From a2177f5b7824f8329200e0a8f9df3ae2570724b5 Mon Sep 17 00:00:00 2001 From: harryswift01 Date: Fri, 27 Mar 2026 14:58:38 +0000 Subject: [PATCH 01/41] tests(regression): consolidate config folders to pure system folder structure --- .../regression/configs/benzaldehyde/{config.yaml => default.yaml} | 0 .../{benzaldehyde_rad/config.yaml => benzaldehyde/rad.yaml} | 0 tests/regression/configs/benzene/{config.yaml => default.yaml} | 0 .../configs/{benzene_rad/config.yaml => benzene/rad.yaml} | 0 .../regression/configs/cyclohexane/{config.yaml => deafult.yaml} | 0 .../configs/{cyclohexane_rad/config.yaml => cyclohexane/rad.yaml} | 0 tests/regression/configs/dna/{config.yaml => deafult.yaml} | 0 .../configs/ethyl-acetate/{config.yaml => deafult.yaml} | 0 .../{ethyl-acetate_rad/config.yaml => ethyl-acetate/rad.yaml} | 0 tests/regression/configs/methane/{config.yaml => deault.yaml} | 0 .../configs/{methane_rad/config.yaml => methane/rad.yaml} | 0 tests/regression/configs/methanol/{config.yaml => deafult.yaml} | 0 .../configs/{methanol_rad/config.yaml => methanol/rad.yaml} | 0 tests/regression/configs/octonol/{config.yaml => default.yaml} | 0 .../configs/{octonol_rad/config.yaml => octonol/rad.yaml} | 0 tests/regression/configs/water/{config.yaml => default.yaml} | 0 .../regression/configs/{water_rad/config.yaml => water/rad.yaml} | 0 17 files changed, 0 insertions(+), 0 deletions(-) rename tests/regression/configs/benzaldehyde/{config.yaml => default.yaml} (100%) rename tests/regression/configs/{benzaldehyde_rad/config.yaml => benzaldehyde/rad.yaml} (100%) rename tests/regression/configs/benzene/{config.yaml => default.yaml} (100%) rename tests/regression/configs/{benzene_rad/config.yaml => benzene/rad.yaml} (100%) rename tests/regression/configs/cyclohexane/{config.yaml => deafult.yaml} (100%) rename tests/regression/configs/{cyclohexane_rad/config.yaml => cyclohexane/rad.yaml} (100%) rename tests/regression/configs/dna/{config.yaml => deafult.yaml} (100%) rename tests/regression/configs/ethyl-acetate/{config.yaml => deafult.yaml} (100%) rename tests/regression/configs/{ethyl-acetate_rad/config.yaml => ethyl-acetate/rad.yaml} (100%) rename tests/regression/configs/methane/{config.yaml => deault.yaml} (100%) rename tests/regression/configs/{methane_rad/config.yaml => methane/rad.yaml} (100%) rename tests/regression/configs/methanol/{config.yaml => deafult.yaml} (100%) rename tests/regression/configs/{methanol_rad/config.yaml => methanol/rad.yaml} (100%) rename tests/regression/configs/octonol/{config.yaml => default.yaml} (100%) rename tests/regression/configs/{octonol_rad/config.yaml => octonol/rad.yaml} (100%) rename tests/regression/configs/water/{config.yaml => default.yaml} (100%) rename tests/regression/configs/{water_rad/config.yaml => water/rad.yaml} (100%) diff --git a/tests/regression/configs/benzaldehyde/config.yaml b/tests/regression/configs/benzaldehyde/default.yaml similarity index 100% rename from tests/regression/configs/benzaldehyde/config.yaml rename to tests/regression/configs/benzaldehyde/default.yaml diff --git a/tests/regression/configs/benzaldehyde_rad/config.yaml b/tests/regression/configs/benzaldehyde/rad.yaml similarity index 100% rename from tests/regression/configs/benzaldehyde_rad/config.yaml rename to tests/regression/configs/benzaldehyde/rad.yaml diff --git a/tests/regression/configs/benzene/config.yaml b/tests/regression/configs/benzene/default.yaml similarity index 100% rename from tests/regression/configs/benzene/config.yaml rename to tests/regression/configs/benzene/default.yaml diff --git a/tests/regression/configs/benzene_rad/config.yaml b/tests/regression/configs/benzene/rad.yaml similarity index 100% rename from tests/regression/configs/benzene_rad/config.yaml rename to tests/regression/configs/benzene/rad.yaml diff --git a/tests/regression/configs/cyclohexane/config.yaml b/tests/regression/configs/cyclohexane/deafult.yaml similarity index 100% rename from tests/regression/configs/cyclohexane/config.yaml rename to tests/regression/configs/cyclohexane/deafult.yaml diff --git a/tests/regression/configs/cyclohexane_rad/config.yaml b/tests/regression/configs/cyclohexane/rad.yaml similarity index 100% rename from tests/regression/configs/cyclohexane_rad/config.yaml rename to tests/regression/configs/cyclohexane/rad.yaml diff --git a/tests/regression/configs/dna/config.yaml b/tests/regression/configs/dna/deafult.yaml similarity index 100% rename from tests/regression/configs/dna/config.yaml rename to tests/regression/configs/dna/deafult.yaml diff --git a/tests/regression/configs/ethyl-acetate/config.yaml b/tests/regression/configs/ethyl-acetate/deafult.yaml similarity index 100% rename from tests/regression/configs/ethyl-acetate/config.yaml rename to tests/regression/configs/ethyl-acetate/deafult.yaml diff --git a/tests/regression/configs/ethyl-acetate_rad/config.yaml b/tests/regression/configs/ethyl-acetate/rad.yaml similarity index 100% rename from tests/regression/configs/ethyl-acetate_rad/config.yaml rename to tests/regression/configs/ethyl-acetate/rad.yaml diff --git a/tests/regression/configs/methane/config.yaml b/tests/regression/configs/methane/deault.yaml similarity index 100% rename from tests/regression/configs/methane/config.yaml rename to tests/regression/configs/methane/deault.yaml diff --git a/tests/regression/configs/methane_rad/config.yaml b/tests/regression/configs/methane/rad.yaml similarity index 100% rename from tests/regression/configs/methane_rad/config.yaml rename to tests/regression/configs/methane/rad.yaml diff --git a/tests/regression/configs/methanol/config.yaml b/tests/regression/configs/methanol/deafult.yaml similarity index 100% rename from tests/regression/configs/methanol/config.yaml rename to tests/regression/configs/methanol/deafult.yaml diff --git a/tests/regression/configs/methanol_rad/config.yaml b/tests/regression/configs/methanol/rad.yaml similarity index 100% rename from tests/regression/configs/methanol_rad/config.yaml rename to tests/regression/configs/methanol/rad.yaml diff --git a/tests/regression/configs/octonol/config.yaml b/tests/regression/configs/octonol/default.yaml similarity index 100% rename from tests/regression/configs/octonol/config.yaml rename to tests/regression/configs/octonol/default.yaml diff --git a/tests/regression/configs/octonol_rad/config.yaml b/tests/regression/configs/octonol/rad.yaml similarity index 100% rename from tests/regression/configs/octonol_rad/config.yaml rename to tests/regression/configs/octonol/rad.yaml diff --git a/tests/regression/configs/water/config.yaml b/tests/regression/configs/water/default.yaml similarity index 100% rename from tests/regression/configs/water/config.yaml rename to tests/regression/configs/water/default.yaml diff --git a/tests/regression/configs/water_rad/config.yaml b/tests/regression/configs/water/rad.yaml similarity index 100% rename from tests/regression/configs/water_rad/config.yaml rename to tests/regression/configs/water/rad.yaml From 50dfaae1be79d0ed3267320958e4f3cdc55ab2d8 Mon Sep 17 00:00:00 2001 From: harryswift01 Date: Fri, 27 Mar 2026 15:07:18 +0000 Subject: [PATCH 02/41] tests(regression): replace hardcoded system list with auto-discovered test cases --- tests/regression/cases.py | 42 ++++++++++++++++++ tests/regression/test_regression.py | 66 +++++++---------------------- 2 files changed, 58 insertions(+), 50 deletions(-) create mode 100644 tests/regression/cases.py diff --git a/tests/regression/cases.py b/tests/regression/cases.py new file mode 100644 index 00000000..245a289b --- /dev/null +++ b/tests/regression/cases.py @@ -0,0 +1,42 @@ +from dataclasses import dataclass +from pathlib import Path +import pytest + + +@dataclass(frozen=True) +class RegressionCase: + system: str + config_path: Path + baseline_path: Path + + +def repo_root() -> Path: + return Path(__file__).resolve().parents[2] + + +def discover_cases(): + configs_root = repo_root() / "tests/regression/configs" + baselines_root = repo_root() / "tests/regression/baselines" + + cases = [] + + for system_dir in sorted(configs_root.iterdir()): + if not system_dir.is_dir(): + continue + + system = system_dir.name + config_path = system_dir / "config.yaml" + baseline_path = baselines_root / f"{system}.json" + + if not config_path.exists(): + continue + + cases.append( + pytest.param( + RegressionCase(system, config_path, baseline_path), + id=system, + marks=pytest.mark.slow if system != "dna" else (), + ) + ) + + return cases \ No newline at end of file diff --git a/tests/regression/test_regression.py b/tests/regression/test_regression.py index 8eecd052..c89c431c 100644 --- a/tests/regression/test_regression.py +++ b/tests/regression/test_regression.py @@ -8,20 +8,11 @@ import pytest from tests.regression.helpers import run_codeentropy_with_config +from tests.regression.cases import discover_cases def _group_index(payload: dict[str, Any]) -> dict[str, dict[str, Any]]: - """Return the groups mapping from a regression payload. - - Args: - payload: Parsed JSON payload. - - Returns: - Mapping of group id to group data. - - Raises: - TypeError: If payload["groups"] is not a dict. - """ + """Return the groups mapping from a regression payload.""" groups = payload.get("groups", {}) if not isinstance(groups, dict): raise TypeError("payload['groups'] must be a dict") @@ -35,17 +26,7 @@ def _compare_grouped( rtol: float, atol: float, ) -> None: - """Compare grouped regression outputs against baseline values. - - Args: - got_payload: Newly produced payload. - baseline_payload: Baseline payload. - rtol: Relative tolerance. - atol: Absolute tolerance. - - Raises: - AssertionError: If any required group/component differs from baseline. - """ + """Compare grouped regression outputs against baseline values.""" got_groups = _group_index(got_payload) base_groups = _group_index(baseline_payload) @@ -100,50 +81,35 @@ def _compare_grouped( @pytest.mark.regression -@pytest.mark.parametrize( - "system", - [ - "dna", - pytest.param("benzaldehyde", marks=pytest.mark.slow), - pytest.param("benzene", marks=pytest.mark.slow), - pytest.param("cyclohexane", marks=pytest.mark.slow), - pytest.param("ethyl-acetate", marks=pytest.mark.slow), - pytest.param("methane", marks=pytest.mark.slow), - pytest.param("methanol", marks=pytest.mark.slow), - pytest.param("octonol", marks=pytest.mark.slow), - pytest.param("water", marks=pytest.mark.slow), - ], -) +@pytest.mark.parametrize("case", discover_cases()) def test_regression_matches_baseline( - tmp_path: Path, system: str, request: pytest.FixtureRequest + tmp_path: Path, case, request: pytest.FixtureRequest ) -> None: - """Run a regression test for one system and compare to its baseline. - - Args: - tmp_path: Pytest-provided temporary directory. - system: System name parameter. - request: Pytest request fixture for reading CLI options. - """ - repo_root = Path(__file__).resolve().parents[2] - config_path = ( - repo_root / "tests" / "regression" / "configs" / system / "config.yaml" - ) - baseline_path = repo_root / "tests" / "regression" / "baselines" / f"{system}.json" + """Run a regression test for one system and compare to its baseline.""" + system = case.system + config_path = case.config_path + baseline_path = case.baseline_path assert config_path.exists(), f"Missing config: {config_path}" assert baseline_path.exists(), f"Missing baseline: {baseline_path}" baseline_payload = json.loads(baseline_path.read_text()) - run = run_codeentropy_with_config(workdir=tmp_path, config_src=config_path) + + run = run_codeentropy_with_config( + workdir=tmp_path, + config_src=config_path, + ) if request.config.getoption("--codeentropy-debug"): print("\n[CodeEntropy regression debug]") + print("system:", system) print("workdir:", run.workdir) print("job_dir:", run.job_dir) print("output_json:", run.output_json) print("payload copy saved:", run.workdir / "codeentropy_output.json") if request.config.getoption("--update-baselines"): + baseline_path.parent.mkdir(parents=True, exist_ok=True) baseline_path.write_text(json.dumps(run.payload, indent=2)) pytest.skip(f"Baseline updated for {system}: {baseline_path}") From a6944c08c5c774c7f82803063032a2fd79df4d77 Mon Sep 17 00:00:00 2001 From: harryswift01 Date: Fri, 27 Mar 2026 15:13:20 +0000 Subject: [PATCH 03/41] tests(regression): use correct file path location for config file --- tests/regression/cases.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/tests/regression/cases.py b/tests/regression/cases.py index 245a289b..a3fb43f4 100644 --- a/tests/regression/cases.py +++ b/tests/regression/cases.py @@ -26,7 +26,7 @@ def discover_cases(): system = system_dir.name config_path = system_dir / "config.yaml" - baseline_path = baselines_root / f"{system}.json" + baseline_path = baselines_root / system / "config.json" if not config_path.exists(): continue From c625c637b614c5fa782685de07953bb97689688d Mon Sep 17 00:00:00 2001 From: harryswift01 Date: Fri, 27 Mar 2026 15:14:09 +0000 Subject: [PATCH 04/41] tests(regression): remove current baseline configurations to reduce future redundancies --- tests/regression/baselines/benzaldehyde.json | 45 -------------- .../baselines/benzaldehyde_rad.json | 45 -------------- tests/regression/baselines/benzene.json | 45 -------------- tests/regression/baselines/benzene_rad.json | 45 -------------- tests/regression/baselines/cyclohexane.json | 45 -------------- .../regression/baselines/cylcohexane_rad.json | 45 -------------- tests/regression/baselines/dna.json | 61 ------------------- tests/regression/baselines/ethyl-acetate.json | 45 -------------- .../baselines/ethyl-acetate_rad.json | 45 -------------- tests/regression/baselines/methane.json | 42 ------------- tests/regression/baselines/methane_rad.json | 42 ------------- tests/regression/baselines/methanol.json | 45 -------------- tests/regression/baselines/methanol_rad.json | 45 -------------- tests/regression/baselines/octonal_rad.json | 45 -------------- tests/regression/baselines/octonol.json | 45 -------------- tests/regression/baselines/water.json | 42 ------------- tests/regression/baselines/water_rad.json | 42 ------------- 17 files changed, 769 deletions(-) delete mode 100644 tests/regression/baselines/benzaldehyde.json delete mode 100644 tests/regression/baselines/benzaldehyde_rad.json delete mode 100644 tests/regression/baselines/benzene.json delete mode 100644 tests/regression/baselines/benzene_rad.json delete mode 100644 tests/regression/baselines/cyclohexane.json delete mode 100644 tests/regression/baselines/cylcohexane_rad.json delete mode 100644 tests/regression/baselines/dna.json delete mode 100644 tests/regression/baselines/ethyl-acetate.json delete mode 100644 tests/regression/baselines/ethyl-acetate_rad.json delete mode 100644 tests/regression/baselines/methane.json delete mode 100644 tests/regression/baselines/methane_rad.json delete mode 100644 tests/regression/baselines/methanol.json delete mode 100644 tests/regression/baselines/methanol_rad.json delete mode 100644 tests/regression/baselines/octonal_rad.json delete mode 100644 tests/regression/baselines/octonol.json delete mode 100644 tests/regression/baselines/water.json delete mode 100644 tests/regression/baselines/water_rad.json diff --git a/tests/regression/baselines/benzaldehyde.json b/tests/regression/baselines/benzaldehyde.json deleted file mode 100644 index 9bd42510..00000000 --- a/tests/regression/baselines/benzaldehyde.json +++ /dev/null @@ -1,45 +0,0 @@ -{ - "args": { - "top_traj_file": [ - "/home/ogo12949/CodeEntropy/.testdata/benzaldehyde/molecules.top", - "/home/ogo12949/CodeEntropy/.testdata/benzaldehyde/trajectory.crd" - ], - "force_file": "/home/ogo12949/CodeEntropy/.testdata/benzaldehyde/forces.frc", - "file_format": "MDCRD", - "kcal_force_units": true, - "selection_string": "all", - "start": 0, - "end": 1, - "step": 1, - "bin_width": 30, - "temperature": 298.0, - "verbose": false, - "output_file": "/tmp/pytest-of-ogo12949/pytest-5/test_regression_matches_baseli1/job001/output_file.json", - "force_partitioning": 0.5, - "water_entropy": true, - "grouping": "molecules", - "combined_forcetorque": true, - "customised_axes": true, - "search_type": "grid" - }, - "provenance": { - "python": "3.13.5", - "platform": "Linux-6.17.0-1012-oem-x86_64-with-glibc2.39", - "codeentropy_version": "2.0.0", - "git_sha": "697cc5da0af766f2f69b0fa31254f2ce7b2b1141" - }, - "groups": { - "0": { - "components": { - "united_atom:Transvibrational": 24.88518233240474, - "united_atom:Rovibrational": 27.950376507672583, - "residue:FTmat-Transvibrational": 71.03412922724692, - "residue:FTmat-Rovibrational": 59.44169664956799, - "united_atom:Conformational": 0.0, - "residue:Conformational": 0.0, - "residue:Orientational": 59.5156759876787 - }, - "total": 242.82706070457093 - } - } -} diff --git a/tests/regression/baselines/benzaldehyde_rad.json b/tests/regression/baselines/benzaldehyde_rad.json deleted file mode 100644 index 84070952..00000000 --- a/tests/regression/baselines/benzaldehyde_rad.json +++ /dev/null @@ -1,45 +0,0 @@ -{ - "args": { - "top_traj_file": [ - "/home/ogo12949/CodeEntropy/.testdata/benzaldehyde/molecules.top", - "/home/ogo12949/CodeEntropy/.testdata/benzaldehyde/trajectory.crd" - ], - "force_file": "/home/ogo12949/CodeEntropy/.testdata/benzaldehyde/forces.frc", - "file_format": "MDCRD", - "kcal_force_units": false, - "selection_string": "all", - "start": 0, - "end": 1, - "step": 1, - "bin_width": 30, - "temperature": 298.0, - "verbose": false, - "output_file": "/tmp/pytest-of-ogo12949/pytest-1/test_regression_matches_baseli1/job001/output_file.json", - "force_partitioning": 0.5, - "water_entropy": true, - "grouping": "molecules", - "combined_forcetorque": true, - "customised_axes": true, - "search_type": "RAD" - }, - "provenance": { - "python": "3.13.5", - "platform": "Linux-6.17.0-1012-oem-x86_64-with-glibc2.39", - "codeentropy_version": "2.0.0", - "git_sha": "3143bcbea9717e13135f61c00e6a0efa7814f82f" - }, - "groups": { - "0": { - "components": { - "united_atom:Transvibrational": 158.90339720185818, - "united_atom:Rovibrational": 143.87250586343512, - "residue:FTmat-Transvibrational": 106.71035236014967, - "residue:FTmat-Rovibrational": 95.07735227595549, - "united_atom:Conformational": 0.0, - "residue:Conformational": 0.0, - "residue:Orientational": 25.3107189764825 - }, - "total": 529.874326677881 - } - } -} diff --git a/tests/regression/baselines/benzene.json b/tests/regression/baselines/benzene.json deleted file mode 100644 index 488248b5..00000000 --- a/tests/regression/baselines/benzene.json +++ /dev/null @@ -1,45 +0,0 @@ -{ - "args": { - "top_traj_file": [ - "/home/ogo12949/CodeEntropy/.testdata/benzene/molecules.top", - "/home/ogo12949/CodeEntropy/.testdata/benzene/trajectory.crd" - ], - "force_file": "/home/ogo12949/CodeEntropy/.testdata/benzene/forces.frc", - "file_format": "MDCRD", - "kcal_force_units": true, - "selection_string": "all", - "start": 0, - "end": 1, - "step": 1, - "bin_width": 30, - "temperature": 298.0, - "verbose": false, - "output_file": "/tmp/pytest-of-ogo12949/pytest-5/test_regression_matches_baseli2/job001/output_file.json", - "force_partitioning": 0.5, - "water_entropy": true, - "grouping": "molecules", - "combined_forcetorque": true, - "customised_axes": true, - "search_type": "grid" - }, - "provenance": { - "python": "3.13.5", - "platform": "Linux-6.17.0-1012-oem-x86_64-with-glibc2.39", - "codeentropy_version": "2.0.0", - "git_sha": "697cc5da0af766f2f69b0fa31254f2ce7b2b1141" - }, - "groups": { - "0": { - "components": { - "united_atom:Transvibrational": 9.081853431559052, - "united_atom:Rovibrational": 27.534380126250227, - "residue:FTmat-Transvibrational": 72.66211800013413, - "residue:FTmat-Rovibrational": 59.93761874375924, - "united_atom:Conformational": 0.0, - "residue:Conformational": 0.0, - "residue:Orientational": 41.237966715197246 - }, - "total": 210.45393701689989 - } - } -} diff --git a/tests/regression/baselines/benzene_rad.json b/tests/regression/baselines/benzene_rad.json deleted file mode 100644 index 7b5e159f..00000000 --- a/tests/regression/baselines/benzene_rad.json +++ /dev/null @@ -1,45 +0,0 @@ -{ - "args": { - "top_traj_file": [ - "/home/ogo12949/CodeEntropy/.testdata/benzene/molecules.top", - "/home/ogo12949/CodeEntropy/.testdata/benzene/trajectory.crd" - ], - "force_file": "/home/ogo12949/CodeEntropy/.testdata/benzene/forces.frc", - "file_format": "MDCRD", - "kcal_force_units": false, - "selection_string": "all", - "start": 0, - "end": 1, - "step": 1, - "bin_width": 30, - "temperature": 298.0, - "verbose": false, - "output_file": "/tmp/pytest-of-ogo12949/pytest-1/test_regression_matches_baseli2/job001/output_file.json", - "force_partitioning": 0.5, - "water_entropy": true, - "grouping": "molecules", - "combined_forcetorque": true, - "customised_axes": true, - "search_type": "RAD" - }, - "provenance": { - "python": "3.13.5", - "platform": "Linux-6.17.0-1012-oem-x86_64-with-glibc2.39", - "codeentropy_version": "2.0.0", - "git_sha": "3143bcbea9717e13135f61c00e6a0efa7814f82f" - }, - "groups": { - "0": { - "components": { - "united_atom:Transvibrational": 93.55450341182438, - "united_atom:Rovibrational": 143.68264201362132, - "residue:FTmat-Transvibrational": 108.34125737284016, - "residue:FTmat-Rovibrational": 95.57598285903227, - "united_atom:Conformational": 0.0, - "residue:Conformational": 0.0, - "residue:Orientational": 12.282076945243183 - }, - "total": 453.43646260256133 - } - } -} diff --git a/tests/regression/baselines/cyclohexane.json b/tests/regression/baselines/cyclohexane.json deleted file mode 100644 index eabf7d83..00000000 --- a/tests/regression/baselines/cyclohexane.json +++ /dev/null @@ -1,45 +0,0 @@ -{ - "args": { - "top_traj_file": [ - 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"/tmp/pytest-of-ogo12949/pytest-5/test_regression_matches_baseli8/job001/output_file.json", - "force_partitioning": 0.5, - "water_entropy": true, - "grouping": "molecules", - "combined_forcetorque": true, - "customised_axes": true, - "search_type": "grid" - }, - "provenance": { - "python": "3.13.5", - "platform": "Linux-6.17.0-1012-oem-x86_64-with-glibc2.39", - "codeentropy_version": "2.0.0", - "git_sha": "697cc5da0af766f2f69b0fa31254f2ce7b2b1141" - }, - "groups": { - "0": { - "components": { - "united_atom:Transvibrational": 43.725393337304425, - "united_atom:Rovibrational": 17.28911070147887, - "united_atom:Conformational": 0.0, - "united_atom:Orientational": 32.00715225476484 - }, - "total": 93.02165629354813 - } - } -} diff --git a/tests/regression/baselines/water_rad.json b/tests/regression/baselines/water_rad.json deleted file mode 100644 index 7e03e61d..00000000 --- a/tests/regression/baselines/water_rad.json +++ /dev/null @@ -1,42 +0,0 @@ -{ - "args": { - "top_traj_file": [ - "/home/ogo12949/CodeEntropy/.testdata/water/molecules.top", - "/home/ogo12949/CodeEntropy/.testdata/water/trajectory.crd" - ], - "force_file": "/home/ogo12949/CodeEntropy/.testdata/water/forces.frc", - "file_format": "MDCRD", - "kcal_force_units": false, - "selection_string": "all", - "start": 0, - "end": 1, - "step": 1, - "bin_width": 30, - "temperature": 298.0, - "verbose": false, - "output_file": "/tmp/pytest-of-ogo12949/pytest-2/test_regression_matches_baseli0/job001/output_file.json", - "force_partitioning": 0.5, - "water_entropy": true, - "grouping": "molecules", - "combined_forcetorque": true, - "customised_axes": true, - "search_type": "RAD" - }, - "provenance": { - "python": "3.13.5", - "platform": "Linux-6.17.0-1012-oem-x86_64-with-glibc2.39", - "codeentropy_version": "2.0.0", - "git_sha": "3143bcbea9717e13135f61c00e6a0efa7814f82f" - }, - "groups": { - "0": { - "components": { - "united_atom:Transvibrational": 79.20298312418278, - "united_atom:Rovibrational": 50.90260688502127, - "united_atom:Conformational": 0.0, - "united_atom:Orientational": 22.599402683404527 - }, - "total": 152.70499269260856 - } - } -} From a6379e3e0813766aadb8e94167dbff948092b4f7 Mon Sep 17 00:00:00 2001 From: harryswift01 Date: Fri, 27 Mar 2026 15:46:28 +0000 Subject: [PATCH 05/41] tests(regression): support baseline generation and missing baseline handling: - Allow regression tests to run in `--update-baselines` mode without requiring existing baseline files - Defer baseline existence checks until after update-mode is considered - Create baseline directories automatically when updating baselines - Ensure `discover_cases` does not fail collection when baselines are missing --- tests/regression/cases.py | 27 +++++++++-------- .../{deafult.yaml => default.yaml} | 0 .../dna/{deafult.yaml => default.yaml} | 0 .../{deafult.yaml => default.yaml} | 0 .../methane/{deault.yaml => default.yaml} | 0 .../methanol/{deafult.yaml => default.yaml} | 0 tests/regression/test_regression.py | 30 ++++++++----------- 7 files changed, 28 insertions(+), 29 deletions(-) rename tests/regression/configs/cyclohexane/{deafult.yaml => default.yaml} (100%) rename tests/regression/configs/dna/{deafult.yaml => default.yaml} (100%) rename tests/regression/configs/ethyl-acetate/{deafult.yaml => default.yaml} (100%) rename tests/regression/configs/methane/{deault.yaml => default.yaml} (100%) rename tests/regression/configs/methanol/{deafult.yaml => default.yaml} (100%) diff --git a/tests/regression/cases.py b/tests/regression/cases.py index a3fb43f4..2ca0c348 100644 --- a/tests/regression/cases.py +++ b/tests/regression/cases.py @@ -15,8 +15,10 @@ def repo_root() -> Path: def discover_cases(): - configs_root = repo_root() / "tests/regression/configs" - baselines_root = repo_root() / "tests/regression/baselines" + base_dir = Path(__file__).resolve().parent + + configs_root = base_dir / "configs" + baselines_root = base_dir / "baselines" cases = [] @@ -25,18 +27,19 @@ def discover_cases(): continue system = system_dir.name - config_path = system_dir / "config.yaml" - baseline_path = baselines_root / system / "config.json" - if not config_path.exists(): - continue + for config_path in sorted(system_dir.glob("*.yaml")): + case_name = config_path.stem + + baseline_path = baselines_root / system / f"{case_name}.json" - cases.append( - pytest.param( - RegressionCase(system, config_path, baseline_path), - id=system, - marks=pytest.mark.slow if system != "dna" else (), + # DO NOT skip if baseline is missing + cases.append( + pytest.param( + RegressionCase(system, config_path, baseline_path), + id=f"{system}-{case_name}", + marks=pytest.mark.slow if system != "dna" else (), + ) ) - ) return cases \ No newline at end of file diff --git a/tests/regression/configs/cyclohexane/deafult.yaml b/tests/regression/configs/cyclohexane/default.yaml similarity index 100% rename from tests/regression/configs/cyclohexane/deafult.yaml rename to tests/regression/configs/cyclohexane/default.yaml diff --git a/tests/regression/configs/dna/deafult.yaml b/tests/regression/configs/dna/default.yaml similarity index 100% rename from tests/regression/configs/dna/deafult.yaml rename to tests/regression/configs/dna/default.yaml diff --git a/tests/regression/configs/ethyl-acetate/deafult.yaml b/tests/regression/configs/ethyl-acetate/default.yaml similarity index 100% rename from tests/regression/configs/ethyl-acetate/deafult.yaml rename to tests/regression/configs/ethyl-acetate/default.yaml diff --git a/tests/regression/configs/methane/deault.yaml b/tests/regression/configs/methane/default.yaml similarity index 100% rename from tests/regression/configs/methane/deault.yaml rename to tests/regression/configs/methane/default.yaml diff --git a/tests/regression/configs/methanol/deafult.yaml b/tests/regression/configs/methanol/default.yaml similarity index 100% rename from tests/regression/configs/methanol/deafult.yaml rename to tests/regression/configs/methanol/default.yaml diff --git a/tests/regression/test_regression.py b/tests/regression/test_regression.py index c89c431c..68794678 100644 --- a/tests/regression/test_regression.py +++ b/tests/regression/test_regression.py @@ -12,7 +12,6 @@ def _group_index(payload: dict[str, Any]) -> dict[str, dict[str, Any]]: - """Return the groups mapping from a regression payload.""" groups = payload.get("groups", {}) if not isinstance(groups, dict): raise TypeError("payload['groups'] must be a dict") @@ -26,7 +25,6 @@ def _compare_grouped( rtol: float, atol: float, ) -> None: - """Compare grouped regression outputs against baseline values.""" got_groups = _group_index(got_payload) base_groups = _group_index(baseline_payload) @@ -41,9 +39,7 @@ def _compare_grouped( base_components = base_g.get("components", {}) got_components = got_g.get("components", {}) - if not isinstance(base_components, dict) or not isinstance( - got_components, dict - ): + if not isinstance(base_components, dict) or not isinstance(got_components, dict): mismatches.append(f"group {gid}: components must be dicts") continue @@ -73,8 +69,7 @@ def _compare_grouped( ) except AssertionError: mismatches.append( - f"group {gid} total: expected={base_g['total']} " - f"got={got_g.get('total')}" + f"group {gid} total: expected={base_g['total']} got={got_g.get('total')}" ) assert not mismatches, "Mismatches:\n" + "\n".join(" " + m for m in mismatches) @@ -85,15 +80,18 @@ def _compare_grouped( def test_regression_matches_baseline( tmp_path: Path, case, request: pytest.FixtureRequest ) -> None: - """Run a regression test for one system and compare to its baseline.""" system = case.system config_path = case.config_path baseline_path = case.baseline_path - assert config_path.exists(), f"Missing config: {config_path}" - assert baseline_path.exists(), f"Missing baseline: {baseline_path}" + update_mode = request.config.getoption("--update-baselines") - baseline_payload = json.loads(baseline_path.read_text()) + if not baseline_path.exists(): + if not update_mode: + raise AssertionError(f"Missing baseline: {baseline_path}") + baseline_payload = {} + else: + baseline_payload = json.loads(baseline_path.read_text()) run = run_codeentropy_with_config( workdir=tmp_path, @@ -101,17 +99,15 @@ def test_regression_matches_baseline( ) if request.config.getoption("--codeentropy-debug"): - print("\n[CodeEntropy regression debug]") + print("\n[DEBUG]") print("system:", system) - print("workdir:", run.workdir) - print("job_dir:", run.job_dir) - print("output_json:", run.output_json) - print("payload copy saved:", run.workdir / "codeentropy_output.json") + print("config:", config_path) + print("baseline:", baseline_path) if request.config.getoption("--update-baselines"): baseline_path.parent.mkdir(parents=True, exist_ok=True) baseline_path.write_text(json.dumps(run.payload, indent=2)) - pytest.skip(f"Baseline updated for {system}: {baseline_path}") + pytest.skip(f"Updated baseline for {system}") _compare_grouped( got_payload=run.payload, From ebd297359ef25ca151dff56ba4029165b2911e41 Mon Sep 17 00:00:00 2001 From: harryswift01 Date: Fri, 27 Mar 2026 16:14:28 +0000 Subject: [PATCH 06/41] tests(regression): add additioanl test cases for regression tests --- .../regression/configs/benzaldehyde/axes_off.yaml | 15 +++++++++++++++ .../configs/benzaldehyde/frame_window.yaml | 14 ++++++++++++++ .../configs/benzaldehyde/selection_subset.yaml | 14 ++++++++++++++ tests/regression/configs/benzene/axes_off.yaml | 15 +++++++++++++++ tests/regression/configs/benzene/default.yaml | 4 ++-- .../regression/configs/benzene/frame_window.yaml | 14 ++++++++++++++ tests/regression/configs/benzene/rad.yaml | 6 +++--- .../configs/benzene/selection_subset.yaml | 14 ++++++++++++++ .../regression/configs/cyclohexane/axes_off.yaml | 15 +++++++++++++++ tests/regression/configs/cyclohexane/default.yaml | 4 ++-- .../configs/cyclohexane/frame_window.yaml | 14 ++++++++++++++ tests/regression/configs/cyclohexane/rad.yaml | 4 ++-- .../configs/cyclohexane/selection_subset.yaml | 14 ++++++++++++++ tests/regression/configs/dna/axes_off.yaml | 14 ++++++++++++++ tests/regression/configs/dna/default.yaml | 6 +++--- tests/regression/configs/dna/frame_window.yaml | 14 ++++++++++++++ tests/regression/configs/dna/rad.yaml | 14 ++++++++++++++ .../regression/configs/dna/selection_subset.yaml | 14 ++++++++++++++ .../configs/ethyl-acetate/axes_off.yaml | 15 +++++++++++++++ .../regression/configs/ethyl-acetate/default.yaml | 4 ++-- .../configs/ethyl-acetate/frame_window.yaml | 14 ++++++++++++++ tests/regression/configs/ethyl-acetate/rad.yaml | 4 ++-- .../configs/ethyl-acetate/selection_subset.yaml | 14 ++++++++++++++ tests/regression/configs/methane/axes_off.yaml | 15 +++++++++++++++ tests/regression/configs/methane/default.yaml | 1 - .../regression/configs/methane/frame_window.yaml | 15 +++++++++++++++ tests/regression/configs/methane/rad.yaml | 1 + .../configs/methane/selection_subset.yaml | 15 +++++++++++++++ tests/regression/configs/methanol/axes_off.yaml | 15 +++++++++++++++ tests/regression/configs/methanol/default.yaml | 4 ++-- .../regression/configs/methanol/frame_window.yaml | 14 ++++++++++++++ tests/regression/configs/methanol/rad.yaml | 4 ++-- .../configs/methanol/selection_subset.yaml | 14 ++++++++++++++ tests/regression/configs/octonol/axes_off.yaml | 15 +++++++++++++++ tests/regression/configs/octonol/default.yaml | 4 ++-- .../regression/configs/octonol/frame_window.yaml | 14 ++++++++++++++ tests/regression/configs/octonol/rad.yaml | 4 ++-- .../configs/octonol/selection_subset.yaml | 14 ++++++++++++++ tests/regression/configs/water/axes_off.yaml | 15 +++++++++++++++ tests/regression/configs/water/frame_window.yaml | 14 ++++++++++++++ .../configs/water/selection_subset.yaml | 14 ++++++++++++++ 41 files changed, 427 insertions(+), 25 deletions(-) create mode 100644 tests/regression/configs/benzaldehyde/axes_off.yaml create mode 100644 tests/regression/configs/benzaldehyde/frame_window.yaml create mode 100644 tests/regression/configs/benzaldehyde/selection_subset.yaml create mode 100644 tests/regression/configs/benzene/axes_off.yaml create mode 100644 tests/regression/configs/benzene/frame_window.yaml create mode 100644 tests/regression/configs/benzene/selection_subset.yaml create mode 100644 tests/regression/configs/cyclohexane/axes_off.yaml create mode 100644 tests/regression/configs/cyclohexane/frame_window.yaml create mode 100644 tests/regression/configs/cyclohexane/selection_subset.yaml create mode 100644 tests/regression/configs/dna/axes_off.yaml create mode 100644 tests/regression/configs/dna/frame_window.yaml create mode 100644 tests/regression/configs/dna/rad.yaml create mode 100644 tests/regression/configs/dna/selection_subset.yaml create mode 100644 tests/regression/configs/ethyl-acetate/axes_off.yaml create mode 100644 tests/regression/configs/ethyl-acetate/frame_window.yaml create mode 100644 tests/regression/configs/ethyl-acetate/selection_subset.yaml create mode 100644 tests/regression/configs/methane/axes_off.yaml create mode 100644 tests/regression/configs/methane/frame_window.yaml create mode 100644 tests/regression/configs/methane/selection_subset.yaml create mode 100644 tests/regression/configs/methanol/axes_off.yaml create mode 100644 tests/regression/configs/methanol/frame_window.yaml create mode 100644 tests/regression/configs/methanol/selection_subset.yaml create mode 100644 tests/regression/configs/octonol/axes_off.yaml create mode 100644 tests/regression/configs/octonol/frame_window.yaml create mode 100644 tests/regression/configs/octonol/selection_subset.yaml create mode 100644 tests/regression/configs/water/axes_off.yaml create mode 100644 tests/regression/configs/water/frame_window.yaml create mode 100644 tests/regression/configs/water/selection_subset.yaml diff --git a/tests/regression/configs/benzaldehyde/axes_off.yaml b/tests/regression/configs/benzaldehyde/axes_off.yaml new file mode 100644 index 00000000..b86eb3bd --- /dev/null +++ b/tests/regression/configs/benzaldehyde/axes_off.yaml @@ -0,0 +1,15 @@ +--- + +run1: + force_file: ".testdata/benzaldehyde/forces.frc" + top_traj_file: + - ".testdata/benzaldehyde/molecules.top" + - ".testdata/benzaldehyde/trajectory.crd" + selection_string: "all" + start: 0 + end: 1 + step: 1 + file_format: "MDCRD" + kcal_force_units: True + search_type: "grid" + customised_axes: false \ No newline at end of file diff --git a/tests/regression/configs/benzaldehyde/frame_window.yaml b/tests/regression/configs/benzaldehyde/frame_window.yaml new file mode 100644 index 00000000..0bfdd9fa --- /dev/null +++ b/tests/regression/configs/benzaldehyde/frame_window.yaml @@ -0,0 +1,14 @@ +--- + +run1: + force_file: ".testdata/benzaldehyde/forces.frc" + top_traj_file: + - ".testdata/benzaldehyde/molecules.top" + - ".testdata/benzaldehyde/trajectory.crd" + selection_string: "all" + start: 0 + end: 5 + step: 2 + file_format: "MDCRD" + kcal_force_units: True + search_type: "grid" \ No newline at end of file diff --git a/tests/regression/configs/benzaldehyde/selection_subset.yaml b/tests/regression/configs/benzaldehyde/selection_subset.yaml new file mode 100644 index 00000000..b9fb06be --- /dev/null +++ b/tests/regression/configs/benzaldehyde/selection_subset.yaml @@ -0,0 +1,14 @@ +--- + +run1: + force_file: ".testdata/benzaldehyde/forces.frc" + top_traj_file: + - ".testdata/benzaldehyde/molecules.top" + - ".testdata/benzaldehyde/trajectory.crd" + selection_string: "protein" + start: 0 + end: 1 + step: 1 + file_format: "MDCRD" + kcal_force_units: True + search_type: "grid" \ No newline at end of file diff --git a/tests/regression/configs/benzene/axes_off.yaml b/tests/regression/configs/benzene/axes_off.yaml new file mode 100644 index 00000000..019128fb --- /dev/null +++ b/tests/regression/configs/benzene/axes_off.yaml @@ -0,0 +1,15 @@ +--- + +run1: + force_file: ".testdata/benzene/forces.frc" + top_traj_file: + - ".testdata/benzene/molecules.top" + - ".testdata/benzene/trajectory.crd" + selection_string: "all" + start: 0 + end: 1 + step: 1 + file_format: "MDCRD" + kcal_force_units: True + search_type: "grid" + customised_axes: false \ No newline at end of file diff --git a/tests/regression/configs/benzene/default.yaml b/tests/regression/configs/benzene/default.yaml index 611e6934..a3f10191 100644 --- a/tests/regression/configs/benzene/default.yaml +++ b/tests/regression/configs/benzene/default.yaml @@ -5,10 +5,10 @@ run1: top_traj_file: - ".testdata/benzene/molecules.top" - ".testdata/benzene/trajectory.crd" - selection_string: 'all' + selection_string: "all" start: 0 end: 1 step: 1 - file_format: 'MDCRD' + file_format: "MDCRD" kcal_force_units: True search_type: "grid" diff --git a/tests/regression/configs/benzene/frame_window.yaml b/tests/regression/configs/benzene/frame_window.yaml new file mode 100644 index 00000000..91e5bc21 --- /dev/null +++ b/tests/regression/configs/benzene/frame_window.yaml @@ -0,0 +1,14 @@ +--- + +run1: + force_file: ".testdata/benzene/forces.frc" + top_traj_file: + - ".testdata/benzene/molecules.top" + - ".testdata/benzene/trajectory.crd" + selection_string: "all" + start: 0 + end: 5 + step: 2 + file_format: "MDCRD" + kcal_force_units: True + search_type: "grid" \ No newline at end of file diff --git a/tests/regression/configs/benzene/rad.yaml b/tests/regression/configs/benzene/rad.yaml index e3862947..ae274209 100644 --- a/tests/regression/configs/benzene/rad.yaml +++ b/tests/regression/configs/benzene/rad.yaml @@ -3,12 +3,12 @@ run1: force_file: ".testdata/benzene/forces.frc" top_traj_file: - - ".testdata/benzene/molecules.top" + - ".testdata/benzaldbenzeneehyde/molecules.top" - ".testdata/benzene/trajectory.crd" - selection_string: 'all' + selection_string: "all" start: 0 end: 1 step: 1 - file_format: 'MDCRD' + file_format: "MDCRD" # kcal_force_units: True search_type: "RAD" diff --git a/tests/regression/configs/benzene/selection_subset.yaml b/tests/regression/configs/benzene/selection_subset.yaml new file mode 100644 index 00000000..8eb2a960 --- /dev/null +++ b/tests/regression/configs/benzene/selection_subset.yaml @@ -0,0 +1,14 @@ +--- + +run1: + force_file: ".testdata/benzene/forces.frc" + top_traj_file: + - ".testdata/benzene/molecules.top" + - ".testdata/benzene/trajectory.crd" + selection_string: "protein" + start: 0 + end: 1 + step: 1 + file_format: "MDCRD" + kcal_force_units: True + search_type: "grid" \ No newline at end of file diff --git a/tests/regression/configs/cyclohexane/axes_off.yaml b/tests/regression/configs/cyclohexane/axes_off.yaml new file mode 100644 index 00000000..1d80c74e --- /dev/null +++ b/tests/regression/configs/cyclohexane/axes_off.yaml @@ -0,0 +1,15 @@ +--- + +run1: + force_file: ".testdata/cyclohexane/forces.frc" + top_traj_file: + - ".testdata/cyclohexane/molecules.top" + - ".testdata/cyclohexane/trajectory.crd" + selection_string: "all" + start: 0 + end: 1 + step: 1 + file_format: "MDCRD" + kcal_force_units: True + search_type: "grid" + customised_axes: false \ No newline at end of file diff --git a/tests/regression/configs/cyclohexane/default.yaml b/tests/regression/configs/cyclohexane/default.yaml index 8c8560f1..b70a05ea 100644 --- a/tests/regression/configs/cyclohexane/default.yaml +++ b/tests/regression/configs/cyclohexane/default.yaml @@ -5,10 +5,10 @@ run1: top_traj_file: - ".testdata/cyclohexane/molecules.top" - ".testdata/cyclohexane/trajectory.crd" - selection_string: 'all' + selection_string: "all" start: 0 end: 1 step: 1 - file_format: 'MDCRD' + file_format: "MDCRD" kcal_force_units: True search_type: "grid" diff --git a/tests/regression/configs/cyclohexane/frame_window.yaml b/tests/regression/configs/cyclohexane/frame_window.yaml new file mode 100644 index 00000000..e4f885f5 --- /dev/null +++ b/tests/regression/configs/cyclohexane/frame_window.yaml @@ -0,0 +1,14 @@ +--- + +run1: + force_file: ".testdata/cyclohexane/forces.frc" + top_traj_file: + - ".testdata/cyclohexane/molecules.top" + - ".testdata/cyclohexane/trajectory.crd" + selection_string: "all" + start: 0 + end: 5 + step: 2 + file_format: "MDCRD" + kcal_force_units: True + search_type: "grid" \ No newline at end of file diff --git a/tests/regression/configs/cyclohexane/rad.yaml b/tests/regression/configs/cyclohexane/rad.yaml index 1fa78cbe..c6b7b598 100644 --- a/tests/regression/configs/cyclohexane/rad.yaml +++ b/tests/regression/configs/cyclohexane/rad.yaml @@ -5,10 +5,10 @@ run1: top_traj_file: - ".testdata/cyclohexane/molecules.top" - ".testdata/cyclohexane/trajectory.crd" - selection_string: 'all' + selection_string: "all" start: 0 end: 1 step: 1 - file_format: 'MDCRD' + file_format: "MDCRD" # kcal_force_units: True search_type: "RAD" diff --git a/tests/regression/configs/cyclohexane/selection_subset.yaml b/tests/regression/configs/cyclohexane/selection_subset.yaml new file mode 100644 index 00000000..2a21ed4a --- /dev/null +++ b/tests/regression/configs/cyclohexane/selection_subset.yaml @@ -0,0 +1,14 @@ +--- + +run1: + force_file: ".testdata/cyclohexane/forces.frc" + top_traj_file: + - ".testdata/cyclohexane/molecules.top" + - ".testdata/cyclohexane/trajectory.crd" + selection_string: "protein" + start: 0 + end: 1 + step: 1 + file_format: "MDCRD" + kcal_force_units: True + search_type: "grid" \ No newline at end of file diff --git a/tests/regression/configs/dna/axes_off.yaml b/tests/regression/configs/dna/axes_off.yaml new file mode 100644 index 00000000..03f5df06 --- /dev/null +++ b/tests/regression/configs/dna/axes_off.yaml @@ -0,0 +1,14 @@ +--- + +run1: + top_traj_file: + - ".testdata/benzaldehyde/molecules.top" + - ".testdata/benzaldehyde/trajectory.crd" + selection_string: "all" + start: 0 + end: 1 + step: 1 + file_format: "MDCRD" + kcal_force_units: True + search_type: "grid" + customised_axes: false \ No newline at end of file diff --git a/tests/regression/configs/dna/default.yaml b/tests/regression/configs/dna/default.yaml index 854dc148..eecc7c9b 100644 --- a/tests/regression/configs/dna/default.yaml +++ b/tests/regression/configs/dna/default.yaml @@ -2,9 +2,9 @@ run1: top_traj_file: - - ".testdata/dna/md_A4_dna.tpr" - - ".testdata/dna/md_A4_dna_xf.trr" - selection_string: 'all' + - ".testdata/dna/molecules.top" + - ".testdata/dna/trajectory.crd" + selection_string: "all" start: 0 end: 1 step: 1 diff --git a/tests/regression/configs/dna/frame_window.yaml b/tests/regression/configs/dna/frame_window.yaml new file mode 100644 index 00000000..0bfdd9fa --- /dev/null +++ b/tests/regression/configs/dna/frame_window.yaml @@ -0,0 +1,14 @@ +--- + +run1: + force_file: ".testdata/benzaldehyde/forces.frc" + top_traj_file: + - ".testdata/benzaldehyde/molecules.top" + - ".testdata/benzaldehyde/trajectory.crd" + selection_string: "all" + start: 0 + end: 5 + step: 2 + file_format: "MDCRD" + kcal_force_units: True + search_type: "grid" \ No newline at end of file diff --git a/tests/regression/configs/dna/rad.yaml b/tests/regression/configs/dna/rad.yaml new file mode 100644 index 00000000..455599b0 --- /dev/null +++ b/tests/regression/configs/dna/rad.yaml @@ -0,0 +1,14 @@ +--- + +run1: + force_file: ".testdata/benzaldehyde/forces.frc" + top_traj_file: + - ".testdata/benzaldehyde/molecules.top" + - ".testdata/benzaldehyde/trajectory.crd" + selection_string: "all" + start: 0 + end: 1 + step: 1 + file_format: "MDCRD" +# kcal_force_units: True + search_type: "RAD" diff --git a/tests/regression/configs/dna/selection_subset.yaml b/tests/regression/configs/dna/selection_subset.yaml new file mode 100644 index 00000000..b9fb06be --- /dev/null +++ b/tests/regression/configs/dna/selection_subset.yaml @@ -0,0 +1,14 @@ +--- + +run1: + force_file: ".testdata/benzaldehyde/forces.frc" + top_traj_file: + - ".testdata/benzaldehyde/molecules.top" + - ".testdata/benzaldehyde/trajectory.crd" + selection_string: "protein" + start: 0 + end: 1 + step: 1 + file_format: "MDCRD" + kcal_force_units: True + search_type: "grid" \ No newline at end of file diff --git a/tests/regression/configs/ethyl-acetate/axes_off.yaml b/tests/regression/configs/ethyl-acetate/axes_off.yaml new file mode 100644 index 00000000..b86eb3bd --- /dev/null +++ b/tests/regression/configs/ethyl-acetate/axes_off.yaml @@ -0,0 +1,15 @@ +--- + +run1: + force_file: ".testdata/benzaldehyde/forces.frc" + top_traj_file: + - ".testdata/benzaldehyde/molecules.top" + - ".testdata/benzaldehyde/trajectory.crd" + selection_string: "all" + start: 0 + end: 1 + step: 1 + file_format: "MDCRD" + kcal_force_units: True + search_type: "grid" + customised_axes: false \ No newline at end of file diff --git a/tests/regression/configs/ethyl-acetate/default.yaml b/tests/regression/configs/ethyl-acetate/default.yaml index d6d29694..4e0c9bc4 100644 --- a/tests/regression/configs/ethyl-acetate/default.yaml +++ b/tests/regression/configs/ethyl-acetate/default.yaml @@ -5,10 +5,10 @@ run1: top_traj_file: - ".testdata/ethyl-acetate/molecules.top" - ".testdata/ethyl-acetate/trajectory.crd" - selection_string: 'all' + selection_string: "all" start: 0 end: 1 step: 1 - file_format: 'MDCRD' + file_format: "MDCRD" kcal_force_units: True search_type: "grid" diff --git a/tests/regression/configs/ethyl-acetate/frame_window.yaml b/tests/regression/configs/ethyl-acetate/frame_window.yaml new file mode 100644 index 00000000..5d165f0e --- /dev/null +++ b/tests/regression/configs/ethyl-acetate/frame_window.yaml @@ -0,0 +1,14 @@ +--- + +run1: + force_file: ".testdata/ethyl-acetate/forces.frc" + top_traj_file: + - ".testdata/ethyl-acetate/molecules.top" + - ".testdata/ethyl-acetate/trajectory.crd" + selection_string: "all" + start: 0 + end: 5 + step: 2 + file_format: "MDCRD" + kcal_force_units: True + search_type: "grid" \ No newline at end of file diff --git a/tests/regression/configs/ethyl-acetate/rad.yaml b/tests/regression/configs/ethyl-acetate/rad.yaml index df09dfe4..97c28228 100644 --- a/tests/regression/configs/ethyl-acetate/rad.yaml +++ b/tests/regression/configs/ethyl-acetate/rad.yaml @@ -5,10 +5,10 @@ run1: top_traj_file: - ".testdata/ethyl-acetate/molecules.top" - ".testdata/ethyl-acetate/trajectory.crd" - selection_string: 'all' + selection_string: "all" start: 0 end: 1 step: 1 - file_format: 'MDCRD' + file_format: "MDCRD" # kcal_force_units: True search_type: "RAD" diff --git a/tests/regression/configs/ethyl-acetate/selection_subset.yaml b/tests/regression/configs/ethyl-acetate/selection_subset.yaml new file mode 100644 index 00000000..fdd0b693 --- /dev/null +++ b/tests/regression/configs/ethyl-acetate/selection_subset.yaml @@ -0,0 +1,14 @@ +--- + +run1: + force_file: ".testdata/ethyl-acetate/forces.frc" + top_traj_file: + - ".testdata/ethyl-acetate/molecules.top" + - ".testdata/ethyl-acetate/trajectory.crd" + selection_string: "protein" + start: 0 + end: 1 + step: 1 + file_format: "MDCRD" + kcal_force_units: True + search_type: "grid" \ No newline at end of file diff --git a/tests/regression/configs/methane/axes_off.yaml b/tests/regression/configs/methane/axes_off.yaml new file mode 100644 index 00000000..7293f41b --- /dev/null +++ b/tests/regression/configs/methane/axes_off.yaml @@ -0,0 +1,15 @@ +--- + +run1: + force_file: ".testdata/methane/forces.frc" + top_traj_file: + - ".testdata/methane/molecules.top" + - ".testdata/methane/trajectory.crd" + selection_string: "all" + start: 0 + end: 1 + step: 1 + file_format: "MDCRD" + kcal_force_units: True + search_type: "grid" + customised_axes: false \ No newline at end of file diff --git a/tests/regression/configs/methane/default.yaml b/tests/regression/configs/methane/default.yaml index 59bba083..720d202d 100644 --- a/tests/regression/configs/methane/default.yaml +++ b/tests/regression/configs/methane/default.yaml @@ -10,6 +10,5 @@ run1: end: 1 step: 1 file_format: "MDCRD" - temperature: 112.0 kcal_force_units: True search_type: "grid" diff --git a/tests/regression/configs/methane/frame_window.yaml b/tests/regression/configs/methane/frame_window.yaml new file mode 100644 index 00000000..a2325705 --- /dev/null +++ b/tests/regression/configs/methane/frame_window.yaml @@ -0,0 +1,15 @@ +--- + +run1: + force_file: ".testdata/methane/forces.frc" + top_traj_file: + - ".testdata/methane/molecules.top" + - ".testdata/methane/trajectory.crd" + selection_string: "all" + start: 0 + end: 5 + step: 2 + file_format: "MDCRD" + temperature: 112.0 + kcal_force_units: True + search_type: "grid" \ No newline at end of file diff --git a/tests/regression/configs/methane/rad.yaml b/tests/regression/configs/methane/rad.yaml index 10e3ea39..07603931 100644 --- a/tests/regression/configs/methane/rad.yaml +++ b/tests/regression/configs/methane/rad.yaml @@ -10,5 +10,6 @@ run1: step: 1 end: 1 file_format: "MDCRD" + temperature: 112.0 # kcal_force_units: True search_type: "RAD" diff --git a/tests/regression/configs/methane/selection_subset.yaml b/tests/regression/configs/methane/selection_subset.yaml new file mode 100644 index 00000000..4734be47 --- /dev/null +++ b/tests/regression/configs/methane/selection_subset.yaml @@ -0,0 +1,15 @@ +--- + +run1: + force_file: ".testdata/methane/forces.frc" + top_traj_file: + - ".testdata/methane/molecules.top" + - ".testdata/methane/trajectory.crd" + selection_string: "protein" + start: 0 + end: 1 + step: 1 + file_format: "MDCRD" + temperature: 112.0 + kcal_force_units: True + search_type: "grid" \ No newline at end of file diff --git a/tests/regression/configs/methanol/axes_off.yaml b/tests/regression/configs/methanol/axes_off.yaml new file mode 100644 index 00000000..3d47e3e8 --- /dev/null +++ b/tests/regression/configs/methanol/axes_off.yaml @@ -0,0 +1,15 @@ +--- + +run1: + force_file: ".testdata/methanol/forces.frc" + top_traj_file: + - ".testdata/methanol/molecules.top" + - ".testdata/methanol/trajectory.crd" + selection_string: "all" + start: 0 + end: 1 + step: 1 + file_format: "MDCRD" + kcal_force_units: True + search_type: "grid" + customised_axes: false \ No newline at end of file diff --git a/tests/regression/configs/methanol/default.yaml b/tests/regression/configs/methanol/default.yaml index 9b7ee6f9..d27f7068 100644 --- a/tests/regression/configs/methanol/default.yaml +++ b/tests/regression/configs/methanol/default.yaml @@ -5,10 +5,10 @@ run1: top_traj_file: - ".testdata/methanol/molecules.top" - ".testdata/methanol/trajectory.crd" - selection_string: 'all' + selection_string: "all" start: 0 end: 1 step: 1 - file_format: 'MDCRD' + file_format: "MDCRD" kcal_force_units: True search_type: "grid" diff --git a/tests/regression/configs/methanol/frame_window.yaml b/tests/regression/configs/methanol/frame_window.yaml new file mode 100644 index 00000000..0bfdd9fa --- /dev/null +++ b/tests/regression/configs/methanol/frame_window.yaml @@ -0,0 +1,14 @@ +--- + +run1: + force_file: ".testdata/benzaldehyde/forces.frc" + top_traj_file: + - ".testdata/benzaldehyde/molecules.top" + - ".testdata/benzaldehyde/trajectory.crd" + selection_string: "all" + start: 0 + end: 5 + step: 2 + file_format: "MDCRD" + kcal_force_units: True + search_type: "grid" \ No newline at end of file diff --git a/tests/regression/configs/methanol/rad.yaml b/tests/regression/configs/methanol/rad.yaml index 1629654a..74831b38 100644 --- a/tests/regression/configs/methanol/rad.yaml +++ b/tests/regression/configs/methanol/rad.yaml @@ -5,10 +5,10 @@ run1: top_traj_file: - ".testdata/methanol/molecules.top" - ".testdata/methanol/trajectory.crd" - selection_string: 'all' + selection_string: "all" start: 0 end: 1 step: 1 - file_format: 'MDCRD' + file_format: "MDCRD" # kcal_force_units: True search_type: "RAD" diff --git a/tests/regression/configs/methanol/selection_subset.yaml b/tests/regression/configs/methanol/selection_subset.yaml new file mode 100644 index 00000000..466ade8b --- /dev/null +++ b/tests/regression/configs/methanol/selection_subset.yaml @@ -0,0 +1,14 @@ +--- + +run1: + force_file: ".testdata/methanol/forces.frc" + top_traj_file: + - ".testdata/methanol/molecules.top" + - ".testdata/methanol/trajectory.crd" + selection_string: "protein" + start: 0 + end: 1 + step: 1 + file_format: "MDCRD" + kcal_force_units: True + search_type: "grid" \ No newline at end of file diff --git a/tests/regression/configs/octonol/axes_off.yaml b/tests/regression/configs/octonol/axes_off.yaml new file mode 100644 index 00000000..7820b878 --- /dev/null +++ b/tests/regression/configs/octonol/axes_off.yaml @@ -0,0 +1,15 @@ +--- + +run1: + force_file: ".testdata/octonol/forces.frc" + top_traj_file: + - ".testdata/octonol/molecules.top" + - ".testdata/octonol/trajectory.crd" + selection_string: "all" + start: 0 + end: 1 + step: 1 + file_format: "MDCRD" + kcal_force_units: True + search_type: "grid" + customised_axes: false \ No newline at end of file diff --git a/tests/regression/configs/octonol/default.yaml b/tests/regression/configs/octonol/default.yaml index 926d03f1..8ee5ee8b 100644 --- a/tests/regression/configs/octonol/default.yaml +++ b/tests/regression/configs/octonol/default.yaml @@ -5,10 +5,10 @@ run1: top_traj_file: - ".testdata/octonol/molecules.top" - ".testdata/octonol/trajectory.crd" - selection_string: 'all' + selection_string: "all" start: 0 end: 1 step: 1 - file_format: 'MDCRD' + file_format: "MDCRD" kcal_force_units: True search_type: "grid" diff --git a/tests/regression/configs/octonol/frame_window.yaml b/tests/regression/configs/octonol/frame_window.yaml new file mode 100644 index 00000000..599ce419 --- /dev/null +++ b/tests/regression/configs/octonol/frame_window.yaml @@ -0,0 +1,14 @@ +--- + +run1: + force_file: ".testdata/octonol/forces.frc" + top_traj_file: + - ".testdata/octonol/molecules.top" + - ".testdata/octonol/trajectory.crd" + selection_string: "all" + start: 0 + end: 5 + step: 2 + file_format: "MDCRD" + kcal_force_units: True + search_type: "grid" \ No newline at end of file diff --git a/tests/regression/configs/octonol/rad.yaml b/tests/regression/configs/octonol/rad.yaml index 918f8c25..a491ec5d 100644 --- a/tests/regression/configs/octonol/rad.yaml +++ b/tests/regression/configs/octonol/rad.yaml @@ -5,10 +5,10 @@ run1: top_traj_file: - ".testdata/octonol/molecules.top" - ".testdata/octonol/trajectory.crd" - selection_string: 'all' + selection_string: "all" start: 0 end: 1 step: 1 - file_format: 'MDCRD' + file_format: "MDCRD" # kcal_force_units: True search_type: "RAD" diff --git a/tests/regression/configs/octonol/selection_subset.yaml b/tests/regression/configs/octonol/selection_subset.yaml new file mode 100644 index 00000000..b6cc3a2e --- /dev/null +++ b/tests/regression/configs/octonol/selection_subset.yaml @@ -0,0 +1,14 @@ +--- + +run1: + force_file: ".testdata/octonol/forces.frc" + top_traj_file: + - ".testdata/octonol/molecules.top" + - ".testdata/octonol/trajectory.crd" + selection_string: "protein" + start: 0 + end: 1 + step: 1 + file_format: "MDCRD" + kcal_force_units: True + search_type: "grid" \ No newline at end of file diff --git a/tests/regression/configs/water/axes_off.yaml b/tests/regression/configs/water/axes_off.yaml new file mode 100644 index 00000000..a3799544 --- /dev/null +++ b/tests/regression/configs/water/axes_off.yaml @@ -0,0 +1,15 @@ +--- + +run1: + force_file: ".testdata/water/forces.frc" + top_traj_file: + - ".testdata/water/molecules.top" + - ".testdata/water/trajectory.crd" + selection_string: "all" + start: 0 + end: 1 + step: 1 + file_format: "MDCRD" + kcal_force_units: True + search_type: "grid" + customised_axes: false \ No newline at end of file diff --git a/tests/regression/configs/water/frame_window.yaml b/tests/regression/configs/water/frame_window.yaml new file mode 100644 index 00000000..9a518e19 --- /dev/null +++ b/tests/regression/configs/water/frame_window.yaml @@ -0,0 +1,14 @@ +--- + +run1: + force_file: ".testdata/water/forces.frc" + top_traj_file: + - ".testdata/water/molecules.top" + - ".testdata/water/trajectory.crd" + selection_string: "all" + start: 0 + end: 5 + step: 2 + file_format: "MDCRD" + kcal_force_units: True + search_type: "grid" \ No newline at end of file diff --git a/tests/regression/configs/water/selection_subset.yaml b/tests/regression/configs/water/selection_subset.yaml new file mode 100644 index 00000000..62a535ad --- /dev/null +++ b/tests/regression/configs/water/selection_subset.yaml @@ -0,0 +1,14 @@ +--- + +run1: + force_file: ".testdata/water/forces.frc" + top_traj_file: + - ".testdata/water/molecules.top" + - ".testdata/water/trajectory.crd" + selection_string: "protein" + start: 0 + end: 1 + step: 1 + file_format: "MDCRD" + kcal_force_units: True + search_type: "grid" \ No newline at end of file From 2a4383fc5ea323b0b6735ad6cb2a940b38c425c8 Mon Sep 17 00:00:00 2001 From: harryswift01 Date: Fri, 27 Mar 2026 16:19:37 +0000 Subject: [PATCH 07/41] tests(regression): include all config files --- tests/regression/configs/methane/default.yaml | 1 + tests/regression/configs/methanol/frame_window.yaml | 6 +++--- 2 files changed, 4 insertions(+), 3 deletions(-) diff --git a/tests/regression/configs/methane/default.yaml b/tests/regression/configs/methane/default.yaml index 720d202d..59bba083 100644 --- a/tests/regression/configs/methane/default.yaml +++ b/tests/regression/configs/methane/default.yaml @@ -10,5 +10,6 @@ run1: end: 1 step: 1 file_format: "MDCRD" + temperature: 112.0 kcal_force_units: True search_type: "grid" diff --git a/tests/regression/configs/methanol/frame_window.yaml b/tests/regression/configs/methanol/frame_window.yaml index 0bfdd9fa..97505686 100644 --- a/tests/regression/configs/methanol/frame_window.yaml +++ b/tests/regression/configs/methanol/frame_window.yaml @@ -1,10 +1,10 @@ --- run1: - force_file: ".testdata/benzaldehyde/forces.frc" + force_file: ".testdata/methanol/forces.frc" top_traj_file: - - ".testdata/benzaldehyde/molecules.top" - - ".testdata/benzaldehyde/trajectory.crd" + - ".testdata/methanol/molecules.top" + - ".testdata/methanol/trajectory.crd" selection_string: "all" start: 0 end: 5 From 9d999b55c8690ca88987e05a94ac4799e22f7c0d Mon Sep 17 00:00:00 2001 From: harryswift01 Date: Fri, 27 Mar 2026 16:22:12 +0000 Subject: [PATCH 08/41] tests(regression): ensure all functions have google style docstrings --- tests/regression/cases.py | 32 +++++++++++++++++++++ tests/regression/conftest.py | 26 +++++++++++++++-- tests/regression/test_regression.py | 44 +++++++++++++++++++++++++++++ 3 files changed, 99 insertions(+), 3 deletions(-) diff --git a/tests/regression/cases.py b/tests/regression/cases.py index 2ca0c348..bb23894d 100644 --- a/tests/regression/cases.py +++ b/tests/regression/cases.py @@ -5,16 +5,48 @@ @dataclass(frozen=True) class RegressionCase: + """ + Represents a single regression test case. + + A regression case corresponds to a specific system and a specific YAML + configuration file, along with its associated baseline file. + + Attributes: + system (str): Name of the system (e.g. "dna", "benzene"). + config_path (Path): Path to the YAML configuration file defining the scenario. + baseline_path (Path): Path to the expected baseline JSON output. + """ system: str config_path: Path baseline_path: Path def repo_root() -> Path: + """ + Return the repository root directory. + + Returns: + Path: Absolute path to the repository root. + """ return Path(__file__).resolve().parents[2] def discover_cases(): + """ + Discover all regression test cases from the configs directory. + + Iterates over each system directory under `tests/regression/configs`, + and collects all YAML configuration files. Each configuration file is + paired with a corresponding baseline JSON file. + + Returns: + list[pytest.Param]: A list of parametrized pytest cases, each wrapping + a RegressionCase instance. + + Notes: + - Cases are automatically marked as slow unless the system is "dna". + - Baseline files are not required to exist at discovery time. + """ base_dir = Path(__file__).resolve().parent configs_root = base_dir / "configs" diff --git a/tests/regression/conftest.py b/tests/regression/conftest.py index 6693f568..9b991d86 100644 --- a/tests/regression/conftest.py +++ b/tests/regression/conftest.py @@ -4,6 +4,15 @@ def pytest_addoption(parser: pytest.Parser) -> None: + """ + Register custom command-line options for pytest. + + Adds options to control regression test execution, baseline updates, + and debugging output. + + Args: + parser (pytest.Parser): Pytest CLI parser. + """ parser.addoption( "--run-slow", action="store_true", @@ -25,6 +34,12 @@ def pytest_addoption(parser: pytest.Parser) -> None: def pytest_configure(config: pytest.Config) -> None: + """ + Register custom pytest markers. + + Args: + config (pytest.Config): Pytest configuration object. + """ config.addinivalue_line("markers", "regression: end-to-end regression tests") config.addinivalue_line("markers", "slow: long-running tests (20-30+ minutes)") @@ -33,9 +48,14 @@ def pytest_collection_modifyitems( config: pytest.Config, items: list[pytest.Item] ) -> None: """ - Regression tests are collected and runnable by default. + Modify collected test items to skip slow tests unless explicitly enabled. + + Only tests marked with `@pytest.mark.slow` are skipped when the + `--run-slow` flag is not provided. - Only @pytest.mark.slow tests are skipped unless you pass --run-slow. + Args: + config (pytest.Config): Pytest configuration object. + items (list[pytest.Item]): Collected test items. """ if config.getoption("--run-slow"): return @@ -43,4 +63,4 @@ def pytest_collection_modifyitems( skip_slow = pytest.mark.skip(reason="Skipped slow test (use --run-slow to run).") for item in items: if "slow" in item.keywords: - item.add_marker(skip_slow) + item.add_marker(skip_slow) \ No newline at end of file diff --git a/tests/regression/test_regression.py b/tests/regression/test_regression.py index 68794678..390c98c6 100644 --- a/tests/regression/test_regression.py +++ b/tests/regression/test_regression.py @@ -12,6 +12,18 @@ def _group_index(payload: dict[str, Any]) -> dict[str, dict[str, Any]]: + """ + Extract the grouped structure from a regression output payload. + + Args: + payload (dict[str, Any]): The full output payload produced by CodeEntropy. + + Returns: + dict[str, dict[str, Any]]: Mapping of group IDs to group data. + + Raises: + TypeError: If the 'groups' field is not a dictionary. + """ groups = payload.get("groups", {}) if not isinstance(groups, dict): raise TypeError("payload['groups'] must be a dict") @@ -25,6 +37,21 @@ def _compare_grouped( rtol: float, atol: float, ) -> None: + """ + Compare grouped regression outputs against baseline data. + + Performs a structured comparison of group components and totals, + using numerical tolerances for floating-point comparisons. + + Args: + got_payload (dict[str, Any]): Output generated by the test run. + baseline_payload (dict[str, Any]): Reference baseline output. + rtol (float): Relative tolerance for numeric comparisons. + atol (float): Absolute tolerance for numeric comparisons. + + Raises: + AssertionError: If any mismatches are found between outputs and baseline. + """ got_groups = _group_index(got_payload) base_groups = _group_index(baseline_payload) @@ -80,6 +107,23 @@ def _compare_grouped( def test_regression_matches_baseline( tmp_path: Path, case, request: pytest.FixtureRequest ) -> None: + """ + Execute a regression test for a single scenario and compare against baseline. + + This test: + 1. Loads a YAML configuration for a given system/scenario + 2. Runs CodeEntropy using that configuration + 3. Compares the output payload against a stored baseline JSON + 4. Optionally updates the baseline if --update-baselines is set + + Args: + tmp_path (Path): Temporary directory provided by pytest. + case (RegressionCase): Parameterized regression case. + request (pytest.FixtureRequest): Pytest request object for accessing CLI options. + + Raises: + AssertionError: If the output does not match the baseline or baseline is missing. + """ system = case.system config_path = case.config_path baseline_path = case.baseline_path From 50ce32587bece9c479f957a4b70e7667879a699a Mon Sep 17 00:00:00 2001 From: harryswift01 Date: Fri, 27 Mar 2026 16:24:14 +0000 Subject: [PATCH 09/41] chore(pre-commit): ensure pre-commit is applied --- tests/regression/cases.py | 4 +++- tests/regression/configs/benzaldehyde/axes_off.yaml | 2 +- .../configs/benzaldehyde/frame_window.yaml | 2 +- .../configs/benzaldehyde/selection_subset.yaml | 2 +- tests/regression/configs/benzene/axes_off.yaml | 2 +- tests/regression/configs/benzene/frame_window.yaml | 2 +- .../configs/benzene/selection_subset.yaml | 2 +- tests/regression/configs/cyclohexane/axes_off.yaml | 2 +- .../configs/cyclohexane/frame_window.yaml | 2 +- .../configs/cyclohexane/selection_subset.yaml | 2 +- tests/regression/configs/dna/axes_off.yaml | 2 +- tests/regression/configs/dna/frame_window.yaml | 2 +- tests/regression/configs/dna/selection_subset.yaml | 2 +- .../regression/configs/ethyl-acetate/axes_off.yaml | 2 +- .../configs/ethyl-acetate/frame_window.yaml | 2 +- .../configs/ethyl-acetate/selection_subset.yaml | 2 +- tests/regression/configs/methane/axes_off.yaml | 2 +- tests/regression/configs/methane/frame_window.yaml | 2 +- .../configs/methane/selection_subset.yaml | 2 +- tests/regression/configs/methanol/axes_off.yaml | 2 +- tests/regression/configs/methanol/frame_window.yaml | 2 +- .../configs/methanol/selection_subset.yaml | 2 +- tests/regression/configs/octonol/axes_off.yaml | 2 +- tests/regression/configs/octonol/frame_window.yaml | 2 +- .../configs/octonol/selection_subset.yaml | 2 +- tests/regression/configs/water/axes_off.yaml | 2 +- tests/regression/configs/water/frame_window.yaml | 2 +- .../regression/configs/water/selection_subset.yaml | 2 +- tests/regression/conftest.py | 2 +- tests/regression/test_regression.py | 13 ++++++++----- 30 files changed, 39 insertions(+), 34 deletions(-) diff --git a/tests/regression/cases.py b/tests/regression/cases.py index bb23894d..39cd7461 100644 --- a/tests/regression/cases.py +++ b/tests/regression/cases.py @@ -1,5 +1,6 @@ from dataclasses import dataclass from pathlib import Path + import pytest @@ -16,6 +17,7 @@ class RegressionCase: config_path (Path): Path to the YAML configuration file defining the scenario. baseline_path (Path): Path to the expected baseline JSON output. """ + system: str config_path: Path baseline_path: Path @@ -74,4 +76,4 @@ def discover_cases(): ) ) - return cases \ No newline at end of file + return cases diff --git a/tests/regression/configs/benzaldehyde/axes_off.yaml b/tests/regression/configs/benzaldehyde/axes_off.yaml index b86eb3bd..3b29c9c7 100644 --- a/tests/regression/configs/benzaldehyde/axes_off.yaml +++ b/tests/regression/configs/benzaldehyde/axes_off.yaml @@ -12,4 +12,4 @@ run1: file_format: "MDCRD" kcal_force_units: True search_type: "grid" - customised_axes: false \ No newline at end of file + customised_axes: false diff --git a/tests/regression/configs/benzaldehyde/frame_window.yaml b/tests/regression/configs/benzaldehyde/frame_window.yaml index 0bfdd9fa..f608b0af 100644 --- a/tests/regression/configs/benzaldehyde/frame_window.yaml +++ b/tests/regression/configs/benzaldehyde/frame_window.yaml @@ -11,4 +11,4 @@ run1: step: 2 file_format: "MDCRD" kcal_force_units: True - search_type: "grid" \ No newline at end of file + search_type: "grid" diff --git a/tests/regression/configs/benzaldehyde/selection_subset.yaml b/tests/regression/configs/benzaldehyde/selection_subset.yaml index b9fb06be..3bf24a46 100644 --- a/tests/regression/configs/benzaldehyde/selection_subset.yaml +++ b/tests/regression/configs/benzaldehyde/selection_subset.yaml @@ -11,4 +11,4 @@ run1: step: 1 file_format: "MDCRD" kcal_force_units: True - search_type: "grid" \ No newline at end of file + search_type: "grid" diff --git a/tests/regression/configs/benzene/axes_off.yaml b/tests/regression/configs/benzene/axes_off.yaml index 019128fb..97a1e9f0 100644 --- a/tests/regression/configs/benzene/axes_off.yaml +++ b/tests/regression/configs/benzene/axes_off.yaml @@ -12,4 +12,4 @@ run1: file_format: "MDCRD" kcal_force_units: True search_type: "grid" - customised_axes: false \ No newline at end of file + customised_axes: false diff --git a/tests/regression/configs/benzene/frame_window.yaml b/tests/regression/configs/benzene/frame_window.yaml index 91e5bc21..cb0f5a6d 100644 --- a/tests/regression/configs/benzene/frame_window.yaml +++ b/tests/regression/configs/benzene/frame_window.yaml @@ -11,4 +11,4 @@ run1: step: 2 file_format: "MDCRD" kcal_force_units: True - search_type: "grid" \ No newline at end of file + search_type: "grid" diff --git a/tests/regression/configs/benzene/selection_subset.yaml b/tests/regression/configs/benzene/selection_subset.yaml index 8eb2a960..91dbb034 100644 --- a/tests/regression/configs/benzene/selection_subset.yaml +++ b/tests/regression/configs/benzene/selection_subset.yaml @@ -11,4 +11,4 @@ run1: step: 1 file_format: "MDCRD" kcal_force_units: True - search_type: "grid" \ No newline at end of file + search_type: "grid" diff --git a/tests/regression/configs/cyclohexane/axes_off.yaml b/tests/regression/configs/cyclohexane/axes_off.yaml index 1d80c74e..ba16e52d 100644 --- a/tests/regression/configs/cyclohexane/axes_off.yaml +++ b/tests/regression/configs/cyclohexane/axes_off.yaml @@ -12,4 +12,4 @@ run1: file_format: "MDCRD" kcal_force_units: True search_type: "grid" - customised_axes: false \ No newline at end of file + customised_axes: false diff --git a/tests/regression/configs/cyclohexane/frame_window.yaml b/tests/regression/configs/cyclohexane/frame_window.yaml index e4f885f5..93ac1b4d 100644 --- a/tests/regression/configs/cyclohexane/frame_window.yaml +++ b/tests/regression/configs/cyclohexane/frame_window.yaml @@ -11,4 +11,4 @@ run1: step: 2 file_format: "MDCRD" kcal_force_units: True - search_type: "grid" \ No newline at end of file + search_type: "grid" diff --git a/tests/regression/configs/cyclohexane/selection_subset.yaml b/tests/regression/configs/cyclohexane/selection_subset.yaml index 2a21ed4a..f544289c 100644 --- a/tests/regression/configs/cyclohexane/selection_subset.yaml +++ b/tests/regression/configs/cyclohexane/selection_subset.yaml @@ -11,4 +11,4 @@ run1: step: 1 file_format: "MDCRD" kcal_force_units: True - search_type: "grid" \ No newline at end of file + search_type: "grid" diff --git a/tests/regression/configs/dna/axes_off.yaml b/tests/regression/configs/dna/axes_off.yaml index 03f5df06..771360f2 100644 --- a/tests/regression/configs/dna/axes_off.yaml +++ b/tests/regression/configs/dna/axes_off.yaml @@ -11,4 +11,4 @@ run1: file_format: "MDCRD" kcal_force_units: True search_type: "grid" - customised_axes: false \ No newline at end of file + customised_axes: false diff --git a/tests/regression/configs/dna/frame_window.yaml b/tests/regression/configs/dna/frame_window.yaml index 0bfdd9fa..f608b0af 100644 --- a/tests/regression/configs/dna/frame_window.yaml +++ b/tests/regression/configs/dna/frame_window.yaml @@ -11,4 +11,4 @@ run1: step: 2 file_format: "MDCRD" kcal_force_units: True - search_type: "grid" \ No newline at end of file + search_type: "grid" diff --git a/tests/regression/configs/dna/selection_subset.yaml b/tests/regression/configs/dna/selection_subset.yaml index b9fb06be..3bf24a46 100644 --- a/tests/regression/configs/dna/selection_subset.yaml +++ b/tests/regression/configs/dna/selection_subset.yaml @@ -11,4 +11,4 @@ run1: step: 1 file_format: "MDCRD" kcal_force_units: True - search_type: "grid" \ No newline at end of file + search_type: "grid" diff --git a/tests/regression/configs/ethyl-acetate/axes_off.yaml b/tests/regression/configs/ethyl-acetate/axes_off.yaml index b86eb3bd..3b29c9c7 100644 --- a/tests/regression/configs/ethyl-acetate/axes_off.yaml +++ b/tests/regression/configs/ethyl-acetate/axes_off.yaml @@ -12,4 +12,4 @@ run1: file_format: "MDCRD" kcal_force_units: True search_type: "grid" - customised_axes: false \ No newline at end of file + customised_axes: false diff --git a/tests/regression/configs/ethyl-acetate/frame_window.yaml b/tests/regression/configs/ethyl-acetate/frame_window.yaml index 5d165f0e..abd8a395 100644 --- a/tests/regression/configs/ethyl-acetate/frame_window.yaml +++ b/tests/regression/configs/ethyl-acetate/frame_window.yaml @@ -11,4 +11,4 @@ run1: step: 2 file_format: "MDCRD" kcal_force_units: True - search_type: "grid" \ No newline at end of file + search_type: "grid" diff --git a/tests/regression/configs/ethyl-acetate/selection_subset.yaml b/tests/regression/configs/ethyl-acetate/selection_subset.yaml index fdd0b693..625cdb33 100644 --- a/tests/regression/configs/ethyl-acetate/selection_subset.yaml +++ b/tests/regression/configs/ethyl-acetate/selection_subset.yaml @@ -11,4 +11,4 @@ run1: step: 1 file_format: "MDCRD" kcal_force_units: True - search_type: "grid" \ No newline at end of file + search_type: "grid" diff --git a/tests/regression/configs/methane/axes_off.yaml b/tests/regression/configs/methane/axes_off.yaml index 7293f41b..0d783d2b 100644 --- a/tests/regression/configs/methane/axes_off.yaml +++ b/tests/regression/configs/methane/axes_off.yaml @@ -12,4 +12,4 @@ run1: file_format: "MDCRD" kcal_force_units: True search_type: "grid" - customised_axes: false \ No newline at end of file + customised_axes: false diff --git a/tests/regression/configs/methane/frame_window.yaml b/tests/regression/configs/methane/frame_window.yaml index a2325705..57de494f 100644 --- a/tests/regression/configs/methane/frame_window.yaml +++ b/tests/regression/configs/methane/frame_window.yaml @@ -12,4 +12,4 @@ run1: file_format: "MDCRD" temperature: 112.0 kcal_force_units: True - search_type: "grid" \ No newline at end of file + search_type: "grid" diff --git a/tests/regression/configs/methane/selection_subset.yaml b/tests/regression/configs/methane/selection_subset.yaml index 4734be47..834b295f 100644 --- a/tests/regression/configs/methane/selection_subset.yaml +++ b/tests/regression/configs/methane/selection_subset.yaml @@ -12,4 +12,4 @@ run1: file_format: "MDCRD" temperature: 112.0 kcal_force_units: True - search_type: "grid" \ No newline at end of file + search_type: "grid" diff --git a/tests/regression/configs/methanol/axes_off.yaml b/tests/regression/configs/methanol/axes_off.yaml index 3d47e3e8..92cb21f5 100644 --- a/tests/regression/configs/methanol/axes_off.yaml +++ b/tests/regression/configs/methanol/axes_off.yaml @@ -12,4 +12,4 @@ run1: file_format: "MDCRD" kcal_force_units: True search_type: "grid" - customised_axes: false \ No newline at end of file + customised_axes: false diff --git a/tests/regression/configs/methanol/frame_window.yaml b/tests/regression/configs/methanol/frame_window.yaml index 97505686..3266624d 100644 --- a/tests/regression/configs/methanol/frame_window.yaml +++ b/tests/regression/configs/methanol/frame_window.yaml @@ -11,4 +11,4 @@ run1: step: 2 file_format: "MDCRD" kcal_force_units: True - search_type: "grid" \ No newline at end of file + search_type: "grid" diff --git a/tests/regression/configs/methanol/selection_subset.yaml b/tests/regression/configs/methanol/selection_subset.yaml index 466ade8b..929a975e 100644 --- a/tests/regression/configs/methanol/selection_subset.yaml +++ b/tests/regression/configs/methanol/selection_subset.yaml @@ -11,4 +11,4 @@ run1: step: 1 file_format: "MDCRD" kcal_force_units: True - search_type: "grid" \ No newline at end of file + search_type: "grid" diff --git a/tests/regression/configs/octonol/axes_off.yaml b/tests/regression/configs/octonol/axes_off.yaml index 7820b878..4317805c 100644 --- a/tests/regression/configs/octonol/axes_off.yaml +++ b/tests/regression/configs/octonol/axes_off.yaml @@ -12,4 +12,4 @@ run1: file_format: "MDCRD" kcal_force_units: True search_type: "grid" - customised_axes: false \ No newline at end of file + customised_axes: false diff --git a/tests/regression/configs/octonol/frame_window.yaml b/tests/regression/configs/octonol/frame_window.yaml index 599ce419..9643ee3d 100644 --- a/tests/regression/configs/octonol/frame_window.yaml +++ b/tests/regression/configs/octonol/frame_window.yaml @@ -11,4 +11,4 @@ run1: step: 2 file_format: "MDCRD" kcal_force_units: True - search_type: "grid" \ No newline at end of file + search_type: "grid" diff --git a/tests/regression/configs/octonol/selection_subset.yaml b/tests/regression/configs/octonol/selection_subset.yaml index b6cc3a2e..3a7d6fa7 100644 --- a/tests/regression/configs/octonol/selection_subset.yaml +++ b/tests/regression/configs/octonol/selection_subset.yaml @@ -11,4 +11,4 @@ run1: step: 1 file_format: "MDCRD" kcal_force_units: True - search_type: "grid" \ No newline at end of file + search_type: "grid" diff --git a/tests/regression/configs/water/axes_off.yaml b/tests/regression/configs/water/axes_off.yaml index a3799544..028a32d5 100644 --- a/tests/regression/configs/water/axes_off.yaml +++ b/tests/regression/configs/water/axes_off.yaml @@ -12,4 +12,4 @@ run1: file_format: "MDCRD" kcal_force_units: True search_type: "grid" - customised_axes: false \ No newline at end of file + customised_axes: false diff --git a/tests/regression/configs/water/frame_window.yaml b/tests/regression/configs/water/frame_window.yaml index 9a518e19..fb313b83 100644 --- a/tests/regression/configs/water/frame_window.yaml +++ b/tests/regression/configs/water/frame_window.yaml @@ -11,4 +11,4 @@ run1: step: 2 file_format: "MDCRD" kcal_force_units: True - search_type: "grid" \ No newline at end of file + search_type: "grid" diff --git a/tests/regression/configs/water/selection_subset.yaml b/tests/regression/configs/water/selection_subset.yaml index 62a535ad..fb91a7e3 100644 --- a/tests/regression/configs/water/selection_subset.yaml +++ b/tests/regression/configs/water/selection_subset.yaml @@ -11,4 +11,4 @@ run1: step: 1 file_format: "MDCRD" kcal_force_units: True - search_type: "grid" \ No newline at end of file + search_type: "grid" diff --git a/tests/regression/conftest.py b/tests/regression/conftest.py index 9b991d86..58249369 100644 --- a/tests/regression/conftest.py +++ b/tests/regression/conftest.py @@ -63,4 +63,4 @@ def pytest_collection_modifyitems( skip_slow = pytest.mark.skip(reason="Skipped slow test (use --run-slow to run).") for item in items: if "slow" in item.keywords: - item.add_marker(skip_slow) \ No newline at end of file + item.add_marker(skip_slow) diff --git a/tests/regression/test_regression.py b/tests/regression/test_regression.py index 390c98c6..99f70df1 100644 --- a/tests/regression/test_regression.py +++ b/tests/regression/test_regression.py @@ -7,8 +7,8 @@ import numpy as np import pytest -from tests.regression.helpers import run_codeentropy_with_config from tests.regression.cases import discover_cases +from tests.regression.helpers import run_codeentropy_with_config def _group_index(payload: dict[str, Any]) -> dict[str, dict[str, Any]]: @@ -66,7 +66,9 @@ def _compare_grouped( base_components = base_g.get("components", {}) got_components = got_g.get("components", {}) - if not isinstance(base_components, dict) or not isinstance(got_components, dict): + if not isinstance(base_components, dict) or not isinstance( + got_components, dict + ): mismatches.append(f"group {gid}: components must be dicts") continue @@ -96,7 +98,8 @@ def _compare_grouped( ) except AssertionError: mismatches.append( - f"group {gid} total: expected={base_g['total']} got={got_g.get('total')}" + f"group {gid} total: expected={base_g['total']} " + f"got={got_g.get('total')}" ) assert not mismatches, "Mismatches:\n" + "\n".join(" " + m for m in mismatches) @@ -119,10 +122,10 @@ def test_regression_matches_baseline( Args: tmp_path (Path): Temporary directory provided by pytest. case (RegressionCase): Parameterized regression case. - request (pytest.FixtureRequest): Pytest request object for accessing CLI options. + request (pytest.FixtureRequest): Pytest request object for accessing CLI options Raises: - AssertionError: If the output does not match the baseline or baseline is missing. + AssertionError: If the output does not match the baseline or baseline is missing """ system = case.system config_path = case.config_path From a82e25446e4a53d14163c152679a3ae5729990c5 Mon Sep 17 00:00:00 2001 From: harryswift01 Date: Fri, 27 Mar 2026 16:32:40 +0000 Subject: [PATCH 10/41] tests(unit): update config paths within unit tests from regression upgrade --- tests/unit/CodeEntropy/levels/test_search.py | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/tests/unit/CodeEntropy/levels/test_search.py b/tests/unit/CodeEntropy/levels/test_search.py index 2e970212..51b15e0c 100644 --- a/tests/unit/CodeEntropy/levels/test_search.py +++ b/tests/unit/CodeEntropy/levels/test_search.py @@ -31,7 +31,7 @@ def test_get_RAD_neighbors(tmp_path: Path): system = "methane" repo_root = Path(__file__).resolve().parents[4] config_path = ( - repo_root / "tests" / "regression" / "configs" / system / "config.yaml" + repo_root / "tests" / "regression" / "configs" / system / "default.yaml" ) tmp_path.mkdir(parents=True, exist_ok=True) @@ -82,7 +82,7 @@ def test_get_grid_neighbors(tmp_path: Path): system = "methane" repo_root = Path(__file__).resolve().parents[4] config_path = ( - repo_root / "tests" / "regression" / "configs" / system / "config.yaml" + repo_root / "tests" / "regression" / "configs" / system / "default.yaml" ) tmp_path.mkdir(parents=True, exist_ok=True) From 06853f41ba1887213fe7ab94c95fe14dab035eaa Mon Sep 17 00:00:00 2001 From: harryswift01 Date: Fri, 27 Mar 2026 16:40:45 +0000 Subject: [PATCH 11/41] tests(regression): use correct file name for dna examples --- tests/regression/configs/dna/axes_off.yaml | 4 ++-- tests/regression/configs/dna/default.yaml | 4 ++-- tests/regression/configs/dna/frame_window.yaml | 8 ++------ tests/regression/configs/dna/rad.yaml | 6 ++---- tests/regression/configs/dna/selection_subset.yaml | 7 ++----- 5 files changed, 10 insertions(+), 19 deletions(-) diff --git a/tests/regression/configs/dna/axes_off.yaml b/tests/regression/configs/dna/axes_off.yaml index 771360f2..a1c763f0 100644 --- a/tests/regression/configs/dna/axes_off.yaml +++ b/tests/regression/configs/dna/axes_off.yaml @@ -2,8 +2,8 @@ run1: top_traj_file: - - ".testdata/benzaldehyde/molecules.top" - - ".testdata/benzaldehyde/trajectory.crd" + - ".testdata/dna/md_A4_dna.tpr" + - ".testdata/dna/md_A4_dna_xf.trr" selection_string: "all" start: 0 end: 1 diff --git a/tests/regression/configs/dna/default.yaml b/tests/regression/configs/dna/default.yaml index eecc7c9b..e1567c7d 100644 --- a/tests/regression/configs/dna/default.yaml +++ b/tests/regression/configs/dna/default.yaml @@ -2,8 +2,8 @@ run1: top_traj_file: - - ".testdata/dna/molecules.top" - - ".testdata/dna/trajectory.crd" + - ".testdata/dna/md_A4_dna.tpr" + - ".testdata/dna/md_A4_dna_xf.trr" selection_string: "all" start: 0 end: 1 diff --git a/tests/regression/configs/dna/frame_window.yaml b/tests/regression/configs/dna/frame_window.yaml index f608b0af..5a0e4516 100644 --- a/tests/regression/configs/dna/frame_window.yaml +++ b/tests/regression/configs/dna/frame_window.yaml @@ -1,14 +1,10 @@ --- run1: - force_file: ".testdata/benzaldehyde/forces.frc" top_traj_file: - - ".testdata/benzaldehyde/molecules.top" - - ".testdata/benzaldehyde/trajectory.crd" + - ".testdata/dna/md_A4_dna.tpr" + - ".testdata/dna/md_A4_dna_xf.trr" selection_string: "all" start: 0 end: 5 step: 2 - file_format: "MDCRD" - kcal_force_units: True - search_type: "grid" diff --git a/tests/regression/configs/dna/rad.yaml b/tests/regression/configs/dna/rad.yaml index 455599b0..79a9979c 100644 --- a/tests/regression/configs/dna/rad.yaml +++ b/tests/regression/configs/dna/rad.yaml @@ -1,14 +1,12 @@ --- run1: - force_file: ".testdata/benzaldehyde/forces.frc" top_traj_file: - - ".testdata/benzaldehyde/molecules.top" - - ".testdata/benzaldehyde/trajectory.crd" + - ".testdata/dna/md_A4_dna.tpr" + - ".testdata/dna/md_A4_dna_xf.trr" selection_string: "all" start: 0 end: 1 step: 1 - file_format: "MDCRD" # kcal_force_units: True search_type: "RAD" diff --git a/tests/regression/configs/dna/selection_subset.yaml b/tests/regression/configs/dna/selection_subset.yaml index 3bf24a46..88dba597 100644 --- a/tests/regression/configs/dna/selection_subset.yaml +++ b/tests/regression/configs/dna/selection_subset.yaml @@ -1,14 +1,11 @@ --- run1: - force_file: ".testdata/benzaldehyde/forces.frc" top_traj_file: - - ".testdata/benzaldehyde/molecules.top" - - ".testdata/benzaldehyde/trajectory.crd" + - ".testdata/dna/md_A4_dna.tpr" + - ".testdata/dna/md_A4_dna_xf.trr" selection_string: "protein" start: 0 end: 1 step: 1 - file_format: "MDCRD" - kcal_force_units: True search_type: "grid" From c9c7e0511b9432d3a9cf4946b852c75403043a22 Mon Sep 17 00:00:00 2001 From: harryswift01 Date: Fri, 27 Mar 2026 16:51:58 +0000 Subject: [PATCH 12/41] tests(regression): add dna regression test into the baselines --- tests/regression/baselines/dna/default.json | 61 +++++++++++++++++++ tests/regression/configs/dna/axes_off.yaml | 14 ----- .../regression/configs/dna/frame_window.yaml | 10 --- tests/regression/configs/dna/rad.yaml | 12 ---- .../configs/dna/selection_subset.yaml | 11 ---- 5 files changed, 61 insertions(+), 47 deletions(-) create mode 100644 tests/regression/baselines/dna/default.json delete mode 100644 tests/regression/configs/dna/axes_off.yaml delete mode 100644 tests/regression/configs/dna/frame_window.yaml delete mode 100644 tests/regression/configs/dna/rad.yaml delete mode 100644 tests/regression/configs/dna/selection_subset.yaml diff --git a/tests/regression/baselines/dna/default.json b/tests/regression/baselines/dna/default.json new file mode 100644 index 00000000..96afc42a --- /dev/null +++ b/tests/regression/baselines/dna/default.json @@ -0,0 +1,61 @@ +{ + "args": { + "top_traj_file": [ + "/home/harry-swift/BioSim/software/CodeEntropy/.testdata/dna/md_A4_dna.tpr", + "/home/harry-swift/BioSim/software/CodeEntropy/.testdata/dna/md_A4_dna_xf.trr" + ], + "force_file": null, + "file_format": null, + "kcal_force_units": false, + "selection_string": "all", + "start": 0, + "end": 1, + "step": 1, + "bin_width": 30, + "temperature": 298.0, + "verbose": false, + "output_file": "/tmp/pytest-of-harry-swift/pytest-25/test_regression_matches_baseli0/job001/output_file.json", + "force_partitioning": 0.5, + "water_entropy": true, + "grouping": "molecules", + "combined_forcetorque": true, + "customised_axes": true, + "search_type": "RAD" + }, + "provenance": { + "python": "3.14.3", + "platform": "Linux-6.17.0-19-generic-x86_64-with-glibc2.39", + "codeentropy_version": "2.1.0", + "git_sha": "06853f41ba1887213fe7ab94c95fe14dab035eaa" + }, + "groups": { + "0": { + "components": { + "united_atom:Transvibrational": 0.0, + "united_atom:Rovibrational": 0.002160679012128457, + "residue:Transvibrational": 0.0, + "residue:Rovibrational": 3.376800684085249, + "polymer:FTmat-Transvibrational": 12.341104347192612, + "polymer:FTmat-Rovibrational": 0.0, + "united_atom:Conformational": 7.0411434528236345, + "residue:Conformational": 0.0, + "polymer:Orientational": 4.758905336627712 + }, + "total": 27.52011449974134 + }, + "1": { + "components": { + "united_atom:Transvibrational": 0.0, + "united_atom:Rovibrational": 0.01846427765949586, + "residue:Transvibrational": 0.0, + "residue:Rovibrational": 2.3863201082544565, + "polymer:FTmat-Transvibrational": 11.11037253388596, + "polymer:FTmat-Rovibrational": 0.0, + "united_atom:Conformational": 6.410455987098191, + "residue:Conformational": 0.46183561256411515, + "polymer:Orientational": 4.758905336627712 + }, + "total": 25.14635385608993 + } + } +} diff --git a/tests/regression/configs/dna/axes_off.yaml b/tests/regression/configs/dna/axes_off.yaml deleted file mode 100644 index a1c763f0..00000000 --- a/tests/regression/configs/dna/axes_off.yaml +++ /dev/null @@ -1,14 +0,0 @@ ---- - -run1: - top_traj_file: - - ".testdata/dna/md_A4_dna.tpr" - - ".testdata/dna/md_A4_dna_xf.trr" - selection_string: "all" - start: 0 - end: 1 - step: 1 - file_format: "MDCRD" - kcal_force_units: True - search_type: "grid" - customised_axes: false diff --git a/tests/regression/configs/dna/frame_window.yaml b/tests/regression/configs/dna/frame_window.yaml deleted file mode 100644 index 5a0e4516..00000000 --- a/tests/regression/configs/dna/frame_window.yaml +++ /dev/null @@ -1,10 +0,0 @@ ---- - -run1: - top_traj_file: - - ".testdata/dna/md_A4_dna.tpr" - - ".testdata/dna/md_A4_dna_xf.trr" - selection_string: "all" - start: 0 - end: 5 - step: 2 diff --git a/tests/regression/configs/dna/rad.yaml b/tests/regression/configs/dna/rad.yaml deleted file mode 100644 index 79a9979c..00000000 --- a/tests/regression/configs/dna/rad.yaml +++ /dev/null @@ -1,12 +0,0 @@ ---- - -run1: - top_traj_file: - - ".testdata/dna/md_A4_dna.tpr" - - ".testdata/dna/md_A4_dna_xf.trr" - selection_string: "all" - start: 0 - end: 1 - step: 1 -# kcal_force_units: True - search_type: "RAD" diff --git a/tests/regression/configs/dna/selection_subset.yaml b/tests/regression/configs/dna/selection_subset.yaml deleted file mode 100644 index 88dba597..00000000 --- a/tests/regression/configs/dna/selection_subset.yaml +++ /dev/null @@ -1,11 +0,0 @@ ---- - -run1: - top_traj_file: - - ".testdata/dna/md_A4_dna.tpr" - - ".testdata/dna/md_A4_dna_xf.trr" - selection_string: "protein" - start: 0 - end: 1 - step: 1 - search_type: "grid" From 9667ae369d796d0db2993d94863897c4701fcc00 Mon Sep 17 00:00:00 2001 From: harryswift01 Date: Mon, 30 Mar 2026 09:36:38 +0100 Subject: [PATCH 13/41] tests(regression): update `benzaldehyde/selection_subset.yaml` to include correct range --- tests/regression/configs/benzaldehyde/selection_subset.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/tests/regression/configs/benzaldehyde/selection_subset.yaml b/tests/regression/configs/benzaldehyde/selection_subset.yaml index 3bf24a46..576c4bac 100644 --- a/tests/regression/configs/benzaldehyde/selection_subset.yaml +++ b/tests/regression/configs/benzaldehyde/selection_subset.yaml @@ -5,7 +5,7 @@ run1: top_traj_file: - ".testdata/benzaldehyde/molecules.top" - ".testdata/benzaldehyde/trajectory.crd" - selection_string: "protein" + selection_string: "resname BENZ and resid 1:10" start: 0 end: 1 step: 1 From fd43daa70b97a0dea0b254e6c20846b17cc7d172 Mon Sep 17 00:00:00 2001 From: harryswift01 Date: Mon, 30 Mar 2026 09:41:30 +0100 Subject: [PATCH 14/41] tests(regression): update `benzene/selection_subset.yaml` to include correct range --- tests/regression/configs/benzene/selection_subset.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/tests/regression/configs/benzene/selection_subset.yaml b/tests/regression/configs/benzene/selection_subset.yaml index 91dbb034..20fa2304 100644 --- a/tests/regression/configs/benzene/selection_subset.yaml +++ b/tests/regression/configs/benzene/selection_subset.yaml @@ -5,7 +5,7 @@ run1: top_traj_file: - ".testdata/benzene/molecules.top" - ".testdata/benzene/trajectory.crd" - selection_string: "protein" + selection_string: "resname BEN and resid 1:10" start: 0 end: 1 step: 1 From ca40b4eede1858e4404e423f9107c4e50b1b71cd Mon Sep 17 00:00:00 2001 From: harryswift01 Date: Mon, 30 Mar 2026 09:43:13 +0100 Subject: [PATCH 15/41] tests(regression): update "cyclohexane/selection_subset.yaml` to include correct range --- tests/regression/configs/cyclohexane/selection_subset.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/tests/regression/configs/cyclohexane/selection_subset.yaml b/tests/regression/configs/cyclohexane/selection_subset.yaml index f544289c..18837f87 100644 --- a/tests/regression/configs/cyclohexane/selection_subset.yaml +++ b/tests/regression/configs/cyclohexane/selection_subset.yaml @@ -5,7 +5,7 @@ run1: top_traj_file: - ".testdata/cyclohexane/molecules.top" - ".testdata/cyclohexane/trajectory.crd" - selection_string: "protein" + selection_string: "resname CHX and resid 1:10" start: 0 end: 1 step: 1 From 0b25cfba3afd3d515993ed9aa39d6e9c18a97a8c Mon Sep 17 00:00:00 2001 From: harryswift01 Date: Mon, 30 Mar 2026 09:50:53 +0100 Subject: [PATCH 16/41] tests(regression): add additional test configurations for DNA example --- tests/regression/configs/dna/axes_off.yaml | 11 +++++++++++ tests/regression/configs/dna/frame_window.yaml | 10 ++++++++++ tests/regression/configs/dna/selection_subset.yaml | 10 ++++++++++ 3 files changed, 31 insertions(+) create mode 100644 tests/regression/configs/dna/axes_off.yaml create mode 100644 tests/regression/configs/dna/frame_window.yaml create mode 100644 tests/regression/configs/dna/selection_subset.yaml diff --git a/tests/regression/configs/dna/axes_off.yaml b/tests/regression/configs/dna/axes_off.yaml new file mode 100644 index 00000000..5583ef15 --- /dev/null +++ b/tests/regression/configs/dna/axes_off.yaml @@ -0,0 +1,11 @@ +--- + +run1: + top_traj_file: + - ".testdata/dna/md_A4_dna.tpr" + - ".testdata/dna/md_A4_dna_xf.trr" + selection_string: "all" + start: 0 + end: 5 + step: 2 + customised_axes: false diff --git a/tests/regression/configs/dna/frame_window.yaml b/tests/regression/configs/dna/frame_window.yaml new file mode 100644 index 00000000..5a0e4516 --- /dev/null +++ b/tests/regression/configs/dna/frame_window.yaml @@ -0,0 +1,10 @@ +--- + +run1: + top_traj_file: + - ".testdata/dna/md_A4_dna.tpr" + - ".testdata/dna/md_A4_dna_xf.trr" + selection_string: "all" + start: 0 + end: 5 + step: 2 diff --git a/tests/regression/configs/dna/selection_subset.yaml b/tests/regression/configs/dna/selection_subset.yaml new file mode 100644 index 00000000..cb6b294c --- /dev/null +++ b/tests/regression/configs/dna/selection_subset.yaml @@ -0,0 +1,10 @@ +--- + +run1: + top_traj_file: + - ".testdata/dna/md_A4_dna.tpr" + - ".testdata/dna/md_A4_dna_xf.trr" + selection_string: "resname DA" + start: 0 + end: 1 + step: 1 From 91c393dc1614937ab2b2984fe9400d74e5833f88 Mon Sep 17 00:00:00 2001 From: harryswift01 Date: Mon, 30 Mar 2026 09:58:24 +0100 Subject: [PATCH 17/41] tests(regression): update `ethyl-acetate/selection_subset.yaml` to include correct range --- tests/regression/configs/ethyl-acetate/selection_subset.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/tests/regression/configs/ethyl-acetate/selection_subset.yaml b/tests/regression/configs/ethyl-acetate/selection_subset.yaml index 625cdb33..e238d1d1 100644 --- a/tests/regression/configs/ethyl-acetate/selection_subset.yaml +++ b/tests/regression/configs/ethyl-acetate/selection_subset.yaml @@ -5,7 +5,7 @@ run1: top_traj_file: - ".testdata/ethyl-acetate/molecules.top" - ".testdata/ethyl-acetate/trajectory.crd" - selection_string: "protein" + selection_string: "resname EA and resid 1:10" start: 0 end: 1 step: 1 From 0c61c989a4f6e76caf4df53f8f5ecdce5e7034ad Mon Sep 17 00:00:00 2001 From: harryswift01 Date: Mon, 30 Mar 2026 10:09:28 +0100 Subject: [PATCH 18/41] tests(regression): add temperature perameter in `methane/axes_off.yaml` configuration --- tests/regression/configs/methane/axes_off.yaml | 1 + 1 file changed, 1 insertion(+) diff --git a/tests/regression/configs/methane/axes_off.yaml b/tests/regression/configs/methane/axes_off.yaml index 0d783d2b..e1b79a8e 100644 --- a/tests/regression/configs/methane/axes_off.yaml +++ b/tests/regression/configs/methane/axes_off.yaml @@ -10,6 +10,7 @@ run1: end: 1 step: 1 file_format: "MDCRD" + temperature: 112.0 kcal_force_units: True search_type: "grid" customised_axes: false From e40ea6fc2eaa9856c83dc1aea28ccc6f1145d3c8 Mon Sep 17 00:00:00 2001 From: harryswift01 Date: Mon, 30 Mar 2026 10:21:46 +0100 Subject: [PATCH 19/41] tests(regression): update `methane/selection_subset.yaml` to include correct range --- tests/regression/configs/methane/selection_subset.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/tests/regression/configs/methane/selection_subset.yaml b/tests/regression/configs/methane/selection_subset.yaml index 834b295f..b2225708 100644 --- a/tests/regression/configs/methane/selection_subset.yaml +++ b/tests/regression/configs/methane/selection_subset.yaml @@ -5,7 +5,7 @@ run1: top_traj_file: - ".testdata/methane/molecules.top" - ".testdata/methane/trajectory.crd" - selection_string: "protein" + selection_string: "resname MET and resid 1:10" start: 0 end: 1 step: 1 From 4bbae02723a83449010a7118d27ee0023a8de8d0 Mon Sep 17 00:00:00 2001 From: harryswift01 Date: Mon, 30 Mar 2026 10:23:48 +0100 Subject: [PATCH 20/41] tests(regression): update `methanol/selection_subset.yaml` to include correct range --- tests/regression/configs/methanol/selection_subset.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/tests/regression/configs/methanol/selection_subset.yaml b/tests/regression/configs/methanol/selection_subset.yaml index 929a975e..6ab616fd 100644 --- a/tests/regression/configs/methanol/selection_subset.yaml +++ b/tests/regression/configs/methanol/selection_subset.yaml @@ -5,7 +5,7 @@ run1: top_traj_file: - ".testdata/methanol/molecules.top" - ".testdata/methanol/trajectory.crd" - selection_string: "protein" + selection_string: "resname MOH and resid 1:10" start: 0 end: 1 step: 1 From 365a64f2ab6ee8c4829d7cb1b72191d6deb453fa Mon Sep 17 00:00:00 2001 From: harryswift01 Date: Mon, 30 Mar 2026 10:25:14 +0100 Subject: [PATCH 21/41] tests(regression): update `octonol/selection_subset.yaml` to include correct range --- tests/regression/configs/octonol/selection_subset.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/tests/regression/configs/octonol/selection_subset.yaml b/tests/regression/configs/octonol/selection_subset.yaml index 3a7d6fa7..2f2587fa 100644 --- a/tests/regression/configs/octonol/selection_subset.yaml +++ b/tests/regression/configs/octonol/selection_subset.yaml @@ -5,7 +5,7 @@ run1: top_traj_file: - ".testdata/octonol/molecules.top" - ".testdata/octonol/trajectory.crd" - selection_string: "protein" + selection_string: "resname OCT and resid 1:10" start: 0 end: 1 step: 1 From 5e93bb2e2a09bca9ad8b974cdcda17e65b5a232d Mon Sep 17 00:00:00 2001 From: harryswift01 Date: Mon, 30 Mar 2026 10:27:25 +0100 Subject: [PATCH 22/41] tests(regression): update `water/selection_subset.yaml` to include correct range --- tests/regression/configs/water/selection_subset.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/tests/regression/configs/water/selection_subset.yaml b/tests/regression/configs/water/selection_subset.yaml index fb91a7e3..1429202f 100644 --- a/tests/regression/configs/water/selection_subset.yaml +++ b/tests/regression/configs/water/selection_subset.yaml @@ -5,7 +5,7 @@ run1: top_traj_file: - ".testdata/water/molecules.top" - ".testdata/water/trajectory.crd" - selection_string: "protein" + selection_string: "resname SOL and resid 1:10" start: 0 end: 1 step: 1 From dd9131752a20ab8aa90dd683f5097920cff05e00 Mon Sep 17 00:00:00 2001 From: harryswift01 Date: Mon, 30 Mar 2026 10:28:53 +0100 Subject: [PATCH 23/41] tests(regression): add configuration file for no waterEntropy within water regression tests --- tests/regression/configs/water/water_off.yaml | 15 +++++++++++++++ 1 file changed, 15 insertions(+) create mode 100644 tests/regression/configs/water/water_off.yaml diff --git a/tests/regression/configs/water/water_off.yaml b/tests/regression/configs/water/water_off.yaml new file mode 100644 index 00000000..322e51f7 --- /dev/null +++ b/tests/regression/configs/water/water_off.yaml @@ -0,0 +1,15 @@ +--- + +run1: + force_file: ".testdata/water/forces.frc" + top_traj_file: + - ".testdata/water/molecules.top" + - ".testdata/water/trajectory.crd" + selection_string: "all" + start: 0 + step: 1 + end: 1 + file_format: "MDCRD" + kcal_force_units: True + search_type: "grid" + water_entropy: False From a2886885fae38252197facec424a756d0544dfcc Mon Sep 17 00:00:00 2001 From: harryswift01 Date: Mon, 30 Mar 2026 10:35:02 +0100 Subject: [PATCH 24/41] tests(regression): add grouping by each as a confiuration file for each of the regression testing systems --- .../configs/benzaldehyde/grouping_each.yaml | 15 +++++++++++++++ .../configs/benzene/grouping_each.yaml | 15 +++++++++++++++ .../configs/cyclohexane/grouping_each.yaml | 15 +++++++++++++++ tests/regression/configs/dna/grouping_each.yaml | 11 +++++++++++ .../configs/ethyl-acetate/grouping_each.yaml | 15 +++++++++++++++ .../configs/methane/grouping_each.yaml | 16 ++++++++++++++++ .../configs/methanol/grouping_each.yaml | 15 +++++++++++++++ .../configs/octonol/grouping_each.yaml | 15 +++++++++++++++ .../regression/configs/water/grouping_each.yaml | 15 +++++++++++++++ 9 files changed, 132 insertions(+) create mode 100644 tests/regression/configs/benzaldehyde/grouping_each.yaml create mode 100644 tests/regression/configs/benzene/grouping_each.yaml create mode 100644 tests/regression/configs/cyclohexane/grouping_each.yaml create mode 100644 tests/regression/configs/dna/grouping_each.yaml create mode 100644 tests/regression/configs/ethyl-acetate/grouping_each.yaml create mode 100644 tests/regression/configs/methane/grouping_each.yaml create mode 100644 tests/regression/configs/methanol/grouping_each.yaml create mode 100644 tests/regression/configs/octonol/grouping_each.yaml create mode 100644 tests/regression/configs/water/grouping_each.yaml diff --git a/tests/regression/configs/benzaldehyde/grouping_each.yaml b/tests/regression/configs/benzaldehyde/grouping_each.yaml new file mode 100644 index 00000000..4cb27c58 --- /dev/null +++ b/tests/regression/configs/benzaldehyde/grouping_each.yaml @@ -0,0 +1,15 @@ +--- + +run1: + force_file: ".testdata/benzaldehyde/forces.frc" + top_traj_file: + - ".testdata/benzaldehyde/molecules.top" + - ".testdata/benzaldehyde/trajectory.crd" + selection_string: "all" + start: 0 + end: 1 + step: 1 + file_format: "MDCRD" + kcal_force_units: True + search_type: "grid" + grouping: "each" diff --git a/tests/regression/configs/benzene/grouping_each.yaml b/tests/regression/configs/benzene/grouping_each.yaml new file mode 100644 index 00000000..f748906e --- /dev/null +++ b/tests/regression/configs/benzene/grouping_each.yaml @@ -0,0 +1,15 @@ +--- + +run1: + force_file: ".testdata/benzene/forces.frc" + top_traj_file: + - ".testdata/benzene/molecules.top" + - ".testdata/benzene/trajectory.crd" + selection_string: "all" + start: 0 + end: 1 + step: 1 + file_format: "MDCRD" + kcal_force_units: True + search_type: "grid" + grouping: "each" diff --git a/tests/regression/configs/cyclohexane/grouping_each.yaml b/tests/regression/configs/cyclohexane/grouping_each.yaml new file mode 100644 index 00000000..eff6bf77 --- /dev/null +++ b/tests/regression/configs/cyclohexane/grouping_each.yaml @@ -0,0 +1,15 @@ +--- + +run1: + force_file: ".testdata/cyclohexane/forces.frc" + top_traj_file: + - ".testdata/cyclohexane/molecules.top" + - ".testdata/cyclohexane/trajectory.crd" + selection_string: "all" + start: 0 + end: 1 + step: 1 + file_format: "MDCRD" + kcal_force_units: True + search_type: "grid" + grouping: "each" diff --git a/tests/regression/configs/dna/grouping_each.yaml b/tests/regression/configs/dna/grouping_each.yaml new file mode 100644 index 00000000..a9e7117c --- /dev/null +++ b/tests/regression/configs/dna/grouping_each.yaml @@ -0,0 +1,11 @@ +--- + +run1: + top_traj_file: + - ".testdata/dna/md_A4_dna.tpr" + - ".testdata/dna/md_A4_dna_xf.trr" + selection_string: "all" + start: 0 + end: 1 + step: 1 + grouping: "each" diff --git a/tests/regression/configs/ethyl-acetate/grouping_each.yaml b/tests/regression/configs/ethyl-acetate/grouping_each.yaml new file mode 100644 index 00000000..84e6eaa0 --- /dev/null +++ b/tests/regression/configs/ethyl-acetate/grouping_each.yaml @@ -0,0 +1,15 @@ +--- + +run1: + force_file: ".testdata/ethyl-acetate/forces.frc" + top_traj_file: + - ".testdata/ethyl-acetate/molecules.top" + - ".testdata/ethyl-acetate/trajectory.crd" + selection_string: "all" + start: 0 + end: 1 + step: 1 + file_format: "MDCRD" + kcal_force_units: True + search_type: "grid" + grouping: "each" diff --git a/tests/regression/configs/methane/grouping_each.yaml b/tests/regression/configs/methane/grouping_each.yaml new file mode 100644 index 00000000..c46f0fbf --- /dev/null +++ b/tests/regression/configs/methane/grouping_each.yaml @@ -0,0 +1,16 @@ +--- + +run1: + force_file: ".testdata/methane/forces.frc" + top_traj_file: + - ".testdata/methane/molecules.top" + - ".testdata/methane/trajectory.crd" + selection_string: "all" + start: 0 + end: 1 + step: 1 + file_format: "MDCRD" + temperature: 112.0 + kcal_force_units: True + search_type: "grid" + grouping: "each" diff --git a/tests/regression/configs/methanol/grouping_each.yaml b/tests/regression/configs/methanol/grouping_each.yaml new file mode 100644 index 00000000..acf952b8 --- /dev/null +++ b/tests/regression/configs/methanol/grouping_each.yaml @@ -0,0 +1,15 @@ +--- + +run1: + force_file: ".testdata/methanol/forces.frc" + top_traj_file: + - ".testdata/methanol/molecules.top" + - ".testdata/methanol/trajectory.crd" + selection_string: "all" + start: 0 + end: 1 + step: 1 + file_format: "MDCRD" + kcal_force_units: True + search_type: "grid" + grouping: "each" diff --git a/tests/regression/configs/octonol/grouping_each.yaml b/tests/regression/configs/octonol/grouping_each.yaml new file mode 100644 index 00000000..2d981af3 --- /dev/null +++ b/tests/regression/configs/octonol/grouping_each.yaml @@ -0,0 +1,15 @@ +--- + +run1: + force_file: ".testdata/octonol/forces.frc" + top_traj_file: + - ".testdata/octonol/molecules.top" + - ".testdata/octonol/trajectory.crd" + selection_string: "all" + start: 0 + end: 1 + step: 1 + file_format: "MDCRD" + kcal_force_units: True + search_type: "grid" + grouping: "each" diff --git a/tests/regression/configs/water/grouping_each.yaml b/tests/regression/configs/water/grouping_each.yaml new file mode 100644 index 00000000..31502301 --- /dev/null +++ b/tests/regression/configs/water/grouping_each.yaml @@ -0,0 +1,15 @@ +--- + +run1: + force_file: ".testdata/water/forces.frc" + top_traj_file: + - ".testdata/water/molecules.top" + - ".testdata/water/trajectory.crd" + selection_string: "all" + start: 0 + step: 1 + end: 1 + file_format: "MDCRD" + kcal_force_units: True + search_type: "grid" + grouping: "each" From 2cafee04802f1722cf11b29cae202b298274f93f Mon Sep 17 00:00:00 2001 From: harryswift01 Date: Mon, 30 Mar 2026 10:42:15 +0100 Subject: [PATCH 25/41] tests(regression): add `combined_forcetorque` configuration file for each regression system --- .../benzaldehyde/combined_forcetorque_false.yaml | 15 +++++++++++++++ .../benzene/combined_forcetorque_off.yaml | 15 +++++++++++++++ .../cyclohexane/combined_forcetorque_off.yaml | 15 +++++++++++++++ .../configs/dna/combined_forcetorque_off.yaml | 11 +++++++++++ .../ethyl-acetate/combined_forcetorque_off.yaml | 15 +++++++++++++++ .../methane/combined_forcetorque_off.yaml | 16 ++++++++++++++++ .../methanol/combined_forcetorque_off.yaml | 15 +++++++++++++++ .../octonol/combined_forcetorque_off.yaml | 15 +++++++++++++++ .../configs/water/combined_forcetorque_off.yaml | 15 +++++++++++++++ 9 files changed, 132 insertions(+) create mode 100644 tests/regression/configs/benzaldehyde/combined_forcetorque_false.yaml create mode 100644 tests/regression/configs/benzene/combined_forcetorque_off.yaml create mode 100644 tests/regression/configs/cyclohexane/combined_forcetorque_off.yaml create mode 100644 tests/regression/configs/dna/combined_forcetorque_off.yaml create mode 100644 tests/regression/configs/ethyl-acetate/combined_forcetorque_off.yaml create mode 100644 tests/regression/configs/methane/combined_forcetorque_off.yaml create mode 100644 tests/regression/configs/methanol/combined_forcetorque_off.yaml create mode 100644 tests/regression/configs/octonol/combined_forcetorque_off.yaml create mode 100644 tests/regression/configs/water/combined_forcetorque_off.yaml diff --git a/tests/regression/configs/benzaldehyde/combined_forcetorque_false.yaml b/tests/regression/configs/benzaldehyde/combined_forcetorque_false.yaml new file mode 100644 index 00000000..99ba8513 --- /dev/null +++ b/tests/regression/configs/benzaldehyde/combined_forcetorque_false.yaml @@ -0,0 +1,15 @@ +--- + +run1: + force_file: ".testdata/benzaldehyde/forces.frc" + top_traj_file: + - ".testdata/benzaldehyde/molecules.top" + - ".testdata/benzaldehyde/trajectory.crd" + selection_string: "all" + start: 0 + end: 1 + step: 1 + file_format: "MDCRD" + kcal_force_units: True + search_type: "grid" + combined_forcetorque: False diff --git a/tests/regression/configs/benzene/combined_forcetorque_off.yaml b/tests/regression/configs/benzene/combined_forcetorque_off.yaml new file mode 100644 index 00000000..e567d07a --- /dev/null +++ b/tests/regression/configs/benzene/combined_forcetorque_off.yaml @@ -0,0 +1,15 @@ +--- + +run1: + force_file: ".testdata/benzene/forces.frc" + top_traj_file: + - ".testdata/benzene/molecules.top" + - ".testdata/benzene/trajectory.crd" + selection_string: "all" + start: 0 + end: 1 + step: 1 + file_format: "MDCRD" + kcal_force_units: True + search_type: "grid" + combined_forcetorque: False diff --git a/tests/regression/configs/cyclohexane/combined_forcetorque_off.yaml b/tests/regression/configs/cyclohexane/combined_forcetorque_off.yaml new file mode 100644 index 00000000..9ec1302f --- /dev/null +++ b/tests/regression/configs/cyclohexane/combined_forcetorque_off.yaml @@ -0,0 +1,15 @@ +--- + +run1: + force_file: ".testdata/cyclohexane/forces.frc" + top_traj_file: + - ".testdata/cyclohexane/molecules.top" + - ".testdata/cyclohexane/trajectory.crd" + selection_string: "all" + start: 0 + end: 1 + step: 1 + file_format: "MDCRD" + kcal_force_units: True + search_type: "grid" + combined_forcetorque: False diff --git a/tests/regression/configs/dna/combined_forcetorque_off.yaml b/tests/regression/configs/dna/combined_forcetorque_off.yaml new file mode 100644 index 00000000..8718682a --- /dev/null +++ b/tests/regression/configs/dna/combined_forcetorque_off.yaml @@ -0,0 +1,11 @@ +--- + +run1: + top_traj_file: + - ".testdata/dna/md_A4_dna.tpr" + - ".testdata/dna/md_A4_dna_xf.trr" + selection_string: "all" + start: 0 + end: 1 + step: 1 + combined_forcetorque: False diff --git a/tests/regression/configs/ethyl-acetate/combined_forcetorque_off.yaml b/tests/regression/configs/ethyl-acetate/combined_forcetorque_off.yaml new file mode 100644 index 00000000..db9f851a --- /dev/null +++ b/tests/regression/configs/ethyl-acetate/combined_forcetorque_off.yaml @@ -0,0 +1,15 @@ +--- + +run1: + force_file: ".testdata/ethyl-acetate/forces.frc" + top_traj_file: + - ".testdata/ethyl-acetate/molecules.top" + - ".testdata/ethyl-acetate/trajectory.crd" + selection_string: "all" + start: 0 + end: 1 + step: 1 + file_format: "MDCRD" + kcal_force_units: True + search_type: "grid" + combined_forcetorque: False diff --git a/tests/regression/configs/methane/combined_forcetorque_off.yaml b/tests/regression/configs/methane/combined_forcetorque_off.yaml new file mode 100644 index 00000000..5e0844be --- /dev/null +++ b/tests/regression/configs/methane/combined_forcetorque_off.yaml @@ -0,0 +1,16 @@ +--- + +run1: + force_file: ".testdata/methane/forces.frc" + top_traj_file: + - ".testdata/methane/molecules.top" + - ".testdata/methane/trajectory.crd" + selection_string: "all" + start: 0 + end: 1 + step: 1 + file_format: "MDCRD" + temperature: 112.0 + kcal_force_units: True + search_type: "grid" + combined_forcetorque: False diff --git a/tests/regression/configs/methanol/combined_forcetorque_off.yaml b/tests/regression/configs/methanol/combined_forcetorque_off.yaml new file mode 100644 index 00000000..0015be5a --- /dev/null +++ b/tests/regression/configs/methanol/combined_forcetorque_off.yaml @@ -0,0 +1,15 @@ +--- + +run1: + force_file: ".testdata/methanol/forces.frc" + top_traj_file: + - ".testdata/methanol/molecules.top" + - ".testdata/methanol/trajectory.crd" + selection_string: "all" + start: 0 + end: 1 + step: 1 + file_format: "MDCRD" + kcal_force_units: True + search_type: "grid" + combined_forcetorque: False diff --git a/tests/regression/configs/octonol/combined_forcetorque_off.yaml b/tests/regression/configs/octonol/combined_forcetorque_off.yaml new file mode 100644 index 00000000..b3f2d51e --- /dev/null +++ b/tests/regression/configs/octonol/combined_forcetorque_off.yaml @@ -0,0 +1,15 @@ +--- + +run1: + force_file: ".testdata/octonol/forces.frc" + top_traj_file: + - ".testdata/octonol/molecules.top" + - ".testdata/octonol/trajectory.crd" + selection_string: "all" + start: 0 + end: 1 + step: 1 + file_format: "MDCRD" + kcal_force_units: True + search_type: "grid" + combined_forcetorque: False diff --git a/tests/regression/configs/water/combined_forcetorque_off.yaml b/tests/regression/configs/water/combined_forcetorque_off.yaml new file mode 100644 index 00000000..4a1419fd --- /dev/null +++ b/tests/regression/configs/water/combined_forcetorque_off.yaml @@ -0,0 +1,15 @@ +--- + +run1: + force_file: ".testdata/water/forces.frc" + top_traj_file: + - ".testdata/water/molecules.top" + - ".testdata/water/trajectory.crd" + selection_string: "all" + start: 0 + step: 1 + end: 1 + file_format: "MDCRD" + kcal_force_units: True + search_type: "grid" + combined_forcetorque: False From 9fd07bf1a85fd57941be17f5b253300da2783e07 Mon Sep 17 00:00:00 2001 From: harryswift01 Date: Mon, 30 Mar 2026 10:59:46 +0100 Subject: [PATCH 26/41] chore(gitignore): update path to regression baseline output files --- .gitignore | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.gitignore b/.gitignore index 20fa8d8f..089b0c31 100644 --- a/.gitignore +++ b/.gitignore @@ -129,4 +129,4 @@ job* .testdata/ !tests/regression/baselines/ -!tests/regression/baselines/*.json +!tests/regression/baselines/*/*.json From 87a97b1f75a6e7456a350a42f15c42fcad44c17c Mon Sep 17 00:00:00 2001 From: harryswift01 Date: Mon, 30 Mar 2026 11:01:29 +0100 Subject: [PATCH 27/41] tests(regression): add all DNA regression baseline results --- tests/regression/baselines/dna/axes_off.json | 61 +++++++++++++++++++ .../dna/combined_forcetorque_off.json | 61 +++++++++++++++++++ tests/regression/baselines/dna/default.json | 4 +- .../baselines/dna/frame_window.json | 61 +++++++++++++++++++ .../baselines/dna/grouping_each.json | 61 +++++++++++++++++++ .../baselines/dna/selection_subset.json | 47 ++++++++++++++ 6 files changed, 293 insertions(+), 2 deletions(-) create mode 100644 tests/regression/baselines/dna/axes_off.json create mode 100644 tests/regression/baselines/dna/combined_forcetorque_off.json create mode 100644 tests/regression/baselines/dna/frame_window.json create mode 100644 tests/regression/baselines/dna/grouping_each.json create mode 100644 tests/regression/baselines/dna/selection_subset.json diff --git a/tests/regression/baselines/dna/axes_off.json b/tests/regression/baselines/dna/axes_off.json new file mode 100644 index 00000000..abefa2d9 --- /dev/null +++ b/tests/regression/baselines/dna/axes_off.json @@ -0,0 +1,61 @@ +{ + "args": { + "top_traj_file": [ + "/home/harry-swift/BioSim/software/CodeEntropy/.testdata/dna/md_A4_dna.tpr", + "/home/harry-swift/BioSim/software/CodeEntropy/.testdata/dna/md_A4_dna_xf.trr" + ], + "force_file": null, + "file_format": null, + "kcal_force_units": false, + "selection_string": "all", + "start": 0, + "end": 5, + "step": 2, + "bin_width": 30, + "temperature": 298.0, + "verbose": false, + "output_file": "/tmp/pytest-of-harry-swift/pytest-1/test_regression_matches_baseli0/job001/output_file.json", + "force_partitioning": 0.5, + "water_entropy": true, + "grouping": "molecules", + "combined_forcetorque": true, + "customised_axes": false, + "search_type": "RAD" + }, + "provenance": { + "python": "3.14.3", + "platform": "Linux-6.17.0-19-generic-x86_64-with-glibc2.39", + "codeentropy_version": "2.1.0", + "git_sha": "2cafee04802f1722cf11b29cae202b298274f93f" + }, + "groups": { + "0": { + "components": { + "united_atom:Transvibrational": 0.0, + "united_atom:Rovibrational": 1.2269044878385265, + "residue:Transvibrational": 0.0, + "residue:Rovibrational": 27.45710747332319, + "polymer:FTmat-Transvibrational": 48.62026970762269, + "polymer:FTmat-Rovibrational": 0.0, + "united_atom:Conformational": 7.0411434528236345, + "residue:Conformational": 0.0, + "polymer:Orientational": 4.758905336627712 + }, + "total": 89.10433045823575 + }, + "1": { + "components": { + "united_atom:Transvibrational": 0.0, + "united_atom:Rovibrational": 1.7972774672527945, + "residue:Transvibrational": 0.0, + "residue:Rovibrational": 25.287669468441067, + "polymer:FTmat-Transvibrational": 60.47397935339153, + "polymer:FTmat-Rovibrational": 0.0, + "united_atom:Conformational": 6.410455987098191, + "residue:Conformational": 0.46183561256411515, + "polymer:Orientational": 4.758905336627712 + }, + "total": 99.1901232253754 + } + } +} diff --git a/tests/regression/baselines/dna/combined_forcetorque_off.json b/tests/regression/baselines/dna/combined_forcetorque_off.json new file mode 100644 index 00000000..ab6af537 --- /dev/null +++ b/tests/regression/baselines/dna/combined_forcetorque_off.json @@ -0,0 +1,61 @@ +{ + "args": { + "top_traj_file": [ + "/home/harry-swift/BioSim/software/CodeEntropy/.testdata/dna/md_A4_dna.tpr", + "/home/harry-swift/BioSim/software/CodeEntropy/.testdata/dna/md_A4_dna_xf.trr" + ], + "force_file": null, + "file_format": null, + "kcal_force_units": false, + "selection_string": "all", + "start": 0, + "end": 1, + "step": 1, + "bin_width": 30, + "temperature": 298.0, + "verbose": false, + "output_file": "/tmp/pytest-of-harry-swift/pytest-1/test_regression_matches_baseli1/job001/output_file.json", + "force_partitioning": 0.5, + "water_entropy": true, + "grouping": "molecules", + "combined_forcetorque": false, + "customised_axes": true, + "search_type": "RAD" + }, + "provenance": { + "python": "3.14.3", + "platform": "Linux-6.17.0-19-generic-x86_64-with-glibc2.39", + "codeentropy_version": "2.1.0", + "git_sha": "2cafee04802f1722cf11b29cae202b298274f93f" + }, + "groups": { + "0": { + "components": { + "united_atom:Transvibrational": 0.0, + "united_atom:Rovibrational": 0.002160679012128457, + "residue:Transvibrational": 0.0, + "residue:Rovibrational": 3.376800684085249, + "polymer:Transvibrational": 21.18266215491188, + "polymer:Rovibrational": 12.837576042626923, + "united_atom:Conformational": 7.0411434528236345, + "residue:Conformational": 0.0, + "polymer:Orientational": 4.758905336627712 + }, + "total": 49.19924835008753 + }, + "1": { + "components": { + "united_atom:Transvibrational": 0.0, + "united_atom:Rovibrational": 0.01846427765949586, + "residue:Transvibrational": 0.0, + "residue:Rovibrational": 2.3863201082544565, + "polymer:Transvibrational": 16.607667396609116, + "polymer:Rovibrational": 12.304363914795593, + "united_atom:Conformational": 6.410455987098191, + "residue:Conformational": 0.46183561256411515, + "polymer:Orientational": 4.758905336627712 + }, + "total": 42.94801263360868 + } + } +} diff --git a/tests/regression/baselines/dna/default.json b/tests/regression/baselines/dna/default.json index 96afc42a..057f306d 100644 --- a/tests/regression/baselines/dna/default.json +++ b/tests/regression/baselines/dna/default.json @@ -14,7 +14,7 @@ "bin_width": 30, "temperature": 298.0, "verbose": false, - "output_file": "/tmp/pytest-of-harry-swift/pytest-25/test_regression_matches_baseli0/job001/output_file.json", + "output_file": "/tmp/pytest-of-harry-swift/pytest-1/test_regression_matches_baseli2/job001/output_file.json", "force_partitioning": 0.5, "water_entropy": true, "grouping": "molecules", @@ -26,7 +26,7 @@ "python": "3.14.3", "platform": "Linux-6.17.0-19-generic-x86_64-with-glibc2.39", "codeentropy_version": "2.1.0", - "git_sha": "06853f41ba1887213fe7ab94c95fe14dab035eaa" + "git_sha": "2cafee04802f1722cf11b29cae202b298274f93f" }, "groups": { "0": { diff --git a/tests/regression/baselines/dna/frame_window.json b/tests/regression/baselines/dna/frame_window.json new file mode 100644 index 00000000..13a87e51 --- /dev/null +++ b/tests/regression/baselines/dna/frame_window.json @@ -0,0 +1,61 @@ +{ + "args": { + "top_traj_file": [ + "/home/harry-swift/BioSim/software/CodeEntropy/.testdata/dna/md_A4_dna.tpr", + "/home/harry-swift/BioSim/software/CodeEntropy/.testdata/dna/md_A4_dna_xf.trr" + ], + "force_file": null, + "file_format": null, + "kcal_force_units": false, + "selection_string": "all", + "start": 0, + "end": 5, + "step": 2, + "bin_width": 30, + "temperature": 298.0, + "verbose": false, + "output_file": "/tmp/pytest-of-harry-swift/pytest-1/test_regression_matches_baseli3/job001/output_file.json", + "force_partitioning": 0.5, + "water_entropy": true, + "grouping": "molecules", + "combined_forcetorque": true, + "customised_axes": true, + "search_type": "RAD" + }, + "provenance": { + "python": "3.14.3", + "platform": "Linux-6.17.0-19-generic-x86_64-with-glibc2.39", + "codeentropy_version": "2.1.0", + "git_sha": "2cafee04802f1722cf11b29cae202b298274f93f" + }, + "groups": { + "0": { + "components": { + "united_atom:Transvibrational": 0.0, + "united_atom:Rovibrational": 1.5821720528374943, + "residue:Transvibrational": 0.0, + "residue:Rovibrational": 27.397449238560412, + "polymer:FTmat-Transvibrational": 48.62026970762269, + "polymer:FTmat-Rovibrational": 0.0, + "united_atom:Conformational": 7.0411434528236345, + "residue:Conformational": 0.0, + "polymer:Orientational": 4.758905336627712 + }, + "total": 89.39993978847194 + }, + "1": { + "components": { + "united_atom:Transvibrational": 0.0, + "united_atom:Rovibrational": 2.5277936366208014, + "residue:Transvibrational": 0.0, + "residue:Rovibrational": 24.80670067454149, + "polymer:FTmat-Transvibrational": 60.47397935339153, + "polymer:FTmat-Rovibrational": 0.0, + "united_atom:Conformational": 6.410455987098191, + "residue:Conformational": 0.46183561256411515, + "polymer:Orientational": 4.758905336627712 + }, + "total": 99.43967060084383 + } + } +} diff --git a/tests/regression/baselines/dna/grouping_each.json b/tests/regression/baselines/dna/grouping_each.json new file mode 100644 index 00000000..36763436 --- /dev/null +++ b/tests/regression/baselines/dna/grouping_each.json @@ -0,0 +1,61 @@ +{ + "args": { + "top_traj_file": [ + "/home/harry-swift/BioSim/software/CodeEntropy/.testdata/dna/md_A4_dna.tpr", + "/home/harry-swift/BioSim/software/CodeEntropy/.testdata/dna/md_A4_dna_xf.trr" + ], + "force_file": null, + "file_format": null, + "kcal_force_units": false, + "selection_string": "all", + "start": 0, + "end": 1, + "step": 1, + "bin_width": 30, + "temperature": 298.0, + "verbose": false, + "output_file": "/tmp/pytest-of-harry-swift/pytest-1/test_regression_matches_baseli4/job001/output_file.json", + "force_partitioning": 0.5, + "water_entropy": true, + "grouping": "each", + "combined_forcetorque": true, + "customised_axes": true, + "search_type": "RAD" + }, + "provenance": { + "python": "3.14.3", + "platform": "Linux-6.17.0-19-generic-x86_64-with-glibc2.39", + "codeentropy_version": "2.1.0", + "git_sha": "2cafee04802f1722cf11b29cae202b298274f93f" + }, + "groups": { + "0": { + "components": { + "united_atom:Transvibrational": 0.0, + "united_atom:Rovibrational": 0.002160679012128457, + "residue:Transvibrational": 0.0, + "residue:Rovibrational": 3.376800684085249, + "polymer:FTmat-Transvibrational": 12.341104347192612, + "polymer:FTmat-Rovibrational": 0.0, + "united_atom:Conformational": 7.0411434528236345, + "residue:Conformational": 0.0, + "polymer:Orientational": 4.758905336627712 + }, + "total": 27.52011449974134 + }, + "1": { + "components": { + "united_atom:Transvibrational": 0.0, + "united_atom:Rovibrational": 0.01846427765949586, + "residue:Transvibrational": 0.0, + "residue:Rovibrational": 2.3863201082544565, + "polymer:FTmat-Transvibrational": 11.11037253388596, + "polymer:FTmat-Rovibrational": 0.0, + "united_atom:Conformational": 6.410455987098191, + "residue:Conformational": 0.46183561256411515, + "polymer:Orientational": 4.758905336627712 + }, + "total": 25.14635385608993 + } + } +} diff --git a/tests/regression/baselines/dna/selection_subset.json b/tests/regression/baselines/dna/selection_subset.json new file mode 100644 index 00000000..eea98843 --- /dev/null +++ b/tests/regression/baselines/dna/selection_subset.json @@ -0,0 +1,47 @@ +{ + "args": { + "top_traj_file": [ + "/home/harry-swift/BioSim/software/CodeEntropy/.testdata/dna/md_A4_dna.tpr", + "/home/harry-swift/BioSim/software/CodeEntropy/.testdata/dna/md_A4_dna_xf.trr" + ], + "force_file": null, + "file_format": null, + "kcal_force_units": false, + "selection_string": "resname DA", + "start": 0, + "end": 1, + "step": 1, + "bin_width": 30, + "temperature": 298.0, + "verbose": false, + "output_file": "/tmp/pytest-of-harry-swift/pytest-1/test_regression_matches_baseli5/job001/output_file.json", + "force_partitioning": 0.5, + "water_entropy": true, + "grouping": "molecules", + "combined_forcetorque": true, + "customised_axes": true, + "search_type": "RAD" + }, + "provenance": { + "python": "3.14.3", + "platform": "Linux-6.17.0-19-generic-x86_64-with-glibc2.39", + "codeentropy_version": "2.1.0", + "git_sha": "2cafee04802f1722cf11b29cae202b298274f93f" + }, + "groups": { + "0": { + "components": { + "united_atom:Transvibrational": 0.0, + "united_atom:Rovibrational": 0.002160679012128457, + "residue:Transvibrational": 0.0, + "residue:Rovibrational": 3.376800684085249, + "polymer:FTmat-Transvibrational": 12.341104347192612, + "polymer:FTmat-Rovibrational": 0.0, + "united_atom:Conformational": 7.0411434528236345, + "residue:Conformational": 0.0, + "polymer:Orientational": 0.0 + }, + "total": 22.761209163113627 + } + } +} From 02e49c842a772890ff79f2a53e4a87b616fc387d Mon Sep 17 00:00:00 2001 From: harryswift01 Date: Mon, 30 Mar 2026 11:41:03 +0100 Subject: [PATCH 28/41] tests(regression): ensure `kcal_force_units` is enabled on all liquids --- tests/regression/configs/benzaldehyde/rad.yaml | 2 +- tests/regression/configs/benzene/rad.yaml | 2 +- tests/regression/configs/cyclohexane/rad.yaml | 2 +- tests/regression/configs/ethyl-acetate/rad.yaml | 2 +- tests/regression/configs/methane/rad.yaml | 2 +- tests/regression/configs/methanol/rad.yaml | 2 +- tests/regression/configs/octonol/rad.yaml | 2 +- 7 files changed, 7 insertions(+), 7 deletions(-) diff --git a/tests/regression/configs/benzaldehyde/rad.yaml b/tests/regression/configs/benzaldehyde/rad.yaml index 455599b0..ab7b3c2f 100644 --- a/tests/regression/configs/benzaldehyde/rad.yaml +++ b/tests/regression/configs/benzaldehyde/rad.yaml @@ -10,5 +10,5 @@ run1: end: 1 step: 1 file_format: "MDCRD" -# kcal_force_units: True + kcal_force_units: True search_type: "RAD" diff --git a/tests/regression/configs/benzene/rad.yaml b/tests/regression/configs/benzene/rad.yaml index ae274209..e6e1c128 100644 --- a/tests/regression/configs/benzene/rad.yaml +++ b/tests/regression/configs/benzene/rad.yaml @@ -10,5 +10,5 @@ run1: end: 1 step: 1 file_format: "MDCRD" -# kcal_force_units: True + kcal_force_units: True search_type: "RAD" diff --git a/tests/regression/configs/cyclohexane/rad.yaml b/tests/regression/configs/cyclohexane/rad.yaml index c6b7b598..bd9cb2f4 100644 --- a/tests/regression/configs/cyclohexane/rad.yaml +++ b/tests/regression/configs/cyclohexane/rad.yaml @@ -10,5 +10,5 @@ run1: end: 1 step: 1 file_format: "MDCRD" -# kcal_force_units: True + kcal_force_units: True search_type: "RAD" diff --git a/tests/regression/configs/ethyl-acetate/rad.yaml b/tests/regression/configs/ethyl-acetate/rad.yaml index 97c28228..47c04aec 100644 --- a/tests/regression/configs/ethyl-acetate/rad.yaml +++ b/tests/regression/configs/ethyl-acetate/rad.yaml @@ -10,5 +10,5 @@ run1: end: 1 step: 1 file_format: "MDCRD" -# kcal_force_units: True + kcal_force_units: True search_type: "RAD" diff --git a/tests/regression/configs/methane/rad.yaml b/tests/regression/configs/methane/rad.yaml index 07603931..353bed7a 100644 --- a/tests/regression/configs/methane/rad.yaml +++ b/tests/regression/configs/methane/rad.yaml @@ -11,5 +11,5 @@ run1: end: 1 file_format: "MDCRD" temperature: 112.0 -# kcal_force_units: True + kcal_force_units: True search_type: "RAD" diff --git a/tests/regression/configs/methanol/rad.yaml b/tests/regression/configs/methanol/rad.yaml index 74831b38..ef0d1b62 100644 --- a/tests/regression/configs/methanol/rad.yaml +++ b/tests/regression/configs/methanol/rad.yaml @@ -10,5 +10,5 @@ run1: end: 1 step: 1 file_format: "MDCRD" -# kcal_force_units: True + kcal_force_units: True search_type: "RAD" diff --git a/tests/regression/configs/octonol/rad.yaml b/tests/regression/configs/octonol/rad.yaml index a491ec5d..ae2bd232 100644 --- a/tests/regression/configs/octonol/rad.yaml +++ b/tests/regression/configs/octonol/rad.yaml @@ -10,5 +10,5 @@ run1: end: 1 step: 1 file_format: "MDCRD" -# kcal_force_units: True + kcal_force_units: True search_type: "RAD" From be46d826f4ae38e3c6e62a7d5bcddeca85e31590 Mon Sep 17 00:00:00 2001 From: harryswift01 Date: Mon, 30 Mar 2026 17:50:57 +0100 Subject: [PATCH 29/41] tests(regression): fix file path for `configs/benzene/rad.yaml` --- tests/regression/configs/benzene/rad.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/tests/regression/configs/benzene/rad.yaml b/tests/regression/configs/benzene/rad.yaml index e6e1c128..8474bf2d 100644 --- a/tests/regression/configs/benzene/rad.yaml +++ b/tests/regression/configs/benzene/rad.yaml @@ -3,7 +3,7 @@ run1: force_file: ".testdata/benzene/forces.frc" top_traj_file: - - ".testdata/benzaldbenzeneehyde/molecules.top" + - ".testdata/benzene/molecules.top" - ".testdata/benzene/trajectory.crd" selection_string: "all" start: 0 From 2ad971fac63bfd7a36513325ff9eda4fc6986444 Mon Sep 17 00:00:00 2001 From: harryswift01 Date: Tue, 31 Mar 2026 16:34:03 +0100 Subject: [PATCH 30/41] tests(regression): update `regression.cases.py` to allow fast and slow testing configs --- tests/regression/cases.py | 42 ++++++++++++++++++++++++++++++--------- 1 file changed, 33 insertions(+), 9 deletions(-) diff --git a/tests/regression/cases.py b/tests/regression/cases.py index 39cd7461..3b36188f 100644 --- a/tests/regression/cases.py +++ b/tests/regression/cases.py @@ -1,5 +1,6 @@ from dataclasses import dataclass from pathlib import Path +from typing import Any import pytest @@ -33,21 +34,41 @@ def repo_root() -> Path: return Path(__file__).resolve().parents[2] -def discover_cases(): +def discover_cases() -> list[Any]: """ Discover all regression test cases from the configs directory. - Iterates over each system directory under `tests/regression/configs`, - and collects all YAML configuration files. Each configuration file is - paired with a corresponding baseline JSON file. + This function scans the regression configuration directory structure and + constructs a list of parametrized pytest cases. Each case corresponds to + a single YAML configuration file and its associated baseline JSON file. + + Directory structure is expected to follow: + + tests/regression/configs//.yaml + tests/regression/baselines//.json + + For each configuration file: + - A `RegressionCase` instance is created. + - A pytest parameter is generated with a unique ID. + - Slow tests are automatically marked using `pytest.mark.slow` + based on configuration naming conventions. + + Slow Test Heuristic: + Configurations considered "slow" are those representing full-system + or full-selection runs. These are explicitly identified by name + (e.g. "default", "rad") and are marked with `pytest.mark.slow`. + All other configurations (typically subset-based runs such as + selection subsets) are treated as fast tests. Returns: - list[pytest.Param]: A list of parametrized pytest cases, each wrapping - a RegressionCase instance. + list[Any]: A list of parametrized pytest cases, each wrapping a + RegressionCase instance and optionally marked as slow. Notes: - - Cases are automatically marked as slow unless the system is "dna". - Baseline files are not required to exist at discovery time. + - Missing baselines will cause failures during test execution unless + `--update-baselines` is used. + - Test IDs are generated in the form: "{system}-{config_name}". """ base_dir = Path(__file__).resolve().parent @@ -56,6 +77,8 @@ def discover_cases(): cases = [] + SLOW_CONFIGS = {"default", "rad"} + for system_dir in sorted(configs_root.iterdir()): if not system_dir.is_dir(): continue @@ -67,12 +90,13 @@ def discover_cases(): baseline_path = baselines_root / system / f"{case_name}.json" - # DO NOT skip if baseline is missing + is_slow = case_name in SLOW_CONFIGS + cases.append( pytest.param( RegressionCase(system, config_path, baseline_path), id=f"{system}-{case_name}", - marks=pytest.mark.slow if system != "dna" else (), + marks=pytest.mark.slow if is_slow else (), ) ) From 01c1f88f4c260d69e11a0f2cd001eaadd7e129ad Mon Sep 17 00:00:00 2001 From: harryswift01 Date: Tue, 31 Mar 2026 16:35:37 +0100 Subject: [PATCH 31/41] tests(regression): update regression testing config files --- tests/regression/configs/benzaldehyde/axes_off.yaml | 2 +- .../configs/benzaldehyde/combined_forcetorque_false.yaml | 2 +- tests/regression/configs/benzaldehyde/frame_window.yaml | 2 +- tests/regression/configs/benzaldehyde/grouping_each.yaml | 2 +- tests/regression/configs/benzaldehyde/selection_subset.yaml | 2 +- tests/regression/configs/benzene/axes_off.yaml | 2 +- tests/regression/configs/benzene/combined_forcetorque_off.yaml | 2 +- tests/regression/configs/benzene/frame_window.yaml | 2 +- tests/regression/configs/benzene/selection_subset.yaml | 2 +- tests/regression/configs/cyclohexane/axes_off.yaml | 2 +- .../configs/cyclohexane/combined_forcetorque_off.yaml | 2 +- tests/regression/configs/cyclohexane/frame_window.yaml | 2 +- tests/regression/configs/cyclohexane/grouping_each.yaml | 2 +- tests/regression/configs/cyclohexane/selection_subset.yaml | 2 +- tests/regression/configs/dna/axes_off.yaml | 2 +- tests/regression/configs/dna/combined_forcetorque_off.yaml | 2 +- tests/regression/configs/dna/frame_window.yaml | 2 +- tests/regression/configs/dna/grouping_each.yaml | 2 +- tests/regression/configs/dna/selection_subset.yaml | 2 +- tests/regression/configs/ethyl-acetate/axes_off.yaml | 2 +- .../configs/ethyl-acetate/combined_forcetorque_off.yaml | 2 +- tests/regression/configs/ethyl-acetate/frame_window.yaml | 2 +- tests/regression/configs/ethyl-acetate/grouping_each.yaml | 2 +- tests/regression/configs/ethyl-acetate/selection_subset.yaml | 2 +- tests/regression/configs/methane/axes_off.yaml | 2 +- tests/regression/configs/methane/combined_forcetorque_off.yaml | 2 +- tests/regression/configs/methane/frame_window.yaml | 2 +- tests/regression/configs/methane/grouping_each.yaml | 2 +- tests/regression/configs/methane/selection_subset.yaml | 2 +- tests/regression/configs/methanol/axes_off.yaml | 2 +- tests/regression/configs/methanol/combined_forcetorque_off.yaml | 2 +- tests/regression/configs/methanol/frame_window.yaml | 2 +- tests/regression/configs/methanol/grouping_each.yaml | 2 +- tests/regression/configs/methanol/selection_subset.yaml | 2 +- tests/regression/configs/octonol/axes_off.yaml | 2 +- tests/regression/configs/octonol/combined_forcetorque_off.yaml | 2 +- tests/regression/configs/octonol/frame_window.yaml | 2 +- tests/regression/configs/octonol/grouping_each.yaml | 2 +- tests/regression/configs/octonol/selection_subset.yaml | 2 +- tests/regression/configs/water/axes_off.yaml | 2 +- tests/regression/configs/water/combined_forcetorque_off.yaml | 2 +- tests/regression/configs/water/frame_window.yaml | 2 +- tests/regression/configs/water/grouping_each.yaml | 2 +- tests/regression/configs/water/selection_subset.yaml | 2 +- tests/regression/configs/water/water_off.yaml | 2 +- 45 files changed, 45 insertions(+), 45 deletions(-) diff --git a/tests/regression/configs/benzaldehyde/axes_off.yaml b/tests/regression/configs/benzaldehyde/axes_off.yaml index 3b29c9c7..a733dda0 100644 --- a/tests/regression/configs/benzaldehyde/axes_off.yaml +++ b/tests/regression/configs/benzaldehyde/axes_off.yaml @@ -5,7 +5,7 @@ run1: top_traj_file: - ".testdata/benzaldehyde/molecules.top" - ".testdata/benzaldehyde/trajectory.crd" - selection_string: "all" + selection_string: "resid 1:10" start: 0 end: 1 step: 1 diff --git a/tests/regression/configs/benzaldehyde/combined_forcetorque_false.yaml b/tests/regression/configs/benzaldehyde/combined_forcetorque_false.yaml index 99ba8513..ea14df32 100644 --- a/tests/regression/configs/benzaldehyde/combined_forcetorque_false.yaml +++ b/tests/regression/configs/benzaldehyde/combined_forcetorque_false.yaml @@ -5,7 +5,7 @@ run1: top_traj_file: - ".testdata/benzaldehyde/molecules.top" - ".testdata/benzaldehyde/trajectory.crd" - selection_string: "all" + selection_string: "resid 1:10" start: 0 end: 1 step: 1 diff --git a/tests/regression/configs/benzaldehyde/frame_window.yaml b/tests/regression/configs/benzaldehyde/frame_window.yaml index f608b0af..8ec3f4e7 100644 --- a/tests/regression/configs/benzaldehyde/frame_window.yaml +++ b/tests/regression/configs/benzaldehyde/frame_window.yaml @@ -5,7 +5,7 @@ run1: top_traj_file: - ".testdata/benzaldehyde/molecules.top" - ".testdata/benzaldehyde/trajectory.crd" - selection_string: "all" + selection_string: "resid 1:10" start: 0 end: 5 step: 2 diff --git a/tests/regression/configs/benzaldehyde/grouping_each.yaml b/tests/regression/configs/benzaldehyde/grouping_each.yaml index 4cb27c58..cb9050bb 100644 --- a/tests/regression/configs/benzaldehyde/grouping_each.yaml +++ b/tests/regression/configs/benzaldehyde/grouping_each.yaml @@ -5,7 +5,7 @@ run1: top_traj_file: - ".testdata/benzaldehyde/molecules.top" - ".testdata/benzaldehyde/trajectory.crd" - selection_string: "all" + selection_string: "resid 1:10" start: 0 end: 1 step: 1 diff --git a/tests/regression/configs/benzaldehyde/selection_subset.yaml b/tests/regression/configs/benzaldehyde/selection_subset.yaml index 576c4bac..f9728c02 100644 --- a/tests/regression/configs/benzaldehyde/selection_subset.yaml +++ b/tests/regression/configs/benzaldehyde/selection_subset.yaml @@ -5,7 +5,7 @@ run1: top_traj_file: - ".testdata/benzaldehyde/molecules.top" - ".testdata/benzaldehyde/trajectory.crd" - selection_string: "resname BENZ and resid 1:10" + selection_string: "resid 1:10" start: 0 end: 1 step: 1 diff --git a/tests/regression/configs/benzene/axes_off.yaml b/tests/regression/configs/benzene/axes_off.yaml index 97a1e9f0..301bc403 100644 --- a/tests/regression/configs/benzene/axes_off.yaml +++ b/tests/regression/configs/benzene/axes_off.yaml @@ -5,7 +5,7 @@ run1: top_traj_file: - ".testdata/benzene/molecules.top" - ".testdata/benzene/trajectory.crd" - selection_string: "all" + selection_string: "resid 1:10" start: 0 end: 1 step: 1 diff --git a/tests/regression/configs/benzene/combined_forcetorque_off.yaml b/tests/regression/configs/benzene/combined_forcetorque_off.yaml index e567d07a..d9e4cfb1 100644 --- a/tests/regression/configs/benzene/combined_forcetorque_off.yaml +++ b/tests/regression/configs/benzene/combined_forcetorque_off.yaml @@ -5,7 +5,7 @@ run1: top_traj_file: - ".testdata/benzene/molecules.top" - ".testdata/benzene/trajectory.crd" - selection_string: "all" + selection_string: "resid 1:10" start: 0 end: 1 step: 1 diff --git a/tests/regression/configs/benzene/frame_window.yaml b/tests/regression/configs/benzene/frame_window.yaml index cb0f5a6d..e48c1cfd 100644 --- a/tests/regression/configs/benzene/frame_window.yaml +++ b/tests/regression/configs/benzene/frame_window.yaml @@ -5,7 +5,7 @@ run1: top_traj_file: - ".testdata/benzene/molecules.top" - ".testdata/benzene/trajectory.crd" - selection_string: "all" + selection_string: "resid 1:10" start: 0 end: 5 step: 2 diff --git a/tests/regression/configs/benzene/selection_subset.yaml b/tests/regression/configs/benzene/selection_subset.yaml index 20fa2304..421b5cb0 100644 --- a/tests/regression/configs/benzene/selection_subset.yaml +++ b/tests/regression/configs/benzene/selection_subset.yaml @@ -5,7 +5,7 @@ run1: top_traj_file: - ".testdata/benzene/molecules.top" - ".testdata/benzene/trajectory.crd" - selection_string: "resname BEN and resid 1:10" + selection_string: "resid 1:10" start: 0 end: 1 step: 1 diff --git a/tests/regression/configs/cyclohexane/axes_off.yaml b/tests/regression/configs/cyclohexane/axes_off.yaml index ba16e52d..de339292 100644 --- a/tests/regression/configs/cyclohexane/axes_off.yaml +++ b/tests/regression/configs/cyclohexane/axes_off.yaml @@ -5,7 +5,7 @@ run1: top_traj_file: - ".testdata/cyclohexane/molecules.top" - ".testdata/cyclohexane/trajectory.crd" - selection_string: "all" + selection_string: "resid 1:10" start: 0 end: 1 step: 1 diff --git a/tests/regression/configs/cyclohexane/combined_forcetorque_off.yaml b/tests/regression/configs/cyclohexane/combined_forcetorque_off.yaml index 9ec1302f..90a7c27b 100644 --- a/tests/regression/configs/cyclohexane/combined_forcetorque_off.yaml +++ b/tests/regression/configs/cyclohexane/combined_forcetorque_off.yaml @@ -5,7 +5,7 @@ run1: top_traj_file: - ".testdata/cyclohexane/molecules.top" - ".testdata/cyclohexane/trajectory.crd" - selection_string: "all" + selection_string: "resid 1:10" start: 0 end: 1 step: 1 diff --git a/tests/regression/configs/cyclohexane/frame_window.yaml b/tests/regression/configs/cyclohexane/frame_window.yaml index 93ac1b4d..e9cf16c3 100644 --- a/tests/regression/configs/cyclohexane/frame_window.yaml +++ b/tests/regression/configs/cyclohexane/frame_window.yaml @@ -5,7 +5,7 @@ run1: top_traj_file: - ".testdata/cyclohexane/molecules.top" - ".testdata/cyclohexane/trajectory.crd" - selection_string: "all" + selection_string: "resid 1:10" start: 0 end: 5 step: 2 diff --git a/tests/regression/configs/cyclohexane/grouping_each.yaml b/tests/regression/configs/cyclohexane/grouping_each.yaml index eff6bf77..ed1f2e4c 100644 --- a/tests/regression/configs/cyclohexane/grouping_each.yaml +++ b/tests/regression/configs/cyclohexane/grouping_each.yaml @@ -5,7 +5,7 @@ run1: top_traj_file: - ".testdata/cyclohexane/molecules.top" - ".testdata/cyclohexane/trajectory.crd" - selection_string: "all" + selection_string: "resid 1:10" start: 0 end: 1 step: 1 diff --git a/tests/regression/configs/cyclohexane/selection_subset.yaml b/tests/regression/configs/cyclohexane/selection_subset.yaml index 18837f87..72baec2e 100644 --- a/tests/regression/configs/cyclohexane/selection_subset.yaml +++ b/tests/regression/configs/cyclohexane/selection_subset.yaml @@ -5,7 +5,7 @@ run1: top_traj_file: - ".testdata/cyclohexane/molecules.top" - ".testdata/cyclohexane/trajectory.crd" - selection_string: "resname CHX and resid 1:10" + selection_string: "resid 1:10" start: 0 end: 1 step: 1 diff --git a/tests/regression/configs/dna/axes_off.yaml b/tests/regression/configs/dna/axes_off.yaml index 5583ef15..4f5de407 100644 --- a/tests/regression/configs/dna/axes_off.yaml +++ b/tests/regression/configs/dna/axes_off.yaml @@ -4,7 +4,7 @@ run1: top_traj_file: - ".testdata/dna/md_A4_dna.tpr" - ".testdata/dna/md_A4_dna_xf.trr" - selection_string: "all" + selection_string: "resid 1:10" start: 0 end: 5 step: 2 diff --git a/tests/regression/configs/dna/combined_forcetorque_off.yaml b/tests/regression/configs/dna/combined_forcetorque_off.yaml index 8718682a..99825c51 100644 --- a/tests/regression/configs/dna/combined_forcetorque_off.yaml +++ b/tests/regression/configs/dna/combined_forcetorque_off.yaml @@ -4,7 +4,7 @@ run1: top_traj_file: - ".testdata/dna/md_A4_dna.tpr" - ".testdata/dna/md_A4_dna_xf.trr" - selection_string: "all" + selection_string: "resid 1:10" start: 0 end: 1 step: 1 diff --git a/tests/regression/configs/dna/frame_window.yaml b/tests/regression/configs/dna/frame_window.yaml index 5a0e4516..c003f83e 100644 --- a/tests/regression/configs/dna/frame_window.yaml +++ b/tests/regression/configs/dna/frame_window.yaml @@ -4,7 +4,7 @@ run1: top_traj_file: - ".testdata/dna/md_A4_dna.tpr" - ".testdata/dna/md_A4_dna_xf.trr" - selection_string: "all" + selection_string: "resid 1:10" start: 0 end: 5 step: 2 diff --git a/tests/regression/configs/dna/grouping_each.yaml b/tests/regression/configs/dna/grouping_each.yaml index a9e7117c..0cc1bdce 100644 --- a/tests/regression/configs/dna/grouping_each.yaml +++ b/tests/regression/configs/dna/grouping_each.yaml @@ -4,7 +4,7 @@ run1: top_traj_file: - ".testdata/dna/md_A4_dna.tpr" - ".testdata/dna/md_A4_dna_xf.trr" - selection_string: "all" + selection_string: "resid 1:10" start: 0 end: 1 step: 1 diff --git a/tests/regression/configs/dna/selection_subset.yaml b/tests/regression/configs/dna/selection_subset.yaml index cb6b294c..637e30f8 100644 --- a/tests/regression/configs/dna/selection_subset.yaml +++ b/tests/regression/configs/dna/selection_subset.yaml @@ -4,7 +4,7 @@ run1: top_traj_file: - ".testdata/dna/md_A4_dna.tpr" - ".testdata/dna/md_A4_dna_xf.trr" - selection_string: "resname DA" + selection_string: "resid 1:10" start: 0 end: 1 step: 1 diff --git a/tests/regression/configs/ethyl-acetate/axes_off.yaml b/tests/regression/configs/ethyl-acetate/axes_off.yaml index 3b29c9c7..a733dda0 100644 --- a/tests/regression/configs/ethyl-acetate/axes_off.yaml +++ b/tests/regression/configs/ethyl-acetate/axes_off.yaml @@ -5,7 +5,7 @@ run1: top_traj_file: - ".testdata/benzaldehyde/molecules.top" - ".testdata/benzaldehyde/trajectory.crd" - selection_string: "all" + selection_string: "resid 1:10" start: 0 end: 1 step: 1 diff --git a/tests/regression/configs/ethyl-acetate/combined_forcetorque_off.yaml b/tests/regression/configs/ethyl-acetate/combined_forcetorque_off.yaml index db9f851a..3bcc649f 100644 --- a/tests/regression/configs/ethyl-acetate/combined_forcetorque_off.yaml +++ b/tests/regression/configs/ethyl-acetate/combined_forcetorque_off.yaml @@ -5,7 +5,7 @@ run1: top_traj_file: - ".testdata/ethyl-acetate/molecules.top" - ".testdata/ethyl-acetate/trajectory.crd" - selection_string: "all" + selection_string: "resid 1:10" start: 0 end: 1 step: 1 diff --git a/tests/regression/configs/ethyl-acetate/frame_window.yaml b/tests/regression/configs/ethyl-acetate/frame_window.yaml index abd8a395..66edeb98 100644 --- a/tests/regression/configs/ethyl-acetate/frame_window.yaml +++ b/tests/regression/configs/ethyl-acetate/frame_window.yaml @@ -5,7 +5,7 @@ run1: top_traj_file: - ".testdata/ethyl-acetate/molecules.top" - ".testdata/ethyl-acetate/trajectory.crd" - selection_string: "all" + selection_string: "resid 1:10" start: 0 end: 5 step: 2 diff --git a/tests/regression/configs/ethyl-acetate/grouping_each.yaml b/tests/regression/configs/ethyl-acetate/grouping_each.yaml index 84e6eaa0..c704af59 100644 --- a/tests/regression/configs/ethyl-acetate/grouping_each.yaml +++ b/tests/regression/configs/ethyl-acetate/grouping_each.yaml @@ -5,7 +5,7 @@ run1: top_traj_file: - ".testdata/ethyl-acetate/molecules.top" - ".testdata/ethyl-acetate/trajectory.crd" - selection_string: "all" + selection_string: "resid 1:10" start: 0 end: 1 step: 1 diff --git a/tests/regression/configs/ethyl-acetate/selection_subset.yaml b/tests/regression/configs/ethyl-acetate/selection_subset.yaml index e238d1d1..9e0a624a 100644 --- a/tests/regression/configs/ethyl-acetate/selection_subset.yaml +++ b/tests/regression/configs/ethyl-acetate/selection_subset.yaml @@ -5,7 +5,7 @@ run1: top_traj_file: - ".testdata/ethyl-acetate/molecules.top" - ".testdata/ethyl-acetate/trajectory.crd" - selection_string: "resname EA and resid 1:10" + selection_string: "resid 1:10" start: 0 end: 1 step: 1 diff --git a/tests/regression/configs/methane/axes_off.yaml b/tests/regression/configs/methane/axes_off.yaml index e1b79a8e..26c36569 100644 --- a/tests/regression/configs/methane/axes_off.yaml +++ b/tests/regression/configs/methane/axes_off.yaml @@ -5,7 +5,7 @@ run1: top_traj_file: - ".testdata/methane/molecules.top" - ".testdata/methane/trajectory.crd" - selection_string: "all" + selection_string: "resid 1:10" start: 0 end: 1 step: 1 diff --git a/tests/regression/configs/methane/combined_forcetorque_off.yaml b/tests/regression/configs/methane/combined_forcetorque_off.yaml index 5e0844be..fa80f4e9 100644 --- a/tests/regression/configs/methane/combined_forcetorque_off.yaml +++ b/tests/regression/configs/methane/combined_forcetorque_off.yaml @@ -5,7 +5,7 @@ run1: top_traj_file: - ".testdata/methane/molecules.top" - ".testdata/methane/trajectory.crd" - selection_string: "all" + selection_string: "resid 1:10" start: 0 end: 1 step: 1 diff --git a/tests/regression/configs/methane/frame_window.yaml b/tests/regression/configs/methane/frame_window.yaml index 57de494f..8050972b 100644 --- a/tests/regression/configs/methane/frame_window.yaml +++ b/tests/regression/configs/methane/frame_window.yaml @@ -5,7 +5,7 @@ run1: top_traj_file: - ".testdata/methane/molecules.top" - ".testdata/methane/trajectory.crd" - selection_string: "all" + selection_string: "resid 1:10" start: 0 end: 5 step: 2 diff --git a/tests/regression/configs/methane/grouping_each.yaml b/tests/regression/configs/methane/grouping_each.yaml index c46f0fbf..95704fcd 100644 --- a/tests/regression/configs/methane/grouping_each.yaml +++ b/tests/regression/configs/methane/grouping_each.yaml @@ -5,7 +5,7 @@ run1: top_traj_file: - ".testdata/methane/molecules.top" - ".testdata/methane/trajectory.crd" - selection_string: "all" + selection_string: "resid 1:10" start: 0 end: 1 step: 1 diff --git a/tests/regression/configs/methane/selection_subset.yaml b/tests/regression/configs/methane/selection_subset.yaml index b2225708..7639faca 100644 --- a/tests/regression/configs/methane/selection_subset.yaml +++ b/tests/regression/configs/methane/selection_subset.yaml @@ -5,7 +5,7 @@ run1: top_traj_file: - ".testdata/methane/molecules.top" - ".testdata/methane/trajectory.crd" - selection_string: "resname MET and resid 1:10" + selection_string: "resid 1:10" start: 0 end: 1 step: 1 diff --git a/tests/regression/configs/methanol/axes_off.yaml b/tests/regression/configs/methanol/axes_off.yaml index 92cb21f5..50124731 100644 --- a/tests/regression/configs/methanol/axes_off.yaml +++ b/tests/regression/configs/methanol/axes_off.yaml @@ -5,7 +5,7 @@ run1: top_traj_file: - ".testdata/methanol/molecules.top" - ".testdata/methanol/trajectory.crd" - selection_string: "all" + selection_string: "resid 1:10" start: 0 end: 1 step: 1 diff --git a/tests/regression/configs/methanol/combined_forcetorque_off.yaml b/tests/regression/configs/methanol/combined_forcetorque_off.yaml index 0015be5a..7aacc1d0 100644 --- a/tests/regression/configs/methanol/combined_forcetorque_off.yaml +++ b/tests/regression/configs/methanol/combined_forcetorque_off.yaml @@ -5,7 +5,7 @@ run1: top_traj_file: - ".testdata/methanol/molecules.top" - ".testdata/methanol/trajectory.crd" - selection_string: "all" + selection_string: "resid 1:10" start: 0 end: 1 step: 1 diff --git a/tests/regression/configs/methanol/frame_window.yaml b/tests/regression/configs/methanol/frame_window.yaml index 3266624d..97c71136 100644 --- a/tests/regression/configs/methanol/frame_window.yaml +++ b/tests/regression/configs/methanol/frame_window.yaml @@ -5,7 +5,7 @@ run1: top_traj_file: - ".testdata/methanol/molecules.top" - ".testdata/methanol/trajectory.crd" - selection_string: "all" + selection_string: "resid 1:10" start: 0 end: 5 step: 2 diff --git a/tests/regression/configs/methanol/grouping_each.yaml b/tests/regression/configs/methanol/grouping_each.yaml index acf952b8..90cb1c66 100644 --- a/tests/regression/configs/methanol/grouping_each.yaml +++ b/tests/regression/configs/methanol/grouping_each.yaml @@ -5,7 +5,7 @@ run1: top_traj_file: - ".testdata/methanol/molecules.top" - ".testdata/methanol/trajectory.crd" - selection_string: "all" + selection_string: "resid 1:10" start: 0 end: 1 step: 1 diff --git a/tests/regression/configs/methanol/selection_subset.yaml b/tests/regression/configs/methanol/selection_subset.yaml index 6ab616fd..bdba7dec 100644 --- a/tests/regression/configs/methanol/selection_subset.yaml +++ b/tests/regression/configs/methanol/selection_subset.yaml @@ -5,7 +5,7 @@ run1: top_traj_file: - ".testdata/methanol/molecules.top" - ".testdata/methanol/trajectory.crd" - selection_string: "resname MOH and resid 1:10" + selection_string: "resid 1:10" start: 0 end: 1 step: 1 diff --git a/tests/regression/configs/octonol/axes_off.yaml b/tests/regression/configs/octonol/axes_off.yaml index 4317805c..361d3619 100644 --- a/tests/regression/configs/octonol/axes_off.yaml +++ b/tests/regression/configs/octonol/axes_off.yaml @@ -5,7 +5,7 @@ run1: top_traj_file: - ".testdata/octonol/molecules.top" - ".testdata/octonol/trajectory.crd" - selection_string: "all" + selection_string: "resid 1:10" start: 0 end: 1 step: 1 diff --git a/tests/regression/configs/octonol/combined_forcetorque_off.yaml b/tests/regression/configs/octonol/combined_forcetorque_off.yaml index b3f2d51e..87c6556b 100644 --- a/tests/regression/configs/octonol/combined_forcetorque_off.yaml +++ b/tests/regression/configs/octonol/combined_forcetorque_off.yaml @@ -5,7 +5,7 @@ run1: top_traj_file: - ".testdata/octonol/molecules.top" - ".testdata/octonol/trajectory.crd" - selection_string: "all" + selection_string: "resid 1:10" start: 0 end: 1 step: 1 diff --git a/tests/regression/configs/octonol/frame_window.yaml b/tests/regression/configs/octonol/frame_window.yaml index 9643ee3d..21d2ada9 100644 --- a/tests/regression/configs/octonol/frame_window.yaml +++ b/tests/regression/configs/octonol/frame_window.yaml @@ -5,7 +5,7 @@ run1: top_traj_file: - ".testdata/octonol/molecules.top" - ".testdata/octonol/trajectory.crd" - selection_string: "all" + selection_string: "resid 1:10" start: 0 end: 5 step: 2 diff --git a/tests/regression/configs/octonol/grouping_each.yaml b/tests/regression/configs/octonol/grouping_each.yaml index 2d981af3..3b38e71b 100644 --- a/tests/regression/configs/octonol/grouping_each.yaml +++ b/tests/regression/configs/octonol/grouping_each.yaml @@ -5,7 +5,7 @@ run1: top_traj_file: - ".testdata/octonol/molecules.top" - ".testdata/octonol/trajectory.crd" - selection_string: "all" + selection_string: "resid 1:10" start: 0 end: 1 step: 1 diff --git a/tests/regression/configs/octonol/selection_subset.yaml b/tests/regression/configs/octonol/selection_subset.yaml index 2f2587fa..46f8fd45 100644 --- a/tests/regression/configs/octonol/selection_subset.yaml +++ b/tests/regression/configs/octonol/selection_subset.yaml @@ -5,7 +5,7 @@ run1: top_traj_file: - ".testdata/octonol/molecules.top" - ".testdata/octonol/trajectory.crd" - selection_string: "resname OCT and resid 1:10" + selection_string: "resid 1:10" start: 0 end: 1 step: 1 diff --git a/tests/regression/configs/water/axes_off.yaml b/tests/regression/configs/water/axes_off.yaml index 028a32d5..0cb2482d 100644 --- a/tests/regression/configs/water/axes_off.yaml +++ b/tests/regression/configs/water/axes_off.yaml @@ -5,7 +5,7 @@ run1: top_traj_file: - ".testdata/water/molecules.top" - ".testdata/water/trajectory.crd" - selection_string: "all" + selection_string: "resid 1:10" start: 0 end: 1 step: 1 diff --git a/tests/regression/configs/water/combined_forcetorque_off.yaml b/tests/regression/configs/water/combined_forcetorque_off.yaml index 4a1419fd..e6cc4984 100644 --- a/tests/regression/configs/water/combined_forcetorque_off.yaml +++ b/tests/regression/configs/water/combined_forcetorque_off.yaml @@ -5,7 +5,7 @@ run1: top_traj_file: - ".testdata/water/molecules.top" - ".testdata/water/trajectory.crd" - selection_string: "all" + selection_string: "resid 1:10" start: 0 step: 1 end: 1 diff --git a/tests/regression/configs/water/frame_window.yaml b/tests/regression/configs/water/frame_window.yaml index fb313b83..651d164a 100644 --- a/tests/regression/configs/water/frame_window.yaml +++ b/tests/regression/configs/water/frame_window.yaml @@ -5,7 +5,7 @@ run1: top_traj_file: - ".testdata/water/molecules.top" - ".testdata/water/trajectory.crd" - selection_string: "all" + selection_string: "resid 1:10" start: 0 end: 5 step: 2 diff --git a/tests/regression/configs/water/grouping_each.yaml b/tests/regression/configs/water/grouping_each.yaml index 31502301..019c3f4b 100644 --- a/tests/regression/configs/water/grouping_each.yaml +++ b/tests/regression/configs/water/grouping_each.yaml @@ -5,7 +5,7 @@ run1: top_traj_file: - ".testdata/water/molecules.top" - ".testdata/water/trajectory.crd" - selection_string: "all" + selection_string: "resid 1:10" start: 0 step: 1 end: 1 diff --git a/tests/regression/configs/water/selection_subset.yaml b/tests/regression/configs/water/selection_subset.yaml index 1429202f..92fe9bc5 100644 --- a/tests/regression/configs/water/selection_subset.yaml +++ b/tests/regression/configs/water/selection_subset.yaml @@ -5,7 +5,7 @@ run1: top_traj_file: - ".testdata/water/molecules.top" - ".testdata/water/trajectory.crd" - selection_string: "resname SOL and resid 1:10" + selection_string: "resid 1:10" start: 0 end: 1 step: 1 diff --git a/tests/regression/configs/water/water_off.yaml b/tests/regression/configs/water/water_off.yaml index 322e51f7..3b138532 100644 --- a/tests/regression/configs/water/water_off.yaml +++ b/tests/regression/configs/water/water_off.yaml @@ -5,7 +5,7 @@ run1: top_traj_file: - ".testdata/water/molecules.top" - ".testdata/water/trajectory.crd" - selection_string: "all" + selection_string: "resid 1:10" start: 0 step: 1 end: 1 From 4d39e9aeeed72fc3993f4a4eb6485da40524ebc5 Mon Sep 17 00:00:00 2001 From: harryswift01 Date: Tue, 31 Mar 2026 16:37:31 +0100 Subject: [PATCH 32/41] ci(workflows): update `weekly-regression.yaml` workflow to run regression systems independently --- .github/workflows/weekly-regression.yaml | 34 ++++++++++++++++++++---- 1 file changed, 29 insertions(+), 5 deletions(-) diff --git a/.github/workflows/weekly-regression.yaml b/.github/workflows/weekly-regression.yaml index fb6b26ee..9326b5ee 100644 --- a/.github/workflows/weekly-regression.yaml +++ b/.github/workflows/weekly-regression.yaml @@ -10,9 +10,32 @@ concurrency: cancel-in-progress: true jobs: + discover: + name: Discover regression systems + runs-on: ubuntu-24.04 + outputs: + systems: ${{ steps.set.outputs.systems }} + + steps: + - name: Checkout repo + uses: actions/checkout@v4 + + - name: Generate system matrix + id: set + run: | + systems=$(ls tests/regression/configs | jq -R -s -c 'split("\n")[:-1]') + echo "systems=$systems" >> $GITHUB_OUTPUT + regression: - name: Regression tests (including slow) + name: Regression (${{ matrix.system }}) + needs: discover runs-on: ubuntu-24.04 + + strategy: + fail-fast: false + matrix: + system: ${{ fromJson(needs.discover.outputs.systems) }} + steps: - name: Checkout repo uses: actions/checkout@8e8c483db84b4bee98b60c0593521ed34d9990e8 # v6 @@ -29,19 +52,20 @@ jobs: path: .testdata key: codeentropy-testdata-${{ runner.os }}-py314 - - name: Install CodeEntropy and its testing dependencies + - name: Install CodeEntropy and dependencies run: | pip install --upgrade pip pip install -e .[testing] - - name: Run regression test suite - run: pytest tests/regression --run-slow + - name: Run regression tests for system + run: | + pytest tests/regression -k "${{ matrix.system }}" --run-slow -vv - name: Upload regression artifacts on failure if: failure() uses: actions/upload-artifact@v4 with: - name: regression-failure-artifacts + name: regression-${{ matrix.system }}-artifacts path: | .testdata/** tests/regression/**/.pytest_cache/** From 40e8a36db44df29720dfc6783865ec87de6ee120 Mon Sep 17 00:00:00 2001 From: harryswift01 Date: Tue, 31 Mar 2026 17:12:09 +0100 Subject: [PATCH 33/41] tests(regression): update all regression baseline results --- .../baselines/benzaldehyde/axes_off.json | 45 + .../combined_forcetorque_false.json | 45 + .../baselines/benzaldehyde/default.json | 45 + .../baselines/benzaldehyde/frame_window.json | 45 + .../baselines/benzaldehyde/grouping_each.json | 153 + .../baselines/benzaldehyde/rad.json | 45 + .../benzaldehyde/selection_subset.json | 45 + .../baselines/benzene/axes_off.json | 45 + .../benzene/combined_forcetorque_off.json | 45 + .../regression/baselines/benzene/default.json | 45 + .../baselines/benzene/frame_window.json | 45 + .../baselines/benzene/grouping_each.json | 6033 +++++++++++++++++ tests/regression/baselines/benzene/rad.json | 45 + .../baselines/benzene/selection_subset.json | 45 + .../baselines/cyclohexane/axes_off.json | 45 + .../cyclohexane/combined_forcetorque_off.json | 45 + .../baselines/cyclohexane/default.json | 45 + .../baselines/cyclohexane/frame_window.json | 45 + .../baselines/cyclohexane/grouping_each.json | 153 + .../regression/baselines/cyclohexane/rad.json | 45 + .../cyclohexane/selection_subset.json | 45 + tests/regression/baselines/dna/axes_off.json | 6 +- .../dna/combined_forcetorque_off.json | 6 +- tests/regression/baselines/dna/default.json | 4 +- .../baselines/dna/frame_window.json | 6 +- .../baselines/dna/grouping_each.json | 6 +- .../baselines/dna/selection_subset.json | 24 +- .../baselines/ethyl-acetate/axes_off.json | 45 + .../combined_forcetorque_off.json | 45 + .../baselines/ethyl-acetate/default.json | 45 + .../baselines/ethyl-acetate/frame_window.json | 45 + .../ethyl-acetate/grouping_each.json | 153 + .../baselines/ethyl-acetate/rad.json | 45 + .../ethyl-acetate/selection_subset.json | 45 + .../baselines/methane/axes_off.json | 42 + .../methane/combined_forcetorque_off.json | 42 + .../regression/baselines/methane/default.json | 42 + .../baselines/methane/frame_window.json | 42 + .../baselines/methane/grouping_each.json | 123 + tests/regression/baselines/methane/rad.json | 42 + .../baselines/methane/selection_subset.json | 42 + .../baselines/methanol/axes_off.json | 45 + .../methanol/combined_forcetorque_off.json | 45 + .../baselines/methanol/default.json | 45 + .../baselines/methanol/frame_window.json | 45 + .../baselines/methanol/grouping_each.json | 153 + tests/regression/baselines/methanol/rad.json | 45 + .../baselines/methanol/selection_subset.json | 45 + .../baselines/octonol/axes_off.json | 45 + .../octonol/combined_forcetorque_off.json | 45 + .../regression/baselines/octonol/default.json | 45 + .../baselines/octonol/frame_window.json | 45 + .../baselines/octonol/grouping_each.json | 153 + tests/regression/baselines/octonol/rad.json | 45 + .../baselines/octonol/selection_subset.json | 45 + .../regression/baselines/water/axes_off.json | 42 + .../water/combined_forcetorque_off.json | 42 + tests/regression/baselines/water/default.json | 42 + .../baselines/water/frame_window.json | 42 + .../baselines/water/grouping_each.json | 123 + tests/regression/baselines/water/rad.json | 42 + 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--- a/tests/regression/baselines/dna/axes_off.json +++ b/tests/regression/baselines/dna/axes_off.json @@ -7,14 +7,14 @@ "force_file": null, "file_format": null, "kcal_force_units": false, - "selection_string": "all", + "selection_string": "resid 1:10", "start": 0, "end": 5, "step": 2, "bin_width": 30, "temperature": 298.0, "verbose": false, - "output_file": "/tmp/pytest-of-harry-swift/pytest-1/test_regression_matches_baseli0/job001/output_file.json", + "output_file": "/tmp/pytest-of-harry-swift/pytest-44/test_regression_matches_baseli0/job001/output_file.json", "force_partitioning": 0.5, "water_entropy": true, "grouping": "molecules", @@ -26,7 +26,7 @@ "python": "3.14.3", "platform": "Linux-6.17.0-19-generic-x86_64-with-glibc2.39", "codeentropy_version": "2.1.0", - "git_sha": "2cafee04802f1722cf11b29cae202b298274f93f" + "git_sha": "be46d826f4ae38e3c6e62a7d5bcddeca85e31590" }, "groups": { "0": { diff --git a/tests/regression/baselines/dna/combined_forcetorque_off.json b/tests/regression/baselines/dna/combined_forcetorque_off.json index ab6af537..aa5253da 100644 --- a/tests/regression/baselines/dna/combined_forcetorque_off.json +++ b/tests/regression/baselines/dna/combined_forcetorque_off.json @@ -7,14 +7,14 @@ "force_file": null, "file_format": null, "kcal_force_units": false, - "selection_string": "all", + "selection_string": "resid 1:10", "start": 0, "end": 1, "step": 1, "bin_width": 30, "temperature": 298.0, "verbose": false, - "output_file": "/tmp/pytest-of-harry-swift/pytest-1/test_regression_matches_baseli1/job001/output_file.json", + "output_file": "/tmp/pytest-of-harry-swift/pytest-44/test_regression_matches_baseli1/job001/output_file.json", "force_partitioning": 0.5, "water_entropy": true, "grouping": "molecules", @@ -26,7 +26,7 @@ "python": "3.14.3", "platform": "Linux-6.17.0-19-generic-x86_64-with-glibc2.39", "codeentropy_version": "2.1.0", - "git_sha": "2cafee04802f1722cf11b29cae202b298274f93f" + "git_sha": "be46d826f4ae38e3c6e62a7d5bcddeca85e31590" }, "groups": { "0": { diff --git a/tests/regression/baselines/dna/default.json b/tests/regression/baselines/dna/default.json index 057f306d..4f1cf692 100644 --- a/tests/regression/baselines/dna/default.json +++ b/tests/regression/baselines/dna/default.json @@ -14,7 +14,7 @@ "bin_width": 30, "temperature": 298.0, "verbose": false, - "output_file": "/tmp/pytest-of-harry-swift/pytest-1/test_regression_matches_baseli2/job001/output_file.json", + "output_file": "/tmp/pytest-of-harry-swift/pytest-44/test_regression_matches_baseli2/job001/output_file.json", "force_partitioning": 0.5, "water_entropy": true, "grouping": "molecules", @@ -26,7 +26,7 @@ "python": "3.14.3", "platform": "Linux-6.17.0-19-generic-x86_64-with-glibc2.39", "codeentropy_version": "2.1.0", - "git_sha": "2cafee04802f1722cf11b29cae202b298274f93f" + "git_sha": "be46d826f4ae38e3c6e62a7d5bcddeca85e31590" }, "groups": { "0": { diff --git a/tests/regression/baselines/dna/frame_window.json b/tests/regression/baselines/dna/frame_window.json index 13a87e51..d9782bc9 100644 --- a/tests/regression/baselines/dna/frame_window.json +++ b/tests/regression/baselines/dna/frame_window.json @@ -7,14 +7,14 @@ "force_file": null, "file_format": null, "kcal_force_units": false, - "selection_string": "all", + "selection_string": "resid 1:10", "start": 0, "end": 5, "step": 2, "bin_width": 30, "temperature": 298.0, "verbose": false, - "output_file": "/tmp/pytest-of-harry-swift/pytest-1/test_regression_matches_baseli3/job001/output_file.json", + "output_file": "/tmp/pytest-of-harry-swift/pytest-44/test_regression_matches_baseli3/job001/output_file.json", "force_partitioning": 0.5, "water_entropy": true, "grouping": "molecules", @@ -26,7 +26,7 @@ "python": "3.14.3", "platform": "Linux-6.17.0-19-generic-x86_64-with-glibc2.39", "codeentropy_version": "2.1.0", - "git_sha": "2cafee04802f1722cf11b29cae202b298274f93f" + "git_sha": 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b/tests/regression/baselines/water/selection_subset.json new file mode 100644 index 00000000..5d188214 --- /dev/null +++ b/tests/regression/baselines/water/selection_subset.json @@ -0,0 +1,42 @@ +{ + "args": { + "top_traj_file": [ + "/home/harry-swift/BioSim/software/CodeEntropy/.testdata/water/molecules.top", + "/home/harry-swift/BioSim/software/CodeEntropy/.testdata/water/trajectory.crd" + ], + "force_file": "/home/harry-swift/BioSim/software/CodeEntropy/.testdata/water/forces.frc", + "file_format": "MDCRD", + "kcal_force_units": true, + "selection_string": "resid 1:10", + "start": 0, + "end": 1, + "step": 1, + "bin_width": 30, + "temperature": 298.0, + "verbose": false, + "output_file": "/tmp/pytest-of-harry-swift/pytest-49/test_regression_matches_baseli6/job001/output_file.json", + "force_partitioning": 0.5, + "water_entropy": true, + "grouping": "molecules", + "combined_forcetorque": true, + "customised_axes": true, + "search_type": "grid" + }, + "provenance": { + "python": 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Date: Wed, 1 Apr 2026 08:58:34 +0100 Subject: [PATCH 34/41] tests(regression): update `regression/configs/benzene/grouping_each.yaml` to use resid selection string --- .../baselines/benzene/grouping_each.json | 5926 +---------------- .../configs/benzene/grouping_each.yaml | 2 +- 2 files changed, 24 insertions(+), 5904 deletions(-) diff --git a/tests/regression/baselines/benzene/grouping_each.json b/tests/regression/baselines/benzene/grouping_each.json index 16c2af12..3c5a91f8 100644 --- a/tests/regression/baselines/benzene/grouping_each.json +++ b/tests/regression/baselines/benzene/grouping_each.json @@ -7,14 +7,14 @@ "force_file": "/home/harry-swift/BioSim/software/CodeEntropy/.testdata/benzene/forces.frc", "file_format": "MDCRD", "kcal_force_units": true, - "selection_string": "all", + "selection_string": "resid 1:10", "start": 0, "end": 1, "step": 1, "bin_width": 30, "temperature": 298.0, "verbose": false, - "output_file": 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".testdata/benzene/trajectory.crd" - selection_string: "all" + selection_string: "resid 1:10" start: 0 end: 1 step: 1 From 954cd3bfdf32e2b03fa65dd17954d2cd182b88d8 Mon Sep 17 00:00:00 2001 From: harryswift01 Date: Wed, 1 Apr 2026 09:16:06 +0100 Subject: [PATCH 35/41] tests(regression): speed up PR regression tests with fast-only selection and parallel execution --- .github/workflows/pr.yaml | 7 ++++++- 1 file changed, 6 insertions(+), 1 deletion(-) diff --git a/.github/workflows/pr.yaml b/.github/workflows/pr.yaml index 851026c3..26cd172c 100644 --- a/.github/workflows/pr.yaml +++ b/.github/workflows/pr.yaml @@ -62,7 +62,12 @@ jobs: python -m pip install -e .[testing] - name: Pytest (regression quick) - run: python -m pytest tests/regression + run: | + python -m pytest tests/regression \ + -m "not slow" \ + -n auto \ + -vv \ + --durations=0 - name: Upload artifacts (failure) if: failure() From 42f2fc628b0f2fcac5631f5b32039b7997bfbe57 Mon Sep 17 00:00:00 2001 From: harryswift01 Date: Wed, 1 Apr 2026 09:55:53 +0100 Subject: [PATCH 36/41] ci: parallelise pytest execution and optimise regression workflows --- .github/workflows/daily.yaml | 8 +++-- .github/workflows/pr.yaml | 38 ++++++++++++------------ .github/workflows/weekly-regression.yaml | 34 +++++++++++---------- conda-recipe/meta.yaml | 1 + pyproject.toml | 6 +++- 5 files changed, 48 insertions(+), 39 deletions(-) diff --git a/.github/workflows/daily.yaml b/.github/workflows/daily.yaml index 95db9c0d..79a5b4b0 100644 --- a/.github/workflows/daily.yaml +++ b/.github/workflows/daily.yaml @@ -11,14 +11,16 @@ concurrency: jobs: unit: - name: Unit (${{ matrix.os }}, ${{ matrix.python-version }}) + name: Unit (${{ matrix.os }}, py${{ matrix.python-version }}) runs-on: ${{ matrix.os }} timeout-minutes: 30 + strategy: fail-fast: false matrix: os: [ubuntu-24.04, macos-15, windows-2025] python-version: ["3.12", "3.13", "3.14"] + steps: - name: Checkout uses: actions/checkout@8e8c483db84b4bee98b60c0593521ed34d9990e8 # v6 @@ -29,10 +31,10 @@ jobs: python-version: ${{ matrix.python-version }} cache: pip - - name: Install (testing) + - name: Install testing dependencies run: | python -m pip install --upgrade pip python -m pip install -e .[testing] - - name: Pytest (unit) • ${{ matrix.os }} • py${{ matrix.python-version }} + - name: Run unit tests run: python -m pytest tests/unit diff --git a/.github/workflows/pr.yaml b/.github/workflows/pr.yaml index 26cd172c..29123bb5 100644 --- a/.github/workflows/pr.yaml +++ b/.github/workflows/pr.yaml @@ -17,6 +17,7 @@ jobs: matrix: os: [ubuntu-24.04, macos-15, windows-2025] python-version: ["3.12", "3.13", "3.14"] + steps: - name: Checkout uses: actions/checkout@8e8c483db84b4bee98b60c0593521ed34d9990e8 # v6 @@ -36,16 +37,17 @@ jobs: run: python -m pytest tests/unit regression-quick: - name: Regression (quick) + name: Regression (fast) needs: unit runs-on: ubuntu-24.04 timeout-minutes: 35 + steps: - name: Checkout - uses: actions/checkout@8e8c483db84b4bee98b60c0593521ed34d9990e8 # v6 + uses: actions/checkout@8e8c483db84b4bee98b60c0593521ed34d9990e8 - name: Set up Python 3.14 - uses: actions/setup-python@a309ff8b426b58ec0e2a45f0f869d46889d02405 # v6.2.0 + uses: actions/setup-python@a309ff8b426b58ec0e2a45f0f869d46889d02405 with: python-version: "3.14" cache: pip @@ -54,20 +56,21 @@ jobs: uses: actions/cache@v4 with: path: .testdata - key: codeentropy-testdata-v1-${{ runner.os }}-py3.14 + key: codeentropy-testdata-${{ runner.os }}-py314 - - name: Install (testing) + - name: Install testing dependencies run: | python -m pip install --upgrade pip python -m pip install -e .[testing] - - name: Pytest (regression quick) + - name: Run fast regression tests (parallel) run: | python -m pytest tests/regression \ -m "not slow" \ -n auto \ + --dist=loadscope \ -vv \ - --durations=0 + --durations=20 - name: Upload artifacts (failure) if: failure() @@ -76,11 +79,7 @@ jobs: name: quick-regression-failure path: | .testdata/** - tests/regression/**/.pytest_cache/** - /tmp/pytest-of-*/pytest-*/**/config.yaml - /tmp/pytest-of-*/pytest-*/**/codeentropy_stdout.txt - /tmp/pytest-of-*/pytest-*/**/codeentropy_stderr.txt - /tmp/pytest-of-*/pytest-*/**/codeentropy_output.json + /tmp/pytest-of-*/pytest-*/** docs: name: Docs @@ -98,7 +97,7 @@ jobs: python-version: "3.14" cache: pip - - name: Install + - name: Install docs dependencies run: | python -m pip install --upgrade pip python -m pip install -e .[docs] @@ -119,6 +118,7 @@ jobs: name: Pre-commit runs-on: ubuntu-24.04 timeout-minutes: 15 + steps: - name: Checkout uses: actions/checkout@8e8c483db84b4bee98b60c0593521ed34d9990e8 # v6 @@ -129,13 +129,12 @@ jobs: python-version: "3.14" cache: pip - - name: Install (pre-commit) + - name: Install pre-commit dependencies run: | python -m pip install --upgrade pip python -m pip install -e .[pre-commit] - name: Run pre-commit - shell: bash run: | pre-commit install pre-commit run --all-files || { @@ -149,8 +148,9 @@ jobs: needs: unit runs-on: ubuntu-24.04 timeout-minutes: 30 + steps: - - name: Checkout repo + - name: Checkout uses: actions/checkout@8e8c483db84b4bee98b60c0593521ed34d9990e8 - name: Set up Python 3.14 @@ -159,12 +159,12 @@ jobs: python-version: "3.14" cache: pip - - name: Install (testing) + - name: Install testing dependencies run: | python -m pip install --upgrade pip python -m pip install -e .[testing] - - name: Run unit test suite with coverage + - name: Run coverage run: | pytest tests/unit \ --cov CodeEntropy \ @@ -172,7 +172,7 @@ jobs: --cov-report xml \ -q - - name: Upload to Coveralls + - name: Upload coverage to Coveralls uses: coverallsapp/github-action@5cbfd81b66ca5d10c19b062c04de0199c215fb6e with: github-token: ${{ secrets.GITHUB_TOKEN }} diff --git a/.github/workflows/weekly-regression.yaml b/.github/workflows/weekly-regression.yaml index 9326b5ee..eebbb11f 100644 --- a/.github/workflows/weekly-regression.yaml +++ b/.github/workflows/weekly-regression.yaml @@ -2,7 +2,7 @@ name: Weekly Regression Tests on: schedule: - - cron: '0 8 * * 1' # Weekly Monday checks + - cron: '0 8 * * 1' workflow_dispatch: concurrency: @@ -13,12 +13,13 @@ jobs: discover: name: Discover regression systems runs-on: ubuntu-24.04 + outputs: systems: ${{ steps.set.outputs.systems }} steps: - - name: Checkout repo - uses: actions/checkout@v4 + - name: Checkout + uses: actions/checkout@8e8c483db84b4bee98b60c0593521ed34d9990e8 - name: Generate system matrix id: set @@ -30,6 +31,7 @@ jobs: name: Regression (${{ matrix.system }}) needs: discover runs-on: ubuntu-24.04 + timeout-minutes: 360 strategy: fail-fast: false @@ -37,39 +39,39 @@ jobs: system: ${{ fromJson(needs.discover.outputs.systems) }} steps: - - name: Checkout repo - uses: actions/checkout@8e8c483db84b4bee98b60c0593521ed34d9990e8 # v6 + - name: Checkout + uses: actions/checkout@8e8c483db84b4bee98b60c0593521ed34d9990e8 - name: Set up Python 3.14 - uses: actions/setup-python@a309ff8b426b58ec0e2a45f0f869d46889d02405 # v6.2.0 + uses: actions/setup-python@a309ff8b426b58ec0e2a45f0f869d46889d02405 with: python-version: "3.14" cache: pip - - name: Cache regression test data downloads + - name: Cache regression test data uses: actions/cache@v4 with: path: .testdata key: codeentropy-testdata-${{ runner.os }}-py314 - - name: Install CodeEntropy and dependencies + - name: Install testing dependencies run: | pip install --upgrade pip pip install -e .[testing] - - name: Run regression tests for system + - name: Run regression tests (slow) run: | - pytest tests/regression -k "${{ matrix.system }}" --run-slow -vv + pytest tests/regression \ + -k "${{ matrix.system }}" \ + --run-slow \ + -vv \ + --durations=20 - - name: Upload regression artifacts on failure + - name: Upload regression artifacts (failure) if: failure() uses: actions/upload-artifact@v4 with: name: regression-${{ matrix.system }}-artifacts path: | .testdata/** - tests/regression/**/.pytest_cache/** - /tmp/pytest-of-*/pytest-*/**/config.yaml - /tmp/pytest-of-*/pytest-*/**/codeentropy_stdout.txt - /tmp/pytest-of-*/pytest-*/**/codeentropy_stderr.txt - /tmp/pytest-of-*/pytest-*/**/codeentropy_output.json + /tmp/pytest-of-*/pytest-*/** diff --git a/conda-recipe/meta.yaml b/conda-recipe/meta.yaml index 7104d80f..28af659e 100644 --- a/conda-recipe/meta.yaml +++ b/conda-recipe/meta.yaml @@ -38,6 +38,7 @@ requirements: - dask >=2026.1.2,<2026.2.0 - distributed >=2026.1.2,<2026.2.0 - dask-jobqueue >=0.9,<0.10 + - pytest-xdist >=3.8, <3.9 test: imports: diff --git a/pyproject.toml b/pyproject.toml index cfccdae5..b32d59e0 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -61,7 +61,8 @@ Documentation = "https://codeentropy.readthedocs.io" testing = [ "pytest>=9.0,<10.0", "pytest-cov>=7.0,<8.0", - "pytest-sugar>=1.1,<2.0" + "pytest-sugar>=1.1,<2.0", + "pytest-xdist" ] pre-commit = [ "pre-commit>=4.5,<5.0", @@ -83,6 +84,9 @@ docs = [ [project.scripts] CodeEntropy = "CodeEntropy.cli:main" +[tool.pytest.ini_options] +addopts = "-n auto -m 'not slow' -vv" + [tool.ruff] line-length = 88 target-version = "py311" From e91dac19c02c4ab45928163b82738cd8da78d6af Mon Sep 17 00:00:00 2001 From: harryswift01 Date: Wed, 1 Apr 2026 10:22:57 +0100 Subject: [PATCH 37/41] ci: move configuration to pyproject.toml and remove pytest.ini --- pyproject.toml | 12 +++++++++++- tests/pytest.ini | 10 ---------- 2 files changed, 11 insertions(+), 11 deletions(-) delete mode 100644 tests/pytest.ini diff --git a/pyproject.toml b/pyproject.toml index b32d59e0..269e47f7 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -85,7 +85,17 @@ docs = [ CodeEntropy = "CodeEntropy.cli:main" [tool.pytest.ini_options] -addopts = "-n auto -m 'not slow' -vv" +addopts = "-n auto -ra -vv --dist=loadscope" + +markers = [ + "regression: end-to-end regression tests against baselines", + "slow: long-running regression tests (20-30+ minutes)" +] + +testpaths = [ + "tests/unit", + "tests/regression" +] [tool.ruff] line-length = 88 diff --git a/tests/pytest.ini b/tests/pytest.ini deleted file mode 100644 index 64a89db8..00000000 --- a/tests/pytest.ini +++ /dev/null @@ -1,10 +0,0 @@ -[pytest] -testpaths = - unit - regression - -markers = - regression: end-to-end regression tests against baselines - slow: long-running regression tests (20-30+ minutes) - -addopts = -ra From 489bd669590a9f9efacec132a94e113d7efb2e3a Mon Sep 17 00:00:00 2001 From: harryswift01 Date: Wed, 1 Apr 2026 10:47:31 +0100 Subject: [PATCH 38/41] tests: update `project.toml` to use parallel flag correctly --- pyproject.toml | 13 +++++------- tests/__init__.py | 5 +---- tests/regression/test_regression.py | 31 +++++++++++++++++++++++++---- 3 files changed, 33 insertions(+), 16 deletions(-) diff --git a/pyproject.toml b/pyproject.toml index 269e47f7..d7b733c9 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -85,16 +85,13 @@ docs = [ CodeEntropy = "CodeEntropy.cli:main" [tool.pytest.ini_options] -addopts = "-n auto -ra -vv --dist=loadscope" +testpaths = ["tests"] -markers = [ - "regression: end-to-end regression tests against baselines", - "slow: long-running regression tests (20-30+ minutes)" -] +addopts = "-n auto -vv -ra" -testpaths = [ - "tests/unit", - "tests/regression" +markers = [ + "regression: end-to-end regression tests against baselines", + "slow: long-running regression tests (20-30+ minutes)", ] [tool.ruff] diff --git a/tests/__init__.py b/tests/__init__.py index 2f065e73..bc68a398 100644 --- a/tests/__init__.py +++ b/tests/__init__.py @@ -1,4 +1 @@ -""" -Empty init file in case you choose a package besides PyTest such as Nose which may look -for such a file. -""" +""" """ diff --git a/tests/regression/test_regression.py b/tests/regression/test_regression.py index 99f70df1..fea359b3 100644 --- a/tests/regression/test_regression.py +++ b/tests/regression/test_regression.py @@ -10,6 +10,27 @@ from tests.regression.cases import discover_cases from tests.regression.helpers import run_codeentropy_with_config +CASES = discover_cases() + + +def pytest_generate_tests(metafunc: pytest.Metafunc) -> None: + """ + Dynamically parametrize regression test cases. + + This hook enables pytest-xdist to distribute individual regression cases + across multiple workers by generating test parametrization at collection time. + + Args: + metafunc (pytest.Metafunc): Pytest metafunction object used to inspect + and modify test function parametrization. + """ + if "case" in metafunc.fixturenames: + metafunc.parametrize( + "case", + CASES, + ids=[c.id for c in CASES], + ) + def _group_index(payload: dict[str, Any]) -> dict[str, dict[str, Any]]: """ @@ -106,9 +127,10 @@ def _compare_grouped( @pytest.mark.regression -@pytest.mark.parametrize("case", discover_cases()) def test_regression_matches_baseline( - tmp_path: Path, case, request: pytest.FixtureRequest + tmp_path: Path, + case, + request: pytest.FixtureRequest, ) -> None: """ Execute a regression test for a single scenario and compare against baseline. @@ -121,8 +143,9 @@ def test_regression_matches_baseline( Args: tmp_path (Path): Temporary directory provided by pytest. - case (RegressionCase): Parameterized regression case. - request (pytest.FixtureRequest): Pytest request object for accessing CLI options + case: A RegressionCase instance containing system, config, and baseline paths. + request (pytest.FixtureRequest): Pytest request object used to access CLI + options. Raises: AssertionError: If the output does not match the baseline or baseline is missing From 07d4016a75bcb29e795a74a359e14d8cc181cda6 Mon Sep 17 00:00:00 2001 From: harryswift01 Date: Wed, 1 Apr 2026 10:56:45 +0100 Subject: [PATCH 39/41] docs: udpdate `developer_guide.rst` to use correct pytest flags --- docs/developer_guide.rst | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/docs/developer_guide.rst b/docs/developer_guide.rst index cb867ae6..edf1b4bf 100644 --- a/docs/developer_guide.rst +++ b/docs/developer_guide.rst @@ -54,7 +54,7 @@ Run regression tests excluding slow systems:: Run slow regression tests:: - pytest tests/regression -m slow + pytest tests/regression --run-slow Run tests with coverage:: From 054b3fc256b9ab96f65b5fd0d0c283298f116394 Mon Sep 17 00:00:00 2001 From: harryswift01 Date: Wed, 1 Apr 2026 12:03:54 +0100 Subject: [PATCH 40/41] ci: parallelize regression tests per system using dynamic matrix --- .github/workflows/pr.yaml | 49 +++++++++++++++++---- .github/workflows/weekly-regression.yaml | 21 +++++++-- tests/regression/conftest.py | 54 ++++++++++++++++-------- tests/regression/list_systems.py | 12 ++++++ 4 files changed, 106 insertions(+), 30 deletions(-) create mode 100644 tests/regression/list_systems.py diff --git a/.github/workflows/pr.yaml b/.github/workflows/pr.yaml index 29123bb5..96aaa0ce 100644 --- a/.github/workflows/pr.yaml +++ b/.github/workflows/pr.yaml @@ -20,10 +20,10 @@ jobs: steps: - name: Checkout - uses: actions/checkout@8e8c483db84b4bee98b60c0593521ed34d9990e8 # v6 + uses: actions/checkout@8e8c483db84b4bee98b60c0593521ed34d9990e8 - name: Set up Python ${{ matrix.python-version }} - uses: actions/setup-python@a309ff8b426b58ec0e2a45f0f869d46889d02405 # v6.2.0 + uses: actions/setup-python@a309ff8b426b58ec0e2a45f0f869d46889d02405 with: python-version: ${{ matrix.python-version }} cache: pip @@ -36,12 +36,44 @@ jobs: - name: Pytest (unit) • ${{ matrix.os }}, ${{ matrix.python-version }} run: python -m pytest tests/unit + discover-systems: + name: Discover regression systems + runs-on: ubuntu-24.04 + outputs: + systems: ${{ steps.set-systems.outputs.systems }} + + steps: + - name: Checkout + uses: actions/checkout@8e8c483db84b4bee98b60c0593521ed34d9990e8 + + - name: Set up Python 3.14 + uses: actions/setup-python@a309ff8b426b58ec0e2a45f0f869d46889d02405 + with: + python-version: "3.14" + cache: pip + + - name: Install testing dependencies + run: | + python -m pip install --upgrade pip + python -m pip install -e .[testing] + + - name: Discover systems + id: set-systems + run: | + SYSTEMS=$(python -m tests.regression.list_systems) + echo "systems=$SYSTEMS" >> $GITHUB_OUTPUT + regression-quick: - name: Regression (fast) - needs: unit + name: Regression (fast) • ${{ matrix.system }} + needs: [unit, discover-systems] runs-on: ubuntu-24.04 timeout-minutes: 35 + strategy: + fail-fast: false + matrix: + system: ${{ fromJson(needs.discover-systems.outputs.systems) }} + steps: - name: Checkout uses: actions/checkout@8e8c483db84b4bee98b60c0593521ed34d9990e8 @@ -63,12 +95,13 @@ jobs: python -m pip install --upgrade pip python -m pip install -e .[testing] - - name: Run fast regression tests (parallel) + - name: Run fast regression tests (per system) run: | python -m pytest tests/regression \ -m "not slow" \ -n auto \ --dist=loadscope \ + -k "${{ matrix.system }}" \ -vv \ --durations=20 @@ -76,7 +109,7 @@ jobs: if: failure() uses: actions/upload-artifact@v4 with: - name: quick-regression-failure + name: quick-regression-failure-${{ matrix.system }} path: | .testdata/** /tmp/pytest-of-*/pytest-*/** @@ -121,10 +154,10 @@ jobs: steps: - name: Checkout - uses: actions/checkout@8e8c483db84b4bee98b60c0593521ed34d9990e8 # v6 + uses: actions/checkout@8e8c483db84b4bee98b60c0593521ed34d9990e8 - name: Set up Python 3.14 - uses: actions/setup-python@a309ff8b426b58ec0e2a45f0f869d46889d02405 # v6.2.0 + uses: actions/setup-python@a309ff8b426b58ec0e2a45f0f869d46889d02405 with: python-version: "3.14" cache: pip diff --git a/.github/workflows/weekly-regression.yaml b/.github/workflows/weekly-regression.yaml index eebbb11f..5f4595be 100644 --- a/.github/workflows/weekly-regression.yaml +++ b/.github/workflows/weekly-regression.yaml @@ -21,10 +21,21 @@ jobs: - name: Checkout uses: actions/checkout@8e8c483db84b4bee98b60c0593521ed34d9990e8 + - name: Set up Python 3.14 + uses: actions/setup-python@a309ff8b426b58ec0e2a45f0f869d46889d02405 + with: + python-version: "3.14" + cache: pip + + - name: Install testing dependencies + run: | + python -m pip install --upgrade pip + python -m pip install -e .[testing] + - name: Generate system matrix id: set run: | - systems=$(ls tests/regression/configs | jq -R -s -c 'split("\n")[:-1]') + systems=$(python -m tests.regression.list_systems) echo "systems=$systems" >> $GITHUB_OUTPUT regression: @@ -56,14 +67,16 @@ jobs: - name: Install testing dependencies run: | - pip install --upgrade pip - pip install -e .[testing] + python -m pip install --upgrade pip + python -m pip install -e .[testing] - - name: Run regression tests (slow) + - name: Run regression tests (slow, per system) run: | pytest tests/regression \ -k "${{ matrix.system }}" \ --run-slow \ + -n auto \ + --dist=loadscope \ -vv \ --durations=20 diff --git a/tests/regression/conftest.py b/tests/regression/conftest.py index 58249369..05be6f7c 100644 --- a/tests/regression/conftest.py +++ b/tests/regression/conftest.py @@ -9,9 +9,6 @@ def pytest_addoption(parser: pytest.Parser) -> None: Adds options to control regression test execution, baseline updates, and debugging output. - - Args: - parser (pytest.Parser): Pytest CLI parser. """ parser.addoption( "--run-slow", @@ -31,14 +28,17 @@ def pytest_addoption(parser: pytest.Parser) -> None: default=False, help="Print CodeEntropy stdout/stderr and paths for easier debugging.", ) + parser.addoption( + "--system", + action="append", + default=None, + help="Run only tests for specified system(s). Can be passed multiple times.", + ) def pytest_configure(config: pytest.Config) -> None: """ Register custom pytest markers. - - Args: - config (pytest.Config): Pytest configuration object. """ config.addinivalue_line("markers", "regression: end-to-end regression tests") config.addinivalue_line("markers", "slow: long-running tests (20-30+ minutes)") @@ -48,19 +48,37 @@ def pytest_collection_modifyitems( config: pytest.Config, items: list[pytest.Item] ) -> None: """ - Modify collected test items to skip slow tests unless explicitly enabled. - - Only tests marked with `@pytest.mark.slow` are skipped when the - `--run-slow` flag is not provided. - - Args: - config (pytest.Config): Pytest configuration object. - items (list[pytest.Item]): Collected test items. + Modify collected test items to: + 1. Skip slow tests unless --run-slow is provided + 2. Filter tests by --system if specified """ - if config.getoption("--run-slow"): + if not config.getoption("--run-slow"): + skip_slow = pytest.mark.skip( + reason="Skipped slow test (use --run-slow to run)." + ) + for item in items: + if "slow" in item.keywords: + item.add_marker(skip_slow) + + selected_systems = config.getoption("--system") + if not selected_systems: return - skip_slow = pytest.mark.skip(reason="Skipped slow test (use --run-slow to run).") + filtered_items = [] + for item in items: - if "slow" in item.keywords: - item.add_marker(skip_slow) + callspec = getattr(item, "callspec", None) + + case = None + if callspec is not None: + case = callspec.params.get("case") + + # Keep non-parametrized tests + if case is None: + filtered_items.append(item) + continue + + if hasattr(case, "system") and case.system in selected_systems: + filtered_items.append(item) + + items[:] = filtered_items diff --git a/tests/regression/list_systems.py b/tests/regression/list_systems.py new file mode 100644 index 00000000..f055457a --- /dev/null +++ b/tests/regression/list_systems.py @@ -0,0 +1,12 @@ +import json + +from tests.regression.cases import discover_cases + + +def main(): + systems = sorted({case.system for case in discover_cases()}) + print(json.dumps(systems)) + + +if __name__ == "__main__": + main() From 54884c64d82fe00efec032a9732943069d462e1d Mon Sep 17 00:00:00 2001 From: harryswift01 Date: Wed, 1 Apr 2026 13:41:49 +0100 Subject: [PATCH 41/41] fix(regression): correctly extract system name from pytest parametrized cases --- tests/regression/list_systems.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/tests/regression/list_systems.py b/tests/regression/list_systems.py index f055457a..0da18eea 100644 --- a/tests/regression/list_systems.py +++ b/tests/regression/list_systems.py @@ -4,7 +4,7 @@ def main(): - systems = sorted({case.system for case in discover_cases()}) + systems = sorted({case.values[0].system for case in discover_cases()}) print(json.dumps(systems))