diff --git a/.DS_Store b/.DS_Store deleted file mode 100644 index ccbc9c3..0000000 Binary files a/.DS_Store and /dev/null differ diff --git a/.github/workflows/conda-build.yml b/.github/workflows/conda-build.yml deleted file mode 100644 index 34dbabb..0000000 --- a/.github/workflows/conda-build.yml +++ /dev/null @@ -1,34 +0,0 @@ -name: Conda Build - -on: [push, pull_request] - -jobs: - build: - runs-on: ubuntu-latest - defaults: - run: - shell: bash -el {0} - steps: - - name: Checkout repository - uses: actions/checkout@v4 # Update to latest version - - - name: Set up Miniconda - uses: conda-incubator/setup-miniconda@v3 - with: - mamba-version: "*" - channels: conda-forge,bioconda - cache-downloads: true - auto-update-conda: false - activate-environment: test - python-version: "3.12" - - - name: Setup conda-build and anaconda-client - run: | - mamba install -q conda-build anaconda-client conda-verify - - - name: Build package - run: | - conda build purge-all - conda config --set solver libmamba - conda config --set channel_priority strict - conda build recipe --suppress-variables --override-channels --channel conda-forge --channel bioconda --no-anaconda-upload --output-folder ./ \ No newline at end of file diff --git a/.github/workflows/python-app.yml b/.github/workflows/python-app.yml index e6975c0..417b96b 100644 --- a/.github/workflows/python-app.yml +++ b/.github/workflows/python-app.yml @@ -26,10 +26,9 @@ jobs: - name: Install dependencies run: | python -m pip install --upgrade pip - python -m pip install flake8 pytest + python -m pip install flake8 pytest build if [ -f requirements.txt ]; then pip install -r requirements.txt; fi - pip install poetry - poetry build + python -m build pip install dist/*.whl - name: Lint with flake8 run: | @@ -39,4 +38,4 @@ jobs: flake8 . --count --exit-zero --max-complexity=10 --max-line-length=127 --statistics - name: Test with pytest run: | - poetry run pytest \ No newline at end of file + pytest \ No newline at end of file diff --git a/.github/workflows/python-package.yml b/.github/workflows/python-package.yml index aeee5d8..d225324 100644 --- a/.github/workflows/python-package.yml +++ b/.github/workflows/python-package.yml @@ -27,10 +27,9 @@ jobs: - name: Install dependencies run: | python -m pip install --upgrade pip - python -m pip install flake8 pytest + python -m pip install flake8 pytest build if [ -f requirements.txt ]; then pip install -r requirements.txt; fi - pip install poetry - poetry build + python -m build pip install dist/*.whl - name: Lint with flake8 run: | diff --git a/.gitignore b/.gitignore index 1f0d4d6..7def66f 100644 --- a/.gitignore +++ b/.gitignore @@ -169,6 +169,9 @@ cython_debug/ .qodo /tests/test_data/RD139_Narrow_UPS1_0_1fmol_inj1.mzML +# macOS metadata files +.DS_Store + # DIA-NN config file generated by tests diann_config.cfg diff --git a/pyproject.toml b/pyproject.toml index 9e30dac..8ea8d5b 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -1,13 +1,13 @@ -[tool.poetry] +[project] name = "quantms-utils" +dynamic = ["version"] description = "Python scripts and helpers for the quantMS workflow" readme = "README.md" license = "MIT" -version = "0.0.28" authors = [ - "Yasset Perez-Riverol ", - "Dai Chengxin ", - "Julianus Pfeuffer " + { name = "Yasset Perez-Riverol", email = "ypriverol@gmail.com" }, + { name = "Dai Chengxin", email = "chengxin2024@126.com" }, + { name = "Julianus Pfeuffer", email = "jule.pf@gmail.com" } ] keywords = [ "quantms", @@ -24,26 +24,22 @@ classifiers = [ "Topic :: Scientific/Engineering :: Bio-Informatics", "Development Status :: 5 - Production/Stable" ] -packages = [ - { include = "quantmsutils" } +dependencies = [ + "click", + "sdrf-pipelines>=0.1.2", + "pyopenms>=3.3.0", + "pandas", + "pyarrow>=16.1.0", + "scipy", ] -[tool.poetry.dependencies] -python = "*" -click = "*" -sdrf-pipelines = ">=0.1.2" -pyopenms = ">=3.3.0" -pandas = "*" -pyarrow = ">=16.1.0" -scipy = "*" - -[tool.poetry.urls] +[project.urls] GitHub = "https://github.com/bigbio/quantms-utils" PyPi = "https://pypi.org/project/quantms-utils/" Quantms = "https://quantms.org" LICENSE = "https://github.com/bigbio/quantms-utils/blob/main/LICENSE" -[tool.poetry.scripts] +[project.scripts] quantmsutilsc = "quantmsutils.quantmsutilsc:main" [tool.isort] @@ -54,5 +50,14 @@ line-length = 99 target-version = ["py39"] [build-system] -requires = ["poetry-core>=1.2.0"] -build-backend = "poetry.core.masonry.api" +requires = ["hatchling", "hatch-vcs"] +build-backend = "hatchling.build" + +[tool.hatch.version] +source = "vcs" + +[tool.hatch.version.raw-options] +local_scheme = "no-local-version" + +[tool.hatch.build.targets.wheel] +packages = ["quantmsutils"] diff --git a/quantmsutils/.DS_Store b/quantmsutils/.DS_Store deleted file mode 100644 index ed96f8a..0000000 Binary files a/quantmsutils/.DS_Store and /dev/null differ diff --git a/recipe/conda_build_config.yaml b/recipe/conda_build_config.yaml deleted file mode 100644 index 81e2ea5..0000000 --- a/recipe/conda_build_config.yaml +++ /dev/null @@ -1,2 +0,0 @@ -python: - - 3.11 diff --git a/recipe/meta.yaml b/recipe/meta.yaml deleted file mode 100644 index b318cac..0000000 --- a/recipe/meta.yaml +++ /dev/null @@ -1,47 +0,0 @@ -# recipe/meta.yaml -package: - name: quantms-utils - version: "0.0.26" - -source: - path: ../ - -build: - entry_points: - - quantmsutilsc=quantmsutils.quantmsutilsc:main - run_exports: - - {{ pin_subpackage('quantms-utils', max_pin="x.x") }} - script: "{{ PYTHON }} -m pip install . --no-deps --no-build-isolation --no-cache-dir -vvv" - number: 0 - noarch: python - -requirements: - host: - - python - - pip - - poetry-core >=1.2.0 - - run: - - python >=3.9,<3.13 - - click - - sdrf-pipelines >=0.1.1 - - pyopenms>=3.3.0 - - pandas - - pyarrow>=16.1.0 - - scipy -test: - imports: - - quantmsutils - commands: - - quantmsutilsc --help - -about: - home: https://www.github.com/bigbio/quantms-utils - summary: Python package with scripts and helpers for the quantms workflow - license: MIT - license_file: LICENSE - dev_url: https://www.github.com/bigbio/quantms-utils - -extra: - recipe-maintainers: - - ypriverol diff --git a/tests/.DS_Store b/tests/.DS_Store deleted file mode 100644 index f0f652e..0000000 Binary files a/tests/.DS_Store and /dev/null differ