updates to MCDC dataset generator

Author: melekderman

.github/workflows/ci.yml

@@ -95,7 +95,7 @@ jobs:
   #     id-token: write
   #   environment:
   #     name: pypi
-  #     url: https://pypi.org/p/pyepics-data
+  #     url: https://pypi.org/p/epics
   #   steps:
   #     - uses: actions/download-artifact@v4
   #       with:

.github/workflows/workflow.yml

@@ -8,6 +8,7 @@ jobs:
   build-n-publish:
     name: Build and publish to PyPI
     runs-on: ubuntu-latest
+    environment: pypi
     permissions:
       id-token: write
       contents: read

CHANGELOG.md

@@ -0,0 +1,46 @@
+# Changelog
+
+All notable changes to PyEPICS are documented in this file.
+
+## [1.0.0] — 2026-02-15
+
+### Added
+
+- **Combined MCDC HDF5 output**: Each element now produces a single HDF5
+  file (e.g. `Fe.h5`) containing `electron_reactions`, `photon_reactions`,
+  and `atomic_relaxation` groups together.
+- `create_combined_mcdc_hdf5()` — new public API for writing combined files.
+- `write_mcdc_combined()` — low-level writer accepting EEDL/EPDL/EADL datasets.
+- Full **EPDL** (photon) support: reader, raw HDF5, MCDC HDF5 — cross sections,
+  form factors, photoelectric subshells, pair production.
+- Full **EADL** (atomic relaxation) support: reader, raw HDF5, MCDC HDF5 —
+  subshell binding energies, radiative/non-radiative transitions,
+  fluorescence and Auger yields.
+- `EPICSClient` — high-level API for querying element properties across
+  all three libraries (EEDL, EPDL, EADL).
+- `ElementProperties` — container with binding energies, cross sections,
+  fluorescence data, and transition energies.
+- CLI tool (`epics`) for download, raw, mcdc, and full pipeline execution.
+- Sphinx documentation with API reference, data-sources guide, and pipeline docs.
+- 164 unit tests covering readers, converters, mapping completeness, and pipeline.
+- PDF regression-test report generator.
+
+### Changed
+
+- **PyPI package name** changed from `pyepics-data` to `epics`.
+  Import name remains `pyepics` (`import pyepics`).
+- Electron-specific constants renamed for clarity:
+  `MF_MT` → `ELECTRON_MF_MT`,
+  `SECTIONS_ABBREVS` → `ELECTRON_SECTIONS_ABBREVS`,
+  `SUBSHELL_LABELS` → `ELECTRON_SUBSHELL_LABELS`.
+  Old names kept as backward-compatible aliases.
+- MCDC CLI now produces one combined file per element in `data/mcdc/`
+  (previously separated into `data/mcdc/electron/`, `photon/`, `atomic/`).
+
+## [0.1.0] — 2026-12-18
+
+### Added
+
+- Initial release with EEDL (electron) reader and HDF5 converter.
+- Basic constant dictionaries and utility functions.
+- PyEEDL backward-compatibility layer (`pyepics.pyeedl_compat`).

INSTALL.md

@@ -7,7 +7,7 @@ PyEPICS requires **Python 3.11 or later** (3.11, 3.12, 3.13).
 ## Quick Install from PyPI
 
 ```bash
-pip install pyepics-data
+pip install epics
 ```
 
 This installs the core package with the minimum required dependencies
@@ -19,23 +19,23 @@ PyEPICS defines optional dependency groups you can install as needed:
 
 | Extra      | What it adds                        | Install command                          |
 |------------|-------------------------------------|------------------------------------------|
-| `download` | `requests`, `beautifulsoup4`        | `pip install "pyepics-data[download]"`   |
-| `pandas`   | `pandas`                            | `pip install "pyepics-data[pandas]"`     |
-| `plot`     | `matplotlib`                        | `pip install "pyepics-data[plot]"`       |
-| `all`      | All optional dependencies           | `pip install "pyepics-data[all]"`        |
-| `dev`      | Testing + linting + docs tooling    | `pip install "pyepics-data[dev]"`        |
+| `download` | `requests`, `beautifulsoup4`        | `pip install "epics[download]"`   |
+| `pandas`   | `pandas`                            | `pip install "epics[pandas]"`     |
+| `plot`     | `matplotlib`                        | `pip install "epics[plot]"`       |
+| `all`      | All optional dependencies           | `pip install "epics[all]"`        |
+| `dev`      | Testing + linting + docs tooling    | `pip install "epics[dev]"`        |
 
 ### Examples
 
 ```bash
 # Core only (reading ENDF files and converting to HDF5)
-pip install pyepics-data
+pip install epics
 
 # With plotting and pandas for interactive exploration
-pip install "pyepics-data[plot,pandas]"
+pip install "epics[plot,pandas]"
 
 # Everything (including download support)
-pip install "pyepics-data[all]"
+pip install "epics[all]"
 ```
 
 ## Developer Install
@@ -99,8 +99,8 @@ This produces:
 
 ```
 dist/
-├── pyepics_data-0.1.0.tar.gz      # sdist
-└── pyepics_data-0.1.0-py3-none-any.whl  # wheel
+├── epics-0.1.0.tar.gz      # sdist
+└── epics-0.1.0-py3-none-any.whl  # wheel
 ```
 
 ## Verifying the Install
@@ -125,5 +125,5 @@ print("EPICSClient loaded successfully")
 
   ```bash
   conda install numpy h5py
-  pip install pyepics-data
+  pip install epics
   ```

README.md

@@ -5,7 +5,7 @@
 [![License: BSD-3](https://img.shields.io/badge/license-BSD--3--Clause-green.svg)](LICENSE)
 [![ReadTheDocs](https://readthedocs.org/projects/pyepics/badge/?version=latest)](https://pyepics.readthedocs.io/en/latest/)
 
-> Python library for reading and converting EPICS (Electron Photon Interaction Cross Sections) nuclear data.
+> Python library for reading and converting EPICS (Electron Photon Interaction Cross Sections) nuclear data by LLNL.
 
 PyEPICS parses EEDL, EPDL, and EADL files from the [LLNL EPICS 2025](https://nuclear.llnl.gov/EPICS/) database (in ENDF-6 format) and converts them into structured HDF5 files suitable for Monte Carlo transport codes such as [MC/DC](https://github.com/CEMeNT-PSAAP/MCDC).
 
@@ -87,10 +87,10 @@ utils ← models ← readers ← converters (raw_hdf5 / mcdc_hdf5)
 
 ```bash
 # From PyPI (when published)
-pip install pyepics-data
+pip install epics
 
 # With all optional dependencies
-pip install "pyepics-data[all]"
+pip install "epics[all]"
 
 # From source (editable, for development)
 git clone https://github.com/melekderman/PyEPICS.git

docs/conf.py

@@ -9,7 +9,7 @@
 project = "PyEPICS"
 copyright = "2026, Melek Derman"
 author = "Melek Derman"
-release = "0.1.0"
+release = "1.0.0"
 
 extensions = [
     "sphinx.ext.autodoc",

docs/getting_started.rst

@@ -4,21 +4,21 @@ Getting Started
 Installation
 ------------
 
-From PyPI (when published):
+From PyPI:
 
 .. code-block:: bash
 
-   pip install pyepics-data
+   pip install epics
 
 With optional extras:
 
 .. code-block:: bash
 
    # Plotting and pandas support
-   pip install "pyepics-data[plot,pandas]"
+   pip install "epics[plot,pandas]"
 
    # All optional dependencies
-   pip install "pyepics-data[all]"
+   pip install "epics[all]"
 
 From source (development):
 

pyepics/__init__.py

@@ -48,12 +48,13 @@
 
 from __future__ import annotations
 
-__version__ = "0.1.0"
+__version__ = "1.0.0"
 __author__ = "Melek Derman"
 
 from pyepics.client import ElementProperties, EPICSClient
 from pyepics.converters.hdf5 import (
     convert_dataset_to_hdf5,
+    create_combined_mcdc_hdf5,
     create_mcdc_hdf5,
     create_raw_hdf5,
 )
@@ -83,6 +84,7 @@
     "convert_dataset_to_hdf5",
     "create_raw_hdf5",
     "create_mcdc_hdf5",
+    "create_combined_mcdc_hdf5",
     # Exceptions
     "PyEPICSError",
     "ParseError",

pyepics/cli.py

@@ -43,9 +43,9 @@
             photon/         ← raw HDF5 (photon)
             atomic/         ← raw HDF5 (atomic)
         mcdc/
-            electron/       ← MCDC HDF5 (electron)
-            photon/         ← MCDC HDF5 (photon)
-            atomic/         ← MCDC HDF5 (atomic)
+            H.h5            ← combined MCDC (electron + photon + atomic)
+            He.h5
+            ...
 """
 
 from __future__ import annotations
@@ -189,52 +189,74 @@ def cmd_raw(args):
 
 
 def cmd_mcdc(args):
-    """Create MCDC-format HDF5 files from ENDF sources."""
-    from pyepics.converters.hdf5 import create_mcdc_hdf5
+    """Create combined MCDC-format HDF5 files (one per element).
+
+    Each output file contains ``electron_reactions``,
+    ``photon_reactions``, and ``atomic_relaxation`` groups — whichever
+    ENDF sources are available for that element.
+    """
+    from pyepics.converters.hdf5 import create_combined_mcdc_hdf5
 
     base = Path(args.data_dir)
-    libraries = args.libraries or list(LIBRARY_CONFIG.keys())
     z_min, z_max = args.z_min, args.z_max
 
-    total_ok = 0
-    total_fail = 0
+    mcdc_dir = base / "data/mcdc"
+    mcdc_dir.mkdir(parents=True, exist_ok=True)
 
-    for lib_name in libraries:
-        cfg = LIBRARY_CONFIG[lib_name]
-        endf_dir = base / cfg["endf_dir"]
-        mcdc_dir = base / cfg["mcdc_dir"]
-        mcdc_dir.mkdir(parents=True, exist_ok=True)
+    # ENDF directories
+    eedl_dir = base / LIBRARY_CONFIG["electron"]["endf_dir"]
+    epdl_dir = base / LIBRARY_CONFIG["photon"]["endf_dir"]
+    eadl_dir = base / LIBRARY_CONFIG["atomic"]["endf_dir"]
 
-        print(f"\n{'=' * 60}")
-        print(f"  Creating MCDC HDF5: {lib_name} ({cfg['dataset_type']})")
-        print(f"  ENDF source:  {endf_dir}")
-        print(f"  Output:       {mcdc_dir}")
-        print(f"  Z range:      {z_min}–{z_max}")
-        print(f"{'=' * 60}")
+    print(f"\n{'=' * 60}")
+    print(f"  Creating combined MCDC HDF5 files")
+    print(f"  Output:  {mcdc_dir}")
+    print(f"  Z range: {z_min}–{z_max}")
+    print(f"{'=' * 60}")
 
-        for Z in range(z_min, z_max + 1):
-            sym = _element_symbol(Z)
-            endf_file = _find_endf_file(endf_dir, cfg["endf_prefix"], Z)
-            if endf_file is None:
-                continue
+    total_ok = 0
+    total_fail = 0
 
-            out_path = mcdc_dir / f"{sym}.h5"
-            print(f"  Z={Z:3d} ({sym:>2s}): {endf_file.name} -> {out_path.name}", end=" ... ", flush=True)
+    for Z in range(z_min, z_max + 1):
+        sym = _element_symbol(Z)
+        eedl_file = _find_endf_file(eedl_dir, "EEDL", Z)
+        epdl_file = _find_endf_file(epdl_dir, "EPDL", Z)
+        eadl_file = _find_endf_file(eadl_dir, "EADL", Z)
+
+        if not any([eedl_file, epdl_file, eadl_file]):
+            continue
+
+        libs = []
+        if eedl_file:
+            libs.append("EEDL")
+        if epdl_file:
+            libs.append("EPDL")
+        if eadl_file:
+            libs.append("EADL")
+
+        out_path = mcdc_dir / f"{sym}.h5"
+        print(
+            f"  Z={Z:3d} ({sym:>2s}): {'+'.join(libs)} -> {out_path.name}",
+            end=" ... ",
+            flush=True,
+        )
 
-            try:
-                create_mcdc_hdf5(
-                    cfg["dataset_type"],
-                    endf_file,
-                    out_path,
-                    overwrite=args.overwrite,
-                )
-                print("OK")
-                total_ok += 1
-            except Exception as exc:
-                print(f"FAIL: {exc}")
-                total_fail += 1
-                if not args.continue_on_error:
-                    return 1
+        try:
+            create_combined_mcdc_hdf5(
+                Z,
+                out_path,
+                eedl_path=eedl_file,
+                epdl_path=epdl_file,
+                eadl_path=eadl_file,
+                overwrite=args.overwrite,
+            )
+            print("OK")
+            total_ok += 1
+        except Exception as exc:
+            print(f"FAIL: {exc}")
+            total_fail += 1
+            if not args.continue_on_error:
+                return 1
 
     print(f"\nMCDC HDF5: {total_ok} OK, {total_fail} failed")
     return 0 if total_fail == 0 else 1

pyepics/converters/__init__.py

@@ -16,14 +16,23 @@
     Writes a "raw" HDF5 preserving original grids and breakpoints.
 * :func:`~pyepics.converters.hdf5.create_mcdc_hdf5`
     Writes an MCDC-optimised HDF5 with common energy grid and PDFs.
+* :func:`~pyepics.converters.hdf5.create_combined_mcdc_hdf5`
+    Creates a single MCDC HDF5 per element with electron, photon,
+    and atomic data combined.
 """
 
 from __future__ import annotations
 
 from pyepics.converters.hdf5 import (
     convert_dataset_to_hdf5,
+    create_combined_mcdc_hdf5,
     create_mcdc_hdf5,
     create_raw_hdf5,
 )
 
-__all__ = ["convert_dataset_to_hdf5", "create_raw_hdf5", "create_mcdc_hdf5"]
+__all__ = [
+    "convert_dataset_to_hdf5",
+    "create_raw_hdf5",
+    "create_mcdc_hdf5",
+    "create_combined_mcdc_hdf5",
+]