Merge pull request #561 from legend-exp/cit

Update citation-related documentation

.github/workflows/distribution.yml

@@ -2,42 +2,47 @@ name: distribute
 
 on:
   workflow_dispatch:
+  pull_request:
   push:
-    tags: "v*"
+    branches:
+      - main
   release:
     types:
       - published
 
-jobs:
+concurrency:
+  group: ${{ github.workflow }}-${{ github.ref }}
+  cancel-in-progress: true
+
+env:
+  FORCE_COLOR: 3
 
+jobs:
   dist:
+    name: Distribution build
     runs-on: ubuntu-latest
-    steps:
-    - uses: actions/checkout@v4
-      with:
-        fetch-depth: 0
 
-    - name: Build SDist and wheel
-      run: pipx run build
-
-    - uses: actions/upload-artifact@v4
-      with:
-        path: dist/*
+    steps:
+      - uses: actions/checkout@v4
+        with:
+          fetch-depth: 0
 
-    - name: Check metadata
-      run: pipx run twine check dist/*
+      - uses: hynek/build-and-inspect-python-package@v2
 
   publish:
     needs: [dist]
+    name: Publish to PyPI
+    environment: pypi
+    permissions:
+      id-token: write
     runs-on: ubuntu-latest
     if: github.event_name == 'release' && github.event.action == 'published'
 
     steps:
-    - uses: actions/download-artifact@v4
-      with:
-        name: artifact
-        path: dist
-
-    - uses: pypa/gh-action-pypi-publish@v1.8.11
-      with:
-        password: ${{ secrets.pypi_password }}
+      - uses: actions/download-artifact@v4
+        with:
+          name: Packages
+          path: dist
+
+      - uses: pypa/gh-action-pypi-publish@release/v1
+        if: github.event_name == 'release' && github.event.action == 'published'

.github/workflows/main.yml

@@ -1,18 +1,19 @@
 name: pygama
 
 on:
+  workflow_dispatch:
+  pull_request:
   push:
     branches:
       - main
-      - 'releases/**'
-  pull_request:
-  release:
+      - "releases/**"
 
 concurrency:
   group: ${{ github.workflow }}-${{ github.ref }}
   cancel-in-progress: true
 
 env:
+  FORCE_COLOR: 3
   TQDM_MININTERVAL: 100
 
 jobs:

.pre-commit-config.yaml

@@ -70,6 +70,7 @@ repos:
       flake8-print,
       pep8-naming
     ]
+    args: ["--extend-ignore", "E203,E501"]
 
 - repo: https://github.com/kynan/nbstripout
   rev: "0.6.1"

CITATION.cff

@@ -1,7 +1,7 @@
 cff-version: 1.2.0
 title: pygama
-doi: FILLME
-date-released: 2024-02-01
+doi: https://doi.org/10.5281/zenodo.10614246
+date-released: 2024-02-03
 url: https://github.com/github-linguist/linguist
 message: "If you use this software, please cite it as below."
 authors:

README.md

@@ -12,6 +12,7 @@
 [![GitHub pull requests](https://img.shields.io/github/issues-pr/legend-exp/pygama?logo=github)](https://github.com/legend-exp/pygama/pulls)
 [![License](https://img.shields.io/github/license/legend-exp/pygama)](https://github.com/legend-exp/pygama/blob/main/LICENSE)
 [![Read the Docs](https://img.shields.io/readthedocs/pygama?logo=readthedocs)](https://pygama.readthedocs.io)
+[![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.10614246.svg)](https://zenodo.org/doi/10.5281/zenodo.10614246)
 
 *pygama* is a Python package for:
 
@@ -28,7 +29,14 @@
 
 Check out the [online documentation](https://pygama.readthedocs.io).
 
+If you are using this software, consider
+[citing](https://zenodo.org/doi/10.5281/zenodo.10614246)!
+
 ## Related repositories
-- [legend-exp/legend-pydataobj](https://github.com/legend-exp/legend-pydataobj) → LEGEND Python Data Objects
-- [legend-exp/legend-daq2lh5](https://github.com/legend-exp/legend-daq2lh5) → Convert digitizer data to LEGEND HDF5
-- [legend-exp/dspeed](https://github.com/legend-exp/dspeed) → Fast Digital Signal Processing for particle detector signals in Python
+
+- [legend-exp/legend-pydataobj](https://github.com/legend-exp/legend-pydataobj)
+  → LEGEND Python Data Objects
+- [legend-exp/legend-daq2lh5](https://github.com/legend-exp/legend-daq2lh5)
+  → Convert digitizer data to LEGEND HDF5
+- [legend-exp/dspeed](https://github.com/legend-exp/dspeed)
+  → Fast Digital Signal Processing for particle detector signals in Python

docs/source/index.rst

@@ -65,5 +65,6 @@ Next steps
 
    Source Code <https://github.com/legend-exp/pygama>
    License <https://github.com/legend-exp/pygama/blob/main/LICENSE>
+   Citation <https://zenodo.org/doi/10.5281/zenodo.10614246>
    Changelog <https://github.com/legend-exp/pygama/releases>
    developer

pyproject.toml

@@ -1,14 +1,121 @@
 [build-system]
 requires = [
-    "setuptools>=42.0.0",
-    "setuptools_scm[toml]>=3.4",
+    "setuptools>=61.2",
+    "setuptools_scm[toml]>=7",
 ]
-
 build-backend = "setuptools.build_meta"
 
+[project]
+name = "pygama"
+description = "Python package for data processing and analysis"
+authors = [
+    { name = "The LEGEND collaboration" },
+]
+maintainers = [
+    { name = "The LEGEND collaboration" },
+]
+readme = "README.md"
+classifiers = [
+    "Development Status :: 4 - Beta",
+    "Intended Audience :: Developers",
+    "Intended Audience :: Science/Research",
+    "License :: OSI Approved :: GNU General Public License v3 (GPLv3)",
+    "Operating System :: MacOS",
+    "Operating System :: POSIX",
+    "Operating System :: Unix",
+    "Programming Language :: Python",
+    "Programming Language :: Python :: 3",
+    "Programming Language :: Python :: 3 :: Only",
+    "Topic :: Scientific/Engineering",
+]
+requires-python = ">=3.9"
+dependencies = [
+    "colorlog",
+    "dspeed>=1.3.0a4",
+    "h5py>=3.2",
+    "iminuit",
+    "legend-daq2lh5>=1.2.0a1",
+    "legend-pydataobj>=1.5.0a5",
+    "matplotlib",
+    "numba!=0.53.*,!=0.54.*,!=0.57",
+    "numpy>=1.21",
+    "pandas>=1.4.4",
+    "pint",
+    "scikit-learn",
+    "scipy>=1.0.1",
+    "tables",
+    "tqdm>=4.27",
+]
+dynamic = [
+    "version",
+]
+
+[project.urls]
+Homepage = "https://github.com/legend-exp/pygama"
+"Bug Tracker" = "https://github.com/legend-exp/pygama/issues"
+Discussions = "https://github.com/legend-exp/pygama/discussions"
+Changelog = "https://github.com/legend-exp/pygama/releases"
+
 [tool.setuptools_scm]
 write_to = "src/pygama/_version.py"
 
+[project.optional-dependencies]
+all = [
+    "pygama[docs,test]",
+]
+docs = [
+    "furo",
+    "jupyter",
+    "myst-parser",
+    "nbsphinx",
+    "sphinx",
+    "sphinx-copybutton",
+    "sphinx-inline-tabs",
+]
+test = [
+    "pre-commit",
+    "pylegendtestdata",
+    "pytest>=6.0",
+    "pytest-cov",
+]
+
+[project.scripts]
+pygama = "pygama.cli:pygama_cli"
+
+[tool.setuptools]
+include-package-data = true
+zip-safe = false
+license-files = [
+    "LICENSE",
+]
+
+[tool.setuptools.package-dir]
+"" = "src"
+
+[tool.setuptools.packages.find]
+where = [
+    "src",
+]
+namespaces = false
+
+[tool.setuptools.package-data]
+"*" = [
+    "*.json",
+]
+
+[tool.coverage]
+run.source = ["pygama"]
+report.exclude_also = [
+  '\.\.\.',
+  'if typing.TYPE_CHECKING:',
+]
+
+[tool.flake8]
+extend-ignore = "E203, E501"
+
+[tool.codespell]
+ignore-words-list = "hist, gaus, nd, ans, crate, nin, puls, spms, fom"
+
 [tool.pytest.ini_options]
 minversion = "6.0"
 addopts = ["-ra", "--showlocals", "--strict-markers", "--strict-config"]

src/pygama/math/__init__.py

@@ -1,3 +1,3 @@
 """
-Subpackage description
+Statistical and mathematical utilities.
 """

src/pygama/pargen/__init__.py

@@ -1,3 +1,4 @@
 """
-Subpackage description
+Utilities to generate and optimize parameters of interest from data (e.g.
+calibration routines)
 """