Merge pull request #563 from SamuelBorden/refactor

Merged in main to refactor, fixed merge conflicts
legend-exp · Mar 8, 2024 · c37ed84 · c37ed84
2 parents 4de5fd4 + 2da52fc
commit c37ed84
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diff --git a/.github/dependabot.yml b/.github/dependabot.yml
@@ -5,5 +5,3 @@ updates:
     directory: "/"
     schedule:
       interval: "monthly"
-    ignore:
-      - dependency-name: "actions/*"
diff --git a/.github/logo.png b/.github/logo.png
diff --git a/.github/workflows/distribution.yml b/.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@v3
-      with:
-        fetch-depth: 0
 
-    - name: Build SDist and wheel
-      run: pipx run build
-
-    - uses: actions/upload-artifact@v3
-      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@v3
-      with:
-        name: artifact
-        path: dist
-
-    - uses: pypa/[email protected]
-      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'
diff --git a/.github/workflows/main.yml b/.github/workflows/main.yml
@@ -1,17 +1,21 @@
 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:
 
   build-and-test:
@@ -24,9 +28,9 @@ jobs:
         os: [ubuntu-latest, macOS-latest]
 
     steps:
-    - uses: actions/checkout@v2
+    - uses: actions/checkout@v4
     - name: Set up Python ${{ matrix.python-version }}
-      uses: actions/setup-python@v2
+      uses: actions/setup-python@v5
       with:
         python-version: ${{ matrix.python-version }}
     - name: Get dependencies and install the package
@@ -35,16 +39,16 @@ jobs:
         python -m pip install --upgrade .[test]
     - name: Run unit tests
       run: |
-        pytest
+        python -m pytest
 
   test-coverage:
     name: Calculate and upload test coverage
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v4
         with:
           fetch-depth: 2
-      - uses: actions/setup-python@v2
+      - uses: actions/setup-python@v5
         with:
           python-version: '3.10'
 
@@ -54,7 +58,7 @@ jobs:
           python -m pip install --upgrade .[test]
           python -m pytest --cov=pygama --cov-report=xml
       - name: Upload Coverage to codecov.io
-        uses: codecov/codecov-action@v3
+        uses: codecov/codecov-action@v4
         with:
           token: ${{ secrets.CODECOV_TOKEN }}
           fail_ci_if_error: false
@@ -63,10 +67,10 @@ jobs:
     name: Build documentation
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v4
         with:
           fetch-depth: 0
-      - uses: actions/setup-python@v2
+      - uses: actions/setup-python@v5
         with:
           python-version: '3.10'
       - name: Setup build environment

diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
@@ -6,7 +6,7 @@ ci:
 exclude: ^(attic|tutorials|src/pygama/math|src/pygama/flow/datagroup.py)
 repos:
 - repo: https://github.com/pre-commit/pre-commit-hooks
-  rev: "v4.4.0"
+  rev: "v4.5.0"
   hooks:
   - id: check-added-large-files
   - id: check-case-conflict
@@ -26,35 +26,35 @@ repos:
   - id: trailing-whitespace
 
 - repo: https://github.com/asottile/setup-cfg-fmt
-  rev: "v2.4.0"
+  rev: "v2.5.0"
   hooks:
   - id: setup-cfg-fmt
 
 - repo: https://github.com/PyCQA/isort
-  rev: "5.12.0"
+  rev: "5.13.2"
   hooks:
   - id: isort
 
 - repo: https://github.com/asottile/pyupgrade
-  rev: "v3.13.0"
+  rev: "v3.15.0"
   hooks:
   - id: pyupgrade
     args: ["--py38-plus"]
 
 - repo: https://github.com/psf/black
-  rev: "23.9.1"
+  rev: "23.12.1"
   hooks:
   - id: black-jupyter
 
 - repo: https://github.com/pre-commit/mirrors-mypy
-  rev: "v1.5.1"
+  rev: "v1.8.0"
   hooks:
   - id: mypy
     files: src
     stages: [manual]
 
 - repo: https://github.com/hadialqattan/pycln
-  rev: "v2.2.2"
+  rev: "v2.4.0"
   hooks:
   - id: pycln
     exclude: ^src/pygama/pargen
@@ -70,6 +70,7 @@ repos:
       flake8-print,
       pep8-naming
     ]
+    args: ["--extend-ignore", "E203,E501"]
 
 - repo: https://github.com/kynan/nbstripout
   rev: "0.6.1"
@@ -85,9 +86,11 @@ repos:
     stages: [manual]
 
 - repo: https://github.com/codespell-project/codespell
-  rev: "v2.2.5"
+  rev: "v2.2.6"
   hooks:
   - id: codespell
+    additional_dependencies:
+      - tomli
 
 - repo: https://github.com/shellcheck-py/shellcheck-py
   rev: "v0.9.0.6"
@@ -103,7 +106,7 @@ repos:
   - id: rst-inline-touching-normal
 
 - repo: https://github.com/pre-commit/mirrors-prettier
-  rev: "v3.0.3"
+  rev: "v4.0.0-alpha.8"
   hooks:
     - id: prettier
       types_or: [json]
diff --git a/CITATION.cff b/CITATION.cff
@@ -0,0 +1,58 @@
+cff-version: 1.2.0
+title: pygama
+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:
+  - family-names: Agostini
+    given-names: Matteo
+    orcid: https://orcid.org/0000-0003-1151-5301
+  - family-names: Detwiler
+    given-names: Jason
+    orcid: https://orcid.org/0000-0002-9050-4610
+  - family-names: Pertoldi
+    given-names: Luigi
+    orcid: https://orcid.org/0000-0002-0467-2571
+  - family-names: Guinn
+    given-names: Ian
+    orcid: https://orcid.org/0000-0002-2424-3272
+  - family-names: Marshall
+    given-names: George
+    orcid: https://orcid.org/0000-0002-5470-5132
+  - family-names: D'Andrea
+    given-names: Valerio
+    orcid: https://orcid.org/0000-0003-2037-4133
+  - family-names: Krause
+    given-names: Patrick
+    orcid: https://orcid.org/0000-0002-9603-7865
+  - family-names: Song
+    given-names: Grace
+    email: [email protected]
+  - family-names: Engelhardt
+    given-names: Erin
+    email: [email protected]
+  - family-names: Borden
+    given-names: Sam
+    orcid: https://orcid.org/0009-0003-2539-4333
+  - family-names: Deckert
+    given-names: Rosanna
+    orcid: https://orcid.org/0009-0006-0431-341X
+  - family-names: Sweigart
+    given-names: David
+    email: [email protected]
+  - family-names: Zschocke
+    given-names: Andreas
+    email: [email protected]
+  - family-names: Wiseman
+    given-names: Clint
+    orcid: https://orcid.org/0000-0002-4232-1326
+  - family-names: Mathew
+    given-names: Tim
+    email: [email protected]
+  - family-names: Kermaïdic
+    given-names: Yoann
+    orcid: https://orcid.org/0000-0001-8007-8016
+  - family-names: Shanks
+    given-names: Ben
+    email: [email protected]
diff --git a/README.md b/README.md
@@ -1,3 +1,5 @@
+<img src=".github/logo.png" alt="pygama logo" align="left" height="150">
+
 # pygama
 
 [![PyPI](https://img.shields.io/pypi/v/pygama?logo=pypi)](https://pypi.org/project/pygama/)
@@ -10,6 +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:
 
@@ -25,3 +28,15 @@
 - generating and selecting high-level event data for further analysis
 
 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
diff --git a/docs/source/conf.py b/docs/source/conf.py
@@ -39,6 +39,7 @@
     "source_directory": "docs/source",
 }
 html_title = f"{project} {version}"
+html_logo = "../../.github/logo.png"
 
 # sphinx-napoleon
 # enforce consistent usage of NumPy-style docstrings
@@ -57,9 +58,11 @@
     "scipy": ("https://docs.scipy.org/doc/scipy", None),
     "pandas": ("https://pandas.pydata.org/docs", None),
     "matplotlib": ("https://matplotlib.org/stable", None),
-    "iminuit": ("https://iminuit.readthedocs.io/en/stable", None),
     "h5py": ("https://docs.h5py.org/en/stable", None),
     "pint": ("https://pint.readthedocs.io/en/stable", None),
+    "lgdo": ("https://legend-pydataobj.readthedocs.io/en/stable", None),
+    "dspeed": ("https://dspeed.readthedocs.io/en/stable", None),
+    "daq2lh5": ("https://legend-daq2lh5.readthedocs.io/en/stable", None),
 }
 
 suppress_warnings = [