Merge pull request #564 from ggmarshall/main

Pargen refactor

.github/workflows/main.yml

@@ -17,29 +17,28 @@ env:
   TQDM_MININTERVAL: 100
 
 jobs:
-
   build-and-test:
     name: Test pygama with Python
     runs-on: ${{ matrix.os }}
     strategy:
       fail-fast: false
       matrix:
-        python-version: ['3.9', '3.10', '3.11']
+        python-version: ["3.9", "3.10", "3.11"]
         os: [ubuntu-latest, macOS-latest]
 
     steps:
-    - uses: actions/checkout@v4
-    - name: Set up Python ${{ matrix.python-version }}
-      uses: actions/setup-python@v5
-      with:
-        python-version: ${{ matrix.python-version }}
-    - name: Get dependencies and install the package
-      run: |
-        python -m pip install --upgrade pip wheel setuptools
-        python -m pip install --upgrade .[test]
-    - name: Run unit tests
-      run: |
-        python -m pytest
+      - uses: actions/checkout@v4
+      - name: Set up Python ${{ matrix.python-version }}
+        uses: actions/setup-python@v5
+        with:
+          python-version: ${{ matrix.python-version }}
+      - name: Get dependencies and install the package
+        run: |
+          python -m pip install --upgrade pip wheel setuptools
+          python -m pip install --upgrade .[test]
+      - name: Run unit tests
+        run: |
+          python -m pytest
 
   test-coverage:
     name: Calculate and upload test coverage
@@ -50,7 +49,7 @@ jobs:
           fetch-depth: 2
       - uses: actions/setup-python@v5
         with:
-          python-version: '3.10'
+          python-version: "3.10"
 
       - name: Generate Report
         run: |
@@ -72,7 +71,7 @@ jobs:
           fetch-depth: 0
       - uses: actions/setup-python@v5
         with:
-          python-version: '3.10'
+          python-version: "3.10"
       - name: Setup build environment
         run: |
           sudo apt-get install -y pandoc

.pre-commit-config.yaml

@@ -36,18 +36,18 @@ repos:
   - id: isort
 
 - repo: https://github.com/asottile/pyupgrade
-  rev: "v3.15.0"
+  rev: "v3.15.2"
   hooks:
   - id: pyupgrade
     args: ["--py38-plus"]
 
 - repo: https://github.com/psf/black
-  rev: "23.12.1"
+  rev: "24.3.0"
   hooks:
   - id: black-jupyter
 
 - repo: https://github.com/pre-commit/mirrors-mypy
-  rev: "v1.8.0"
+  rev: "v1.9.0"
   hooks:
   - id: mypy
     files: src
@@ -57,14 +57,12 @@ repos:
   rev: "v2.4.0"
   hooks:
   - id: pycln
-    exclude: ^src/pygama/pargen
     args: [--all]
 
 - repo: https://github.com/PyCQA/flake8
-  rev: "6.1.0"
+  rev: "7.0.0"
   hooks:
   - id: flake8
-    exclude: ^src/pygama/pargen
     additional_dependencies: [
       flake8-bugbear>=23.1.17,
       flake8-print,
@@ -73,7 +71,7 @@ repos:
     args: ["--extend-ignore", "E203,E501"]
 
 - repo: https://github.com/kynan/nbstripout
-  rev: "0.6.1"
+  rev: "0.7.1"
   hooks:
     - id: nbstripout
       args: ["--drop-empty-cells",
@@ -93,7 +91,7 @@ repos:
       - tomli
 
 - repo: https://github.com/shellcheck-py/shellcheck-py
-  rev: "v0.9.0.6"
+  rev: "v0.10.0.1"
   hooks:
   - id: shellcheck
 

CITATION.cff

@@ -2,7 +2,6 @@ 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

codecov.yml

@@ -9,7 +9,7 @@ coverage:
     patch: false
 
 github_checks:
-    annotations: false
+  annotations: false
 
 comment:
   require_changes: true

docs/source/conf.py

@@ -76,7 +76,7 @@
 autodoc_default_options = {"ignore-module-all": True}
 # Include __init__() docstring in class docstring
 autoclass_content = "both"
-autodoc_typehints = "both"
+autodoc_typehints = "description"
 autodoc_typehints_description_target = "documented_params"
 autodoc_typehints_format = "short"
 

docs/source/extensions/numbadoc.py

@@ -5,6 +5,7 @@
 
 Adapted from https://github.com/numba/numba/issues/5755#issuecomment-646587651
 """
+
 from copy import copy
 from typing import Iterator, List
 

pyproject.toml

@@ -35,13 +35,14 @@ dependencies = [
     "dspeed>=1.3",
     "h5py>=3.2",
     "iminuit",
-    "legend-daq2lh5>=1.2",
-    "legend-pydataobj>=1.5",
+    "legend-daq2lh5>=1.2.1",
+    "legend-pydataobj>=1.6",
     "matplotlib",
     "numba!=0.53.*,!=0.54.*,!=0.57",
     "numpy>=1.21",
     "pandas>=1.4.4",
     "pint",
+    "pyyaml",
     "scikit-learn",
     "scipy>=1.0.1",
     "tables",
@@ -115,7 +116,7 @@ report.exclude_also = [
 extend-ignore = "E203, E501"
 
 [tool.codespell]
-ignore-words-list = "hist, gaus, nd, ans, crate, nin, puls, spms, fom"
+ignore-words-list = "hist, gaus, nd, ans, crate, nin, puls, spms, fom, FOM"
 
 [tool.pytest.ini_options]
 minversion = "6.0"

src/pygama/cli.py

@@ -1,6 +1,7 @@
 """
 pygama's command line interface utilities.
 """
+
 import argparse
 import logging
 import os