Merge pull request #532 from SamuelBorden/math_refactor

Math Refactor + Merged Main Into Refactor

.github/pull_request_template.md

@@ -1,6 +1,10 @@
+<!---
+
 Before submitting a pull request, please make sure you've read and understood the pygama developer's guide: https://pygama.readthedocs.io/en/latest/developer.html. In particular, do not forget to:
 
-- [ ] Conform to our **coding conventions**
-- [ ] Update existing or add new **tests**
-- [ ] Update existing or add new **documentation**
-- [ ] Address any issue reported by GitHub checks
+- Conform to our coding conventions
+- Update existing or add new tests
+- Update existing or add new documentation
+- Address any issue reported by GitHub checks
+
+--->

.github/workflows/distribution.yml

@@ -38,6 +38,6 @@ jobs:
         name: artifact
         path: dist
 
-    - uses: pypa/gh-action-pypi-publish@v1.5.1
+    - uses: pypa/gh-action-pypi-publish@v1.8.10
       with:
         password: ${{ secrets.pypi_password }}

.github/workflows/main.yml

@@ -4,7 +4,6 @@ on:
   push:
     branches:
       - main
-      - refactor
       - 'releases/**'
   pull_request:
   release:
@@ -21,7 +20,7 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        python-version: ['3.9', '3.10']
+        python-version: ['3.9', '3.10', '3.11']
         os: [ubuntu-latest, macOS-latest]
 
     steps:
@@ -53,12 +52,12 @@ jobs:
         run: |
           python -m pip install --upgrade pip wheel setuptools
           python -m pip install --upgrade .[test]
-          pytest --cov=pygama --cov-report=xml
+          python -m pytest --cov=pygama --cov-report=xml
       - name: Upload Coverage to codecov.io
         uses: codecov/codecov-action@v3
         with:
           token: ${{ secrets.CODECOV_TOKEN }}
-          fail_ci_if_error: true
+          fail_ci_if_error: false
 
   test-docs:
     name: Build documentation

.pre-commit-config.yaml

@@ -1,12 +1,12 @@
 ci:
   autoupdate_commit_msg: "chore: update pre-commit hooks"
-  autoupdate_schedule: "monthly"
+  autoupdate_schedule: "quarterly"
   autofix_commit_msg: "style: pre-commit fixes"
 
 exclude: ^(attic|tutorials|src/pygama/math|src/pygama/flow/datagroup.py)
 repos:
 - repo: https://github.com/pre-commit/pre-commit-hooks
-  rev: "v4.3.0"
+  rev: "v4.4.0"
   hooks:
   - id: check-added-large-files
   - id: check-case-conflict
@@ -17,6 +17,7 @@ repos:
   - id: check-json
   - id: check-toml
   - id: check-docstring-first
+    exclude: ^src/pygama/raw/(fc/fc_event_decoder.py|compass/compass_event_decoder.py)$
   - id: debug-statements
   - id: end-of-file-fixer
   - id: forbid-new-submodules
@@ -25,52 +26,50 @@ repos:
   - id: trailing-whitespace
 
 - repo: https://github.com/asottile/setup-cfg-fmt
-  rev: "v2.2.0"
+  rev: "v2.4.0"
   hooks:
   - id: setup-cfg-fmt
 
 - repo: https://github.com/PyCQA/isort
-  rev: "5.10.1"
+  rev: "5.12.0"
   hooks:
   - id: isort
 
 - repo: https://github.com/asottile/pyupgrade
-  rev: "v3.2.0"
+  rev: "v3.13.0"
   hooks:
   - id: pyupgrade
     args: ["--py38-plus"]
 
 - repo: https://github.com/psf/black
-  rev: "22.10.0"
+  rev: "23.9.1"
   hooks:
   - id: black-jupyter
 
 - repo: https://github.com/pre-commit/mirrors-mypy
-  rev: "v0.982"
+  rev: "v1.5.1"
   hooks:
   - id: mypy
     files: src
     stages: [manual]
 
 - repo: https://github.com/hadialqattan/pycln
-  rev: "v2.1.1"
+  rev: "v2.2.2"
   hooks:
   - id: pycln
     exclude: ^src/pygama/pargen
     args: [--all]
 
 - repo: https://github.com/PyCQA/flake8
-  rev: "5.0.4"
+  rev: "6.1.0"
   hooks:
   - id: flake8
     exclude: ^src/pygama/pargen
     additional_dependencies: [
-      flake8-bugbear,
+      flake8-bugbear>=23.1.17,
       flake8-print,
-      # flake8-docstrings,
       pep8-naming
     ]
-    # args: ["--docstring-convention", "numpy"]
 
 - repo: https://github.com/kynan/nbstripout
   rev: "0.6.1"
@@ -80,31 +79,31 @@ repos:
              "--extra-keys", "metadata.kernelspec metadata.language_info"]
 
 - repo: https://github.com/mgedmin/check-manifest
-  rev: "0.48"
+  rev: "0.49"
   hooks:
   - id: check-manifest
     stages: [manual]
 
 - repo: https://github.com/codespell-project/codespell
-  rev: "v2.2.2"
+  rev: "v2.2.5"
   hooks:
   - id: codespell
 
 - repo: https://github.com/shellcheck-py/shellcheck-py
-  rev: "v0.8.0.4"
+  rev: "v0.9.0.6"
   hooks:
   - id: shellcheck
 
 - repo: https://github.com/pre-commit/pygrep-hooks
-  rev: "v1.9.0"
+  rev: "v1.10.0"
   hooks:
   - id: python-no-log-warn
   - id: rst-backticks
   - id: rst-directive-colons
   - id: rst-inline-touching-normal
 
 - repo: https://github.com/pre-commit/mirrors-prettier
-  rev: "v3.0.0-alpha.4"
+  rev: "v3.0.3"
   hooks:
     - id: prettier
       types_or: [json]