Refactor and modernize python packaging

.codeclimate.yml

@@ -46,7 +46,7 @@ plugins:
     config:
       minimum_severity: major
       tests_patterns:
-        - pythresh/test/**
+        - tests/**
 exclude_patterns:
   - "examples/"
-  - "**/test/"
+  - "tests/"

.gitattributes

@@ -0,0 +1,2 @@
+# Force consistent line endings everywhere
+* text=auto eol=lf

.github/workflows/python-package.yml → .github/workflows/ci.yml

@@ -28,22 +28,23 @@ jobs:
       uses: actions/setup-python@v6
       with:
         python-version: ${{ matrix.python-version }}
-    - name: Install dependencies
+    - name: Install libomp (macOS)
+      if: runner.os == 'macOS'
       run: |
-        python -m pip install --upgrade pip wheel setuptools setuptools-scm
-        python -m pip install flake8 pytest-cov mypy cython
-        python -m pip install -r requirements-test.txt --use-pep517
-    - name: Lint with flake8
+        brew install libomp
+    - name: Install dependencies
       run: |
-        # stop the build if there are Python syntax errors or undefined names
-        flake8 . --count --select=E9,F63,F7,F82 --show-source --statistics
-        # exit-zero treats all errors as warnings. The GitHub editor is 127 chars wide
-        flake8 . --count --exit-zero --max-complexity=10 --max-line-length=127 --statistics
+        python -m pip install --upgrade pip wheel setuptools>=77.0.3 uv
+        uv pip install --system -e '.[dev]' --no-build-isolation
+    - name: Lint with Ruff
+      run: ruff check .
+    - name: Check formatting
+      run: ruff format --check .
     - name: Test with pytest
       run: |
-        pytest -vs --doctest-modules --cov-fail-under=90 --cov-branch --cov=pythresh --cov-report term-missing --pyargs pythresh --continue-on-collection-errors
+        pytest -q -r f --doctest-modules --cov-fail-under=90 --cov-branch --cov=pythresh --cov-report=term-missing --cov-report=xml --continue-on-collection-errors
     - name: Upload coverage to Codecov (partial)
-      uses: codecov/codecov-action@v5
+      uses: codecov/codecov-action@v6
       with:
         files: ./coverage.xml
         flags: ${{ matrix.os }}-${{ matrix.python-version }}
@@ -58,7 +59,7 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - name: Finalize Codecov uploads
-        uses: codecov/codecov-action@v5
+        uses: codecov/codecov-action@v6
         with:
           finalize: true
         env:

.github/workflows/python-publish.yml

@@ -13,64 +13,67 @@ on:
 
 jobs:
   release:
-    if: contains(github.event.head_commit.message, 'bump') && github.actor == 'KulikDM'
+    if: contains(github.event.head_commit.message, 'release') && github.actor == 'KulikDM'
     runs-on: ubuntu-latest
     steps:
       - name: Checkout repository
         uses: actions/checkout@v6
+        with:
+          token: ${{ secrets.GIT_TOKEN }}
 
       - name: Set up Python
         uses: actions/setup-python@v6
         with:
           python-version: "3.12"
 
-      - name: Increment version number
+      - name: Install dependencies
         run: |
-          printf "Reading the current version from the file\n"
-
-          current_version=$(grep -oP "__version__ = '\K(\d+\.\d+\.\d+)" pythresh/version.py)
-
-          if [[ -z $current_version ]]; then
-              current_version="0.0.0"
-              printf "\nIssue fetching current version $current_version\n"
-              exit 1
-          fi
-
-          printf "\nIncrementing the version number\n"
+          set -euo pipefail
+          pip install --upgrade pip setuptools wheel
+          pip install bump-my-version build twine
 
-          IFS='.' read -r -a version_parts <<< "$current_version"
-          patch=$(( ${version_parts[2]} + 1 ))
+      - name: Configure Git
+        run: |
+          git config --global user.name "${{ secrets.GIT_USER }}"
+          git config --global user.email "${{ secrets.GIT_EMAIL }}"
 
-          printf "\nHandling version part overflow\n"
+      - name: Bump version
+        run: |
+          set -euo pipefail
 
-          if (( patch > 9 )); then
-              patch=0
-              minor=$(( ${version_parts[1]} + 1 ))
+          COMMIT_MSG="${{ github.event.head_commit.message }}"
+          echo "Commit message: $COMMIT_MSG"
 
-              if (( minor > 9 )); then
-                  minor=0
-                  major=$(( ${version_parts[0]} + 1 ))
-              else
-                  major=${version_parts[0]}
-              fi
+          if [[ "$COMMIT_MSG" =~ patch ]]; then
+              BUMP_TYPE="patch"
+          elif [[ "$COMMIT_MSG" =~ minor ]]; then
+              BUMP_TYPE="minor"
+          elif [[ "$COMMIT_MSG" =~ major ]]; then
+              BUMP_TYPE="major"
           else
-              minor=${version_parts[1]}
-              major=${version_parts[0]}
+              echo "No bump type found, defaulting to patch."
+              BUMP_TYPE="patch"
           fi
 
-          new_version="${major}.${minor}.$patch"
+          echo "Bumping version type: $BUMP_TYPE"
+          bump-my-version bump "$BUMP_TYPE" \
+            --no-tag \
+            --commit \
+            --message "Bump version: {current_version} → {new_version} [skip ci]"
 
-          printf "\nUpdating the file with the new version number\n"
+      - name: Push version bump
+        run: |
+          set -euo pipefail
+          git push --follow-tags
 
-          sed -i "s/__version__ = '${current_version}'/__version__ = '${new_version}'/" pythresh/version.py
+          new_version=$(PYTHONPATH=. python -c "import pythresh; print(pythresh.__version__)")
 
           echo "new_version=$new_version" >> $GITHUB_ENV
           echo "WORK_DIR=$(pwd)" >> $GITHUB_ENV
 
-          printf "\nNew version updated from $current_version to $new_version\n"
-
       - name: Validate new PyPi version
         run: |
+          set -euo pipefail
           printf "Getting lastest pypi information\n"
 
           url="https://pypi.org/pypi/pythresh/json"
@@ -84,50 +87,37 @@ jobs:
           fi
 
           printf "\nNew version validated\n"
-
-      - name: Commit and push changes
-        env:
-          GIT_USER: ${{ secrets.GIT_USER }}
-          GIT_EMAIL: ${{ secrets.GIT_EMAIL }}
-          GIT_TOKEN: ${{ secrets.GIT_TOKEN }}
-        run: |
-          printf "Preparing to commit\n"
-
-          git config --global user.name $GIT_USER
-          git config --global user.email $GIT_EMAIL
-          git commit -a -m "Updated to version ${{ env.new_version }}"
-
-          printf "\nPushing the changes to the repository\n"
-
-          git push origin main
-
-          printf "\nNew version commited\n"
           sleep 1m
 
       - name: Publish to PyPI
         env:
           TWINE_USERNAME: __token__
           TWINE_PASSWORD: ${{ secrets.PYPI_API_TOKEN }}
         run: |
+          set -euo pipefail
           printf "Preparing to install dependancies\n"
 
-          python -m pip install --upgrade pip setuptools wheel twine build
           python -m build
 
           printf "\nPackage created locally\n"
 
+          twine check --strict dist/*
+
+          printf "\nChecks passed\n"
+
           twine upload dist/*
 
           printf "\nNew PyPi release created\n"
           sleep 10m
 
       - name: Validate new Conda version
         run: |
+          set -euo pipefail
           printf "Getting lastest pypi information\n"
 
           url="https://pypi.org/pypi/pythresh/json"
           latest_version=$(curl -s "$url" | jq -r '.info.version')
-          latest_sha256=$(curl -s "$url" | jq -r '.releases."'"$latest_version"'"[1].digests."sha256"')
+          latest_sha256=$(curl -s "$url" | jq -r '.releases."'"$latest_version"'"[] | select(.packagetype == "sdist") | .digests.sha256')
 
           echo "Validating version update"
 
@@ -144,13 +134,11 @@ jobs:
       - name: Update Conda feedstock repository
         env:
           GIT_USER: ${{ secrets.GIT_USER }}
-          GIT_EMAIL: ${{ secrets.GIT_EMAIL }}
           GIT_TOKEN: ${{ secrets.GIT_TOKEN }}
         run: |
+          set -euo pipefail
           printf "Preparing to clone feedstock repository\n"
 
-          git config --global user.name $GIT_USER
-          git config --global user.email $GIT_EMAIL
           git clone https://$GIT_USER:$GIT_TOKEN@github.com/conda-forge/pythresh-feedstock.git
 
           cd pythresh-feedstock
@@ -181,6 +169,7 @@ jobs:
         env:
           GIT_TOKEN: ${{ secrets.GIT_TOKEN }}
         run: |
+          set -euo pipefail
           printf "Preparing to create new GitHub release\n"
 
           cd "${{ env.WORK_DIR }}"

.pre-commit-config.yaml

@@ -9,13 +9,17 @@ repos:
       - id: name-tests-test
         always_run: true
         args: [--pytest-test-first]
+        exclude: ^tests/utils\.py$
       - id: mixed-line-ending
         args: [--fix=lf]
 
   - repo: https://github.com/charliermarsh/ruff-pre-commit
     rev: v0.15.12
     hooks:
       - id: ruff
+        name: Fix code
         args: [--exit-non-zero-on-fix, --fix, --line-length=180]
         exclude: "\\.ipynb$"
-        name: Lint code
+      - id: ruff-format
+        name: Format code
+        exclude: "\\.ipynb$"

.readthedocs.yaml

@@ -9,7 +9,7 @@ version: 2
 build:
   os: ubuntu-22.04
   tools:
-    python: "3.10"
+    python: "3.12"
     # You can also specify other tool versions:
     # nodejs: "19"
     # rust: "1.64"
@@ -25,5 +25,7 @@ formats:
 
 # Optionally declare the Python requirements required to build your docs
 python:
-   install:
-   - requirements: docs/requirements.txt
+  install:
+    - method: pip
+      path: .
+      extra_requirements: all, docs

README.rst

@@ -46,7 +46,7 @@
 
 .. |badge_licence| image:: https://img.shields.io/github/license/KulikDM/pythresh.svg?logo=data:image/svg+xml;base64,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
    :alt: License
-   :target: https://github.com/KulikDM/pythresh/blob/master/LICENSE
+   :target: https://github.com/KulikDM/pythresh/blob/main/LICENSE
 
 .. |badge_citation| image:: https://zenodo.org/badge/497683169.svg
    :alt: Zenodo DOI