Merge pull request #580 from ISA-tools/develop

Develop

Author: knirirr

.github/workflows/buildandtestpython.yml

@@ -3,51 +3,45 @@ name: Python package
 on:
   pull_request:
   push:
-
 jobs:
   build:
-
     runs-on: ubuntu-latest
     strategy:
       matrix:
-        python-version: ['3.9', '3.10', '3.11', '3.12']
-
+        python-version: [ '3.9', '3.10', '3.11', '3.12', '3.13' ]
     steps:
-      - uses: actions/checkout@v4
-      - name: Set up Python ${{ matrix.python-version }}
-        uses: actions/setup-python@v4
-        with:
-          python-version: ${{ matrix.python-version }}
-      - name: Download Test Data
-        run: |
-          bash -x get_test_data.sh
-      - name: Install dependencies
-        run: |
-          python -m pip install --upgrade pip
-          pip install flake8 pytest
-          if [ -f requirements.txt ]; then pip install -r requirements.txt; fi
-      - name: Lint with flake8
-        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
-      - name: Test with python unittest
-        run: |
-          behave --no-capture --no-capture-stderr --format=progress features/isa-file-handler.feature
-          coverage run -m unittest discover -s tests/
-          coverage report -m
-      - name: Coveralls
-        uses: AndreMiras/coveralls-python-action@develop
-        with:
-          parallel: true
-          flag-name: Unit Test
+    - uses: actions/checkout@v4.2.2
+    - name: Download Test Data
+      run: |
+        bash -x get_test_data.sh
+    - name: Install uv
+      uses: astral-sh/setup-uv@v6.3.0
+      with:
+        enable-cache: true
+        cache-dependency-glob: uv.lock
+    - name: Sync dependencies
+      run: |
+        uv python pin ${{ matrix.python-version }} 
+        uv sync --group dev
+    - uses: astral-sh/ruff-action@v3
+    - run: ruff check
+    - run: ruff format
+    - name: Test with python unittest
+      run: |
+        uv run --python ${{ matrix.python-version }} pytest
+        uv run --python ${{ matrix.python-version }} coverage run -m unittest discover -s tests/
+        uv run --python ${{ matrix.python-version }} coverage report -m
+    - name: Coveralls
+      uses: AndreMiras/coveralls-python-action@develop
+      with:
+        parallel: true
+        flag-name: Unit Test
 
   coveralls_finish:
     needs: build
     runs-on: ubuntu-latest
     steps:
-      - name: Coveralls Finished
-        uses: AndreMiras/coveralls-python-action@develop
-        with:
-          parallel-finished: true
+    - name: Coveralls Finished
+      uses: AndreMiras/coveralls-python-action@develop
+      with:
+        parallel-finished: true

.github/workflows/pythonpublish.yml

@@ -13,14 +13,15 @@ jobs:
       uses: actions/setup-python@v4
       with:
         python-version: '3.x'
-    - name: Install dependencies
+    - name: Install uv
+      uses: astral-sh/setup-uv@v6.3.0
+      with:
+        enable-cache: true
+        cache-dependency-glob: uv.lock
+    - name: Sync dependencies
       run: |
-        python -m pip install --upgrade pip
-        pip install setuptools wheel twine
+        uv sync --no-dev
     - name: Build and publish
-      env:
-        TWINE_USERNAME: ${{ secrets.PYPI_USERNAME }}
-        TWINE_PASSWORD: ${{ secrets.PYPI_PASSWORD }}
       run: |
-        python setup.py sdist bdist_wheel
-        twine upload --verbose dist/*
+        echo "Publishing to PyPI..."
+        uv publish -t ${{ secrets.PYPI_TOKEN }}

.pre-commit-config.yaml

@@ -0,0 +1,72 @@
+default_language_version:
+  python: python3.13
+repos:
+- repo: https://github.com/abravalheri/validate-pyproject
+  rev: v0.24.1
+  hooks:
+  - id: validate-pyproject
+    name: 🔍 Validate pyproject.toml
+- repo: https://github.com/gitleaks/gitleaks
+  rev: v8.28.0
+  hooks:
+  - id: gitleaks
+    name: "🔒 Security · Detect hardcoded secrets"
+- repo: https://github.com/hukkin/mdformat
+  rev: 0.7.22
+  hooks:
+  - id: mdformat
+    name: "🟢  Markdown · Format markdown"
+- repo: https://github.com/pre-commit/pre-commit-hooks
+  rev: v6.0.0
+  hooks:
+  - id: check-added-large-files
+    name: 🟢  Check large files
+    args: [ "--maxkb=2000" ]
+  - id: check-toml
+    name: 🟢  Check toml files
+  - id: check-json
+    name: 🟢  Check json files
+  - id: pretty-format-json
+    name: 🟢  Format json files
+    args:
+    - "--autofix"
+    - "--indent=4"
+    - "--no-sort-keys"
+  - id: check-yaml
+    name: 🟢  Check yaml files
+    args:
+    - --unsafe
+  - id: end-of-file-fixer
+    name: 🟢 Check end of file character
+    exclude: resources/.+\.(js|css)$
+  - id: trailing-whitespace
+    name: 🟢  Check trailing whitespaces
+    exclude: (tests/data/.+|resources/.+\.(js|css))$
+- repo: https://github.com/astral-sh/uv-pre-commit
+  rev: 0.9.1
+  hooks:
+  - id: uv-lock
+    name: ✅ Check uv.lock file
+- repo: https://github.com/lk16/detect-missing-init
+  rev: v0.1.6
+  hooks:
+  - id: detect-missing-init
+    name: 🔍 Detect missing __init__.py files
+    args: [ "--create", "--track", "--python-folders", "isatools" ]
+- repo: https://github.com/astral-sh/ruff-pre-commit
+  rev: v0.14.0
+  hooks:
+  - id: ruff-check
+    name: 🔍 Check Format with Ruff
+    args:
+    - --exit-non-zero-on-fix
+    - --no-cache
+  - id: ruff-format
+    name: 🐍 python · Format with Ruff
+- repo: https://github.com/seddonym/import-linter.git
+  rev: "v2.5.2"
+  hooks:
+  - id: import-linter
+    name: 🪵 architecture and package structure check (lint-imports)
+    language: python
+    args: [ "--no-cache" ]

.python-version

@@ -1 +1 @@
-3.9.0
+3.13

README.md

@@ -62,6 +62,76 @@ The documentation to install and use the ISA-API (v0.14.3 and above) can be foun
 
 For the previous versions (up to v0.11) check the documentation [here](https://isatools.readthedocs.io/en/latest/).
 
+
 Contributing
 ------------
 The ISA-API is still in development. We would be very happy to receive any help and contributions (testing, feature requests, pull requests). Please feel free to contact our development team at [isatools@googlegroups.com](mailto:isatools@googlegroups.com), or ask a question, report a bug or file a feature request in the GitHub issue tracker at [https://github.com/ISA-tools/isa-api/issues](https://github.com/ISA-tools/isa-api/issues).
+
+
+Setup Development Environment
+-----------------------------
+
+```bash
+# install python package manager uv
+curl -LsSf https://astral.sh/uv/install.sh | sh
+
+# add $HOME/.local/bin to your PATH, either restart your shell or run
+export PATH=$HOME/.local/bin:$PATH
+
+# install git from https://git-scm.com/downloads
+# Linux command
+apt update; apt install git -y
+
+# Mac command
+# brew install git
+
+# clone project from github
+git clone https://github.com/ISA-tools/isa-api.git
+
+cd isa-api
+
+# install python if it is not installed
+uv python install 3.13
+
+# uv python install 3.12
+# uv python install 3.11
+# uv python install 3.10
+
+# pin a python version
+uv python pin 3.13
+
+# install python dependencies
+uv sync
+
+# install pre-commit to check repository integrity and format checking
+uv run pre-commit
+
+# run package and module dependencies
+uv run lint-imports
+
+# list all possible linters. selected linters are defined in pyproject.toml
+uv run ruff linter
+
+# run lint tool
+uv run ruff check
+
+# check specific linter
+uv run ruff check --select I
+
+# check specific lint rule
+uv run ruff check --select F841
+
+# check imports and update imports order
+uv run ruff check --select I --fix
+
+# run format check
+uv run ruff format --check
+
+# run unit tests with specific version
+uv run --python 3.11 pytest
+
+uv run --python 3.13 pytest
+
+# open your IDE (vscode, pycharm, etc.) and set python interpreter as .venv/bin/python
+
+```