Merge branch 'main' into atom-line-template

.deepsource.toml

@@ -0,0 +1,11 @@
+version = 1
+
+[[analyzers]]
+name = "shell"
+
+[[analyzers]]
+name = "python"
+
+  [analyzers.meta]
+  runtime_version = "3.x.x"
+  max_line_length = 100

.editorconfig

@@ -0,0 +1,18 @@
+# EditorConfig is awesome: https://EditorConfig.org
+
+root = true
+
+[*]
+end_of_line = lf
+insert_final_newline = true
+charset = utf-8
+indent_style = space
+indent_size = 4
+max_line_length = 100
+
+[Makefile]
+indent_style = tab
+
+[{*.json,*.yml,*.yaml}]
+indent_style = space
+indent_size = 2

.github/workflows/pytest.yaml

@@ -0,0 +1,28 @@
+name: pytest
+on:
+  push:
+    branches:
+    # Run tests for change on the main branch ...
+    - main
+    tags-ignore:
+    # ... but not for tags (avoids duplicate work).
+    - '**'
+  pull_request:
+  # Run tests on pull requests
+jobs:
+  tests:
+    strategy:
+      matrix:
+        os: [ubuntu-latest, macos-latest, windows-latest]
+        python-version: ["3.9", "3.12"]
+    runs-on: ${{ matrix.os }}
+    steps:
+      - uses: actions/checkout@v4
+      - name: Set up Python ${{ matrix.python-version }}
+        uses: actions/setup-python@v5
+        with:
+          python-version: ${{ matrix.python-version }}
+      - name: Install development version
+        run: pip install -e .[dev]
+      - name: Run Pytest
+        run: pytest -vv

.github/workflows/release.yaml

@@ -0,0 +1,128 @@
+# This workflow is adapted from:
+# https://packaging.python.org/en/latest/guides/publishing-package-distribution-releases-using-github-actions-ci-cd-workflows/
+# Changed made:
+# - Remove emoticons
+# - Update some actions to more recent versions
+
+name: release
+
+on: push
+
+env:
+  # This is not critical
+  # It is used only for showing URLs in GitHub Actions web interface.
+  PYPI_NAME: qc-iodata
+
+jobs:
+  build:
+    name: Build distribution
+    runs-on: ubuntu-latest
+
+    steps:
+    - uses: actions/checkout@v4
+      with:
+        fetch-depth: 0
+    - name: Set up Python
+      uses: actions/setup-python@v5
+      with:
+        python-version: "3.9"
+    - name: Install pypa/build
+      run: >-
+        python -m pip install build
+    - name: Build package
+      run: >-
+        python -m build
+    - name: Store the distribution packages
+      uses: actions/upload-artifact@v4
+      with:
+        name: python-package-distributions
+        path: dist/
+
+  publish-to-pypi:
+    name: Publish Python distribution to PyPI
+    if: startsWith(github.ref, 'refs/tags/')  # only publish to PyPI on tag pushes
+    needs:
+    - build
+    runs-on: ubuntu-latest
+    environment:
+      name: pypi
+      url: https://pypi.org/p/${{ env.PYPI_NAME }}
+    permissions:
+      id-token: write
+
+    steps:
+    - name: Download all the dists
+      uses: actions/download-artifact@v4
+      with:
+        name: python-package-distributions
+        path: dist/
+    - name: Publish distribution to PyPI
+      uses: pypa/gh-action-pypi-publish@release/v1
+
+  github-release:
+    name: >-
+      Sign the Python distribution with Sigstore
+      and upload them to GitHub Release
+    needs:
+    - publish-to-pypi
+    runs-on: ubuntu-latest
+
+    permissions:
+      contents: write
+      id-token: write
+
+    steps:
+    - name: Download all the dists
+      uses: actions/download-artifact@v4
+      with:
+        name: python-package-distributions
+        path: dist/
+    - name: Sign the dists with Sigstore
+      uses: sigstore/gh-action-sigstore-python@v2.1.1
+      with:
+        inputs: >-
+          ./dist/*.tar.gz
+          ./dist/*.whl
+    - name: Create GitHub Release
+      env:
+        GITHUB_TOKEN: ${{ github.token }}
+      run: >-
+        gh release create
+        '${{ github.ref_name }}'
+        --repo '${{ github.repository }}'
+        --notes ""
+    - name: Upload artifact signatures to GitHub Release
+      env:
+        GITHUB_TOKEN: ${{ github.token }}
+      # Upload to GitHub Release using the `gh` CLI.
+      # `dist/` contains the built packages, and the
+      # sigstore-produced signatures and certificates.
+      run: >-
+        gh release upload
+        '${{ github.ref_name }}' dist/**
+        --repo '${{ github.repository }}'
+
+  publish-to-testpypi:
+    name: Publish Python distribution to TestPyPI
+    if: ${{ github.ref == 'refs/heads/main' &&  github.repository_owner == 'theochem'}}
+    needs:
+    - build
+    runs-on: ubuntu-latest
+
+    environment:
+      name: testpypi
+      url: https://test.pypi.org/p/${{ env.PYPI_NAME }}
+
+    permissions:
+      id-token: write
+
+    steps:
+    - name: Download all the dists
+      uses: actions/download-artifact@v4
+      with:
+        name: python-package-distributions
+        path: dist/
+    - name: Publish distribution to TestPyPI
+      uses: pypa/gh-action-pypi-publish@release/v1
+      with:
+        repository-url: https://test.pypi.org/legacy/

.gitignore

@@ -94,6 +94,9 @@ celerybeat-schedule
 # dotenv
 .env
 
+# direnv
+.envrc
+
 # virtualenv
 .venv
 venv/

.pre-commit-config.yaml

@@ -0,0 +1,38 @@
+exclude: 'iodata/test/data/.*'
+repos:
+- repo: https://github.com/pre-commit/pre-commit-hooks
+  rev: v4.6.0
+  hooks:
+    - id: check-added-large-files
+    - id: check-ast
+    - id: check-case-conflict
+    - id: check-executables-have-shebangs
+    - id: check-json
+    - id: check-yaml
+    - id: check-merge-conflict
+    - id: check-symlinks
+    - id: check-toml
+    - id: check-vcs-permalinks
+    - id: debug-statements
+    - id: detect-private-key
+    - id: destroyed-symlinks
+    - id: end-of-file-fixer
+    - id: fix-byte-order-marker
+    - id: mixed-line-ending
+    - id: pretty-format-json
+      args: ["--autofix", "--no-sort-keys"]
+    - id: trailing-whitespace
+- repo: https://github.com/Lucas-C/pre-commit-hooks
+  rev: v1.5.5
+  hooks:
+    - id: remove-crlf
+- repo: https://github.com/python-jsonschema/check-jsonschema
+  rev: 0.28.4
+  hooks:
+    - id: check-github-workflows
+- repo: https://github.com/astral-sh/ruff-pre-commit
+  rev: v0.4.5
+  hooks:
+    - id: ruff-format
+    - id: ruff
+      args: ["--fix", "--show-fixes"]