qc-PyCI 0.6.1a2__tar.gz

qc_pyci-0.6.1a2/.clang-format

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+---
+Language:        Cpp
+# BasedOnStyle:  LLVM
+AccessModifierOffset: -4
+AlignAfterOpenBracket: Align
+AlignConsecutiveMacros: false
+AlignConsecutiveAssignments: false
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+AllowShortLambdasOnASingleLine: All
+AllowShortIfStatementsOnASingleLine: Never
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+AlwaysBreakAfterReturnType: None
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+AlwaysBreakTemplateDeclarations: true
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+BinPackParameters: true
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+BreakBeforeBraces: Attach
+BreakBeforeInheritanceComma: false
+BreakInheritanceList: BeforeColon
+BreakBeforeTernaryOperators: true
+BreakConstructorInitializersBeforeComma: false
+BreakConstructorInitializers: BeforeColon
+BreakAfterJavaFieldAnnotations: false
+BreakStringLiterals: true
+ColumnLimit:     100
+CommentPragmas:  '^ IWYU pragma:'
+CompactNamespaces: false
+ConstructorInitializerAllOnOneLineOrOnePerLine: false
+ConstructorInitializerIndentWidth: 4
+ContinuationIndentWidth: 4
+Cpp11BracedListStyle: true
+DeriveLineEnding: true
+DerivePointerAlignment: false
+DisableFormat:   false
+ExperimentalAutoDetectBinPacking: false
+FixNamespaceComments: true
+ForEachMacros:
+  - foreach
+  - Q_FOREACH
+  - BOOST_FOREACH
+IncludeBlocks:   Preserve
+IncludeCategories:
+  - Regex:           '^"(llvm|llvm-c|clang|clang-c)/'
+    Priority:        2
+    SortPriority:    0
+  - Regex:           '^(<|"(gtest|gmock|isl|json)/)'
+    Priority:        3
+    SortPriority:    0
+  - Regex:           '.*'
+    Priority:        1
+    SortPriority:    0
+IncludeIsMainRegex: '(Test)?$'
+IncludeIsMainSourceRegex: ''
+IndentCaseLabels: false
+IndentGotoLabels: true
+IndentPPDirectives: None
+IndentWidth:     4
+IndentWrappedFunctionNames: false
+JavaScriptQuotes: Leave
+JavaScriptWrapImports: true
+KeepEmptyLinesAtTheStartOfBlocks: true
+MacroBlockBegin: ''
+MacroBlockEnd:   ''
+MaxEmptyLinesToKeep: 1
+NamespaceIndentation: None
+ObjCBinPackProtocolList: Auto
+ObjCBlockIndentWidth: 2
+ObjCSpaceAfterProperty: false
+ObjCSpaceBeforeProtocolList: true
+PenaltyBreakAssignment: 2
+PenaltyBreakBeforeFirstCallParameter: 19
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+PenaltyExcessCharacter: 1000000
+PenaltyReturnTypeOnItsOwnLine: 60
+PointerAlignment: Right
+ReflowComments:  true
+SortIncludes:    true
+SortUsingDeclarations: true
+SpaceAfterCStyleCast: false
+SpaceAfterLogicalNot: false
+SpaceAfterTemplateKeyword: false
+SpaceBeforeAssignmentOperators: true
+SpaceBeforeCpp11BracedList: false
+SpaceBeforeCtorInitializerColon: true
+SpaceBeforeInheritanceColon: true
+SpaceBeforeParens: ControlStatements
+SpaceBeforeRangeBasedForLoopColon: true
+SpaceInEmptyBlock: false
+SpaceInEmptyParentheses: false
+SpacesBeforeTrailingComments: 1
+SpacesInAngles:  false
+SpacesInConditionalStatement: false
+SpacesInContainerLiterals: true
+SpacesInCStyleCastParentheses: false
+SpacesInParentheses: false
+SpacesInSquareBrackets: false
+SpaceBeforeSquareBrackets: false
+Standard:        Latest
+StatementMacros:
+  - Q_UNUSED
+  - QT_REQUIRE_VERSION
+TabWidth:        8
+UseCRLF:         false
+UseTab:          Never
+...
+

qc_pyci-0.6.1a2/.github/workflows/pypi_release.yaml

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+# This workflow is adapted from:
+# https://packaging.python.org/en/latest/guides/publishing-package-distribution-releases-using-github-actions-ci-cd-workflows/
+
+name: PyPI Release
+on:
+  push:
+    tags:
+      # Trigger on version tags (e.g., v1.0.0)
+      - "v[0-9].[0-9].[0-9]*"
+      - "[0-9].[0-9].[0-9]*"
+      # Trigger on pre-release tags (e.g., v1.0.0-alpha.1)
+      - "v[0-9].[0-9].[0-9]*-*"
+      - "[0-9].[0-9].[0-9]*-*"
+
+env:
+  # The name of the package to be published to PyPI and TestPyPI.
+  PYPI_NAME: qc-PyCI
+
+jobs:
+  build:
+    name: Build distribution
+    runs-on: ${{ matrix.os }}
+    strategy:
+      matrix:
+        # os: [ubuntu-latest, macos-latest]
+        # python-version: ["3.9", "3.10", "3.11", "3.12"]
+        os: [ubuntu-latest]
+        python-version: ["3.12"]
+
+    steps:
+    #   # TODO: Add C++ compliers
+    #   # Fetch CUDA toolkit using Jimver/cuda-toolkit
+    #   - name: Fetch CUDA toolkit
+    #     uses: Jimver/cuda-toolkit@v0.2.18
+    #     id: cuda-toolkit
+    #     with:
+    #       cuda: "12.1.0"
+
+    #   - name: Check nvcc version
+    #     run: nvcc -V
+
+      - uses: actions/checkout@v4
+        with:
+          fetch-depth: 0
+
+      - name: Set up Python
+        uses: actions/setup-python@v5
+        # with:
+        #   python-version: "3.12"
+        with:
+          python-version: ${{ matrix.python-version }}
+
+      - name: Install system dependencies (Ubuntu)
+        if: runner.os == 'Linux'
+        run: |
+          sudo apt-get update
+          sudo apt-get install -y make gcc g++ python3-dev
+
+      - name: Install system dependencies (macOS)
+        if: runner.os == 'macOS'
+        run: |
+          brew install gcc make
+
+      - name: Install development and distributions version
+        run: |
+          pip install --upgrade pip
+          pip install -v .
+          pip install pytest build
+
+      - name: Build Source Distribution
+        run: |
+          make
+          make test
+          python -m build --sdist
+
+      - name: Store the distribution packages
+        uses: actions/upload-artifact@v4
+        with:
+          name: python-package-distributions
+          path: dist/
+
+  publish-to-pypi:
+    name: Publish Python distribution to PyPI
+    # only publish to PyPI on tag pushes
+    if: startsWith(github.ref, 'refs/tags/')
+    needs:
+      - build
+    runs-on: ubuntu-latest
+    environment:
+      name: PyPI-Release
+      url: https://pypi.org/project/${{ 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
+        env:
+          TWINE_USERNAME: "__token__"
+          TWINE_PASSWORD: ${{ secrets.PYPI_TOKEN }}
+
+  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@v3.0.0
+        with:
+          inputs: >-
+            ./dist/*.tar.gz
+
+      - 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: ${{ github.token }}
+        run: >-
+          gh release upload
+          "${{ github.ref_name }}" dist/**
+          --repo "${{ github.repository }}"
+
+  publish-to-testpypi:
+    name: Publish Python distribution to TestPyPI
+    # if: ${{ github.ref == "refs/heads/master" && github.repository_owner == "theochem" }}
+    needs:
+      - build
+    runs-on: ubuntu-latest
+
+    environment:
+      name: TestPyPI
+      url: https://test.pypi.org/project/${{ 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/
+        env:
+          TWINE_USERNAME: "__token__"
+          TWINE_PASSWORD: ${{ secrets.TEST_PYPI_TOKEN }}

qc_pyci-0.6.1a2/.github/workflows/python-app.yml

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+name: Test PyCI
+
+on:
+  push:
+    branches: [ master ]
+  pull_request:
+    branches: [ master ]
+
+jobs:
+  build:
+
+    runs-on: ubuntu-latest
+
+    steps:
+    - uses: actions/checkout@v2
+    - name: Set up Python 3.10
+      uses: actions/setup-python@v2
+      with:
+        python-version: "3.10"
+    - name: Install dependencies and make C++ library
+      run: |
+        python3 -m pip install --user numpy scipy pytest
+        PYTHON=python3 make
+    - name: Run PyCI tests
+      run: |
+        PYTHON=python3 make test

qc_pyci-0.6.1a2/.github/workflows/website.yml

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+name: deploy-book
+
+# Only run this when the master branch changes
+on:
+  push:
+    branches:
+      - master
+      - website
+
+  pull_request:
+    types: [opened, synchronize, reopened, closed]
+    branches:
+      - main
+    # If your git repository has the Jupyter Book within some-subfolder next to
+    # unrelated files, you can make this run only if a file within that specific
+    # folder has been modified.
+    #
+    #paths:
+    #- book/
+
+# This job installs dependencies, builds the book, and pushes it to `gh-pages`
+jobs:
+  deploy-book:
+    runs-on: ubuntu-latest
+    permissions:
+      pages: write
+      # https://github.com/JamesIves/github-pages-deploy-action/issues/1110
+      contents: write
+
+    steps:
+      - uses: actions/checkout@v2
+      - name: Set up Python 3.10
+        uses: actions/setup-python@v2
+        with:
+          python-version: "3.10"
+      - name: Install dependencies and make C++ library
+        run: |
+          python3 -m pip install --user numpy scipy pytest pycodestyle pydocstyle
+          PYTHON=python3 make
+          python3 -m pip install .
+
+      - name: Install dependencies
+        run: |
+          python3 -m pip install -r website/requirements.txt
+
+
+      # Add soft links to the notebooks
+      - name: Add soft links to the notebooks
+        run: |
+          cd website
+          ln -s ../notebooks ./examples
+          ln -s ../doc/source ./api
+          cd ../
+
+      # Build the book
+      - name: Build the website
+        run: |
+          jupyter-book build ./website/
+
+      # Push the book's HTML to github-pages
+      # inspired by https://github.com/orgs/community/discussions/26724
+      # only push to gh-pages if the master branch has been updated
+      - name: GitHub Pages Action
+        # if: ${{ github.event_name == 'push' && github.ref == 'refs/heads/master' }}
+        uses: peaceiris/actions-gh-pages@v3
+        with:
+          github_token: ${{ secrets.GITHUB_TOKEN }}
+          publish_dir: ./website/_build/html
+          publish_branch: gh-pages
+          cname: pyci.qcdevs.org

qc_pyci-0.6.1a2/.gitignore

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+# Prerequisites
+*.d
+
+# Compiled object files
+*.slo
+*.lo
+*.o
+*.obj
+
+# Precompiled headers
+*.gch
+*.pch
+
+# Compiled dynamic libraries
+*.so
+*.so.[0-9]*
+*.dylib
+*.dll
+
+# Fortran module files
+*.mod
+*.smod
+
+# Compiled static libraries
+*.lai
+*.la
+*.a
+*.lib
+
+# Executables
+*.exe
+*.out
+*.app
+
+# Byte-compiled / optimized / DLL files
+__pycache__/
+*.py[cod]
+*$py.class
+
+# Distribution / packaging
+.Python
+build/
+cover/
+develop-eggs/
+dist/
+downloads/
+eggs/
+.eggs/
+parts/
+sdist/
+var/
+wheels/
+.installed.cfg
+MANIFEST
+*.egg-info/
+*.egg
+*.manifest
+*.spec
+pip-log.txt
+pip-delete-this-directory.txt
+.pytest_cache/
+.coverage
+
+# Environments
+.env
+.venv
+env/
+venv/
+ENV/
+
+# Editor junk
+tags
+[._]*.s[a-v][a-z]
+[._]*.sw[a-p]
+[._]s[a-v][a-z]
+[._]sw[a-p]
+*~
+\#*\#
+.\#*
+.ropeproject
+.idea/
+.spyderproject
+.spyproject
+.vscode/
+
+# Documentation
+doc/build/
+
+# Clangd
+compile_flags.txt
+
+# Libraries
+deps/
+
+# Jupyter Notebooks
+.ipynb_checkpoints

qc_pyci-0.6.1a2/.pre-commit-config.yaml

@@ -0,0 +1,7 @@
+# See https://pre-commit.com for more information
+# See https://pre-commit.com/hooks.html for more hooks
+repos:
+-   repo: https://github.com/pre-commit/pre-commit-hooks
+    rev: v3.2.0
+    hooks:
+    -   id: check-added-large-files

qc_pyci-0.6.1a2/.travis.yml

@@ -0,0 +1,24 @@
+language: python
+
+python:
+  - "3.6"
+
+os:
+  - linux
+
+dist:
+  - bionic
+
+branches:
+  only:
+    - master
+
+install:
+  - python -m pip install numpy scipy pytest pycodestyle pydocstyle
+  - make
+  - python -m pip install .
+
+script:
+  - python -m pycodestyle pyci
+  - python -m pydocstyle pyci
+  - PYCI_NUM_THREADS=2 python -m pytest pyci

qc_pyci-0.6.1a2/CONTRIBUTORS

@@ -0,0 +1,5 @@
+Michael Richer <richerm@mcmaster.ca>
+Gabriela Sanchez-Diaz <diazg1@mcmaster.ca>
+Ali Tehrani <alirezatehrani24@gmail.com>
+Farnaz Heidar-Zadeh <farnaz_chem@yahoo.com>
+Taewon D. Kim <davidkim91@gmail.com>