qccompute 0.13.0__tar.gz

qccompute-0.13.0/.github/ISSUE_TEMPLATE/bug_report.md

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+---
+name: Bug report
+about: Create a report to help us improve
+title: "[BUG] - "
+labels: bug
+assignees: ''
+
+---
+
+**Describe the bug**
+A clear and concise description of what the bug is.
+
+**To Reproduce**
+Steps to reproduce the behavior. Please provide all necessary data and a runable python script that reproduces your error:
+1. Go to '...'
+2. Click on '....'
+3. Scroll down to '....'
+4. See error
+
+**Expected behavior**
+A clear and concise description of what you expected to happen.
+
+**Screenshots**
+If applicable, add screenshots to help explain your problem.
+
+**Additional context**
+Add any other context about the problem here.

qccompute-0.13.0/.github/ISSUE_TEMPLATE/feature_request.md

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+---
+name: Feature request
+about: Suggest an idea for this project
+title: "[FEATURE] - "
+labels: enhancement
+assignees: ''
+
+---
+
+**Is your feature request related to a problem? Please describe.**
+A clear and concise description of what the problem is. Ex. I'm always frustrated when [...]
+
+**Describe the solution you'd like**
+A clear and concise description of what you want to happen.
+
+**Describe alternatives you've considered**
+A clear and concise description of any alternative solutions or features you've considered.
+
+**Additional context**
+Add any other context or screenshots about the feature request here.

qccompute-0.13.0/.github/workflows/basic-code-quality.yaml

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+name: Basic Code Quality
+
+on: [push]
+
+jobs:
+  ruff:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v3
+      - name: Set up Python
+        uses: actions/setup-python@v5
+        with:
+          python-version-file: ".python-version"
+      - name: Install ruff
+        run: pip install ruff
+      - name: ruff
+        run: ruff check .
+
+  mypy:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v3
+      - name: Set up Python
+        uses: actions/setup-python@v5
+        with:
+          python-version-file: ".python-version"
+      - name: Install uv
+        uses: astral-sh/setup-uv@v5
+      - name: Install the project
+        run: uv sync --all-extras --dev
+      - name: mypy
+        run: uv run mypy .
+
+  detect-secrets:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v3
+      - name: Set up Python
+        uses: actions/setup-python@v5
+        with:
+          python-version-file: ".python-version"
+      - name: Install detect secrets
+        run: pip install detect-secrets
+      - name: Look for secrets
+        run: git ls-files -z | xargs -0 detect-secrets-hook -v
+
+  typos:
+    name: "spell check"
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v3
+      - uses: crate-ci/typos@master
+        with:
+          files: .

qccompute-0.13.0/.github/workflows/create-release.yaml

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+name: Create Release
+
+on:
+  push:
+    tags:
+      - "*" # Match any tag
+  workflow_dispatch: # Enable manual triggering
+
+jobs:
+  create-release:
+    name: Create GitHub Release
+    runs-on: ubuntu-latest
+    environment: release # Link to the protected environment
+
+    steps:
+      - name: Checkout code
+        uses: actions/checkout@v4
+
+      - name: Extract Release Notes
+        id: extract_notes
+        run: |
+          VERSION=${{ github.ref_name }}
+          sed -n "/## \\[$VERSION\\]/,/## \\[/p" CHANGELOG.md | sed '$d' | sed "s/## \\[$VERSION\\]/## $VERSION/" > RELEASE_NOTES.md
+
+      - name: Create GitHub Release
+        id: create_release
+        uses: actions/create-release@v1
+        with:
+          tag_name: ${{ github.ref_name }}
+          release_name: Release ${{ github.ref_name }}
+          body_path: ./RELEASE_NOTES.md
+          draft: false
+          prerelease: false
+        env:
+          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+
+      - name: Output release URL
+        run: |
+          echo "Release URL: ${{ steps.create_release.outputs.html_url }}"

qccompute-0.13.0/.github/workflows/publish-to-pypi.yaml

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+# https://github.com/marketplace/actions/pypi-publish
+
+name: Publish to PyPI
+
+on:
+  push:
+    tags: # Only publish on tagged commits
+      - "*"
+
+jobs:
+  build-and-publish:
+    name: Build and publish Python 🐍 distributions 📦 to PyPI
+    runs-on: ubuntu-latest
+    environment:
+      name: pypi
+      url: https://pypi.org/project/qcop/
+    permissions:
+      id-token: write # IMPORTANT: this permission is mandatory for trusted publishing
+
+    steps:
+      - name: Check out source repository
+        uses: actions/checkout@v2
+
+      - name: Set up Python
+        uses: actions/setup-python@v5
+        with:
+          python-version-file: ".python-version"
+
+      - name: Install uv
+        uses: astral-sh/setup-uv@v5
+
+      - name: Build distribution 📦
+        run: uv build
+
+      - name: Publish package 📤 to PyPI
+        uses: pypa/gh-action-pypi-publish@release/v1

qccompute-0.13.0/.github/workflows/test.yaml

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+name: Tests
+
+on:
+  push:
+    branches: [master]
+  pull_request:
+    branches: [master]
+
+jobs:
+  tests:
+    runs-on: ubuntu-latest
+    strategy:
+      fail-fast: false
+      matrix:
+        python-version: ["3.10", "3.11", "3.12", "3.13", "3.14"]
+        include:
+          - python-version: "3.12"
+            coverage: true
+    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 uv
+        uses: astral-sh/setup-uv@v5
+
+      # uv pip resolves & installs deps like pip (not an environment sync)
+      - name: Install package + test deps (uv pip)
+        run: uv pip install --system --group dev .
+
+      - name: Run tests
+        run: python -m pytest --cov-report=term-missing --cov-report html:htmlcov --cov-config=pyproject.toml --cov=qcop --cov=tests .
+
+      - name: Upload coverage HTML
+        if: ${{ matrix.coverage == true }}
+        uses: actions/upload-artifact@v4
+        with:
+          name: htmlcov-py${{ matrix.python-version }}
+          path: htmlcov
+
+      # To catch manifest issues, we build and install from sdist on one version
+      - name: Build sdist (only on 3.12)
+        if: ${{ matrix.coverage == true }}
+        run: python -m pip install build && python -m build --sdist
+
+      - name: Install from sdist (only on 3.12)
+        if: ${{ matrix.coverage == true }}
+        run: python -m pip install dist/*.tar.gz

qccompute-0.13.0/.gitignore

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+# Byte-compiled / optimized / DLL files
+__pycache__/
+*.py[cod]
+*$py.class
+
+# C extensions
+*.so
+
+# Distribution / packaging
+.Python
+build/
+develop-eggs/
+dist/
+downloads/
+eggs/
+.eggs/
+lib/
+lib64/
+parts/
+sdist/
+var/
+wheels/
+share/python-wheels/
+*.egg-info/
+.installed.cfg
+*.egg
+MANIFEST
+
+# PyInstaller
+#  Usually these files are written by a python script from a template
+#  before PyInstaller builds the exe, so as to inject date/other infos into it.
+*.manifest
+*.spec
+
+# Installer logs
+pip-log.txt
+pip-delete-this-directory.txt
+
+# Unit test / coverage reports
+htmlcov/
+.tox/
+.nox/
+.coverage
+.coverage.*
+.cache
+nosetests.xml
+coverage.xml
+*.cover
+*.py,cover
+.hypothesis/
+.pytest_cache/
+cover/
+
+# Translations
+*.mo
+*.pot
+
+# Django stuff:
+*.log
+local_settings.py
+db.sqlite3
+db.sqlite3-journal
+
+# Flask stuff:
+instance/
+.webassets-cache
+
+# Scrapy stuff:
+.scrapy
+
+# Sphinx documentation
+docs/_build/
+
+# PyBuilder
+.pybuilder/
+target/
+
+# Jupyter Notebook
+.ipynb_checkpoints
+
+# IPython
+profile_default/
+ipython_config.py
+
+# pyenv
+#   For a library or package, you might want to ignore these files since the code is
+#   intended to run in multiple environments; otherwise, check them in:
+# .python-version
+
+# pipenv
+#   According to pypa/pipenv#598, it is recommended to include Pipfile.lock in version control.
+#   However, in case of collaboration, if having platform-specific dependencies or dependencies
+#   having no cross-platform support, pipenv may install dependencies that don't work, or not
+#   install all needed dependencies.
+#Pipfile.lock
+
+# poetry
+#   Similar to Pipfile.lock, it is generally recommended to include poetry.lock in version control.
+#   This is especially recommended for binary packages to ensure reproducibility, and is more
+#   commonly ignored for libraries.
+#   https://python-poetry.org/docs/basic-usage/#commit-your-poetrylock-file-to-version-control
+#poetry.lock
+
+# pdm
+#   Similar to Pipfile.lock, it is generally recommended to include pdm.lock in version control.
+#pdm.lock
+#   pdm stores project-wide configurations in .pdm.toml, but it is recommended to not include it
+#   in version control.
+#   https://pdm.fming.dev/#use-with-ide
+.pdm.toml
+
+# PEP 582; used by e.g. github.com/David-OConnor/pyflow and github.com/pdm-project/pdm
+__pypackages__/
+
+# Celery stuff
+celerybeat-schedule
+celerybeat.pid
+
+# SageMath parsed files
+*.sage.py
+
+# Environments
+.env
+.venv
+env/
+venv/
+ENV/
+env.bak/
+venv.bak/
+
+# Spyder project settings
+.spyderproject
+.spyproject
+
+# Rope project settings
+.ropeproject
+
+# mkdocs documentation
+/site
+
+# mypy
+.mypy_cache/
+.dmypy.json
+dmypy.json
+
+# Pyre type checker
+.pyre/
+
+# pytype static type analyzer
+.pytype/
+
+# Cython debug symbols
+cython_debug/
+
+# PyCharm
+#  JetBrains specific template is maintained in a separate JetBrains.gitignore that can
+#  be found at https://github.com/github/gitignore/blob/main/Global/JetBrains.gitignore
+#  and can be added to the global gitignore or merged into this file.  For a more nuclear
+#  option (not recommended) you can uncomment the following to ignore the entire idea folder.
+#.idea/
+
+# qcop specific ignores
+# TeraChem scratch files
+scr.*
+tc.in
+*.xyz
+# Keep example file
+!examples/h2o.xyz
+# Psi4 scratch files
+*.dat

qccompute-0.13.0/.pre-commit-config.yaml

@@ -0,0 +1,44 @@
+# 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: v4.4.0
+    hooks:
+      - id: check-yaml
+        exclude: mkdocs.yml
+      - id: check-added-large-files
+        args: ["--maxkb=250"]
+        exclude: caffeine.frequencies.out
+  - repo: https://github.com/Yelp/detect-secrets
+    rev: v1.4.0
+    hooks:
+      - id: detect-secrets
+        stages: [commit]
+        exclude: uv.lock
+  - repo: https://github.com/charliermarsh/ruff-pre-commit
+    # Ruff version.
+    rev: "v0.5.7"
+    hooks:
+      - id: ruff
+        args: [--fix, --exit-non-zero-on-fix]
+  - repo: https://github.com/pre-commit/mirrors-mypy
+    rev: v1.15.0
+    hooks:
+      - id: mypy
+        args: [.]
+        pass_filenames: false
+        additional_dependencies:
+          [pydantic>=2.0.0, qcdata>=0.17.0, types-toml]
+  - repo: https://github.com/crate-ci/typos
+    rev: v1.24.5
+    hooks:
+      - id: typos
+  - repo: local
+    hooks:
+      - id: tests
+        name: tests
+        stages: [push]
+        language: system
+        entry: uv run pytest
+        types: [python]
+        pass_filenames: false

qccompute-0.13.0/.python-version

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+3.10

qccompute-0.13.0/.vscode/settings.json

@@ -0,0 +1,41 @@
+{
+    "cSpell.words": [
+        "acetonitrile",
+        "addcart",
+        "allclose",
+        "alpb",
+        "arange",
+        "calcspec",
+        "calctype",
+        "calctypes",
+        "coordsys",
+        "Delocalized",
+        "dockerized",
+        "excinfo",
+        "gfnff",
+        "hostcpus",
+        "htmlcov",
+        "libxtb",
+        "mrchem",
+        "numhess",
+        "pstdout",
+        "psutil",
+        "pyenv",
+        "qcconst",
+        "qcdata",
+        "qcel",
+        "qcio",
+        "qcop",
+        "qcparse",
+        "rotamer",
+        "rotamers",
+        "singlepoint",
+        "spinmult",
+        "TCPB",
+        "terachem",
+        "terachemd",
+        "tmpdir",
+        "wfns",
+        "xyzout"
+    ]
+}