molcrys-kit 0.3.0__tar.gz

molcrys_kit-0.3.0/.dockerignore

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+# .dockerignore — keep the build context lean
+# The local build still sends a context to Docker, even though the main Dockerfile
+# installs the package and extracts notebooks/scripts from the GitHub archive.
+
+# Python build artefacts
+__pycache__/
+*.py[cod]
+*.pyo
+*.pyd
+*.egg-info/
+*.egg
+dist/
+build/
+.eggs/
+.installed.cfg
+MANIFEST
+
+# Coverage / test outputs
+.coverage
+htmlcov/
+.pytest_cache/
+output/
+
+# Jupyter artefacts
+.ipynb_checkpoints/
+# NOTE: do NOT exclude *.ipynb here. The current Dockerfile downloads the
+# notebook/ tree from the GitHub archive rather than COPY'ing it from the local
+# context, but keeping notebooks in the context avoids future surprises if the
+# build strategy changes again.
+
+# Editor / OS
+.vscode/
+.idea/
+*.swp
+*.swo
+.DS_Store
+Thumbs.db
+
+# Git
+.git/
+.gitignore
+
+# Docs / CI (not needed in the image)
+docs/
+benchmarks/

molcrys_kit-0.3.0/.gitattributes

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+*.ipynb linguist-generated=true

molcrys_kit-0.3.0/.github/workflows/publish-ghcr.yml

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+name: publish-ghcr
+
+on:
+  push:
+    tags:
+      - "v*"
+  workflow_dispatch:
+    inputs:
+      git_ref:
+        description: "GitHub archive ref to build from (for example refs/heads/main or refs/tags/v0.2.0)"
+        required: true
+        default: "refs/heads/main"
+        type: string
+      image_tag:
+        description: "GHCR image tag to push (for example dev260326 or v0.2.0)"
+        required: true
+        default: "dev"
+        type: string
+
+permissions:
+  contents: read
+  packages: write
+
+jobs:
+  publish:
+    runs-on: ubuntu-latest
+
+    steps:
+      - name: Check out repository
+        uses: actions/checkout@v4
+        with:
+          fetch-depth: 0
+
+      - name: Resolve build ref and output image coordinates
+        id: prep
+        shell: bash
+        run: |
+          set -euo pipefail
+
+          OWNER_LC="$(echo "${GITHUB_REPOSITORY_OWNER}" | tr '[:upper:]' '[:lower:]')"
+          IMAGE="ghcr.io/${OWNER_LC}/molcryskit"
+
+          if [[ "${GITHUB_EVENT_NAME}" == "push" && "${GITHUB_REF}" == refs/tags/* ]]; then
+            GIT_REF="refs/tags/${GITHUB_REF_NAME}"
+            IMAGE_TAG="${GITHUB_REF_NAME}"
+          else
+            GIT_REF="${{ github.event.inputs.git_ref }}"
+            IMAGE_TAG="${{ github.event.inputs.image_tag }}"
+          fi
+
+          if [[ "${GIT_REF}" != refs/heads/* && "${GIT_REF}" != refs/tags/* ]]; then
+            echo "git_ref must start with refs/heads/ or refs/tags/: ${GIT_REF}" >&2
+            exit 1
+          fi
+
+          if [[ ! "${IMAGE_TAG}" =~ ^[A-Za-z0-9_][A-Za-z0-9_.-]{0,127}$ ]]; then
+            echo "image_tag is not a valid Docker tag: ${IMAGE_TAG}" >&2
+            exit 1
+          fi
+
+          PROMOTE_LATEST="false"
+          if [[ "${GITHUB_EVENT_NAME}" == "push" && "${GITHUB_REF}" == refs/tags/* && "${GITHUB_REF_NAME}" != *-* ]]; then
+            PROMOTE_LATEST="true"
+          fi
+
+          echo "image=${IMAGE}" >> "${GITHUB_OUTPUT}"
+          echo "git_ref=${GIT_REF}" >> "${GITHUB_OUTPUT}"
+          echo "image_tag=${IMAGE_TAG}" >> "${GITHUB_OUTPUT}"
+          echo "promote_latest=${PROMOTE_LATEST}" >> "${GITHUB_OUTPUT}"
+
+      - name: Log in to GHCR
+        uses: docker/login-action@v3
+        with:
+          registry: ghcr.io
+          username: ${{ github.actor }}
+          password: ${{ secrets.GITHUB_TOKEN }}
+
+      - name: Generate image metadata
+        id: meta
+        uses: docker/metadata-action@v5
+        with:
+          images: ${{ steps.prep.outputs.image }}
+          tags: |
+            type=raw,value=${{ steps.prep.outputs.image_tag }}
+            type=sha,prefix=sha-
+            type=raw,value=latest,enable=${{ steps.prep.outputs.promote_latest == 'true' }}
+          labels: |
+            org.opencontainers.image.source=${{ github.server_url }}/${{ github.repository }}
+            org.opencontainers.image.revision=${{ github.sha }}
+            org.opencontainers.image.version=${{ steps.prep.outputs.image_tag }}
+
+      - name: Set up Docker Buildx
+        uses: docker/setup-buildx-action@v3
+
+      - name: Build and push image
+        id: build
+        uses: docker/build-push-action@v6
+        with:
+          context: .
+          file: ./Dockerfile
+          push: true
+          build-args: |
+            MOLCRYSKIT_REF=${{ steps.prep.outputs.git_ref }}
+          tags: ${{ steps.meta.outputs.tags }}
+          labels: ${{ steps.meta.outputs.labels }}
+          cache-from: type=gha
+          cache-to: type=gha,mode=max
+
+      - name: Write publish summary
+        shell: bash
+        run: |
+          {
+            echo "## GHCR publish result"
+            echo
+            echo "- Image: \`${{ steps.prep.outputs.image }}\`"
+            echo "- Git ref inside build: \`${{ steps.prep.outputs.git_ref }}\`"
+            echo "- Primary tag: \`${{ steps.prep.outputs.image_tag }}\`"
+            echo "- Digest: \`${{ steps.build.outputs.digest }}\`"
+          } >> "${GITHUB_STEP_SUMMARY}"

molcrys_kit-0.3.0/.github/workflows/publish-pypi.yml

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+name: publish-pypi
+
+on:
+  push:
+    tags:
+      - "v*"
+  workflow_dispatch:
+    inputs:
+      target:
+        description: "Package index to publish to"
+        required: true
+        default: "testpypi"
+        type: choice
+        options:
+          - testpypi
+          - pypi
+
+permissions:
+  contents: read
+
+jobs:
+  build:
+    runs-on: ubuntu-latest
+
+    steps:
+      - name: Check out repository
+        uses: actions/checkout@v4
+
+      - name: Set up Python
+        uses: actions/setup-python@v5
+        with:
+          python-version: "3.10"
+          cache: pip
+
+      - name: Install build frontend
+        run: |
+          python -m pip install --upgrade pip
+          python -m pip install build
+
+      - name: Build source and wheel distributions
+        run: python -m build
+
+      - name: Upload distributions
+        uses: actions/upload-artifact@v4
+        with:
+          name: python-package-distributions
+          path: dist/
+          if-no-files-found: error
+
+  publish-testpypi:
+    needs: build
+    runs-on: ubuntu-latest
+    if: github.event_name == 'workflow_dispatch' && github.event.inputs.target == 'testpypi'
+    environment:
+      name: testpypi
+      url: https://test.pypi.org/project/molcrys-kit/
+    permissions:
+      contents: read
+      id-token: write
+
+    steps:
+      - name: Download distributions
+        uses: actions/download-artifact@v4
+        with:
+          name: python-package-distributions
+          path: dist/
+
+      - name: Publish to TestPyPI
+        uses: pypa/gh-action-pypi-publish@release/v1
+        with:
+          repository-url: https://test.pypi.org/legacy/
+          packages-dir: dist/
+
+  publish-pypi:
+    needs: build
+    runs-on: ubuntu-latest
+    if: startsWith(github.ref, 'refs/tags/v') || (github.event_name == 'workflow_dispatch' && github.event.inputs.target == 'pypi')
+    environment:
+      name: pypi
+      url: https://pypi.org/project/molcrys-kit/
+    permissions:
+      contents: read
+      id-token: write
+
+    steps:
+      - name: Download distributions
+        uses: actions/download-artifact@v4
+        with:
+          name: python-package-distributions
+          path: dist/
+
+      - name: Publish to PyPI
+        uses: pypa/gh-action-pypi-publish@release/v1
+        with:
+          packages-dir: dist/

molcrys_kit-0.3.0/.github/workflows/unit-tests.yml

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+name: unit-tests
+
+on:
+  push:
+  pull_request:
+    branches:
+      - main
+  workflow_dispatch:
+
+permissions:
+  contents: read
+
+jobs:
+  unit-tests:
+    runs-on: ubuntu-latest
+
+    steps:
+      - name: Check out repository
+        uses: actions/checkout@v4
+
+      - name: Set up Python
+        uses: actions/setup-python@v5
+        with:
+          python-version: "3.10"
+          cache: pip
+
+      - name: Install test dependencies
+        run: |
+          python -m pip install --upgrade pip
+          python -m pip install -e ".[test]"
+
+      - name: Run unit tests
+        run: pytest tests/unit

molcrys_kit-0.3.0/.gitignore

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+# Byte-compiled / optimized / DLL files
+__pycache__/
+*.pyc
+*.py[codz]
+*$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
+
+# UV
+#   Similar to Pipfile.lock, it is generally recommended to include uv.lock in version control.
+#   This is especially recommended for binary packages to ensure reproducibility, and is more
+#   commonly ignored for libraries.
+#uv.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
+#poetry.toml
+
+# pdm
+#   Similar to Pipfile.lock, it is generally recommended to include pdm.lock in version control.
+#   pdm recommends including project-wide configuration in pdm.toml, but excluding .pdm-python.
+#   https://pdm-project.org/en/latest/usage/project/#working-with-version-control
+#pdm.lock
+#pdm.toml
+.pdm-python
+.pdm-build/
+
+# pixi
+#   Similar to Pipfile.lock, it is generally recommended to include pixi.lock in version control.
+#pixi.lock
+#   Pixi creates a virtual environment in the .pixi directory, just like venv module creates one
+#   in the .venv directory. It is recommended not to include this directory in version control.
+.pixi
+
+# 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
+.envrc
+.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/
+
+# Abstra
+# Abstra is an AI-powered process automation framework.
+# Ignore directories containing user credentials, local state, and settings.
+# Learn more at https://abstra.io/docs
+.abstra/
+
+# Visual Studio Code
+#  Visual Studio Code specific template is maintained in a separate VisualStudioCode.gitignore
+#  that can be found at https://github.com/github/gitignore/blob/main/Global/VisualStudioCode.gitignore
+#  and can be added to the global gitignore or merged into this file. However, if you prefer,
+#  you could uncomment the following to ignore the entire vscode folder
+# .vscode/
+
+# Ruff stuff:
+.ruff_cache/
+
+# PyPI configuration file
+.pypirc
+
+# Cursor
+#  Cursor is an AI-powered code editor. `.cursorignore` specifies files/directories to
+#  exclude from AI features like autocomplete and code analysis. Recommended for sensitive data
+#  refer to https://docs.cursor.com/context/ignore-files
+.cursorignore
+.cursorindexingignore
+
+# Marimo
+marimo/_static/
+marimo/_lsp/
+__marimo__/
+
+# Local planning notes (scratch only; not part of the published source)
+plans/

molcrys_kit-0.3.0/.pre-commit-config.yaml

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+repos:
+  - repo: https://github.com/pre-commit/pre-commit-hooks
+    rev: v4.4.0
+    hooks:
+      - id: trailing-whitespace
+      - id: end-of-file-fixer
+      - id: check-yaml
+      - id: check-added-large-files
+
+  - repo: https://github.com/astral-sh/ruff-pre-commit
+    rev: v0.1.6
+    hooks:
+      - id: ruff
+        args: [--fix, --exit-non-zero-on-fix]
+      - id: ruff-format
+
+  - repo: https://github.com/kynan/nbstripout
+    rev: 0.6.1
+    hooks:
+      - id: nbstripout