pdb2reaction 0.3.0__tar.gz

pdb2reaction-0.3.0/.github/workflows/docs.yml

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+name: Deploy Documentation
+
+on:
+  push:
+    branches: [main]
+  workflow_dispatch:
+
+permissions:
+  contents: read
+  pages: write
+  id-token: write
+
+concurrency:
+  group: "pages"
+  cancel-in-progress: false
+
+jobs:
+  build:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+
+      - name: Set up Python
+        uses: actions/setup-python@v5
+        with:
+          python-version: '3.11'
+
+      - name: Install dependencies
+        run: |
+          pip install -r docs/requirements_docs.txt
+
+      - name: Build documentation
+        run: |
+          cd docs
+          make html
+
+      - name: Upload artifact
+        uses: actions/upload-pages-artifact@v3
+        with:
+          path: docs/_build/html
+
+  deploy:
+    needs: build
+    runs-on: ubuntu-latest
+    environment:
+      name: github-pages
+      url: ${{ steps.deployment.outputs.page_url }}
+    steps:
+      - name: Deploy to GitHub Pages
+        id: deployment
+        uses: actions/deploy-pages@v4

pdb2reaction-0.3.0/.github/workflows/docs_quality.yml

@@ -0,0 +1,42 @@
+name: Docs Quality
+
+on:
+  pull_request:
+  push:
+    branches: [main]
+
+jobs:
+  reference-and-smoke:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+
+      - name: Set up Python
+        uses: actions/setup-python@v5
+        with:
+          python-version: "3.11"
+
+      - name: Install minimal dependencies
+        run: |
+          python -m pip install --upgrade pip
+          pip install torch --index-url https://download.pytorch.org/whl/cpu
+          pip install -e . --no-deps
+          pip install click pyyaml numpy biopython scipy ase \
+            autograd dask distributed h5py fabric jinja2 joblib \
+            matplotlib natsort psutil rmsd sympy scikit-learn \
+            pandas tabulate plotly
+
+      - name: Run docs quality suite
+        timeout-minutes: 20
+        env:
+          DOCS_DUMP_CASE_TIMEOUT_SEC: "180"
+        run: |
+          set -o pipefail
+          python scripts/run_docs_quality.py --skip-dump | tee docs_quality_timing.log
+
+      - name: Upload docs quality timing log
+        if: always()
+        uses: actions/upload-artifact@v4
+        with:
+          name: docs_quality_timing_log
+          path: docs_quality_timing.log

pdb2reaction-0.3.0/.github/workflows/release.yml

@@ -0,0 +1,41 @@
+name: Publish to PyPI
+
+on:
+  release:
+    types:
+      - published
+
+permissions:
+  contents: read
+  id-token: write
+
+jobs:
+  publish:
+    name: Build and publish
+    runs-on: ubuntu-latest
+    steps:
+      - name: Checkout
+        uses: actions/checkout@v4
+        with:
+          fetch-depth: 0
+
+      - name: Setup Python
+        uses: actions/setup-python@v5
+        with:
+          python-version: "3.11"
+
+      - name: Install build dependencies
+        run: python -m pip install --upgrade build twine
+
+      - name: Build package
+        run: |
+          rm -rf dist
+          python -m build
+
+      - name: Verify distribution
+        run: python -m twine check dist/*
+
+      - name: Publish to PyPI (Trusted Publishing)
+        uses: pypa/gh-action-pypi-publish@release/v1
+        with:
+          packages-dir: dist/

pdb2reaction-0.3.0/.github/workflows/test.yml

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+name: Tests
+
+on:
+  pull_request:
+  push:
+    branches: [main]
+
+jobs:
+  unit-tests:
+    runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        python-version: ["3.11", "3.12"]
+    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 minimal test dependencies
+        run: |
+          python -m pip install --upgrade pip
+          pip install torch --index-url https://download.pytorch.org/whl/cpu
+          pip install -e . --no-deps
+          pip install click pyyaml numpy biopython scipy ase \
+            autograd dask distributed h5py fabric jinja2 joblib \
+            matplotlib natsort psutil rmsd sympy scikit-learn \
+            pandas tabulate plotly pytest pytest-cov
+
+      - name: Run unit tests (CPU-only, no GPU)
+        timeout-minutes: 10
+        run: |
+          pytest tests/ -v --tb=short -x --cov=pdb2reaction --cov-report=term-missing --cov-fail-under=15

pdb2reaction-0.3.0/.gitignore

@@ -0,0 +1,45 @@
+.history/
+
+__pycache__/
+.pytest_cache/
+*.pyc
+*.pyo
+*.pyd
+
+venv/
+env/
+env.bak/
+env1/
+env2/
+.env
+
+.vscode/
+*.code-workspace
+
+*.log
+improvement_plan.md
+
+build/
+dist/
+*.egg-info/
+*.egg
+
+# setuptools-scm generated version file
+pdb2reaction/_version.py
+
+test-reports/
+.coverage
+
+# Sphinx documentation
+docs/_build/
+docs/_static/*.css.map
+docs/_static/*.js.map
+docs/_autosummary/
+docs/.myst_cache/
+docs/.ipynb_checkpoints/
+
+*.bak
+*.swp
+*.tmp
+*.tmp.*
+*~

pdb2reaction-0.3.0/CHANGELOG.md

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+# Changelog
+
+All notable changes to **pdb2reaction** will be documented in this file.
+
+The format follows [Keep a Changelog](https://keepachangelog.com/).
+
+## [Unreleased]
+
+### Added
+- `logging.getLogger(__name__)` in all CLI modules for structured logging.
+- `CONTRIBUTING.md` and `CHANGELOG.md`.
+- `show_default=True` on all `--backend`, `--solvent`, and `--solvent-model` CLI options.
+- Coverage reporting (`pytest-cov`) in CI.
+- Additional unit tests for `summary_log`, `align`, `cli_utils`, and `defaults`.
+
+### Fixed
+- `_mep_skipped_by_resume` variable used before definition in `all.py`.
+- Temporary directory leaks in `scan2d` and `scan3d` (added `finally: shutil.rmtree`).
+- All `WARNING` messages in `all.py` now write to stderr (`err=True`).
+- `ja/all.md` documented wrong default for `--opt-mode` (`hess` → `grad`).
+- Duplicated `_is_param_explicit` helper replaced with `cli_param_overridden` from `utils`.
+- Version banner no longer printed during `--help` tab completion (`ctx.resilient_parsing` guard).
+
+### Changed
+- Centralized Click parameter-source checking via `cli_param_overridden(ctx, name)`.

pdb2reaction-0.3.0/CONTRIBUTING.md

@@ -0,0 +1,47 @@
+# Contributing to pdb2reaction
+
+Thank you for your interest in contributing to **pdb2reaction**.
+
+## Development Setup
+
+```bash
+# Clone the repository
+git clone https://github.com/t-0hmura/pdb2reaction.git
+cd pdb2reaction
+
+# Create a conda environment
+conda create -n pdb2reaction python=3.11
+conda activate pdb2reaction
+
+# Install in editable mode
+pip install -e .
+```
+
+## Running Tests
+
+```bash
+# Run the full test suite
+pytest tests/ -v --tb=short
+
+# Run with coverage
+pytest tests/ -v --tb=short --cov=pdb2reaction --cov-report=term-missing
+```
+
+## Code Style
+
+- Use `from __future__ import annotations` in all modules.
+- Use `logging.getLogger(__name__)` for structured logging; avoid bare `print()`.
+- CLI options should include `show_default=True` where applicable.
+- Warning messages via `click.echo()` should use `err=True` to write to stderr.
+
+## Submitting Changes
+
+1. Fork the repository and create a feature branch.
+2. Make your changes and add tests where appropriate.
+3. Ensure all tests pass locally.
+4. Open a pull request with a clear description of the changes.
+
+## License
+
+By contributing, you agree that your contributions will be licensed under the
+[GPL-3.0 License](LICENSE).