protein-quest 0.10.0__tar.gz

protein_quest-0.10.0/.github/workflows/ci.yml

@@ -0,0 +1,84 @@
+name: CI
+
+on:
+  push:
+    branches:
+      - main
+  pull_request:
+
+concurrency:
+  group: ${{ github.workflow }}-${{ github.ref }}
+  cancel-in-progress: true
+
+jobs:
+  test:
+    name: test
+    runs-on: ubuntu-latest
+    permissions:
+      id-token: write
+    steps:
+      - uses: actions/checkout@v4
+      - name: Install uv
+        uses: astral-sh/setup-uv@v6
+      - name: Install the project
+        run: uv sync --locked --dev --extra mcp
+      - name: Install pocl
+        run: uv pip install pocl-binary-distribution==3.0
+      - name: Cache downloaded test data
+        uses: actions/cache@v4
+        with:
+            path: ~/.cache/protein-quest-tests
+            key: cached-protein-quest-tests
+      - name: Run tests
+        run: |
+          uv run pytest --cov --cov-report=xml
+      - name: Run codacy-coverage-reporter
+        uses: codacy/codacy-coverage-reporter-action@v1.3.0
+        with:
+          project-token: ${{ secrets.CODACY_PROJECT_TOKEN }}
+          coverage-reports: coverage.xml
+
+  build:
+    name: build
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+      - name: Install uv
+        uses: astral-sh/setup-uv@v6
+      - name: Build the project
+        run: uv build
+  lint:
+    name: lint
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+      - name: Install uv
+        uses: astral-sh/setup-uv@v6
+      - name: Run linters
+        run: uvx ruff check
+  typing:
+    name: typing
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+      - name: Install uv
+        uses: astral-sh/setup-uv@v6
+      - name: Install the project
+        run: uv sync --locked --dev --extra mcp
+      - name: Run type checkers
+        run: uv run pyrefly check src tests
+  typing-docs:
+    name: typing-docs
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+      - name: Install uv
+        uses: astral-sh/setup-uv@v6
+      - name: Install the project
+        run: uv sync --group docs-type
+      - name: Convert notebooks to Python scripts
+        run: |
+          find docs/ -name "*.ipynb" -exec uv run --group docs-type marimo convert {} -o {}.py \;
+      - name: Run type checkers on docs
+        run: uv run --group docs-type pyrefly check docs/notebooks/*.ipynb.py
+

protein_quest-0.10.0/.github/workflows/pages.yml

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+name: Deploy MkDocs to GitHub Pages
+
+on:
+  push:
+    branches:
+      - main
+  workflow_dispatch:
+  pull_request:
+
+permissions:
+  contents: read
+  pages: write
+  id-token: write
+
+# Only have one deployment in progress at a time
+concurrency:
+  group: pages
+  cancel-in-progress: true
+
+jobs:
+  build:
+    runs-on: ubuntu-latest
+    steps:
+      - name: Checkout
+        uses: actions/checkout@v4
+        
+      - name: Install uv
+        uses: astral-sh/setup-uv@v6
+        
+      - name: Install dependencies
+        run: uv sync --locked --group docs
+        
+      - name: Build MkDocs site
+        run: |
+          uv run mkdocs build
+        env:
+          # Force colored output from rich library
+          TTY_COMPATIBLE: '1'
+          TTY_INTERACTIVE: '0'
+
+      - name: Upload artifact
+        uses: actions/upload-pages-artifact@v3
+        with:
+          path: site
+
+  deploy:
+    # Add a dependency to the build job
+    needs: build
+
+    # Only deploy on pushes to main or manual trigger of main branch
+    if: github.ref == 'refs/heads/main'
+
+    # Grant GITHUB_TOKEN the permissions required to make a Pages deployment
+    permissions:
+      pages: write      # to deploy to Pages
+      id-token: write   # to verify the deployment originates from an appropriate source
+
+    # Deploy to the github-pages environment
+    environment:
+      name: github-pages
+      url: ${{ steps.deployment.outputs.page_url }}
+
+    # Specify runner + deployment step
+    runs-on: ubuntu-latest
+    steps:          
+      - name: Deploy to GitHub Pages
+        id: deployment
+        uses: actions/deploy-pages@v4

protein_quest-0.10.0/.github/workflows/pypi-publish.yml

@@ -0,0 +1,26 @@
+name: Publish to PyPI
+
+on:
+  release:
+    types: [published]
+
+jobs:
+  publish:
+    name: Build and Publish to PyPI
+    runs-on: ubuntu-latest
+    environment:
+      name: pypi
+      url: https://pypi.org/p/protein-quest
+    permissions:
+      id-token: write  # IMPORTANT: mandatory for trusted publishing
+    steps:
+      - uses: actions/checkout@v4
+      
+      - name: Install uv
+        uses: astral-sh/setup-uv@v6
+      
+      - name: Build package
+        run: uv build
+      
+      - name: Publish to PyPI
+        uses: pypa/gh-action-pypi-publish@release/v1

protein_quest-0.10.0/.gitignore

@@ -0,0 +1,89 @@
+# Byte-compiled / optimized / DLL files
+*.py[cod]
+*$py.class
+__pycache__
+
+# Distribution / packaging
+.Python
+build/
+develop-eggs/
+dist/
+downloads/
+eggs/
+.eggs/
+lib/
+lib64/
+parts/
+sdist/
+var/
+wheels/
+share/python-wheels/
+*.egg-info/
+.installed.cfg
+*.egg
+
+# jupyter notebook
+.ipynb_checkpoints
+
+# Unit test / coverage reports
+htmlcov/
+.coverage
+.coverage.*
+coverage.xml
+.cache
+.pytest_cache
+.tox/
+
+# Sphinx documentation
+docs/_build
+
+# ide
+# 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/
+.spyderproject
+.spyproject
+
+# Mac
+.DS_Store
+
+# virtual environments
+env
+.env
+env3
+.env3
+venv
+.venv
+venv3
+.venv3
+ENV/
+env.bak/
+venv.bak/
+
+# vim
+*.swp
+*.swo
+*.orig
+
+/docs/session1/
+/docs/alphafold_files/
+/docs/pdb_files/
+/docs/density_filtered/
+/site
+/mysession/
+# Paths generated in README.md examples
+uniprot_accs.txt
+pdbe.csv
+alphafold.csv
+emdbs.csv
+interaction-partners-of-Q05471.txt
+complexes.csv
+downloads-af/
+downloads-emdb/
+downloads-pdbe/
+filtered/
+filtered-chains/
+filtered-ss/

protein_quest-0.10.0/.python-version

@@ -0,0 +1 @@
+3.13

protein_quest-0.10.0/.vscode/extensions.json

@@ -0,0 +1,8 @@
+{
+    "recommendations": [
+        "ms-toolsai.jupyter",
+        "ms-python.vscode-pylance",
+        "ms-python.python",
+        "charliermarsh.ruff"
+    ]
+}

protein_quest-0.10.0/CITATION.cff

@@ -0,0 +1,26 @@
+# YAML 1.2
+---
+cff-version: 1.2.0
+title: protein quest
+message: >-
+  If you use this software, please cite it using the
+  metadata from this file.
+type: software
+authors:
+  - affiliation: "Netherlands eScience Center"
+    family-names: Verhoeven
+    given-names: Stefan
+    orcid: "https://orcid.org/0000-0002-5821-2060"
+  - given-names: Anna
+    family-names: Engel
+    affiliation: '@UtrechtUniversity'
+    orcid: "https://orcid.org/0009-0002-1806-7951"
+  - given-names: Alexandre
+    family-names: Bonvin
+    affiliation: '@UtrechtUniversity'    
+    orcid: "https://orcid.org/0000-0001-7369-1322"
+repository-code: https://github.com/haddocking/protein-quest
+identifiers:
+  - description: Latest version of software
+    type: doi
+    value: 10.5281/zenodo.16941288

protein_quest-0.10.0/CODE_OF_CONDUCT.md

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+# Contributor Covenant Code of Conduct
+
+## Our Pledge
+
+We as members, contributors, and leaders pledge to make participation in our
+community a harassment-free experience for everyone, regardless of age, body
+size, visible or invisible disability, ethnicity, sex characteristics, gender
+identity and expression, level of experience, education, socio-economic status,
+nationality, personal appearance, race, religion, or sexual identity
+and orientation.
+
+We pledge to act and interact in ways that contribute to an open, welcoming,
+diverse, inclusive, and healthy community.
+
+## Our Standards
+
+Examples of behavior that contributes to a positive environment for our
+community include:
+
+* Demonstrating empathy and kindness toward other people
+* Being respectful of differing opinions, viewpoints, and experiences
+* Giving and gracefully accepting constructive feedback
+* Accepting responsibility and apologizing to those affected by our mistakes,
+  and learning from the experience
+* Focusing on what is best not just for us as individuals, but for the
+  overall community
+
+Examples of unacceptable behavior include:
+
+* The use of sexualized language or imagery, and sexual attention or
+  advances of any kind
+* Trolling, insulting or derogatory comments, and personal or political attacks
+* Public or private harassment
+* Publishing others' private information, such as a physical or email
+  address, without their explicit permission
+* Other conduct which could reasonably be considered inappropriate in a
+  professional setting
+
+## Enforcement Responsibilities
+
+Community leaders are responsible for clarifying and enforcing our standards of
+acceptable behavior and will take appropriate and fair corrective action in
+response to any behavior that they deem inappropriate, threatening, offensive,
+or harmful.
+
+Community leaders have the right and responsibility to remove, edit, or reject
+comments, commits, code, wiki edits, issues, and other contributions that are
+not aligned to this Code of Conduct, and will communicate reasons for moderation
+decisions when appropriate.
+
+## Scope
+
+This Code of Conduct applies within all community spaces, and also applies when
+an individual is officially representing the community in public spaces.
+Examples of representing our community include using an official e-mail address,
+posting via an official social media account, or acting as an appointed
+representative at an online or offline event.
+
+## Enforcement
+
+Instances of abusive, harassing, or otherwise unacceptable behavior may be
+reported to the community leaders responsible for enforcement at
+s.verhoeven@esciencecenter.nl.
+All complaints will be reviewed and investigated promptly and fairly.
+
+All community leaders are obligated to respect the privacy and security of the
+reporter of any incident.
+
+## Enforcement Guidelines
+
+Community leaders will follow these Community Impact Guidelines in determining
+the consequences for any action they deem in violation of this Code of Conduct:
+
+### 1. Correction
+
+**Community Impact**: Use of inappropriate language or other behavior deemed
+unprofessional or unwelcome in the community.
+
+**Consequence**: A private, written warning from community leaders, providing
+clarity around the nature of the violation and an explanation of why the
+behavior was inappropriate. A public apology may be requested.
+
+### 2. Warning
+
+**Community Impact**: A violation through a single incident or series
+of actions.
+
+**Consequence**: A warning with consequences for continued behavior. No
+interaction with the people involved, including unsolicited interaction with
+those enforcing the Code of Conduct, for a specified period of time. This
+includes avoiding interactions in community spaces as well as external channels
+like social media. Violating these terms may lead to a temporary or
+permanent ban.
+
+### 3. Temporary Ban
+
+**Community Impact**: A serious violation of community standards, including
+sustained inappropriate behavior.
+
+**Consequence**: A temporary ban from any sort of interaction or public
+communication with the community for a specified period of time. No public or
+private interaction with the people involved, including unsolicited interaction
+with those enforcing the Code of Conduct, is allowed during this period.
+Violating these terms may lead to a permanent ban.
+
+### 4. Permanent Ban
+
+**Community Impact**: Demonstrating a pattern of violation of community
+standards, including sustained inappropriate behavior,  harassment of an
+individual, or aggression toward or disparagement of classes of individuals.
+
+**Consequence**: A permanent ban from any sort of public interaction within
+the community.
+
+## Attribution
+
+This Code of Conduct is adapted from the [Contributor Covenant][homepage],
+version 2.0, available at
+https://www.contributor-covenant.org/version/2/0/code_of_conduct.html.
+
+Community Impact Guidelines were inspired by [Mozilla's code of conduct
+enforcement ladder](https://github.com/mozilla/diversity).
+
+[homepage]: https://www.contributor-covenant.org
+
+For answers to common questions about this code of conduct, see the FAQ at
+https://www.contributor-covenant.org/faq. Translations are available at
+https://www.contributor-covenant.org/translations.

protein_quest-0.10.0/CONTRIBUTING.md

@@ -0,0 +1,108 @@
+# Contributing guidelines
+
+We welcome any kind of contribution to our software, from simple comment or question to a full fledged [pull request](https://help.github.com/articles/about-pull-requests/). Please read and follow our [Code of Conduct](CODE_OF_CONDUCT.md).
+
+A contribution can be one of the following cases:
+
+1. you have a question;
+1. you think you may have found a bug (including unexpected behavior);
+1. you want to make some kind of change to the code base (e.g. to fix a bug, to add a new feature, to update documentation);
+1. you want to make a new release of the code base.
+
+The sections below outline the steps in each case.
+
+## You have a question
+
+1. use the search functionality [here](https://github.com/haddocking/protein-quest/issues) to see if someone already filed the same issue;
+2. if your issue search did not yield any relevant results, make a new issue;
+3. apply the "Question" label; apply other labels when relevant.
+
+## You think you may have found a bug
+
+1. use the search functionality [here](https://github.com/haddocking/protein-quest/issues) to see if someone already filed the same issue;
+1. if your issue search did not yield any relevant results, make a new issue, making sure to provide enough information to the rest of the community to understand the cause and context of the problem. Depending on the issue, you may want to include:
+    - the [SHA hashcode](https://help.github.com/articles/autolinked-references-and-urls/#commit-shas) of the commit that is causing your problem;
+    - some identifying information (name and version number) for dependencies you're using;
+    - information about the operating system;
+1. apply relevant labels to the newly created issue.
+
+## You want to make some kind of change to the code base
+
+1. (**important**) announce your plan to the rest of the community *before you start working*. This announcement should be in the form of a (new) issue;
+1. (**important**) wait until some kind of consensus is reached about your idea being a good idea;
+1. if needed, fork the repository to your own Github profile and create your own feature branch off of the latest main commit. While working on your feature branch, make sure to stay up to date with the main branch by pulling in changes, possibly from the 'upstream' repository (follow the instructions [here](https://help.github.com/articles/configuring-a-remote-for-a-fork/) and [here](https://help.github.com/articles/syncing-a-fork/));
+1. install [uv](https://docs.astral.sh/uv) to manage this packages development environment);
+1. Make sure `uv sync --all-extras --all-groups && . .venv/bin/activate && protein-quest --help` works;
+1. make sure the existing tests still work by running `uv run pytest`;
+1. add your own tests (if necessary);
+1. format your code with `uvx ruff format` and sort imports with `uvx ruff check --select I --fix`;
+1. lint your code with `uvx ruff check` (use `uvx ruff check --fix` to fix issues automatically);
+1. type check your code with `uv run pyrefly check src tests`;
+1. update or expand the documentation (see [Contributing with documentation](#contributing-with-documentation) section below);
+1. [push](http://rogerdudler.github.io/git-guide/) your feature branch to (your fork of) the protein-quest repository on GitHub;
+1. create the pull request, e.g. following the instructions [here](https://help.github.com/articles/creating-a-pull-request/).
+
+In case you feel like you've made a valuable contribution, but you don't know how to write or run tests for it, or how to generate the documentation: don't let this discourage you from making the pull request; we can help you! Just go ahead and submit the pull request, but keep in mind that you might be asked to append additional commits to your pull request.
+
+## You want to make a new release of the code base
+
+To create a release you need write permission on the repository.
+
+1. Bump the version in [src/protein_quest/__version__.py](src/protein_quest/__version__.py).
+2. Check the author list in [`CITATION.cff`](CITATION.cff)
+3. Go to the [GitHub release page](https://github.com/haddocking/protein-quest/releases)
+4. Press draft a new release button
+5. Fill tag, title and description field. For tag use version from `src/protein_quest/__version__.py` and prepend with "v" character. For description use "Python package to search/retrieve/filter proteins and protein structures." line plus press "Generate release notes" button.
+6. Press the Publish Release button
+7. Wait until [Build and upload to PyPI](https://github.com/haddocking/protein-quest/actions/workflows/pypi-publish.yml) has completed
+8. Verify new release is on [PyPi](https://pypi.org/project/protein-quest/#history)
+9. Verify new Zenodo record has been created.
+
+## Contributing to documentation
+
+To work on notebooks in the docs/ directory:
+
+```shell
+uv sync --group docs
+# Open a notebook with VS code and select .venv/bin/python as kernel
+```
+
+Start the live-reloading docs server with:
+
+```shell
+uv run mkdocs serve
+```
+
+Build the documentation site with:
+
+```shell
+uv run mkdocs build
+# The site will be built in the `site/` directory.
+# You can preview it with
+python3 -m http.server -d site
+```
+
+<details>
+<summary>Type checking notebooks</summary>
+
+[Pyrefly](https://pyrefly.org/) does not support notebooks yet, so we need to convert them to python scripts and then run pyrefly on them.
+
+```shell
+find docs/ -name "*.ipynb" -exec uv run --group docs-type marimo convert {} -o {}.py \;
+uv run --group docs-type pyrefly check docs/notebooks/*.ipynb.py
+rm docs/notebooks/*.ipynb.py
+```
+
+</details>
+
+
+## Contributing to tests
+
+The code coverage is stored at [https://app.codacy.com/gh/haddocking/protein-quest/coverage](https://app.codacy.com/gh/haddocking/protein-quest/coverage) .
+
+The search functions of the protein-quest package talk to web services on the Internet.
+To have fast tests we use [pytest-recording](https://github.com/kiwicom/pytest-recording) to record and replay HTTP interactions.
+See [pytest-recording documentation](https://github.com/kiwicom/pytest-recording) for more details on how to use it.
+Like overwrite previous recordings in test/cassettes/**.yaml files with `--record-mode=rewrite`.
+
+The files downloaded for tests are cached in `~/.cache/protein-quest-tests`.