protein-quest 1.0.0__tar.gz → 1.1.0__tar.gz

{protein_quest-1.0.0 → protein_quest-1.1.0}/.github/workflows/ci.yml

@@ -17,9 +17,9 @@ jobs:
     permissions:
       id-token: write
     steps:
-      - uses: actions/checkout@v4
+      - uses: actions/checkout@v6
       - name: Install uv
-        uses: astral-sh/setup-uv@v6
+        uses: astral-sh/setup-uv@v7
       - name: Install the project
         run: uv sync --locked --dev --extra mcp
       - name: Install pocl
@@ -27,8 +27,8 @@ jobs:
       - name: Cache downloaded test data
         uses: actions/cache@v4
         with:
-            path: ~/.cache/protein-quest-tests
-            key: cached-protein-quest-tests
+          path: ~/.cache/protein-quest-tests
+          key: cached-protein-quest-tests
       - name: Run tests
         run: |
           uv run pytest --cov --cov-report=xml
@@ -42,27 +42,27 @@ jobs:
     name: build
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v4
+      - uses: actions/checkout@v6
       - name: Install uv
-        uses: astral-sh/setup-uv@v6
+        uses: astral-sh/setup-uv@v7
       - name: Build the project
         run: uv build
   lint:
     name: lint
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v4
+      - uses: actions/checkout@v6
       - name: Install uv
-        uses: astral-sh/setup-uv@v6
+        uses: astral-sh/setup-uv@v7
       - name: Run linters
         run: uvx ruff check
   typing:
     name: typing
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v4
+      - uses: actions/checkout@v6
       - name: Install uv
-        uses: astral-sh/setup-uv@v6
+        uses: astral-sh/setup-uv@v7
       - name: Install the project
         run: uv sync --locked --dev --extra mcp
       - name: Run type checkers
@@ -71,9 +71,9 @@ jobs:
     name: typing-docs
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v4
+      - uses: actions/checkout@v6
       - name: Install uv
-        uses: astral-sh/setup-uv@v6
+        uses: astral-sh/setup-uv@v7
       - name: Install the project
         run: uv sync --group docs-type
       - name: Convert notebooks to Python scripts
@@ -81,13 +81,12 @@ jobs:
           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
-  duplicated-code:
+  pre-commit:
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v4
-      - name: Install NodeJS
+      - uses: actions/checkout@v6
+      - name: Install nodejs
         uses: actions/setup-node@v6
         with:
-          node-version: '24'
-      - name: Run jscpd to detect duplicated code
-        run: npx jscpd src
+          node-version: "24"
+      - uses: j178/prek-action@v1

{protein_quest-1.0.0 → protein_quest-1.1.0}/.github/workflows/pages.yml

@@ -23,20 +23,20 @@ jobs:
     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'
+          TTY_COMPATIBLE: "1"
+          TTY_INTERACTIVE: "0"
 
       - name: Upload artifact
         uses: actions/upload-pages-artifact@v3
@@ -52,8 +52,8 @@ jobs:
 
     # 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
+      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:
@@ -62,7 +62,7 @@ jobs:
 
     # Specify runner + deployment step
     runs-on: ubuntu-latest
-    steps:          
+    steps:
       - name: Deploy to GitHub Pages
         id: deployment
         uses: actions/deploy-pages@v4

{protein_quest-1.0.0 → protein_quest-1.1.0}/.github/workflows/pypi-publish.yml

@@ -12,15 +12,15 @@ jobs:
       name: pypi
       url: https://pypi.org/p/protein-quest
     permissions:
-      id-token: write  # IMPORTANT: mandatory for trusted publishing
+      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-1.0.0 → protein_quest-1.1.0}/.howfairis.yml

@@ -1 +1 @@
-skip_checklist_checks_reason: "I'm using the fairsoftwarechecklist"
+skip_checklist_checks_reason: "I'm using the fairsoftwarechecklist"

protein_quest-1.1.0/.markdownlint-cli2.yaml

@@ -0,0 +1,16 @@
+# markdownlint-cli2 configuration file
+# See https://github.com/DavidAnson/markdownlint-cli2 for documentation
+
+# Disable rules that conflict with Prettier formatting
+config:
+  no-trailing-spaces: false
+  no-hard-tabs: false
+  no-multiple-blanks: false
+  line-length: false
+  blanks-around-headings: false
+  list-marker-space: false
+  blanks-around-fences: false
+  blanks-around-lists: false
+  no-inline-html: false
+  single-trailing-newline: false
+  descriptive-link-text: false

protein_quest-1.1.0/.pre-commit-config.yaml

@@ -0,0 +1,87 @@
+# Keeping pytest and pyrefly out of pre-commit as they need full venv.
+# To run needs docker and nodejs installed.
+
+# Do not check or fix downloaded files
+exclude: ^tests/.*(\.yaml|\.pdb)$
+
+repos:
+  - repo: https://github.com/adamchainz/blacken-docs
+    rev: "1.20.0"
+    hooks:
+      - id: blacken-docs
+        additional_dependencies: [black==25.*]
+
+  - repo: https://github.com/pre-commit/pre-commit-hooks
+    rev: "v6.0.0"
+    hooks:
+      - id: check-added-large-files
+      - id: check-case-conflict
+      - id: check-merge-conflict
+      - id: check-symlinks
+      - id: check-yaml
+      - id: debug-statements
+      - id: end-of-file-fixer
+      - id: mixed-line-ending
+      - id: name-tests-test
+        args: ["--pytest-test-first"]
+      - id: requirements-txt-fixer
+      - id: trailing-whitespace
+
+  - repo: https://github.com/pre-commit/pygrep-hooks
+    rev: "v1.10.0"
+    hooks:
+      - id: rst-backticks
+      - id: rst-directive-colons
+      - id: rst-inline-touching-normal
+
+  - repo: https://github.com/rbubley/mirrors-prettier
+    rev: "v3.7.4"
+    hooks:
+      - id: prettier
+        types_or: [yaml, markdown, html, css, scss, javascript, json]
+        args: [--prose-wrap=always]
+
+  - repo: https://github.com/astral-sh/ruff-pre-commit
+    rev: "v0.14.10"
+    hooks:
+      - id: ruff-check
+        args: ["--fix", "--show-fixes"]
+      - id: ruff-format
+
+  - repo: https://github.com/codespell-project/codespell
+    rev: "v2.4.1"
+    hooks:
+      - id: codespell
+        additional_dependencies:
+          - tomli; python_version<'3.11'
+
+  - repo: https://github.com/shellcheck-py/shellcheck-py
+    rev: "v0.11.0.1"
+    hooks:
+      - id: shellcheck
+
+  - repo: https://github.com/python-jsonschema/check-jsonschema
+    rev: "0.36.0"
+    hooks:
+      - id: check-github-workflows
+      - id: check-citation-file-format
+      # Not checking mkdocs.yml as hook does not support custom YAML tags like !!python/....
+      # see https://github.com/python-jsonschema/check-jsonschema/issues/489
+      # mkdocs schema exists at https://www.schemastore.org/mkdocs-1.6.json
+
+  # Tried to use official jscpd repo, but got jscpd not found error
+  - repo: local
+    hooks:
+      - id: jscpd
+        name: jscpd code duplication checker
+        entry: npx jscpd
+        language: node
+        args: ["--gitignore", "--exitCode=1", "src"]
+        types: [text]
+        pass_filenames: false
+
+  - repo: https://github.com/DavidAnson/markdownlint-cli2
+    rev: v0.20.0
+    hooks:
+      - id: markdownlint-cli2
+        args: ["--fix"]

protein_quest-1.1.0/.vscode/extensions.json

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

{protein_quest-1.0.0 → protein_quest-1.1.0}/CITATION.cff

@@ -17,7 +17,7 @@ authors:
     orcid: "https://orcid.org/0009-0002-1806-7951"
   - given-names: Alexandre
     family-names: Bonvin
-    affiliation: '@UtrechtUniversity'    
+    affiliation: '@UtrechtUniversity'
     orcid: "https://orcid.org/0000-0001-7369-1322"
 repository-code: https://github.com/haddocking/protein-quest
 identifiers:

{protein_quest-1.0.0 → protein_quest-1.1.0}/CODE_OF_CONDUCT.md

@@ -6,8 +6,8 @@ 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.
+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.
@@ -17,23 +17,23 @@ diverse, inclusive, and healthy community.
 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,
+- 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
+- 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
+- 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
@@ -60,8 +60,8 @@ representative at an online or offline event.
 
 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.
+<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.
@@ -82,15 +82,15 @@ behavior was inappropriate. A public apology may be requested.
 
 ### 2. Warning
 
-**Community Impact**: A violation through a single incident or series
-of actions.
+**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.
+like social media. Violating these terms may lead to a temporary or permanent
+ban.
 
 ### 3. Temporary Ban
 
@@ -106,23 +106,23 @@ 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
+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.
+**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.
+<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).
+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.
+<https://www.contributor-covenant.org/faq>. Translations are available at
+<https://www.contributor-covenant.org/translations>.

protein_quest-1.1.0/CONTRIBUTING.md

@@ -0,0 +1,185 @@
+# 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. apply more formatting and linting with `uvx prek run --all-files`;
+1. update or expand the documentation (see
+   [Contributing to documentation](#contributing-to-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`.
+
+## Automated code quality checks on git commit
+
+This step is **optional** but recommended for developers who want to
+automatically check code quality before committing.
+
+We use [prek](https://github.com/j178/prek) to run pre-commit hooks. If you want
+to set up automated checks:
+
+1. Install prek if you haven't already:
+
+   ```shell
+   uv tool install prek
+   ```
+
+1. Install git hooks:
+
+   ```shell
+   prek install
+   ```
+
+1. Now every `git commit` will automatically run `prek run` on the files you're
+   committing. The hooks will check for common issues like trailing whitespace,
+   file endings, and run all configured linters.
+
+1. If you ever want to disable the hooks, run:
+   ```shell
+   prek uninstall
+   ```