pid4cat-model 0.3.0__tar.gz

pid4cat_model-0.3.0/.copier-answers.yml

@@ -0,0 +1,15 @@
+# Changes here will be overwritten by Copier
+_commit: v0.4.0
+_src_path: gh:dalito/linkml-project-copier
+add_example: false
+copyright_year: '2023'
+email: david.linke@catalysis.de
+full_name: David Linke
+gh_action_docs_preview: false
+gh_action_pypi: true
+github_org: nfdi4cat
+license: MIT
+project_description: LinkML model for handle-based PIDs for resources in catalysis
+    (pid4cat)
+project_name: pid4cat-model
+project_slug: pid4cat_model

pid4cat_model-0.3.0/.editorconfig

@@ -0,0 +1,18 @@
+# Check http://editorconfig.org for more information
+# This is the main config file for this project:
+root = true
+
+[*]
+charset = utf-8
+end_of_line = lf
+insert_final_newline = true
+indent_style = space
+indent_size = 2
+trim_trailing_whitespace = true
+
+[*.py]
+indent_style = space
+indent_size = 4
+
+[*.md]
+trim_trailing_whitespace = false

pid4cat_model-0.3.0/.github/dependabot.yml

@@ -0,0 +1,9 @@
+# Please see the documentation for all configuration options:
+# https://docs.github.com/github/administering-a-repository/configuration-options-for-dependency-updates
+
+version: 2
+updates:
+  - package-ecosystem: github-actions
+    directory: "/"
+    schedule:
+      interval: monthly

pid4cat_model-0.3.0/.github/workflows/deploy-docs.yaml

@@ -0,0 +1,86 @@
+---
+name: Deploy docs
+on:  # yamllint disable-line rule:truthy
+  push:
+    tags:
+      - 'v[0-9]+.[0-9]+.[0-9]+'
+      - 'v[0-9]+.[0-9]+.[0-9]+rc[0-9]'
+    branches:
+      - main
+  pull_request:
+    branches:
+      - main
+  workflow_dispatch:
+
+permissions: {}
+
+jobs:
+  build-docs:
+    runs-on: ubuntu-latest
+
+    # Grant GITHUB_TOKEN the permissions required to make a gh-pages deployment
+    permissions:
+      contents: write  # to let mkdocs write the new docs
+      pages: write     # to deploy to Pages
+      id-token: write  # allow to generate an OpenID Connect (OIDC) token
+
+    steps:
+      - name: Checkout
+        uses: actions/checkout@11bd71901bbe5b1630ceea73d27597364c9af683
+        with:
+          fetch-depth: 0  # otherwise, you will fail to push refs to dest repo
+
+      - name: Configure git for the bot
+        # Gives the bot that commits to gh-pages a name & email address
+        # so that the commits have an author in the commit log.
+        run: |
+          git config user.name github-actions[bot]
+          git config user.email github-actions[bot]@users.noreply.github.com
+
+      - name: Install uv
+        uses: astral-sh/setup-uv@0c5e2b8115b80b4c7c5ddf6ffdd634974642d182
+        with:
+          python-version: 3.12
+          enable-cache: true
+          cache-dependency-glob: "uv.lock"
+
+      - name: Set up Python
+        uses: actions/setup-python@8d9ed9ac5c53483de85588cdf95a591a75ab9f55
+        with:
+          python-version: 3.12
+
+      - name: Install just
+        run: |
+          uv tool install rust-just
+
+      - name: Install dependencies
+        run: uv sync --dev --no-progress
+
+      - name: Generate schema documentation
+        run: |
+          # TODO Check if version is injected into the schema.
+          just gen-doc
+
+      # The if-conditions below make sure to select the right step, depending
+      # on the job trigger. Only one of the steps below will run at a time.
+      # The others will be skipped.
+
+      - name: Check docs in pull requests with strict mode
+        if: github.event_name == 'pull_request'
+        run: |
+          # XXX Enable strict mode once docs are clean
+          echo "Strict check of docs disabled."
+          # uv run mkdocs build --strict
+
+      # yamllint disable rule:line-length
+      - name: Build & deploy "dev" docs for a new commit to master
+        if: github.event_name == 'push' && github.ref_type != 'tag'
+        run: |
+          export SHORT_SHA=$(echo "${GITHUB_SHA}" | cut -c1-7)
+          uv run mike deploy --push --update-aliases --title "dev (${SHORT_SHA})" dev
+
+      - name: Build & deploy docs for a new version tag
+        if: github.ref_type == 'tag' && github.event_name == 'push'
+        run: |
+          uv run mike deploy --push --update-aliases ${{ github.ref_name }} latest
+          uv run mike set-default latest --push

pid4cat_model-0.3.0/.github/workflows/main.yaml

@@ -0,0 +1,55 @@
+# Built from:
+# https://docs.github.com/en/actions/guides/building-and-testing-python
+---
+name: Build and test
+
+on:  # yamllint disable-line rule:truthy
+  push:
+    branches: [main]
+  pull_request:
+
+env:
+  FORCE_COLOR: "1" # Make tools pretty.
+
+permissions: {}
+
+jobs:
+  test:
+
+    runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        # re-enable when linkml-runtime is realesed with
+        #   https://github.com/linkml/linkml-runtime/pull/357
+        # python-version: ["3.9", "3.10", "3.11", "3.12"]
+        python-version: ["3.11", "3.12"]
+      fail-fast: false
+
+    steps:
+
+      - name: Check out repository
+        uses: actions/checkout@11bd71901bbe5b1630ceea73d27597364c9af683
+        with:
+          persist-credentials: false
+
+      - name: Install uv
+        uses: astral-sh/setup-uv@0c5e2b8115b80b4c7c5ddf6ffdd634974642d182
+        with:
+          python-version: ${{ matrix.python-version }}
+          enable-cache: true
+          cache-dependency-glob: "uv.lock"
+
+      - name: Set up Python ${{ matrix.python-version }}
+        uses: actions/setup-python@8d9ed9ac5c53483de85588cdf95a591a75ab9f55
+        with:
+          python-version: ${{ matrix.python-version }}
+
+      - name: Install just
+        run: |
+          uv tool install rust-just
+
+      - name: Install project
+        run: uv sync --dev
+
+      - name: Run test suite
+        run: just test

pid4cat_model-0.3.0/.github/workflows/pypi-publish.yaml

@@ -0,0 +1,94 @@
+---
+name: Publish Python Package
+
+# Publishes with trusted publishing to
+# - PyPI on releases created in GitHub UI if status is published.
+#   For draft status, nothing happens.
+# - TestPyPI on new tags "v1.2.3" or "v1.2.3.something" on main branch
+#
+# More on trusted publishing: https://docs.pypi.org/trusted-publishers/
+
+on:  # yamllint disable-line rule:truthy
+  push:
+    tags:
+      # GitHub glob matching is limited [1]. So we can't define a pattern matching
+      # pep 440 version definition [N!]N(.N)*[{a|b|rc}N][.postN][.devN]
+      - 'v[0-9]+.[0-9]+.[0-9]+.?*'
+      - 'v[0-9]+.[0-9]+.[0-9]+rc[0-9]'
+  release:
+    types: [published]
+
+permissions: {}
+
+jobs:
+  build:
+    name: Build Python 🐍 distributions 📦 for publishing
+    runs-on: ubuntu-latest
+
+    steps:
+      - name: Check out repository
+        uses: actions/checkout@11bd71901bbe5b1630ceea73d27597364c9af683
+        with:
+          persist-credentials: false
+
+      - name: Install uv
+        uses: astral-sh/setup-uv@0c5e2b8115b80b4c7c5ddf6ffdd634974642d182
+        with:
+          python-version: 3.12
+          enable-cache: true
+
+      - name: Set up Python
+        uses: actions/setup-python@8d9ed9ac5c53483de85588cdf95a591a75ab9f55
+        with:
+          python-version: 3.12
+
+      - name: Install just
+        run: |
+          uv tool install rust-just
+
+      - name: Build source and wheel archives
+        run: uv build
+
+      - name: Store built distribution
+        uses: actions/upload-artifact@ea165f8d65b6e75b540449e92b4886f43607fa02
+        with:
+          name: distribution-files
+          path: dist/
+
+  pypi-publish:
+    name: Build and publish Python 🐍 package 📦 to PyPI and TestPyPI
+    needs: build
+    runs-on: ubuntu-latest
+    environment:
+      name: pypi-release
+      url: https://pypi.org/p/pid4cat_model
+    permissions:
+      id-token: write  # this permission is mandatory for trusted publishing
+    steps:
+      - name: Download built distribution
+        uses: actions/download-artifact@95815c38cf2ff2164869cbab79da8d1f422bc89e
+        with:
+          name: distribution-files
+          path: dist
+
+      - name: Publish package 📦 to Test PyPI
+        if: github.event_name == 'push'
+        uses: pypa/gh-action-pypi-publish@76f52bc884231f62b9a034ebfe128415bbaabdfc
+        with:
+          repository-url: https://test.pypi.org/legacy/
+          verbose: true
+
+      - name: Publish package 📦 to PyPI
+        if: github.event_name == 'release'
+        uses: pypa/gh-action-pypi-publish@76f52bc884231f62b9a034ebfe128415bbaabdfc
+        with:
+          verbose: true
+
+# [1] https://docs.github.com/en/actions/using-workflows/workflow-syntax-for-github-actions#filter-pattern-cheat-sheet
+# Used actions: (updates managed by dependabot)
+# - https://github.com/actions/checkout
+# - https://github.com/astral-sh/setup-uv
+# - https://github.com/actions/setup-python
+# - https://github.com/actions/upload-artifact
+# - https://github.com/actions/download-artifact
+# - https://github.com/pypa/gh-action-pypi-publish/

pid4cat_model-0.3.0/.gitignore

@@ -0,0 +1,151 @@
+docs/local-js-pkgs
+
+# generated part of documentation
+docs/elements/*.md
+
+# generated merged schema
+docs/schema/*
+!docs/schema/README.md
+
+# linkml-run-examples output (not useful to have in git in its current form)
+examples/output/
+
+# Derived schemas, generated from the schema.yaml
+tmp/
+project/
+!project/README.md
+
+# 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/
+pip-wheel-metadata/
+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/
+
+# 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
+target/
+
+# Jupyter Notebook
+.ipynb_checkpoints
+
+# IPython
+profile_default/
+ipython_config.py
+
+# pyenv
+.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
+
+# PEP 582; used by e.g. github.com/David-OConnor/pyflow
+__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/
+
+# pycharm
+.idea/
+# Local vscode editor config
+.vscode/

pid4cat_model-0.3.0/.linkmllint.yaml

@@ -0,0 +1,11 @@
+# Use the recommended rule set except for the standard_naming rule
+extends: recommended
+
+rules:
+  standard_naming:
+    level: disabled
+    # permissible_values_upper_case: true
+    # class_pattern: snake_case
+  canonical_prefixes:
+    # Superfluous warnings for https-refixes, https://github.com/linkml/linkml/issues/2492
+    level: disabled

pid4cat_model-0.3.0/.pre-commit-config.yaml

@@ -0,0 +1,45 @@
+---
+# https://pre-commit.com/
+repos:
+  - repo: https://github.com/pre-commit/pre-commit-hooks
+    rev: v5.0.0
+    hooks:
+      - id: check-toml
+      - id: check-yaml
+      - id: end-of-file-fixer
+      - id: trailing-whitespace
+        args: [--markdown-linebreak-ext=md]
+
+  - repo: https://github.com/adrienverge/yamllint.git
+    rev: v1.37.0
+    hooks:
+      - id: yamllint
+        args: [-c=.yamllint.yaml]
+
+  - repo: https://github.com/codespell-project/codespell
+    rev: v2.4.1
+    hooks:
+      - id: codespell
+        additional_dependencies:
+          - tomli
+
+  - repo: https://github.com/crate-ci/typos
+    rev: v1.31.1
+    hooks:
+      - id: typos
+
+  - repo: https://github.com/astral-sh/ruff-pre-commit
+    # Ruff version.
+    rev: v0.11.3
+    hooks:
+      # Run the linter.
+      - id: ruff
+        args: [--fix, --exit-non-zero-on-fix]
+      # Run the formatter.
+      - id: ruff-format
+
+  - repo: https://github.com/astral-sh/uv-pre-commit
+    # uv version.
+    rev: 0.6.12
+    hooks:
+      - id: uv-lock

pid4cat_model-0.3.0/.yamllint.yaml

@@ -0,0 +1,12 @@
+# Configuration for https://github.com/adrienverge/yamllint
+
+extends: default
+
+rules:
+  document-start: disable  # Don't check if document has a start marker (---).
+  line-length:
+    max: 80
+    level: warning
+    allow-non-breakable-words: true
+    allow-non-breakable-inline-mappings: true
+  new-lines: disable  # Don't check for type of new line characters.

pid4cat_model-0.3.0/CODE_OF_CONDUCT.md

@@ -0,0 +1,76 @@
+# Contributor Covenant Code of Conduct
+
+## Our Pledge
+
+In the interest of fostering an open and welcoming environment, we as
+contributors and maintainers pledge to make participation in our project and
+our community a harassment-free experience for everyone, regardless of age,
+body size, disability, ethnicity, gender identity and expression, level of
+experience, nationality, personal appearance, race, religion, or sexual
+identity and orientation.
+
+## Our Standards
+
+Examples of behavior that contributes to creating a positive environment
+include:
+
+* Using welcoming and inclusive language
+* Being respectful of differing viewpoints and experiences
+* Gracefully accepting constructive criticism
+* Focusing on what is best for the community
+* Showing empathy towards other community members
+
+Examples of unacceptable behavior by participants include:
+
+* The use of sexualized language or imagery and unwelcome sexual attention or
+  advances
+* Trolling, insulting/derogatory comments, and personal or political attacks
+* Public or private harassment
+* Publishing others' private information, such as a physical or electronic
+  address, without explicit permission
+* Other conduct which could reasonably be considered inappropriate in a
+  professional setting
+
+## Our Responsibilities
+
+Project maintainers are responsible for clarifying the standards of acceptable
+behavior and are expected to take appropriate and fair corrective action in
+response to any instances of unacceptable behavior.
+
+Project maintainers 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, or to ban temporarily or
+permanently any contributor for other behaviors that they deem inappropriate,
+threatening, offensive, or harmful.
+
+## Scope
+
+This Code of Conduct applies both within project spaces and in public spaces
+when an individual is representing the project or its community. Examples of
+representing a project or community include using an official project e-mail
+address, posting via an official social media account, or acting as an
+appointed representative at an online or offline event. Representation of a
+project may be further defined and clarified by project maintainers.
+
+## Enforcement
+
+Instances of abusive, harassing, or otherwise unacceptable behavior may be
+reported by [contacting the project team](contact.md). All complaints will be
+reviewed and investigated and will result in a response that is deemed
+necessary and appropriate to the circumstances. The project team is obligated
+to maintain confidentiality with regard to the reporter of an incident. Further
+details of specific enforcement policies may be posted separately.
+
+Project maintainers who do not follow or enforce the Code of Conduct in good
+faith may face temporary or permanent repercussions as determined by other
+members of the project's leadership.
+
+## Attribution
+
+This code of conduct has been derived from the excellent code of conduct of the
+[ATOM project](https://github.com/atom/atom/blob/master/CODE_OF_CONDUCT.md)
+which in turn is adapted from the [Contributor Covenant][homepage], version
+1.4, available at [https://contributor-covenant.org/version/1/4][version]
+
+[homepage]: https://contributor-covenant.org
+[version]: https://contributor-covenant.org/version/1/4/

pid4cat_model-0.3.0/CONTRIBUTING.md

@@ -0,0 +1,113 @@
+# Contributing to pid4cat-model
+
+:+1: First of all: Thank you for taking the time to contribute!
+
+The following is a set of guidelines for contributing to
+pid4cat-model. These guidelines are not strict rules.
+Use your best judgment, and feel free to propose changes to this document
+in a pull request.
+
+## Table Of Contents
+
+- [Contributing to pid4cat-model](#contributing-to-pid4cat-model)
+  - [Table Of Contents](#table-of-contents)
+  - [Code of Conduct](#code-of-conduct)
+  - [Guidelines for Contributions and Requests](#guidelines-for-contributions-and-requests)
+    - [Reporting problems with the data model](#reporting-problems-with-the-data-model)
+    - [Adding new elements](#adding-new-elements)
+  - [Best Practices](#best-practices)
+    - [GitHub Best Practice](#github-best-practice)
+    - [Understanding LinkML](#understanding-linkml)
+    - [Modeling Best Practice](#modeling-best-practice)
+
+<a id="code-of-conduct"></a>
+
+## Code of Conduct
+
+The pid4cat-model team strives to create a
+welcoming environment for editors, users and other contributors.
+Please carefully read our [Code of Conduct](CODE_OF_CONDUCT.md).
+
+<a id="contributions"></a>
+
+## Guidelines for Contributions and Requests
+
+<a id="reporting-bugs"></a>
+
+### Reporting problems with the data model
+
+Please use our [Issue Tracker][issues] to report problems with the data model.
+
+<a id="requesting-terms"></a>
+
+### Adding new elements
+
+Please submit a [Pull Request][pulls] with the proposed changes or create an [Issue][issues].
+
+<a id="best-practices"></a>
+
+## Best Practices
+
+<a id="great-issues"></a>
+
+### GitHub Best Practice
+
+- Creating and curating issues
+    - Read ["About Issues"][[about-issues]]
+    - Issues should be focused and actionable
+    - Complex issues should be broken down into simpler issues where possible
+- Pull Requests
+    - Read ["About Pull Requests"][about-pulls]
+    - Read [GitHub Pull Requests: 10 Tips to Know](https://blog.mergify.com/github-pull-requests-10-tips-to-know/)
+    - Pull Requests (PRs) should be atomic and aim to close a single issue
+    - Long running PRs should be avoided where possible
+    - PRs should reference issues following standard conventions (e.g. “fixes #123”)
+    - Schema developers should always be working on a single issue at any one time
+    - Never work on the main branch, always work on an issue/feature branch
+    - Core developers can work on branches off origin rather than forks
+    - Always create a PR on a branch to maximize transparency of what you are doing
+    - PRs should be reviewed and merged in a timely fashion by the pid4cat-model technical leads
+    - PRs that do not pass GitHub actions should never be merged
+    - In the case of git conflicts, the contributor should try and resolve the conflict
+    - If a PR fails a GitHub action check, the contributor should try and resolve the issue in a timely fashion
+
+### Understanding LinkML
+
+Core developers should read the material on the [LinkML site](https://linkml.io/linkml), in particular:
+
+- [Overview](https://linkml.io/linkml/intro/overview.html)
+- [Tutorial](https://linkml.io/linkml/intro/tutorial.html)
+- [Schemas](https://linkml.io/linkml/schemas/index.html)
+- [FAQ](https://linkml.io/linkml/faq/index.html)
+
+### Modeling Best Practice
+
+- Follow Naming conventions
+    - Standard LinkML naming conventions should be followed (UpperCamelCase for classes and enums, snake_case for slots)
+    - Know how to use the LinkML linter to check style and conventions
+    - The names for classes should be nouns or noun-phrases: Person, GenomeAnnotation, Address, Sample
+    - Spell out abbreviations and short forms, except where this goes against convention (e.g. do not spell out DNA)
+    - Elements that are imported from outside (e.g. schema.org) need not follow the same naming conventions
+    - Multivalued slots should be named as plurals
+- Document model elements
+    - All model elements should have documentation (descriptions) and other textual annotations (e.g. comments, notes)
+    - Textual annotations on classes, slots and enumerations should be written with minimal jargon, clear grammar and no misspellings
+- Include examples and counter-examples (intentionally invalid examples)
+    - Rationale: these serve as documentation and unit tests
+    - These will be used by the automated test suite
+    - Invalid example data files should be invalid for one single reason, which should be reflected in the filename. It should be possible to render the invalid example files valid by addressing that single fault.
+- Use enums for categorical values
+    - Rationale: Open-ended string ranges encourage multiple values to represent the same entity, like “water”, “H2O” and “HOH”
+    - Any slot whose values could be constrained to a finite set should use an Enum
+    - Non-categorical values, e.g. descriptive fields like `name` or `description` fall outside of this.
+- Reuse
+    - Existing scheme elements should be reused where appropriate, rather than making duplicative elements
+    - More specific classes can be created by refining classes using inheritance (`is_a`)
+
+[about-branches]: https://docs.github.com/en/pull-requests/collaborating-with-pull-requests/proposing-changes-to-your-work-with-pull-requests/about-branches
+[about-issues]: https://docs.github.com/en/issues/tracking-your-work-with-issues/about-issues
+[about-pulls]: https://docs.github.com/en/pull-requests/collaborating-with-pull-requests/proposing-changes-to-your-work-with-pull-requests/about-pull-requests
+[issues]: https://github.com/nfdi4cat/pid4cat-model/issues/
+[pulls]: https://github.com/nfdi4cat/pid4cat-model/pulls/
+
+We recommend also reading [GitHub Pull Requests: 10 Tips to Know](https://blog.mergify.com/github-pull-requests-10-tips-to-know/)