pid4cat-model 0.4.2__tar.gz → 0.4.3__tar.gz

{pid4cat_model-0.4.2 → pid4cat_model-0.4.3}/.copier-answers.yml

@@ -1,9 +1,10 @@
 # Changes here will be overwritten by Copier
-_commit: v0.4.0
+_commit: v0.5.0
 _src_path: gh:dalito/linkml-project-copier
 add_example: false
 copyright_year: '2023'
 email: david.linke@catalysis.de
+existing_license_file: ''
 full_name: David Linke
 gh_action_docs_preview: false
 gh_action_pypi: true
@@ -13,3 +14,4 @@ project_description: LinkML model for handle-based PIDs for resources in catalys
     (pid4cat)
 project_name: pid4cat-model
 project_slug: pid4cat_model
+

pid4cat_model-0.4.3/.github/dependabot.yml

@@ -0,0 +1,15 @@
+# Please see the documentation for all configuration options:
+# https://docs.github.com/en/code-security/dependabot/working-with-dependabot/dependabot-options-reference
+
+version: 2
+updates:
+  - package-ecosystem: github-actions
+    directory: "/"
+    schedule:
+      interval: monthly
+    assignees:
+      - "dalito"
+    groups:
+      github-actions:
+        patterns:
+          - "*"

{pid4cat_model-0.4.2 → pid4cat_model-0.4.3}/.github/workflows/deploy-docs.yaml

@@ -18,6 +18,10 @@ jobs:
   build-docs:
     runs-on: ubuntu-latest
 
+    strategy:
+      matrix:
+        pyversion: ["3.13"]
+
     # Grant GITHUB_TOKEN the permissions required to make a gh-pages deployment
     permissions:
       contents: write  # to let mkdocs write the new docs
@@ -25,8 +29,9 @@ jobs:
       id-token: write  # allow to generate an OpenID Connect (OIDC) token
 
     steps:
+      # https://github.com/actions/checkout
       - name: Checkout
-        uses: actions/checkout@11bd71901bbe5b1630ceea73d27597364c9af683
+        uses: actions/checkout@v6.0.2
         with:
           fetch-depth: 0  # otherwise, you will fail to push refs to dest repo
 
@@ -37,24 +42,26 @@ jobs:
           git config user.name github-actions[bot]
           git config user.email github-actions[bot]@users.noreply.github.com
 
+      # https://github.com/astral-sh/setup-uv
       - name: Install uv
-        uses: astral-sh/setup-uv@6b9c6063abd6010835644d4c2e1bef4cf5cd0fca
+        uses: astral-sh/setup-uv@v8.1.0
         with:
-          python-version: 3.12
+          python-version: ${{ matrix.pyversion }}
           enable-cache: true
           cache-dependency-glob: "uv.lock"
 
+      # https://github.com/actions/setup-python
       - name: Set up Python
-        uses: actions/setup-python@a26af69be951a213d495a4c3e4e4022e16d87065
+        uses: actions/setup-python@v6.2.0
         with:
-          python-version: 3.12
+          python-version: ${{ matrix.pyversion }}
 
       - name: Install just
         run: |
           uv tool install rust-just
 
       - name: Install dependencies
-        run: uv sync --dev --no-progress
+        run: uv sync --group dev --no-progress
 
       - name: Generate schema documentation
         run: |

{pid4cat_model-0.4.2 → pid4cat_model-0.4.3}/.github/workflows/main.yaml

@@ -9,7 +9,7 @@ on:  # yamllint disable-line rule:truthy
   pull_request:
 
 env:
-  FORCE_COLOR: "1" # Make tools pretty.
+  FORCE_COLOR: "1"  # Make tools pretty.
 
 permissions: {}
 
@@ -19,28 +19,28 @@ jobs:
     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"]
+        python-version: ["3.10", "3.11", "3.12", "3.13", "3.14"]
       fail-fast: false
 
     steps:
 
+      # https://github.com/actions/checkout
       - name: Check out repository
-        uses: actions/checkout@11bd71901bbe5b1630ceea73d27597364c9af683
+        uses: actions/checkout@v6.0.2
         with:
           persist-credentials: false
 
+      # https://github.com/astral-sh/setup-uv
       - name: Install uv
-        uses: astral-sh/setup-uv@6b9c6063abd6010835644d4c2e1bef4cf5cd0fca
+        uses: astral-sh/setup-uv@v8.1.0
         with:
           python-version: ${{ matrix.python-version }}
           enable-cache: true
           cache-dependency-glob: "uv.lock"
 
+      # https://github.com/actions/setup-python
       - name: Set up Python ${{ matrix.python-version }}
-        uses: actions/setup-python@a26af69be951a213d495a4c3e4e4022e16d87065
+        uses: actions/setup-python@v6.2.0
         with:
           python-version: ${{ matrix.python-version }}
 
@@ -49,7 +49,7 @@ jobs:
           uv tool install rust-just
 
       - name: Install project
-        run: uv sync --dev
+        run: uv sync --group dev
 
       - name: Run test suite
         run: just test

{pid4cat_model-0.4.2 → pid4cat_model-0.4.3}/.github/workflows/pypi-publish.yaml

@@ -11,7 +11,7 @@ name: Publish Python Package
 on:  # yamllint disable-line rule:truthy
   push:
     tags:
-      # GitHub glob matching is limited [1]. So we can't define a pattern matching
+      # GitHub glob matching is limited. 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]'
@@ -25,22 +25,29 @@ jobs:
     name: Build Python 🐍 distributions 📦 for publishing
     runs-on: ubuntu-latest
 
+    strategy:
+      matrix:
+        pyversion: ["3.13"]
+
     steps:
+      # https://github.com/actions/checkout
       - name: Check out repository
-        uses: actions/checkout@11bd71901bbe5b1630ceea73d27597364c9af683
+        uses: actions/checkout@v6.0.2
         with:
           persist-credentials: false
 
+      # https://github.com/astral-sh/setup-uv
       - name: Install uv
-        uses: astral-sh/setup-uv@6b9c6063abd6010835644d4c2e1bef4cf5cd0fca
+        uses: astral-sh/setup-uv@v8.1.0
         with:
-          python-version: 3.12
+          python-version: ${{ matrix.pyversion }}
           enable-cache: true
 
+      # https://github.com/actions/setup-python
       - name: Set up Python
-        uses: actions/setup-python@a26af69be951a213d495a4c3e4e4022e16d87065
+        uses: actions/setup-python@v6.2.0
         with:
-          python-version: 3.12
+          python-version: ${{ matrix.pyversion }}
 
       - name: Install just
         run: |
@@ -49,8 +56,9 @@ jobs:
       - name: Build source and wheel archives
         run: uv build
 
+      # https://github.com/actions/upload-artifact
       - name: Store built distribution
-        uses: actions/upload-artifact@ea165f8d65b6e75b540449e92b4886f43607fa02
+        uses: actions/upload-artifact@v7.0.1
         with:
           name: distribution-files
           path: dist/
@@ -65,30 +73,23 @@ jobs:
     permissions:
       id-token: write  # this permission is mandatory for trusted publishing
     steps:
+      # https://github.com/actions/download-artifact
       - name: Download built distribution
-        uses: actions/download-artifact@d3f86a106a0bac45b974a628896c90dbdf5c8093
+        uses: actions/download-artifact@v8.0.1
         with:
           name: distribution-files
           path: dist
 
+      # https://github.com/pypa/gh-action-pypi-publish
       - name: Publish package 📦 to Test PyPI
         if: github.event_name == 'push'
-        uses: pypa/gh-action-pypi-publish@76f52bc884231f62b9a034ebfe128415bbaabdfc
+        uses: pypa/gh-action-pypi-publish@v1.14.0
         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
+        uses: pypa/gh-action-pypi-publish@v1.14.0
         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-0.4.2 → pid4cat_model-0.4.3}/.linkmllint.yaml

@@ -7,5 +7,6 @@ rules:
     # permissible_values_upper_case: true
     # class_pattern: snake_case
   canonical_prefixes:
-    # Superfluous warnings for https-refixes, https://github.com/linkml/linkml/issues/2492
+    # Suppress warnings for https-prefixes
+    # related: https://github.com/linkml/linkml/issues/2492
     level: disabled

{pid4cat_model-0.4.2 → pid4cat_model-0.4.3}/.pre-commit-config.yaml

@@ -2,35 +2,40 @@
 # https://pre-commit.com/
 repos:
   - repo: https://github.com/pre-commit/pre-commit-hooks
-    rev: v5.0.0
+    rev: v6.0.0
     hooks:
       - id: check-toml
       - id: check-yaml
+        # mkdocs.yml uses !!python/name tags unsupported by the safe YAML loader
+        exclude: ^mkdocs\.yml$
       - id: end-of-file-fixer
+        exclude: ^\.copier-answers\.yml$
       - id: trailing-whitespace
         args: [--markdown-linebreak-ext=md]
 
   - repo: https://github.com/adrienverge/yamllint.git
-    rev: v1.37.0
+    rev: v1.38.0
     hooks:
       - id: yamllint
         args: [-c=.yamllint.yaml]
+        exclude: ^\.copier-answers\.yml$
+        verbose: true  # Show warnings.
 
   - repo: https://github.com/codespell-project/codespell
-    rev: v2.4.1
+    rev: v2.4.2
     hooks:
       - id: codespell
         additional_dependencies:
           - tomli
 
   - repo: https://github.com/crate-ci/typos
-    rev: v1.31.1
+    rev: v1.46.3
     hooks:
       - id: typos
 
   - repo: https://github.com/astral-sh/ruff-pre-commit
     # Ruff version.
-    rev: v0.11.3
+    rev: v0.15.14
     hooks:
       # Run the linter.
       - id: ruff
@@ -40,6 +45,6 @@ repos:
 
   - repo: https://github.com/astral-sh/uv-pre-commit
     # uv version.
-    rev: 0.6.12
+    rev: 0.11.16
     hooks:
       - id: uv-lock

pid4cat_model-0.4.3/.yamlfix.toml

@@ -0,0 +1,8 @@
+# Config for the yaml formatter https://github.com/lyz-code/yamlfix
+# install: "uv tool install yamlfix"
+line_length = 88
+sequence_style = "block_style"
+
+# order is important: keep whiteline before section_whitelines
+whitelines = 1
+section_whitelines = 1

{pid4cat_model-0.4.2 → pid4cat_model-0.4.3}/.yamllint.yaml

@@ -2,10 +2,17 @@
 
 extends: default
 
+# Specify files to ignore.
+ignore:
+  # Ignore autogenerated file that does not conform to yamllint rules.
+  - .copier-answers.yml
+  # Ignore schema files that may not conform due to imports.
+  - docs/schema/*.yaml
+
 rules:
   document-start: disable  # Don't check if document has a start marker (---).
   line-length:
-    max: 80
+    max: 88
     level: warning
     allow-non-breakable-words: true
     allow-non-breakable-inline-mappings: true

{pid4cat_model-0.4.2 → pid4cat_model-0.4.3}/PKG-INFO

@@ -1,15 +1,15 @@
 Metadata-Version: 2.4
 Name: pid4cat-model
-Version: 0.4.2
+Version: 0.4.3
 Summary: Python model equivalent of LinkML datamodel for handle-based PIDs for resources in catalysis (pid4cat)
 Author-email: David Linke <david.linke@catalysis.de>
 Maintainer-email: David Linke <david.linke@catalysis.de>
 License-Expression: MIT
 License-File: LICENSE
-Requires-Python: <4.0,>=3.11
-Requires-Dist: click<8.2.0,>=8.1.7
+Requires-Python: >=3.10
+Requires-Dist: click>8.2.0
 Requires-Dist: httpx<0.29.0,>=0.28.1
-Requires-Dist: linkml-runtime>=1.9.2
+Requires-Dist: linkml-runtime>=1.9.4
 Description-Content-Type: text/markdown
 
 [![CI - main](https://github.com/nfdi4cat/pid4cat-model/actions/workflows/main.yaml/badge.svg)](https://github.com/nfdi4cat/pid4cat-model/actions/workflows/main.yaml)

{pid4cat_model-0.4.2 → pid4cat_model-0.4.3}/config.public.mk

@@ -20,13 +20,10 @@ LINKML_GENERATORS_CONFIG_YAML=config.yaml
 LINKML_GENERATORS_DOC_ARGS="--truncate-descriptions False --hierarchical-class-view --subfolder-type-separation --index-name overview"
 
 ## pass args to workaround genowl rdfs config bug (linkml#1453)
-##   (i.e. --no-type-objects --no-metaclasses --metadata-profile rdfs)
+##   (i.e. --no-type-objects --no-metaclasses --metadata-profile=rdfs)
+# LINKML_GENERATORS_OWL_ARGS="--no-type-objects --no-metaclasses --metadata-profile=rdfs"
 LINKML_GENERATORS_OWL_ARGS=
 
-## pass args to trigger experimental java/typescript generation
-LINKML_GENERATORS_JAVA_ARGS=
-LINKML_GENERATORS_TYPESCRIPT_ARGS=
-
 ## pass args to pydantic generator which isn't supported by gen-project
 ## https://github.com/linkml/linkml/issues/2537
 LINKML_GENERATORS_PYDANTIC_ARGS=

{pid4cat_model-0.4.2 → pid4cat_model-0.4.3}/config.yaml

@@ -19,10 +19,10 @@ generator_args:
     mergeimports: true
   owl:
     mergeimports: true
-    metaclasses: true
-    type_objects: true
-    # throws 'Cannot handle metadata profile: rdfs'
-    # metadata_profile: rdfs
+    metaclasses: false
+    type_objects: false
+    add_root_classes: true
+    mixins_as_expressions: true
   markdown:
     mergeimports: true
     directory: "docs/elements"

pid4cat_model-0.4.3/docs/hooks/theme_overrides_priority.py

@@ -0,0 +1,18 @@
+"""Give docs/overrides priority over plugin-supplied theme dirs.
+
+The mkdocs_pymdownx_material_extras plugin inserts its own theme directory at
+position 0 of theme.dirs in its on_config hook, which shadows the user's
+custom_dir. This hook runs after plugins and moves custom_dir back to the
+front so files under docs/overrides win against the plugin's templates.
+"""
+
+
+def on_config(config):
+    custom_dir = config["theme"].custom_dir
+    if not custom_dir:
+        return config
+    dirs = config["theme"].dirs
+    if custom_dir in dirs and dirs[0] != custom_dir:
+        dirs.remove(custom_dir)
+        dirs.insert(0, custom_dir)
+    return config

pid4cat_model-0.4.3/docs/js/extra-loader.js

@@ -0,0 +1,2 @@
+// See https://facelessuser.github.io/pymdown-extensions/extras/mermaid/#custom-loader
+// And https://github.com/facelessuser/pymdown-extensions/blob/main/docs/src/js/material-extra-3rdparty.js

pid4cat_model-0.4.3/docs/overrides/partials/header.html

@@ -0,0 +1,71 @@
+{#-
+  Copied from mkdocs-material to bypass the header.html provided by
+  mkdocs_pymdownx_material_extras (which forces a dracula-based palette).
+  This restores Material's standard palette toggle using default/slate.
+-#}
+{% set class = "md-header" %}
+{% if "navigation.tabs.sticky" in features %}
+  {% set class = class ~ " md-header--shadow md-header--lifted" %}
+{% elif "navigation.tabs" not in features %}
+  {% set class = class ~ " md-header--shadow" %}
+{% endif %}
+<header class="{{ class }}" data-md-component="header">
+  <nav class="md-header__inner md-grid" aria-label="{{ lang.t('header') }}">
+    <a href="{{ config.extra.homepage | d(nav.homepage.url, true) | url }}" title="{{ config.site_name | e }}" class="md-header__button md-logo" aria-label="{{ config.site_name }}" data-md-component="logo">
+      {% include "partials/logo.html" %}
+    </a>
+    <label class="md-header__button md-icon" for="__drawer">
+      {% set icon = config.theme.icon.menu or "material/menu" %}
+      {% include ".icons/" ~ icon ~ ".svg" %}
+    </label>
+    <div class="md-header__title" data-md-component="header-title">
+      <div class="md-header__ellipsis">
+        <div class="md-header__topic">
+          <span class="md-ellipsis">
+            {{ config.site_name }}
+          </span>
+        </div>
+        <div class="md-header__topic" data-md-component="header-topic">
+          <span class="md-ellipsis">
+            {% if page.meta and page.meta.title %}
+              {{ page.meta.title }}
+            {% else %}
+              {{ page.title }}
+            {% endif %}
+          </span>
+        </div>
+      </div>
+    </div>
+    {% if config.theme.palette %}
+      {% if not config.theme.palette is mapping %}
+        {% include "partials/palette.html" %}
+      {% endif %}
+    {% endif %}
+    {% if not config.theme.palette is mapping %}
+      {% include "partials/javascripts/palette.html" %}
+    {% endif %}
+    {% if config.extra.alternate %}
+      {% include "partials/alternate.html" %}
+    {% endif %}
+    {% if "material/search" in config.plugins %}
+      {% set search = config.plugins["material/search"] | attr("config") %}
+      {% if search.enabled %}
+        <label class="md-header__button md-icon" for="__search">
+          {% set icon = config.theme.icon.search or "material/magnify" %}
+          {% include ".icons/" ~ icon ~ ".svg" %}
+        </label>
+        {% include "partials/search.html" %}
+      {% endif %}
+    {% endif %}
+    {% if config.repo_url %}
+      <div class="md-header__source">
+        {% include "partials/source.html" %}
+      </div>
+    {% endif %}
+  </nav>
+  {% if "navigation.tabs.sticky" in features %}
+    {% if "navigation.tabs" in features %}
+      {% include "partials/tabs.html" %}
+    {% endif %}
+  {% endif %}
+</header>

pid4cat_model-0.4.3/docs/stylesheets/extra.css

@@ -0,0 +1,27 @@
+#logo_light_mode {
+  display: var(--md-footer-logo-light-mode);
+}
+
+#logo_dark_mode {
+  display: var(--md-footer-logo-dark-mode);
+}
+
+[data-md-color-scheme="default"] {
+  --md-footer-logo-dark-mode: none;
+  --md-footer-logo-light-mode: block;
+}
+
+/* The mkdocs_pymdownx_material_extras plugin ships an
+   extra-c6ab11540a.css with a `:root>* { --md-typeset-a-color: #00bcd4; }`
+   rule that forces light-mode links to bright cyan, ignoring the configured
+   accent color. We override it with a higher-specificity selector
+   (body[attr] = 0,1,1 beats :root>* = 0,1,0) so light-mode links use the
+   configured accent color (indigo via mkdocs.yml palette). */
+body[data-md-color-scheme="default"] {
+  --md-typeset-a-color: var(--md-accent-fg-color);
+}
+
+[data-md-color-scheme="slate"] {
+  --md-footer-logo-dark-mode: none;
+  --md-footer-logo-light-mode: block;
+}

pid4cat_model-0.4.3/examples/PID4CatRecord-001.yaml

@@ -0,0 +1,87 @@
+---
+contains_pids:
+  - responseCode: 1
+    handle: 21.T12995/lik-1
+    values:
+      - index: 1
+        type: URL
+        data:
+          format: string
+          value: https://pid4cat.example.org/lik-1
+        ttl: 86400
+        timestamp: '2024-05-15T15:51:15Z'
+      - index: 2
+        type: STATUS
+        data:
+          format: string
+          value: REGISTERED
+        ttl: 86400
+        timestamp: '2024-05-15T15:51:15Z'
+      - index: 3
+        type: SCHEMA_VER
+        data:
+          format: string
+          value: v0.1.0
+        ttl: 86400
+        timestamp: '2024-05-15T15:51:15Z'
+      - index: 4
+        type: METADATA_LICENSE
+        data:
+          format: string
+          value: CC0-1.0
+        ttl: 86400
+        timestamp: '2024-05-15T15:51:15Z'
+      - index: 5
+        type: EMAIL
+        data:
+          format: string
+          value: datafuzzi@example.org
+        ttl: 86400
+        timestamp: '2024-05-15T15:51:15Z'
+      - index: 6
+        type: RESOURCE_INFO
+        data:
+          format: string
+          value:
+            - resource_info:
+                label: Resource label
+                description: Resource description
+                resource_category: SAMPLE
+                representation_variants:
+                  - variant_url: https://example.org/resource
+                    media_type: text/turtle
+                    encoding_format: UTF-8
+                    size: 12345
+        ttl: 86400
+        timestamp: '2024-05-15T15:51:15Z'
+      - index: 7
+        type: RELATED
+        data:
+          format: string
+          value:
+            - related_identifiers:
+                - relation_type: IS_PART_OF
+                  related_identifier: https://example.org/collection
+                  datetime_log: '2024-02-19T00:00:00Z'
+                - relation_type: IS_REFERENCED_BY
+                  related_identifier: https://example.org/referenced
+                  datetime_log: '2024-02-19T00:00:00Z'
+        ttl: 86400
+        timestamp: '2024-05-15T15:51:15Z'
+      - index: 8
+        type: CHANGES
+        data:
+          format: string
+          value:
+            - change_log:
+                - datetime_log: '2024-02-19T00:00:00Z'
+                  has_agent:
+                    name: Data Fuzzi
+                    email: datafuzzi@example.org
+                    orcid: 0000-0000-0000-0000
+                    affiliation_ror: https://ror.org/029hg0311
+                    role: TRUSTEE
+                  changed_field: STATUS
+                  description: 'as requested in issue #123'
+        ttl: 86400
+        timestamp: '2024-05-15T15:51:15Z'