First fixes 131: components, $(MAKE) and reports

Changes.md

@@ -1,3 +1,26 @@
+# v1.3.1 (unpublished, target date 24 May 2022)
+
+- Added shortcut make commands for recreating components: `recreate-components` and `recreate-%` ([pull](https://github.com/INCATools/ontology-development-kit/pull/570)).
+- Added new shortcut command for fast releases: `make prepare_release_fast`.
+- Added the [Ontology Access Kit](https://github.com/INCATools/ontology-access-kit), a python library for interacting with ontologies, the the ODK ([pull](https://github.com/INCATools/ontology-development-kit/pull/586)).
+- New tools: [gh](https://github.com/cli/cli), [j2cli](https://github.com/kolypto/j2cli)
+- The ontology diff GitHub action, a tool that allows you to create diffs for you ontology pull requests, is now automatically synced with your ODK setup ([pull](https://github.com/INCATools/ontology-development-kit/pull/564)).
+- Added `workflows` option to ODK config. This allows users to choose which workflows (at the moment GitHub actions-based) should be automatically synchronised.
+- Custom ROBOT SPARQL reports now consider the imports by default ([pull](https://github.com/INCATools/ontology-development-kit/pull/570))
+- Technical
+   - Run internal `make` and $(MAKE) to ensure that parameters are propagated correctly ([issue](https://github.com/INCATools/ontology-development-kit/issues/554)).
+   - Mirror goal is only run when mirrors have been downloaded ([pull](https://github.com/INCATools/ontology-development-kit/pull/570))
+- Documentation
+   - Some improved documentation on components ([pull](https://github.com/INCATools/ontology-development-kit/pull/577))
+   - All ODK-related general docs now moved to https://oboacademy.github.io/obook.
+   - DOSDP documentation pages are now only created when dosdp is configured.
+- Bugs
+   - The automatic docs workflow now correctly `uses: mhausenblas/mkdocs-deploy-gh-pages@master`.
+   - In ODK 1.3.0 `prepare_release` depended on `all`, which caused some cyclicity for some customised setups. This is now changed to a separate `all_odk` goal.
+   - Simple ontology release artefacts now correctly depend on the `simple seed`.
+   - Similar to subset declarations, ODK now injects synonymtype declarations when extracting a module.
+
+
 # v1.3.0 (24 February 2022)
 
 ### New features:

Dockerfile

@@ -12,6 +12,10 @@ ENV ODK_VERSION $ODK_VERSION
 # docker run -v $HOME/.coursier/cache/v1:/tools/.coursier-cache ...
 ENV COURSIER_CACHE "/tools/.coursier-cache"
 
+# Install GH
+RUN curl -fsSL https://cli.github.com/packages/githubcli-archive-keyring.gpg | dd of=/usr/share/keyrings/githubcli-archive-keyring.gpg
+RUN echo "deb [arch=$(dpkg --print-architecture) signed-by=/usr/share/keyrings/githubcli-archive-keyring.gpg] https://cli.github.com/packages stable main" | tee /etc/apt/sources.list.d/github-cli.list > /dev/null
+
 # Install tools provided by Ubuntu.
 RUN apt-get update && DEBIAN_FRONTEND="noninteractive" apt-get install -y --no-install-recommends  \
     build-essential \
@@ -27,6 +31,7 @@ RUN apt-get update && DEBIAN_FRONTEND="noninteractive" apt-get install -y --no-i
     libjson-perl \
     pkg-config \
     xlsx2csv \
+    gh \
     nodejs \
     npm \
     graphviz

odk/odk.py

@@ -513,6 +513,9 @@ class OntologyProject(JsonSchemaMixin):
     ci : Optional[List[str]] = field(default_factory=lambda: ['github_actions'])
     """continuous integration defaults; currently available: travis, github_actions"""
 
+    workflows : Optional[List[str]] = field(default_factory=lambda: ['docs'])
+    """Workflows that are synced when updating the repo. Currently available: docs, diff, qc."""
+
     import_pattern_ontology : bool = False
     """if true import pattern.owl"""
 

requirements.txt.lite

@@ -11,3 +11,5 @@ pyyaml
 ruamel.yaml
 dosdp
 tsvalid
+j2cli[yaml]
+j2cli

template/_dynamic_files.jinja2

@@ -626,7 +626,7 @@ jobs:
         run: cd src/ontology && make ROBOT_ENV='ROBOT_JAVA_ARGS=-Xmx6G' test IMP=false PAT=false
 {% endif -%}
 {% endif -%}
-{% if 'github_actions' in project.ci %}
+{% if (('github_actions' in project.ci) and ('diff' in project.workflows)) %}
 ^^^ .github/workflows/diff.yml
 name: 'Create ROBOT diffs on Pull requests'
 
@@ -1450,11 +1450,12 @@ The documentation is _not_ automatically updated from the Markdown, and needs to
    ```
 3. Just to double check, you can now navigate to your documentation pages (usually https://{{ project.github_org }}.github.io/{{ project.repo }}/). 
    Just make sure you give GitHub 2-5 minutes to build the pages!
-
+{% if project.use_dosdps %}
 ^^^ docs/templates/dosdp.md
 # DOSDP documentation stub
 
-Do not overwrite, contents will be generated automatically,
+Do not overwrite, contents will be generated automatically.
+{% endif %}
 ^^^ mkdocs.yaml
 site_name: {{ project.title }}
 theme: material
@@ -1477,8 +1478,8 @@ nav:
       - Contributing: contributing.md{% if project.use_dosdps %}
   - Reference:
     - Design Patterns:
-      - Design Patterns Overview: dosdp.md{% endif %}
-{% if 'github_actions' in project.ci %}
+      - Design Patterns Overview: dosdp.md{% endif %}{% endif %}
+{% if (('github_actions' in project.ci) and ('docs' in project.workflows)) %}
 ^^^ .github/workflows/docs.yml
 # Basic ODK workflow
 name: Docs
@@ -1501,10 +1502,9 @@ jobs:
         uses: actions/checkout@v2
 
       - name: Deploy docs
-        uses: mhausenblas/mkdocs-deploy-gh-pages@{{ project.git_main_branch }}
+        uses: mhausenblas/mkdocs-deploy-gh-pages@master
         # Or use mhausenblas/mkdocs-deploy-gh-pages@nomaterial to build without the mkdocs-material theme
         env:
           GITHUB_TOKEN: {% raw %}${{ secrets.GITHUB_TOKEN }}{% endraw %}
           CONFIG_FILE: mkdocs.yaml
 {% endif -%}
-{% endif -%}