Merge branch 'main' into experimental-base-model-transformer

.git-blame-ignore-revs

@@ -0,0 +1,2 @@
+# Reformat with black and isort
+ef566b7942153a2f29b626976bf04d15854f3cf1

.github/workflows/check_external_links.yaml

@@ -0,0 +1,33 @@
+name: Check Sphinx external links
+on:
+  pull_request:
+  schedule:
+    - cron: '0 5 * * 1'  # at 05:00 UTC every Monday
+  workflow_dispatch:
+
+jobs:
+  check-external-links:
+    runs-on: ubuntu-latest
+    steps:
+      - name: Checkout
+        uses: actions/checkout@v3.1.0
+        with:
+          fetch-depth: 0
+
+      - name: Set up Python 3.
+        uses: actions/setup-python@v4
+        with:
+          python-version: 3.9
+
+      - name: Install Poetry
+        uses: snok/install-poetry@v1
+        with:
+          version: 1.3.2
+
+      - name: install
+        run: poetry install -E docs
+
+      - name: Build documentation.
+        run: |
+          cd docs/
+          poetry run sphinx-build -b linkcheck . _build | grep "broken"

.github/workflows/docker-build.yaml

@@ -12,6 +12,7 @@ on:
 
 jobs:
   docker:
+    if: github.repository == 'linkml/linkml'
     runs-on: ubuntu-latest
     steps:
       - name: Checkout
@@ -48,4 +49,4 @@ jobs:
           platforms: linux/amd64,linux/arm64/v8
           push: ${{ github.event_name != 'pull_request' }}
           tags: ${{ steps.meta.outputs.tags }}
-          labels: ${{ steps.meta.outputs.labels }}
+          labels: ${{ steps.meta.outputs.labels }}

.github/workflows/main.yaml

@@ -20,9 +20,16 @@ jobs:
       matrix:
         os: [ubuntu-latest, windows-latest]
         python-version: ["3.8", "3.9", "3.10"]
+        pydantic-version: ["1", "2"]
         exclude:
           - os: windows-latest
             python-version: "3.8"
+          - os: windows-latest
+            pydantic-version: "2"
+          - python-version: "3.8"
+            pydantic-version: "2"
+          - python-version: "3.9"
+            pydantic-version: "2"
 
     # See https://github.com/snok/install-poetry#running-on-windows
     defaults:
@@ -70,31 +77,40 @@ jobs:
         if: steps.cached-poetry-dependencies.outputs.cache-hit != 'true'
         run: poetry install --no-interaction --no-root
 
+      #----------------------------------------------
+      # install pydantic
+      #----------------------------------------------
+      - name: Install Pydantic
+        run: poetry add pydantic@^${{ matrix.pydantic-version }}
+
       #----------------------------------------------
       #         setup and install graphviz
       #----------------------------------------------
       - name: Setup Graphviz
         uses: ts-graphviz/setup-graphviz@v1
 
       #----------------------------------------------
-      #    Linting
+      #    Linting & code quality
       #----------------------------------------------
-      - name: Lint with black and isort
+      - name: Check common spelling errors
+        run: poetry run tox -e codespell
+      - name: Check with flake8
         run: poetry run tox -e lint
 
       #----------------------------------------------
       #              coverage report
       #----------------------------------------------
       - name: Generate coverage results
         run: |
-          poetry run coverage run -m unittest discover
+          poetry run coverage run -m pytest
           poetry run coverage xml
           poetry run coverage report -m
         shell: bash
       #----------------------------------------------
       #           upload coverage results
       #----------------------------------------------
       - name: Upload coverage report
+        if: github.repository == 'linkml/linkml'
         uses: codecov/codecov-action@v3.1.0
         with:
           name: codecov-results-${{ matrix.os }}-${{ matrix.python-version }}

.gitignore

@@ -6,8 +6,8 @@ output/
 docs/_sources
 docs/_modules
 docs/_images
-sphinx/_build/
-sphinx/source/
+docs/_build/
+docs/source/
 
 # Jekyll
 Gemfile.lock

.pre-commit-config.yaml

@@ -0,0 +1,28 @@
+default_language_version:
+  python: python3
+repos:
+- repo: https://github.com/pre-commit/pre-commit-hooks
+  rev: v4.4.0
+  hooks:
+  - id: end-of-file-fixer
+    exclude: __snapshots__
+  - id: check-yaml
+    exclude: __snapshots__
+  - id: check-toml
+  - id: trailing-whitespace
+    exclude: __snapshots__
+- repo: https://github.com/psf/black
+  rev: 23.7.0
+  hooks:
+  - id: black
+- repo: https://github.com/astral-sh/ruff-pre-commit
+  rev: v0.0.278
+  hooks:
+  - id: ruff
+    args: [--fix, --exit-non-zero-on-fix]
+- repo: https://github.com/codespell-project/codespell
+  rev: v2.2.4
+  hooks:
+  - id: codespell
+    additional_dependencies:
+      - tomli

Dockerfile

@@ -7,7 +7,7 @@ ENV PYTHONFAULTHANDLER=1 \
   PIP_NO_CACHE_DIR=off \
   PIP_DISABLE_PIP_VERSION_CHECK=on \
   PIP_DEFAULT_TIMEOUT=100 \
-  POETRY_VERSION=1.2.1
+  POETRY_VERSION=1.6.0
 
 # Install Poetry
 RUN pip install "poetry==$POETRY_VERSION"
@@ -19,11 +19,15 @@ WORKDIR /code
 COPY ./.git ./.git
 COPY pyproject.toml poetry.lock README.md .
 COPY linkml linkml/
-RUN poetry build 
+RUN poetry build
 
 #######################################
 FROM python:3.9-slim-bullseye as runner
 
+ENV DEBIAN_FRONTEND=noninteractive
+RUN apt update
+RUN apt update && apt install -y gcc musl-dev python3-dev && rm -rf /var/lib/apt/lists/*
+
 RUN useradd --create-home linkmluser
 WORKDIR /home/linkmluser
 USER linkmluser

Makefile

@@ -14,7 +14,7 @@ all-examples-%:  examples/%.py examples/%.schema.json  examples/%.shex  examples
 RUN=poetry run
 
 test:
-	$(RUN) python -m unittest discover
+	$(RUN) pytest
 
 ## Example schema products
 examples/%.py: examples/%.yaml
@@ -58,13 +58,13 @@ linkml/linter/config/datamodel/config.py: linkml/linter/config/datamodel/config.
 
 TUTORIALS = 01 02 03 04 05 06 07 08 09 10
 test-tutorials: $(patsubst %, test-tutorial-%, $(TUTORIALS))
-test-tutorial-%: sphinx/intro/tutorial%.md
-	pipenv run python -m linkml.utils.execute_tutorial -d /tmp/tutorial $<
+test-tutorial-%: docs/intro/tutorial%.md
+	$(RUN) python -m linkml.utils.execute_tutorial -d /tmp/tutorial $<
 
 rtd:
-	cd sphinx && $(RUN) make html
+	cd docs && $(RUN) make html
 deploy-rtd:
-	cd sphinx && $(RUN) make deploy
+	cd docs && $(RUN) make deploy
 
 ################################################
 #### Commands for building the Docker image ####
@@ -86,7 +86,7 @@ docker-build-use-cache-dev:
 
 docker-clean:
 	docker kill $(IM) || echo not running ;
-	docker rm $(IM) || echo not made 
+	docker rm $(IM) || echo not made
 
 docker-publish-no-build:
 	@docker push $(IM):$(VERSION) \
@@ -101,4 +101,4 @@ docker-publish: docker-build
 	&& docker push $(IM):latest
 
 docker-run:
-	@docker run  -v $(PWD):/work -w /work -ti $(IM):$(VERSION) 
+	@docker run  -v $(PWD):/work -w /work -ti $(IM):$(VERSION)

SPECIFICATION.md

@@ -163,7 +163,7 @@ prefixes:
   qud: http://qudt.org/1.1/schema/qudt#
 ```
 
-The CURIE `wgs:lat` will exand to http://www.w3.org/2003/01/geo/wgs84_pos#lat.
+The CURIE `wgs:lat` will expand to http://www.w3.org/2003/01/geo/wgs84_pos#lat.
 
 * an external CURIE map specified via a [default_curi_maps](https://w3id.org/linkml/meta/default_curi_maps) section.
 

codecov.yml

@@ -0,0 +1,9 @@
+# https://docs.codecov.com/docs/codecov-yaml
+coverage:
+  status:
+    project:
+      default:
+        informational: true
+    patch:
+      default:
+        informational: true

docs/README.md

@@ -4,7 +4,7 @@ These instructions are for the core developers of the LinkML framework.
 
 Documentation source:
 
- * [sphinx/ folder](https://github.com/linkml/linkml/tree/main/sphinx)
+ * [docs/ folder](https://github.com/linkml/linkml/tree/main/docs)
  * deployed to: [https://linkml.io/linkml/](https://linkml.io/linkml/)
 
 We use the sphinx framework.

docs/conf.py

@@ -18,7 +18,7 @@
 # -- Project information -----------------------------------------------------
 
 project = 'linkml'
-copyright = '2021, LinkML Authors'
+copyright = '2021-2023, LinkML Authors'
 author = 'LinkML Authors'
 
 
@@ -75,7 +75,12 @@
 # Options for the linkcheck builder
 linkcheck_ignore = [
     'https://w3id.org/linkml/*',
+    'https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5819722',
+    'https://doi.org/10.1093/database/bax105',
+    'https://github.com/linkml/prefixmaps/*#*',
+    'https://docs.google.com/presentation/d/*#*'
 ]
 
+
 # Options for autosectionlabel
 autosectionlabel_prefix_document = True