working examples

.cruft.json

@@ -0,0 +1,27 @@
+{
+  "template": "https://github.com/linkml/linkml-project-cookiecutter",
+  "commit": "ef7ff16925321a2abdbaa5a2ba5db8aa83ebf24f",
+  "checkout": null,
+  "context": {
+    "cookiecutter": {
+      "project_name": "mixs-6-2-for-merge",
+      "__project_slug": "mixs_6_2_for_merge",
+      "github_org": "GenomicsStandardsConsortium",
+      "__source_path": "src/mixs_6_2_for_merge/schema/mixs_6_2_for_merge.yaml",
+      "project_description": "MIxS: the Minimum Information about any (X) Sequence standard",
+      "full_name": "Mark Andrew Miller",
+      "email": "[email protected]",
+      "__author": "Mark Andrew Miller <[email protected]>",
+      "license": "MIT",
+      "main_schema_class": "Checklist",
+      "create_python_classes": "Yes",
+      "use_schemasheets": "No",
+      "google_sheet_id": "1wVoaiFg47aT9YWNeRfTZ8tYHN8s8PAuDx5i2HUcDpvQ",
+      "google_sheet_tabs": "personinfo enums",
+      "__google_sheet_module": "personinfo_enums",
+      "github_token_for_pypi_deployment": "PYPI_PASSWORD",
+      "_template": "https://github.com/linkml/linkml-project-cookiecutter"
+    }
+  },
+  "directory": null
+}

.github/workflows/deploy-docs.yaml

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+---
+name: Auto-deployment of mixs_6_2_for_merge Documentation
+on:
+  push:
+    branches: [main]
+
+jobs:
+  build-docs:
+    runs-on: ubuntu-latest
+    steps:
+      - name: Checkout
+        uses: actions/checkout@v3
+        with:
+          fetch-depth: 0  # otherwise, you will failed to push refs to dest repo
+
+      - name: Set up Python 3.
+        uses: actions/setup-python@v4
+        with:
+          python-version: 3.9
+
+      - name: Install Poetry.
+        uses: snok/[email protected]
+
+      - name: Install dependencies.
+        run: poetry install -E docs
+
+      - name: Build documentation.
+        run: |
+          mkdir -p docs
+          touch docs/.nojekyll
+          make gendoc
+          ([ ! -f docs/about.md ] && cp src/docs/about.md docs/) || true
+          make mkd-gh-deploy
+
+...

.github/workflows/main.yaml

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+# Built from:
+# https://docs.github.com/en/actions/guides/building-and-testing-python
+# https://github.com/snok/install-poetry#workflows-and-tips
+---
+name: Build and test mixs_6_2_for_merge
+
+on: [pull_request]
+
+jobs:
+  test:
+
+    runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        python-version: ["3.9", "3.10"]
+
+    steps:
+
+      - name: Check out repository
+        uses: actions/checkout@v3
+
+      - name: Set up Python ${{ matrix.python-version }}
+        uses: actions/setup-python@v4
+        with:
+          python-version: ${{ matrix.python-version }}
+
+      - name: Install Poetry
+        uses: snok/[email protected]
+
+      - name: Install dependencies
+        run: poetry install --no-interaction --no-root
+
+      - name: Install project
+        run: poetry install --no-interaction
+
+      - name: Run test suite
+        run: make test

.github/workflows/pypi-publish.yaml

@@ -0,0 +1,40 @@
+---
+name: Publish Python Package
+
+on:
+  release:
+    types: [created]
+
+jobs:
+  build-n-publish:
+    name: Build and publish Python 🐍 distributions 📦 to PyPI
+    runs-on: ubuntu-latest
+
+    steps:
+      - uses: actions/checkout@v3
+
+      - name: Set up Python
+        uses: actions/setup-python@v4
+        with:
+          python-version: 3.9
+
+      - name: Install Poetry
+        run: |
+          pip install poetry
+          poetry self add "poetry-dynamic-versioning[plugin]"
+        # uses: snok/[email protected]
+        # with:
+        #   virtualenvs-create: true
+        #   virtualenvs-in-project: true
+
+      # - name: Install dependencies
+      #   run: poetry install --no-interaction
+
+      - name: Build source and wheel archives
+        run: poetry build
+
+      - name: Publish distribution 📦 to PyPI
+        uses: pypa/[email protected]
+        with:
+          user: __token__
+          password: ${{ secrets.PYPI_PASSWORD }}

.gitignore

@@ -1,3 +1,6 @@
+.idea
+.idea/
+
 /docs/
 /project/docs/
 /tmp/

config.env

@@ -0,0 +1,8 @@
+LINKML_GENERATORS_PROJECT_ARGS=--config-file config.yaml
+
+### Extra layer of configuration for Makefile beyond
+### what 'gen-project --config-file config.yaml' provides.
+### Uncomment and set environment variables as needed.
+
+# LINKML_GENERATORS_MARKDOWN_ARGS=--no-mergeimports
+

config.yaml

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+# Configuration of generators (defaults illustrated)
+---
+generator_args:
+  excel:
+    mergeimports: true
+  owl:
+    mergeimports: true
+    metaclasses: true
+    type_objects: true
+    # throws 'Cannot handle metadata profile: rdfs'
+    # metadata_profile: rdfs
+  markdown:
+    mergeimports: true
+  graphql:
+    mergeimports: true
+  java:
+    mergeimports: true
+    metadata: true
+  jsonld:
+    mergeimports: true
+  jsonschema:
+    mergeimports: true
+  jsonldcontext:
+    mergeimports: true
+  python:
+    mergeimports: true
+  prefixmap:
+    mergeimports: true
+  proto:
+    mergeimports: true
+  shacl:
+    mergeimports: true
+  shex:
+    mergeimports: true
+  sqlddl:
+    mergeimports: true
+  typescript:
+    mergeimports: true
+    metadata: true
+
+...

examples/MixsCompliantData-MimsSoil-example.yaml

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+mims_soil_data:
+  - collection_date: "2013-03-25T12:42:31+01:00"
+    depth: 1.234 units
+    elev: 1.234 units
+    env_broad_scale: term [ONTOLOGY:123]
+    env_local_scale: term [ONTOLOGY:123]
+    env_medium: term [ONTOLOGY:123]
+    geo_loc_name: "text: text, text"
+    lat_lon: 45.1 45.9
+    project_name: absolutely any text
+    samp_name: msd1
+    samp_taxon_id: Gut Metagenome [NCBITaxon:749906]
+    seq_meth: absolutely any text
+  - collection_date: "2013-03-25T12:42:31+01:00"
+    depth: 1.234 units
+    elev: 1.234 units
+    env_broad_scale: term [ONTOLOGY:123]
+    env_local_scale: term [ONTOLOGY:123]
+    env_medium: term [ONTOLOGY:123]
+    geo_loc_name: "text: text, text"
+    lat_lon: 45.1 45.9
+    project_name: absolutely any text
+    samp_name: msd2
+    samp_taxon_id: Gut Metagenome [NCBITaxon:749906]
+    seq_meth: absolutely any text

project.Makefile

@@ -1 +1,5 @@
 ## Add your own custom Makefile targets here
+
+# we won't need to rerun this once we agree that we are done with bulk updating
+src/mixs_6_2_for_merge/schema/mixs_6_2_for_merge.yaml:
+	curl https://raw.githubusercontent.com/GenomicsStandardsConsortium/mixs6.2_release_candidate/main/generated-schema/mixs_6_2_rc.yaml > $@

src/data/examples/MixsCompliantData-MimsSoil-example.yaml

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+mims_soil_data:
+  - collection_date: "2013-03-25T12:42:31+01:00"
+    depth: 1.234 units
+    elev: 1.234 units
+    env_broad_scale: term [ONTOLOGY:123]
+    env_local_scale: term [ONTOLOGY:123]
+    env_medium: term [ONTOLOGY:123]
+    geo_loc_name: "text: text, text"
+    lat_lon: 45.1 45.9
+    project_name: absolutely any text
+    samp_name: msd1
+    samp_taxon_id: Gut Metagenome [NCBITaxon:749906]
+    seq_meth: absolutely any text
+  - collection_date: "2013-03-25T12:42:31+01:00"
+    depth: 1.234 units
+    elev: 1.234 units
+    env_broad_scale: term [ONTOLOGY:123]
+    env_local_scale: term [ONTOLOGY:123]
+    env_medium: term [ONTOLOGY:123]
+    geo_loc_name: "text: text, text"
+    lat_lon: 45.1 45.9
+    project_name: absolutely any text
+    samp_name: msd2
+    samp_taxon_id: Gut Metagenome [NCBITaxon:749906]
+    seq_meth: absolutely any text

src/data/examples/invalid/MixsCompliantData-MimsSoil-example-undefined-slot.yaml

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+undefined_slot:
+  - collection_date: "2013-03-25T12:42:31+01:00"
+    depth: 1.234 units
+    elev: 1.234 units
+    env_broad_scale: term [ONTOLOGY:123]
+    env_local_scale: term [ONTOLOGY:123]
+    env_medium: term [ONTOLOGY:123]
+    geo_loc_name: "text: text, text"
+    lat_lon: 45.1 45.9
+    project_name: absolutely any text
+    samp_name: msd1
+    samp_taxon_id: Gut Metagenome [NCBITaxon:749906]
+    seq_meth: absolutely any text
+  - collection_date: "2013-03-25T12:42:31+01:00"
+    depth: 1.234 units
+    elev: 1.234 units
+    env_broad_scale: term [ONTOLOGY:123]
+    env_local_scale: term [ONTOLOGY:123]
+    env_medium: term [ONTOLOGY:123]
+    geo_loc_name: "text: text, text"
+    lat_lon: 45.1 45.9
+    project_name: absolutely any text
+    samp_name: msd2
+    samp_taxon_id: Gut Metagenome [NCBITaxon:749906]
+    seq_meth: absolutely any text

src/data/examples/valid/MixsCompliantData-MimsSoil-example.yaml

@@ -0,0 +1,25 @@
+mims_soil_data:
+  - collection_date: "2013-03-25T12:42:31+01:00"
+    depth: 1.234 units
+    elev: 1.234 units
+    env_broad_scale: term [ONTOLOGY:123]
+    env_local_scale: term [ONTOLOGY:123]
+    env_medium: term [ONTOLOGY:123]
+    geo_loc_name: "text: text, text"
+    lat_lon: 45.1 45.9
+    project_name: absolutely any text
+    samp_name: msd1
+    samp_taxon_id: Gut Metagenome [NCBITaxon:749906]
+    seq_meth: absolutely any text
+  - collection_date: "2013-03-25T12:42:31+01:00"
+    depth: 1.234 units
+    elev: 1.234 units
+    env_broad_scale: term [ONTOLOGY:123]
+    env_local_scale: term [ONTOLOGY:123]
+    env_medium: term [ONTOLOGY:123]
+    geo_loc_name: "text: text, text"
+    lat_lon: 45.1 45.9
+    project_name: absolutely any text
+    samp_name: msd2
+    samp_taxon_id: Gut Metagenome [NCBITaxon:749906]
+    seq_meth: absolutely any text