From d07b34e2f492a304a4b7217f0b24d7f300903fad Mon Sep 17 00:00:00 2001 From: Yelena Cox <107718499+yelenacox@users.noreply.github.com> Date: Mon, 29 Jun 2026 15:45:19 -0500 Subject: [PATCH 1/3] Modifying 'meaning' to match LinkML prefixes Updated SNOMED CT codes to use 'snomedct' prefix. --- .../schema/EnumConsanguinityAssertion.yaml | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/src/cam_source_enums/schema/EnumConsanguinityAssertion.yaml b/src/cam_source_enums/schema/EnumConsanguinityAssertion.yaml index 0a47e27..183fcfd 100644 --- a/src/cam_source_enums/schema/EnumConsanguinityAssertion.yaml +++ b/src/cam_source_enums/schema/EnumConsanguinityAssertion.yaml @@ -8,16 +8,16 @@ enums: not_suspected: title: not-suspected description: Not suspected - meaning: snomed_ct:428263003 + meaning: snomedct:428263003 suspected: title: suspected description: Suspected - meaning: snomed_ct:415684004 + meaning: snomedct:415684004 known_present: title: known-present description: Known Present - meaning: snomed_ct:410515003 + meaning: snomedct:410515003 unknown: title: unknown description: Unknown - meaning: snomed_ct:261665006 + meaning: snomedct:261665006 From 58ba345d374c928a8608f59df325e05846fba530 Mon Sep 17 00:00:00 2001 From: Yelena Cox <107718499+yelenacox@users.noreply.github.com> Date: Wed, 1 Jul 2026 11:23:30 -0500 Subject: [PATCH 2/3] Modifying Copier for GH Actions * Modifying docs * Copier answers * Copier modifications to add GH actions --- .copier-answers.yml | 16 ++++++ .github/dependabot.yml | 13 +++++ .github/workflows/deploy-docs.yaml | 62 +++++++++++++++++++++ .github/workflows/main.yaml | 55 +++++++++++++++++++ .github/workflows/test_pages_build.yaml | 71 +++++++++++++++++++++++++ src/README.md | 4 ++ 6 files changed, 221 insertions(+) create mode 100644 .copier-answers.yml create mode 100644 .github/dependabot.yml create mode 100644 .github/workflows/deploy-docs.yaml create mode 100644 .github/workflows/main.yaml create mode 100644 .github/workflows/test_pages_build.yaml create mode 100644 src/README.md diff --git a/.copier-answers.yml b/.copier-answers.yml new file mode 100644 index 0000000..ee84780 --- /dev/null +++ b/.copier-answers.yml @@ -0,0 +1,16 @@ +# Changes here will be overwritten by Copier +_commit: v0.5.0 +_src_path: https://github.com/linkml/linkml-project-copier +add_example: false +copyright_year: '2026' +email: yelena.cox@vumc.org +existing_license_file: '' +full_name: Yelena Cox +gh_action_docs_preview: true +gh_action_pypi: false +github_org: include-dcc +license: MIT +project_description: Source enumerations for the INCLUDE Common Access Model +project_name: cam-source-enums +project_slug: cam_source_enums + diff --git a/.github/dependabot.yml b/.github/dependabot.yml new file mode 100644 index 0000000..127295b --- /dev/null +++ b/.github/dependabot.yml @@ -0,0 +1,13 @@ +# 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 + groups: + github-actions: + patterns: + - "*" diff --git a/.github/workflows/deploy-docs.yaml b/.github/workflows/deploy-docs.yaml new file mode 100644 index 0000000..fbf11d5 --- /dev/null +++ b/.github/workflows/deploy-docs.yaml @@ -0,0 +1,62 @@ +--- +name: Deploy docs +on: # yamllint disable-line rule:truthy + push: + branches: [main] + workflow_dispatch: + +permissions: {} + +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 + pages: write # to deploy to Pages + id-token: write # allow to generate an OpenID Connect (OIDC) token + + steps: + # https://github.com/actions/checkout + - name: Checkout + uses: actions/checkout@v6.0.2 + 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 + + # https://github.com/astral-sh/setup-uv + - name: Install uv + uses: astral-sh/setup-uv@v8.1.0 + with: + 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@v6.2.0 + with: + python-version: ${{ matrix.pyversion }} + + - name: Install just + run: | + uv tool install rust-just + + - name: Install dependencies + run: uv sync --group dev --no-progress + + - name: Generate schema documentation + run: | + just gen-doc + uv run mkdocs gh-deploy --force diff --git a/.github/workflows/main.yaml b/.github/workflows/main.yaml new file mode 100644 index 0000000..349c7d8 --- /dev/null +++ b/.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: + 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@v6.0.2 + with: + persist-credentials: false + + # https://github.com/astral-sh/setup-uv + - name: Install uv + 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@v6.2.0 + with: + python-version: ${{ matrix.python-version }} + + - name: Install just + run: | + uv tool install rust-just + + - name: Install project + run: uv sync --group dev + + - name: Run test suite + run: just test diff --git a/.github/workflows/test_pages_build.yaml b/.github/workflows/test_pages_build.yaml new file mode 100644 index 0000000..d2927e0 --- /dev/null +++ b/.github/workflows/test_pages_build.yaml @@ -0,0 +1,71 @@ +name: Preview documentation build + +on: # yamllint disable-line rule:truthy + pull_request: + types: + - opened + - reopened + - synchronize + +env: + CLICOLOR: 1 + +concurrency: preview-${{ github.ref }} + +permissions: {} + +jobs: + run: + # Don't run for PRs from forks which fails due to lack of permissions. + if: github.event.pull_request.head.repo.full_name == github.repository + # 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 + pull-requests: write # add comment on the PR with the preview URL + runs-on: ubuntu-latest + + strategy: + matrix: + pyversion: ["3.13"] + + steps: + # https://github.com/actions/checkout + - name: Checkout + uses: actions/checkout@v5.0.0 + with: + fetch-depth: 0 + + # https://github.com/actions/setup-python + - name: Set up Python + uses: actions/setup-python@v6.0.0 + with: + python-version: ${{ matrix.pyversion }} + # https://github.com/astral-sh/setup-uv + - name: Install uv + uses: astral-sh/setup-uv@v7.1.2 + with: + python-version: ${{ matrix.pyversion }} + enable-cache: true + cache-dependency-glob: "uv.lock" + + - name: Install just + run: | + uv tool install rust-just + + - name: Install dependencies + run: uv sync --dev --no-progress + + - name: Build documentation + run: | + just gen-doc + uv run mkdocs build -d site + touch site/.nojekyll + + # https://github.com/rossjrw/pr-preview-action + - name: Deploy preview + uses: rossjrw/pr-preview-action@v1.6.2 + with: + source-dir: site/ + preview-branch: gh-pages diff --git a/src/README.md b/src/README.md new file mode 100644 index 0000000..e006d1c --- /dev/null +++ b/src/README.md @@ -0,0 +1,4 @@ +# The linkML model and its Python representations + +This directory holds the schema, its Python representations +and optionally also additional Python code for the project. From 632a273ec61942b199fffc57d869ccc61bd21222 Mon Sep 17 00:00:00 2001 From: Yelena Cox <107718499+yelenacox@users.noreply.github.com> Date: Wed, 1 Jul 2026 11:24:58 -0500 Subject: [PATCH 3/3] Fix formatting of 'traverse_up' support note --- docs/term-expansion.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/docs/term-expansion.md b/docs/term-expansion.md index b974f61..b6f7843 100644 --- a/docs/term-expansion.md +++ b/docs/term-expansion.md @@ -12,4 +12,4 @@ This is the source of the enumeration files to be materialized by the [Term-Weav - include_self - true/false -* It does not currently support 'traverse_up' +*It does not currently support 'traverse_up'