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Fix GHAs #203

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Merged
ialarmedalien merged 6 commits into from
Mar 18, 2025
Merged

Fix GHAs #203

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ad920c2
updating GHAs to remove all the code checks (for now) and run docs de…
ialarmedalien Mar 18, 2025
1906c98
remove accidental line addition
ialarmedalien Mar 18, 2025
387fffc
gha fix
ialarmedalien Mar 18, 2025
a40338d
adding in uv lock file, fixing a few bits and pieces in the GHA and m…
ialarmedalien Mar 18, 2025
b71ec07
adding in uv lock file, fixing a few bits and pieces in the GHA and m…
ialarmedalien Mar 18, 2025
b303a1e
remove comments
ialarmedalien Mar 18, 2025
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6 changes: 2 additions & 4 deletions .github/workflows/deploy-docs.yaml
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Original file line number Diff line number Diff line change
Expand Up @@ -24,13 +24,11 @@ jobs:
# Install a specific version of uv.
version: "0.6.6"

- name: Install dependencies.
run: uv sync --all-extras

- name: Build documentation.
run: |
mkdir -p docs
touch docs/.nojekyll
uv sync --group docs
make gendoc
([ ! -f docs/about.md ] && cp src/docs/*.md docs/) || true
# ([ ! -f docs/about.md ] && cp src/docs/*.md docs/) || true
make mkd-gh-deploy
15 changes: 9 additions & 6 deletions .github/workflows/on_branch_merge.yaml
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Expand Up @@ -10,11 +10,14 @@
run_unit_tests:
uses: ./.github/workflows/run_tests.yaml

run_code_ql:
uses: ./.github/workflows/codeql.yaml
run_linkml_tasks:
uses: ./.github/workflows/run_tests.yaml

# run_code_ql:
# uses: ./.github/workflows/codeql.yaml

run_codacy:
uses: ./.github/workflows/codacy.yaml
# run_codacy:
# uses: ./.github/workflows/codacy.yaml

run_trivy:
uses: ./.github/workflows/trivy.yaml
# run_trivy:
# uses: ./.github/workflows/trivy.yaml
Comment on lines +14 to +23

Check warning

Code scanning / CodeQL

Workflow does not contain permissions Medium

Actions job or workflow does not limit the permissions of the GITHUB_TOKEN. Consider setting an explicit permissions block, using the following as a minimal starting point: {}
15 changes: 9 additions & 6 deletions .github/workflows/on_pr.yaml
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Expand Up @@ -12,11 +12,14 @@
run_unit_tests:
uses: ./.github/workflows/run_tests.yaml

run_code_ql:
uses: ./.github/workflows/codeql.yaml
run_linkml_tasks:
uses: ./.github/workflows/run_tests.yaml

# run_code_ql:
# uses: ./.github/workflows/codeql.yaml

run_codacy:
uses: ./.github/workflows/codacy.yaml
# run_codacy:
# uses: ./.github/workflows/codacy.yaml

run_trivy:
uses: ./.github/workflows/trivy.yaml
# run_trivy:
# uses: ./.github/workflows/trivy.yaml
Comment on lines +16 to +25

Check warning

Code scanning / CodeQL

Workflow does not contain permissions Medium

Actions job or workflow does not limit the permissions of the GITHUB_TOKEN. Consider setting an explicit permissions block, using the following as a minimal starting point: {}
41 changes: 41 additions & 0 deletions .github/workflows/test_pages_build.yaml
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@@ -0,0 +1,41 @@
name: Preview credit_engine documentation build

on:
pull_request:
types:
- opened
- reopened
- synchronize

concurrency: preview-${{ github.ref }}

jobs:
run:
runs-on: ubuntu-latest
steps:
- name: Checkout
uses: actions/checkout@main
with:
fetch-depth: 0

- name: Set up Python 3
uses: actions/setup-python@main
with:
python-version: 3.12

- name: Install uv
uses: astral-sh/setup-uv@v5

- name: Build documentation
run: |
mkdir -p site
touch site/.nojekyll
uv sync --group docs
make gendoc
uv run mkdocs build -d site

- name: Deploy preview
uses: rossjrw/pr-preview-action@v1
with:
source-dir: site/
preview-branch: gh-pages
6 changes: 4 additions & 2 deletions Makefile
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Expand Up @@ -197,10 +197,12 @@ $(DOCDIR):
mkdir -p $@

gendoc: $(DOCDIR)
cp -rf $(SRC)/docs/files/* $(DOCDIR) ; \
# cp -rf $(SRC)/docs/files/* $(DOCDIR) ; \
$(RUN) gen-doc ${GEN_DOC_ARGS} -d $(DOCDIR) --template-directory $(DOCTEMPLATES) $(SOURCE_SCHEMA_PATH)
mkdir -p $(DOCDIR)/js
$(RUN) cp $(SRC)/docs/js/*.js $(DOCDIR)/js/
cp $(SRC)/docs/js/*.js $(DOCDIR)/js/
mkdir -p $(DOCDIR)/pages
cp $(SRC)/docs/pages/*.md $(DOCDIR)/pages/

testdoc: gendoc serve

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3 changes: 2 additions & 1 deletion mkdocs.yml
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Expand Up @@ -13,8 +13,9 @@ plugins:
- mermaid2
nav:
- Index: index.md
- About: pages/about.md
- KBase DOIs: pages/kbase_dois.md
- GitHub Repo: https://github.com/kbase/credit_engine
# - KBase DOIs: docs/kbase_dois.md

site_url: https://kbase.github.io/credit_engine
repo_url: https://github.com/kbase/credit_engine
Expand Down
2,767 changes: 0 additions & 2,767 deletions poetry.lock
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This file was deleted.

0 src/docs/files/about.md → src/docs/pages/about.md
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0 src/docs/files/kbase_dois.md → src/docs/pages/kbase_dois.md
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1,640 changes: 1,640 additions & 0 deletions uv.lock
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