docs: refresh docs

cancervariants · Mar 30, 2024 · 31f037c · 31f037c
1 parent 0c7b328
commit 31f037c
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diff --git a/.github/workflows/checks.yaml b/.github/workflows/checks.yaml
@@ -35,3 +35,23 @@ jobs:
 
       - name: Check style
         run: python3 -m ruff check . && python3 -m ruff format --check .
+  docs:
+    runs-on: ubuntu-latest
+    env:
+      SPHINX_GITHUB_CHANGELOG_TOKEN: ${{ secrets.SPHINX_GITHUB_CHANGELOG_TOKEN }}
+    steps:
+      - uses: actions/checkout@v3
+
+      - name: Set up Python
+        uses: actions/setup-python@v4
+        with:
+          python-version: 3.11
+
+      - name: Install dependencies
+        run: |
+          python3 -m pip install --upgrade pip
+          python3 -m pip install '.[docs]'
+
+      - name: Attempt docs build
+        working-directory: ./docs
+        run: make html
diff --git a/LICENSE b/LICENSE
@@ -1,6 +1,6 @@
 MIT License
 
-Copyright (c) 2018 VICC
+Copyright (c) 2018-2024 VICC
 
 Permission is hereby granted, free of charge, to any person obtaining a copy
 of this software and associated documentation files (the "Software"), to deal

diff --git a/docs/Makefile b/docs/Makefile
@@ -1,11 +1,12 @@
 # Minimal makefile for Sphinx documentation
 #
 
-# You can set these variables from the command line.
-SPHINXOPTS    =
-SPHINXBUILD   = sphinx-build
-SOURCEDIR     = .
-BUILDDIR      = _build
+# You can set these variables from the command line, and also
+# from the environment for the first two.
+SPHINXOPTS    ?=
+SPHINXBUILD   ?= sphinx-build
+SOURCEDIR     = source
+BUILDDIR      = build
 
 # Put it first so that "make" without argument is like "make help".
 help:
@@ -16,4 +17,4 @@ help:
 # Catch-all target: route all unknown targets to Sphinx using the new
 # "make mode" option.  $(O) is meant as a shortcut for $(SPHINXOPTS).
 %: Makefile
-	@$(SPHINXBUILD) -M $@ "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)
+	@$(SPHINXBUILD) -M $@ "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)
diff --git a/docs/__authors__.py b/docs/__authors__.py
diff --git a/docs/cite.rst b/docs/cite.rst
diff --git a/docs/cite_files/metakb-preprint.bib b/docs/cite_files/metakb-preprint.bib
diff --git a/docs/cite_files/metakb-preprint.enw b/docs/cite_files/metakb-preprint.enw
diff --git a/docs/cite_files/metakb-preprint.ris b/docs/cite_files/metakb-preprint.ris
diff --git a/docs/cite_files/metakb-preprint.xml b/docs/cite_files/metakb-preprint.xml
diff --git a/docs/cli/README.md b/docs/cli/README.md