Merge pull request #90 from compgenomicslab/dev-repo

update dev repo to main

Author: dengzq1234

.cache/v/cache/lastfailed

@@ -0,0 +1,8 @@
+{
+  "tests/test_alignment.py": true, 
+  "tests/test_annotate.py": true, 
+  "tests/test_emapper.py": true, 
+  "tests/test_plot.py": true, 
+  "tests/test_prune.py": true, 
+  "tests/test_taxonomic.py": true
+}

.github/workflows/deploy.yml

@@ -0,0 +1,44 @@
+name: Deploy Sphinx docs to GitHub Pages
+
+on:
+  push:
+    branches:
+      - main
+
+jobs:
+  build-and-deploy:
+    runs-on: ubuntu-latest
+
+    steps:
+      - name: Check out the code
+        uses: actions/checkout@v2
+
+      - name: Set up Python
+        uses: actions/setup-python@v2
+        with:
+          python-version: '3.x'
+
+      - name: Install dependencies
+        run: |
+          python -m pip install --upgrade pip
+          pip install sphinx sphinx-rtd-theme
+
+      - name: Build the documentation
+        run: make html
+        working-directory: ./docs
+
+      - name: Post-process HTML files
+        run: python post_process_html.py
+        working-directory: ./docs
+        
+      - name: Deploy to GitHub Pages
+        env:
+          ACTIONS_DEPLOY_KEY: ${{ secrets.ACTIONS_DEPLOY_KEY }}
+        run: |
+          cd docs/build/html
+          git init
+          git config user.name 'github-actions[bot]'
+          git config user.email 'github-actions[bot]@users.noreply.github.com'
+          git add .
+          git commit -m "Deploy documentation"
+          git push --force --quiet "https://${{ secrets.ACTIONS_DEPLOY_KEY }}@github.com/${{ github.repository }}.git" master:gh-pages

.gitignore

@@ -1,8 +1,14 @@
 *.pyc
 dist/
 dist/*
-build/
-build/*
+# Ignore build artifacts
+/build/
+/build/*
+/docs/build/
+/docs/build/*
+# Ignore Sphinx static files (if necessary)
+docs/source/_static/
+docs/source/_templates/
 *.egg-info/
 __pycache__/
 __pycache__/*

README.md

@@ -0,0 +1,20 @@
+# Minimal makefile for Sphinx documentation
+#
+
+# 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:
+	@$(SPHINXBUILD) -M help "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)
+
+.PHONY: help Makefile
+
+# 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)

docs/Makefile

@@ -0,0 +1,4 @@
+# Sphinx build info version 1
+# This file hashes the configuration used when building these files. When it is not found, a full rebuild will be done.
+config: 71c3667afe7096ee3bfc9c1417ac3e30
+tags: 645f666f9bcd5a90fca523b33c5a78b7