chore: Merge branch 'main' into iss-129

.github/workflows/docs-mkdocs.yml

@@ -0,0 +1,25 @@
+name: docs
+on:
+  workflow_dispatch:
+  release:
+    types:
+      - published
+  push:
+    branches:
+      - main
+    paths:
+      - "docs/**"
+      - "**.md"
+      - .github/workflows/docs-mkdocs.yml
+      - mkdocs.yml
+
+jobs:
+  mkdocs:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+        with:
+          fetch-depth: 0
+      - uses: CCBR/actions/mkdocs-mike@main
+        with:
+          github-token: ${{ github.token }}

CHANGELOG.md

@@ -1,13 +1,25 @@
 ## RENEE development version
 
-- Minor documentation improvements. (#132, #135, @kelly-sovacool)
+### New features
+
 - Support hg38 release 45 on biowulf & FRCE. (#127, @kelly-sovacool)
-- Show the name of the pipeline rather than the python script for CLI help messages. (#131, @kelly-sovacool)
 - hg38 genome index files now include decoy & virus sequences. (#136, @kelly-sovacool)
   - Additionally, `--genome` is no longer required and is set to `hg38_36` by default.
-- Add GUI instructions to the documentation website. (#38, @samarth8392)
+- Set default shared singularity SIF directory for biowulf and frce. (#94, @kelly-sovacool)
+- Add `renee gui` subcommand to launch the graphical user interface. (#94, @kelly-sovacool)
+  - Previously, `renee_gui` (with an underscore) was a command in the `ccbrpipeliner` module.
+
+### Bug fixes
+
 - Ensure `renee build` creates necessary `config` directory during initialization. (#139, @kelly-sovacool)
 
+### Documentation updates
+
+- Minor documentation improvements. (#132, #135, @kelly-sovacool)
+- Add GUI instructions to the documentation website. (#38, @samarth8392)
+- The docs website now has a dropdown menu to select which version to view. The latest release is shown by default. (#150, @kelly-sovacool)
+- Show the name of the pipeline rather than the python script for CLI help messages. (#131, @kelly-sovacool)
+
 ## RENEE 2.5.12
 
 - Minor documentation improvements. (#100, @kelly-sovacool)

README.md

@@ -3,7 +3,7 @@
 An open-source, reproducible, and scalable solution for analyzing RNA-seq data.
 
 [![Tests](https://github.com/CCBR/RENEE/actions/workflows/main.yaml/badge.svg)](https://github.com/CCBR/RENEE/actions/workflows/main.yaml)
-[![mkdocs](https://github.com/CCBR/RENEE/actions/workflows/docs.yml/badge.svg)](https://github.com/CCBR/RENEE/actions/workflows/docs.yml)
+[![docs](https://github.com/CCBR/RENEE/actions/workflows/docs-mkdocs.yml/badge.svg)](https://github.com/CCBR/RENEE/actions/workflows/docs-mkdocs.yml)
 [![DOI](https://zenodo.org/badge/447297455.svg)](https://zenodo.org/doi/10.5281/zenodo.10553198)
 
 ### Table of Contents

bin/redirect

@@ -67,4 +67,4 @@ elif [[ $ISFRCE == true ]];then
 	export PATH="/mnt/projects/CCBR-Pipelines/bin:$PATH"
 fi
 
-${TOOLDIR}/src/renee/__main__.py "$@" || true
+${TOOLDIR}/main.py "$@" || true

docs/requirements.txt

@@ -1,34 +1,13 @@
-Babel==2.8.0
-click==7.1.2
-future==0.18.2
-gitdb==4.0.5
-GitPython==3.1.7
-htmlmin==0.1.12
-importlib-metadata==1.7.0
-Jinja2==2.11.2
-joblib==0.16.0
-jsmin==3.0.0
-livereload==2.6.1
-lunr==0.5.8
-Markdown==3.2.2
-MarkupSafe==1.1.1
-mkdocs==1.1.2
-mkdocs-awesome-pages-plugin==2.2.1
-mkdocs-git-revision-date-localized-plugin==0.7
+mkdocs
+#https://pypi.org/project/mkdocs-git-revision-date-localized-plugin/
+mkdocs-git-revision-date-localized-plugin
+#https://pypi.org/project/mkdocs-minify-plugin/
+mkdocs-minify-plugin
+#https://pypi.org/project/mkdocs-git-revision-date-plugin/
+mkdocs-git-revision-date-plugin
+#https://pypi.org/project/mkdocs-material/
 mkdocs-material
+#https://pypi.org/project/mkdocs-material-extensions/
 mkdocs-material-extensions
-mkdocs-minify-plugin==0.3.0
-mkdocs-redirects==1.0.1
-nltk==3.5
-Pygments==2.6.1
-pymdown-extensions==7.1
-pytz==2020.1
-PyYAML==5.3.1
-regex==2020.7.14
-six==1.15.0
-smmap==3.0.4
-tornado==6.0.4
-tqdm==4.48.2
-zipp==3.1.0
-mkdocs-git-revision-date-plugin
+#https://github.com/jimporter/mike
 mike

main.py

@@ -0,0 +1,16 @@
+#!/usr/bin/env python
+import os
+import re
+import sys
+from src.renee.__main__ import main
+
+# add script directory to the path to allow the CLI to work out-of-the-box
+# without the need to install it via pip first
+SCRIPT_DIR = os.path.join(os.path.dirname(os.path.abspath(__file__)), "src", "renee")
+sys.path.append(SCRIPT_DIR)
+
+if (
+    __name__ == "__main__"
+):  # this block is adapted from the executable file created by `pip install`
+    sys.argv[0] = re.sub(r"(-script\.pyw|\.exe)?$", "", sys.argv[0])
+    sys.exit(main())

mkdocs.yml

@@ -42,6 +42,10 @@ plugins:
   - git-revision-date
   - minify:
       minify_html: true
+  - mike:
+      alias_type: symlink
+      canonical_version: latest
+      version_selector: true
 
 # Customization
 extra:

pyproject.toml

@@ -33,12 +33,13 @@ classifiers = [
     "Programming Language :: Python :: 3.9",
     "Topic :: Scientific/Engineering :: Bio-Informatics",
 ]
-requires-python = ">=3.8"
+requires-python = ">=3.11"
 dependencies = [
+    "argparse",
     "Click >= 8.1.3",
+    "PySimpleGui < 5",
     "snakemake >= 7, < 8",
     "snaketool-utils >= 0.0.5",
-    "argparse"
 ]
 
 [project.optional-dependencies]