Merge pull request #647 from jashapiro/jashapiro/prep0.1.0

Add release notes for 0.1.0

.github/ISSUE_TEMPLATE/create-a-semantic-version-release.md

@@ -10,15 +10,17 @@ If issues must be resolved before creating a release, mark them as blockers in Z
 **Pre-release checklist:**
 
 - [ ] Any mentions of the release tag in the repository have been updated
-- [ ] All scheduled workflows are passing
-  - [ ] [Run all analysis modules](https://github.com/AlexsLemonade/OpenScPCA-analysis/actions/workflows/all_modules.yml) (trigger manually if needed)
+- [ ] All maintenance workflows are passing
+  - [ ] [Run all analysis modules](https://github.com/AlexsLemonade/OpenScPCA-analysis/actions/workflows/run_all-modules.yml) (trigger manually if needed)
   - [ ] [Spellcheck](https://github.com/AlexsLemonade/OpenScPCA-analysis/actions/workflows/spellcheck.yml) (trigger manually if needed)
-  - [ ] Code styling
+  - [ ] [Code styling](https://github.com/AlexsLemonade/OpenScPCA-analysis/actions/workflows/code-styling.yml) (optional, trigger manually)
 - [ ] All blocking issues have been resolved
-- [ ] Write release notes, which should include the following:
+- [ ] Write release notes and add them to [`CHANGELOG.md`](https://github.com/AlexsLemonade/OpenScPCA-analysis/blob/main/CHANGELOG.md), which should include the following:
   - Which modules have been added, if any?
   - Which modules have been deprecated, if any?
   - What has changed in the repo documentation, if anything?
   - Are there any _major_ shifts in project dependencies?
     For example, is there a package that was used throughout Docker environments that has been replaced?
   - Have there been any changes in repo file organization?
+- [ Create a release on GitHub ](https://github.com/AlexsLemonade/OpenScPCA-analysis/releases/new)
+  - populate the contents with the release notes added to the changelog.

.github/cron-issue-templates/create-periodic-release-template.md

@@ -3,7 +3,6 @@ Create a periodic release using [the periodic release workflow](https://github.c
 #### Pre-release checklist
 
 - [ ] All scheduled workflows are passing
-  - [ ] [Run all analysis modules](https://github.com/AlexsLemonade/OpenScPCA-analysis/actions/workflows/all_modules.yml) (trigger manually if needed)
+  - [ ] [Run all analysis modules](https://github.com/AlexsLemonade/OpenScPCA-analysis/actions/workflows/run_all-modules.yml) (trigger manually if needed)
   - [ ] [Spellcheck](https://github.com/AlexsLemonade/OpenScPCA-analysis/actions/workflows/spellcheck.yml) (trigger manually if needed)
-  - [ ] Code styling
 - [ ] All blocking issues have been resolved

.github/workflows/spellcheck.yml

@@ -6,6 +6,7 @@ on:
       - feature/*
     paths:
       - docs/**
+      - "*.md"
   workflow_dispatch:
   schedule:
     - cron: "0 0 15 * *" # 15th of every month at midnight
@@ -33,7 +34,7 @@ jobs:
         id: spell
         with:
           dictionary: .github/components/dictionary.txt
-          files: ${{ github.event_name == 'pull_request' && 'docs/* docs/*/* docs/*/*/*' || null }}
+          files: ${{ github.event_name == 'pull_request' && 'docs/* docs/*/* docs/*/*/* *.md' || null }}
 
       - name: Upload spell check errors
         uses: actions/upload-artifact@v4

CHANGELOG.md

@@ -0,0 +1,35 @@
+# Release notes for OpenScPCA-analysis
+
+This document contains release notes for versioned releases of the OpenScPCA-analysis repository.
+We will also periodically release and tag dated snapshots of the repository, but these will not be reflected in this document.
+
+<!--
+Add new release notes in reverse numerical order (newest first) below this comment
+
+You may want to add temporary notes here for tracking as features are added, before a new release is ready.
+-->
+
+
+## v0.1.0
+
+This is the initial versioned release of the OpenScPCA-analysis repository.
+The repository at this stage should be generally complete with respect to infrastructure, but the analysis is still only in the early stages.
+
+With respect to infrastructure, the repository contains the following components:
+
+- detailed documentation in the `docs` directory explaining how to interact with the OpenScPCA project and how to set up and run analyses (published at https://openscpca.readthedocs.io/)
+- a `create-analysis-module.py` script for setting up new analysis modules
+- `download-data.py` and `download-results.py` scripts to download data and results from the OpenScPCA project
+- template notebooks, scripts, environment files, and Docker images for analysis modules
+
+The repository contains the following analysis modules that are now in a relatively mature state:
+
+- `hello-R`
+- `hello-python`
+- `simulate-sce`
+- `doublet-detection`
+
+The following additional modules are in active development:
+
+- `cell-type-ewings`
+- `metacells`