Merge branch 'main' of https://github.com/theislab/single-cell-best-practices

Author: Zethson

.github/workflows/build_book.yml

@@ -35,6 +35,9 @@ jobs:
             v1-${{ github.ref }}
             v1-refs/heads/master
 
+      - name: Insert env-setup dropdown to all chapters
+        run: make dropdown
+
       - name: Build the JupyterBook
         run: make
 

.github/workflows/build_environments.yml

@@ -10,7 +10,7 @@ jobs:
         environments:
           [
             "jupyter-book/introduction/analysis_tools.yml",
-            "jupyter-book/preprocessing_visualization/preprocessing.yml",
+            "jupyter-book/preprocessing_visualization/preprocessing_visualization.yml",
             "jupyter-book/cellular_structure/clustering.yml",
             "jupyter-book/cellular_structure/annotation.yml",
             "jupyter-book/cellular_structure/integration.yml",

.pre-commit-config.yaml

@@ -7,11 +7,11 @@ default_stages:
 minimum_pre_commit_version: 2.16.0
 repos:
   - repo: https://github.com/pre-commit/mirrors-prettier
-    rev: v2.5.1
+    rev: v3.1.0
     hooks:
       - id: prettier
   - repo: https://github.com/astral-sh/ruff-pre-commit
-    rev: v0.8.6
+    rev: v0.9.7
     hooks:
       - id: ruff
         args: [--fix, --exit-non-zero-on-fix, --unsafe-fixes]

CONTRIBUTING.md

@@ -75,6 +75,57 @@ All chapters are available as Jupyter Notebooks and end-to-end executable.
 The diverse requirements of tools for the chapters do not allow it for us to provide a single environment that can build all chapters.
 Hence, we decided to provide minimal Conda environments per chapter. These can be found in the respective folders.
 
+## Adding changelog entries with `towncrier`
+
+We use `towncrier` to manage our changelog. Here’s how to include a changelog entry when making a PR:
+
+1. Install `towncrier` (only once):
+
+```bash
+pip install towncrier
+```
+
+2. Make your pull request as usual.
+
+3. After opening your PR, note the PR number (e.g., 34), and create a changelog fragment:
+
+```bash
+towncrier create -c 'update blah blah ([#34](https://github.com/theislab/single-cell-best-practices/pull/34)) <sub>@seohyonkim</sub>' 34.changed.md
+```
+
+Replace "update blah blah" with a brief description of your change, PR number with your PR number, and the author of the PR with your github tag.
+Valid categories for the filename of the `markdown` are:
+
+`added`
+`changed`
+`fixed`
+`removed`
+
+4. This will create a `.md` file (e.g., `34.changed.md`) in the `changelog.d/` directory (at the root of the repo). Make sure this file is included in your commit.
+
+5. Push your changes again.
+
+### Releasing a new version (maintainers only)
+
+To release a new version:
+
+1. Run Towncrier to build the changelog:
+
+```bash
+towncrier build --yes --version 2.0.0
+```
+
+This will update `CHANGELOG.md` and remove the `changelog.d/` directory.
+
+2. Add contributor names and links to the PR manually under each relevant PR entry in the generated `CHANGELOG.md`.
+
+3. Recreate the `changelog.d/` directory for future PRs:
+
+```bash
+mkdir changelog.d
+touch changelog.d/.gitkeep
+```
+
 ## Environment setup
 
 Run the following command with the environment file of choice to create the environment for the chapter that you want to build.

Makefile

@@ -4,6 +4,9 @@ JUPYTER_KERNEL := python3
 build:
 	jupyter-book build $(JUPYTER_BOOK_DIR)
 
+dropdown:
+	python3 scripts/insert_dropdown.py 	
+
 clean:
 	jupyter-book clean --all $(JUPYTER_BOOK_DIR)
 

changelog.d/345.added.md

@@ -1 +1 @@
-Add `release notes`
+Add new feature `changelog`. Changelog fragments will be added in `changelog` chapter. ([#345](https://github.com/theislab/single-cell-best-practices/pull/345)) <sub>@seohyonkim</sub>

changelog.d/347.changed.md

@@ -0,0 +1 @@
+Add dataset generator and updatae texts in `Interoperability` chapter. ([#347](https://github.com/theislab/single-cell-best-practices/pull/347)) <sub>@seohyonkim</sub>

changelog.d/348.added.md

@@ -0,0 +1 @@
+Add env- and lamin-setup dropdown with `make dropdown`. ([#348](https://github.com/theislab/single-cell-best-practices/pull/348)) <sub>@LuisHenzlmeier</sub>

changelog.d/351.added.md

@@ -0,0 +1 @@
+Add manual to use `towncrier` in `CONTRIBUTING.md`. ([#351](https://github.com/theislab/single-cell-best-practices/pull/351)) <sub>@seohyonkim</sub>

jupyter-book/_static/book.js

@@ -18,7 +18,7 @@
     document.querySelector(".prev-next-bottom").remove();
     document.querySelector(".footer").remove();
     var elementsToRemove = document.querySelectorAll(
-      ".remove-from-content-only"
+      ".remove-from-content-only",
     );
     elementsToRemove.forEach(function (el) {
       el.remove();
@@ -30,8 +30,8 @@
     var style = document.createElement("style");
     style.appendChild(
       document.createTextNode(
-        "hypothesis-sidebar, hypothesis-notebook, hypothesis-adder{display:none!important;}"
-      )
+        "hypothesis-sidebar, hypothesis-notebook, hypothesis-adder{display:none!important;}",
+      ),
     );
     document.getElementsByTagName("head")[0].appendChild(style);
   }