Merge branch 'main' into main

Author: grst

.github/workflows/make-json.yml

@@ -16,16 +16,15 @@ jobs:
     steps:
       - name: Checkout repository
         uses: actions/checkout@v4
-      - name: setup-yq
-        run: |
-          sudo curl -L "https://github.com/mikefarah/yq/releases/download/v4.28.2/yq_linux_amd64" > /usr/local/bin/yq
-          sudo chmod +x /usr/local/bin/yq
-      - name: convert to json
+      - name: Install uv
+        uses: astral-sh/setup-uv@v7
+        with:
+          cache-dependency-glob: scripts/pyproject.toml
+      - name: Execute validation script and create output directory
         run: |
-          mkdir build
-          touch build/.nojekyll
-          cat packages/**/meta.yaml
-          yq -o=json packages/**/meta.yaml | jq -s . > build/ecosystem.json
+          uvx --from ./scripts validate-registry --registry-dir packages --outdir=build
+        env:
+          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
       - name: Upload GitHub Pages artifact
         uses: actions/upload-pages-artifact@v3
         with:

.github/workflows/register-template-repos.yml

@@ -13,20 +13,16 @@ jobs:
       - uses: actions/checkout@v4
         with:
           token: ${{ secrets.BOT_GH_TOKEN }}
-      - name: Set up Python 3.13
-        uses: actions/setup-python@v6
+      - name: Install uv
+        uses: astral-sh/setup-uv@v7
         with:
-          python-version: "3.13"
-          cache: "pip"
-          cache-dependency-path: "**/pyproject.toml"
-      - name: Install build dependencies
-        run: python -m pip install --upgrade pip wheel
-      - name: Install package with scripts
-        run: pip install ./scripts
+          cache-dependency-glob: scripts/pyproject.toml
       - name: Update template repo registry
-        run: register-template-repos template-repos.yml
+        run: uvx --from ./scripts register-template-repos template-repos.yml
         env:
           GITHUB_TOKEN: "${{ secrets.BOT_GH_TOKEN }}"
+          FORCE_COLOR: "1"
+          COLUMNS: "150"
       - uses: EndBug/add-and-commit@v9
         with:
           add: ./template-repos.yml

.gitignore

@@ -3,3 +3,5 @@ __pycache__/
 .*cache/
 
 /.vscode/
+.venv
+schema.pyi

.pre-commit-config.yaml

@@ -21,19 +21,23 @@ repos:
     rev: v3.6.2
     hooks:
       - id: prettier
+  - repo: https://github.com/tox-dev/pyproject-fmt
+    rev: v2.6.0
+    hooks:
+      - id: pyproject-fmt
   # package metadata
   - repo: https://github.com/python-jsonschema/check-jsonschema
-    rev: 0.34.1
+    rev: 0.35.0
     hooks:
       - id: check-jsonschema
-        files: "schema.json"
+        files: "scripts/src/ecosystem_scripts/schema.json"
         args: ["--check-metaschema"]
   - repo: https://github.com/python-jsonschema/check-jsonschema
-    rev: 0.34.1
+    rev: 0.35.0
     hooks:
       - id: check-jsonschema
         files: "packages/.*/meta.yaml"
-        args: ["--schemafile", "schema.json"]
+        args: ["--schemafile", "scripts/src/ecosystem_scripts/schema.json"]
   - repo: local
     hooks:
       - id: forbid-to-commit
@@ -45,7 +49,7 @@ repos:
         exclude: "^packages/.*/meta.yaml$"
   # template repo registry
   - repo: https://github.com/astral-sh/ruff-pre-commit
-    rev: v0.14.2
+    rev: v0.14.5
     hooks:
       - id: ruff-check
         args: [--fix, --exit-non-zero-on-fix]

README.md

@@ -16,9 +16,10 @@ It **does not** imply endorsement or that an in-depth review has been performed.
 
 Submit a pull-request adding a `meta.yaml` file for your package to the `packages` directory.
 
-- Please refer to other entries for examples
-- The full definition of available fields is available in [`schema.json`](schema.json)
 - Please copy the checklist from below into the pull request description and answer all questions.
+- Please refer to other entries for examples
+- The full definition of available fields is available in [`schema.json`](scripts/src/ecosystem_scripts/schema.json)
+- You can add a logo in svg/png/webp format if you like. Currently it is not used on our website, though.
 
 ## What are the requirements for an ecosystem package?
 

packages/CellAnnotator/meta.yaml

@@ -1,6 +1,6 @@
 name: CellAnnotator
 description: |
-  CellAnnotator is a leightweight tool to query large language models for cell type labels in scRNA-seq data. It can incorporate prior knowledge, and it creates consistent labels across samples in your study.
+  CellAnnotator is a lightweight tool to query large language models for cell type labels in scRNA-seq data. It can incorporate prior knowledge, and it creates consistent labels across samples in your study.
 project_home: https://github.com/quadbio/cell-annotator
 documentation_home: https://cell-annotator.readthedocs.io/en/latest/
 install:
@@ -13,6 +13,6 @@ tags:
   - cell state
 license: MIT
 version: v0.1.3
-authors:
+contact:
   - Marius1311
 test_command: pip install -e '.[test]' && pytest

packages/CellCharter/meta.yaml

@@ -15,7 +15,7 @@ tags:
   - gaussian mixture model
 license: BSD-3-Clause
 version: v0.3.1
-authors:
+contact:
   - marcovarrone
 test_command: |
   pip install ".[test]" && pytest

packages/CellMapper/meta.yaml

@@ -12,6 +12,6 @@ tags:
   - query-to-reference
 license: MIT
 version: v0.1.2
-authors:
+contact:
   - Marius1311
 test_command: pip install -e '.[test]' && pytest

packages/CellOracle/meta.yaml

@@ -14,8 +14,8 @@ tags:
   - TF
 license: Apache-2.0
 version: v0.10.12
-authors:
-  - KenjiKamimoto-wustl122
+contact:
+  - KenjiKamimoto-ac
   - sam-morris
   - cmhct7
 test_command: |

packages/CellRank/meta.yaml

@@ -17,7 +17,7 @@ tags:
   - trajectory-generation
 license: BSD-3-Clause
 version: v1.5.1
-authors:
+contact:
   - Marius1311
   - michalk8
   - WeilerP