Merge branch 'main' into main

Author: grst

.github/workflows/make-json.yml

@@ -6,28 +6,24 @@ on:
     branches: [main]
 
 concurrency:
-  group: "pages"
+  group: ${{ github.workflow }}-${{ github.ref }}
   cancel-in-progress: true
 
 jobs:
   mkjson:
     runs-on: ubuntu-latest
-
     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
+      - uses: actions/checkout@v5
+      - uses: astral-sh/setup-uv@v7
+      - 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 }}
+          FORCE_COLOR: "1"
+          COLUMNS: "150"
       - name: Upload GitHub Pages artifact
-        uses: actions/upload-pages-artifact@v3
+        uses: actions/upload-pages-artifact@v4
         with:
           path: "build"
 

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

@@ -10,23 +10,17 @@ jobs:
   register-template-repos:
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v4
+      - uses: actions/checkout@v5
         with:
           token: ${{ secrets.BOT_GH_TOKEN }}
-      - name: Set up Python 3.11
-        uses: actions/setup-python@v5
-        with:
-          python-version: "3.11"
-          cache: "pip"
-          cache-dependency-path: "**/pyproject.toml"
-      - name: Install build dependencies
-        run: python -m pip install --upgrade pip wheel
-      - name: Install package with scripts
-        run: pip install ./scripts
+      - name: Install uv
+        uses: astral-sh/setup-uv@v7
       - name: Update template repo registry
-        run: register-template-repos template-repos.yml
+        run: uvx --from ./scripts register-template-repos template-repos.yml
         env:
           GITHUB_TOKEN: "${{ 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

@@ -8,7 +8,7 @@ minimum_pre_commit_version: 2.16.0
 repos:
   # all files
   - repo: https://github.com/pre-commit/pre-commit-hooks
-    rev: v5.0.0
+    rev: v6.0.0
     hooks:
       - id: detect-private-key
       - id: check-ast
@@ -17,36 +17,64 @@ repos:
         args: [--fix=lf]
       - id: trailing-whitespace
       - id: check-case-conflict
-  - repo: https://github.com/pre-commit/mirrors-prettier
-    rev: v4.0.0-alpha.8
+  - repo: https://github.com/rbubley/mirrors-prettier
+    rev: v3.6.2
     hooks:
       - id: prettier
   # package metadata
   - repo: https://github.com/python-jsonschema/check-jsonschema
-    rev: 0.33.2
+    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: 0.33.2
+    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
         name: Check files in `packages` directory
         entry: |
-          Only files named `meta.yaml` are permitted in the packages directory
+          Only `meta.yaml` and logo files are permitted in the packages directory
         language: fail
         files: "^packages/.*$"
-        exclude: "^packages/.*/meta.yaml$"
-  # template repo registry
+        exclude: "^packages/.*/(meta.yaml|logo\\..*)$"
+  # scripts
   - repo: https://github.com/astral-sh/ruff-pre-commit
-    rev: v0.12.4
+    rev: v0.14.6
     hooks:
-      - id: ruff
+      - id: ruff-check
         args: [--fix, --exit-non-zero-on-fix]
+        files: ^scripts/.*$
       - id: ruff-format
+        files: ^scripts/.*$
+  - repo: https://github.com/tox-dev/pyproject-fmt
+    rev: v2.11.1
+    hooks:
+      - id: pyproject-fmt
+  - repo: https://github.com/camptocamp/jsonschema-gentypes
+    rev: "2.12.0"
+    hooks:
+      - id: jsonschema-gentypes
+        args:
+          - --json-schema=scripts/src/ecosystem_scripts/schema.json
+          - --python=scripts/src/ecosystem_scripts/schema.pyi
+        files: ^scripts/.*/schema.json$
+  - repo: https://github.com/pre-commit/mirrors-mypy
+    rev: v1.18.2
+    hooks:
+      - id: mypy
+        args: [--config-file=scripts/pyproject.toml, scripts]
+        pass_filenames: false
+        additional_dependencies:
+          - httpx
+          - types-jsonschema
+          - pillow
+          - pygithub
+          - types-PyYAML
+          - rich
+        files: ^scripts/.*$

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 +13,7 @@ tags:
   - cell state
 license: MIT
 version: v0.1.3
-authors:
+contact:
   - Marius1311
 test_command: pip install -e '.[test]' && pytest
+category: ecosystem

packages/CellCharter/meta.yaml

@@ -15,7 +15,8 @@ tags:
   - gaussian mixture model
 license: BSD-3-Clause
 version: v0.3.1
-authors:
+contact:
   - marcovarrone
 test_command: |
   pip install ".[test]" && pytest
+category: ecosystem

packages/CellMapper/meta.yaml

@@ -12,6 +12,7 @@ tags:
   - query-to-reference
 license: MIT
 version: v0.1.2
-authors:
+contact:
   - Marius1311
 test_command: pip install -e '.[test]' && pytest
+category: ecosystem

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: |
@@ -42,3 +42,4 @@ test_command: |
   pip install .
   # command to run tests
   pytest -v
+category: ecosystem

packages/CellRank/meta.yaml

@@ -17,9 +17,10 @@ tags:
   - trajectory-generation
 license: BSD-3-Clause
 version: v1.5.1
-authors:
+contact:
   - Marius1311
   - michalk8
   - WeilerP
 test_command: |
   pip install ".[test]" && pytest
+category: ecosystem