Merge branch 'concatenation-of-unimodal-data' of https://github.com/m…

…ikelkou/scverse-tutorials into concatenation-of-unimodal-data
scverse · Aug 3, 2023 · cd978a9 · cd978a9
2 parents 322adcc + 81e835e
commit cd978a9
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diff --git a/.github/workflows/execute-nbs.yaml b/.github/workflows/execute-nbs.yaml
@@ -2,6 +2,9 @@ name: Execute notebooks
 on:
     pull_request_target:
         branches: [main]
+        paths:
+            - "docs/**"
+            - "environment.yml"
 
 jobs:
     runnbs:

diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
@@ -7,15 +7,15 @@ default_stages:
 minimum_pre_commit_version: 2.16.0
 repos:
     - repo: https://github.com/psf/black
-      rev: "23.3.0"
+      rev: "23.7.0"
       hooks:
           - id: black-jupyter
     - repo: https://github.com/asottile/blacken-docs
-      rev: 1.13.0
+      rev: 1.15.0
       hooks:
           - id: blacken-docs
     - repo: https://github.com/pre-commit/mirrors-prettier
-      rev: v3.0.0-alpha.9-for-vscode
+      rev: v3.0.0
       hooks:
           - id: prettier
             # Newer versions of node don't work on systems that have an older version of GLIBC
@@ -24,8 +24,8 @@ repos:
             # See https://github.com/scverse/cookiecutter-scverse/issues/143 and
             # https://github.com/jupyterlab/jupyterlab/issues/12675
             language_version: "17.9.1"
-    - repo: https://github.com/charliermarsh/ruff-pre-commit
-      rev: v0.0.272
+    - repo: https://github.com/astral-sh/ruff-pre-commit
+      rev: v0.0.281
       hooks:
           - id: ruff
             args: [--fix, --exit-non-zero-on-fix]
@@ -49,13 +49,13 @@ repos:
             language: fail
             files: '.*\.rej$'
     - repo: https://github.com/python-jsonschema/check-jsonschema
-      rev: 0.23.1
+      rev: 0.23.3
       hooks:
           - id: check-jsonschema
             files: "tutorial-registry/schema.json"
             args: ["--check-metaschema"]
     - repo: https://github.com/python-jsonschema/check-jsonschema
-      rev: 0.23.1
+      rev: 0.23.3
       hooks:
           - id: check-jsonschema
             files: "tutorial-registry/tutorials/.*/meta.yaml"

diff --git a/docs/notebooks/basic-scrna-tutorial.ipynb b/docs/notebooks/basic-scrna-tutorial.ipynb
diff --git a/tutorial-registry/schema.json b/tutorial-registry/schema.json
@@ -55,8 +55,11 @@
                     "data structures",
                     "differential expression",
                     "functional analysis",
-                    "concatenation"
-
+                    "concatenation",
+                    "preprocessing",
+                    "cell-type annotation",
+                    "quality control",
+                    "visualization"
                 ]
             },
             "uniqueItems": true

diff --git a/tutorial-registry/tutorials/preprocessing-and-clustering/icon.webp b/tutorial-registry/tutorials/preprocessing-and-clustering/icon.webp
diff --git a/tutorial-registry/tutorials/preprocessing-and-clustering/meta.yaml b/tutorial-registry/tutorials/preprocessing-and-clustering/meta.yaml
@@ -0,0 +1,22 @@
+name: Preprocessing, clustering and cell-type annotation
+description: |
+    This fundamental single-cell tutorial guides you through the most common analysis steps, including quality control,
+    normalization, feature selection, dimensionality reduction, clustering and cell-type annotation.
+link: https://scverse-tutorials.readthedocs.io/en/latest/notebooks/basic-scrna-tutorial.html
+image: icon.webp
+primary_category: scRNA-seq
+tags:
+    - preprocessing
+    - cell-type annotation
+    - quality control
+    - visualization
+packages:
+    - anndata
+    - scanpy
+    - celltypist
+    - decoupler
+authors:
+    - ivirshup
+    - dbdimitrov
+    - AnnaChristina
+    - Hrovatin