restore env.yml

Author: flying-sheep

.cruft.json

@@ -20,6 +20,7 @@
       ],
       "_exclude_on_template_update": [
         ".github/ISSUE_TEMPLATE/**",
+        "environment.yml",
         "*.md",
         "src/**",
         "docs/*.md",

environment.yml

@@ -0,0 +1,25 @@
+# declare dependencies for binder and for executing notebooks on CI
+name: tutorials
+channels:
+  - conda-forge
+dependencies:
+  - python=3.12
+  - jupyter-cache
+  - ipykernel
+  - ipython
+  - jupyterlab-myst
+  - jupytext
+  - pip>=24.2
+  - pip:
+      - scanpy>=1.10
+      - scrublet
+      - leidenalg
+      # We need this commit: https://github.com/saezlab/decoupler-py/commit/0b3d9a975e06230ebbc32a6f97810be1730b8562
+      - decoupler @ git+https://github.com/saezlab/decoupler-py.git
+      - celltypist
+      - seaborn
+      - mudata
+      - muon
+      - mudatasets
+      - omnipath
+      - pooch

pyproject.toml

@@ -114,6 +114,7 @@ lint.pydocstyle.convention = "numpy"
 [tool.cruft]
 skip = [
   ".github/ISSUE_TEMPLATE",
+  "environment.yml",
   "*.md",
   "src",
   "docs/*.md",