Move to scanpy 1.9.8

.github/workflows/python-package.yml

@@ -13,20 +13,31 @@ jobs:
     runs-on: ubuntu-latest
     strategy:
       matrix:
-        python-version: ["3.8", "3.9"]
+        python-version: ["3.12"]
 
     steps:
     - uses: actions/checkout@v2
 
     - name: Setup mamba
-      uses: mamba-org/provision-with-micromamba@main
+      uses: mamba-org/setup-micromamba@v1
       with:
         environment-file: test-env.yaml
         cache-downloads: true
-        channels: conda-forge, bioconda, defaults
+        condarc: |
+          channels:
+            - conda-forge
+            - bioconda
+            - defaults
+          channel_priority: flexible
         extra-specs: |
           python=${{ matrix.python-version }}
 
+    - name: Debug Micromamba
+      run: |
+        micromamba env list
+        micromamba info
+        micromamba env export -n test-env
+
     - name: Run black manually
       run: |
         black --check --verbose ./

test-env.yaml

@@ -4,18 +4,18 @@ channels:
   - bioconda
   - defaults
 dependencies:
-  - scanpy=1.9.3
+  - scanpy=1.10.3
   - louvain
   - igraph
   - leidenalg
   - loompy
   - Click <8
   - harmonypy>=0.0.5
-  - bbknn>=1.5.0,<1.6.0
+  - bbknn >=1.6.0
   - mnnpy>=0.1.9.5
-  # for mnnpy using n_jobs
-  - scipy <1.9.0
-  - scikit-learn <1.3.0
+  # Current Scipy installed requires certain numpy restrictions
+  - numpy >=1.17.3,<1.25.0
+  - scipy
   - scrublet
   - fa2
   # for testing