Merge branch 'main' into dev

abearab · Jan 7, 2025 · 3f3e1c7 · 3f3e1c7
2 parents 5551058 + ce87ac5
commit 3f3e1c7
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Showing 3 changed files with 6 additions and 7 deletions.
diff --git a/.github/workflows/main.yml b/.github/workflows/main.yml
@@ -17,7 +17,7 @@ jobs:
       max-parallel: 5
       matrix:
         os-version: ["ubuntu-latest"]
-        python-version: ["3.9", "3.10", "3.11", "3.12"]
+        python-version: ["3.9", "3.10", "3.11"] # "3.12" "3.13"
 
     steps:
     - uses: actions/checkout@v3
@@ -35,11 +35,10 @@ jobs:
         # exit-zero treats all errors as warnings. The GitHub editor is 127 chars wide
         flake8 . --count --exit-zero --max-complexity=10 --max-line-length=127 --statistics
     - name: "Install miniconda"
-      uses: conda-incubator/setup-miniconda@v2
+      uses: conda-incubator/setup-miniconda@v3
       with:
           miniconda-version: "latest"
           auto-update-conda: true
-          mamba-version: "*"
           python-version: ${{ matrix.python-version }}
           channels: conda-forge,bioconda
           environment-file: environment.yml

diff --git a/.github/workflows/python-publish.yml b/.github/workflows/python-publish.yml
@@ -16,7 +16,7 @@ jobs:
       max-parallel: 5
       matrix:
         os-version: ["ubuntu-latest"]
-        python-version: ["3.12"]  # ["3.9", "3.10", "3.11", "3.12"]
+        python-version: ["3.11"]  # "3.9", "3.10", "3.11", "3.12", "3.13"
 
     steps:
     - uses: actions/checkout@v3
@@ -34,11 +34,10 @@ jobs:
         # exit-zero treats all errors as warnings. The GitHub editor is 127 chars wide
         flake8 . --count --exit-zero --max-complexity=10 --max-line-length=127 --statistics
     - name: "Install miniconda"
-      uses: conda-incubator/setup-miniconda@v2
+      uses: conda-incubator/setup-miniconda@v3
       with:
         miniconda-version: "latest"
         auto-update-conda: true
-        mamba-version: "*"
         python-version: ${{ matrix.python-version }}
         channels: conda-forge,bioconda
         environment-file: environment.yml

diff --git a/environment.yml b/environment.yml
@@ -11,6 +11,7 @@ dependencies:
   - anndata
   - scipy
   - scar
+  - scikit-learn==1.2.2
   - matplotlib
   - ipykernel
   - mscorefonts
@@ -21,4 +22,4 @@ dependencies:
       - adpbulk
       - pydeseq2
       - adjustText
-      - watermark
+      - watermark