test jax dependecies

.github/workflows/ingestion-ci.yml

@@ -18,7 +18,7 @@ jobs:
       fail-fast: false
       matrix:
         os: ["ubuntu-latest"] # , "macos-latest", "windows-latest"
-        python-version: ["3.9"]
+        python-version: ["3.11"]
 
     steps:
       - uses: actions/checkout@v4

.github/workflows/spatial-ci.yml

@@ -0,0 +1,71 @@
+name: Spatial CI
+
+on:
+  push:
+    branches:
+      - main
+  pull_request:
+    branches:
+      - main
+
+env:
+  debug: 'true'
+
+jobs:
+  ingestion:
+    runs-on: ubuntu-latest
+    strategy:
+      fail-fast: false
+      matrix:
+        os: ["ubuntu-latest"] # , "macos-latest", "windows-latest"
+        python-version: ["3.11"]
+
+    steps:
+      - uses: actions/checkout@v4
+
+      - name: File tree
+        if: env.debug == 'true'
+        run: tree
+
+      - uses: conda-incubator/setup-miniconda@v3
+        with:
+          miniforge-version: latest
+          auto-activate-base: true
+          auto-update-conda: true
+          channels: conda-forge
+          channel-priority: strict
+          activate-environment: pipeline_env
+          environment-file: pipeline_env.yaml
+
+      - name: Install Panpipes
+        shell: bash -el {0}
+        run: |
+          pip install '.[spatial]'
+          conda list
+
+      - name: Conda info
+        if: env.debug == 'true'
+        shell: bash -el {0}
+        run: conda info
+
+      - name: Conda list
+        if: env.debug == 'true'
+        shell: pwsh
+        run: conda list
+
+      # Note: all three files are renamed during the download to trim the "subsample_" prefix
+      - name: Preparing the data
+        run: |
+          mkdir -p teaseq/ingest/data.dir
+          cd teaseq/ingest/data.dir
+          curl -L -o adt.h5ad https://figshare.com/ndownloader/files/41671551
+          curl -L -o atac.h5ad https://figshare.com/ndownloader/files/41671554
+          curl -L -o rna.h5ad https://figshare.com/ndownloader/files/41671557
+
+      # Note: we run the following to test that the commands works
+      # However, the following task will replacing the file anyway
+      - name: Preparing the configuration file
+        shell: bash -el {0}
+        run: |
+          cd teaseq/ingest
+          panpipes ingest config

pyproject.toml

@@ -36,7 +36,7 @@ dependencies = [
     "drmaa", 
     "gevent",
     "harmonypy",
-    "jax<=0.4.23",
+    "jax<=0.4.23", # temp for scvi https://github.com/theislab/scvelo/issues/1186
     "jaxlib<=0.4.23",
     "leidenalg", 
     "louvain",