pip install -e

DendrouLab · Feb 9, 2024 · b5d6e41 · b5d6e41
1 parent 265e8c3
commit b5d6e41
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Showing 3 changed files with 31 additions and 29 deletions.
diff --git a/.github/workflows/ingestion-ci.yml b/.github/workflows/ingestion-ci.yml
@@ -21,9 +21,14 @@ jobs:
         python-version: ["3.9"]
 
     steps:
-      # - uses: actions/checkout@v4
-      - name: Download Conda YAML file
-        run: curl -o pipeline_env.yaml https://raw.githubusercontent.com/DendrouLab/panpipes/kra-gha/pipeline_env.yaml
+      - uses: actions/checkout@v4
+
+      - name: File tree
+        if: env.debug == 'true'
+        run: tree
+
+      # - name: Download Conda YAML file
+      #   run: curl -o pipeline_env.yaml https://raw.githubusercontent.com/DendrouLab/panpipes/kra-gha/pipeline_env.yaml
 
       - uses: conda-incubator/setup-miniconda@v3
         with:
@@ -33,21 +38,27 @@ jobs:
           channels: conda-forge
           channel-priority: strict
           activate-environment: pipeline_env
-          environment-file: pipeline_env.yaml # consider moving to etc/pipeline_env.yaml
+          environment-file: pipeline_env.yaml
 
-      # Note: the pinned versions in pipeline_env.yaml are not respected during the miniconda step above
-      - name: Pin version of pip dependencies
+      - name: Install Panpipes
         shell: bash -el {0}
-        run: pip install --force-reinstall -v \
-          boto3==1.34.34 \
-          botocore==1.34.34 \
-          flax==0.8.0 \
-          fonttools==4.47.2 \
-          jax==0.4.23 \
-          jaxlib==0.4.23 \
-          numpy==1.22.4 \
-          orbax-checkpoint==0.5.2 \
-          pytorch-lightning==2.1.4
+        run: |
+          pip install -e .
+          conda list
+
+      # Note: the pinned versions in pipeline_env.yaml are not respected during the miniconda step above
+      # - name: Pin version of pip dependencies
+      #   shell: bash -el {0}
+      #   run: pip install --force-reinstall -v \
+      #     boto3==1.34.34 \
+      #     botocore==1.34.34 \
+      #     flax==0.8.0 \
+      #     fonttools==4.47.2 \
+      #     jax==0.4.23 \
+      #     jaxlib==0.4.23 \
+      #     numpy==1.22.4 \
+      #     orbax-checkpoint==0.5.2 \
+      #     pytorch-lightning==2.1.4
 
       - name: Conda info
         if: env.debug == 'true'

diff --git a/pipeline_env.yaml b/pipeline_env.yaml
@@ -14,15 +14,4 @@ dependencies:
   - r-xtable
   - pip
   - pip:
-    - panpipes[spatial]
     - pytest
-    - boto3==1.34.34
-    - botocore==1.34.34
-    - flax==0.8.0
-    - fonttools==4.47.2
-    - jax==0.4.23
-    - jaxlib==0.4.23
-    - numpy==1.22.4
-    - orbax-checkpoint==0.5.2
-    - pytorch-lightning==2.1.4
-
diff --git a/pyproject.toml b/pyproject.toml
@@ -35,14 +35,16 @@ dependencies = [
     "cgatcore", 
     "drmaa", 
     "gevent",
-    "harmonypy", 
+    "harmonypy",
+    "jax<=0.4.23",
+    "jaxlib<=0.4.23",
     "leidenalg", 
     "louvain",
     "matplotlib<=3.7.3",
     "mofapy2",
     "mudata>=0.2.1",
     "muon",
-    "numpy>=1.22.4", 
+    "numpy==1.22.4", 
     "openpyxl",
     "packaging", 
     "pandas>=1.0",