fix github action and yml

.github/workflows/integration-ci.yml

@@ -21,9 +21,11 @@ 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/main/pipeline_env.yaml
+      - uses: actions/checkout@v4
+
+      - name: File tree
+        if: env.debug == 'true'
+        run: tree
 
       - uses: conda-incubator/setup-miniconda@v3
         with:
@@ -33,21 +35,13 @@ 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
           
       - name: Conda info
         if: env.debug == 'true'
@@ -85,7 +79,7 @@ jobs:
                
       - name: File tree
         if: env.debug == 'true'
-        run: tree
+        run: tree teaseq
 
       - name: Review pipeline tasks
         shell: bash -el {0}
@@ -101,4 +95,4 @@ jobs:
         
       - name: File tree
         if: env.debug == 'true'
-        run: tree
+        run: tree teaseq

pipeline_env.yaml

@@ -14,5 +14,4 @@ dependencies:
   - r-xtable
   - pip
   - pip:
-    - panpipes[spatial]
     - pytest