🐛 run some diagnostics

RasmussenLab · Oct 24, 2024 · 50031f2 · 50031f2
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commit 50031f2
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Showing 4 changed files with 19 additions and 16 deletions.
diff --git a/.github/workflows/ci.yaml b/.github/workflows/ci.yaml
@@ -2,8 +2,8 @@ name: Run unit tests, integration tests, and publish package if tagged
 on:
   push:
     branches: [main, dev]
-  pull_request:
-    branches: [main, dev]
+  # pull_request:
+  #   branches: [main, dev]
   release:
     types: [published]
   schedule:
@@ -27,7 +27,7 @@ jobs:
       uses: actions/checkout@v4
     - name: Set up Miniconda
       uses: conda-incubator/setup-miniconda@v3
-      with: 
+      with:
         python-version: ${{ matrix.python-version }}
         channel-priority: strict
         environment-file: snakemake_env.yml
@@ -42,21 +42,21 @@ jobs:
         conda env export --no-builds
         conda env export --no-builds > environment_w_versions.yml
     - name: Dry-Run demo workflow (integration test)
-      run: | 
+      run: |
        cd project
        snakemake -p -c1 --configfile config/single_dev_dataset/example/config.yaml --use-conda -n
     - name: Run demo workflow (integration test)
       continue-on-error: true
-      run: | 
+      run: |
        cd project
        snakemake -p -c4 -k --configfile config/single_dev_dataset/example/config.yaml --use-conda
     - name: Run demo workflow again (in case of installation issues)
       continue-on-error: true
-      run: | 
+      run: |
         cd project
         snakemake -p -c4 -k --configfile config/single_dev_dataset/example/config.yaml --use-conda
     - name: Run demo workflow again (in case of installation issues) - one thread
-      run: | 
+      run: |
         cd project
         snakemake -p -c1 --configfile config/single_dev_dataset/example/config.yaml --use-conda
     - name: Archive results
@@ -92,13 +92,13 @@ jobs:
 
       - name: Install pytest
         run: pip install pytest pytest-cov
-      
+
       - name: Run pytest
         run: pytest .
 
       - name: Install papermill
         run: pip install papermill ipykernel
-      
+
       - name: View papermill help message for notebooks (as scripts)
         run: |
           cd project
@@ -123,7 +123,7 @@ jobs:
 
     steps:
       - uses: actions/checkout@v4
-  
+
       - uses: actions/setup-python@v5
         with:
           python-version: "3.8"

diff --git a/.github/workflows/ci_workflow.yaml b/.github/workflows/ci_workflow.yaml
@@ -2,8 +2,8 @@ name: run workflow (v1) with conda envs
 on:
   push:
     branches: [main, dev]
-  pull_request:
-    branches: [main, dev]
+  # pull_request:
+  #   branches: [main, dev]
   release:
     types: [published]
   schedule:

diff --git a/.github/workflows/test_pkg_on_colab.yaml b/.github/workflows/test_pkg_on_colab.yaml
@@ -23,15 +23,18 @@ jobs:
         - name: Install pimms-learn (from branch) and papermill
           if: github.event_name == 'pull_request'
           run: | 
-            pip install .
-            pip install papermill 
+            pip install --user .
+            pip install papermill
+            python3 -c "import pandas"
+            python3 -c "import pimmslearn"
         - name: Install pimms-learn (from PyPI) and papermill
           if: github.event_name == 'schedule'
           run: | 
             pip install pimms-learn papermill
         - name: Run tutorial
           run: |
             cd project
+            which papermill
             papermill 04_1_train_pimms_models.ipynb 04_1_train_pimms_models_output.ipynb
             papermill 04_1_train_pimms_models.ipynb 04_1_train_pimms_models_no_val.ipynb -p sample_splits False
 
diff --git a/.github/workflows/workflow_website.yaml b/.github/workflows/workflow_website.yaml
@@ -1,7 +1,7 @@
 name: Build workflow (v2) website on public Alzheimer dataset (for protein groups)
 on:
-  pull_request:
-    branches: [main, dev]
+  # pull_request:
+  #   branches: [main, dev]
   release:
       types: [published]
   schedule: