From 6986e38ce290c7672836348e0de36fab68be03f9 Mon Sep 17 00:00:00 2001
From: Henry Webel <kzl465@ku.dk>
Date: Mon, 28 Oct 2024 14:18:16 +0100
Subject: [PATCH] :bug: fix installation issue of pimms on PR using colab image
 (#82)

* :bug: fix installation issue of pimms on PR

- solved by installing directly from GitHub PullRequest
---
 .github/workflows/ci.yaml                | 16 ++++++++--------
 .github/workflows/test_pkg_on_colab.yaml | 11 ++++++++---
 pimmslearn/__init__.py                   |  1 +
 3 files changed, 17 insertions(+), 11 deletions(-)

diff --git a/.github/workflows/ci.yaml b/.github/workflows/ci.yaml
index 7cb8b26a3..a0d594b5e 100644
--- a/.github/workflows/ci.yaml
+++ b/.github/workflows/ci.yaml
@@ -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/test_pkg_on_colab.yaml b/.github/workflows/test_pkg_on_colab.yaml
index 6109c0810..5f6fafe3a 100644
--- a/.github/workflows/test_pkg_on_colab.yaml
+++ b/.github/workflows/test_pkg_on_colab.yaml
@@ -19,9 +19,13 @@ jobs:
         - uses: actions/checkout@v4
         - name: Install pimms-learn (from branch) and papermill
           if: github.event_name == 'pull_request'
-          run: | 
-            pip install .
-            pip install papermill 
+          run: |
+            echo $GITHUB_REF
+            pip install git+https://github.com/RasmussenLab/pimms.git@$GITHUB_REF
+            pip install papermill
+            cd project
+            echo python3 -c "import pimmslearn; print(pimmslearn.__version__)"
+            python3 -c "import pimmslearn; print(pimmslearn.__version__)"
         - name: Install pimms-learn (from PyPI) and papermill
           if: github.event_name == 'schedule'
           run: | 
@@ -29,6 +33,7 @@ jobs:
         - 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/pimmslearn/__init__.py b/pimmslearn/__init__.py
index 95021ccad..262462099 100644
--- a/pimmslearn/__init__.py
+++ b/pimmslearn/__init__.py
@@ -17,6 +17,7 @@
 
 import njab
 
+import pimmslearn.io
 import pimmslearn.logging
 import pimmslearn.nb
 import pimmslearn.pandas