From 50372a48f48c093a2ea11e35e73d37e1d7f76695 Mon Sep 17 00:00:00 2001
From: Daniel Danis <daniel.gordon.danis@protonmail.com>
Date: Thu, 22 Aug 2024 16:32:06 +0200
Subject: [PATCH 1/2] We will not run the notebooks anymore. The docs are the
 source of truth.

---
 .github/workflows/notebooks.yml | 33 ---------------------------------
 .github/workflows/python_ci.yml |  2 +-
 2 files changed, 1 insertion(+), 34 deletions(-)
 delete mode 100644 .github/workflows/notebooks.yml

diff --git a/.github/workflows/notebooks.yml b/.github/workflows/notebooks.yml
deleted file mode 100644
index dc62fc44..00000000
--- a/.github/workflows/notebooks.yml
+++ /dev/null
@@ -1,33 +0,0 @@
-name: Notebooks
-
-on:
-    push:
-      branches: [ develop ]
-    pull_request:
-      branches: [ main, develop ]
-
-jobs:
-    run-notebook:
-      runs-on: ubuntu-latest
-
-      steps:
-        - uses: actions/checkout@v4
-        - name: Initialize Python
-          uses: actions/setup-python@v4.3.1
-          with:
-            python-version: '3.11'
-        - name: Setup Python
-          run: |
-            python -m pip install --upgrade pip jupyter
-            python -m pip install .
-            python -m ipykernel install --user --name run-notebook --display-name "Run notebook"
-        - name: Run notebooks
-          run: |
-            # The functional annotation of RPGRIP1, STXBP1, and KBG takes too long.
-            # However, we can add them later, if we will really want that.
-            cohorts=(MAPK8IP3 PPP2R1A SUOX)
-            for cohort in ${cohorts[@]}; do
-              nb="notebooks/${cohort}/${cohort}.ipynb"
-              printf "Processing notebook at %s\n" ${nb}
-              jupyter execute --kernel_name run-notebook ${nb}
-            done
diff --git a/.github/workflows/python_ci.yml b/.github/workflows/python_ci.yml
index cdd8b20b..aa715096 100644
--- a/.github/workflows/python_ci.yml
+++ b/.github/workflows/python_ci.yml
@@ -21,7 +21,7 @@ jobs:
             python-version: ${{ matrix.python-version }}
         - name: Install package
           run: |
-            python3 -m pip install --editable .[test]
+            python3 -m pip install .[test]
         - name: Run pytest tests
           run: |
             export MPLBACKEND=Agg

From da21a175feb37ac3eb7f5605b8c6873c152c839a Mon Sep 17 00:00:00 2001
From: Daniel Danis <daniel.gordon.danis@protonmail.com>
Date: Thu, 22 Aug 2024 16:34:15 +0200
Subject: [PATCH 2/2] Revert back to the editable install.

---
 .github/workflows/python_ci.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/python_ci.yml b/.github/workflows/python_ci.yml
index aa715096..cdd8b20b 100644
--- a/.github/workflows/python_ci.yml
+++ b/.github/workflows/python_ci.yml
@@ -21,7 +21,7 @@ jobs:
             python-version: ${{ matrix.python-version }}
         - name: Install package
           run: |
-            python3 -m pip install .[test]
+            python3 -m pip install --editable .[test]
         - name: Run pytest tests
           run: |
             export MPLBACKEND=Agg