Python 3.12 support (#794)

* Change CI to python 3.12

* Change notebook CI to python 3.12

* Updated submodule

* Add graphviz dependency

* Fixed estimator data retrieval

* Obtain data based on dowhy version

* Estimate data retrieval only for latest dowhy versions

* Move graphviz installation

* More latest python 3.12

Signed-off-by: zethson <lukas.heumos@posteo.net>

---------

Signed-off-by: zethson <lukas.heumos@posteo.net>
Co-authored-by: Lukas Heumos <lukas.heumos@posteo.net>

.github/workflows/build.yml

@@ -16,12 +16,10 @@ jobs:
         steps:
             - uses: actions/checkout@v3
 
-            - name: Set up Python 3.11
+            - name: Set up Python 3.12
               uses: actions/setup-python@v5
               with:
-                  python-version: "3.11"
-                  cache: "pip"
-                  cache-dependency-path: "**/pyproject.toml"
+                  python-version: "3.12"
 
             - name: Install build dependencies
               run: python -m pip install --upgrade pip wheel twine build

.github/workflows/release.yml

@@ -13,10 +13,10 @@ jobs:
             - name: Checkout code
               uses: actions/checkout@v3
 
-            - name: Set up Python 3.11
+            - name: Set up Python 3.12
               uses: actions/setup-python@v5
               with:
-                  python-version: "3.11"
+                  python-version: "3.12"
 
             - name: Install hatch
               run: pip install hatch

.github/workflows/run_notebooks.yml

@@ -26,13 +26,13 @@ jobs:
             - name: Set up Python
               uses: actions/setup-python@v5
               with:
-                  python-version: "3.11"
+                  python-version: "3.12"
 
             - name: Install UV
               run: pip install uv
 
             - name: Install ehrapy and additional dependencies
-              run: uv pip install --system . cellrank nbconvert ipykernel
+              run: uv pip install --system . cellrank nbconvert ipykernel graphviz
 
             - name: Install scvelo from Github
               run: uv pip install --system git+https://github.com/theislab/scvelo.git

.github/workflows/test.yml

@@ -24,9 +24,9 @@ jobs:
                     - os: ubuntu-latest
                       python: "3.10"
                     - os: ubuntu-latest
-                      python: "3.11"
+                      python: "3.12"
                     - os: ubuntu-latest
-                      python: "3.11"
+                      python: "3.12"
                       pip-flags: "--pre"
 
         env:

.readthedocs.yml

@@ -1,8 +1,8 @@
 version: 2
 build:
-    os: ubuntu-22.04
+    os: ubuntu-24.04
     tools:
-        python: "3.11"
+        python: "3.12"
     commands:
         - asdf plugin add uv
         - asdf install uv latest