Merge pull request #412 from JohT/feature/update-python-setuptools

Update Python setuptools to 80.9.* to fix security issue

Author: JohT

.github/workflows/internal-check-links-in-documentation.yml

@@ -13,7 +13,7 @@ on:
       - 'CHANGELOG.md'
       - '.github/workflows/internal-check-links-in-documentation.yml' # also run when this file was changed
   schedule:
-    - cron: "15 6 1 * *" # On the first day of each month at 6:15 o'clock
+    - cron: "42 7 * * 1" # Every week at 07:40 AM on Monday 
 
 jobs:
   reports:

.github/workflows/internal-java-code-analysis.yml

@@ -8,6 +8,7 @@ on:
     paths-ignore: 
       - '**/*.md'
       - '**/*.txt'
+      - '!requirements.txt'
       - '**/*.css'
       - '**/*.html'
       - '**/*.js'
@@ -26,6 +27,7 @@ on:
     paths-ignore: 
       - '**/*.md'
       - '**/*.txt'
+      - '!requirements.txt'
       - '**/*.css'
       - '**/*.html'
       - '**/*.js'

.github/workflows/internal-typescript-code-analysis.yml

@@ -8,6 +8,7 @@ on:
     paths-ignore: 
       - '**/*.md'
       - '**/*.txt'
+      - '!requirements.txt'
       - '**/*.css'
       - '**/*.html'
       - '**/*.js'
@@ -26,6 +27,7 @@ on:
     paths-ignore: 
       - '**/*.md'
       - '**/*.txt'
+      - '!requirements.txt'
       - '**/*.css'
       - '**/*.html'
       - '**/*.js'

conda-environment.yml

@@ -1,3 +1,4 @@
+# NOTE: Keep this file in sync with requirements.txt
 name: codegraph
 channels:
   - conda-forge/label/python_rc # Needed on Mac since Python >= 3.12
@@ -13,7 +14,7 @@ dependencies:
   - numpy=1.26.*
   - pandas=2.2.*
   - pip=25.0.*
-  - setuptools=75.8.* # opentsne uses sklearn.base uses joblib uses distutils missing in Python >= 12 (TODO use native openTSNE?) 
+  - setuptools=80.9.* # opentsne uses sklearn.base uses joblib uses distutils missing in Python >= 12 (TODO use native openTSNE?) 
   - typing-extensions=4.12.* # Also needed for opentsne and Python >= 3.12
   - opentsne=1.0.* # to visualize node embeddings in 2D (t-SNE dimensionality reduction)
   - wordcloud=1.9.*

requirements.txt

@@ -1,6 +1,7 @@
 # --- Core Python version ---
 # NOTE: Python version must be >= 3.12 for compatibility
 # This should be enforced by the user/environment, not pip
+# NOTE: Keep this file in sync with conda-environment.yml
 
 # --- Core tools ---
 jupyter==1.1.*
@@ -9,7 +10,7 @@ nbconvert[webpdf]==7.16.*
 numpy==1.26.*
 pandas==2.2.*
 pip==25.0.*
-setuptools==75.8.* # opentsne uses sklearn.base uses joblib uses distutils missing in Python >= 12 (TODO use native openTSNE?) 
+setuptools==80.9.* # opentsne uses sklearn.base uses joblib uses distutils missing in Python >= 12 (TODO use native openTSNE?) 
 typing-extensions==4.12.* # Needed for opentsne and Python >= 3.12
 
 # --- Visualization ---