From 3a36754ed1b1b88266ba87b56a1356122ce9f236 Mon Sep 17 00:00:00 2001
From: JohT <7671054+JohT@users.noreply.github.com>
Date: Wed, 6 Aug 2025 21:55:34 +0200
Subject: [PATCH 1/3] Run the whole pipeline when dependencies change

---
 .github/workflows/internal-java-code-analysis.yml       | 2 ++
 .github/workflows/internal-typescript-code-analysis.yml | 2 ++
 2 files changed, 4 insertions(+)

diff --git a/.github/workflows/internal-java-code-analysis.yml b/.github/workflows/internal-java-code-analysis.yml
index ca61dc01a..66f7ac375 100644
--- a/.github/workflows/internal-java-code-analysis.yml
+++ b/.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'
diff --git a/.github/workflows/internal-typescript-code-analysis.yml b/.github/workflows/internal-typescript-code-analysis.yml
index ebf5d773d..df59feca3 100644
--- a/.github/workflows/internal-typescript-code-analysis.yml
+++ b/.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'

From 047c1e9ac11b36c9d577896d2536b7773d39623b Mon Sep 17 00:00:00 2001
From: JohT <7671054+JohT@users.noreply.github.com>
Date: Wed, 6 Aug 2025 21:59:31 +0200
Subject: [PATCH 2/3] Check links every week instead of every month

---
 .github/workflows/internal-check-links-in-documentation.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/internal-check-links-in-documentation.yml b/.github/workflows/internal-check-links-in-documentation.yml
index 0aaf08110..6bc347f03 100644
--- a/.github/workflows/internal-check-links-in-documentation.yml
+++ b/.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:

From 5126bc804eef062b87cb8c85c739a5175b437a4c Mon Sep 17 00:00:00 2001
From: JohT <7671054+JohT@users.noreply.github.com>
Date: Thu, 7 Aug 2025 07:44:31 +0200
Subject: [PATCH 3/3] Update Python setuptools to 80.9.*

---
 conda-environment.yml | 3 ++-
 requirements.txt      | 3 ++-
 2 files changed, 4 insertions(+), 2 deletions(-)

diff --git a/conda-environment.yml b/conda-environment.yml
index 789d92b6c..bc0dcea86 100644
--- a/conda-environment.yml
+++ b/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.*
diff --git a/requirements.txt b/requirements.txt
index 5a8642692..6d912e39a 100644
--- a/requirements.txt
+++ b/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 ---