From 0dd7905fa4bf77ea522d2a2048da4510546087db Mon Sep 17 00:00:00 2001
From: ilan-gold <ilanbassgold@gmail.com>
Date: Fri, 23 Jan 2026 12:23:48 +0100
Subject: [PATCH 1/4] feat: pre release job

---
 .github/workflows/integration-test.yml | 5 ++++-
 overrides.txt                          | 1 +
 2 files changed, 5 insertions(+), 1 deletion(-)
 create mode 100644 overrides.txt

diff --git a/.github/workflows/integration-test.yml b/.github/workflows/integration-test.yml
index 2733c52..3c929bb 100644
--- a/.github/workflows/integration-test.yml
+++ b/.github/workflows/integration-test.yml
@@ -18,6 +18,7 @@ jobs:
       fail-fast: false
       matrix:
         python: ["3.12", "3.13"]
+        is_pre: [true, false]
         package:
           # extras should be a comma seperated list of strings, like `extras: "lazy,accelerated"`
           # The 'test' extra is always installed
@@ -31,6 +32,8 @@ jobs:
           - {name: "pertpy", extras: "de"}
           - {name: "decoupler", extras: ""}
           - {name: "SnapATAC2", extras: ""}
+        exclude:
+          - { python: 3.12, is_pre: true }
 
     defaults:
       run:
@@ -89,7 +92,7 @@ jobs:
               EXTRAS="test"
             fi
           fi
-          uv pip install --compile --system ".[$EXTRAS]" git+https://github.com/scverse/anndata -c ../integration-testing/constraints.txt $GROUP -v
+          uv pip install ${{ matrix.is_pre else && '--prerelease allow' ||  '' }} --compile --system ".[$EXTRAS]" git+https://github.com/scverse/anndata -c ../integration-testing/constraints.txt --override ../integration-testing/overrides.txt $GROUP -v
         working-directory: ${{ matrix.package.name }}
       
       - name: Set failure type for install
diff --git a/overrides.txt b/overrides.txt
new file mode 100644
index 0000000..789f724
--- /dev/null
+++ b/overrides.txt
@@ -0,0 +1 @@
+pandas>=3
\ No newline at end of file

From ff1c4edbdda05695522c8e510c8aaccd5d09eb1f Mon Sep 17 00:00:00 2001
From: ilan-gold <ilanbassgold@gmail.com>
Date: Fri, 23 Jan 2026 12:24:47 +0100
Subject: [PATCH 2/4] fix: ah there's else!

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

diff --git a/.github/workflows/integration-test.yml b/.github/workflows/integration-test.yml
index 3c929bb..bd28395 100644
--- a/.github/workflows/integration-test.yml
+++ b/.github/workflows/integration-test.yml
@@ -92,7 +92,7 @@ jobs:
               EXTRAS="test"
             fi
           fi
-          uv pip install ${{ matrix.is_pre else && '--prerelease allow' ||  '' }} --compile --system ".[$EXTRAS]" git+https://github.com/scverse/anndata -c ../integration-testing/constraints.txt --override ../integration-testing/overrides.txt $GROUP -v
+          uv pip install ${{ matrix.is_pre && '--prerelease allow' ||  '' }} --compile --system ".[$EXTRAS]" git+https://github.com/scverse/anndata -c ../integration-testing/constraints.txt --override ../integration-testing/overrides.txt $GROUP -v
         working-directory: ${{ matrix.package.name }}
       
       - name: Set failure type for install

From ef228d6c25759a41af59ef328401c8373ac5fb7d Mon Sep 17 00:00:00 2001
From: ilan-gold <ilanbassgold@gmail.com>
Date: Fri, 23 Jan 2026 13:22:04 +0100
Subject: [PATCH 3/4] oops no overrides unless pre

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

diff --git a/.github/workflows/integration-test.yml b/.github/workflows/integration-test.yml
index bd28395..078a10c 100644
--- a/.github/workflows/integration-test.yml
+++ b/.github/workflows/integration-test.yml
@@ -92,7 +92,7 @@ jobs:
               EXTRAS="test"
             fi
           fi
-          uv pip install ${{ matrix.is_pre && '--prerelease allow' ||  '' }} --compile --system ".[$EXTRAS]" git+https://github.com/scverse/anndata -c ../integration-testing/constraints.txt --override ../integration-testing/overrides.txt $GROUP -v
+          uv pip install ${{ matrix.is_pre && '--prerelease allow' ||  '' }} --compile --system ".[$EXTRAS]" git+https://github.com/scverse/anndata -c ../integration-testing/constraints.txt ${{ matrix.is_pre && '--override ../integration-testing/overrides.txt' || ''}} $GROUP -v
         working-directory: ${{ matrix.package.name }}
       
       - name: Set failure type for install

From ae1e930fdf42d228a7ead7298396e7a9be991d5e Mon Sep 17 00:00:00 2001
From: ilan-gold <ilanbassgold@gmail.com>
Date: Mon, 26 Jan 2026 13:55:02 +0100
Subject: [PATCH 4/4] fix: issue title

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

diff --git a/.github/workflows/integration-test.yml b/.github/workflows/integration-test.yml
index 078a10c..b50b088 100644
--- a/.github/workflows/integration-test.yml
+++ b/.github/workflows/integration-test.yml
@@ -122,7 +122,7 @@ jobs:
         if: failure() && github.event_name == 'schedule'
         id: find_issue
         run: |
-          ISSUE_TITLE="Integration Testing CI ${failure_type^} Failure on python ${{ matrix.python }}"
+          ISSUE_TITLE="Integration Testing CI ${failure_type^} Failure on python ${{ matrix.python }}${{matrix.is_pre && ' with prerelease dependencies' || ''}}"
           echo "Checking for existing issue: $ISSUE_TITLE"
           ISSUE_COUNT=$(gh issue list --repo scverse/${{ matrix.package.name }} --state open --search "${ISSUE_TITLE}" --json number --jq 'length')
           if [[ "$ISSUE_COUNT" -gt 0 ]]; then