From 4b4c92fa8fc61e71413a70b6978ab180ab54db80 Mon Sep 17 00:00:00 2001
From: Severin Dicks <37635888+Intron7@users.noreply.github.com>
Date: Wed, 7 Feb 2024 15:07:39 +0100
Subject: [PATCH] added yaml for gpu_ci (#1359)

* Set 30min timeout for GPU tests

* added yaml for gpu_ci

* fixes typo

* [pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci

* List pip packages too

---------

Co-authored-by: Isaac Virshup <ivirshup@gmail.com>
Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
---
 .ci/gpu_ci.yml                 | 12 ++++++++++++
 .github/workflows/test-gpu.yml | 20 ++++++++++----------
 2 files changed, 22 insertions(+), 10 deletions(-)
 create mode 100644 .ci/gpu_ci.yml

diff --git a/.ci/gpu_ci.yml b/.ci/gpu_ci.yml
new file mode 100644
index 000000000..9776ec3d5
--- /dev/null
+++ b/.ci/gpu_ci.yml
@@ -0,0 +1,12 @@
+name: cupy_env
+channels:
+  - nvidia
+  - conda-forge
+dependencies:
+  - python=3.12
+  - cuda-version=11.8
+  - cupy
+  - numba
+  - pytest
+  - pytest-cov
+  - pytest-xdist
diff --git a/.github/workflows/test-gpu.yml b/.github/workflows/test-gpu.yml
index 104396116..5d93f10d9 100644
--- a/.github/workflows/test-gpu.yml
+++ b/.github/workflows/test-gpu.yml
@@ -35,9 +35,14 @@ jobs:
     name: GPU Tests
     needs: check
     runs-on: "cirun-aws-gpu--${{ github.run_id }}"
+    # Setting a timeout of 30 minutes, as the AWS costs money
+    # At time of writing, a typical run takes about 5 minutes
+    timeout-minutes: 30
+
     defaults:
       run:
         shell: bash -el {0}
+
     steps:
       - uses: actions/checkout@v3
         with:
@@ -49,14 +54,7 @@ jobs:
       - uses: mamba-org/setup-micromamba@v1
         with:
           micromamba-version: "1.3.1-0"
-          environment-name: anndata-gpu-ci
-          create-args: >-
-            python=3.11
-            cupy
-            numba
-            pytest
-            pytest-cov
-            pytest-xdist
+          environment-file: .ci/gpu_ci.yml
           init-shell: >-
             bash
           generate-run-shell: false
@@ -64,8 +62,10 @@ jobs:
       - name: Install AnnData
         run: pip install .[dev,test,gpu]
 
-      - name: Mamba list
-        run: micromamba list
+      - name: Env list
+        run: |
+          micromamba list
+          pip list
 
       - name: Run test
         run: pytest -m gpu --cov --cov-report=xml --cov-context=test -n 4