From 134bcc9d96ad6977368a7da1bc355e041577635c Mon Sep 17 00:00:00 2001
From: Intron7 <severin.dicks@icloud.com>
Date: Mon, 16 Dec 2024 15:24:48 +0100
Subject: [PATCH 01/14] test

---
 .readthedocs.yml | 6 ++----
 hatch.toml       | 5 +++++
 2 files changed, 7 insertions(+), 4 deletions(-)

diff --git a/.readthedocs.yml b/.readthedocs.yml
index 668b1931..30b5452f 100644
--- a/.readthedocs.yml
+++ b/.readthedocs.yml
@@ -12,11 +12,9 @@ build:
     - asdf install uv latest
     - asdf global uv latest
 
-    # Use uv to synchronize dependencies
-    - uv pip install --system .[doc]
+    - uv sync --extra doc
+    - uv run -m sphinx -T -b html -d docs/_build/doctrees -D language=en docs $READTHEDOCS_OUTPUT/html
 
-    # Build documentation using sphinx
-    - python -m sphinx -T -b html -d docs/_build/doctrees -D language=en docs $READTHEDOCS_OUTPUT/html
 
 sphinx:
   configuration: docs/conf.py
diff --git a/hatch.toml b/hatch.toml
index 7d11867b..46538fe6 100644
--- a/hatch.toml
+++ b/hatch.toml
@@ -9,3 +9,8 @@ features = ["test", "rapids12"]
 features = ["doc"]
 scripts.build = "sphinx-build -M html docs docs/_build {args}"
 scripts.clean = "git clean -fXd docs"
+
+[envs.hatch-test.pip]
+extra_index_urls = [
+  "https://pypi.nvidia.com"
+]

From ae7cae4e5b9fe712c3a07d653116cf42f8b780aa Mon Sep 17 00:00:00 2001
From: Intron7 <severin.dicks@icloud.com>
Date: Mon, 16 Dec 2024 15:26:41 +0100
Subject: [PATCH 02/14] update

---
 .readthedocs.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.readthedocs.yml b/.readthedocs.yml
index 30b5452f..c5852e2c 100644
--- a/.readthedocs.yml
+++ b/.readthedocs.yml
@@ -5,7 +5,7 @@ submodules:
 build:
   os: ubuntu-24.04
   tools:
-    python: "3.12"
+    python: "3.11"
   commands:
     # Install and set up uv
     - asdf plugin add uv

From 6bc95d2f90efde1610f57f40a1fb57e67e669298 Mon Sep 17 00:00:00 2001
From: Intron7 <severin.dicks@icloud.com>
Date: Mon, 16 Dec 2024 15:29:35 +0100
Subject: [PATCH 03/14] update hatch

---
 hatch.toml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/hatch.toml b/hatch.toml
index 46538fe6..e3b2ce0c 100644
--- a/hatch.toml
+++ b/hatch.toml
@@ -10,7 +10,7 @@ features = ["doc"]
 scripts.build = "sphinx-build -M html docs docs/_build {args}"
 scripts.clean = "git clean -fXd docs"
 
-[envs.hatch-test.pip]
+[envs.default.pip]
 extra_index_urls = [
   "https://pypi.nvidia.com"
 ]

From 4dfdf23f891f61ff0321bc1ac2a7ac122872c9b1 Mon Sep 17 00:00:00 2001
From: Intron7 <severin.dicks@icloud.com>
Date: Mon, 16 Dec 2024 15:31:52 +0100
Subject: [PATCH 04/14] update read the docs

---
 .readthedocs.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.readthedocs.yml b/.readthedocs.yml
index c5852e2c..5cff94ca 100644
--- a/.readthedocs.yml
+++ b/.readthedocs.yml
@@ -12,7 +12,7 @@ build:
     - asdf install uv latest
     - asdf global uv latest
 
-    - uv sync --extra doc
+    - uv sync --extra docs
     - uv run -m sphinx -T -b html -d docs/_build/doctrees -D language=en docs $READTHEDOCS_OUTPUT/html
 
 

From 8658421d9a61d1f91457f3c0d7bfcdc82d839ab5 Mon Sep 17 00:00:00 2001
From: Intron7 <severin.dicks@icloud.com>
Date: Mon, 16 Dec 2024 16:04:35 +0100
Subject: [PATCH 05/14] test rapids

---
 pyproject.toml | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/pyproject.toml b/pyproject.toml
index acb60ac9..fca05e44 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -5,7 +5,7 @@ build-backend = "hatchling.build"
 [project]
 name = "rapids_singlecell"
 description = "running single cell analysis on Nvidia GPUs"
-requires-python = ">=3.10"
+requires-python =  ">=3.10, <3.13"
 license = {file = "LICENSE"}
 authors = [{name = "Severin Dicks"}]
 readme = {file = "README.md", content-type="text/markdown"}
@@ -26,8 +26,8 @@ dependencies = [
 ]
 
 [project.optional-dependencies]
-rapids11 = ["cupy-cuda11x","cudf-cu11==24.10.*", "cuml-cu11==24.10.*", "cugraph-cu11==24.10.*"]
-rapids12 = ["cupy-cuda12x","cudf-cu12==24.10.*", "cuml-cu12==24.10.*", "cugraph-cu12==24.10.*"]
+#rapids11 = ["cupy-cuda11x","cudf-cu11==24.10.*", "cuml-cu11==24.10.*", "cugraph-cu11==24.10.*"]
+rapids12 = ["cupy-cuda12x","cudf-cu12==24.12.*", "cuml-cu12==24.12.*", "cugraph-cu12==24.12.*"]
 doc = [
     "sphinx>=4.5.0",
     "sphinx-copybutton",

From 67335608d0118d160b53394fcf8037ce1b6aaf73 Mon Sep 17 00:00:00 2001
From: Intron7 <severin.dicks@icloud.com>
Date: Mon, 16 Dec 2024 16:12:01 +0100
Subject: [PATCH 06/14] update for rapids-24.12

---
 .readthedocs.yml | 8 +++++---
 pyproject.toml   | 2 +-
 2 files changed, 6 insertions(+), 4 deletions(-)

diff --git a/.readthedocs.yml b/.readthedocs.yml
index 5cff94ca..668b1931 100644
--- a/.readthedocs.yml
+++ b/.readthedocs.yml
@@ -5,16 +5,18 @@ submodules:
 build:
   os: ubuntu-24.04
   tools:
-    python: "3.11"
+    python: "3.12"
   commands:
     # Install and set up uv
     - asdf plugin add uv
     - asdf install uv latest
     - asdf global uv latest
 
-    - uv sync --extra docs
-    - uv run -m sphinx -T -b html -d docs/_build/doctrees -D language=en docs $READTHEDOCS_OUTPUT/html
+    # Use uv to synchronize dependencies
+    - uv pip install --system .[doc]
 
+    # Build documentation using sphinx
+    - python -m sphinx -T -b html -d docs/_build/doctrees -D language=en docs $READTHEDOCS_OUTPUT/html
 
 sphinx:
   configuration: docs/conf.py
diff --git a/pyproject.toml b/pyproject.toml
index fca05e44..e32d47ed 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -26,7 +26,7 @@ dependencies = [
 ]
 
 [project.optional-dependencies]
-#rapids11 = ["cupy-cuda11x","cudf-cu11==24.10.*", "cuml-cu11==24.10.*", "cugraph-cu11==24.10.*"]
+#rapids11 = ["cupy-cuda11x","cudf-cu11==24.12.*", "cuml-cu11==24.12.*", "cugraph-cu11==24.12.*"]
 rapids12 = ["cupy-cuda12x","cudf-cu12==24.12.*", "cuml-cu12==24.12.*", "cugraph-cu12==24.12.*"]
 doc = [
     "sphinx>=4.5.0",

From a1bd7f810b84f7ea5081c2de0fefa474dac6edb6 Mon Sep 17 00:00:00 2001
From: Intron7 <severin.dicks@icloud.com>
Date: Mon, 16 Dec 2024 16:20:00 +0100
Subject: [PATCH 07/14] use python-3.12 for tests

---
 .github/workflows/test-gpu-dev.yml | 2 +-
 .github/workflows/test-gpu.yml     | 2 +-
 pyproject.toml                     | 2 +-
 3 files changed, 3 insertions(+), 3 deletions(-)

diff --git a/.github/workflows/test-gpu-dev.yml b/.github/workflows/test-gpu-dev.yml
index b47355fa..5abaf615 100644
--- a/.github/workflows/test-gpu-dev.yml
+++ b/.github/workflows/test-gpu-dev.yml
@@ -42,7 +42,7 @@ jobs:
       - name: Install Python
         uses: actions/setup-python@v5
         with:
-          python-version: "3.11"
+          python-version: "3.12"
 
       - name: Install UV
         uses: hynek/setup-cached-uv@v2
diff --git a/.github/workflows/test-gpu.yml b/.github/workflows/test-gpu.yml
index f2fef56a..1ff2011c 100644
--- a/.github/workflows/test-gpu.yml
+++ b/.github/workflows/test-gpu.yml
@@ -42,7 +42,7 @@ jobs:
       - name: Install Python
         uses: actions/setup-python@v5
         with:
-          python-version: "3.11"
+          python-version: "3.12"
 
       - name: Install UV
         uses: hynek/setup-cached-uv@v2
diff --git a/pyproject.toml b/pyproject.toml
index e32d47ed..9a5612e8 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -26,7 +26,7 @@ dependencies = [
 ]
 
 [project.optional-dependencies]
-#rapids11 = ["cupy-cuda11x","cudf-cu11==24.12.*", "cuml-cu11==24.12.*", "cugraph-cu11==24.12.*"]
+rapids11 = ["cupy-cuda11x","cudf-cu11==24.12.*", "cuml-cu11==24.12.*", "cugraph-cu11==24.12.*"]
 rapids12 = ["cupy-cuda12x","cudf-cu12==24.12.*", "cuml-cu12==24.12.*", "cugraph-cu12==24.12.*"]
 doc = [
     "sphinx>=4.5.0",

From f71ebac7ffcf6a754e7b09831be2aa1318c4e4a7 Mon Sep 17 00:00:00 2001
From: Intron7 <severin.dicks@icloud.com>
Date: Mon, 16 Dec 2024 16:33:57 +0100
Subject: [PATCH 08/14] test CI

---
 .github/workflows/test-gpu-dev.yml | 1 +
 .github/workflows/test-gpu.yml     | 2 +-
 2 files changed, 2 insertions(+), 1 deletion(-)

diff --git a/.github/workflows/test-gpu-dev.yml b/.github/workflows/test-gpu-dev.yml
index 5abaf615..84f76858 100644
--- a/.github/workflows/test-gpu-dev.yml
+++ b/.github/workflows/test-gpu-dev.yml
@@ -55,6 +55,7 @@ jobs:
           "scanpy @ git+https://github.com/scverse/scanpy.git"
           "anndata @ git+https://github.com/scverse/anndata.git"
           --extra-index-url=https://pypi.nvidia.com
+          --index-strategy  unsafe-best-match
 
       - name: Run test
         run: pytest
diff --git a/.github/workflows/test-gpu.yml b/.github/workflows/test-gpu.yml
index 1ff2011c..450b361b 100644
--- a/.github/workflows/test-gpu.yml
+++ b/.github/workflows/test-gpu.yml
@@ -50,7 +50,7 @@ jobs:
           cache-dependency-path: pyproject.toml
 
       - name: Install rapids-singlecell
-        run: uv pip install --system -e .[test,rapids12] --extra-index-url=https://pypi.nvidia.com
+        run: uv pip install --system -e .[test,rapids12] --extra-index-url=https://pypi.nvidia.com --index-strategy  unsafe-best-match
 
       - name: Pip list
         run: pip list

From eb632e77adb4a92ab2c51ca7516cb7c5ee43bd85 Mon Sep 17 00:00:00 2001
From: Intron7 <severin.dicks@icloud.com>
Date: Mon, 16 Dec 2024 16:54:28 +0100
Subject: [PATCH 09/14] add flag to install

---
 docs/Installation.md | 4 ++++
 1 file changed, 4 insertions(+)

diff --git a/docs/Installation.md b/docs/Installation.md
index bce93e67..64bc5507 100644
--- a/docs/Installation.md
+++ b/docs/Installation.md
@@ -21,6 +21,10 @@ pip install 'rapids-singlecell[rapids12]' --extra-index-url=https://pypi.nvidia.
 ```
 It is important to ensure that the CUDA environment is set up correctly so that RAPIDS and Cupy can locate the necessary libraries.
 
+```{note}
+If you are using `python=3.12` with `uv`, you might need to add the `--index-strategy unsafe-best-match` flag to ensure compatibility.
+```
+
 ## Docker
 
 We also offer a Docker container for `rapids-singlecell`. This container includes all the necessary dependencies, making it even easier to get started with `rapids-singlecell`.

From 33cf94491a2876f99bbe3fe4a2a24b6d3acb3ca0 Mon Sep 17 00:00:00 2001
From: Intron7 <severin.dicks@icloud.com>
Date: Mon, 16 Dec 2024 16:55:33 +0100
Subject: [PATCH 10/14] update install

---
 conda/{rsc_rapids_24.08.yml => rsc_rapids_24.12.yml} | 4 ++--
 docs/Installation.md                                 | 4 ++--
 2 files changed, 4 insertions(+), 4 deletions(-)
 rename conda/{rsc_rapids_24.08.yml => rsc_rapids_24.12.yml} (91%)

diff --git a/conda/rsc_rapids_24.08.yml b/conda/rsc_rapids_24.12.yml
similarity index 91%
rename from conda/rsc_rapids_24.08.yml
rename to conda/rsc_rapids_24.12.yml
index 8f3b3f38..b57125df 100644
--- a/conda/rsc_rapids_24.08.yml
+++ b/conda/rsc_rapids_24.12.yml
@@ -5,8 +5,8 @@ channels:
  - conda-forge
  - bioconda
 dependencies:
- - rapids=24.08
- - python=3.11
+ - rapids=24.12
+ - python=3.12
  - cuda-version=12.5
  - cudnn
  - cutensor
diff --git a/docs/Installation.md b/docs/Installation.md
index 64bc5507..cb8c5c39 100644
--- a/docs/Installation.md
+++ b/docs/Installation.md
@@ -2,9 +2,9 @@
 ## Conda
 The easiest way to install *rapids-singlecell* is to use one of the *yaml* file provided in the [conda](https://github.com/scverse/rapids_singlecell/tree/main/conda) folder. These *yaml* files install everything needed to run the example notebooks and get you started.
 ```
-conda env create -f conda/rsc_rapids_24.06.yml #default CUDA-11.8
+conda env create -f conda/rsc_rapids_24.08.yml #default CUDA-11.8
 # or
-mamba env create -f conda/rsc_rapids_24.08.yml #default CUDA-12.5
+mamba env create -f conda/rsc_rapids_24.12.yml #default CUDA-12.5
 ```
 ## PyPI
 As of version 0.4.0 *rapids-singlecell* is now on PyPI.

From c15ecf72addb4fe1ff35877b1f088ddf9625bf51 Mon Sep 17 00:00:00 2001
From: Intron7 <severin.dicks@icloud.com>
Date: Mon, 16 Dec 2024 16:59:17 +0100
Subject: [PATCH 11/14] keep rapids-24.08

---
 conda/{rsc_rapids_24.10.yml => rsc_rapids_24.08.yml} | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)
 rename conda/{rsc_rapids_24.10.yml => rsc_rapids_24.08.yml} (95%)

diff --git a/conda/rsc_rapids_24.10.yml b/conda/rsc_rapids_24.08.yml
similarity index 95%
rename from conda/rsc_rapids_24.10.yml
rename to conda/rsc_rapids_24.08.yml
index c21bf794..8f3b3f38 100644
--- a/conda/rsc_rapids_24.10.yml
+++ b/conda/rsc_rapids_24.08.yml
@@ -5,7 +5,7 @@ channels:
  - conda-forge
  - bioconda
 dependencies:
- - rapids=24.10
+ - rapids=24.08
  - python=3.11
  - cuda-version=12.5
  - cudnn

From 6e9b0869825949eef05be5a668121f41f875cc3b Mon Sep 17 00:00:00 2001
From: Severin Dicks <37635888+Intron7@users.noreply.github.com>
Date: Mon, 16 Dec 2024 17:43:21 +0100
Subject: [PATCH 12/14] Update .github/workflows/test-gpu-dev.yml

Co-authored-by: Philipp A. <flying-sheep@web.de>
---
 .github/workflows/test-gpu-dev.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/test-gpu-dev.yml b/.github/workflows/test-gpu-dev.yml
index 84f76858..2d5cd25f 100644
--- a/.github/workflows/test-gpu-dev.yml
+++ b/.github/workflows/test-gpu-dev.yml
@@ -55,7 +55,7 @@ jobs:
           "scanpy @ git+https://github.com/scverse/scanpy.git"
           "anndata @ git+https://github.com/scverse/anndata.git"
           --extra-index-url=https://pypi.nvidia.com
-          --index-strategy  unsafe-best-match
+          --index-strategy=unsafe-best-match
 
       - name: Run test
         run: pytest

From c1b35a4011e38c79c79318085dd3fd647c332a67 Mon Sep 17 00:00:00 2001
From: Severin Dicks <37635888+Intron7@users.noreply.github.com>
Date: Mon, 16 Dec 2024 17:43:26 +0100
Subject: [PATCH 13/14] Update .github/workflows/test-gpu.yml

Co-authored-by: Philipp A. <flying-sheep@web.de>
---
 .github/workflows/test-gpu.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/test-gpu.yml b/.github/workflows/test-gpu.yml
index 450b361b..40d0c931 100644
--- a/.github/workflows/test-gpu.yml
+++ b/.github/workflows/test-gpu.yml
@@ -50,7 +50,7 @@ jobs:
           cache-dependency-path: pyproject.toml
 
       - name: Install rapids-singlecell
-        run: uv pip install --system -e .[test,rapids12] --extra-index-url=https://pypi.nvidia.com --index-strategy  unsafe-best-match
+        run: uv pip install --system -e .[test,rapids12] --extra-index-url=https://pypi.nvidia.com --index-strategy=unsafe-best-match
 
       - name: Pip list
         run: pip list

From 247f75a584899c4b6db0198b76d6375eb16728e3 Mon Sep 17 00:00:00 2001
From: Severin Dicks <37635888+Intron7@users.noreply.github.com>
Date: Mon, 16 Dec 2024 17:43:31 +0100
Subject: [PATCH 14/14] Update docs/Installation.md

Co-authored-by: Philipp A. <flying-sheep@web.de>
---
 docs/Installation.md | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/docs/Installation.md b/docs/Installation.md
index cb8c5c39..54b01c5c 100644
--- a/docs/Installation.md
+++ b/docs/Installation.md
@@ -22,7 +22,7 @@ pip install 'rapids-singlecell[rapids12]' --extra-index-url=https://pypi.nvidia.
 It is important to ensure that the CUDA environment is set up correctly so that RAPIDS and Cupy can locate the necessary libraries.
 
 ```{note}
-If you are using `python=3.12` with `uv`, you might need to add the `--index-strategy unsafe-best-match` flag to ensure compatibility.
+If you are using `python=3.12` with `uv`, you might need to add the `--index-strategy=unsafe-best-match` flag to ensure compatibility.
 ```
 
 ## Docker