From 72c06198d2cede532b6c456e5b0a462a59e1f85e Mon Sep 17 00:00:00 2001
From: Derrik Gratz <46037149+derrik-gratz@users.noreply.github.com>
Date: Mon, 11 May 2026 14:05:23 -0700
Subject: [PATCH 1/2] Add apptainer conda loading instructions

Some users have issues loading the package inside the container which can be fixed by explicitly activating the base conda environment
---
 docs/installation.md | 45 ++++++++++++++++++++++++++++++++++++++++++++
 1 file changed, 45 insertions(+)

diff --git a/docs/installation.md b/docs/installation.md
index 2487613d..6295084d 100644
--- a/docs/installation.md
+++ b/docs/installation.md
@@ -203,6 +203,51 @@ Then run the following command to execute the container:
 apptainer run --nv rsc.sif
 ```
 
+If you encounter errors importing the package inside the container, you may need to activate the conda environment inside the container:
+
+<details><summary>Example loading error:</summary>
+  ```python
+  >>> import rapids_singlecell as rsc
+Traceback (most recent call last):
+  File "<python-input-0>", line 1, in <module>
+    import rapids_singlecell as rsc
+  File "/src/rapids_singlecell/src/rapids_singlecell/__init__.py", line 3, in <module>
+    import cuml.internals.logger as logger
+  File "/opt/conda/lib/python3.14/site-packages/cuml/__init__.py", line 16, in <module>
+    import cupy
+  File "/opt/conda/lib/python3.14/site-packages/cupy/__init__.py", line 18, in <module>
+    from cupy import _core  # NOQA
+    ^^^^^^^^^^^^^^^^^^^^^^
+  File "/opt/conda/lib/python3.14/site-packages/cupy/_core/__init__.py", line 5, in <module>
+    from cupy._core import core  # NOQA
+    ^^^^^^^^^^^^^^^^^^^^^^^^^^^
+  File "cupy/_core/core.pyx", line 1, in init cupy._core.core
+  File "cupy/_core/_routines_math.pyx", line 7, in init cupy._core._routines_math
+  File "cupy/_core/_reduction.pyx", line 1, in init cupy._core._reduction
+  File "cupy/_core/_cub_reduction.pyx", line 260, in init cupy._core._cub_reduction
+  File "/opt/conda/lib/python3.14/site-packages/cupy/_environment.py", line 86, in get_nvcc_path
+    _nvcc_path = _get_nvcc_path()
+  File "/opt/conda/lib/python3.14/site-packages/cupy/_environment.py", line 198, in _get_nvcc_path
+    cuda_path = get_cuda_path()
+  File "/opt/conda/lib/python3.14/site-packages/cupy/_environment.py", line 78, in get_cuda_path
+    _cuda_path = _get_cuda_path()
+  File "/opt/conda/lib/python3.14/site-packages/cupy/_environment.py", line 151, in _get_cuda_path
+    conda_cuda_path = _get_conda_cuda_path()
+  File "/opt/conda/lib/python3.14/site-packages/cupy/_environment.py", line 130, in _get_conda_cuda_path
+    cuda_path = os.path.join(conda_prefix, 'targets', arch)
+  File "<frozen posixpath>", line 77, in join
+TypeError: expected str, bytes or os.PathLike object, not NoneType
+>>> 
+  ```
+</details>
+
+```bash
+source /opt/conda/etc/profile.d/conda.sh
+conda activate base
+python3
+...
+```
+
 
 # System requirements
 

From 12a41aec03cd49f5a6b09df87875cbc92fe11def Mon Sep 17 00:00:00 2001
From: "pre-commit-ci[bot]"
 <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Date: Mon, 11 May 2026 21:05:51 +0000
Subject: [PATCH 2/2] [pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci
---
 docs/installation.md | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/docs/installation.md b/docs/installation.md
index 6295084d..24af48bd 100644
--- a/docs/installation.md
+++ b/docs/installation.md
@@ -237,7 +237,7 @@ Traceback (most recent call last):
     cuda_path = os.path.join(conda_prefix, 'targets', arch)
   File "<frozen posixpath>", line 77, in join
 TypeError: expected str, bytes or os.PathLike object, not NoneType
->>> 
+>>>
   ```
 </details>