Feature/pixi and conda installation

README.md

@@ -1,8 +1,30 @@
 # Installation
 
-## pip
+We recommend CUDA 12.1 with `cu*` packages version ≥24.2 and <26.0. Ensure your CUDA driver version matches or exceeds your toolkit version (≥12.1 for CUDA 12.1). 
+Adjust package versions in the environment files below if your system requires a different package versions.
 
-Before installing **segger**, please install GPU-accelerated versions of PyTorch, RAPIDS, and related packages compatible with your system. *Please ensure all CUDA-enabled packages are compiled for the same CUDA version.*
+## Clone the repository
+```bash
+git clone https://github.com/dpeerlab/segger.git segger && cd segger
+```
+
+## Using `conda`
+```bash
+conda env create -n segger -f environment_cuda121.yml
+```
+
+Adjust `environment_cuda121.yml` for other CUDA versions (e.g., `environment_cuda118.yml` for CUDA 11.8).
+
+## Using `pixi`
+```bash
+pixi install -e cuda121
+```
+
+Adjust the environment name in `pixi.toml` as needed for other CUDA versions.
+
+## `pip`
+
+Install GPU-accelerated PyTorch and RAPIDS compatible with your CUDA version before installing **segger**. All CUDA-enabled packages must be compiled for the same CUDA version.
 
 - **PyTorch & torchvision:** [Installation guide](https://pytorch.org/get-started/locally/)
 - **torch_scatter:** [Installation guide](https://github.com/rusty1s/pytorch_scatter#installation)
@@ -28,7 +50,6 @@ pip install cupy-cuda12x
 
 ```bash
 # Clone segger repo and install locally
-git clone https://github.com/dpeerlab/segger.git segger && cd segger
 pip install -e .
 ```
 

environment_cuda121.yml

@@ -0,0 +1,29 @@
+channels:
+  - pytorch
+  - nvidia
+  - rapidsai
+  - conda-forge
+
+dependencies:
+  - python>=3.11,<3.12
+
+  # RAPIDS 24.10 — last release compatible with CUDA 12.1 runtime
+  - cuspatial=24.10
+  - cudf=24.10
+  - cuml=24.10
+  - cugraph=24.10
+  - cupy
+
+  - pip
+  - pip:
+      - --extra-index-url https://pypi.nvidia.com
+      - --extra-index-url https://download.pytorch.org/whl/cu121
+      - --find-links https://data.pyg.org/whl/torch-2.5.0+cu121.html
+      - torch==2.5.*
+      - torchvision==0.20.*
+      - lightning
+      - torch-geometric
+      - torch-scatter
+      - torch-sparse
+      - cupy-cuda12x>=12.2,<13.0
+      - --editable .

pixi.toml

@@ -0,0 +1,45 @@
+[workspace]
+channels = ["pytorch", "nvidia", "rapidsai", "conda-forge"]
+platforms = ["linux-64"]
+
+[dependencies]
+python = ">=3.11"
+
+[pypi-dependencies]
+segger = { path = ".", editable = true }
+
+[feature.cuda121.dependencies]
+python = ">=3.11,<3.12"
+
+[feature.cuda121.system-requirements]
+cuda = "12"
+
+[feature.cuda121.pypi-options]
+index-strategy = "unsafe-best-match"
+index-url = "https://pypi.org/simple"
+extra-index-urls = [
+    "https://pypi.nvidia.com",
+    "https://download.pytorch.org/whl/cu121"
+]
+find-links = [
+    { url = "https://data.pyg.org/whl/torch-2.5.0+cu121.html" }
+]
+
+[feature.cuda121.pypi-dependencies]
+torch = "==2.5.*"
+torchvision = "==0.20.*"
+lightning = "*"
+torch_geometric = "*"
+torch-scatter = "*"
+torch-sparse = "*"
+cuspatial-cu12 = "==24.10.*"
+cudf-cu12 = "==24.10.*"
+cuml-cu12 = "==24.10.*"
+cugraph-cu12 = "==24.10.*"
+cupy-cuda12x = ">=12.2,<13.0"
+
+[tool.uv.extra-build-dependencies]
+torch-scatter = ["torch"]
+
+[environments]
+cuda121 = ["cuda121"]

pyproject.toml

@@ -15,7 +15,6 @@ dependencies = [
     "anndata",
     "cyclopts",
     "geopandas",
-    "lightning",
     "numba",
     "numpy",
     "opencv-python",
@@ -27,8 +26,7 @@ dependencies = [
     "shapely",
     "scikit-image",
     "scikit-learn",
-    "tifffile",
-    "torch_geometric",
+    "tifffile"
 ]
 
 [build-system]

src/segger/cli/main.py

@@ -10,4 +10,3 @@
 
 # Debugging utilities
 app.command(debug)
-

tmp.txt

@@ -0,0 +1,189 @@
+Package                  Version         Editable project location
+------------------------ --------------- --------------------------------------------------------------
+aiohappyeyeballs         2.6.1
+aiohttp                  3.13.3
+aiosignal                1.4.0
+anndata                  0.12.7
+array-api-compat         1.13.0
+asttokens                3.0.1
+attrs                    25.4.0
+cachetools               6.2.4
+certifi                  2026.1.4
+charset-normalizer       3.4.4
+click                    8.3.1
+cloudpickle              3.1.2
+comm                     0.2.3
+contourpy                1.3.3
+cuda-bindings            12.9.5
+cuda-pathfinder          1.3.3
+cuda-python              12.9.5
+cudf-cu12                25.4.0
+cugraph-cu12             25.4.1
+cuml-cu12                25.4.0
+cupy-cuda12x             13.6.0
+cuspatial-cu12           25.4.0
+cuvs-cu12                25.4.0
+cycler                   0.12.1
+cyclopts                 4.4.5
+dask                     2025.2.0
+dask-cuda                25.4.0
+dask-cudf-cu12           25.4.0
+debugpy                  1.8.20
+decorator                5.2.1
+diptest                  0.10.0
+distributed              2025.2.0
+distributed-ucxx-cu12    0.43.0
+docstring_parser         0.17.0
+docutils                 0.22.4
+donfig                   0.8.1.post1
+executing                2.2.1
+fastrlock                0.8.3
+filelock                 3.20.0
+fonttools                4.61.1
+frozenlist               1.8.0
+fsspec                   2025.12.0
+geopandas                1.1.2
+gh                       0.0.4
+gitdb                    4.0.12
+GitPython                3.1.46
+google-crc32c            1.8.0
+h5py                     3.15.1
+idna                     3.11
+ImageIO                  2.37.2
+ipykernel                7.2.0
+ipython                  9.10.0
+ipython_pygments_lexers  1.1.1
+jedi                     0.19.2
+Jinja2                   3.1.6
+joblib                   1.5.3
+jupyter_client           8.8.0
+jupyter_core             5.9.1
+kiwisolver               1.4.9
+lazy_loader              0.4
+legacy-api-wrap          1.5
+libcudf-cu12             25.4.0
+libcugraph-cu12          25.4.1
+libcuml-cu12             25.4.0
+libcuspatial-cu12        25.4.0
+libcuvs-cu12             25.4.0
+libkvikio-cu12           25.4.0
+libraft-cu12             25.4.0
+librmm-cu12              25.4.0
+libucx-cu12              1.18.1
+libucxx-cu12             0.43.0
+lightning                2.6.0
+lightning-utilities      0.15.2
+llvmlite                 0.43.0
+locket                   1.0.0
+markdown-it-py           4.0.0
+MarkupSafe               2.1.5
+matplotlib               3.10.8
+matplotlib-inline        0.2.1
+mdurl                    0.1.2
+memory-profiler          0.61.0
+mpmath                   1.3.0
+msgpack                  1.1.2
+multidict                6.7.0
+natsort                  8.4.0
+nest_asyncio             1.6.0
+networkx                 3.6.1
+numba                    0.60.0
+numba-cuda               0.4.0
+numcodecs                0.16.5
+numpy                    2.0.2
+nvidia-cublas-cu12       12.1.3.1
+nvidia-cuda-cupti-cu12   12.1.105
+nvidia-cuda-nvrtc-cu12   12.1.105
+nvidia-cuda-runtime-cu12 12.1.105
+nvidia-cudnn-cu12        9.1.0.70
+nvidia-cufft-cu12        11.0.2.54
+nvidia-curand-cu12       10.3.2.106
+nvidia-cusolver-cu12     11.4.5.107
+nvidia-cusparse-cu12     12.1.0.106
+nvidia-ml-py             12.575.51
+nvidia-nccl-cu12         2.21.5
+nvidia-nvcomp-cu12       4.2.0.11
+nvidia-nvjitlink-cu12    12.9.86
+nvidia-nvtx-cu12         12.1.105
+nvtx                     0.2.14
+opencv-python            4.12.0.88
+packaging                26.0
+pandas                   2.2.3
+parso                    0.8.6
+partd                    1.4.2
+patsy                    1.0.2
+pexpect                  4.9.0
+pillow                   12.0.0
+pip                      26.0.1
+platformdirs             4.9.2
+polars                   1.37.1
+polars-runtime-32        1.37.1
+prompt_toolkit           3.0.52
+propcache                0.4.1
+psutil                   7.2.2
+ptyprocess               0.7.0
+pure_eval                0.2.3
+pyarrow                  19.0.1
+Pygments                 2.19.2
+pylibcudf-cu12           25.4.0
+pylibcugraph-cu12        25.4.1
+pylibraft-cu12           25.4.0
+pynndescent              0.6.0
+pynvjitlink-cu12         0.7.0
+pynvml                   12.0.0
+pyogrio                  0.12.1
+pyparsing                3.3.1
+pyproj                   3.7.2
+python-dateutil          2.9.0.post0
+pytorch-lightning        2.6.0
+pytz                     2025.2
+PyYAML                   6.0.3
+pyzmq                    27.1.0
+raft-dask-cu12           25.4.0
+rapids-dask-dependency   25.4.0
+rapids-logger            0.1.19
+requests                 2.32.5
+rich                     14.2.0
+rich-rst                 1.3.2
+rmm-cu12                 25.4.0
+scanpy                   1.11.5
+scikit-image             0.26.0
+scikit-learn             1.8.0
+scipy                    1.17.0
+seaborn                  0.13.2
+segger                   0.1.0           /data1/collab002/sail/projects/ongoing/segger_dev/tools/segger
+session-info2            0.3
+setuptools               82.0.0
+shapely                  2.1.2
+six                      1.17.0
+smmap                    5.0.2
+sortedcontainers         2.4.0
+stack_data               0.6.3
+statsmodels              0.14.6
+sympy                    1.13.1
+tblib                    3.2.2
+threadpoolctl            3.6.0
+tifffile                 2025.12.20
+toolz                    1.1.0
+torch                    2.5.0+cu121
+torch-geometric          2.7.0
+torch_scatter            2.1.2+pt25cu121
+torchmetrics             1.8.2
+torchvision              0.20.0+cu121
+tornado                  6.5.3
+tqdm                     4.67.1
+traitlets                5.14.3
+treelite                 4.4.1
+triton                   3.1.0
+typing_extensions        4.15.0
+tzdata                   2025.3
+ucx-py-cu12              0.43.0
+ucxx-cu12                0.43.0
+umap-learn               0.5.11
+urllib3                  2.6.3
+wcwidth                  0.6.0
+wheel                    0.46.3
+xxhash                   3.6.0
+yarl                     1.22.0
+zarr                     3.1.5
+zict                     3.0.0