Uv installation

.readthedocs.yaml

@@ -1,14 +1,13 @@
 version: 2
 
 build:
-  os: "ubuntu-20.04"
+  os: "ubuntu-22.04"
   tools:
     python: "3.11"
-
-python:
-  # Install our python package before building the docs
-  install:
-    - method: pip
-      path: . 
-      extra_requirements:
-        - docs
+  commands:
+    # Install uv
+    - pip install uv
+    # Sync dependencies with uv (includes docs extras)
+    - uv sync --extra docs
+    # Build docs
+    - uv run sphinx-build -b html docs $READTHEDOCS_OUTPUT/html

README.md

@@ -20,18 +20,43 @@ Extensive documentation and tutorials are available at [read the docs](https://s
 
 ## Installing
 
-To install SCENIC+ (in a Linux environment):
+### Recommended: Install with uv (Fast & Cross-Platform)
 
-We highly recommend to install SCENIC+ in a new conda environment.
+[uv](https://github.com/astral-sh/uv) is a fast Python package installer and resolver. It's the recommended way to install SCENIC+ as it handles dependencies efficiently and works on macOS, Linux, and Windows.
+
+**Requirements:**
+- Python 3.11 (Python 3.12 not yet supported due to dependency incompatibilities)
+- HDF5 library (see platform-specific instructions in [UV_SETUP.md](UV_SETUP.md))
+
+**Quick Start:**
 
 ```bash
+# Install uv
+curl -LsSf https://astral.sh/uv/install.sh | sh
+
+# Clone the repository
+git clone https://github.com/aertslab/scenicplus
+cd scenicplus
 
-$ conda create --name scenicplus python=3.11 -y
-$ conda activate scenicplus
-$ git clone https://github.com/aertslab/scenicplus
-$ cd scenicplus
-$ pip install .
+# Install dependencies and SCENIC+
+uv sync
+
+# Run Python with uv
+uv run python your_script.py
+```
 
+For detailed setup instructions, troubleshooting, and platform-specific requirements, see [UV_SETUP.md](UV_SETUP.md).
+
+### Alternative: Install with conda/pip
+
+If you prefer conda, you can install SCENIC+ in a new conda environment:
+
+```bash
+conda create --name scenicplus python=3.11 -y
+conda activate scenicplus
+git clone https://github.com/aertslab/scenicplus
+cd scenicplus
+pip install .
 ```
 
 ## Questions?

UV_SETUP.md

@@ -0,0 +1,103 @@
+# UV Setup for SCENIC+
+
+This project is now configured to use `uv`, a fast Python package installer and resolver.
+
+## Prerequisites
+
+1. **Python Version**: This project currently requires **Python 3.11**. Python 3.12 is not yet supported due to the `sinfo` package incompatibility (used by `scanpy`).
+
+2. Install HDF5 (required for tables package):
+
+   **macOS:**
+   ```bash
+   brew install hdf5
+   ```
+
+   **Linux:**
+   ```bash
+   # Ubuntu/Debian
+   sudo apt-get install libhdf5-dev
+
+   # Fedora/RHEL
+   sudo dnf install hdf5-devel
+   ```
+
+   **Windows:**
+
+   On Windows, the pre-built wheels for `tables` 3.10+ should work without manually installing HDF5. If you encounter issues, you can install HDF5 via conda:
+   ```bash
+   conda install -c conda-forge hdf5
+   ```
+
+## Installation
+
+1. Install uv:
+   ```bash
+   curl -LsSf https://astral.sh/uv/install.sh | sh
+   ```
+
+2. Sync dependencies:
+   ```bash
+   uv sync
+   ```
+
+The project includes a dependency override for the `tables` package to use version 3.10+ instead of the problematic 3.9.2, avoiding compilation issues on macOS.
+
+## Running Python with uv
+
+Use `uv run` to execute Python commands in the managed environment:
+
+```bash
+uv run python your_script.py
+uv run python -c "import scenicplus"
+```
+
+## How It Works
+
+The `pyproject.toml` file includes a `[tool.uv]` section with an override:
+
+```toml
+[tool.uv]
+override-dependencies = [
+    "tables>=3.10"
+]
+```
+
+This ensures that even though some dependencies (like `scanpy`) pin `tables==3.9.2`, uv will use version 3.10+ which has pre-built wheels for Apple Silicon and avoids compilation errors.
+
+## Troubleshooting
+
+### tables Compilation Errors
+
+If you see compilation errors mentioning `fdopen` or `zutil.c`, the `tables` package is trying to build from source. This should not happen with the current setup, but if it does:
+
+1. Ensure your `pyproject.toml` has the override-dependencies section shown above
+2. Delete `uv.lock` and regenerate:
+   ```bash
+   rm uv.lock
+   uv lock
+   uv sync
+   ```
+
+### Verifying Installation
+
+Check that tables 3.10+ is installed:
+```bash
+uv run python -c "import tables; print(tables.__version__)"
+```
+
+You should see version 3.10.2 or later.
+
+## Development
+
+The project uses:
+- Python 3.11 (3.12 support blocked by `sinfo` package used by `scanpy`)
+- uv for package management and virtual environment
+- All dependencies specified in `requirements.txt`
+- Dependency overrides in `pyproject.toml` for compatibility:
+  - `tables>=3.10` (fixes macOS compilation issues)
+  - `ray>=2.51.0` (adds Python 3.12 wheel support, ready for when Python 3.12 is supported)
+
+### Python 3.12 Status
+
+Python 3.12 support is currently blocked by the `sinfo` package (v0.3.4), which uses `configparser.SafeConfigParser` (removed in Python 3.12). This package is a dependency of `scanpy` v1.8.2 and is only used for the optional `sc.logging.print_versions()` function. Once `scanpy` updates or removes this dependency, Python 3.12 will be supported.

constraints.txt

@@ -0,0 +1 @@
+tables>=3.10

pyproject.toml

@@ -11,7 +11,7 @@ authors = [
 description = "SCENIC+ is a python package to build gene regulatory networks (GRNs) using combined or separate single-cell gene expression (scRNA-seq) and single-cell chromatin accessibility (scATAC-seq) data."
 readme = "README.md"
 version = "1.0a2"
-requires-python = ">=3.8,<=3.11.8"
+requires-python = ">=3.11,<3.12"
 keywords = ["scATAC", "GRN inference", "eGRN inference"]
 license = { file = "LICENCE.txt" }
 classifiers = [
@@ -23,9 +23,6 @@ classifiers = [
   "Programming Language :: Python",
   "Programming Language :: Python :: 3",
   "Programming Language :: Python :: 3 :: Only",
-  "Programming Language :: Python :: 3.8",
-  "Programming Language :: Python :: 3.9",
-  "Programming Language :: Python :: 3.10",
   "Programming Language :: Python :: 3.11",
   "Topic :: Scientific/Engineering :: Bio-Informatics",
 ]
@@ -34,6 +31,12 @@ dynamic = ["dependencies"]
 [tool.setuptools.dynamic]
 dependencies = {file = ["requirements.txt"]}
 
+[tool.uv]
+override-dependencies = [
+    "tables>=3.10",
+    "ray>=2.51.0"
+]
+
 [project.optional-dependencies]
 docs = [
     "sphinx_rtd_theme",

requirements.txt

@@ -748,7 +748,8 @@ seaborn==0.13.2
     #   pycistopic
     #   scanpy
     #   scenicplus (pyproject.toml)
-sinfo==0.3.4
+# sinfo==0.3.4 removed - not compatible with Python 3.12
+# scanpy will work without it (only used for session_info.show() function)
     # via scanpy
 six==1.16.0
     # via