Installation procedure (#70)

* Replace setup.py with pyproject.toml

* Update CI workflows to install with just pip install

* Change tests pip install to editable and update install instructions on readme.md

* Add macos to test

* Update path for lib in macos

Author: CalCraven

.github/workflows/run_test.yml

@@ -14,11 +14,12 @@ jobs:
   test:
     if: github.event.pull_request.draft == false
     name: Grouper Tests (python)
-    runs-on: ubuntu-latest
+    runs-on: ${{ matrix.os }}
 
     strategy:
       fail-fast: false
       matrix:
+        os: [macOS-latest, ubuntu-latest]
         python-version: [3.9, 3.12]
 
     defaults:
@@ -27,7 +28,7 @@ jobs:
 
     steps:
     - name: Checkout code
-      uses: actions/checkout@v2
+      uses: actions/checkout@v4
 
     - name: Install environment
       uses: mamba-org/setup-micromamba@v2
@@ -40,10 +41,10 @@ jobs:
       run: micromamba activate grouper-dev
 
     - name: List libraries in grouper-dev
-      run: ls /home/runner/micromamba/envs/grouper-dev/lib | grep omp
+      run: ls ${MAMBA_ROOT_PREFIX}/envs/grouper-dev/lib | grep omp
 
     - name: Install package
-      run: micromamba run -n grouper-dev python setup.py build_ext --inplace;micromamba run -n grouper-dev pip install .
+      run: micromamba run -n grouper-dev pip install -e .
 
     - name: Run tests with pytest
       run: micromamba run -n grouper-dev pytest Grouper/tests

.gitignore

@@ -7,7 +7,6 @@ notebooks
 foo
 .benchmarks
 # Data files
-*.txt
 *.pkl
 
 foo.ipynb

CMakeLists.txt

@@ -0,0 +1,79 @@
+cmake_minimum_required(VERSION 3.15)
+project(${SKBUILD_PROJECT_NAME} LANGUAGES CXX)
+
+# Set C++ standard
+set(CMAKE_CXX_STANDARD 17)
+set(CMAKE_CXX_STANDARD_REQUIRED ON)
+
+# Find required packages
+find_package(pybind11 REQUIRED CONFIG)
+
+# Get conda prefix
+if(DEFINED ENV{CONDA_PREFIX})
+    set(CONDA_PREFIX $ENV{CONDA_PREFIX})
+else()
+    message(FATAL_ERROR "CONDA_PREFIX environment variable not set")
+endif()
+
+# Platform-specific settings
+if(APPLE)
+    set(CMAKE_OSX_ARCHITECTURES "arm64")
+    set(PLATFORM_COMPILE_FLAGS "-Xpreprocessor" "-fopenmp")
+elseif(UNIX AND NOT APPLE)
+    set(PLATFORM_COMPILE_FLAGS "-D_Thread_local=thread_local")
+endif()
+
+# Include directories
+set(INCLUDE_DIRS
+    ${CONDA_PREFIX}/include
+    ${CONDA_PREFIX}/include/cairo
+    ${CONDA_PREFIX}/include/boost
+    ${CONDA_PREFIX}/include/rdkit
+    ${CONDA_PREFIX}/include/omp
+    ${CONDA_PREFIX}/include/nauty
+    ${CONDA_PREFIX}/include/libpq
+    ${CMAKE_CURRENT_SOURCE_DIR}/Grouper
+)
+
+# Library directories
+set(LIBRARY_DIRS
+    ${CONDA_PREFIX}/lib
+    ${CONDA_PREFIX}/lib/cairo
+)
+
+# Libraries to link
+set(LIBRARIES
+    RDKitFileParsers
+    RDKitSmilesParse
+    RDKitGraphMol
+    RDKitRDGeneral
+    omp
+    nauty
+    pq
+)
+
+# Source files
+set(SOURCES
+    Grouper/dataStructures.cpp
+    Grouper/binding.cpp
+    Grouper/processColoredGraphs.cpp
+    Grouper/generate.cpp
+    Grouper/fragmentation.cpp
+)
+
+# Create pybind11 module
+pybind11_add_module(_Grouper ${SOURCES})
+
+# Set target properties
+target_include_directories(_Grouper PRIVATE ${INCLUDE_DIRS})
+target_link_directories(_Grouper PRIVATE ${LIBRARY_DIRS})
+target_link_libraries(_Grouper PRIVATE ${LIBRARIES})
+
+# Compiler flags
+target_compile_options(_Grouper PRIVATE 
+    -fPIC
+    ${PLATFORM_COMPILE_FLAGS}
+)
+
+# Install the module
+install(TARGETS _Grouper DESTINATION Grouper)

README.md

@@ -13,7 +13,7 @@
 <!-- PROJECT LOGO -->
 <br />
 <div align="center">
-  <a href="https://github.com/kierannp/Grouper">
+  <a href="https://github.com/mosdef-hub/Grouper">
     <img src="images/grouper.jpeg" alt="Logo" width="700" height="300">
   </a>
 
@@ -22,14 +22,14 @@
   <p align="center">
     A software package for creating and manipulating graphs of molecular groups.
     <br />
-    <a href="https://github.com/kierannp/Grouper"><strong>Explore the docs »</strong></a>
+    <a href="https://github.com/mosdef-hub/Grouper"><strong>Explore the docs »</strong></a>
     <br />
     <br />
-    <a href="https://github.com/kierannp/Grouper">View Demo</a>
+    <a href="https://github.com/mosdef-hub/Grouper">View Demo</a>
     ·
-    <a href="https://github.com/kierannp/Grouper/issues">Report Bug</a>
+    <a href="https://github.com/mosdef-hub/Grouper/issues">Report Bug</a>
     ·
-    <a href="https://github.com/kierannp/Grouper/issues">Request Feature</a>
+    <a href="https://github.com/mosdef-hub/Grouper/issues">Request Feature</a>
   </p>
 </div>
 
@@ -71,20 +71,13 @@ The fundamental data structure behind this package is based on a port graph, loo
 
 ### Installation
 
-1. Clone the repo
 ```sh
-conda create -n Grouper python=3.9
-conda activate Grouper
-conda install librdkit-dev librdkit rdkit-dev rdkit-postgresql boost cmake rdkit eigen pybind11 openmp
-conda install -c conda-forge nauty nlohmann_json
-
-git clone https://github.com/kierannp/Grouper
+git clone https://github.com/mosdef-hub/Grouper
 cd Grouper
-```
-2. Install with `pip`
-```python
-python setup.py build_ext --inplace
-python setup.py install
+conda create -f environment.yml
+conda activate grouper-dev
+pip install -e . 
+python -m pytest Grouper/tests
 ```
 
 <p align="right">(<a href="#readme-top">back to top</a>)</p>

pyproject.toml

@@ -0,0 +1,17 @@
+[build-system]
+requires = ["scikit-build-core>=0.3.3", "pybind11"]
+build-backend = "scikit_build_core.build"
+
+[project]
+name = "Grouper"
+version = "0.1"
+description = "A package for working with group graphs"
+authors = [{name = "Kieran Nehil-Puleo"}]
+requires-python = ">=3.9"
+
+[tool.scikit-build]
+cmake.minimum-version = "3.15"
+wheel.expand-macos-universal-tags = true
+
+[tool.setuptools]
+packages = ["Grouper"]