Revamped build system to minimal autoconf + scikit-build

.github/workflows/autoreconf.yml

@@ -21,17 +21,11 @@ jobs:
       run: |
         autoreconf -fiv
         ./configure
-        make dist
-
-    - name: Extract dist files
-      run: |
-        tar -zxvf scdemon-*.tar.gz
-        cp -r scdemon-*/* .
 
     - name: Push to Main Branch
       run: |
         git config --global user.name 'GitHub Action'
         git config --global user.email '[email protected]'
-        git add config.guess config.sub configure configure.ac Makefile.in Makefile.am install-sh aclocal.m4 missing DESCRIPTION VERSION
+        git add configure DESCRIPTION VERSION docs/sphinx/conf.py
         git commit -m "Auto-update Autotools files" || echo "No changes to commit"
         git push origin HEAD:main -f

.gitignore

@@ -1,3 +1,6 @@
+## makevars
+src/Makevars
+
 ## autoconf
 autom4te.cache/
 config.status

CMakeLists.txt

@@ -0,0 +1,31 @@
+cmake_minimum_required(VERSION 3.15...3.27)
+project(
+  ${SKBUILD_PROJECT_NAME}
+  VERSION ${SKBUILD_PROJECT_VERSION}
+  LANGUAGES CXX)
+
+# Set C++ standard
+set(CMAKE_CXX_STANDARD 17)
+set(CMAKE_CXX_STANDARD_REQUIRED ON)
+
+find_package(Python REQUIRED COMPONENTS Interpreter Development.Module)
+find_package(pybind11 CONFIG REQUIRED)
+
+# Find OpenMP
+find_package(OpenMP REQUIRED)
+if(OpenMP_CXX_FOUND)
+  set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} ${OpenMP_CXX_FLAGS}")
+endif()
+
+# Include Eigen
+find_package(Eigen3 3.3 REQUIRED NO_MODULE)
+
+python_add_library(_core MODULE scdemon/py_se.cpp WITH_SOABI)
+target_link_libraries(_core PRIVATE pybind11::headers)
+target_link_libraries(_core PRIVATE Eigen3::Eigen)
+
+target_compile_definitions(_core PRIVATE VERSION_INFO=${PROJECT_VERSION})
+
+# Include the C++ headers
+include_directories(${CMAKE_CURRENT_SOURCE_DIR}/src)
+install(TARGETS _core DESTINATION ${SKBUILD_PROJECT_NAME})

README.org

@@ -34,6 +34,11 @@ BigCLAM/Leiden
 - .varp: PCA based ANN (bool)
 - .varp: filtered graph (CSR, data=tvalue)
 - .var / .varm: clustering / cluster loadings
+****  Minimal conda environment
+#+BEGIN_SRC bash
+mamba create -n scdemonpy conda-forge::gxx_linux-64 conda-forge::gcc_linux-64 conda-forge::gfortran_linux-64 conda-forge::eigen conda-forge::gsl conda-forge::anndata conda-forge::tqdm conda-forge::pybind11 conda-forge::pip conda-forge::igraph conda-forge::umap-learn
+mamba create -n scdemonr conda-forge::gxx_linux-64 conda-forge::gcc_linux-64 conda-forge::gfortran_linux-64 conda-forge::r-devtools conda-forge::r-rcppeigen conda-forge::r-rcppprogress conda-forge::gsl bioconda::bioconductor-rhdf5 conda-forge::r-igraph conda-forge::r-uwot conda-forge::r-irlba
+#+END_SRC
 **** API
 ***** build_nn_graph
 1. extract dimreduc, variables, covariates using params. Order obs/obsm based statistics if applicable.
@@ -46,11 +51,21 @@ BigCLAM/Leiden
 *** DONE C++ demo code linked to python and R
 *** DONE HC0 SE in C++
 **** DONE Eigen::MatrixBase<T> type
-*** TODO KNN interface in R/Python
-**** Sparse matrix conversion: 0/1 indexing
+*** TODO CircleCI and codecov
+*** DONE Sparse matrix conversion: 0/1 indexing
+*** TODO simplify setup
+use data.table https://github.com/Rdatatable/data.table/blob/master/configure and nloptr https://github.com/astamm/nloptr/blob/master/configure as templates
+- scikit-build + CMake for python
+- configure.ac/configure/cleanup scripts for R  
 *** TODO pkgdown website
+- github action https://github.com/r-lib/actions/blob/v2/examples/pkgdown.yaml
+*** TODO CI circleCI like bioconda?
+*** TODO testing/codecov
+*** TODO linting
+- lintr action https://github.com/r-lib/actions/blob/v2/examples/lint.yaml
+- python linting like anndata
 *** TODO sphinx/readthedocs
-*** TODO threaded implementation
+*** DONE threaded implementation
 **** OpenMP vs STL parallel
 *** TODO CMake build for R and python
 *** TODO vignettes in R and python
@@ -62,3 +77,8 @@ BigCLAM/Leiden
 **** bootstrapped cluster SE
 *** TODO Newey-West in C++ : sort by sample depth to account for depth autocorrelation
 *** TODO Submit to bioconda (R, python versions)
+*** TODO Add to bioconductor?, seurat-wrappers, scanpy.external.tl
+*** TODO Single-cell Multi-omic: Use CCA or OPA; combine graphs
+*** TODO metacell support instead of using PCA based
+*** TODO support for WGCNA
+

cleanup

@@ -0,0 +1,2 @@
+#!/usr/bin/env sh
+rm -f src/Makevars

configure.ac

@@ -1,47 +1,25 @@
-AC_INIT([scdemon], [0.0.2])
+AC_INIT([scdemon], [0.0.3])
 
 AC_MSG_NOTICE([Creating VERSION file])
 echo m4_defn([AC_PACKAGE_VERSION]) > VERSION
 
-AC_CANONICAL_BUILD
-AC_CANONICAL_HOST
-AC_CANONICAL_TARGET
+: ${R_HOME=$(R RHOME)}
+if test -z "${R_HOME}"; then
+   AC_MSG_ERROR([Could not determine R_HOME.])
+fi
 
+CXX=`"${R_HOME}/bin/R" CMD config CXX`
+if test -z "${CXX}"; then
+    AC_MSG_ERROR([No C++ compiler available])
+fi
+CXXFLAGS=`"${R_HOME}/bin/R" CMD config CXXFLAGS`
+CPPFLAGS=`"${R_HOME}/bin/R" CMD config CPPFLAGS`
 AC_LANG([C++])
+AC_REQUIRE_CPP
 AC_PROG_CXX
 
-PKG_PROG_PKG_CONFIG
-PKG_CHECK_MODULES([EIGEN], [eigen3 >= 3.3.9], [], [AC_MSG_WARN([Eigen flags may not be set for python])])
-PKG_CHECK_MODULES([HDF5], [hdf5], [], [AC_MSG_WARN([HDF5 may not be set for testing])])
-PKG_CHECK_MODULES([GSL], [gsl], [], [AC_MSG_ERROR([GSL is required, please install])])
 AC_OPENMP
-
-AC_CHECK_PROG([R_FOUND], [R], [yes], [no])
-if test "x$R_FOUND" = xno; then
-  AC_MSG_WARN([R is not installed.])
-fi
-AC_PROG_MAKE_SET
-
-AM_INIT_AUTOMAKE([foreign subdir-objects])
-AM_MAINTAINER_MODE
-
-
-AC_ARG_ENABLE([cxxtest],
-    [AS_HELP_STRING([--enable-cxxtest], [Enable the compilation of c++ binary])],
-    [cxxtest=$enableval],
-    [cxxtest=no])
-
-AM_CONDITIONAL([ENABLE_CXX_TEST], [test "x$cxxtest" = "xyes"])
-
-AC_SUBST([PKG_CXXFLAGS], ["$CXXFLAGS $OPENMP_CXXFLAGS $GSL_CFLAGS"])
-AC_SUBST([PKG_LIBS], ["$LDFLAGS $OPENMP_CXXFLAGS $GSL_LIBS"]) 
-AC_SUBST([EIGEN_CXXFLAGS], ["$EIGEN_CFLAGS"])
-AC_SUBST([EIGEN_LIBS], ["$EIGEN_LIBS"])
-AC_SUBST([OPENMP_CXXFLAGS], ["$OPENMP_CXXFLAGS"])
-AC_SUBST([OPENMP_LIBS], ["$OPENMP_CXXFLAGS"])
-AC_SUBST([HDF5_CXXFLAGS], ["$HDF5_CXXFLAGS"])
-AC_SUBST([HDF5_LIBS], ["$HDF5_LIBS"])
-AC_SUBST([GSL_CXXFLAGS], ["$GSL_CFLAGS"])
-AC_SUBST([GSL_LIBS], ["$GSL_LIBS"])
-AC_CONFIG_FILES([src/Makevars Makefile DESCRIPTION docs/sphinx/conf.py])
+AC_SUBST([PKG_CXXFLAGS], ["$CXXFLAGS $OPENMP_CXXFLAGS"])
+AC_SUBST([PKG_LIBS], ["$LDFLAGS $OPENMP_CXXFLAGS"]) 
+AC_CONFIG_FILES([src/Makevars DESCRIPTION])
 AC_OUTPUT

docs/sphinx/conf.py.in → docs/sphinx/conf.py

@@ -5,11 +5,11 @@
 
 # -- Project information -----------------------------------------------------
 # https://www.sphinx-doc.org/en/master/usage/configuration.html#project-information
-
+from scdemon import __version__
 project = 'scdemon'
 copyright = '2024, Benjamin James'
 author = 'Benjamin James'
-release = '@VERSION@'
+release = __version__
 
 # -- General configuration ---------------------------------------------------
 # https://www.sphinx-doc.org/en/master/usage/configuration.html#general-configuration

pyproject.toml

@@ -0,0 +1,19 @@
+[build-system]
+requires = ["scikit-build-core>=0.3.3", "pybind11"] 
+build-backend = "scikit_build_core.build"
+
+[project]
+name = "scdemon"
+version = "0.0.3"
+description = "Single cell decomposition into networks"
+authors = [{name = "Benjamin James", email = "[email protected]"},
+           {name = "Carles Boix", email = "[email protected]"}]
+license = {file = "LICENSE"}
+requires-python = ">=3.7"
+dependencies = ["numpy", "pandas", "scipy", "tqdm"]
+
+[project.optional-dependencies]
+test = ["pytest"]
+
+[tool.scikit-build]
+wheel.expand-macos-universal-tags = true

scdemon/__init__.py

@@ -1,6 +1,6 @@
-import scdemon_ext
+#from _core import *
 import sys
-
+from ._core import *
 from tqdm.auto import tqdm
 class ProgressManager:
     def __init__(self):

scdemon/py_se.cpp

@@ -28,7 +28,7 @@ Eigen::MatrixXd py_ols_beta(const py::EigenDRef<Eigen::MatrixXd> &X,
         return ols_beta(X, Y);
 }
 
-PYBIND11_MODULE(scdemon_ext, m) {
+PYBIND11_MODULE(_core, m) {
 	m.def("ols_beta", &py_ols_beta);
 	m.def("robust_se_X", &py_robust_se_X);
 	m.def("robust_se", &py_robust_se);

src/Makevars.in

@@ -1,8 +1,2 @@
 PKG_CXXFLAGS = @PKG_CXXFLAGS@
 PKG_LIBS = @PKG_LIBS@
-OPENMP_CXXFLAGS = @OPENMP_CXXFLAGS@
-OPENMP_LIBS = @OPENMP_LIBS@
-EIGEN_CXXFLAGS = @EIGEN_CXXFLAGS@
-EIGEN_LIBS = @EIGEN_LIBS@
-GSL_CXXFLAGS = @GSL_CXXFLAGS@
-GSL_LIBS = @GSL_LIBS@

src/Makevars.win

@@ -0,0 +1,2 @@
+PKG_CXXFLAGS = $(SHLIB_OPENMP_CXXFLAGS)
+PKG_LIBS = $(SHLIB_OPENMP_CXXFLAGS)