Update packaging

.gitmodules

@@ -1,3 +1,3 @@
-[submodule "gemmi"]
-	path = gemmi
-	url = git@github.com:project-gemmi/gemmi.git
+[submodule "pybind11"]
+	path = pybind11
+	url = https://github.com/pybind/pybind11

CMakeLists.txt

@@ -1,8 +1,17 @@
-cmake_minimum_required(VERSION 3.11.0)
+##############################################################################
+# Build file for amplus project
+##############################################################################
+
+cmake_minimum_required(VERSION 3.17.0)
 
 # Set the project name
 project(amplus CXX)
 
+# Set the build type to release
+if(NOT CMAKE_BUILD_TYPE)
+  set(CMAKE_BUILD_TYPE Release)
+endif()
+
 # Set the cmake module path
 set(CMAKE_MODULE_PATH ${PROJECT_SOURCE_DIR}/cmake)
 
@@ -11,28 +20,18 @@ set(CMAKE_MODULE_PATH ${PROJECT_SOURCE_DIR}/cmake)
 # clusters which may not allow export of LD_LIBRARY_PATH
 set(CMAKE_INSTALL_RPATH_USE_LINK_PATH True)
 
-# Find Pybind11
-find_package(pybind11 REQUIRED)
+# Add pybind sub directory
+add_subdirectory(pybind11)
 
 # Add a C/C++ extension
-pybind11_add_module(freeze_ext 
+pybind11_add_module(amplus_ext 
   amplus/freeze/freeze_ext.cc)
 
 # Ensure we are using C++11
-target_compile_features(freeze_ext PUBLIC cxx_std_11)
+target_compile_features(amplus_ext PUBLIC cxx_std_11)
 
 # Set the include directory
-target_include_directories(freeze_ext PUBLIC .)
-
-# Set the coverage compile and link flags for gcc or clang
-set(COVERAGE_COMPILE_FLAGS -coverage)
-set(COVERAGE_LINK_FLAGS    -coverage)
-
-# Set the coverage compile and link flags in the debug build
-target_compile_options(freeze_ext 
-  PUBLIC "$<$<CONFIG:DEBUG>:${COVERAGE_COMPILE_FLAGS}>")
-target_link_options(freeze_ext 
-  PUBLIC "$<$<CONFIG:DEBUG>:${COVERAGE_LINK_FLAGS}>")
+target_include_directories(amplus_ext PUBLIC .)
 
 # Install the python extension
-install(TARGETS freeze_ext LIBRARY DESTINATION amplus/freeze)
+install(TARGETS amplus_ext LIBRARY DESTINATION ${CMAKE_LIBRARY_OUTPUT_DIRECTORY})

README.md

@@ -3,25 +3,56 @@
 
 ![Code style: black](https://img.shields.io/badge/code%20style-black-000000.svg)
 
-## Dependencies
+## Installation
 
-The packages depends on the python-multem package being installed. To do this,
-follow the instructions [here](https://github.com/rosalindfranklininstitute/python-multem).
+In order to build this package, the following dependencies are required:
 
-## Installation
+- The CUDA toolkit
+- FFTW
+
+To install from the github repository do the following
+
+```sh
+export CUDACXX=${PATH_TO_CUDA}/bin/nvcc
+python -m pip install git+https://github.com/rosalindfranklininstitute/amplus-digital-twin.git@master#egg=amplus-digital-twin
+```
+
+To install from source, clone this repository. The repository has a submodule
+for pybind11 so after cloning the repository run
+
+```sh
+git submodule update --init --recursive
+```
+
+Then do the following:
+
+```sh
+export CUDACXX=${PATH_TO_CUDA}/bin/nvcc
+python -m pip install .
+```
+
+If you would like to run the tests then, clone this repository and then do the following:
+
+```sh
+export CUDACXX=${PATH_TO_CUDA}/bin/nvcc
+python -m pip install .[test]
+```
+
+## Installation for developers
 
-To install from source, clone this repository and then do the following:
+To install for development, clone this repository and then do the following:
 
 ```sh
-python setup.py install
+export CUDACXX=${PATH_TO_CUDA}/bin/nvcc
+python -m pip install -e .
 ```
 
 ## Testing
 
-To run the tests, clone this repository and the do the following:
+To run the tests, follow the installation instructions for developers and then do the following:
 
 ```sh
-python setup.py test
+pytest
 ```
 
 ## Usage

pyproject.toml

@@ -1,2 +1,3 @@
 [build-system]
-requires = ["setuptools", "wheel", "scikit-build", "cmake", "ninja"]
+requires = ["setuptools", "wheel", "cmake", "ninja"]
+build-backend = "setuptools.build_meta"

requirements.txt

@@ -1,4 +1,7 @@
-scikit-build
+setuptools
 cmake
 ninja
 wheel
+pytest
+pytest-cov
+mock

setup.py

@@ -3,8 +3,48 @@
 #
 # This code is distributed under the BSD license.
 #
-from skbuild import setup
-from setuptools import find_packages
+import os
+import subprocess
+import sys
+from setuptools import setup, find_packages, Extension
+from setuptools.command.build_ext import build_ext
+
+
+class CMakeBuild(build_ext):
+    """
+    Build the extensions
+
+    """
+
+    def build_extensions(self):
+
+        # Set the cmake directory
+        cmake_lists_dir = os.path.abspath(".")
+
+        # Ensure the build directory exists
+        if not os.path.exists(self.build_temp):
+            os.makedirs(self.build_temp)
+
+        # Run Cmake once
+        ext = self.extensions[0]
+
+        # Get the directory
+        extdir = os.path.abspath(os.path.dirname(self.get_ext_fullpath(ext.name)))
+
+        # Arguments to cmake
+        cmake_args = [
+            "-DCMAKE_BUILD_TYPE=%s" % "Release",
+            "-DCMAKE_LIBRARY_OUTPUT_DIRECTORY=%s" % extdir,
+            "-DPYTHON_EXECUTABLE=%s" % sys.executable,
+        ]
+
+        # Config and the extension
+        subprocess.check_call(
+            ["cmake", cmake_lists_dir] + cmake_args, cwd=self.build_temp
+        )
+
+        # Build the extension
+        subprocess.check_call(["cmake", "--build", "."], cwd=self.build_temp)
 
 
 def main():
@@ -21,17 +61,20 @@ def main():
             "distributed",
             "dask_jobqueue",
             "gemmi",
+            "guanaco @ git+https://github.com/rosalindfranklininstitute/guanaco.git@master#egg=guanaco",
             "h5py",
             "mrcfile",
             "numpy",
             "pandas",
             "pillow",
-            "python-multem @ https://github.com/rosalindfranklininstitute/python-multem/tarball/master#egg=python-multem",
+            "python-multem @ git+https://github.com/rosalindfranklininstitute/python-multem.git@master#egg=python-multem", 
             "scipy",
             "pyyaml",
         ],
         tests_require=tests_require,
         test_suite="tests",
+        ext_modules=[Extension("amplus_ext", [])],
+        cmdclass={"build_ext": CMakeBuild},
         entry_points={
             "console_scripts": [
                 "amplus.read_pdb=amplus.command_line:read_pdb",