cmake build

.dockerignore

@@ -1,2 +1,2 @@
 .git/
-docker/
+build

.github/workflows/ci-test.yml

@@ -3,12 +3,14 @@ name: CI-Test
 on: [push, pull_request]
 
 jobs:
+
   lint:
     runs-on: ubuntu-latest
     steps:
-    - uses: actions/checkout@v2
-    - uses: actions/setup-python@v2
-    - uses: pre-commit/[email protected]
+    - uses: actions/checkout@v4
+    - uses: actions/setup-python@v4
+    - uses: pre-commit/[email protected]
+
   test:
     name: Tests
     runs-on: ${{ matrix.host-os }}
@@ -19,23 +21,37 @@ jobs:
         python-version: ["3.7", "3.8", "3.9", "3.10", "3.11"]
       fail-fast: false
     steps:
+      - name: Set env.REPOSITORY_NAME  # just the repo, as opposed to org/repo
+        run: |
+          export REPOSITORY_NAME=${GITHUB_REPOSITORY#*/}
+          echo "REPOSITORY_NAME=${REPOSITORY_NAME}" >> $GITHUB_ENV
+
       - name: Checkout the code
-        uses: actions/checkout@v2
+        uses: actions/checkout@v4
 
       - name: Set up Python ${{ matrix.python-version }}
-        uses: actions/setup-python@v2
+        uses: actions/setup-python@v4
         with:
           python-version: ${{ matrix.python-version }}
 
       - name: Install dependencies
         run: |
           set -vxeuo pipefail
           bash ./scripts/install-deps.sh
+          ls -Al .
+          ls -Al ./dist/
+          tree .
+
+      - uses: actions/upload-artifact@v3
+        with:
+          name: ${{ env.REPOSITORY_NAME }}-wheels
+          path: dist/*.whl
 
       - name: Test with pytest
         run: |
           set -vxeuo pipefail
           bash ./scripts/run-tests.sh
+
   docs:
     name: Documentation
     runs-on: ubuntu-latest
@@ -46,11 +62,16 @@ jobs:
       fail-fast: false
 
     steps:
+      - name: Set env.REPOSITORY_NAME  # just the repo, as opposed to org/repo
+        run: |
+          export REPOSITORY_NAME=${GITHUB_REPOSITORY#*/}
+          echo "REPOSITORY_NAME=${REPOSITORY_NAME}" >> $GITHUB_ENV
+
       - name: Checkout the code
-        uses: actions/checkout@v2
+        uses: actions/checkout@v4
 
       - name: Set up Python ${{ matrix.python-version }}
-        uses: actions/setup-python@v2
+        uses: actions/setup-python@v4
         with:
           python-version: ${{ matrix.python-version }}
 
@@ -63,3 +84,8 @@ jobs:
         run: |
           set -vxeuo pipefail
           bash ./scripts/build-docs.sh
+
+      - uses: actions/upload-artifact@v3
+        with:
+          name: ${{ env.REPOSITORY_NAME }}-docs
+          path: docs/build/html/

.github/workflows/docs-publish.yml

@@ -21,10 +21,10 @@ jobs:
           echo "REPOSITORY_NAME=${REPOSITORY_NAME}" >> $GITHUB_ENV
 
       - name: Checkout the code
-        uses: actions/checkout@v2
+        uses: actions/checkout@v4
 
       - name: Set up Python ${{ matrix.python-version }}
-        uses: actions/setup-python@v2
+        uses: actions/setup-python@v4
         with:
           python-version: ${{ matrix.python-version }}
 
@@ -38,6 +38,11 @@ jobs:
           set -vxeuo pipefail
           bash ./scripts/build-docs.sh
 
+      - uses: actions/upload-artifact@v3
+        with:
+          name: ${{ env.REPOSITORY_NAME }}-docs
+          path: docs/build/html/
+
       - name: Deploy documentation to nsls-ii.github.io
         # We pin to the SHA, not the tag, for security reasons.
         # https://docs.github.com/en/free-pro-team@latest/actions/learn-github-actions/security-hardening-for-github-actions#using-third-party-actions

.gitignore

@@ -96,6 +96,7 @@ target/
 #pycharm
 .idea/*
 
+.vscode/*
 
 #Ipython Notebook
 .ipynb_checkpoints

.pre-commit-config.yaml

@@ -1,6 +1,6 @@
 repos:
   - repo: https://github.com/pre-commit/pre-commit-hooks
-    rev: v4.1.0
+    rev: v4.4.0
     hooks:
       - id: check-yaml
       - id: check-toml
@@ -10,18 +10,16 @@ repos:
         exclude: |
           (?x)^(
             src/|
-            docs/|
-            github_deploy_key_nsls_ii_edrixs.enc
+            docs/
           )
       - id: trailing-whitespace
         exclude: |
           (?x)^(
             src/|
-            docs/|
-            github_deploy_key_nsls_ii_edrixs.enc
+            docs/
           )
   - repo: https://github.com/PyCQA/flake8.git
-    rev: 4.0.1
+    rev: 6.1.0
     hooks:
       - id: flake8
         exclude: ^examples/

CMakeLists.txt

@@ -0,0 +1,65 @@
+cmake_minimum_required(VERSION 3.17.3 FATAL_ERROR) # 3.17 > for Python3_SOABI
+
+project (EDRIXS C Fortran)
+
+if (NOT CMAKE_BUILD_TYPE)
+  set(CMAKE_BUILD_TYPE RelWithDebInfo CACHE STRING "Build type configuration" FORCE)
+  message(STATUS "Setting default build type: ${CMAKE_BUILD_TYPE}")
+endif()
+
+message(STATUS "CMAKE_COMMAND: ${CMAKE_COMMAND}")
+message(STATUS "CMAKE_BUILD_TYPE: ${CMAKE_BUILD_TYPE}")
+
+set(CMAKE_POSITION_INDEPENDENT_CODE ON)
+
+list(APPEND CMAKE_MODULE_PATH ${CMAKE_SOURCE_DIR}/cmake)
+
+find_package(MPI REQUIRED)
+
+find_package(LAPACK REQUIRED)
+
+option(EDRIXS_PYINTERFACE "Build python interface" OFF)
+
+# see https://gitlab.kitware.com/cmake/cmake/-/issues/21779
+if (CMAKE_VERSION VERSION_LESS 3.20)
+  if(LAPACK_FOUND)
+    set(_lapack_libs "${LAPACK_LIBRARIES}")
+    if(_lapack_libs AND TARGET BLAS::BLAS)
+      # remove the ${BLAS_LIBRARIES} from the interface and replace it
+      # with the BLAS::BLAS target
+      list(REMOVE_ITEM _lapack_libs "${BLAS_LIBRARIES}")
+      list(APPEND _lapack_libs BLAS::BLAS)
+    endif()
+    if(_lapack_libs)
+      set_target_properties(LAPACK::LAPACK PROPERTIES
+        INTERFACE_LINK_LIBRARIES "${_lapack_libs}"
+      )
+    endif()
+    unset(_lapack_libs)
+  endif()
+endif()
+
+# use a custom find module because arpack-ng config module doesn't provide full paths to libs
+# see https://github.com/opencollab/arpack-ng/pull/311
+find_package(arpack MODULE REQUIRED COMPONENTS serial parallel)
+
+
+if (EDRIXS_PY_INTERFACE)
+  message(STATUS "Building python interface")
+  find_package(Python3 3.7 REQUIRED COMPONENTS Interpreter Development NumPy)
+
+  # Grab the variables from a local Python installation
+  # F2PY headers
+  execute_process(
+    COMMAND "${Python3_EXECUTABLE}"
+    -c "import numpy.f2py; print(numpy.f2py.get_include())"
+    OUTPUT_VARIABLE F2PY_INCLUDE_DIR
+    OUTPUT_STRIP_TRAILING_WHITESPACE
+  )
+
+  message(STATUS "Python3_INCLUDE_DIRS: ${Python3_INCLUDE_DIRS}")
+  message(STATUS "F2PY_INCLUDE_DIR: ${F2PY_INCLUDE_DIR}")
+  message(STATUS "Python3_NumPy_INCLUDE_DIRS: ${Python3_NumPy_INCLUDE_DIRS}")
+endif()
+
+add_subdirectory(src)

README.rst

@@ -103,31 +103,13 @@ Install from source
 
   Be sure to compile OpenBLAS, arpack-ng, mpi4py and edrixs with the same (MPI) Fortran compiler.
 
-* Install Fortran parts of edrixs
+* Install edrixs
 
     .. code-block:: bash
 
-       $ cd src
-       $ make F90=mpif90 LIBS="-L/usr/local/lib -lopenblas -lparpack -larpack"
-       $ make install
+       $ pip install -v .
 
-  where, you may need to change ``F90`` and ``LIBS`` according to your specific environment. There will be problems when using gfortran with MKL, so we recommend ``gfortran+OpenBLAS`` or ``ifort+MKL``. ``libedrixsfortran.a`` will be generated, which will be used when building python interface. The executable ``.x`` files will be installed in ``edrixs/bin`` directory and add the following line in ``.bashrc`` or ``.bash_profile`` file,
-
-    .. code-block:: bash
-
-       export PATH=/root_dir_of_edrixs/edrixs/bin:$PATH
-
-* Install Python parts of edrixs
-
-  Be sure to first make ``libedrixsfortran.a`` in src.
-
-    .. code-block:: bash
-
-       $ python setup.py config_fc --f77exec=mpif90 --f90exec=mpif90 build_ext \
-         --libraries=openblas,parpack,arpack --library-dirs=/usr/lib:/usr/local/lib:/opt/local/lib \
-         --link-objects=./src/libedrixsfortran.a
-       $ pip install .
-
-  where, ``--library-dirs`` ares the paths to search ``--libraries``, please set it according to your environments.
+  There will be problems when using gfortran with MKL, so we recommend ``gfortran+OpenBLAS`` or ``ifort+MKL``. The executable ``.x`` files will be installed in the ``bin`` directory of the active python environment.
+  The fortran library and compiled python extension are built using ``cmake`` which can be configured by setting the ``CMAKE_CONFIGURE_ARGS`` environment variable.
 
 Please see our `online documentation <https://nsls-ii.github.io/edrixs/user/installation.html>`_ for more details of installation.

cmake/Findarpack.cmake

@@ -0,0 +1,50 @@
+include(FindPackageHandleStandardArgs)
+
+message(STATUS "Finding arpack")
+
+# if components not specified default to serial library
+set(_supported_components serial parallel)
+if(NOT arpack_FIND_COMPONENTS)
+  set(arpack_FIND_COMPONENTS serial)
+endif()
+
+# check request components
+foreach(_component ${arpack_FIND_COMPONENTS})
+  if (NOT ${_component} IN_LIST _supported_components)
+    message(FATAL_ERROR "${_component} is not a valid component (serial,parallel)")
+  endif()
+endforeach()
+
+message(STATUS "${arpack_FIND_COMPONENTS}")
+
+if(DEFINED ENV{ARPACK_ROOT})
+  set(ARPACK_ROOT "$ENV{ARPACK_ROOT}")
+endif()
+
+set(arpack_serial_FOUND FALSE)
+set(arpack_parallel_FOUND FALSE)
+set(arpack_LIBRARIES "")
+
+if ("serial" IN_LIST arpack_FIND_COMPONENTS)
+  find_library(ARPACK_LIBRARY NAMES arpack HINTS ${ARPACK_ROOT})
+  if(ARPACK_LIBRARY)
+    set(arpack_serial_FOUND TRUE)
+    message(STATUS "ARPACK_LIBRARY: ${ARPACK_LIBRARY}")
+    add_library(ARPACK::ARPACK INTERFACE IMPORTED)
+    set_target_properties(ARPACK::ARPACK PROPERTIES INTERFACE_LINK_LIBRARIES "${ARPACK_LIBRARY}")
+    list(APPEND arpack_LIBRARIES ${ARPACK_LIBRARY})
+  endif()
+endif()
+
+if ("parallel" IN_LIST arpack_FIND_COMPONENTS)
+  find_library(PARPACK_LIBRARY NAMES parpack HINTS ${ARPACK_ROOT})
+  if(PARPACK_LIBRARY)
+    set(arpack_parallel_FOUND TRUE)
+    message(STATUS "PARPACK_LIBRARY: ${PARPACK_LIBRARY}")
+    add_library(PARPACK::PARPACK INTERFACE IMPORTED)
+    set_target_properties(PARPACK::PARPACK PROPERTIES INTERFACE_LINK_LIBRARIES "${PARPACK_LIBRARY}")
+    list(APPEND arpack_LIBRARIES ${PARPACK_LIBRARY})
+  endif()
+endif()
+
+find_package_handle_standard_args(arpack REQUIRED_VARS "arpack_LIBRARIES" HANDLE_COMPONENTS)

docker/Dockerfile

@@ -1,20 +1,69 @@
-FROM edrixs/edrixs_base
-WORKDIR /project
-
-COPY . ./src/edrixs
-
-    # build fortran part of edrixs
-RUN export LD_LIBRARY_PATH="/usr/local/lib:\$LD_LIBRARY_PATH" \
-    && make -C src/edrixs/src F90=mpif90 LIBS="-L/usr/local/lib -lopenblas -lparpack -larpack" \
-    && make install -C src/edrixs/src \
-    # build python part of edrixs
-    && cd src/edrixs \
-    && python setup.py build_ext --library-dirs=/usr/local/lib \
-    && pip install . \
-    && cd ../../  \
-    # set env
-    && echo "export PATH=/project/src/edrixs/bin:\$PATH" >> ~/.bashrc  \
-    && echo "export PATH=/project/src/edrixs/bin:\$PATH" >> /home/rixs/.bashrc  \
-    # copy examples to /home/rixs
-    && cp -r src/edrixs/examples /home/rixs/edrixs_examples \
-    && chown -R rixs:rixs /home/rixs/edrixs_examples
+FROM ubuntu:22.04 as base
+
+# general environment for docker
+ENV DEBIAN_FRONTEND=noninteractive
+
+# base packages
+RUN apt-get update && apt-get install -y --no-install-recommends sudo curl vim libgfortran-11-dev libopenmpi-dev libopenblas-dev python3 libpython3-dev python3-pip python3-venv && rm -rf /var/lib/apt/lists/*
+
+# create docker user
+RUN useradd -m -s /bin/bash -u 1999 docker && echo "docker:docker" | chpasswd && adduser docker sudo
+
+# enable passwordless sudo
+RUN echo "docker ALL=(ALL) NOPASSWD:ALL" > /etc/sudoers.d/docker
+
+# allow docker user to install into /opt
+RUN sudo chown docker:docker /opt
+
+USER    docker
+WORKDIR /home/docker
+
+# create venv
+ENV VIRTUAL_ENV=/opt/edrixs
+RUN python3 -m venv $VIRTUAL_ENV
+ENV PATH="$VIRTUAL_ENV/bin:$PATH"
+
+FROM base as dep_builder
+
+ENV LD_LIBRARY_PATH="/opt/edrixs/lib" \
+    CMAKE_PREFIX_PATH="/opt/edrixs"
+
+# install build tools
+RUN sudo apt-get update && sudo apt-get install -y --no-install-recommends \
+    autoconf \
+    build-essential \
+    gfortran \
+    ca-certificates \
+    coreutils \
+    curl \
+    git \
+    cmake
+
+RUN curl -L https://github.com/opencollab/arpack-ng/archive/refs/tags/3.8.0.tar.gz | tar xvz && \
+  cd arpack-ng-3.8.0 && \
+  mkdir build && \
+  cd build && \
+  cmake -DMPI=ON -DCMAKE_INSTALL_PREFIX=/opt/edrixs .. && \
+  make -j4 && \
+  make test && \
+  make install
+
+FROM dep_builder as app_builder
+
+RUN pip install --upgrade pip setuptools
+RUN pip install numpy scipy sympy matplotlib sphinx mpi4py ipython jupyter jupyterlab
+
+COPY --chown=docker . edrixs
+
+RUN export VERBOSE=1 FFLAGS="-Wall -Wunused -Wextra -Wno-maybe-uninitialized -Ofast -faggressive-loop-optimizations -fno-tree-pre" && \
+  pip install -v ./edrixs
+
+from base as app
+
+# see https://github.com/open-mpi/ompi/issues/4948
+ENV LD_LIBRARY_PATH="/opt/edrixs/lib" \
+    CMAKE_PREFIX_PATH="/opt/edrixs" \
+    OMPI_MCA_btl_vader_single_copy_mechanism="none"
+
+COPY --from=app_builder /opt /opt
+COPY --from=app_builder --chown=docker /home/docker/edrixs/examples examples