Merge pull request #248 from phonopy/release

Set version 3.3.0
phonopy · Jul 8, 2024 · 3f90329 · 3f90329
2 parents d52aae6 + c40299e
commit 3f90329
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diff --git a/.github/workflows/publish-to-test-pypi.yml b/.github/workflows/publish-to-test-pypi.yml
@@ -9,30 +9,21 @@ on:
 jobs:
   build-linux:
     runs-on: ubuntu-latest
-    defaults:
-      run:
-        shell: bash -l {0}
     strategy:
       matrix:
-        python-version: ["3.10", ]
+        python-version: [3.12, ]
 
     steps:
     - uses: actions/checkout@v4
-    # Use conda-incubator/setup-miniconda for precise control of conda infrastructure
-    - uses: conda-incubator/setup-miniconda@v3
+    - name: Set up Python ${{ matrix.python-version }}
+      uses: actions/setup-python@v5
       with:
-        auto-update-conda: true
-        channels: conda-forge
-        channel-priority: strict
         python-version: ${{ matrix.python-version }}
     - name: Make sdist
       run: |
-        conda activate test
-        conda install --yes python=${{ matrix.python-version }}
-        conda install --yes "libblas=*=*openblas" openblas cmake c-compiler numpy
-        ./get_nanoversion.sh
-        cat __nanoversion__.txt
-        python setup.py sdist
+        git tag v`grep __version__ phono3py/version.py|awk -F'"' '{print($2)}'`
+        pip install build
+        python -m build --sdist
     - name: Publish package to TestPyPI
       if: github.event_name == 'push' && startsWith(github.ref, 'refs/heads/rc')
       uses: pypa/gh-action-pypi-publish@release/v1

diff --git a/CMakeLists.txt b/CMakeLists.txt
@@ -1,27 +1,27 @@
 cmake_minimum_required(VERSION 3.20)
 
-option(PHPHCALC "Option to build phph calculation module" OFF)
-option(PHONONCALC "Option to build phonon calculation module" OFF)
-option(GRIDSYS "Option to build gridsys module" OFF)
-option(WITH_Fortran "enable fortran interface" OFF)
+option(BUILD_PHPHCALC_LIB "Option to build phph calculation module" OFF)
+option(BUILD_PHONONCALC_LIB "Option to build phonon calculation module" OFF)
+option(BUILD_GRIDSYS_LIB "Option to build gridsys module" OFF)
+option(PHONO3PY_WITH_Fortran "enable fortran interface" OFF)
 option(PHONO3PY_USE_OMP "Option to search OpenMP library" ON)
-option(PHPHCALC_USE_MTBLAS "Use multithread BLAS is it exists" OFF)
-option(WITH_TESTS "build unit tests" OFF)
+option(PHONO3PY_USE_MTBLAS "Use multithread BLAS if it exists" ON)
+option(PHONO3PY_WITH_TESTS "build unit tests" OFF)
 option(BUILD_SHARED_LIBS "Option to build shared library" OFF)
 
-if(WITH_Fortran)
+if(PHONO3PY_WITH_Fortran)
     enable_language(Fortran)
-    set(GRIDSYS ON)
+    set(BUILD_GRIDSYS_LIB ON)
 endif()
 
-if(WITH_TESTS)
+if(PHONO3PY_WITH_TESTS)
     set(BUILD_SHARED_LIBS ON)
-    set(GRIDSYS ON)
+    set(BUILD_GRIDSYS_LIB ON)
 endif()
 
-if((NOT PHPHCALC)
-   AND (NOT PHONONCALC)
-   AND (NOT GRIDSYS))
+if((NOT BUILD_PHPHCALC_LIB)
+   AND (NOT BUILD_PHONONCALC_LIB)
+   AND (NOT BUILD_GRIDSYS_LIB))
     set(BUILD_NANOBIND_MODULE ON)
     message(STATUS "Build nanobind module of ${SKBUILD_PROJECT_NAME}")
 else()
@@ -86,8 +86,8 @@ else()
     set(OpenMP_FOUND OFF) # cmake-lint: disable=C0103
 endif()
 
-if(PHPHCALC
-   OR PHONONCALC
+if(BUILD_PHPHCALC_LIB
+   OR BUILD_PHONONCALC_LIB
    OR BUILD_NANOBIND_MODULE)
     find_package(BLAS REQUIRED) # set BLAS_LIBRARIES
 
@@ -104,28 +104,30 @@ if(PHPHCALC
     endif()
 
     if(BLAS_LIBRARIES MATCHES "libmkl")
-        message(STATUS "MKL detected: Set C-macros MKL_LAPACKE MULTITHREADED_BLAS")
-        message(STATUS "Use multithreaded BLAS for phonon calculation.")
+        message(STATUS "MKL detected: Set C-macro MKL_LAPACKE.")
 
-        if(PHPHCALC_USE_MTBLAS)
-            message(STATUS "Use multithreaded BLAS for ph-ph calculation.")
+        if(PHONO3PY_USE_MTBLAS)
+            message(
+                STATUS "Set C-macro MULTITHREADED_BLAS to avoid nested OpenMP calls."
+            )
         endif()
     endif()
 
     if(BLAS_LIBRARIES MATCHES "libopenblas")
-        message(STATUS "OpenBLAS detected: Set C-macro MULTITHREADED_BLAS")
-        message(STATUS "Use multithreaded BLAS for phonon calculation.")
+        message(STATUS "OpenBLAS detected.")
 
-        if(PHPHCALC_USE_MTBLAS)
-            message(STATUS "Use multithreaded BLAS for ph-ph calculation.")
+        if(PHONO3PY_USE_MTBLAS)
+            message(
+                STATUS "Set C-macro MULTITHREADED_BLAS to avoid nested OpenMP calls."
+            )
         endif()
     endif()
 endif()
 
 # ###################################################################################
 # Build phphcalc module #
 # ###################################################################################
-if(PHPHCALC OR BUILD_NANOBIND_MODULE)
+if(BUILD_PHPHCALC_LIB OR BUILD_NANOBIND_MODULE)
     # Source code
     set(SOURCES_PHPHCALC
         ${PROJECT_SOURCE_DIR}/c/bzgrid.c
@@ -163,7 +165,7 @@ if(PHPHCALC OR BUILD_NANOBIND_MODULE)
         target_include_directories(phphcalc_lib PRIVATE ${MY_INCLUDES})
 
         if(BLAS_LIBRARIES MATCHES "libmkl")
-            if(PHPHCALC_USE_MTBLAS)
+            if(PHONO3PY_USE_MTBLAS)
                 target_compile_definitions(
                     phphcalc_lib PRIVATE MKL_LAPACKE MULTITHREADED_BLAS
                                          THM_EPSILON=1e-10)
@@ -174,7 +176,7 @@ if(PHPHCALC OR BUILD_NANOBIND_MODULE)
         endif()
 
         if(BLAS_LIBRARIES MATCHES "libopenblas")
-            if(PHPHCALC_USE_MTBLAS)
+            if(PHONO3PY_USE_MTBLAS)
                 target_compile_definitions(phphcalc_lib PRIVATE MULTITHREADED_BLAS
                                                                 THM_EPSILON=1e-10)
             else()
@@ -195,7 +197,7 @@ if(PHPHCALC OR BUILD_NANOBIND_MODULE)
         target_include_directories(phphcalc_lib PRIVATE ${MY_INCLUDES})
 
         if(BLAS_LIBRARIES MATCHES "libmkl")
-            if(PHPHCALC_USE_MTBLAS)
+            if(PHONO3PY_USE_MTBLAS)
                 target_compile_definitions(
                     phphcalc_lib PRIVATE MKL_LAPACKE MULTITHREADED_BLAS
                                          THM_EPSILON=1e-10)
@@ -206,7 +208,7 @@ if(PHPHCALC OR BUILD_NANOBIND_MODULE)
         endif()
 
         if(BLAS_LIBRARIES MATCHES "libopenblas")
-            if(PHPHCALC_USE_MTBLAS)
+            if(PHONO3PY_USE_MTBLAS)
                 target_compile_definitions(phphcalc_lib PRIVATE MULTITHREADED_BLAS
                                                                 THM_EPSILON=1e-10)
             else()
@@ -236,7 +238,7 @@ endif()
 # ###################################################################################
 # phononcalc #
 # ###################################################################################
-if(PHONONCALC OR BUILD_NANOBIND_MODULE)
+if(BUILD_PHONONCALC_LIB OR BUILD_NANOBIND_MODULE)
     # Source code
     set(SOURCES_PHONONCALC
         ${PROJECT_SOURCE_DIR}/c/dynmat.c ${PROJECT_SOURCE_DIR}/c/lapack_wrapper.c
@@ -311,7 +313,7 @@ endif()
 # ###################################################################################
 # grid #
 # ###################################################################################
-if(GRIDSYS)
+if(BUILD_GRIDSYS_LIB)
     # Source code
     set(SOURCES_GRIDSYS
         ${PROJECT_SOURCE_DIR}/c/bzgrid.c
@@ -360,12 +362,12 @@ if(GRIDSYS)
             DESTINATION ${CMAKE_INSTALL_INCLUDEDIR})
 endif()
 
-if(WITH_Fortran)
+if(PHONO3PY_WITH_Fortran)
     add_subdirectory(fortran)
 endif()
 
-if(WITH_TESTS)
-    if(WITH_Fortran)
+if(PHONO3PY_WITH_TESTS)
+    if(PHONO3PY_WITH_Fortran)
         set(LIB_MOD_DIR ${CMAKE_CURRENT_BINARY_DIR}/fortran)
     endif()
 

diff --git a/doc/changelog.md b/doc/changelog.md
@@ -2,6 +2,12 @@
 
 # Change Log
 
+## Jul-8-2024: Version 3.3.0
+
+- Build system of phono3py was renewed. Now nanobind, cmake, and
+  scikit-build-core are used for the building, and the receipt is written in
+  `CMakeLists.txt` and `pyproject.toml`.
+
 ## Jun-29-2024: Version 3.2.0
 
 - `--rd` and `--rd-fc2` options for generating random directional displacements.

diff --git a/doc/conf.py b/doc/conf.py
@@ -58,9 +58,9 @@
 # built documents.
 #
 # The short X.Y version.
-version = "3.2"
+version = "3.3"
 # The full version, including alpha/beta/rc tags.
-release = "3.2.0"
+release = "3.3.0"
 
 # The language for content autogenerated by Sphinx. Refer to documentation
 # for a list of supported languages.

diff --git a/doc/install.md b/doc/install.md
@@ -30,18 +30,23 @@ All dependent packages should be installed.
 (install_from_source_code)=
 ## Installation from source code
 
-When installing phono3py using `setup.py` from the source code, a few libraries
-are required before running `setup.py` script.
+When installing phono3py from the source code, a few libraries are required
+before running `pip install`.
+
+Note that at version 3.3.0, the build system of phono3py was modernized.
+Nanobind, cmake, and scikit-build-core are used for the building. The receipt is
+written in `CMakeLists.txt` and `pyproject.toml`. The old `setup.py` was
+removed.
+
+If phono3py is compiled with a special compiler or special options, manual
+modification of `CMakeLists.txt` may be needed.
 
 - {ref}`Linear algebra library <install_lapacke>`: BLAS, LAPACK, and LAPACKE
 - {ref}`OpenMP library <install_openmp>`: For the multithreding support.
 
 These packages may be installed by the package manager of OS (e.g. `apt`) or
 conda environment. Automatic search of required libraries and flags that are
-already on the system is performed by cmake. If cmake is installed on the
-system, this automatic search is invoked as default. For the installation with
-custom configurations without using cmake, the environment variable
-`PHONO3PY_USE_CMAKE=false` has to be set.
+already on the system is performed by cmake.
 
 (install_with_cmake)=
 ### Build with automatic search of library configurations by cmake
@@ -56,57 +61,6 @@ See an example at {ref}`install_an_example`. In the standard output, flags and
 libraries found by cmake are shown. Please carefully check if those
 configurations are expected ones or not.
 
-(install_custom)=
-### Build with custom library configurations by `site.cfg` file
-
-Custom installation is achieved by creating `site.cfg` file on the same
-directory as `setup.py`. Users will write configurations of compiler flags and
-linked libraries in `site.cfg`. If `setup.py` finds `site.cfg`, the
-configurations are used as the default configurations. If cmake is found in the
-system, cmake tries to find required libraries and found configurations are
-appended. To deactivate cmake's library search, the environment variable
-`PHONO3PY_USE_CMAKE=false` has to be set before running the phono3py build:
-```
-% export PHONO3PY_USE_CMAKE=false
-```
-In previous versions, `site.cfg` was processed by numpy,
-but from version 2.4.0, it is processed by script in `setup.py`.
-`extra_link_args`, `extra_compile_args`, `extra_objects`, and `include_dirs` can
-be specified. How they used is found at [setuptools web
-site](https://setuptools.pypa.io/en/latest/userguide/ext_modules.html#extension-api-reference).
-
-In most cases, users want to enable multithreading support with OpenMP. Its
-minimum setting with gcc as the compiler is:
-
-```
-extra_compile_args = -fopenmp
-```
-
-Additional configuration can be necessary. It is recommended first starting only
-with `extra_compile_args = -fopenmp` and run `setup.py`, then check if phono3py
-works properly or not without error or warning. When phono3py doesn't work with
-the above setting, add another configuration one by one to test compilation.
-Some examples are given below.
-
-For MKL (for gcc and clang), `site.cfg`
-
-```
-extra_compile_args = -fopenmp
-```
-
-For openblas and clang
-
-```
-extra_compile_args = -fopenmp
-```
-
-For openblas and gcc
-
-```
-extra_compile_args = -fopenmp
-extra_link_args = -lgomp
-```
-
 (install_an_example)=
 
 ## Installation instruction of latest development version of phono3py
@@ -117,7 +71,8 @@ wrong python libraries can be imported.
 1. Download miniforge
 
    Miniforge is downloaded at https://github.com/conda-forge/miniforge. The
-   detailed installation instruction is found in the same page. If usual conda or miniconda is used, the following `~/.condarc` setting is recommended:
+   detailed installation instruction is found in the same page. If usual conda
+   or miniconda is used, the following `~/.condarc` setting is recommended:
 
    ```
    channel_priority: strict
@@ -148,7 +103,7 @@ wrong python libraries can be imported.
    For x86-64 system:
 
    ```bash
-   % conda install numpy scipy h5py pyyaml matplotlib-base c-compiler "libblas=*=*mkl" spglib mkl-include cmake
+   % conda install numpy scipy h5py pyyaml matplotlib-base c-compiler cxx-compiler "libblas=*=*mkl" spglib mkl-include cmake
    ```
 
    A libblas library can be chosen among `[openblas, mkl, blis, netlib]`. If
@@ -161,7 +116,7 @@ wrong python libraries can be imported.
    For macOS ARM64 system, currently only openblas can be chosen:
 
    ```bash
-   % conda install numpy scipy h5py pyyaml matplotlib-base c-compiler spglib cmake openblas
+   % conda install numpy scipy h5py pyyaml matplotlib-base c-compiler cxx-compiler spglib cmake openblas
    ```
 
    Note that using hdf5 files on NFS mounted file system, you may have to disable
@@ -179,10 +134,8 @@ wrong python libraries can be imported.
    % git clone https://github.com/phonopy/phonopy.git
    % git clone https://github.com/phonopy/phono3py.git
    % cd phonopy
-   % git checkout develop
    % pip install -e . -vvv
    % cd ../phono3py
-   % git checkout develop
    % pip install -e . -vvv
    ```
 
@@ -215,23 +168,6 @@ Ubuntu package manager (`liblapacke` and `liblapacke-dev`):
 % sudo apt-get install liblapack-dev liblapacke-dev
 ```
 
-### Compiling Netlib LAPACKE
-
-The compilation procedure is found at the LAPACKE web site. After creating the
-LAPACKE library, `liblapacke.a` (or the dynamic link library), `setup.py` must
-be properly modified to link it. As an example, the procedure of compiling
-LAPACKE is shown below.
-
-```bash
-% tar xvfz lapack-3.6.0.tgz
-% cd lapack-3.6.0
-% cp make.inc.example make.inc
-% make lapackelib
-```
-
-BLAS, LAPACK, and LAPACKE, these all may have to be compiled with `-fPIC` option
-to use it with python.
-
 (install_openmp)=
 ## Multithreading and its controlling by C macro
 

diff --git a/phono3py/scripts/phono3py-coleigplot → phono3py/scripts/phono3py_coleigplot.py b/phono3py/scripts/phono3py-coleigplot → phono3py/scripts/phono3py_coleigplot.py
@@ -1,5 +1,3 @@
-#!/usr/bin/env python
-
 import argparse
 import os
 import sys
@@ -139,5 +137,6 @@ def main(args: argparse.Namespace):
         plot(args)
 
 
-if __name__ == "__main__":
+def run():
+    """Run phono3py-coleigplot script."""
     main(get_options())