phono3py 3.2.0__tar.gz → 3.3.0__tar.gz

phono3py-3.3.0/CMakeLists.txt

@@ -0,0 +1,398 @@
+cmake_minimum_required(VERSION 3.20)
+
+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(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(PHONO3PY_WITH_Fortran)
+    enable_language(Fortran)
+    set(BUILD_GRIDSYS_LIB ON)
+endif()
+
+if(PHONO3PY_WITH_TESTS)
+    set(BUILD_SHARED_LIBS ON)
+    set(BUILD_GRIDSYS_LIB ON)
+endif()
+
+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 ${SKBUILD_PROJECT_NAME}")
+else()
+    set(BUILD_NANOBIND_MODULE OFF)
+endif()
+
+if(BUILD_NANOBIND_MODULE)
+    project(${SKBUILD_PROJECT_NAME})
+    set(DEV_MODULE Development.Module)
+    find_package(
+        Python 3.8 REQUIRED
+        COMPONENTS Interpreter ${DEV_MODULE}
+        OPTIONAL_COMPONENTS Development.SABIModule)
+else()
+    project(phono3py C)
+    set(CMAKE_MACOSX_RPATH 1)
+    set(CMAKE_C_FLAGS_RELEASE "-Wall -O2")
+    set(CMAKE_C_FLAGS_DEBUG "-g -DLAGWARNING -DTHMWARNING")
+
+    # Version numbers
+    file(READ ${PROJECT_SOURCE_DIR}/phono3py/version.py version_file)
+    string(REGEX MATCH "__version__.*([0-9]+)[.]([0-9]+)[.]([0-9]+)"
+                 phono3py_version ${version_file})
+    set(MAJOR_VERSION ${CMAKE_MATCH_1})
+    set(MINOR_VERSION ${CMAKE_MATCH_2})
+    set(MICRO_VERSION ${CMAKE_MATCH_3})
+    set(SERIAL "${MAJOR_VERSION}.${MINOR_VERSION}.${MICRO_VERSION}")
+    set(SOSERIAL "1")
+    include(GNUInstallDirs)
+endif()
+
+if(NOT CMAKE_BUILD_TYPE AND NOT CMAKE_CONFIGURATION_TYPES)
+    set(CMAKE_BUILD_TYPE
+        Release
+        CACHE STRING "Choose the type of build." FORCE)
+    set_property(CACHE CMAKE_BUILD_TYPE PROPERTY STRINGS "Debug" "Release"
+                                                 "MinSizeRel" "RelWithDebInfo")
+endif()
+
+message(STATUS "Build type: ${CMAKE_BUILD_TYPE}")
+message(STATUS "CMAKE_SYSTEM_PREFIX_PATH: ${CMAKE_SYSTEM_PREFIX_PATH}")
+
+if(USE_CONDA_PATH AND DEFINED ENV{CONDA_PREFIX})
+    message(STATUS "$ENV{CONDA_PREFIX}")
+    set(CMAKE_MODULE_PATH $ENV{CONDA_PREFIX})
+    set(MY_INCLUDES $ENV{CONDA_PREFIX}/include ${PROJECT_SOURCE_DIR}/c)
+    link_directories($ENV{CONDA_PREFIX}/lib)
+else()
+    set(MY_INCLUDES ${PROJECT_SOURCE_DIR}/c)
+endif()
+
+if(PHONO3PY_USE_OMP)
+    message(STATUS "Find OpenMP library")
+    find_package(OpenMP)
+
+    if(OpenMP_FOUND)
+        message(STATUS "OpenMP libs: ${OpenMP_C_LIBRARIES}")
+        message(STATUS "OpenMP flags: ${OpenMP_C_FLAGS}")
+    endif()
+else()
+    message(STATUS "OpenMP is not used.")
+    set(OpenMP_FOUND OFF) # cmake-lint: disable=C0103
+endif()
+
+if(BUILD_PHPHCALC_LIB
+   OR BUILD_PHONONCALC_LIB
+   OR BUILD_NANOBIND_MODULE)
+    find_package(BLAS REQUIRED) # set BLAS_LIBRARIES
+
+    if(BLAS_FOUND)
+        message(STATUS "BLAS libs: ${BLAS_LIBRARIES}")
+        message(STATUS "BLAS flags: ${BLAS_LINKER_FLAGS}")
+    endif()
+
+    find_package(LAPACK REQUIRED) # set LAPACK_LIBRARIES
+
+    if(LAPACK_FOUND)
+        message(STATUS "LAPACK libs: ${LAPACK_LIBRARIES}")
+        message(STATUS "LAPACK flags: ${LAPACK_LINKER_FLAGS}")
+    endif()
+
+    if(BLAS_LIBRARIES MATCHES "libmkl")
+        message(STATUS "MKL detected: Set C-macro MKL_LAPACKE.")
+
+        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.")
+
+        if(PHONO3PY_USE_MTBLAS)
+            message(
+                STATUS "Set C-macro MULTITHREADED_BLAS to avoid nested OpenMP calls."
+            )
+        endif()
+    endif()
+endif()
+
+# ###################################################################################
+# Build phphcalc module #
+# ###################################################################################
+if(BUILD_PHPHCALC_LIB OR BUILD_NANOBIND_MODULE)
+    # Source code
+    set(SOURCES_PHPHCALC
+        ${PROJECT_SOURCE_DIR}/c/bzgrid.c
+        ${PROJECT_SOURCE_DIR}/c/collision_matrix.c
+        ${PROJECT_SOURCE_DIR}/c/fc3.c
+        ${PROJECT_SOURCE_DIR}/c/grgrid.c
+        ${PROJECT_SOURCE_DIR}/c/imag_self_energy_with_g.c
+        ${PROJECT_SOURCE_DIR}/c/interaction.c
+        ${PROJECT_SOURCE_DIR}/c/isotope.c
+        ${PROJECT_SOURCE_DIR}/c/lagrid.c
+        ${PROJECT_SOURCE_DIR}/c/lapack_wrapper.c
+        ${PROJECT_SOURCE_DIR}/c/phono3py.c
+        ${PROJECT_SOURCE_DIR}/c/phonoc_utils.c
+        ${PROJECT_SOURCE_DIR}/c/pp_collision.c
+        ${PROJECT_SOURCE_DIR}/c/real_self_energy.c
+        ${PROJECT_SOURCE_DIR}/c/real_to_reciprocal.c
+        ${PROJECT_SOURCE_DIR}/c/reciprocal_to_normal.c
+        ${PROJECT_SOURCE_DIR}/c/snf3x3.c
+        ${PROJECT_SOURCE_DIR}/c/tetrahedron_method.c
+        ${PROJECT_SOURCE_DIR}/c/triplet.c
+        ${PROJECT_SOURCE_DIR}/c/triplet_grid.c
+        ${PROJECT_SOURCE_DIR}/c/triplet_iw.c)
+
+    if(BUILD_SHARED_LIBS)
+        # Shared library
+        add_library(phphcalc_lib SHARED ${SOURCES_PHPHCALC})
+
+        if(OpenMP_FOUND)
+            target_link_libraries(phphcalc_lib PRIVATE BLAS::BLAS LAPACK::LAPACK
+                                                       OpenMP::OpenMP_C)
+        else()
+            target_link_libraries(phphcalc_lib PRIVATE BLAS::BLAS LAPACK::LAPACK)
+        endif()
+
+        target_include_directories(phphcalc_lib PRIVATE ${MY_INCLUDES})
+
+        if(BLAS_LIBRARIES MATCHES "libmkl")
+            if(PHONO3PY_USE_MTBLAS)
+                target_compile_definitions(
+                    phphcalc_lib PRIVATE MKL_LAPACKE MULTITHREADED_BLAS
+                                         THM_EPSILON=1e-10)
+            else()
+                target_compile_definitions(phphcalc_lib PRIVATE MKL_LAPACKE
+                                                                THM_EPSILON=1e-10)
+            endif()
+        endif()
+
+        if(BLAS_LIBRARIES MATCHES "libopenblas")
+            if(PHONO3PY_USE_MTBLAS)
+                target_compile_definitions(phphcalc_lib PRIVATE MULTITHREADED_BLAS
+                                                                THM_EPSILON=1e-10)
+            else()
+                target_compile_definitions(phphcalc_lib PRIVATE THM_EPSILON=1e-10)
+            endif()
+        endif()
+    else()
+        # Static link library
+        add_library(phphcalc_lib STATIC ${SOURCES_PHPHCALC})
+
+        if(OpenMP_FOUND)
+            target_link_libraries(phphcalc_lib BLAS::BLAS LAPACK::LAPACK
+                                  OpenMP::OpenMP_C)
+        else()
+            target_link_libraries(phphcalc_lib BLAS::BLAS LAPACK::LAPACK)
+        endif()
+
+        target_include_directories(phphcalc_lib PRIVATE ${MY_INCLUDES})
+
+        if(BLAS_LIBRARIES MATCHES "libmkl")
+            if(PHONO3PY_USE_MTBLAS)
+                target_compile_definitions(
+                    phphcalc_lib PRIVATE MKL_LAPACKE MULTITHREADED_BLAS
+                                         THM_EPSILON=1e-10)
+            else()
+                target_compile_definitions(phphcalc_lib PRIVATE MKL_LAPACKE
+                                                                THM_EPSILON=1e-10)
+            endif()
+        endif()
+
+        if(BLAS_LIBRARIES MATCHES "libopenblas")
+            if(PHONO3PY_USE_MTBLAS)
+                target_compile_definitions(phphcalc_lib PRIVATE MULTITHREADED_BLAS
+                                                                THM_EPSILON=1e-10)
+            else()
+                target_compile_definitions(phphcalc_lib PRIVATE THM_EPSILON=1e-10)
+            endif()
+        endif()
+    endif()
+
+    if(NOT BUILD_NANOBIND_MODULE)
+        if(BUILD_SHARED_LIBS)
+            set_property(TARGET phphcalc_lib PROPERTY VERSION ${SERIAL})
+            set_property(TARGET phphcalc_lib PROPERTY SOVERSION ${SOSERIAL})
+            install(TARGETS phphcalc_lib LIBRARY DESTINATION ${CMAKE_INSTALL_LIBDIR})
+        else()
+            set_property(TARGET phphcalc_lib PROPERTY VERSION ${SERIAL})
+            set_property(TARGET phphcalc_lib PROPERTY SOVERSION ${SOSERIAL})
+            set_property(TARGET phphcalc_lib PROPERTY OUTPUT_NAME phphcalc_lib)
+            install(TARGETS phphcalc_lib ARCHIVE DESTINATION ${CMAKE_INSTALL_LIBDIR})
+        endif()
+
+        # Header file
+        install(FILES ${PROJECT_SOURCE_DIR}/c/phono3py.h
+                DESTINATION ${CMAKE_INSTALL_INCLUDEDIR})
+    endif()
+endif()
+
+# ###################################################################################
+# phononcalc #
+# ###################################################################################
+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
+        ${PROJECT_SOURCE_DIR}/c/phonon.c ${PROJECT_SOURCE_DIR}/c/phononcalc.c)
+
+    if(BUILD_SHARED_LIBS)
+        # Shared library
+        add_library(phononcalc_lib SHARED ${SOURCES_PHONONCALC})
+
+        if(OpenMP_FOUND)
+            target_link_libraries(phononcalc_lib BLAS::BLAS LAPACK::LAPACK
+                                  OpenMP::OpenMP_C)
+        else()
+            target_link_libraries(phononcalc_lib BLAS::BLAS LAPACK::LAPACK)
+        endif()
+
+        target_include_directories(phononcalc_lib PRIVATE ${MY_INCLUDES})
+
+        if(BLAS_LIBRARIES MATCHES "libmkl")
+            target_compile_definitions(phononcalc_lib PRIVATE MKL_LAPACKE
+                                                              MULTITHREADED_BLAS)
+        endif()
+
+        if(BLAS_LIBRARIES MATCHES "libopenblas")
+            target_compile_definitions(phononcalc_lib PRIVATE MULTITHREADED_BLAS)
+        endif()
+
+    else()
+        # Static link library
+        add_library(phononcalc_lib STATIC ${SOURCES_PHONONCALC})
+
+        if(OpenMP_FOUND)
+            target_link_libraries(phononcalc_lib PRIVATE BLAS::BLAS LAPACK::LAPACK
+                                                         OpenMP::OpenMP_C)
+        else()
+            target_link_libraries(phononcalc_lib PRIVATE BLAS::BLAS LAPACK::LAPACK)
+        endif()
+
+        target_include_directories(phononcalc_lib PRIVATE ${MY_INCLUDES})
+
+        if(BLAS_LIBRARIES MATCHES "libmkl")
+            target_compile_definitions(phononcalc_lib PRIVATE MKL_LAPACKE
+                                                              MULTITHREADED_BLAS)
+        endif()
+
+        if(BLAS_LIBRARIES MATCHES "libopenblas")
+            target_compile_definitions(phononcalc_lib PRIVATE MULTITHREADED_BLAS)
+        endif()
+    endif()
+
+    if(NOT BUILD_NANOBIND_MODULE)
+        if(BUILD_SHARED_LIBS)
+            set_property(TARGET phononcalc_lib PROPERTY VERSION ${SERIAL})
+            set_property(TARGET phononcalc_lib PROPERTY SOVERSION ${SOSERIAL})
+            install(TARGETS phononcalc_lib
+                    LIBRARY DESTINATION ${CMAKE_INSTALL_LIBDIR})
+
+        else()
+            set_property(TARGET phononcalc_lib PROPERTY VERSION ${SERIAL})
+            set_property(TARGET phononcalc_lib PROPERTY SOVERSION ${SOSERIAL})
+            set_property(TARGET phononcalc_lib PROPERTY OUTPUT_NAME phononcalc_lib)
+            install(TARGETS phononcalc_lib
+                    ARCHIVE DESTINATION ${CMAKE_INSTALL_LIBDIR})
+        endif()
+
+        # Header file
+        install(FILES ${PROJECT_SOURCE_DIR}/c/phononcalc.h
+                DESTINATION ${CMAKE_INSTALL_INCLUDEDIR})
+    endif()
+endif()
+
+# ###################################################################################
+# grid #
+# ###################################################################################
+if(BUILD_GRIDSYS_LIB)
+    # Source code
+    set(SOURCES_GRIDSYS
+        ${PROJECT_SOURCE_DIR}/c/bzgrid.c
+        ${PROJECT_SOURCE_DIR}/c/grgrid.c
+        ${PROJECT_SOURCE_DIR}/c/gridsys.c
+        ${PROJECT_SOURCE_DIR}/c/lagrid.c
+        ${PROJECT_SOURCE_DIR}/c/niggli.c
+        ${PROJECT_SOURCE_DIR}/c/phonoc_utils.c
+        ${PROJECT_SOURCE_DIR}/c/snf3x3.c
+        ${PROJECT_SOURCE_DIR}/c/tetrahedron_method.c
+        ${PROJECT_SOURCE_DIR}/c/triplet.c
+        ${PROJECT_SOURCE_DIR}/c/triplet_grid.c
+        ${PROJECT_SOURCE_DIR}/c/triplet_iw.c)
+
+    if(BUILD_SHARED_LIBS)
+        # Shared library
+        add_library(gridsys SHARED ${SOURCES_GRIDSYS})
+
+        if(OpenMP_FOUND)
+            target_link_libraries(gridsys PRIVATE OpenMP::OpenMP_C)
+        endif()
+
+        target_include_directories(gridsys PRIVATE ${MY_INCLUDES})
+        target_compile_definitions(gridsys PRIVATE THM_EPSILON=1e-10)
+        set_property(TARGET gridsys PROPERTY VERSION ${SERIAL})
+        set_property(TARGET gridsys PROPERTY SOVERSION ${SOSERIAL})
+        install(TARGETS gridsys LIBRARY DESTINATION ${CMAKE_INSTALL_LIBDIR})
+    else()
+        # Static link library
+        add_library(gridsys_static STATIC ${SOURCES_GRIDSYS})
+
+        if(OpenMP_FOUND)
+            target_link_libraries(gridsys_static PRIVATE OpenMP::OpenMP_C)
+        endif()
+
+        target_include_directories(gridsys_static PRIVATE ${MY_INCLUDES})
+        target_compile_definitions(gridsys_static PRIVATE THM_EPSILON=1e-10)
+        set_property(TARGET gridsys_static PROPERTY VERSION ${SERIAL})
+        set_property(TARGET gridsys_static PROPERTY SOVERSION ${SOSERIAL})
+        set_property(TARGET gridsys_static PROPERTY OUTPUT_NAME gridsys)
+        install(TARGETS gridsys_static ARCHIVE DESTINATION ${CMAKE_INSTALL_LIBDIR})
+    endif()
+
+    # Header file
+    install(FILES ${PROJECT_SOURCE_DIR}/c/gridsys.h
+            DESTINATION ${CMAKE_INSTALL_INCLUDEDIR})
+endif()
+
+if(PHONO3PY_WITH_Fortran)
+    add_subdirectory(fortran)
+endif()
+
+if(PHONO3PY_WITH_TESTS)
+    if(PHONO3PY_WITH_Fortran)
+        set(LIB_MOD_DIR ${CMAKE_CURRENT_BINARY_DIR}/fortran)
+    endif()
+
+    add_subdirectory(ctest)
+endif()
+
+if(BUILD_NANOBIND_MODULE)
+    set_target_properties(phphcalc_lib PROPERTIES POSITION_INDEPENDENT_CODE ON)
+    set_target_properties(phononcalc_lib PROPERTIES POSITION_INDEPENDENT_CODE ON)
+
+    execute_process(
+        COMMAND "${Python_EXECUTABLE}" -m nanobind --cmake_dir
+        OUTPUT_STRIP_TRAILING_WHITESPACE
+        OUTPUT_VARIABLE NB_DIR)
+    list(APPEND CMAKE_PREFIX_PATH "${NB_DIR}")
+    find_package(nanobind CONFIG REQUIRED)
+    nanobind_add_module(_phono3py STABLE_ABI ${PROJECT_SOURCE_DIR}/c/phono3py.h
+                        ${PROJECT_SOURCE_DIR}/c/_phono3py.cpp)
+    nanobind_add_module(_phononcalc STABLE_ABI ${PROJECT_SOURCE_DIR}/c/phononcalc.h
+                        ${PROJECT_SOURCE_DIR}/c/_phononcalc.cpp)
+
+    target_link_libraries(_phono3py PRIVATE phphcalc_lib)
+    target_link_libraries(_phononcalc PRIVATE phononcalc_lib)
+
+    target_compile_definitions(_phono3py PRIVATE THM_EPSILON=1e-10)
+    install(TARGETS _phono3py LIBRARY DESTINATION ${SKBUILD_PROJECT_NAME})
+    install(TARGETS _phononcalc LIBRARY DESTINATION ${SKBUILD_PROJECT_NAME})
+endif()

phono3py-3.3.0/PKG-INFO

@@ -0,0 +1,107 @@
+Metadata-Version: 2.1
+Name: phono3py
+Version: 3.3.0
+Summary: This is the phono3py module.
+Author-Email: Atsushi Togo <atztogo@gmail.com>
+License: Copyright (c) 2015-2024, Phonopy. All rights reserved.
+        
+        Redistribution and use in source and binary forms, with or without
+        modification, are permitted provided that the following conditions
+        are met:
+        
+        * Redistributions of source code must retain the above copyright
+          notice, this list of conditions and the following disclaimer.
+        * Redistributions in binary form must reproduce the above copyright
+          notice, this list of conditions and the following disclaimer in the
+          documentation and/or other materials provided with the distribution.
+        * Neither the name of the phonopy project nor the
+          names of its contributors may be used to endorse or promote products
+          derived from this software without specific prior written permission.
+        
+        THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS
+        "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT
+        LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR
+        A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL <COPYRIGHT
+        HOLDER> BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+        EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+        PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR
+        PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF
+        LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING
+        NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS
+        SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+Project-URL: Homepage, https://phonopy.github.io/phono3py/
+Project-URL: Repository, https://github.com/phonopy/phono3py
+Requires-Python: >=3.8
+Requires-Dist: numpy>=1.17.0
+Requires-Dist: scipy
+Requires-Dist: PyYAML>=5.3
+Requires-Dist: matplotlib>=2.2.2
+Requires-Dist: h5py>=3.0
+Requires-Dist: spglib>=2.3
+Requires-Dist: phonopy<2.27,>=2.26
+Description-Content-Type: text/markdown
+
+[![Version Badge](https://anaconda.org/conda-forge/phono3py/badges/version.svg)](https://anaconda.org/conda-forge/phono3py)
+[![Downloads Badge](https://anaconda.org/conda-forge/phono3py/badges/downloads.svg)](https://anaconda.org/conda-forge/phono3py)
+[![PyPI version](https://badge.fury.io/py/phono3py.svg)](https://badge.fury.io/py/phono3py)
+[![PyPI](https://img.shields.io/pypi/dm/phono3py.svg?maxAge=2592000)](https://pypi.python.org/pypi/phono3py)
+[![codecov](https://codecov.io/gh/phonopy/phono3py/branch/develop/graph/badge.svg)](https://codecov.io/gh/phonopy/phono3py)
+
+# phono3py
+
+A simulation package of phonon-phonon interaction related properties mainly
+written in python. Phono3py user documentation is found at
+http://phonopy.github.io/phono3py/.
+
+## Mailing list for questions
+
+Usual phono3py questions should be sent to phonopy mailing list
+(https://sourceforge.net/p/phonopy/mailman/).
+
+## Dependency
+
+See `requirements.txt`. Optionally `symfc` and `scipy` are required
+for using additional features.
+
+## Development
+
+The development of phono3py is managed on the `develop` branch of github
+phono3py repository.
+
+- Github issues is the place to discuss about phono3py issues.
+- Github pull request is the place to request merging source code.
+- Formatting rules are found in `pyproject.toml`.
+- Not strictly, but VSCode's `settings.json` may be written like below
+
+  ```json
+  "ruff.lint.args": [
+      "--config=${workspaceFolder}/pyproject.toml",
+  ],
+  "[python]": {
+      "editor.defaultFormatter": "charliermarsh.ruff",
+      "editor.codeActionsOnSave": {
+          "source.organizeImports": "explicit"
+      }
+  },
+  ```
+
+- Use of pre-commit (https://pre-commit.com/) is encouraged.
+  - Installed by `pip install pre-commit`, `conda install pre_commit` or see
+    https://pre-commit.com/#install.
+  - pre-commit hook is installed by `pre-commit install`.
+  - pre-commit hook is run by `pre-commit run --all-files`.
+
+## Documentation
+
+Phono3py user documentation is written using python sphinx. The source files are
+stored in `doc` directory. Please see how to write the documentation at
+`doc/README.md`.
+
+## How to run tests
+
+Tests are written using pytest. To run tests, pytest has to be installed. The
+tests can be run by
+
+```bash
+% pytest
+```