Merge branch 'master' into weekly-build

mir-group · Sep 20, 2024 · c582a7e · c582a7e
2 parents 9d9ce8b + 060248e
commit c582a7e
Show file tree

Hide file tree

Showing 10 changed files with 96 additions and 287 deletions.
diff --git a/.github/workflows/flare.yml b/.github/workflows/flare.yml
@@ -56,7 +56,6 @@ jobs:
 
         cmake ..
         cmake --build . -j4
-        cp _C_flare* ../flare/bffs/sgp
         cd ctests
         ./tests
 
@@ -89,8 +88,7 @@ jobs:
 
     - name: Pip install
       run: |
-        pip install -U codecov pytest pytest-cov pytest_mock Sphinx sphinx-rtd-theme breathe nbsphinx
-        pip install -r requirements.txt
+          pip install -e .[docs,tests]
 
     - name: Patch ASE
       run: |
@@ -121,11 +119,6 @@ jobs:
         python tutorial.py
         rm Al* aluminum.txt aspirin.txt md17_aspirin.npz tutorial.ipynb tutorial.py
 
-    - name: Install Sphinx and Breathe
-      run: |
-        sudo apt-get update
-        sudo apt-get install python3-sphinx python3-sphinx-rtd-theme python3-breathe python3-nbsphinx
-
     - name: Run Doxygen
       uses: mattnotmitt/[email protected]
       with:
@@ -134,6 +127,7 @@ jobs:
 
     - name: Run Sphinx
       run: |
+        sudo apt-get install pandoc
         export PYTHONPATH=$PYTHONPATH:$PWD/lammps/python
         cd docs
         pwd

diff --git a/CMakeLists.txt b/CMakeLists.txt
@@ -1,4 +1,4 @@
-cmake_minimum_required(VERSION 3.14.5)
+cmake_minimum_required(VERSION 3.18...3.26)
 
 set(CMAKE_DISABLE_SOURCE_CHANGES ON)
 set(CMAKE_DISABLE_IN_SOURCE_BUILD ON)
@@ -15,8 +15,6 @@ set(CMAKE_CXX_EXTENSIONS OFF)
 
 set(CMAKE_OSX_ARCHITECTURES "x86_64")
 
-set(FLARE_PYTHON_VERSION "" CACHE STRING "Python version to use for compiling modules")
-
 if(NOT CMAKE_BUILD_TYPE)
   message(STATUS "[flare] CMAKE_BUILD_TYPE not specified, setting it to "
                  "Release. Use `-DCMAKE_BUILD_TYPE=...` to overwrite.")
@@ -32,13 +30,15 @@ include(FetchContent)
 # googletest
 ################################################################################
 
-FetchContent_Declare(googletest
-    GIT_REPOSITORY https://github.com/google/googletest.git
-    GIT_TAG release-1.11.0
-    SOURCE_DIR ${CMAKE_CURRENT_BINARY_DIR}/External/googletest
-    UPDATE_COMMAND ""
-)
-FetchContent_MakeAvailable(googletest)
+if(NOT DEFINED SKBUILD)
+    FetchContent_Declare(googletest
+        GIT_REPOSITORY https://github.com/google/googletest.git
+        GIT_TAG release-1.11.0
+        SOURCE_DIR ${CMAKE_CURRENT_BINARY_DIR}/External/googletest
+        UPDATE_COMMAND ""
+    )
+    FetchContent_MakeAvailable(googletest)
+endif()
 
 # Json
 ################################################################################
@@ -53,19 +53,6 @@ FetchContent_Populate(json)
 add_subdirectory(${json_SOURCE_DIR} ${json_BINARY_DIR})
 include_directories(${json_SOURCE_DIR})
 
-# Kokkos
-################################################################################
-
-#FetchContent_Declare(kokkos
-#    GIT_REPOSITORY https://github.com/kokkos/kokkos
-#    SOURCE_DIR ${CMAKE_CURRENT_BINARY_DIR}/External/kokkos
-#    UPDATE_COMMAND ""
-#)
-#FetchContent_GetProperties(kokkos)
-#FetchContent_Populate(kokkos)
-#add_subdirectory(${kokkos_SOURCE_DIR} ${kokkos_BINARY_DIR})
-#include_directories(${Kokkos_SOURCE_DIR})
-
 
 # Eigen3
 ################################################################################
@@ -140,37 +127,24 @@ add_dependencies(flare eigen_project)
 # Link to json.
 target_link_libraries(flare PUBLIC nlohmann_json::nlohmann_json)
 
-# Add conda include directories
-if (DEFINED ENV{CONDA_PREFIX})
-  message(STATUS "Adding conda include directories.")
-  include_directories($ENV{CONDA_PREFIX}/include)
-endif()
-
 # Link to OpenMP.
-if (DEFINED ENV{OMP_LOC})
-    target_link_libraries(flare PUBLIC $ENV{OMP_LOC})
-    message(STATUS "Linking to user-specified OpenMP library.")
-elseif(DEFINED ENV{NO_OMP})
-    message(STATUS "Building without OpenMP.")
-else()
+if(NOT DEFINED ENV{NO_OMP})
     find_package(OpenMP)
     if(OpenMP_CXX_FOUND)
         target_link_libraries(flare PUBLIC OpenMP::OpenMP_CXX)
     endif()
 endif()
 
-# Check for user-specified MKL package.
-if (DEFINED ENV{MKL_INCLUDE} AND DEFINED ENV{MKL_LIBS})
-  message(STATUS "Linking Eigen to user-specified MKL libraries.")
-  include_directories($ENV{MKL_INCLUDE})
-  target_link_libraries(flare PUBLIC $ENV{MKL_LIBS})
-  target_compile_definitions(flare PUBLIC EIGEN_USE_MKL_ALL=1)
-# Give the option to do a "bare-bones" build without Lapack/Lapacke.
-elseif(DEFINED ENV{NO_LAPACK})
-  message(STATUS "Building without Lapack.")
-else()
+# Add conda include directories TODO: MKL issue if not
+if(DEFINED ENV{CONDA_PREFIX})
+  message(STATUS "Adding conda include directories.")
+  include_directories($ENV{CONDA_PREFIX}/include)
+endif()
+
+
+if(NOT DEFINED ENV{NO_LAPACK})
   find_package(LAPACK REQUIRED)
-  target_link_libraries(flare PUBLIC ${LAPACK_LIBRARIES})
+  target_link_libraries(flare PUBLIC LAPACK::LAPACK)
 
   if (LAPACK_LIBRARIES MATCHES mkl)
     message(STATUS "Linking Eigen to MKL.")
@@ -179,16 +153,18 @@ else()
     find_package(LAPACKE)
     if(LAPACKE_FOUND)
       target_link_libraries(flare PUBLIC ${LAPACKE_LIBRARIES})
+      message(STATUS "Linking Eigen to LAPACKE.")
+      target_compile_definitions(flare PUBLIC EIGEN_USE_LAPACKE=1)
     endif()
-    message(STATUS "Linking Eigen to LAPACKE.")
-    target_compile_definitions(flare PUBLIC EIGEN_USE_LAPACKE=1)
   endif()
 endif()
 
-# Create pybind module.
 pybind11_add_module(flare_module ${PYBIND_SOURCES})
 target_link_libraries(flare_module PUBLIC flare)
 set_target_properties(flare_module PROPERTIES OUTPUT_NAME "_C_flare")
+install(TARGETS flare_module LIBRARY DESTINATION flare/bffs/sgp)
 
 # Add test directory.
-add_subdirectory(ctests)
+if(NOT DEFINED SKBUILD)
+  add_subdirectory(ctests)
+endif()
diff --git a/MANIFEST.in b/MANIFEST.in
diff --git a/flare/descriptors/env.py b/flare/descriptors/env.py
@@ -192,7 +192,7 @@ def setup_mask(self, cutoffs_mask):
                     self.cut3b_mask = cutoffs_mask.get("cut3b_mask", None)
                     if "threebody_cutoff_list" in cutoffs_mask:
                         self.threebody_cutoff_list = np.array(
-                            cutoffs_mask["threebody_cutoff_list"], dtype=np.float
+                            cutoffs_mask["threebody_cutoff_list"], dtype=np.float64
                         )
 
     def compute_env(self):

diff --git a/flare/utils/parameter_helper.py b/flare/utils/parameter_helper.py
@@ -839,7 +839,7 @@ def summarize_group(self, group_type):
                 for ele in self.groups["specie"][idt]:
                     atom_n = atomic_numbers[ele]
                     if atom_n >= len(self.species_mask):
-                        new_mask = np.ones(atom_n, dtype=np.int) * (nspecie - 1)
+                        new_mask = np.ones(atom_n, dtype=np.int8) * (nspecie - 1)
                         new_mask[: len(self.species_mask)] = self.species_mask
                         self.species_mask = new_mask
                     self.species_mask[atom_n] = idt

diff --git a/flare/utils/parameters.py b/flare/utils/parameters.py
@@ -196,7 +196,7 @@ def check_instantiation(hyps, cutoffs, kernels, param_dict):
 
                 # check mask has the right dimension and values
                 mask = param_dict[f"{kernel}_mask"]
-                param_dict[f"{kernel}_mask"] = nparray(mask, dtype=np.int)
+                param_dict[f"{kernel}_mask"] = nparray(mask, dtype=np.int8)
 
                 assert npmax(mask) < n
                 dim = Parameters.ndim[kernel]
@@ -247,7 +247,7 @@ def check_instantiation(hyps, cutoffs, kernels, param_dict):
 
             # Ensure typed correctly as numpy array
             param_dict["original_hyps"] = nparray(
-                param_dict["original_hyps"], dtype=np.float
+                param_dict["original_hyps"], dtype=np.float64
             )
             if (len(param_dict["original_hyps"]) - 1) not in param_dict["map"]:
                 assert (

diff --git a/pyproject.toml b/pyproject.toml
@@ -0,0 +1,60 @@
+[build-system]
+requires = ["scikit-build-core", "pybind11"]
+build-backend = "scikit_build_core.build"
+
+[project]
+name = "mir-flare"
+version = "1.4.2"
+description = "Fast Learning of Atomistic Rare Events"
+readme = "README.md"
+requires-python = ">=3.7"
+authors = [
+    { name = "Materials Intelligence Research", email = "[email protected]" },
+]
+classifiers = [
+    "Development Status :: 4 - Beta",
+    "License :: OSI Approved :: MIT License",
+    "Topic :: Scientific/Engineering :: Artificial Intelligence",
+    "Topic :: Scientific/Engineering :: Physics",
+]
+dependencies = [
+    "ase==3.22",
+    "nptyping",
+    "numba",
+    "numpy",
+    "pyyaml",
+    "scipy",
+    "wandb",
+]
+
+[project.scripts]
+flare-otf = "flare.scripts.otf_train:main"
+
+[project.urls]
+Homepage = "https://github.com/mir-group/flare"
+
+[project.optional-dependencies]
+tests = [
+    "pytest-mock",
+    "pytest>=4.6",
+    "IPython",
+]
+dev = [
+    "jupyter",
+    "memory_profiler",
+]
+docs = [
+    "babel",
+    "docutils==0.17.1",
+    "nbconvert",
+    "nbsphinx",
+    "pandoc",
+    "pygments==2.15.0",
+    "codecov",
+    "Sphinx",
+    "sphinx-rtd-theme",
+    "breathe"
+]
+
+[tool.scikit-build]
+wheel.packages = ["flare"]
diff --git a/requirements.txt b/requirements.txt