Scipy optimizer module

.github/workflows/merge.yaml

@@ -0,0 +1,46 @@
+# Licensed to the Apache Software Foundation (ASF) under one
+# or more contributor license agreements.  See the NOTICE file
+# distributed with this work for additional information
+# regarding copyright ownership.  The ASF licenses this file
+# to you under the Apache License, Version 2.0 (the
+# "License"); you may not use this file except in compliance
+# with the License.  You may obtain a copy of the License at
+#
+#   http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing,
+# software distributed under the License is distributed on an
+# "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY
+# KIND, either express or implied.  See the License for the
+# specific language governing permissions and limitations
+# under the License.
+
+# Copyright 2023 NWChemEx-Project
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+# http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+#
+
+name: .github Merge Workflow
+
+on:
+  push:
+    branches:
+      - master
+
+jobs:
+  Common-Merge:
+    uses: NWChemEx-Project/.github/.github/workflows/common_merge.yaml@master
+    with:
+      doc_target: 'Sphinx'
+      generate_module_docs: false
+    secrets: inherit

.github/workflows/pull_request.yaml

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+# Licensed to the Apache Software Foundation (ASF) under one
+# or more contributor license agreements.  See the NOTICE file
+# distributed with this work for additional information
+# regarding copyright ownership.  The ASF licenses this file
+# to you under the Apache License, Version 2.0 (the
+# "License"); you may not use this file except in compliance
+# with the License.  You may obtain a copy of the License at
+#
+#   http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing,
+# software distributed under the License is distributed on an
+# "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY
+# KIND, either express or implied.  See the License for the
+# specific language governing permissions and limitations
+# under the License.
+
+# Copyright 2023 NWChemEx-Project
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+# http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+#
+
+name: .github Pull Request Workflow
+
+on:
+  pull_request:
+    branches:
+      - master
+
+jobs:
+  Common-Pull-Request:
+    uses: NWChemEx-Project/.github/.github/workflows/common_pull_request.yaml@master
+    with:
+      config_file: '.github/.licenserc.yaml'
+      source_dir: ''
+      compilers: ''
+      doc_target: 'Sphinx'
+    secrets: inherit

CMakeLists.txt

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+# Copyright 2022 NWChemEx-Project
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+# http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+
+cmake_minimum_required(VERSION 3.14)
+set(VERSION 1.0.0) #TODO: get from git
+project(structurefinder VERSION "${VERSION}" LANGUAGES CXX)
+
+include(FetchContent)
+FetchContent_Declare(
+    nwx_cmake
+    GIT_REPOSITORY https://github.com/NWChemEx-Project/NWXCMake
+)
+FetchContent_MakeAvailable(nwx_cmake)
+list(APPEND CMAKE_MODULE_PATH "${nwx_cmake_SOURCE_DIR}/cmake")
+
+set(
+    CMAKE_MODULE_PATH "${CMAKE_MODULE_PATH}" "${PROJECT_SOURCE_DIR}/cmake"
+    CACHE STRING "" FORCE
+)
+
+include(get_cmaize)
+include(nwx_versions)
+
+### Options ###
+option(BUILD_TESTING "Should we build the tests?" OFF)
+option(BUILD_PYBIND11_PYBINDINGS "Use Pybind11 to build Python bindings?" ON)
+option(ENABLE_NWCHEM "Should we build supporf for friend: NWChem ?" ON)
+
+## Build StructureFinder's dependencies ##
+cpp_find_or_build_dependency(
+    nwchemex
+    URL github.com/NWChemEx-Project/NWChemEx
+    PRIVATE TRUE
+    VERSION ${NWX_SIMDE_VERSION}
+    BUILD_TARGET nwchemex
+    FIND_TARGET nwx::nwchemex
+    CMAKE_ARGS BUILD_TESTING=OFF
+)
+
+if("${NWX_MODULE_DIRECTORY}" STREQUAL "")
+    message(
+        FATAL_ERROR "NWX_MODULE_DIRECTORY must be set to the directory "
+                    "where you would like the Python modules installed."
+    )
+endif()
+
+
+if("${BUILD_TESTING}")
+    include(CTest)
+    include(nwx_pybind11)
+
+# override
+function(nwx_pybind11_tests npt_name npt_driver)
+    if(NOT "${BUILD_PYBIND11_PYBINDINGS}")
+        return()
+    endif()
+
+    set(_npt_options "")
+    set(_npt_one_val "")
+    set(_npt_lists SUBMODULES)
+    cmake_parse_arguments(
+        "_npt" "${_npt_options}" "${_npt_one_val}" "${_npt_lists}" ${ARGN}
+    )
+
+    if("${BUILD_TESTING}")
+        include(CTest)
+        find_package(Python COMPONENTS Interpreter REQUIRED)
+
+        # Build the PYTHONPATH for the test
+        set(_npt_py_path "PYTHONPATH=${NWX_MODULE_DIRECTORY}")
+        set(_npt_py_path "${_npt_py_path}:${CMAKE_BINARY_DIR}")
+        foreach(_npt_submod ${_npt_SUBMODULES})
+            set(_npt_dep_dir "${CMAKE_BINARY_DIR}/_deps/${_npt_submod}-build")
+            set(_npt_py_path "${_npt_py_path}:${_npt_dep_dir}")
+        endforeach()
+        if(NOT "${NWX_PYTHON_EXTERNALS}" STREQUAL "")
+            set(_npt_py_path "${_npt_py_path}:${NWX_PYTHON_EXTERNALS}")
+        endif()
+
+        add_test(
+            NAME "${npt_name}"
+            COMMAND "${Python_EXECUTABLE}" "${npt_driver}"
+        )
+
+        set_tests_properties(
+            "${npt_name}"
+            PROPERTIES ENVIRONMENT "${_npt_py_path}"
+        )
+    endif()
+endfunction()
+
+#
+
+    set(PYTHON_TEST_DIR "${CMAKE_CURRENT_LIST_DIR}/tests/python")
+
+    message("calling nwx_pybind11_tests")
+    nwx_pybind11_tests(
+        pyStructureFinder_unit_tests
+        "${PYTHON_TEST_DIR}/unit_tests/test_structurefinder.py"
+        SUBMODULES nwchemex simde chemist pluginplay parallelzone
+    )
+endif()
+
+install(
+    DIRECTORY "${python_src_directory}/structurefinder"
+    DESTINATION "${NWX_MODULE_DIRECTORY}"
+)

src/python/structurefinder/__init__.py

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+# Licensed to the Apache Software Foundation (ASF) under one
+# or more contributor license agreements.  See the NOTICE file
+# distributed with this work for additional information
+# regarding copyright ownership.  The ASF licenses this file
+# to you under the Apache License, Version 2.0 (the
+# "License"); you may not use this file except in compliance
+# with the License.  You may obtain a copy of the License at
+#
+#   http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing,
+# software distributed under the License is distributed on an
+# "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY
+# KIND, either express or implied.  See the License for the
+# specific language governing permissions and limitations
+# under the License.
+