Pyberny addition

.github/.licenserc.yaml

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+# Copyright 2021 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.
+#
+header:
+  license:
+    spdx-id: Apache-2.0
+    copyright-owner: NWChemEx Community
+
+  paths-ignore:
+    - .github/
+    - LICENSE
+    - version.txt
+    - docs/source/nitpick_exceptions
+
+  comment: never

.github/workflows/merge.yaml

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+# Copyright 2024 NWChemEx Community
+#
+# 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/.github/.github/workflows/common_merge.yaml@master
+    with:
+      doc_target: 'structure_finder_cxx_api'
+      generate_module_docs: true
+    secrets: inherit

.github/workflows/pull_request.yaml

@@ -0,0 +1,31 @@
+# Copyright 2024 NWChemEx Community
+#
+# 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/.github/.github/workflows/common_pull_request.yaml@master
+    with:
+      config_file: '.github/.licenserc.yaml'
+      source_dir: ''
+      compilers: '["gcc-11", "clang-14"]'
+      doc_target: 'structure_finder_cxx_api'
+    secrets: inherit

.gitignore

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+# Copyright 2024 NWChemEx Community
+#
+# 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.
+
+__pycache__/
+build/
+venv/
+install/

CMakeLists.txt

@@ -0,0 +1,88 @@
+# Copyright 2024 NWChemEx Community
+#
+# 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 Project and Version
+file(STRINGS "${CMAKE_CURRENT_SOURCE_DIR}/version.txt" VERSION)
+project(structurefinder VERSION "${VERSION}" LANGUAGES CXX)
+
+## Get CMaize
+include(cmake/get_cmaize.cmake)
+
+## Paths ##
+set(${PROJECT_NAME}_INC_DIR "${CMAKE_CURRENT_LIST_DIR}/include/${PROJECT_NAME}")
+set(${PROJECT_NAME}_SRC_DIR "${CMAKE_CURRENT_LIST_DIR}/src/${PROJECT_NAME}")
+set(${PROJECT_NAME}_TESTS_DIR "${CMAKE_CURRENT_SOURCE_DIR}/tests")
+set(${PROJECT_NAME}_PYTHON_DIR "${CMAKE_CURRENT_SOURCE_DIR}/src/python")
+set(${PROJECT_NAME}_PYTHON_TEST_DIR "${${PROJECT_NAME}_TESTS_DIR}/python")
+
+## Options ##
+cmaize_option_list(
+    BUILD_TESTING OFF "Should the tests be built?"
+    BUILD_PYBIND11_PYBINDINGS ON "Use Pybind11 to build Python bindings?"
+)
+
+## Find or build dependencies ##
+cmaize_find_or_build_dependency(
+    simde
+    URL github.com/NWChemEx/SimDE
+    VERSION master
+    BUILD_TARGET simde
+    FIND_TARGET nwx::simde
+    CMAKE_ARGS BUILD_TESTING=OFF
+               BUILD_PYBIND11_PYBINDINGS=${BUILD_PYBIND11_PYBINDINGS}
+)
+
+cmaize_find_or_build_dependency(
+    pyberny
+    PACKAGE_MANAGER pip
+)
+
+# Builds C++ API documentation
+include(nwx_cxx_api_docs)
+nwx_cxx_api_docs("${${PROJECT_NAME}_INC_DIR}" "${${PROJECT_NAME}_SRC_DIR}")
+
+## Add libraries ##
+add_library(${PROJECT_NAME} INTERFACE)
+target_link_libraries(${PROJECT_NAME} INTERFACE simde pyberny)
+
+## Build tests ##
+if("${BUILD_TESTING}")
+    include(CTest)
+    include(nwx_pybind11)
+
+    ## Add Tests ##
+    cmaize_find_or_build_dependency(
+        nwchemex
+        URL github.com/NWChemEx/NWChemEx
+        BUILD_TARGET nwchemex
+        FIND_TARGET nwx::nwchemex
+        CMAKE_ARGS BUILD_TESTING=OFF
+    )
+
+    nwx_pybind11_tests(
+        py_${PROJECT_NAME}
+        "${${PROJECT_NAME}_PYTHON_TEST_DIR}/unit_tests/test_${PROJECT_NAME}.py"
+        DEPENDS nwchemex
+        SUBMODULES simde chemist pluginplay parallelzone friendzone chemcache nwchemex
+    )
+
+endif()
+
+## Add package ##
+install(
+    DIRECTORY "${${PROJECT_NAME}_PYTHON_DIR}/${PROJECT_NAME}"
+    DESTINATION "${NWX_MODULE_DIRECTORY}"
+)

README.md

@@ -1,2 +1,18 @@
+<!--
+  ~ Copyright 2024 NWChemEx Community
+  ~
+  ~ 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.
+-->
+
 # StructureFinder
 Repo for geometry optimization, transition states, etc. Much of this repo will be Python based, providing interfaces to geomeTRIC, pyBerny, ASE NEB, etc.

cmake/get_cmaize.cmake

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+# Copyright 2024 NWChemEx Community
+#
+# 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.
+
+function(get_cmaize)
+
+    if("${CMAIZE_VERSION}" STREQUAL "")
+        set(CMAIZE_VERSION v1.1.0 )
+    endif()
+
+    # Store whether we are building tests or not, then turn off the tests
+    if(BUILD_TESTING)
+        set(build_testing_old "${BUILD_TESTING}")
+    endif()
+    set(BUILD_TESTING OFF CACHE BOOL "" FORCE)
+
+    # Download CMakePP and bring it into scope
+    include(FetchContent)
+    FetchContent_Declare(
+        cmaize
+        GIT_REPOSITORY https://github.com/CMakePP/CMaize
+        GIT_TAG ${CMAIZE_VERSION}
+    )
+    FetchContent_MakeAvailable(cmaize)
+
+    # Restore the previous value, if set
+    # Unset otherwise
+    if(build_testing_old)
+        set(BUILD_TESTING "${build_testing_old}" CACHE BOOL "" FORCE)
+    else()
+        unset(BUILD_TESTING CACHE)
+    endif()
+endfunction()
+
+# Call the function we just wrote to get CMaize
+get_cmaize()
+
+# Include CMaize
+include(cmaize/cmaize)

docs/Makefile

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+# Copyright 2024 NWChemEx Community
+#
+# 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.
+
+# Minimal makefile for Sphinx documentation
+#
+
+# You can set these variables from the command line.
+SPHINXOPTS    =
+SPHINXBUILD   = sphinx-build
+SPHINXPROJ    = structurefinder
+SOURCEDIR     = source
+BUILDDIR      = build
+
+# Put it first so that "make" without argument is like "make help".
+help:
+	@$(SPHINXBUILD) -M help "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)
+
+.PHONY: help Makefile
+
+# Catch-all target: route all unknown targets to Sphinx using the new
+# "make mode" option.  $(O) is meant as a shortcut for $(SPHINXOPTS).
+%: Makefile
+	@$(SPHINXBUILD) -M $@ "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)

docs/README.md

@@ -0,0 +1,18 @@
+<!--
+  ~ Copyright 2024 NWChemEx Community
+  ~
+  ~ 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.
+-->
+
+General instructions for building documentation found throughout the NWChemEx project are available at:
+https://github.com/NWChemEx/NWChemEx/blob/master/docs/README.md

docs/requirements.txt

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+sphinx==v7.2.6
+sphinx_rtd_theme==1.3.0
+sphinxcontrib-bibtex
+sphinx_tabs
+sphinx-autoapi