Scipy optimizer module

.github/.licenserc.yaml

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+header:
+  license:
+    spdx-id: Apache-2.0
+    copyright-owner: NWChemEx-Project
+
+  paths-ignore:
+    - .github/
+    - docs/Makefile
+    - LICENSE
+    - docs/requirements.txt
+    - docs/source/bibliography/*.bib
+    - version.txt
+    - cmake/friends.py.in
+
+  comment: never

.github/workflows/merge.yaml

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+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

@@ -0,0 +1,16 @@
+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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+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)
+
+## Build StructureFinder's dependencies ##
+cpp_find_or_build_dependency(
+    nwchemex
+    URL github.com/NWChemEx-Project/NWChemEx
+    PRIVATE TRUE
+    VERSION master
+    BUILD_TARGET nwchemex
+    FIND_TARGET nwx::nwchemex
+    CMAKE_ARGS BUILD_TESTING=OFF
+)
+
+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}"
+)

README.md

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

docs/Makefile

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+# 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 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.
+-->
+
+General instructions for building documentation found throughout the NWChemEx project are available at:
+https://github.com/NWChemEx-Project/NWChemEx/blob/master/docs/README.md

docs/requirements.txt

@@ -0,0 +1,5 @@
+sphinx
+sphinx_rtd_theme==1.3.0
+sphinxcontrib-bibtex
+sphinx_tabs
+sphinx-autoapi==3.0.0

docs/source/conf.py

@@ -0,0 +1,174 @@
+# -*- coding: utf-8 -*-
+# 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.
+
+#
+# Configuration file for the Sphinx documentation builder.
+#
+# This file does only contain a selection of the most common options. For a
+# full list see the documentation:
+# http://www.sphinx-doc.org/en/master/config
+
+import os
+import sys
+
+# -- Project information -----------------------------------------------------
+
+project = u'structurefinder'
+copyright = u'2023, NWChemEx Team'
+author = u'NWChemEx Team'
+
+# Get the version from version.txt
+version = '1.0.0'
+# The full version, including alpha/beta/rc tags
+release = version
+
+# -- General configuration ---------------------------------------------------
+
+# We use numref which is introduced in Sphinx 1.3
+needs_sphinx = '1.3'
+
+# Add any Sphinx extension module names here, as strings. They can be
+# extensions coming with Sphinx (named 'sphinx.ext.*') or your custom
+# ones.
+extensions = [
+    'sphinx.ext.autodoc', 'sphinx.ext.autosummary', 'sphinx_tabs.tabs',
+    'sphinx.ext.doctest', 'sphinx.ext.todo', 'sphinx.ext.coverage',
+    'sphinx.ext.mathjax', 'sphinx.ext.githubpages', 'autoapi.extension'
+]
+dir_path = os.path.dirname(os.path.realpath(__file__))
+doc_path = os.path.dirname(dir_path)
+root_path = os.path.dirname(doc_path)
+
+# Add any paths that contain templates here, relative to this directory.
+#templates_path = ['_templates']
+
+# The suffix(es) of source filenames.
+# You can specify multiple suffix as a list of string:
+#
+# source_suffix = ['.rst', '.md']
+source_suffix = '.rst'
+
+# The master toctree document.
+master_doc = 'index'
+
+# The language for content autogenerated by Sphinx. Refer to documentation
+# for a list of supported languages.
+#
+# This is also used if you do content translation via gettext catalogs.
+# Usually you set "language" from the command line for these cases.
+language = 'en'
+
+# List of patterns, relative to source directory, that match files and
+# directories to ignore when looking for source files.
+# This pattern also affects html_static_path and html_extra_path .
+exclude_patterns = []
+
+# The name of the Pygments (syntax highlighting) style to use.
+pygments_style = 'sphinx'
+
+# Should figures be numbered?
+numfig = True
+
+# -- Options for HTML output -------------------------------------------------
+
+# The theme to use for HTML and HTML Help pages.  See the documentation for
+# a list of builtin themes.
+#
+html_theme = 'sphinx_rtd_theme'
+
+# Theme options are theme-specific and customize the look and feel of a theme
+# further.  For a list of options available for each theme, see the
+# documentation.
+#
+# html_theme_options = {}
+
+# Add any paths that contain custom static files (such as style sheets) here,
+# relative to this directory. They are copied after the builtin static files,
+# so a file named "default.css" will overwrite the builtin "default.css".
+#html_static_path = ['_static']
+
+# Custom sidebar templates, must be a dictionary that maps document names
+# to template names.
+#
+# The default sidebars (for documents that don't match any pattern) are
+# defined by theme itself.  Builtin themes are using these templates by
+# default: ``['localtoc.html', 'relations.html', 'sourcelink.html',
+# 'searchbox.html']``.
+#
+# html_sidebars = {}
+
+# -- Options for HTMLHelp output ---------------------------------------------
+
+# Output file base name for HTML help builder.
+htmlhelp_basename = project + 'doc'
+
+# -- Options for LaTeX output ------------------------------------------------
+
+latex_elements = {
+    # The paper size ('letterpaper' or 'a4paper').
+    #
+    # 'papersize': 'letterpaper',
+
+    # The font size ('10pt', '11pt' or '12pt').
+    #
+    # 'pointsize': '10pt',
+
+    # Additional stuff for the LaTeX preamble.
+    #
+    # 'preamble': '',
+
+    # Latex figure (float) alignment
+    #
+    # 'figure_align': 'htbp',
+}
+
+# Grouping the document tree into LaTeX files. List of tuples
+# (source start file, target name, title,
+#  author, documentclass [howto, manual, or own class]).
+latex_documents = [
+    (master_doc, project + '.tex', project + ' Documentation', author,
+     'manual'),
+]
+
+# -- Options for manual page output ------------------------------------------
+
+# One entry per manual page. List of tuples
+# (source start file, name, description, authors, manual section).
+man_pages = [(master_doc, project.lower(), project + ' Documentation',
+              [author], 1)]
+
+# -- Options for Texinfo output ----------------------------------------------
+
+# Grouping the document tree into Texinfo files. List of tuples
+# (source start file, target name, title, author,
+#  dir menu entry, description, category)
+texinfo_documents = [
+    (master_doc, project, project + ' Documentation', author, project,
+     'One line description of project.', 'Miscellaneous'),
+]
+
+# -- Extension configuration -------------------------------------------------
+autoapi_dirs = ['../../src', '../../tests']
+autoapi_add_toctree_entry = False
+
+# -- Options for intersphinx extension ---------------------------------------
+
+# Example configuration for intersphinx: refer to the Python standard library.
+intersphinx_mapping = {'https://docs.python.org/': None}
+
+# -- Options for todo extension ----------------------------------------------
+
+# If true, `todo` and `todoList` produce output, else they produce nothing.
+todo_include_todos = True