.. README targets
.. include:: README.txt
   :start-after: target-start-do-not-remove
   :end-before: target-end-do-not-remove

.. General references
.. _`AEA Compute environment`: https://aea.re-pages.lanl.gov/developer-operations/aea_compute_environment/aea_compute_environment.html
.. _`AEA Conda channel`: https://aea.re-pages.lanl.gov/developer-operations/aea_compute_environment/aea_compute_environment.html#aea-conda-channel
.. _`AEA Gitlab group members`: https://re-git.lanl.gov/groups/aea/-/group_members
.. _`AEA Gitlab group`: https://re-git.lanl.gov/aea
.. _`ASC RE Gitlab HPC Accounts`: https://hpcaccounts.lanl.gov/projects/request/asc-re-gitlab
.. _`ASC RE Gitlab User Documentation`: https://re-git.lanl.gov/help/user/index.md
.. _`ASC RE Gitlab`: https://re-git.lanl.gov/
.. _`Anaconda Documentation`: https://docs.conda.io/projects/conda/en/latest/user-guide/tasks/manage-environments.html
.. _`Argparse type`: https://docs.python.org/3.12/library/argparse.html#type
.. _`Argparse tutorial`: https://docs.python.org/3/howto/argparse.html
.. _`Bash Arrays`: https://www.gnu.org/savannah-checkouts/gnu/bash/manual/bash.html#Arrays
.. _`Bash Exit Status`: https://www.gnu.org/software/bash/manual/html_node/Exit-Status.html
.. _`Bash Parameter Expansion`: https://www.gnu.org/savannah-checkouts/gnu/bash/manual/bash.html#Shell-Parameter-Expansion
.. _`Bash Variables`: https://www.gnu.org/savannah-checkouts/gnu/bash/manual/bash.html#Bash-Variables
.. _`CMake`: https://cmake.org/cmake/help/latest/
.. _`CalculiX`: http://www.dhondt.de/
.. _`Cartesian Product`: https://en.wikipedia.org/wiki/Cartesian_product
.. _`Charm++`: https://charmplusplus.org/
.. _`CheckProg`: https://scons.org/doc/production/HTML/scons-user/ch21s07.html
.. _`Confluence`: https://www.atlassian.com/software/confluence
.. _`Cubit`: https://cubit.sandia.gov/public/documentation.html
.. _`ccx2paraview`: https://github.com/calculix/ccx2paraview
.. _`Sierra`: https://www.osti.gov/biblio/1886996
.. _`Quinoa`: https://quinoacomputing.github.io/index.html
.. _`Fierro`: https://lanl.github.io/Fierro/index.html
.. _`FierroMechanics`: https://anaconda.org/fierromechanics
.. _`Environment modules`: https://modules.readthedocs.io/en/stable/modulefile.html
.. _`GNU Make`: https://www.gnu.org/software/make/
.. _`GNU sed`: https://www.gnu.org/software/sed/
.. _`GNU tar`: https://www.gnu.org/software/tar/
.. _`conda-forge sed`: https://anaconda.org/conda-forge/sed
.. _`Gitlab`: https://about.gitlab.com/
.. _`Gitlab Flow`: https://docs.gitlab.com/ee/topics/gitlab_flow.html
.. _`GitHub`: https://github.com/
.. _`Bitbucket`: https://www.atlassian.com/software/bitbucket
.. _`Gmsh`: https://gmsh.info/
.. _`Granta STK`: https://int.lanl.gov/projects/W13docs/GrantaSTK/#t=streamlined%2Fwelcome_to_v2.htm
.. _`Granta/MIMS`: http://grantami.lanl.gov/mi
.. _`pytest JUnit XML output`: https://docs.pytest.org/en/7.1.x/how-to/output.html#creating-junitxml-format-files
.. _`LaTeX`: https://www.latex-project.org/
.. _`Markdown`: https://daringfireball.net/projects/markdown/
.. _`Material Database`: https://ddw-confluence.lanl.gov/display/MD/Material+Database
.. _`Material Models members`: https://re-git.lanl.gov/groups/aea/material-models/-/group_members
.. _`Material Models`: https://re-git.lanl.gov/aea/material-models
.. _`meshio`: https://github.com/nschloe/meshio
.. _`MPI`: https://www.mpi-forum.org/
.. _`pandas`: https://pandas.pydata.org/
.. _`PEP-257`: https://peps.python.org/pep-0257/
.. _`PEP-287`: https://peps.python.org/pep-0287/
.. _`PEP-440`: https://www.python.org/dev/peps/pep-0440/
.. _`PEP-8`: https://www.python.org/dev/peps/pep-0008/
.. _`pytest`: https://docs.pytest.org/
.. _`PYTHONPATH`: https://docs.python.org/3/library/sys.html#sys.path
.. _`Python 2.7 argparse`: https://docs.python.org/2.7/library/argparse.html
.. _`Python 3 argparse`: https://docs.python.org/3/library/argparse.html
.. _`Python 2`: https://docs.python.org/2.7/
.. _`Python 3`: https://docs.python.org/3.12/
.. _`Python Modules`: https://docs.python.org/3/tutorial/modules.html
.. _`Python Template Strings`: https://docs.python.org/3/library/string.html#template-strings
.. _`Python Top-Level Code Environment`: https://docs.python.org/3/library/__main__.html
.. _`Python argparse`: https://docs.python.org/3/library/argparse.html
.. _`Python documentation`: https://docs.python.org/3/index.html
.. _`Python pathlib`: https://docs.python.org/3/library/pathlib.html
.. _`Python sys`: https://docs.python.org/3/library/sys.html
.. _`Python`: https://www.python.org/
.. _`Python lambda expression`: https://docs.python.org/3/tutorial/controlflow.html#lambda-expressions
.. _`Python generator expressions`: https://docs.python.org/3/tutorial/classes.html#generator-expressions
.. _`SALib.sample`: https://salib.readthedocs.io/en/latest/api.html#
.. _`SALib.analyze`: https://salib.readthedocs.io/en/latest/api/SALib.analyze.html
.. _`SALib sobol`: https://salib.readthedocs.io/en/latest/api.html#sobol-sensitivity-analysis
.. _`SALib morris`: https://salib.readthedocs.io/en/latest/api.html#method-of-morris
.. _`scipy Sobol`: https://docs.scipy.org/doc/scipy/reference/generated/scipy.stats.qmc.Sobol.html
.. _`scipy Latin Hypercube`: https://docs.scipy.org/doc/scipy/reference/generated/scipy.stats.qmc.LatinHypercube.html
.. _`scipy.stats`: https://docs.scipy.org/doc/scipy/reference/stats.html
.. _`scipy.stats.qmc`: https://docs.scipy.org/doc/scipy/reference/stats.qmc.html
.. _`SCons AddPostAction`: https://scons.org/doc/production/HTML/scons-user.html#app-functions
.. _`SCons AddPreAction`: https://scons.org/doc/production/HTML/scons-user.html#app-functions
.. _`SCons Builders`: https://scons.org/doc/production/HTML/scons-user/ch17.html
.. _`SCons Emitters`: https://scons.org/doc/production/HTML/scons-user.html#id1459
.. _`SCons Command`: https://scons.org/doc/production/HTML/scons-user/ch18.html
.. _`SCons CheckProg`: https://scons.org/doc/production/HTML/scons-user.html#id1476
.. _`SCons Copy`: https://scons.org/doc/production/HTML/scons-user/ch12.html#id1406
.. _`SCons Pseudo-Builder`: https://scons.org/doc/production/HTML/scons-user/ch19.html
.. _`SCons AddMethod`: https://scons.org/doc/production/HTML/scons-user/ch19.html
.. _`SCons Help`: https://scons.org/doc/production/HTML/scons-user/ch09.html#idp105548827004112
.. _`SCons Python build function`: https://scons.org/doc/production/HTML/scons-user/ch17s04.html
.. _`SCons PrependENVPath`: https://scons.org/doc/production/HTML/scons-user/apd.html#f-PrependENVPath
.. _`SCons AppendENVPath`: https://scons.org/doc/production/HTML/scons-user/apd.html#f-AppendENVPath
.. _`SCons Substfile`: https://scons.org/doc/production/HTML/scons-user.html#b-Substfile
.. _`SCons Alias`: https://scons.org/doc/production/HTML/scons-user/ch23.html
.. _`SCons command-line build options`: https://scons.org/doc/production/HTML/scons-user/ch10.html#idm46358236334624
.. _`SCons command-line build variables`: https://scons.org/doc/production/HTML/scons-user/ch10s02.html
.. _`SCons construction environment`: https://scons.org/doc/production/HTML/scons-user/ch07s02.html
.. _`SCons Attaching a Builder to a Construction Environment`: https://scons.org/doc/production/HTML/scons-user/ch17s02.html
.. _`SCons custom builders`: https://scons.org/doc/production/HTML/scons-user/ch17.html
.. _`SCons hierarchical build`: https://scons.org/doc/production/HTML/scons-user/ch14.html
.. _`SCons project build help`: https://scons.org/doc/production/HTML/scons-user/ch09.html#idm46358284707920
.. _`SCons sharing environments`: https://scons.org/doc/production/HTML/scons-user/ch14s05.html
.. _`SCons Node Package`: https://scons.org/doc/production/HTML/scons-api/SCons.Node/?highlight=file+object
.. _`SCons Appendix D`: https://scons.org/doc/production/HTML/scons-user/apd.html
.. _`SCons FindFile`: https://scons.org/doc/production/HTML/scons-user/ch26s04.html
.. _`SCons Python function builder`: https://scons.org/doc/production/HTML/scons-user.html#id1477
.. _`SCons SConscript`: https://scons.org/doc/production/HTML/scons-user/ch14.html
.. _`SCons Special Variables`: https://scons.org/doc/production/HTML/scons-man.html#special_variables
.. _`SCons Variable Substitution`: https://scons.org/doc/production/HTML/scons-man.html#variable_substitution
.. _`SCons Tar`: https://scons.org/doc/production/HTML/scons-man.html#b-Tar
.. _`setuptools_scm`: https://setuptools-scm.readthedocs.io/en/latest/
.. _`Tutorial: setuptools_scm`: https://lanl-aea.github.io/waves/tutorial_setuptools_scm.html
.. _`Software Carpentry`: https://software-carpentry.org/
.. _`Software Carpentry: Python Novice`: https://swcarpentry.github.io/python-novice-inflammation/
.. _`Sphinx automodule`: https://www.sphinx-doc.org/en/master/usage/extensions/autodoc.html#directive-automodule
.. _`Sphinx style guide`: https://documentation-style-guide-sphinx.readthedocs.io/en/latest/style-guide.html#
.. _`SLURM`: https://slurm.schedmd.com/
.. _`sbatch`: https://slurm.schedmd.com/sbatch.html
.. _`vtk`: https://vtk.org/
.. _`h5py`: https://www.h5py.org/
.. _`The HDF5 Group command-line-tools`: https://docs.hdfgroup.org/hdf5/develop/_view_tools_view.html
.. _`matplotlib`: https://matplotlib.org/stable/
.. _`Xarray`: https://docs.xarray.dev/en/stable/
.. _`automated build system`: https://en.wikipedia.org/wiki/List_of_build_automation_software
.. _`conda-forge`: https://conda-forge.org/
.. _`custom conda channel`: https://docs.conda.io/projects/conda/en/latest/user-guide/tasks/create-custom-channels.html
.. _`directed acyclic graph`: https://en.wikipedia.org/wiki/Directed_acyclic_graph
.. _`Git`: https://git-scm.com/
.. _`Git-LFS`: https://git-lfs.com/
.. _`numpy.corrcoef`: https://numpy.org/doc/stable/reference/generated/numpy.corrcoef.html
.. _`re docs`: https://docs.python.org/3.6/library/re.html
.. _`reStructuredText`: https://docutils.sourceforge.io/rst.html
.. _`reStructuredText Primer`: https://www.sphinx-doc.org/en/master/usage/restructuredtext/basics.html
.. _`seaborn.pairplot`: https://seaborn.pydata.org/generated/seaborn.pairplot.html
.. _`shebang`: https://en.wikipedia.org/wiki/Shebang_(Unix)
.. _`shell environment`: https://www.gnu.org/software/bash/manual/html_node/Environment.html
.. _`Sphinx`: https://www.sphinx-doc.org/en/master/
.. _`Unittest Mock`: https://docs.python.org/3/library/unittest.mock.html
.. _`xarray dataset`: https://xarray.pydata.org/en/v2022.03.0/generated/xarray.Dataset.html

.. PDM/PLM
.. _`Windchill`: https://www.ptc.com/en/products/windchill
.. _`Teamcenter`: https://plm.sw.siemens.com/en-US/teamcenter/
.. _`SOLIDWORKS PDM`: https://www.solidworks.com/product/solidworks-pdm
.. _`Minerva`: https://www.ansys.com/products/connect/ansys-minerva
.. _`ENOVIA`: https://www.3ds.com/products/enovia

.. Project specific links
.. _`Gitlab project issues`: https://re-git.lanl.gov/aea/python-projects/waves/-/issues
.. _`WAVES tutorials abaqus source files`: https://github.com/lanl-aea/waves/tree/main/waves/tutorials/modsim_package/abaqus
.. _`WAVES quickstart source files`: https://github.com/lanl-aea/waves/tree/main/waves/tutorials/waves_quickstart
.. _`SCons quickstart source files`: https://github.com/lanl-aea/waves/tree/main/waves/tutorials/scons_quickstart
.. _`WAVES tutorials`: https://github.com/lanl-aea/waves/tree/main/waves/tutorials
.. _`MODSIM-TEMPLATE environment file`: https://github.com/lanl-aea/waves/blob/main/waves/modsim_template/environment.yml
.. _`upstream repository`: https://re-git.lanl.gov/aea/python-projects/waves
.. _`CITATION`: https://github.com/lanl-aea/waves/blob/main/CITATION.bib

.. Abaqus reference links
.. _`Abaqus *INCLUDE`: https://help.3ds.com/2023/english/dssimulia_established/SIMACAEKEYRefMap/simakey-r-include.htm
.. _`Abaqus Assembly Definition`: https://help.3ds.com/2023/english/dssimulia_established/SIMACAEMODRefMap/simamod-c-partassy.htm
.. _`Abaqus Element Sets`: https://help.3ds.com/2023/english/dssimulia_established/SIMACAEMODRefMap/simamod-c-element.htm?contextscope=all#simamod-c-element-t-GroupingElementsIntoElementSets-sma-topic9
.. _`Abaqus Elements Guide`: https://help.3ds.com/2023/english/dssimulia_established/SIMACAEELMRefMap/simaelm-c-ov.htm
.. _`Abaqus File Extension Definitions`: https://help.3ds.com/2023/english/dssimulia_established/SIMACAEEXCRefMap/simaexc-c-fileextensions.htm
.. _`Abaqus Model Object`: https://help.3ds.com/2023/english/dssimulia_established/SIMACAEKERRefMap/simaker-c-modelpyc.htm
.. _`Abaqus Node Sets`: https://help.3ds.com/2023/english/dssimulia_established/SIMACAEMODRefMap/simamod-c-node.htm?contextscope=all#simamod-c-node-t-GroupingNodesIntoNodeSets-sma-topic8
.. _`Abaqus Precision Level for Executables`: https://help.3ds.com/2023/english/dssimulia_established/SIMACAEANLRefMap/simaanl-c-over.htm?contextscope=all#simaanl-c-over-precision
.. _`Abaqus Python Environment`: https://help.3ds.com/2023/english/dssimulia_established/SIMACAECMDRefMap/simacmd-m-PdeUsing-sb.htm
.. _`Abaqus Scripting`: https://help.3ds.com/2023/english/dssimulia_established/SIMACAECMDRefMap/simacmd-c-ov.htm
.. _`Abaqus Standard/Explicit Execution`: https://help.3ds.com/2023/english/dssimulia_established/simacaeexcrefmap/simaexc-c-analysisproc.htm
.. _`Mesh Convergence`: https://help.3ds.com/2023/english/dssimulia_established/simacaegsarefmap/simagsa-c-ctmmeshconverg.htm

.. email addresses
.. _`w13dev`: w13dev@lanl.gov
.. _`Christopher Long`: cclong@lanl.gov
