tardigrade_vector_tools

Project Description

A collection of tools for C++ that make interfacing with vectors easier and less prone to error. These tools also allow the user access to the powerful Eigen library which provides matrix utilities in such a way that Eigen does not need to be used explicitly in the user's code.

Information

• Documentation: https://aea.re-pages.lanl.gov/material-models/tardigrade_vector_tools
• Wiki: https://re-git.lanl.gov/aea/material-models/tardigrade_vector_tools/-/wikis/home

Developers

• Nathan Miller [email protected]
• Kyle Brindley [email protected]

Dependencies

Executables

• CMake >= 3.14
• Doxygen >= 1.8.5
• LaTeX >= 2017

Python Modules (for documentation)

For convenience, the minimal Python environment requirements for the documentation build are included in configuration_files/environment.yaml. This file was created from the pipreqs command line tool and Sphinx configuration inspection, e.g. the extension packages.

$ pwd
path/to/tardigrade_vector_tools/
$ pipreqs --use-local --print --no-pin .

A minimal anaconda environment for building the documentation can be created from an existing anaconda installation with the following commands.

$ conda create --file environment.txt

You can learn more about Anaconda Python environment creation and management in the Anaconda Documentation.

C++ Libraries

> NOTE: Non-admin installations for Eigen and Boost are no longer required. This project is built and deployed > against C++ libraries managed in Conda. See the Conda environment file and README discussion for non-admin environment > management.

• Eigen >= 3.3.7
• BOOST >= 1.53.0

Building the documentation

Warning

API Health Note: The Sphinx API docs are a work-in-progress. The doxygen API is much more useful

Build on sstelmo

1. Activate the correct python environment

   $ module use /projects/aea_compute/modulefiles
   $ module load tardigrade_vector_tools-env

2. Create the build directory and move there

   $ pwd
   /path/to/tardigrade_vector_tools/
   $ mkdir build/
   $ cd build/

3. Run cmake configuration

   $ pwd
   /path/to/tardigrade_vector_tools/build/
   $ cmake ..

4. Display target options

   $ pwd
   /path/to/cpp_stub/build
   $ cmake --build . --target help

4. Build various portions of the project

   Most of the project will re-build only as necessary after source updates. Some portions of the documentation require a cmake --build . --target clean after documentation source file updates to force a re-build.

   $ pwd
   /path/to/cpp_stub/build
   
   # Build everything (either or)
   $ cmake --build .
   $ cmake --build . --target all

5. Sphinx HTML Documentation builds to:

   tardigrade_vector_tools/build/docs/sphinx/html/index.html

6. Display docs

   $ pwd
   /path/to/tardigrade_vector_tools/build/
   $ firefox docs/sphinx/html/index.html &

7. While the Sphinx API is still a WIP, try the doxygen API

   $ pwd
   /path/to/tardigrade_vector_tools/build/
   $ firefox docs/doxygen/html/index.html &

---

Install the library

Build the entire before performing the installation.

4. Build the entire project

   $ pwd
   /path/to/cpp_stub/build
   $ cmake --build .

5. Install the library

   $ pwd
   /path/to/cpp_stub/build
   $ cmake --install . --prefix path/to/root/install
   
   # Example local user (non-admin) Linux install
   $ cmake --install . --prefix /home/$USER/.local
   
   # Example install to conda environment
   $ conda activate my_env
   $ cmake --install . --prefix ${CONDA_PREFIX}

Contribution Guidelines

Git Commit Message

Begin Git commit messages with one of the following headings:

• BUG: bug fix
• DOC: documentation
• FEAT: feature
• MAINT: maintenance
• TST: tests
• REL: release
• WIP: work-in-progress

For example:

git commit -m "DOC: adds documentation for feature"

Git Branch Names

When creating branches use one of the following naming conventions. When in doubt use feature/<description>.

• bugfix/\<description>
• feature/\<description>
• release/\<description>

reStructured Text

Sphinx reads in docstrings and other special portions of the code as reStructured text. Developers should follow styles in this Sphinx style guide`_.

Style Guide

This project does not yet have a full style guide. Generally, wherever a style can't be inferred from surrounding code this project falls back to PEP-8 -like styles. There are two notable exceptions to the notional PEP-8 fall back:

1. Doxygen style docstrings are required for automated, API from source documentation.
2. This project prefers expansive whitespace surrounding parentheses, braces, and brackets.
   • No leading space between a function and the argument list.
   • One space following an open paranthesis (, brace {, or bracket [
   • One space leading a close paranthesis ), brace }, or bracket ]

An example of the whitespace style:

my_function( arg1, { arg2, arg3 }, arg4 );

The following sed commands may be useful for updating white space, but must be used with care. The developer is recommended to use a unique git commit between each command with a corresponding review of the changes and a unit test run.

• Trailing space for open paren/brace/bracket

  sed -i 's/\([({[]\)\([^ ]\)/\1 \2/g' <list of files to update>

• Leading space for close paren/brace/bracket

  sed -i 's/\([^ ]\)\([)}\]]\)/\1 \2/g' <list of files to update>

• White space between adjacent paren/brace/bracket

  sed -i 's/\([)}\]]\)\([)}\]]\)/\1 \2/g' <list of files to update>