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# Developer Manual

## Clone

- GitHub

      $ git clone git@github.com:lanl-aea/waves.git

- LANL

      $ git clone ssh://git@re-git.lanl.gov:10022/aea/python-projects/waves.git

## Dependencies

The development environment dependencies are found in the project’s `environment.yml` file. For convenience, the file is reproduced here

     1channels:
     2  - fierromechanics
     3  - conda-forge
     4  - nodefaults
     5
     6dependencies:
     7  - black
     8  - boa
     9  - calculix
    10  - ccx2paraview
    11  - fierro-fe-cpu
    12  # Remove trilinos-cpu explicit requirement when Fierro package(s) resolve the missing library issue
    13  # https://re-git.lanl.gov/aea/python-projects/waves/-/issues/865
    14  - trilinos-cpu <=15
    15  - flake8
    16  - glab >=1.52
    17  - h5netcdf
    18  - h5py
    19  - ipython
    20  - lazy_loader >=0.4
    21  - matplotlib-base
    22  - meshio
    23  - mypy
    24  - networkx
    25  # Required to satisfy undocumented SALib dependencies on numpy version
    26  - numpy >=2
    27  - pandas
    28  - pip
    29  - pytest >=6
    30  - pytest-cov
    31  - pytest-xdist
    32  - python-build
    33  - python-gmsh
    34  - pyyaml
    35  # Required to satisfy undocumented SALib dependencies on numpy version
    36  - salib >=1.5.1
    37  - scipy >=1
    38  - scons >=4.6
    39  - seaborn
    40  - setuptools >=77
    41  - setuptools_scm >=8
    42  - sphinx >=7.1
    43  - sphinx-argparse
    44  - sphinx-book-theme
    45  - sphinx-copybutton >=0.5.1
    46  - sphinx-design
    47  - sphinxcontrib-bibtex
    48  - xarray >=2024.10.0
    49  # Twine from conda-forge is killed with an invalid signature on macOS
    50  - pip:
    51    - twine >=5

In addition to the Conda environment managed packages, this project also requires a separately managed installation of TeXLive to build the PDF documentation.

The tutorials in this project may also require:

1. Abaqus

2. Cubit

3. Matlab

## Activate Environment

The Conda packages found in `environment.yml` are reproduced in the Dependencies section.

### Local development environments

SCons can be installed in a Conda environment with the Conda package manager. See the Conda installation and Conda environment management documentation for more details about using Conda.

1. Create the environment if it doesn’t exist

       $ pwd
       path/to/local/git/clone/waves
       $ conda env create --name waves-env --file environment.yml

2. Activate the environment

       $ conda activate waves-env

In addition to the primary development environment file `environment.yml`, several other environment files are maintained for CI jobs. For Windows developers, `environment-win.yml` removes packages that are not available for Windows and packages that are only necessary for deployment jobs. The `conda-build.yml` and `pip-build.yml` are stripped down to the bare essentials for building Conda and pip packages, respectively.

### AEA CI server environment

The AEA CI server environment is created under the default Gitlab-Runner user in the Gitlab-Runner build directory and is not available for developers. The AEA CI jobs use a mix of the `environment.yml`, `conda-build.yml`, and `pip-build.yml` files. AEA RHEL developers may use the full `environment.yml` file to create a local development environment that closely mirrors the linux CI environment.

By default, Conda creates `~/.conda/pkgs` for the package cache, which can grow quite large. If a user’s home directory space is limited, developers are highly encouraged to configure Conda to use their projects space for the package cache, e.g. with a `~/.condarc` file using the template below, where the text `${user}` is replaced by the user name.

    envs_dirs:
      - /projects/${user}/conda/envs

    pkgs_dirs:
      - /projects/${user}/conda/pkgs

AEA developers may then create a local development environment with the following commands

    $ source /apps/miniconda3/3.13-miniconda-25.5.1/etc/profile.d/conda.sh
    $ conda env create --name waves-env --file environment.yml
    $ conda activate waves-env

See the CI job Anaconda `conda_installation` path in `.pipeline-common.yml` for the current AEA Anaconda path and version used by the AEA CI server.

### HPC CI server environment

For computing policy reasons, HPC CI pipelines are owned by the launching user and launched with the user’s account. The HPC CI server environment is created in the user owned CI job directory, which is cleaned out for each CI job. This means there is no shared environment available on HPC and developers must create and mantain their own development environment. It is strongly recommended that developers create this environment in their scratch space, e.g. `${system_scratch}/$USER/conda/envs/waves-env`.

Because the CI pipeline runs as the launching user, Conda will create a package and environment cache according to the user’s HPC Conda configuration. By default, Conda creates `~/.conda/pkgs` for the package cache, which can grow quite large. If a user’s home directory space is limited, developers are highly encouraged to configure Conda to use their scratch space for the package cache, e.g. with a `~/.condarc` file using the template below, where the text `${user_scratch}` is replaced by the absolute path to the user’s scratch directory.

    envs_dirs:
      - ${user_scratch}/conda/envs

    pkgs_dirs:
      - ${user_scratch}/conda/pkgs

You can read more about managing the Conda package and environment cache configuration here: https://conda.io/projects/conda/en/latest/user-guide/configuration/custom-env-and-pkg-locations.html

HPC developers may then create a local development environment with the following commands

    $ source /udsl/udsl1/hpcsoft/common/x86_64/anaconda/2024.10-python-3.12/etc/profile.d/conda.sh
    $ conda env create --name waves-env --file environment.yml
    $ conda activate waves

See the CI job Anaconda `conda_installation` path in `.pipeline-hpc.yml` for the current AEA Anaconda path and version used by the AEA CI server.

### Windows CI environment

The Windows CI server must have a system (or Gitlab-Runner user) installation of the following software separately from the Conda environment.

- Git

- Git-LFS

- TeXLive

- Anaconda/Miniconda/Miniforge

The Windows CI server environment is created under the default Gitlab-Runner user in the Gitlab-Runner build directory and is not available for developers. The Windows CI jobs use a mix of the `environment-win.yml`, `conda-build.yml`, and `pip-build.yml` files. Windows developers may use `environment-win.yml` to create a local development environment that closely mirrors the linux CI environment.

### MacOS CI environment

The MacOS CI server must have a system (or Gitlab-Runner user) installation of the following software separately from the Conda environment.

- Git

- Git-LFS

- TeXLive

- Anaconda/Miniconda/Miniforge

The MacOS CI server environment is created under the default Gitlab-Runner user in the Gitlab-Runner build directory and is not available for developers. The MacOS CI jobs use a mix of the `environment.yml`, `conda-build.yml`, and `pip-build.yml` files. MacOS developers may use the full `environment.yml` file to create a local development environment that closely mirrors the linux CI environment.

## Contribution Guidelines

The WAVES project uses the Gitlab Flow [25] workflow model.

### 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 "FEAT: short intent of new feature"
    git commit -m "BUG: fixes nasty bug"
    git commit -m "DOC: adds documentation for feature"

### 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:

## Build

This project uses the SCons build system. This section will discuss some common build operations. For a full list of SCons command-line options and target build behavior, see the SCons manpage. The SCons manpage is also installed with Scons in the environment and can be opened from the command-line as `man scons` in the AEA Compute environment.

- View project specific command-line options, default targets, and aliases

      $ scons -h

- Build all default targets

      $ scons

- Build a specific target

      $ scons <target name>

- Remove the default targets’ artifacts

      $ scons --clean

- Remove all targets’ artifacts

      $ scons . --clean

This project may be built as a Conda or pip package. The Conda package is the preferred distribution and takes the default distribution name `waves`. The Conda recipe(s) will call the pip build commands directly, so it is not necessary to build the pip package first.

### pip

To build the pip package, use the `build` alias. The package artifacts will live in `build/dist`.

    $ scons build

The package distribution name may be changed from the default `waves` to something else. For instance, on PyPI the distribution name `waves` is taken by another project, so the PyPI distribution name of this project is `waves-workflows`.

    $ scons build --distribution-name=waves-workflows

For this reason the `pyproject.toml` file has been templated in the source tree as `pyproject.toml.in`. The necessary `pyproject.toml` file will be generated as necessary with the specified distribution name by the SCons `build`, `install`, `style`, and test aliases.

The `install` alias is provided for packaging in ecosystems which support data file installation outside the package directory, e.g. man pages. By default, this alias installs to a local `install/` directory, but the prefix may be set to match the recipe’s installation prefix. For instance, the Conda recipe must install to the `${PREFIX}` variable managed by `conda-build`.

    $ scons install --prefix=${PREFIX}

If a `pyproject.toml` file has been generated, the package may be built with the usual `py-build` and `pip` commands, as well. Such an installation will not include the man pages or HTML documentation and the `waves docs` subcommand will not work to launch locally installed documentation. Direct pip builds should be avoided as general practice, but may be desirable for package maintainers that require more direct control over the build and install options.

    $ scons pyproject.toml
    $ python -m build .
    $ python -m pip install dist/waves-*.tar.gz

### Conda

To build the Conda package activate the development environment and run the conda build command found in the CI configuration file. The current command may be found as

    $ sed -n '/output_folder=/,/VERSION/p' .gitlab-ci.yml .pipeline*.yml
    ...

    $ output_folder='conda-bld'
    $ mkdir ${output_folder}
    $ VERSION=$(python -m setuptools_scm) conda build recipe --channel conda-forge --no-anaconda-upload --output-folder ${output_folder}

A second recipe that bundles the LANL internally linked documentation is found in `waves/recipe-internal` and can be built similarly by replacing `recipe` with `recipe-internal` in the above command.

### Tutorials

This project contains several, separate SCons project configurations, where the `SConstruct` file name indicates an SCons project by convention. The WAVES package and documentation are defined in the `waves/SConstruct` file. The modsim template and regression tests are defined in a separate `waves/modsim_template/Sconstruct` file. The WAVES tutorials each have a tutorial specific configuration file `waves/tutorials/*SConstruct`. The following build commands apply to each, but must be run from their respective project configuration parent directories, `waves`, `waves/modsim_template` and `waves/tutorials`. The available targets and aliases differ accordingly.

When executing the tutorials or modsim template build commands directly in the repository, the WAVES project root repository must be put on `PYTHONPATH`. In personal (but not shared) virtual environments, the preferred method is to run `conda develop .` once from the project root directory. See the Conda documentation for more information about “development” mode installs. For shared environments, the preferred solution is to prefix the build commands with `PYTHONPATH=.. ``, where it is assumed that the ``PWD` is the tutorial or modsim template root directory.

    $ pwd
    /home/roppenheimer/repos/waves/waves/modsim_template
    $ PYTHONPATH=/home/roppenheimer/repos/waves scons -h

## Test

The project regression suite is collected under the `regression` alias and can be run as

    $ scons regression

By default, the system tests are configured to run with permissive skips for missing third-party software. This allows developers to run as much of the system test suite as possible on local systems with incomplete third-party software installations. To force the full execution of the system tests, a pass-through `--unconditional-build` flag may be added. This forces the documentation build, even if `sphinx-build` is missing, and passes through pytest to the system tests and tutorials as an SCons CLI option of the same name. The AEA RHEL CI server contains all necessary third-party software, so the CI tests on this server require the full build as

    $ scons regression --unconditional-build

The continuous integration server also performs a separate style guide check using `flake8` and `black` with associated aliases or the collector alias `style`.

    $ scons style

If `black` reports files that should be formatted, the following alias will format files using the same command line options as the check alias. `black` can also be run directly, but this may miss files without the `.py` extension, such as SConstruct and SConscript files. After formatting, the developer must review the changes and commit them to their branch.

    $ scons black-format

WAVES has dedicated target aliases for the unit and system tests. To run the unit tests, activate a conda environment and run

    $ scons pytest

XML and HTML coverage reports are always generated for the `pytest` alias. The XML output is used to provide coverage visualization on merge requests. The HTML output can be opened with a browser to explore coverage interactively and is uploaded to the internally hosted Gitlab-Pages documentation at: https://aea.re-pages.lanl.gov/python-projects/waves/coverage/index.html.

    $ scons pytest
    $ ls build/pytest/coverage.xml build/pytest/coverage/index.html
    build/pytest/coverage.xml  build/pytest/coverage/index.html
    $ find build/pytest -name coverage.xml -o -name index.html
    build/pytest/coverage.xml
    build/pytest/coverage/index.html

Warning

Since a v0.12.9 pre-release, the `pyproject.toml` file is templated from `pyproject.toml.in` to allow distribution name changes during packaging with `scons build`. The SCons aliases which depend on `pyproject.toml` will automatically create this templated file as necessary. However, if this file has not yet been generated, it is not possible to run the `pytest` executable directly. Run `scons pyproject.toml` or any of the testing aliases before running the test suite directly with the `pytest` command.

    $ scons pyproject.toml
    $ pytest -v -n 4 waves/_tests/test_scons_extensions.py

The tutorials and modsim template are run as system tests and require third-party software not available on conda-forge. To run the system tests, install the third-party software and make them available in your `PATH`, activate a conda environment and run

    $ scons systemtest

The full list of continuous integration test commands can be found in the Gitlab-CI files.

    $ pwd
    path/to/local/git/clone/waves/
    $ sed -n '/developer-test/,/tags/p' .gitlab-ci.yml .pipeline-*.yml

The WAVES unit and system tests may also be executed from the installation directory. These tests use pytest directly and may require non-default pytest options and markers to execute the system tests serially. The full list of CI commands may be found in the internal recipe file, `recipe-internal/meta.yaml`, under the `test` keyword. The following grep command will show the pytest commands and options.

    $ grep "pytest " recipe-internal/*

### Test Local Package

When testing CLI changes locally, the waves module must be run as a script. We must also set the `PYTHONPATH` in order to include the current waves module when operating on a configuration that imports waves.

Below is an example of a visualization test of an SConstruct file using the local waves module.

    $ pwd
    path/to/local/git/clone/waves/
    $ PYTHONPATH=$PWD python -m waves._main visualize . --sconstruct /path/to/local/SConstruct

## Documentation

The documentation build is automated with SCons as the `documentation` target. The HTML documentation builds to `waves/build/docs/html/index.html`

- Build the WAVES documentation

      $ pwd
      path/to/local/git/clone/waves/
      $ scons documentation

- Build the MODSIM-TEMPLATE documentation. The WAVES package must be on `PYTHONPATH`. For developers, the least disruptive solution is a per-command modification of `PYTHONPATH`.

      $ pwd
      path/to/local/git/clone/waves/modsim_template
      $ PYTHONPATH=/path/to/local/git/clone/waves:$PYTHONPATH scons documentation

## Windows users

This project uses symbolic links to minimize duplication of files where possible. Some files, such as the tutorial and modsim template package files, can not be shared in common due to their applications and the necessary directory structure for each. However, if the file content is identical, a symbolic link is used to avoid duplicating the entire file.

Symbolic links require special handling on Windows computers. If contributors are developing from a Windows machine, they are encouraged to

1. Read about `mklink` and “developer mode” for Windows 10/11

2. Use an up-to-date version of git

3. Use one of the following git configurations

       # Global configuration. Run from anywhere.
       > git config --global core.symlinks true

       # Local configuration. Run from repository root directory after cloning.
       > git config core.symlinks true

4. Use unix line endings with one of the following git configurations

       # Global configuration. Run from anywhere.
       > git config --global core.autocrlf true

       # Local configuration. Run from repository root directory after cloning.
       > git config core.autocrlf true

## Gitlab-CI

### AEA RHEL

There are several known AEA RHEL CI fragile false-negative failure mechanisms. If one of these failures is observed, try re-running the CI job without change.

- Conda environment creation fails in `conda-build` jobs. The shared conda command sometimes interferes with itself while running simultaneous `conda-build` jobs.

### HPC

While the system tests are run with an HPC CI pipeline, the machine and runner uptime and system test runtime are considered too fragile for reliable use. The AEA RHEL system tests pass in less than 8 minutes, but the HPC system test job has been observed to complete in under 15 minutes or time out after an hour. The HPC CI system tests are always run for merge-requests and scheduled pipelines, but the pass/fail status is not used to mark CI tests as failing. Developers are encouraged to check the HPC system test results, but not required to address failing HPC CI pipelines.

The HPC CI jobs usually run in 15-25 minutes when it runs successfully.

There are several known HPC CI fragile false-negative failure mechanisms. If one of these failures is observed, try re-running the CI job without change.

- Timeout at 1 hour

### Windows

While the system tests are run with a Windows CI pipeline, the Windows CI server does not have the full suite of third-party software required to run the full system tests. The pipeline is always run for merge-requests and scheduled pipelines, but it is considered experimental and the pass/fail status is not used to mark CI tests as failing. Developers are encouraged to check the Windows test results, but not required to address failing Windows CI pipelines.

The Windows CI jobs usually run in under 6 minutes.

There are several known Windows CI fragile false-negative failure mechanisms. If one of these failures is observed, try re-running the CI job without change.

- Incorrect or imcomplete CI environment build: `Script file 'C:\ProgramData\anaconda3\envs\waves-dev\Scripts\sphinx-build-script.py' is not present.`

### MacOS

While the system tests are run with a MacOS CI pipeline, the MacOS CI server does not have the full suite of third-party software required to run the full system tests. The pipeline is always run for merge-requests and scheduled pipelines, but it is considered experimental and the pass/fail status is not used to mark CI tests as failing. Developers are encouraged to check the MacOS test results, but not required to address failing MacOS CI pipelines.

The MacOS CI jobs usually run in under 3 minutes.