memote.suite.cli.runner
¶
Provide commands for running the test suite on a metabolic model.
Module Contents¶
Functions¶
cli () |
Metabolic model testing command line tool. |
run (model, collect, filename, location, ignore_git, pytest_args, exclusive, skip, solver, solver_timeout, experimental, custom_tests, deployment, skip_unchanged) |
Run the test suite on a single model and collect results. |
new (directory, replay) |
Create a suitable model repository structure from a template. |
_model_from_stream (stream, filename) |
|
_test_history (model, sbml_ver, solver, solver_timeout, manager, commit, pytest_args, skip, exclusive, experimental) |
|
history (model, message, rewrite, solver, solver_timeout, location, pytest_args, deployment, commits, skip, exclusive, experimental=None) |
Re-compute test results for the git branch history. |
_setup_gh_repo (github_repository, github_username, note) |
|
_setup_travis_ci (gh_repo_name, auth_token, repo_access_token) |
|
online (note, github_repository, github_username) |
Upload the repository to GitHub and enable testing on Travis CI. |
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memote.suite.cli.runner.
cli
()[source]¶ Metabolic model testing command line tool.
In its basic invocation memote runs a test suite on a metabolic model. Through various subcommands it can further generate three types of pretty HTML reports (snapshot, diff and history), generate a model repository structure for starting a new project, and recreate the test result history.
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memote.suite.cli.runner.
run
(model, collect, filename, location, ignore_git, pytest_args, exclusive, skip, solver, solver_timeout, experimental, custom_tests, deployment, skip_unchanged)[source]¶ Run the test suite on a single model and collect results.
MODEL: Path to model file. Can also be supplied via the environment variable MEMOTE_MODEL or configured in ‘setup.cfg’ or ‘memote.ini’.
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memote.suite.cli.runner.
new
(directory, replay)[source]¶ Create a suitable model repository structure from a template.
By using a cookiecutter template, memote will ask you a couple of questions and set up a new directory structure that will make your life easier. The new directory will be placed in the current directory or respect the given –directory option.
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memote.suite.cli.runner.
_test_history
(model, sbml_ver, solver, solver_timeout, manager, commit, pytest_args, skip, exclusive, experimental)[source]¶
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memote.suite.cli.runner.
history
(model, message, rewrite, solver, solver_timeout, location, pytest_args, deployment, commits, skip, exclusive, experimental=None)[source]¶ Re-compute test results for the git branch history.
MODEL is the path to the model file.
MESSAGE is a commit message in case results were modified or added.
[COMMIT] … It is possible to list out individual commits that should be re-computed or supply a range <oldest commit>..<newest commit>, for example,
memote history model.xml “chore: re-compute history” 6b84d05..cd49c85There are two distinct modes:
1. Completely re-compute test results for each commit in the git history.
This should only be necessary when memote is first used with existing model repositories.- By giving memote specific commit hashes, it will re-compute test results for those only. This can also be achieved by supplying a commit range.