cli¶
Bioconda Utils Command Line Interface
Functions
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Updates recipes in recipe_folder |
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Build a Bioconductor recipe. |
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Locally accedd bioconda-bot command API |
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Cleans skeletons created by |
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Export the DAG of packages to a graph format file for visualization |
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Print recipes dependent on a package |
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Lint recipes |
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Detect packages in bioconda that have duplicates in the other defined channels. |
Adds the paremeter |
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Adds the parameter |
Adds the parameter |
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Gets list of paths to recipe folders to be built |
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Gets list of modified recipes according to git_range and blacklist |
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Adds optional positional arguments recipe_folder and config |
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Bump a package build number and all dependencies as required due to a change in pinnings |
Documentation
- bioconda_utils.cli.enable_logging(default_loglevel='info', default_file_loglevel='debug')[source]¶
Adds the parameter
--loglevel
and sets up logging- Parameters:
default_loglevel – loglevel used when –loglevel is not passed
- bioconda_utils.cli.enable_debugging()[source]¶
Adds the paremeter
--pdb
(or-P
) to enable dropping into PDB
- bioconda_utils.cli.enable_threads()[source]¶
Adds the parameter
--threads
(or-t
) to limit parallelism
- bioconda_utils.cli.recipe_folder_and_config(allow_missing_for=None)[source]¶
Adds optional positional arguments recipe_folder and config
Requires that func has synopsis
def x(recipe_folder, config,...)
.
- bioconda_utils.cli.get_recipes_to_build(git_range, recipe_folder)[source]¶
Gets list of modified recipes according to git_range and blacklist
- bioconda_utils.cli.get_recipes(config, recipe_folder, packages, git_range)[source]¶
Gets list of paths to recipe folders to be built
Considers all recipes matching globs in packages, constrains to recipes modified or unblacklisted in the git_range if given, then removes blacklisted recipes.
- bioconda_utils.cli.duplicates(config, strict_version=False, strict_build=False, dryrun=False, remove=False, url=False, channel='bioconda')[source]¶
Detect packages in bioconda that have duplicates in the other defined channels.
- bioconda_utils.cli.do_lint(recipe_folder, config, packages='*', cache=None, list_checks=False, exclude=None, push_status=False, user='bioconda', commit=None, push_comment=False, pull_request=None, repo='bioconda-recipes', git_range=None, full_report=False, try_fix=False)[source]¶
Lint recipes
If –push-status is not set, reports a TSV of linting results to stdout. Otherwise pushes a commit status to the specified commit on github.
- bioconda_utils.cli.dag(recipe_folder, config, packages='*', format='gml', hide_singletons=False)[source]¶
Export the DAG of packages to a graph format file for visualization
- bioconda_utils.cli.update_pinning(recipe_folder, config, packages='*', skip_additional_channels=None, skip_variants=None, max_bumps=None, no_leaves=False, cache=None)[source]¶
Bump a package build number and all dependencies as required due to a change in pinnings
- bioconda_utils.cli.dependent(recipe_folder, config, restrict=False, dependencies=None, reverse_dependencies=None)[source]¶
Print recipes dependent on a package
- bioconda_utils.cli.bioconductor_skeleton(recipe_folder, config, package, bioc_data_packages, versioned=False, force=False, pkg_version=None, bioc_version=None, recursive=False, skip_if_in_channels=['conda-forge', 'bioconda'])[source]¶
Build a Bioconductor recipe. The recipe will be created in the ‘recipes’ directory and will be prefixed by “bioconductor-”. If –recursive is set, then any R dependency recipes will be prefixed by “r-“.
These R recipes must be evaluated on a case-by-case basis to determine if they are relevant to biology (in which case they should be submitted to bioconda) or not (submit to conda-forge).
- Biology-related:
‘bioconda-utils clean-cran-skeleton <recipe> –no-windows’ and submit to Bioconda.
- Not bio-related:
‘bioconda-utils clean-cran-skeleton <recipe>’ and submit to conda-forge.
- bioconda_utils.cli.clean_cran_skeleton(recipe, no_windows=False)[source]¶
Cleans skeletons created by
conda skeleton cran
.Before submitting to conda-forge or Bioconda, recipes generated with
conda skeleton cran
need to be cleaned up: comments removed, licenses fixed, and other linting.Use –no-windows for a Bioconda submission.
- bioconda_utils.cli.autobump(recipe_folder, config, packages='*', exclude=None, cache=None, failed_urls=None, unparsed_urls=None, recipe_status=None, exclude_subrecipes=None, exclude_channels='conda-forge', ignore_blacklists=False, fetch_requirements=False, check_branch=False, create_branch=False, create_pr=False, only_active=False, no_shuffle=False, max_updates=0, dry_run=False, no_check_pinnings=False, no_follow_graph=False, no_check_version_update=False, no_check_pending_deps=False, sign=0, commit_as=None)[source]¶
Updates recipes in recipe_folder
- bioconda_utils.cli.bot(loglevel='info')[source]¶
Locally accedd bioconda-bot command API
To run the bot locally, use:
$ gunicorn bioconda_utils.bot:init_app_internal_celery –worker-class aiohttp.worker.GunicornWebWorker
You can append –reload to have gunicorn reload if any of the python files change.