biosimulators_utils.gh_action package

Submodules

biosimulators_utils.gh_action.core module

Utilities for GitHub action workflows for reviewing and committing simulators to the BioSimulators registry

Author:

Jonathan Karr <karr@mssm.edu>

Date:

2020-12-08

Copyright:

2020, Center for Reproducible Biomedical Modeling

License:

MIT

class biosimulators_utils.gh_action.core.GitHubAction

Bases: ABC

A GitHub continuous integration action

gh_auth

authorization for GitHub (user and access token

Type:

tuple of str

gh_repo

owner and name of the repository which triggered the action

Type:

str

GH_ACTION_RUN_URL = 'https://github.com/{}/actions/runs/{}'

ISSUE_ASIGNEES_ENDPOINT = 'https://api.github.com/repos/{}/issues/{}/assignees'

ISSUE_COMMENTS_ENDPOINT = 'https://api.github.com/repos/{}/issues/{}/comments'

ISSUE_ENDPOINT = 'https://api.github.com/repos/{}/issues/{}'

ISSUE_LABELS_ENDPOINT = 'https://api.github.com/repos/{}/issues/{}/labels'

classmethod add_comment_to_issue(issue_number: str, comment: str)

Post a comment to the GitHub issue

Parameters:

• issue_number (str) – issue number

• comment (str) – comment

classmethod add_error_comment_to_issue(issue_number, comments, raise_error=True)

Post an error to the GitHub issue

Parameters:

• issue_number (str) – issue number

• comments (list of Comment) – comment

• raise_error (bool, optional) – if True, raise error

Raises:

ValueError –

classmethod add_labels_to_issue(issue_number: str, labels: list[str]) → None

Add one or more labels to an issue

Parameters:

• issue_number (str) – issue number

• labels (list of str) – labels to add to the issue

classmethod assign_issue(issue_number, users)

Assign an issue to a list of users

Parameters:

• issue_number (str) – issue number

• users (list of str) – GitHub ids of users to assign to issue

classmethod close_issue(issue_number)

Close a GitHub issue

Parameters:

issue_number (str) – issue number

classmethod format_error_comment(comment)

Format comment to display as error

Parameters:

comment (str) – comment to format as error

Returns:

formatted comment

Return type:

str

static get_data_in_issue(issue: Dict[str, _JSONValue])

Get the YAML-structured data in an issue

Parameters:

issue (dict) – properties of the GitHub issue for the submission in json format

Returns:

YAML-structured data in an issue (as dict)

Return type:

object

static get_gh_action_run_id()

Get the id for the current GitHub action run

Returns:

GitHub action run id

Return type:

str

classmethod get_gh_action_run_url()

Get the URL for a GitHub action run

Returns:

URL for a GitHub action run

Return type:

str

static get_gh_auth()

Get authorization for GitHub

Returns:

authorization for GitHub (user and access token)

Return type:

tuple of str

static get_gh_repo() → str

Get the owner and name of the repository which triggered the action

Returns:

owner and name of the repository which triggered the action

Return type:

str

classmethod get_issue(issue_number: str) → Dict[str, _JSONValue]

Get the properties of the GitHub issue for the submission

Parameters:

issue_number (str) – issue number

Returns:

properties of the GitHub issue for the submission in json format

Return type:

dict

static get_issue_number() → str

Get the number of the issue which triggered the action

Returns:

issue number

Return type:

str

classmethod get_labels_for_issue(issue_number: str) → list[str]

Get the labels for an issue

Parameters:

issue_number (str) – issue number

Returns:

labels

Return type:

list of str

classmethod remove_label_from_issue(issue_number: str, label)

Remove a label from an issue

Parameters:

• issue_number (str) – issue number

• label (str) – label to remove from the issue

classmethod reset_issue_labels(issue_number: str, labels_to_remove: list[str])

Reset the labels for an issue

Parameters:

• issue_number (str) – issue number

• labels_to_remove (list of str) – labels to remove

abstract run()

class biosimulators_utils.gh_action.core.GitHubActionErrorHandling

Bases: object

Methods for handing errors in the execution of GitHu actions

classmethod catch_errors(uncaught_exception_msg_func=None, caught_error_labels=None, uncaught_error_labels=None)

Generator for a decorator for CI actions that catches errors and reports them as comments to an issue

Parameters:

• uncaught_exception_msg_func (types.FunctionType, optional) – function to calculate error message to display to users

• caught_error_labels (list of str, optional) – labels to apply to caught errors

• uncaught_error_labels (list of str, optional) – labels to apply to uncaught errors

get_uncaught_exception_msg()

Create an error message to display to users for all exceptions not caught during the exception of the run method for a GitHub action workflow (exceptions of all types except GitHubActionCaughtError)

Parameters:

exception (Exception) – a failure encountered during the exception of the run method for the workflow

Returns:

error message to display to users

Return type:

str

biosimulators_utils.gh_action.data_model module

Data model for GitHub action workflows

Author:

Jonathan Karr <karr@mssm.edu>

Date:

2020-12-08

Copyright:

2020, Center for Reproducible Biomedical Modeling

License:

MIT

class biosimulators_utils.gh_action.data_model.Comment(text: str | None = None, error: bool | None = None)

Bases: object

A comment on an issue

text

text

Type:

str

error

if True, format as error

Type:

bool

exception biosimulators_utils.gh_action.data_model.GitHubActionCaughtError

Bases: BioSimulatorsException

An error caught during the execution of a GitHub action