bridge.pipelines.bt2gh_for_pr_issues.map_funcs.functions module

bridge.pipelines.bt2gh_for_pr_issues.map_funcs.functions module#

Map function annotations from bio.tools to GitHub.

This module compares the function annotations recorded in bio.tools with the GitHub README and, when appropriate, proposes a GitHub issue suggesting that the bio.tools function annotations be added to the README.

bridge.pipelines.bt2gh_for_pr_issues.map_funcs.functions.map_functions(gh_readme, bt_functions)[source]#

Propose a GitHub issue to add function annotations based on bio.tools metadata.

Steps performed: 1. Check if the README already mentions functions using the FUNCTION_PATTERN.

If it does, no issue is needed.

  1. If no functions are found in bio.tools, no issue is needed.

  2. If functions are present in bio.tools but not mentioned in the README, build

    a function string for each function and propose an issue to add them to the README.

Parameters:

  • gh_readme (str | None) – The current README content from GitHub, or None if the file does not exist yet.

  • bt_functions (list[FunctionItem] | None) – The list of FunctionItems from bio.tools metadata, or None if no functions are defined.

Returns:

A dictionary with the issue title as key and the issue body as value, or None if no issue is to be created.

Return type:

dict[str, str] | None

bridge.pipelines.bt2gh_for_pr_issues.map_funcs.functions.map_functions_to_readme(gh_readme, bt_functions)[source]#

Propose an updated README content by adding function annotations from bio.tools metadata.

Steps performed: 1. Check if README exists; if not, no update is needed. 2. Check if the README already mentions functions using the FUNCTION_PATTERN.

If it does not, no update is needed.

  1. If no functions are found in bio.tools, no update is needed.

  2. If functions are present in bio.tools and the README mentions functions,

    remove all existing function blocks from the README.

  3. In their place, add new function blocks for each function from bio.tools.

    The new function blocks are built using the FUNCTION_TEMPLATE and the function data from bio.tools.

This function is intended to be used in the construction of a README update for a PR, where the updated README content is proposed directly rather than suggesting the update via an issue. See readme module for the usage of this function in the context of a README update.

Parameters:

  • gh_readme (str | None) – The current README content from GitHub, or None if the file does not exist yet.

  • bt_functions (list[FunctionItem] | None) – The list of FunctionItems from bio.tools metadata, or None if no functions are defined.

Returns:

The updated README content with function annotations added, or the original README content if no update is needed.

Return type:

str | None

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