From 183a1029f2d8368a5c7899cd1306abe6677ba448 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?B=C3=A9r=C3=A9nice=20Batut?= Date: Tue, 31 Oct 2023 14:56:10 +0100 Subject: [PATCH] Apply suggestions from code review Co-authored-by: Nicola Soranzo --- bin/extract_galaxy_tools.py | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/bin/extract_galaxy_tools.py b/bin/extract_galaxy_tools.py index 15dcfb24..eb905ae4 100644 --- a/bin/extract_galaxy_tools.py +++ b/bin/extract_galaxy_tools.py @@ -144,8 +144,8 @@ def check_categories(ts_categories, ts_cat): return True -def get_tool_metadata(tool, repo): - """" " +def get_tool_metadata(tool: ContentFile, repo: Repository) -> : + """ Get tool metadata from the .shed.yaml, requirements in the macros or xml file, bio.tools information if available in the macros or xml, EDAM annotations using bio.tools API, recent conda version using conda API @@ -274,7 +274,7 @@ def get_tool_metadata(tool, repo): return metadata -def parse_tools(repo): +def parse_tools(repo: Repository): """ Parse tools in a GitHub repository, extract them and their metadata @@ -352,7 +352,7 @@ def export_tools(tools: list, output_fp: str) -> None: df.to_csv(output_fp, sep="\t", index=False) -def filter_tools(tools, ts_cat, excluded_tools, keep_tools): +def filter_tools(tools, ts_cat: List[str], excluded_tools: List[str], keep_tools: List[str]): """ Filter tools for specific ToolShed categories and add information if to keep or to exclude