From b806367aa7c83199ba51e98a75bcfea5120f5216 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?B=C3=A9r=C3=A9nice=20Batut?= <bebatut@gmail.com>
Date: Tue, 31 Oct 2023 13:08:38 +0100
Subject: [PATCH] Fix linting

---
 bin/extract_galaxy_tools.py | 33 +++++++++++++++++++++------------
 1 file changed, 21 insertions(+), 12 deletions(-)

diff --git a/bin/extract_galaxy_tools.py b/bin/extract_galaxy_tools.py
index e28449ac..e0656f5c 100644
--- a/bin/extract_galaxy_tools.py
+++ b/bin/extract_galaxy_tools.py
@@ -135,7 +135,7 @@ def check_categories(ts_categories, ts_cat):
     :param ts_cat: list of ToolShed categories to keep in the extraction
     """
     if ts_categories is not None and len(ts_cat) > 0:
-        ts_cats = ts_categories.split(', ')
+        ts_cats = ts_categories.split(", ")
         to_keep = False
         for cat in ts_cats:
             if cat in ts_cat:
@@ -145,12 +145,10 @@ def check_categories(ts_categories, ts_cat):
 
 
 def get_tool_metadata(tool, repo):
-    """"
-    Get tool information
-    - Check the `.shed.yaml` file
-    - Extract metadata from the `.shed.yaml`
-    - Extract the requirements in the macros or xml file to get tool version supported in Galaxy
-    - Extract bio.tools information if available in the macros or xml
+    """" "
+    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
 
     :param tool: GitHub ContentFile object
     :param repo: GitHub Repository object
@@ -174,7 +172,7 @@ def get_tool_metadata(tool, repo):
         "Galaxy wrapper source": None,
         "Galaxy wrapper version": None,
         "Conda id": None,
-        "Conda version": None
+        "Conda version": None,
     }
     # extract .shed.yml information and check macros.xml
     try:
@@ -368,7 +366,9 @@ def filter_tools(tools, ts_cat, excluded_tools, keep_tools):
 
 
 if __name__ == "__main__":
-    parser = argparse.ArgumentParser(description="Extract Galaxy tools from GitHub repositories together with biotools and conda metadata")
+    parser = argparse.ArgumentParser(
+        description="Extract Galaxy tools from GitHub repositories together with biotools and conda metadata"
+    )
     subparser = parser.add_subparsers(dest="command")
     # Extract tools
     extractools = subparser.add_parser("extractools", help="Extract tools")
@@ -376,10 +376,19 @@ def filter_tools(tools, ts_cat, excluded_tools, keep_tools):
     extractools.add_argument("--all_tools", "-o", required=True, help="Filepath to CSV with all extracted tools")
     # Filter tools
     filtertools = subparser.add_parser("filtertools", help="Filter tools")
-    filtertools.add_argument("--tools", "-t", required=True, help="Filepath to CSV with all extracted tools, generated by extractools command")
+    filtertools.add_argument(
+        "--tools",
+        "-t",
+        required=True,
+        help="Filepath to CSV with all extracted tools, generated by extractools command",
+    )
     filtertools.add_argument("--filtered_tools", "-f", required=True, help="Filepath to CSV with filtered tools")
-    filtertools.add_argument("--categories", "-c", help="Path to a file with ToolShed category to keep in the extraction (one per line)")
-    filtertools.add_argument("--exclude", "-e", help="Path to a file with ToolShed ids of tools to exclude (one per line)")
+    filtertools.add_argument(
+        "--categories", "-c", help="Path to a file with ToolShed category to keep in the extraction (one per line)"
+    )
+    filtertools.add_argument(
+        "--exclude", "-e", help="Path to a file with ToolShed ids of tools to exclude (one per line)"
+    )
     filtertools.add_argument("--keep", "-k", help="Path to a file with ToolShed ids of tools to keep (one per line)")
     args = parser.parse_args()