Fix linting (#161)

* Add docstrings

* Fix linting

* Black/isort formatting

* Type annotate functions

* More type annotations

* Fix line break

subdomains/scripts/parse_tools_to_produce_yml_files.py

@@ -2,45 +2,47 @@
 installation.
 """
 
-import yaml
+import argparse
 import os
 import re
-import argparse
 
 import tools_au
+import yaml
 
 parser = argparse.ArgumentParser(
-    description='Create installation yaml files from a Yaml file containing'
-    ' the panel_view/Toolkit data')
-parser.add_argument('--tk', action="store", dest='toolkit',
-                    help='Path of the toolkit.yaml file')
-parser.add_argument('--yml-folder', action="store", dest='dest',
-                    help='Folder containing the yml files with tool installed'
-                    ' in the target instance')
+    description="Create installation yaml files from a Yaml file containing the panel_view/Toolkit data"
+)
+parser.add_argument("--tk", action="store", dest="toolkit", help="Path of the toolkit.yaml file")
+parser.add_argument(
+    "--yml-folder",
+    action="store",
+    dest="dest",
+    help="Folder containing the yml files with tool installed" " in the target instance",
+)
 args = parser.parse_args()
 
 print(args.toolkit)
 print(args.dest)
 
-with open(args.toolkit, 'r') as stream:
+with open(args.toolkit) as stream:
     data_loaded = yaml.safe_load(stream)
 
-for i in range(3, len(data_loaded['items']) - 2):
-    section = data_loaded['items'][i]['id']
-    name = data_loaded['items'][i]['name']
+for i in range(3, len(data_loaded["items"]) - 2):
+    section = data_loaded["items"][i]["id"]
+    name = data_loaded["items"][i]["name"]
     f = open(section + ".yml", "w")
     f.write("tool_panel_section_label: " + name + "\ntools:\n")
-    for j in data_loaded['items'][i]['items']:  # for loop on toolkit sections
-        path = j['id']
-        infos = path.replace('toolshed.g2.bx.psu.edu/repos/', "")
+    for j in data_loaded["items"][i]["items"]:  # for loop on toolkit sections
+        path = j["id"]
+        infos = path.replace("toolshed.g2.bx.psu.edu/repos/", "")
         # extract the owner (group1) and the name of the tool (group2)
         pattern = re.compile(r"([^\/]+)\/([^\/]+)\/")
         for match in pattern.finditer(infos):  # for each tool in the seection
             owner = match.group(1)
             tool = match.group(2)
             # verify the tool is not already installed
             installed = os.popen('grep -r "' + tool + '" ' + args.dest).read()
-            if installed == '':  # if tool not installed
+            if installed == "":  # if tool not installed
                 f.write("- name: " + tool + "\n")
                 f.write("  owner: " + owner + "\n")
     f.close()

subdomains/scripts/tools_au.py

@@ -1,49 +1,59 @@
 """Convert YAML files for install on AU.
 
-Assumes that wdir contains tool yaml files.
+Assumes that wdir contains tool yaml files produced by the
+parse_tools_to_produce_yml_files.py script, they should look like:
+<tool_section_1>.yml
+<tool_section_1>.yml.lock
+<tool_section_2>.yml
+<tool_section_2>.yml.lock
+...
+
+See subdomains/singlecell/tool_panel for example.
 """
 
-import yaml
 from pathlib import Path
 
+import yaml
+
 WDIR = Path(__file__).parent
 EXCLUDE_KEYS = [
-    'install_repository_dependencies',
-    'tool_panel_section_label',
+    "install_repository_dependencies",
+    "tool_panel_section_label",
 ]
-OUTPUT_FILE = WDIR / 'usegalaxy.org.au.yml'
+OUTPUT_FILE = WDIR / "usegalaxy.org.au.yml"
 
 
-def parse():
-    data = {'tools': []}
-    for f in WDIR.glob('*.yml.lock'):
-        if not f.name.endswith('.yml.lock'):
+def parse() -> None:
+    """Parse tools list from YAML files."""
+    data: dict = {"tools": []}
+    for f in WDIR.glob("*.yml.lock"):
+        if not f.name.endswith(".yml.lock"):
             continue
         print(f"Extracting data from {f}...")
-        with open(f, 'r') as handle:
+        with open(f) as handle:
             section_data = yaml.safe_load(handle)
-        section_data['tools'] = [
-            _transcribe_to_au(x) for x in section_data['tools']
-        ]
+        section_data["tools"] = [_transcribe_to_au(x) for x in section_data["tools"]]
         for key in EXCLUDE_KEYS:
             section_data.pop(key)
-        data['tools'] += section_data['tools']
-    for key in ('install_resolver_dependencies', 'install_tool_dependencies'):
+        data["tools"] += section_data["tools"]
+    for key in ("install_resolver_dependencies", "install_tool_dependencies"):
         data[key] = section_data[key]
     write_data(data)
-    print(f'Data transcribed and written to {OUTPUT_FILE}')
+    print(f"Data transcribed and written to {OUTPUT_FILE}")
 
 
-def _transcribe_to_au(tool):
-    tool['tool_panel_section_label'] = 'Single-Cell'
-    tool.pop('tool_panel_section_id')
+def _transcribe_to_au(tool: dict) -> dict:
+    """Convert keys to AU installation format."""
+    tool["tool_panel_section_label"] = "Single-Cell"
+    tool.pop("tool_panel_section_id")
     return tool
 
 
-def write_data(data):
-    with open(OUTPUT_FILE, 'w') as handle:
+def write_data(data: dict) -> None:
+    """Write data to YAML output file."""
+    with open(OUTPUT_FILE, "w") as handle:
         yaml.dump(data, handle, default_flow_style=False)
 
 
-if __name__ == '__main__':
+if __name__ == "__main__":
     parse()