Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Feature/python typing/list.py #2214

Merged
merged 15 commits into from
Oct 18, 2023
Merged

Feature/python typing/list.py #2214

Changes from 4 commits
Commits
Show all changes
15 commits
Select commit Hold shift + click to select a range
d39ded8
test 1
NovakApis Mar 28, 2023
7b1da94
Update list.py
NovakApis Mar 28, 2023
962e60d
black + isort applied
NovakApis Mar 28, 2023
7e5aa06
Delete my_pytest.yml
NovakApis Mar 28, 2023
05dd3fe
Update nf_core/components/list.py
NovakApis Mar 28, 2023
bba34d2
__init__ arguments update
NovakApis Mar 28, 2023
9608ce9
Merge branch 'dev' into feature/python-typing/list.py
kedhammar Oct 17, 2023
4b7750a
Use casting to assume outcome of recursive .get() calls
kedhammar Oct 17, 2023
df52e63
add mypy and types to req-dev
kedhammar Oct 17, 2023
933eb76
mypy fix
kedhammar Oct 17, 2023
1a650f8
This flag is already in the .toml config
kedhammar Oct 17, 2023
48c2260
black
kedhammar Oct 17, 2023
d9fd75e
newline
kedhammar Oct 17, 2023
94704fa
Motivate cast() usage
kedhammar Oct 18, 2023
c699bb5
Merge branch 'dev' into feature/python-typing/list.py
kedhammar Oct 18, 2023
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
16 changes: 9 additions & 7 deletions nf_core/components/list.py
View file
Open in desktop
Original file line number Diff line number Diff line change
@@ -1,5 +1,6 @@
import json
import logging
from typing import Dict, List, Optional, Tuple, Union

import rich

Expand All @@ -11,11 +12,11 @@


class ComponentList(ComponentCommand):
def __init__(self, component_type, pipeline_dir, remote=True, remote_url=None, branch=None, no_pull=False):
def __init__(self, component_type, pipeline_dir, remote=True, remote_url=None, branch=None, no_pull=False) -> None:
NovakApis marked this conversation as resolved.
Show resolved Hide resolved
super().__init__(component_type, pipeline_dir, remote_url, branch, no_pull)
self.remote = remote

def list_components(self, keywords=None, print_json=False):
def list_components(self, keywords: Optional[List[str]] = None, print_json=False) -> rich.table.Table:
keywords = keywords or []
"""
Get available modules/subworkflows names from GitHub tree for repo
Expand All @@ -25,11 +26,11 @@ def list_components(self, keywords=None, print_json=False):
# self.check_component_structure(self.component_type)

# Initialise rich table
table = rich.table.Table()
table: rich.table.Table = rich.table.Table()
table.add_column(f"{self.component_type[:-1].capitalize()} Name")
components = []
components: List[str] = []

def pattern_msg(keywords):
def pattern_msg(keywords: List[str]):
if len(keywords) == 0:
return ""
if len(keywords) == 1:
Expand Down Expand Up @@ -78,11 +79,11 @@ def pattern_msg(keywords):
return ""

# Verify that 'modules.json' is consistent with the installed modules
modules_json = ModulesJson(self.dir)
modules_json: ModulesJson = ModulesJson(self.dir)
modules_json.check_up_to_date()

# Filter by keywords
repos_with_comps = {
repos_with_comps: Dict[str, List[Tuple[str, str]]] = {
repo_url: [comp for comp in components if all(k in comp[1] for k in keywords)]
for repo_url, components in modules_json.get_all_components(self.component_type).items()
}
Expand All @@ -101,6 +102,7 @@ def pattern_msg(keywords):
modules_json = modules_json.modules_json

for repo_url, component_with_dir in sorted(repos_with_comps.items()):
repo_entry: Dict[str, Dict[str, Dict[str, Dict[str, Union[str, List[str]]]]]]
repo_entry = modules_json["repos"].get(repo_url, {})
for install_dir, component in sorted(component_with_dir):
repo_modules = repo_entry.get(self.component_type)
Expand Down