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

Make module/subworkflow names case insensitive #2869

Merged
merged 2 commits into from
Mar 21, 2024
+25 −16
Merged

Make module/subworkflow names case insensitive #2869

Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
2 commits
Select commit Hold shift + click to select a range
3b2aaa9
Make cli-provided module/subworkflow names case insensitive
pmoris Mar 20, 2024
2cdb907
Rename subworkflow argument in subworkflows info command
pmoris Mar 20, 2024
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
1 change: 1 addition & 0 deletions CHANGELOG.md
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -41,6 +41,7 @@
- Fix issue with config resolution that was causing nested configs to behave unexpectedly ([#2862](https://github.com/nf-core/tools/pull/2862))
- Fix schema docs console output truncating ([#2880](https://github.com/nf-core/tools/pull/2880))
- fix: ensure path object converted to string before stripping quotes ([#2878](https://github.com/nf-core/tools/pull/2878))
- Make cli-provided module/subworkflow names case insensitive ([#2869](https://github.com/nf-core/tools/pull/2869))

## [v2.13.1 - Tin Puppy Patch](https://github.com/nf-core/tools/releases/tag/2.13) - [2024-02-29]

Expand Down
40 changes: 24 additions & 16 deletions nf_core/__main__.py
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -103,6 +103,14 @@ def selective_traceback_hook(exctype, value, traceback):
sys.excepthook = selective_traceback_hook


# Define callback function to normalize the case of click arguments,
# which is used to make the module/subworkflow names, provided by the
# user on the cli, case insensitive.
def normalize_case(ctx, param, component_name):
if component_name is not None:
return component_name.casefold()


def run_nf_core():
# print nf-core header if environment variable is not set
if os.environ.get("_NF_CORE_COMPLETE") is None:
Expand Down Expand Up @@ -786,7 +794,7 @@ def modules_list_local(ctx, keywords, json, dir): # pylint: disable=redefined-b
# nf-core modules install
@modules.command("install")
@click.pass_context
@click.argument("tool", type=str, required=False, metavar="<tool> or <tool/subtool>")
@click.argument("tool", type=str, callback=normalize_case, required=False, metavar="<tool> or <tool/subtool>")
@click.option(
"-d",
"--dir",
Expand Down Expand Up @@ -838,7 +846,7 @@ def modules_install(ctx, tool, dir, prompt, force, sha):
# nf-core modules update
@modules.command("update")
@click.pass_context
@click.argument("tool", type=str, required=False, metavar="<tool> or <tool/subtool>")
@click.argument("tool", type=str, callback=normalize_case, required=False, metavar="<tool> or <tool/subtool>")
@click.option(
"-d",
"--dir",
Expand Down Expand Up @@ -930,7 +938,7 @@ def modules_update(
# nf-core modules patch
@modules.command()
@click.pass_context
@click.argument("tool", type=str, required=False, metavar="<tool> or <tool/subtool>")
@click.argument("tool", type=str, callback=normalize_case, required=False, metavar="<tool> or <tool/subtool>")
@click.option(
"-d",
"--dir",
Expand Down Expand Up @@ -967,7 +975,7 @@ def patch(ctx, tool, dir, remove):
# nf-core modules remove
@modules.command("remove")
@click.pass_context
@click.argument("tool", type=str, required=False, metavar="<tool> or <tool/subtool>")
@click.argument("tool", type=str, callback=normalize_case, required=False, metavar="<tool> or <tool/subtool>")
@click.option(
"-d",
"--dir",
Expand Down Expand Up @@ -1121,7 +1129,7 @@ def create_module(
# nf-core modules test
@modules.command("test")
@click.pass_context
@click.argument("tool", type=str, required=False, metavar="<tool> or <tool/subtool>")
@click.argument("tool", type=str, callback=normalize_case, required=False, metavar="<tool> or <tool/subtool>")
@click.option(
"-d",
"--dir",
Expand Down Expand Up @@ -1180,7 +1188,7 @@ def test_module(ctx, tool, dir, no_prompts, update, once, profile):
# nf-core modules lint
@modules.command("lint")
@click.pass_context
@click.argument("tool", type=str, required=False, metavar="<tool> or <tool/subtool>")
@click.argument("tool", type=str, callback=normalize_case, required=False, metavar="<tool> or <tool/subtool>")
@click.option(
"-d",
"--dir",
Expand Down Expand Up @@ -1267,7 +1275,7 @@ def modules_lint(ctx, tool, dir, registry, key, all, fail_warned, local, passed,
# nf-core modules info
@modules.command("info")
@click.pass_context
@click.argument("tool", type=str, required=False, metavar="<tool> or <tool/subtool>")
@click.argument("tool", type=str, callback=normalize_case, required=False, metavar="<tool> or <tool/subtool>")
@click.option(
"-d",
"--dir",
Expand Down Expand Up @@ -1306,7 +1314,7 @@ def modules_info(ctx, tool, dir):
# nf-core modules bump-versions
@modules.command()
@click.pass_context
@click.argument("tool", type=str, required=False, metavar="<tool> or <tool/subtool>")
@click.argument("tool", type=str, callback=normalize_case, required=False, metavar="<tool> or <tool/subtool>")
@click.option(
"-d",
"--dir",
Expand Down Expand Up @@ -1392,7 +1400,7 @@ def create_subworkflow(ctx, subworkflow, dir, author, force, migrate_pytest):
# nf-core subworkflows test
@subworkflows.command("test")
@click.pass_context
@click.argument("subworkflow", type=str, required=False, metavar="subworkflow name")
@click.argument("subworkflow", type=str, callback=normalize_case, required=False, metavar="subworkflow name")
@click.option(
"-d",
"--dir",
Expand Down Expand Up @@ -1519,7 +1527,7 @@ def subworkflows_list_local(ctx, keywords, json, dir): # pylint: disable=redefi
# nf-core subworkflows lint
@subworkflows.command("lint")
@click.pass_context
@click.argument("subworkflow", type=str, required=False, metavar="subworkflow name")
@click.argument("subworkflow", type=str, callback=normalize_case, required=False, metavar="subworkflow name")
@click.option(
"-d",
"--dir",
Expand Down Expand Up @@ -1600,15 +1608,15 @@ def subworkflows_lint(ctx, subworkflow, dir, registry, key, all, fail_warned, lo
# nf-core subworkflows info
@subworkflows.command("info")
@click.pass_context
@click.argument("tool", type=str, required=False, metavar="subworkflow name")
@click.argument("subworkflow", type=str, callback=normalize_case, required=False, metavar="subworkflow name")
@click.option(
"-d",
"--dir",
type=click.Path(exists=True),
default=".",
help=r"Pipeline directory. [dim]\[default: Current working directory][/]",
)
def subworkflows_info(ctx, tool, dir):
def subworkflows_info(ctx, subworkflow, dir):
"""
Show developer usage information about a given subworkflow.

Expand All @@ -1625,7 +1633,7 @@ def subworkflows_info(ctx, tool, dir):
try:
subworkflow_info = SubworkflowInfo(
dir,
tool,
subworkflow,
ctx.obj["modules_repo_url"],
ctx.obj["modules_repo_branch"],
ctx.obj["modules_repo_no_pull"],
Expand All @@ -1639,7 +1647,7 @@ def subworkflows_info(ctx, tool, dir):
# nf-core subworkflows install
@subworkflows.command("install")
@click.pass_context
@click.argument("subworkflow", type=str, required=False, metavar="subworkflow name")
@click.argument("subworkflow", type=str, callback=normalize_case, required=False, metavar="subworkflow name")
@click.option(
"-d",
"--dir",
Expand Down Expand Up @@ -1697,7 +1705,7 @@ def subworkflows_install(ctx, subworkflow, dir, prompt, force, sha):
# nf-core subworkflows remove
@subworkflows.command("remove")
@click.pass_context
@click.argument("subworkflow", type=str, required=False, metavar="subworkflow name")
@click.argument("subworkflow", type=str, callback=normalize_case, required=False, metavar="subworkflow name")
@click.option(
"-d",
"--dir",
Expand Down Expand Up @@ -1727,7 +1735,7 @@ def subworkflows_remove(ctx, dir, subworkflow):
# nf-core subworkflows update
@subworkflows.command("update")
@click.pass_context
@click.argument("subworkflow", type=str, required=False, metavar="subworkflow name")
@click.argument("subworkflow", type=str, callback=normalize_case, required=False, metavar="subworkflow name")
@click.option(
"-d",
"--dir",
Expand Down
Loading