Merge pull request #2016 from ewels/top-level-hide-progress

Refactor `--hide-progress` to be at the top level CLI

.github/workflows/create-lint-wf.yml

@@ -86,7 +86,7 @@ jobs:
 
       # Run nf-core linting
       - name: nf-core lint
-        run: nf-core --log-file log.txt lint --dir nf-core-testpipeline --fail-ignored --fail-warned
+        run: nf-core --log-file log.txt --hide-progress lint --dir nf-core-testpipeline --fail-ignored --fail-warned
 
       # Run the other nf-core commands
       - name: nf-core list
@@ -102,7 +102,7 @@ jobs:
         run: nf-core --log-file log.txt bump-version --dir nf-core-testpipeline/ 1.1
 
       - name: nf-core lint in release mode
-        run: nf-core --log-file log.txt lint --dir nf-core-testpipeline --fail-ignored --fail-warned --release
+        run: nf-core --log-file log.txt --hide-progress lint --dir nf-core-testpipeline --fail-ignored --fail-warned --release
 
       - name: nf-core modules install
         run: nf-core --log-file log.txt modules install fastqc --dir nf-core-testpipeline/ --force

CHANGELOG.md

@@ -12,6 +12,7 @@
 
 ### General
 
+- Refactor CLI flag `--hide-progress` to be at the top-level group, like `--verbose` ([#2016](https://github.com/nf-core/tools/pull/2016))
 - Fix error in tagging GitPod docker images during releases
 - `nf-core sync` now supports the template YAML file using `-t/--template-yaml`.
 - Fix bug when updating modules from old version in old folder structure

nf_core/__main__.py

@@ -104,23 +104,13 @@ def run_nf_core():
     nf_core_cli(auto_envvar_prefix="NFCORE")
 
 
-# taken from https://github.com/pallets/click/issues/108#issuecomment-194465429
-_common_options = [
-    click.option("--hide-progress", is_flag=True, default=False, help="Don't show progress bars."),
-]
-
-
-def common_options(func):
-    for option in reversed(_common_options):
-        func = option(func)
-    return func
-
-
 @click.group(context_settings=dict(help_option_names=["-h", "--help"]))
 @click.version_option(nf_core.__version__)
 @click.option("-v", "--verbose", is_flag=True, default=False, help="Print verbose output to the console.")
+@click.option("--hide-progress", is_flag=True, default=False, help="Don't show progress bars.")
 @click.option("-l", "--log-file", help="Save a verbose log to a file.", metavar="<filename>")
-def nf_core_cli(verbose, log_file):
+@click.pass_context
+def nf_core_cli(ctx, verbose, hide_progress, log_file):
     """
     nf-core/tools provides a set of helper tools for use with nf-core Nextflow pipelines.
 
@@ -147,6 +137,11 @@ def nf_core_cli(verbose, log_file):
         log_fh.setFormatter(logging.Formatter("[%(asctime)s] %(name)-20s [%(levelname)-7s]  %(message)s"))
         log.addHandler(log_fh)
 
+    ctx.obj = {
+        "verbose": verbose,
+        "hide_progress": hide_progress or verbose,  # Always hide progress bar with verbose logging
+    }
+
 
 # nf-core list
 @nf_core_cli.command()
@@ -329,8 +324,8 @@ def create(name, description, author, version, no_git, force, outdir, template_y
 @click.option("-w", "--fail-warned", is_flag=True, help="Convert warn tests to failures")
 @click.option("--markdown", type=str, metavar="<filename>", help="File to write linting results to (Markdown)")
 @click.option("--json", type=str, metavar="<filename>", help="File to write linting results to (JSON)")
-@common_options
-def lint(dir, release, fix, key, show_passed, fail_ignored, fail_warned, markdown, json, hide_progress):
+@click.pass_context
+def lint(ctx, dir, release, fix, key, show_passed, fail_ignored, fail_warned, markdown, json):
     """
     Check pipeline code against nf-core guidelines.
 
@@ -352,7 +347,7 @@ def lint(dir, release, fix, key, show_passed, fail_ignored, fail_warned, markdow
     # Run the lint tests!
     try:
         lint_obj, module_lint_obj = nf_core.lint.run_linting(
-            dir, release, fix, key, show_passed, fail_ignored, fail_warned, markdown, json, hide_progress
+            dir, release, fix, key, show_passed, fail_ignored, fail_warned, markdown, json, ctx.obj["hide_progress"]
         )
         if len(lint_obj.failed) + len(module_lint_obj.failed) > 0:
             sys.exit(1)
@@ -730,10 +725,7 @@ def create_test_yml(ctx, tool, run_tests, output, force, no_prompts):
 @click.option("--local", is_flag=True, help="Run additional lint tests for local modules")
 @click.option("--passed", is_flag=True, help="Show passed tests")
 @click.option("--fix-version", is_flag=True, help="Fix the module version if a newer version is available")
-@common_options
-def lint(
-    ctx, tool, dir, key, all, fail_warned, local, passed, fix_version, hide_progress
-):  # pylint: disable=redefined-outer-name
+def lint(ctx, tool, dir, key, all, fail_warned, local, passed, fix_version):  # pylint: disable=redefined-outer-name
     """
     Lint one or more modules in a directory.
 
@@ -750,13 +742,13 @@ def lint(
             ctx.obj["modules_repo_url"],
             ctx.obj["modules_repo_branch"],
             ctx.obj["modules_repo_no_pull"],
-            hide_progress,
+            ctx.obj["hide_progress"],
         )
         module_lint.lint(
             module=tool,
             key=key,
             all_modules=all,
-            hide_progress=hide_progress,
+            hide_progress=ctx.obj["hide_progress"],
             print_results=True,
             local=local,
             show_passed=passed,

nf_core/modules/lint/__init__.py

@@ -72,7 +72,9 @@ def __init__(
         no_pull=False,
         hide_progress=False,
     ):
-        super().__init__("modules", dir=dir, remote_url=remote_url, branch=branch, no_pull=no_pull, hide_progress=False)
+        super().__init__(
+            "modules", dir=dir, remote_url=remote_url, branch=branch, no_pull=no_pull, hide_progress=hide_progress
+        )
 
         self.fail_warned = fail_warned
         self.passed = []

tests/test_cli.py

@@ -273,7 +273,6 @@ def test_lint(self, mock_lint, mock_is_pipeline):
             "fail-warned": None,
             "markdown": "output_file.md",
             "json": "output_file.json",
-            "hide-progress": None,
         }
 
         cmd = ["lint"] + self.assemble_params(params)