enable env variables for options, move hide-progress into decorator g…

…roup

.github/workflows/rich-codex.yml

@@ -22,6 +22,9 @@ jobs:
 
       - name: Generate terminal images with rich-codex
         uses: ewels/rich-codex@v1
+        env:
+          NFCORE_LINT_HIDE_PROGRESS: true
+          NFCORE_MODULES_LINT_HIDE_PROGRESS: true
         with:
           commit_changes: "true"
           clean_img_paths: docs/images/*.svg
@@ -31,4 +34,4 @@ jobs:
             which nf-core &&
             nextflow -version &&
             nf-core --version
-            PY_COLORS=true
+

README.md

@@ -428,7 +428,7 @@ before_command: >
 fake_command: nf-core lint
 -->
 
-![`nf-core lint --hide-progress`](docs/images/nf-core-lint.svg)
+![`nf-core lint`](docs/images/nf-core-lint.svg)
 
 You can use the `-k` / `--key` flag to run only named tests for faster debugging, eg: `nf-core lint -k files_exist -k files_unchanged`. The `nf-core lint` command lints the current working directory by default, to specify another directory you can use `--dir <directory>`.
 
@@ -824,7 +824,7 @@ working_dir: tmp/modules
 before_command: sed 's/1.13a/1.10/g' modules/multiqc/main.nf > modules/multiqc/main.nf.tmp && mv modules/multiqc/main.nf.tmp modules/multiqc/main.nf
 -->
 
-![`nf-core modules lint multiqc --hide-progress`](docs/images/nf-core-modules-lint.svg)
+![`nf-core modules lint multiqc`](docs/images/nf-core-modules-lint.svg)
 
 ### Run the tests for a module using pytest
 

nf_core/__main__.py

@@ -90,7 +90,19 @@ def run_nf_core():
     stderr.print("\n")
 
     # Lanch the click cli
-    nf_core_cli()
+    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"]))
@@ -304,7 +316,7 @@ 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)")
-@click.option("--hide-progress", is_flag=True, help="Don't show progress bars")
+@common_options
 def lint(dir, release, fix, key, show_passed, fail_ignored, fail_warned, markdown, json, hide_progress):
     """
     Check pipeline code against nf-core guidelines.
@@ -667,7 +679,7 @@ 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")
-@click.option("--hide-progress", is_flag=True, help="Don't show progress bars")
+@common_options
 def lint(ctx, tool, dir, key, all, fail_warned, local, passed, fix_version, hide_progress):
     """
     Lint one or more modules in a directory.