Add customisation option to remove all GitHub support with nf-core create

.github/workflows/rich-codex.yml

@@ -1,5 +1,10 @@
 name: Generate images for docs
-on: [push]
+on:
+  push:
+    branches-ignore:
+      - "master"
+      - "dev"
+  workflow_dispatch:
 jobs:
   rich_codex:
     runs-on: ubuntu-latest
@@ -22,6 +27,10 @@ jobs:
 
       - name: Generate terminal images with rich-codex
         uses: ewels/rich-codex@v1
+        env:
+          COLUMNS: 100
+          NFCORE_LINT_HIDE_PROGRESS: true
+          NFCORE_MODULES_LINT_HIDE_PROGRESS: true
         with:
           commit_changes: "true"
           clean_img_paths: docs/images/*.svg
@@ -31,4 +40,3 @@ jobs:
             which nf-core &&
             nextflow -version &&
             nf-core --version
-            PY_COLORS=true

CHANGELOG.md

@@ -13,6 +13,7 @@
 - Make `nf-core create` fail if Git default branch name is dev or TEMPLATE ([#1705](https://github.com/nf-core/tools/pull/1705))
 - Convert `console` snippets to `bash` snippets in the template where applicable ([#1729](https://github.com/nf-core/tools/pull/1729))
 - Add `branch` field to module entries in `modules.json` to record what branch a module was installed from ([#1728](https://github.com/nf-core/tools/issues/1728))
+- Add customisation option to remove all GitHub support with `nf-core create` ([#1766](https://github.com/nf-core/tools/pull/1766))
 
 ### Linting
 
@@ -49,6 +50,7 @@
 - Replace use of the deprecated `distutils` Version object with that from `packaging` ([#1735](https://github.com/nf-core/tools/pull/1735))
 - Add code to cancel CI run if a new run starts ([#1760](https://github.com/nf-core/tools/pull/1760))
 - CI for the API docs generation now uses the ubuntu-latest base image ([#1762](https://github.com/nf-core/tools/pull/1762))
+- Add option to hide progress bars in `nf-core lint` and `nf-core modules lint` with `--hide-progress`.
 
 ### Modules
 

README.md

@@ -287,6 +287,10 @@ working_dir: tmp
 
 Once downloaded, you will see something like the following file structure for the downloaded pipeline:
 
+<!-- RICH-CODEX
+working_dir: tmp
+-->
+
 ![`tree -L 2 nf-core-rnaseq/`](docs/images/nf-core-download-tree.svg)
 
 You can run the pipeline by simply providing the directory path for the `workflow` folder to your `nextflow run` command:

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 +316,8 @@ 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)")
-def lint(dir, release, fix, key, show_passed, fail_ignored, fail_warned, markdown, json):
+@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.
 
@@ -326,7 +339,7 @@ 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
+            dir, release, fix, key, show_passed, fail_ignored, fail_warned, markdown, json, hide_progress
         )
         if len(lint_obj.failed) + len(module_lint_obj.failed) > 0:
             sys.exit(1)
@@ -666,7 +679,8 @@ 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")
-def lint(ctx, tool, dir, key, all, fail_warned, local, passed, fix_version):
+@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.
 
@@ -683,11 +697,13 @@ def lint(ctx, tool, dir, key, all, fail_warned, local, passed, fix_version):
             ctx.obj["modules_repo_url"],
             ctx.obj["modules_repo_branch"],
             ctx.obj["modules_repo_no_pull"],
+            hide_progress,
         )
         module_lint.lint(
             module=tool,
             key=key,
             all_modules=all,
+            hide_progress=hide_progress,
             print_results=True,
             local=local,
             show_passed=passed,

nf_core/create.py

@@ -58,6 +58,10 @@ def __init__(
         )
 
         skippable_paths = {
+            "github": [
+                ".github/",
+                ".gitignore",
+            ],
             "ci": [".github/workflows/"],
             "igenomes": ["conf/igenomes.config"],
             "branded": [
@@ -74,7 +78,9 @@ def __init__(
         self.name = self.template_params["name"]
 
         # Set fields used by the class methods
-        self.no_git = no_git
+        self.no_git = (
+            no_git if self.template_params["github"] else True
+        )  # Set to True if template was configured without github hosting
         self.force = force
         if outdir is None:
             outdir = os.path.join(os.getcwd(), self.template_params["name_noslash"])
@@ -110,6 +116,7 @@ def create_param_dict(self, name, description, author, version, template_yaml_pa
         # Define the different template areas, and what actions to take for each
         # if they are skipped
         template_areas = {
+            "github": {"name": "GitHub hosting", "file": True, "content": False},
             "ci": {"name": "GitHub CI", "file": True, "content": False},
             "github_badges": {"name": "GitHub badges", "file": False, "content": True},
             "igenomes": {"name": "iGenomes config", "file": True, "content": True},
@@ -313,9 +320,10 @@ def render_template(self):
             # Make a logo and save it, if it is a nf-core pipeline
             self.make_pipeline_logo()
         else:
-            # Remove field mentioning nf-core docs
-            # in the github bug report template
-            self.remove_nf_core_in_bug_report_template()
+            if self.template_params["github"]:
+                # Remove field mentioning nf-core docs
+                # in the github bug report template
+                self.remove_nf_core_in_bug_report_template()
 
             # Update the .nf-core.yml with linting configurations
             self.fix_linting()
@@ -395,6 +403,15 @@ def fix_linting(self):
             "multiqc_config": ["report_comment"],
         }
 
+        # Add GitHub hosting specific configurations
+        if not self.template_params["github"]:
+            lint_config["files_exist"].extend(
+                [
+                    ".github/ISSUE_TEMPLATE/bug_report.yml",
+                ]
+            )
+            lint_config["files_unchanged"] = [".github/ISSUE_TEMPLATE/bug_report.yml"]
+
         # Add CI specific configurations
         if not self.template_params["ci"]:
             lint_config["files_exist"].extend(

nf_core/lint/__init__.py

@@ -40,6 +40,7 @@ def run_linting(
     fail_warned=False,
     md_fn=None,
     json_fn=None,
+    hide_progress=False,
 ):
     """Runs all nf-core linting checks on a given Nextflow pipeline project
     in either `release` mode or `normal` mode (default). Returns an object
@@ -77,15 +78,15 @@ def run_linting(
         pipeline_keys = None
 
     # Create the lint object
-    lint_obj = PipelineLint(pipeline_dir, release_mode, fix, pipeline_keys, fail_ignored, fail_warned)
+    lint_obj = PipelineLint(pipeline_dir, release_mode, fix, pipeline_keys, fail_ignored, fail_warned, hide_progress)
 
     # Load the various pipeline configs
     lint_obj._load_lint_config()
     lint_obj._load_pipeline_config()
     lint_obj._list_files()
 
     # Create the modules lint object
-    module_lint_obj = nf_core.modules.lint.ModuleLint(pipeline_dir)
+    module_lint_obj = nf_core.modules.lint.ModuleLint(pipeline_dir, hide_progress=hide_progress)
 
     # Verify that the pipeline is correctly configured and has  a modules.json file
     module_lint_obj.has_valid_directory()
@@ -182,7 +183,9 @@ class PipelineLint(nf_core.utils.Pipeline):
     from .template_strings import template_strings
     from .version_consistency import version_consistency
 
-    def __init__(self, wf_path, release_mode=False, fix=(), key=None, fail_ignored=False, fail_warned=False):
+    def __init__(
+        self, wf_path, release_mode=False, fix=(), key=None, fail_ignored=False, fail_warned=False, hide_progress=False
+    ):
         """Initialise linting object"""
 
         # Initialise the parent object
@@ -192,6 +195,7 @@ def __init__(self, wf_path, release_mode=False, fix=(), key=None, fail_ignored=F
         self.release_mode = release_mode
         self.fail_ignored = fail_ignored
         self.fail_warned = fail_warned
+        self.hide_progress = hide_progress
         self.failed = []
         self.ignored = []
         self.fixed = []
@@ -307,6 +311,7 @@ def _lint_pipeline(self):
             rich.progress.BarColumn(bar_width=None),
             "[magenta]{task.completed} of {task.total}[reset] » [bold yellow]{task.fields[test_name]}",
             transient=True,
+            disable=self.hide_progress,
         )
         with self.progress_bar:
             lint_progress = self.progress_bar.add_task(

nf_core/modules/lint/__init__.py

@@ -64,7 +64,15 @@ class ModuleLint(ModuleCommand):
     from .module_todos import module_todos
     from .module_version import module_version
 
-    def __init__(self, dir, fail_warned=False, remote_url=None, branch=None, no_pull=False):
+    def __init__(
+        self,
+        dir,
+        fail_warned=False,
+        remote_url=None,
+        branch=None,
+        no_pull=False,
+        hide_progress=False,
+    ):
         self.dir = dir
         try:
             self.dir, self.repo_type = nf_core.modules.module_utils.get_repo_type(self.dir)
@@ -75,7 +83,8 @@ def __init__(self, dir, fail_warned=False, remote_url=None, branch=None, no_pull
         self.passed = []
         self.warned = []
         self.failed = []
-        self.modules_repo = ModulesRepo(remote_url, branch, no_pull)
+        self.hide_progress = hide_progress
+        self.modules_repo = ModulesRepo(remote_url, branch, no_pull, hide_progress)
         self.lint_tests = self.get_all_lint_tests(self.repo_type == "pipeline")
 
         if self.repo_type == "pipeline":
@@ -131,6 +140,7 @@ def lint(
         module=None,
         key=(),
         all_modules=False,
+        hide_progress=False,
         print_results=True,
         show_passed=False,
         local=False,
@@ -153,6 +163,7 @@ def lint(
         :param print_results:   Whether to print the linting results
         :param show_passed:     Whether passed tests should be shown as well
         :param fix_version:     Update the module version if a newer version is available
+        :param hide_progress:   Don't show progress bars
 
         :returns:               A ModuleLint object containing information of
                                 the passed, warned and failed tests
@@ -261,6 +272,7 @@ def lint_modules(self, modules, local=False, fix_version=False):
             "[magenta]{task.completed} of {task.total}[reset] » [bold yellow]{task.fields[test_name]}",
             transient=True,
             console=console,
+            disable=self.hide_progress,
         )
         with progress_bar:
             lint_progress = progress_bar.add_task(

nf_core/modules/modules_json.py

@@ -253,7 +253,7 @@ def determine_module_branches_and_shas(self, repo_name, remote_url, modules):
                         break
                     # Create a new modules repo with the selected branch, and retry find the sha
                     modules_repo = nf_core.modules.modules_repo.ModulesRepo(
-                        remote_url=remote_url, branch=branch, no_pull=True, no_progress=True
+                        remote_url=remote_url, branch=branch, no_pull=True, hide_progress=True
                     )
                 else:
                     found_sha = True

nf_core/modules/modules_repo.py

@@ -111,7 +111,7 @@ def get_remote_branches(remote_url):
                     branches[sha] = branch_name
             return set(branches.values())
 
-    def __init__(self, remote_url=None, branch=None, no_pull=False, no_progress=False):
+    def __init__(self, remote_url=None, branch=None, no_pull=False, hide_progress=False):
         """
         Initializes the object and clones the git repository if it is not already present
         """
@@ -127,7 +127,7 @@ def __init__(self, remote_url=None, branch=None, no_pull=False, no_progress=Fals
 
         self.fullname = nf_core.modules.module_utils.path_from_remote(self.remote_url)
 
-        self.setup_local_repo(remote_url, branch, no_progress)
+        self.setup_local_repo(remote_url, branch, hide_progress)
 
         # Verify that the repo seems to be correctly configured
         if self.fullname != NF_CORE_MODULES_NAME or self.branch:
@@ -138,7 +138,7 @@ def __init__(self, remote_url=None, branch=None, no_pull=False, no_progress=Fals
 
         self.avail_module_names = None
 
-    def setup_local_repo(self, remote, branch, no_progress=True):
+    def setup_local_repo(self, remote, branch, hide_progress=True):
         """
         Sets up the local git repository. If the repository has been cloned previously, it
         returns a git.Repo object of that clone. Otherwise it tries to clone the repository from
@@ -152,21 +152,19 @@ def setup_local_repo(self, remote, branch, no_progress=True):
         self.local_repo_dir = os.path.join(NFCORE_DIR, self.fullname)
         if not os.path.exists(self.local_repo_dir):
             try:
-                if no_progress:
-                    self.repo = git.Repo.clone_from(remote, self.local_repo_dir)
-                else:
-                    pbar = rich.progress.Progress(
-                        "[bold blue]{task.description}",
-                        rich.progress.BarColumn(bar_width=None),
-                        "[bold yellow]{task.fields[state]}",
-                        transient=True,
+                pbar = rich.progress.Progress(
+                    "[bold blue]{task.description}",
+                    rich.progress.BarColumn(bar_width=None),
+                    "[bold yellow]{task.fields[state]}",
+                    transient=True,
+                    disable=hide_progress,
+                )
+                with pbar:
+                    self.repo = git.Repo.clone_from(
+                        remote,
+                        self.local_repo_dir,
+                        progress=RemoteProgressbar(pbar, self.fullname, self.remote_url, "Cloning"),
                     )
-                    with pbar:
-                        self.repo = git.Repo.clone_from(
-                            remote,
-                            self.local_repo_dir,
-                            progress=RemoteProgressbar(pbar, self.fullname, self.remote_url, "Cloning"),
-                        )
                 ModulesRepo.update_local_repo_status(self.fullname, True)
             except GitCommandError:
                 raise LookupError(f"Failed to clone from the remote: `{remote}`")
@@ -179,19 +177,17 @@ def setup_local_repo(self, remote, branch, no_progress=True):
                 ModulesRepo.update_local_repo_status(self.fullname, True)
             # If the repo is already cloned, fetch the latest changes from the remote
             if not ModulesRepo.local_repo_synced(self.fullname):
-                if no_progress:
-                    self.repo.remotes.origin.fetch()
-                else:
-                    pbar = rich.progress.Progress(
-                        "[bold blue]{task.description}",
-                        rich.progress.BarColumn(bar_width=None),
-                        "[bold yellow]{task.fields[state]}",
-                        transient=True,
+                pbar = rich.progress.Progress(
+                    "[bold blue]{task.description}",
+                    rich.progress.BarColumn(bar_width=None),
+                    "[bold yellow]{task.fields[state]}",
+                    transient=True,
+                    disable=hide_progress,
+                )
+                with pbar:
+                    self.repo.remotes.origin.fetch(
+                        progress=RemoteProgressbar(pbar, self.fullname, self.remote_url, "Pulling")
                     )
-                    with pbar:
-                        self.repo.remotes.origin.fetch(
-                            progress=RemoteProgressbar(pbar, self.fullname, self.remote_url, "Pulling")
-                        )
                 ModulesRepo.update_local_repo_status(self.fullname, True)
 
             # Before verifying the branch, fetch the changes