Merge pull request #4130 from ewels/modules-install-no-tty

Author: ewels

nf_core/__main__.py

@@ -456,12 +456,13 @@ def command_pipelines_download(
     default=False,
     help="Show hidden params which don't normally need changing",
 )
+@click.option("-n", "--no-prompts", is_flag=True, default=False, help="Run without prompting for user input")
 @click.pass_context
-def command_pipelines_create_params_file(ctx, pipeline, revision, output, force, show_hidden):
+def command_pipelines_create_params_file(ctx, pipeline, revision, output, force, show_hidden, no_prompts):
     """
     Build a parameter file for a pipeline.
     """
-    pipelines_create_params_file(ctx, pipeline, revision, output, force, show_hidden)
+    pipelines_create_params_file(ctx, pipeline, revision, output, force, show_hidden, no_prompts)
 
 
 # nf-core pipelines launch
@@ -515,6 +516,7 @@ def command_pipelines_create_params_file(ctx, pipeline, revision, output, force,
     default="https://nf-co.re/launch",
     help="Customise the builder URL (for development work)",
 )
+@click.option("-n", "--no-prompts", is_flag=True, default=False, help="Run without prompting for user input")
 @click.pass_context
 def command_pipelines_launch(
     ctx,
@@ -527,11 +529,14 @@ def command_pipelines_launch(
     save_all,
     show_hidden,
     url,
+    no_prompts,
 ):
     """
     Launch a pipeline using a web GUI or command line prompts.
     """
-    pipelines_launch(ctx, pipeline, id, revision, command_only, params_in, params_out, save_all, show_hidden, url)
+    pipelines_launch(
+        ctx, pipeline, id, revision, command_only, params_in, params_out, save_all, show_hidden, url, no_prompts
+    )
 
 
 # nf-core pipelines list
@@ -626,14 +631,33 @@ def rocrate(
 @click.option("-u", "--username", type=str, help="GitHub PR: auth username.")
 @click.option("-t", "--template-yaml", help="Pass a YAML file to customize the template")
 @click.option("-b", "--blog-post", type=str, help="Link to the blog post")
+@click.option("-n", "--no-prompts", is_flag=True, default=False, help="Run without prompting for user input")
 def command_pipelines_sync(
-    ctx, directory, from_branch, pull_request, github_repository, username, template_yaml, force_pr, blog_post
+    ctx,
+    directory,
+    from_branch,
+    pull_request,
+    github_repository,
+    username,
+    template_yaml,
+    force_pr,
+    blog_post,
+    no_prompts,
 ):
     """
     Sync a pipeline [cyan i]TEMPLATE[/] branch with the nf-core template.
     """
     pipelines_sync(
-        ctx, directory, from_branch, pull_request, github_repository, username, template_yaml, force_pr, blog_post
+        ctx,
+        directory,
+        from_branch,
+        pull_request,
+        github_repository,
+        username,
+        template_yaml,
+        force_pr,
+        blog_post,
+        no_prompts,
     )
 
 
@@ -2142,14 +2166,27 @@ def command_create_logo(logo_text, directory, name, theme, width, format, force)
 @click.option("-g", "--github-repository", type=str, help="GitHub PR: target repository.")
 @click.option("-u", "--username", type=str, help="GitHub PR: auth username.")
 @click.option("-t", "--template-yaml", help="Pass a YAML file to customize the template")
-def command_sync(ctx, directory, from_branch, pull_request, github_repository, username, template_yaml, force_pr):
+@click.option("-n", "--no-prompts", is_flag=True, default=False, help="Run without prompting for user input")
+def command_sync(
+    ctx, directory, from_branch, pull_request, github_repository, username, template_yaml, force_pr, no_prompts
+):
     """
     Use `nf-core pipelines sync` instead.
     """
     log.warning(
         "The `[magenta]nf-core sync[/]` command is deprecated. Use `[magenta]nf-core pipelines sync[/]` instead."
     )
-    pipelines_sync(ctx, directory, from_branch, pull_request, github_repository, username, template_yaml, force_pr)
+    pipelines_sync(
+        ctx,
+        directory,
+        from_branch,
+        pull_request,
+        github_repository,
+        username,
+        template_yaml,
+        force_pr,
+        no_prompts=no_prompts,
+    )
 
 
 # nf-core bump-version (deprecated)
@@ -2250,6 +2287,7 @@ def command_list(ctx, keywords, sort, json, show_archived):
     default="https://nf-co.re/launch",
     help="Customise the builder URL (for development work)",
 )
+@click.option("-n", "--no-prompts", is_flag=True, default=False, help="Run without prompting for user input")
 @click.pass_context
 def command_launch(
     ctx,
@@ -2262,14 +2300,17 @@ def command_launch(
     save_all,
     show_hidden,
     url,
+    no_prompts,
 ):
     """
     Use `nf-core pipelines launch` instead.
     """
     log.warning(
         "The `[magenta]nf-core launch[/]` command is deprecated. Use `[magenta]nf-core pipelines launch[/]` instead."
     )
-    pipelines_launch(ctx, pipeline, id, revision, command_only, params_in, params_out, save_all, show_hidden, url)
+    pipelines_launch(
+        ctx, pipeline, id, revision, command_only, params_in, params_out, save_all, show_hidden, url, no_prompts
+    )
 
 
 # nf-core create-params-file (deprecated)
@@ -2292,14 +2333,15 @@ def command_launch(
     default=False,
     help="Show hidden params which don't normally need changing",
 )
-def command_create_params_file(pipeline, revision, output, force, show_hidden):
+@click.option("-n", "--no-prompts", is_flag=True, default=False, help="Run without prompting for user input")
+def command_create_params_file(pipeline, revision, output, force, show_hidden, no_prompts):
     """
     Use `nf-core pipelines create-params-file` instead.
     """
     log.warning(
         "The `[magenta]nf-core create-params-file[/]` command is deprecated. Use `[magenta]nf-core pipelines create-params-file[/]` instead."
     )
-    pipelines_create_params_file(pipeline, revision, output, force, show_hidden)
+    pipelines_create_params_file(pipeline, revision, output, force, show_hidden, no_prompts)
 
 
 # nf-core download (deprecated)

nf_core/commands_pipelines.py

@@ -5,6 +5,7 @@
 
 import rich
 
+import nf_core.utils
 from nf_core.pipelines.params_file import ParamsFileBuilder
 from nf_core.utils import rich_force_colors
 
@@ -53,6 +54,12 @@ def pipelines_create(ctx, name, description, author, version, force, outdir, tem
         )
         sys.exit(1)
     else:
+        if not nf_core.utils.is_interactive():
+            log.error(
+                "No pipeline arguments provided and session is not interactive (no TTY detected). "
+                "Please provide at least --name, --description, and --author to run non-interactively."
+            )
+            sys.exit(1)
         log.info("Launching interactive nf-core pipeline creation tool.")
         app = PipelineCreateApp()
         app.run()
@@ -206,7 +213,7 @@ def pipelines_download(
 
 
 # nf-core pipelines create-params-file
-def pipelines_create_params_file(ctx, pipeline, revision, output, force, show_hidden):
+def pipelines_create_params_file(ctx, pipeline, revision, output, force, show_hidden, no_prompts=False):
     """
     Build a parameter file for a pipeline.
 
@@ -218,7 +225,7 @@ def pipelines_create_params_file(ctx, pipeline, revision, output, force, show_hi
     Run using a remote pipeline name (such as GitHub `user/repo` or a URL),
     a local pipeline directory.
     """
-    builder = ParamsFileBuilder(pipeline, revision)
+    builder = ParamsFileBuilder(pipeline, revision, no_prompts)
 
     if not builder.write_params_file(Path(output), show_hidden=show_hidden, force=force):
         sys.exit(1)
@@ -236,6 +243,7 @@ def pipelines_launch(
     save_all,
     show_hidden,
     url,
+    no_prompts=False,
 ):
     """
     Launch a pipeline using a web GUI or command line prompts.
@@ -262,6 +270,7 @@ def pipelines_launch(
         show_hidden,
         url,
         id,
+        no_prompts,
     )
     if not launcher.launch_pipeline():
         sys.exit(1)
@@ -309,7 +318,16 @@ def pipelines_rocrate(
 
 # nf-core pipelines sync
 def pipelines_sync(
-    ctx, directory, from_branch, pull_request, github_repository, username, template_yaml, force_pr, blog_post
+    ctx,
+    directory,
+    from_branch,
+    pull_request,
+    github_repository,
+    username,
+    template_yaml,
+    force_pr,
+    blog_post,
+    no_prompts=False,
 ):
     """
     Sync a pipeline [cyan i]TEMPLATE[/] branch with the nf-core template.
@@ -331,7 +349,15 @@ def pipelines_sync(
         is_pipeline_directory(directory)
         # Sync the given pipeline dir
         sync_obj = PipelineSync(
-            directory, from_branch, pull_request, github_repository, username, template_yaml, force_pr, blog_post
+            directory,
+            from_branch,
+            pull_request,
+            github_repository,
+            username,
+            template_yaml,
+            force_pr,
+            blog_post,
+            no_prompts,
         )
         sync_obj.sync()
     except (SyncExceptionError, PullRequestExceptionError) as e:

nf_core/components/components_command.py

@@ -35,11 +35,16 @@ def __init__(
         self.directory: Path = Path(directory)
         self.modules_repo = ModulesRepo(remote_url, branch, no_pull, hide_progress)
         self.hide_progress: bool = hide_progress
-        self.no_prompts: bool = no_prompts
+        self.no_prompts: bool = no_prompts or not nf_core.utils.is_interactive()
         self.repo_type: str | None = None
         self.org: str = ""
         self._configure_repo_and_paths()
 
+    def require_prompts(self, msg: str) -> None:
+        """Raise UserWarning if prompts are disabled (via --no-prompts or non-interactive session)."""
+        if self.no_prompts:
+            raise UserWarning(f"{msg} and prompts are disabled.")
+
     def _configure_repo_and_paths(self, nf_dir_req: bool = True) -> None:
         """
         Determine the repo type and set some default paths.

nf_core/components/components_test.py

@@ -122,6 +122,7 @@ def check_inputs(self) -> None:
                 except LookupError:
                     raise
 
+        assert self.component_name is not None  # Set above by user input, prompt, or guard
         self.component_dir = Path(self.component_type, self.modules_repo.repo_path, *self.component_name.split("/"))
 
         # First, sanity check that the module directory exists
@@ -170,7 +171,6 @@ def display_nftest_output(self, nftest_out: bytes, nftest_err: bytes) -> None:
                 print("Displaying nf-test error")
             if "Different Snapshot:" in nftest_err.decode():
                 log.error("nf-test failed due to differences in the snapshots")
-                # prompt to update snapshot
                 if self.no_prompts:
                     log.info("Updating snapshot")
                     self.update = True

nf_core/components/components_utils.py

@@ -70,7 +70,7 @@ def get_repo_info(directory: Path, use_prompt: bool | None = True) -> tuple[Path
     # Check for org if modules repo
     if repo_type == "modules":
         org = getattr(tools_config, "org_path", "") or ""
-        if org == "":
+        if org == "" and use_prompt:
             log.warning("Organisation path not defined in %s [key: org_path]", config_fn.name)
             org = questionary.text(
                 "What is the organisation path under which modules and subworkflows are stored?",
@@ -107,6 +107,8 @@ def prompt_component_version_sha(
     Returns:
         git_sha (str): The selected version of the module/subworkflow
     """
+    if not nf_core.utils.is_interactive():
+        raise UserWarning("Cannot interactively select a version and session is not interactive (no TTY detected).")
     older_commits_choice = questionary.Choice(
         title=[("fg:ansiyellow", "older commits"), ("class:choice-default", "")], value=""
     )

nf_core/components/create.py

@@ -231,6 +231,12 @@ def _get_bioconda_tool(self):
                 log.warning(
                     f"Could not find Conda dependency using the Anaconda API: '{self.tool_conda_name if self.tool_conda_name else self.component}'"
                 )
+                if self.no_prompts:
+                    log.warning(
+                        f"{e}\nBioconda package not found and prompts are disabled. "
+                        "Building module without tool software and meta."
+                    )
+                    break
                 if rich.prompt.Confirm.ask("[violet]Do you want to enter a different Bioconda package name?"):
                     self.tool_conda_name = rich.prompt.Prompt.ask("[violet]Name of Bioconda package").strip()
                     continue
@@ -272,6 +278,7 @@ def _get_module_structure_components(self):
                 "For example: {}".format(", ".join(process_label_defaults))
             )
         while self.process_label is None:
+            self.require_prompts("Process label not provided.\nPlease provide the `--process-label` option")
             self.process_label = questionary.autocomplete(
                 "Process resource label:",
                 choices=process_label_defaults,
@@ -287,6 +294,9 @@ def _get_module_structure_components(self):
                 "[link=https://github.com/nf-core/modules/blob/master/modules/nf-core/bwa/index/main.nf]indexing reference genome files[/link]."
             )
         while self.has_meta is None:
+            self.require_prompts(
+                "Meta map requirement not specified.\nPlease provide the `--has-meta` or `--no-meta` option"
+            )
             self.has_meta = rich.prompt.Confirm.ask(
                 "[violet]Will the module require a meta map of sample information?",
                 default=True,
@@ -346,7 +356,7 @@ def _collect_name_prompt(self):
                 elif self.component_type == "subworkflows":
                     log.warning("Subworkflow name must be lower-case letters only, with no punctuation")
                 name_clean = re.sub(r"[^a-z\d/]", "", self.component.lower())
-                if rich.prompt.Confirm.ask(f"[violet]Change '{self.component}' to '{name_clean}'?"):
+                if self.no_prompts or rich.prompt.Confirm.ask(f"[violet]Change '{self.component}' to '{name_clean}'?"):
                     self.component = name_clean
                 else:
                     self.component = ""
@@ -363,6 +373,10 @@ def _collect_name_prompt(self):
 
             # Prompt for new entry if we reset
             if self.component == "":
+                self.require_prompts(
+                    f"No {self.component_type[:-1]} name provided.\n"
+                    f"Please provide the {self.component_type[:-1]} name as a command-line argument"
+                )
                 if self.component_type == "modules":
                     self.component = rich.prompt.Prompt.ask("[violet]Name of tool/subtool").strip()
                 elif self.component_type == "subworkflows":
@@ -435,6 +449,7 @@ def _get_username(self):
         while self.author is None or not github_username_regex.match(self.author):
             if self.author is not None and not github_username_regex.match(self.author):
                 log.warning("Does not look like a valid GitHub username (must start with an '@')!")
+            self.require_prompts("GitHub username not provided.\nPlease provide the `--author` option")
             self.author = rich.prompt.Prompt.ask(
                 f"[violet]GitHub Username:[/]{' (@author)' if author_default is None else ''}",
                 default=author_default,
@@ -486,10 +501,15 @@ def _copy_old_files(self, component_old_path):
     def _print_and_delete_pytest_files(self):
         """Prompt if pytest files should be deleted and printed to stdout"""
         pytest_dir = Path(self.directory, "tests", self.component_type, self.org, self.component_dir)
-        if rich.prompt.Confirm.ask(
-            "[violet]Do you want to delete the pytest files?[/]\nPytest file 'main.nf' will be printed to standard output to allow migrating the tests manually to 'main.nf.test'.",
-            default=False,
-        ):
+        if self.no_prompts:
+            log.info("Prompts disabled: skipping pytest file deletion prompt.")
+            delete_pytest = False
+        else:
+            delete_pytest = rich.prompt.Confirm.ask(
+                "[violet]Do you want to delete the pytest files?[/]\nPytest file 'main.nf' will be printed to standard output to allow migrating the tests manually to 'main.nf.test'.",
+                default=False,
+            )
+        if delete_pytest:
             with open(pytest_dir / "main.nf") as fh:
                 log.info(fh.read())
             if pytest_dir.is_symlink():

nf_core/components/info.py

@@ -97,6 +97,10 @@ def init_mod_name(self, component: str | None) -> str:
             module: str: Module name to check
         """
         if component is None:
+            self.require_prompts(
+                f"No {self.component_type[:-1]} name provided.\n"
+                f"Please provide the {self.component_type[:-1]} name as a command-line argument"
+            )
             self.local = questionary.confirm(
                 f"Is the {self.component_type[:-1]} locally installed?", style=nf_core.utils.nfcore_question_style
             ).unsafe_ask()