Add TTY detection to prevent CLI hanging in non-interactive sessions

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()

nf_core/components/components_test.py

@@ -112,6 +112,11 @@ def check_inputs(self) -> None:
                 raise UserWarning(
                     f"{self.component_type[:-1].title()} name not provided and prompts deactivated. Please provide the {self.component_type[:-1]} name{' as TOOL/SUBTOOL or TOOL' if self.component_type == 'modules' else ''}."
                 )
+            elif not nf_core.utils.is_interactive():
+                nf_core.utils.require_interactive(
+                    f"{self.component_type[:-1].title()} name not provided.\n"
+                    f"Please provide the {self.component_type[:-1]} name as a command-line argument."
+                )
             else:
                 try:
                     self.component_name = questionary.autocomplete(
@@ -122,6 +127,7 @@ 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
@@ -139,6 +145,12 @@ def check_inputs(self) -> None:
                     "To use Singularity set 'export PROFILE=singularity' in your shell before running this command."
                 )
                 os.environ["PROFILE"] = "docker"
+            elif not nf_core.utils.is_interactive():
+                log.info(
+                    "Setting environment variable '$PROFILE' to Docker as session is not interactive.\n"
+                    "To use Singularity set 'export PROFILE=singularity' in your shell before running this command."
+                )
+                os.environ["PROFILE"] = "docker"
             else:
                 question = {
                     "type": "list",
@@ -175,15 +187,18 @@ def display_nftest_output(self, nftest_out: bytes, nftest_err: bytes) -> None:
                     log.info("Updating snapshot")
                     self.update = True
                 elif self.update is None:
-                    answer = Confirm.ask(
-                        "[bold][blue]?[/] nf-test found differences in the snapshot. Do you want to update it?",
-                        default=True,
-                    )
-                    if answer:
-                        log.info("Updating snapshot")
-                        self.update = True
+                    if not nf_core.utils.is_interactive():
+                        log.warning("Snapshot differences found in non-interactive session. Not updating.")
                     else:
-                        log.debug("Snapshot not updated")
+                        answer = Confirm.ask(
+                            "[bold][blue]?[/] nf-test found differences in the snapshot. Do you want to update it?",
+                            default=True,
+                        )
+                        if answer:
+                            log.info("Updating snapshot")
+                            self.update = True
+                        else:
+                            log.debug("Snapshot not updated")
                 if self.update:
                     # update snapshot using nf-test --update-snapshot
                     self.generate_snapshot()
@@ -250,8 +265,10 @@ def check_snapshot_stability(self) -> bool:
         else:
             if self.obsolete_snapshots:
                 # ask if the user wants to remove obsolete snapshots using nf-test --clean-snapshot
-                if self.no_prompts or Confirm.ask(
-                    "nf-test found obsolete snapshots. Do you want to remove them?", default=True
+                if (
+                    self.no_prompts
+                    or not nf_core.utils.is_interactive()
+                    or Confirm.ask("nf-test found obsolete snapshots. Do you want to remove them?", default=True)
                 ):
                     profile = self.profile if self.profile else os.environ["PROFILE"]
                     log.info("Removing obsolete snapshots")

nf_core/components/components_utils.py

@@ -42,6 +42,10 @@ def get_repo_info(directory: Path, use_prompt: bool | None = True) -> tuple[Path
 
     # If not set, prompt the user
     if not repo_type and use_prompt:
+        nf_core.utils.require_interactive(
+            f"'repository_type' not defined in '{config_fn.name}'.\n"
+            f"Please add 'repository_type' to your {config_fn.name} file."
+        )
         log.warning("'repository_type' not defined in %s", config_fn.name)
         repo_type = questionary.select(
             "Is this repository a pipeline or a modules repository?",
@@ -71,6 +75,9 @@ def get_repo_info(directory: Path, use_prompt: bool | None = True) -> tuple[Path
     if repo_type == "modules":
         org = getattr(tools_config, "org_path", "") or ""
         if org == "":
+            nf_core.utils.require_interactive(
+                f"'org_path' not defined in '{config_fn.name}'.\nPlease add 'org_path' to your {config_fn.name} file."
+            )
             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 +114,9 @@ def prompt_component_version_sha(
     Returns:
         git_sha (str): The selected version of the module/subworkflow
     """
+    nf_core.utils.require_interactive(
+        "Cannot interactively select a version.\nPlease use the '--sha' option to specify a version."
+    )
     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 not nf_core.utils.is_interactive():
+                    log.warning(
+                        f"{e}\nBioconda package not found and session is not interactive. "
+                        "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 +278,9 @@ def _get_module_structure_components(self):
                 "For example: {}".format(", ".join(process_label_defaults))
             )
         while self.process_label is None:
+            nf_core.utils.require_interactive(
+                "Process label not provided.\nPlease provide the '--process-label' option."
+            )
             self.process_label = questionary.autocomplete(
                 "Process resource label:",
                 choices=process_label_defaults,
@@ -287,6 +296,9 @@ 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:
+            nf_core.utils.require_interactive(
+                "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 +358,9 @@ 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 not nf_core.utils.is_interactive():
+                    self.component = name_clean
+                elif rich.prompt.Confirm.ask(f"[violet]Change '{self.component}' to '{name_clean}'?"):
                     self.component = name_clean
                 else:
                     self.component = ""
@@ -363,6 +377,10 @@ def _collect_name_prompt(self):
 
             # Prompt for new entry if we reset
             if self.component == "":
+                nf_core.utils.require_interactive(
+                    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 +453,7 @@ 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 '@')!")
+            nf_core.utils.require_interactive("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 +505,15 @@ 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 not nf_core.utils.is_interactive():
+            log.info("Non-interactive session: 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:
+            nf_core.utils.require_interactive(
+                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()

nf_core/components/install.py

@@ -223,6 +223,11 @@ def collect_and_verify_name(
         Check that the supplied name is an available module/subworkflow.
         """
         if component is None:
+            nf_core.utils.require_interactive(
+                f"No {self.component_type[:-1]} name provided.\n"
+                f"Please provide the {self.component_type[:-1]} name as a command-line argument:\n"
+                f"  nf-core {self.component_type} install <name>"
+            )
             component = questionary.autocomplete(
                 f"{'Tool' if self.component_type == 'modules' else 'Subworkflow'} name:",
                 choices=sorted(modules_repo.get_avail_components(self.component_type, commit=self.current_sha)),
@@ -274,6 +279,11 @@ def check_component_installed(self, component, current_version, component_dir, m
                 log.info(f"{self.component_type[:-1].title()} '{component}' is already installed.")
 
             if prompt:
+                nf_core.utils.require_interactive(
+                    f"{self.component_type[:-1].title()} '{component}' is already installed and '--prompt' "
+                    "cannot be used.\n"
+                    "Use '--force' to force reinstallation in headless environments."
+                )
                 message = (
                     "?" if self.component_type == "modules" else " of this subworkflow and all it's imported modules?"
                 )
@@ -304,6 +314,11 @@ def get_version(self, component, sha, prompt, current_version, modules_repo):
         if sha:
             version = sha
         elif prompt:
+            nf_core.utils.require_interactive(
+                f"Cannot interactively select a version for '{component}'.\n"
+                "Please specify the version using the '--sha' option:\n"
+                f"  nf-core {self.component_type} install --sha <commit_sha> {component}"
+            )
             try:
                 version = prompt_component_version_sha(
                     component,

nf_core/components/patch.py

@@ -52,6 +52,10 @@ def patch(self, component=None):
         components = self.modules_json.get_all_components(self.component_type).get(self.modules_repo.remote_url)
 
         if component is None:
+            nf_core.utils.require_interactive(
+                f"No {self.component_type[:-1]} name provided.\n"
+                f"Please provide the {self.component_type[:-1]} name as a command-line argument."
+            )
             choices = [
                 component if directory == self.modules_repo.repo_path else f"{directory}/{component}"
                 for directory, component in components
@@ -94,6 +98,9 @@ def patch(self, component=None):
         patch_path = Path(self.directory, patch_relpath)
 
         if patch_path.exists():
+            nf_core.utils.require_interactive(
+                f"Patch already exists for '{component_fullname}'.\nPlease remove the existing patch file first."
+            )
             remove = questionary.confirm(
                 f"Patch exists for {self.component_type[:-1]} '{component_fullname}'. Do you want to regenerate it?",
                 style=nf_core.utils.nfcore_question_style,
@@ -157,6 +164,10 @@ def remove(self, component):
         components = self.modules_json.get_all_components(self.component_type).get(self.modules_repo.remote_url)
 
         if component is None:
+            nf_core.utils.require_interactive(
+                f"No {self.component_type[:-1]} name provided.\n"
+                f"Please provide the {self.component_type[:-1]} name as a command-line argument."
+            )
             choices = [
                 component if directory == self.modules_repo.repo_path else f"{directory}/{component}"
                 for directory, component in components
@@ -199,6 +210,9 @@ def remove(self, component):
         component_path = Path(self.directory, component_relpath)
 
         if patch_path.exists():
+            nf_core.utils.require_interactive(
+                f"Patch exists for '{component_fullname}'.\nPlease remove the existing patch file first."
+            )
             remove = questionary.confirm(
                 f"Patch exists for {self.component_type[:-1]} '{component_fullname}'. Are you sure you want to remove?",
                 style=nf_core.utils.nfcore_question_style,

nf_core/components/remove.py

@@ -53,6 +53,10 @@ def remove(self, component, repo_url=None, repo_path=None, removed_by=None, remo
         if repo_url is None:
             repo_url = self.modules_repo.remote_url
         if component is None:
+            nf_core.utils.require_interactive(
+                f"No {self.component_type[:-1]} name provided.\n"
+                f"Please provide the {self.component_type[:-1]} name as a command-line argument."
+            )
             component = questionary.autocomplete(
                 f"{self.component_type[:-1]} name:",
                 choices=self.components_from_repo(repo_path),
@@ -130,6 +134,10 @@ def remove(self, component, repo_url=None, repo_path=None, removed_by=None, remo
                     )
                 # ask the user if they still want to remove the component, add it back otherwise
                 if not force:
+                    nf_core.utils.require_interactive(
+                        f"{self.component_type[:-1].title()} '{component}' is still included in workflow files.\n"
+                        "Use '--force' to force removal."
+                    )
                     if not questionary.confirm(
                         f"Do you still want to remove the {self.component_type[:-1]} '{component}'?",
                         style=nf_core.utils.nfcore_question_style,