Bump versions failing #3382
Description
Description of the bug
In 3.1.0 and 3.1.1 there is the following error when trying to bump versions:
NotADirectoryError: [Errno 20] Not a directory: 'modules/nf-core/cellranger/.gitignore/main.nf'
It seems that this is because some tools have files within their module directories, but the code does not verify whether the directory contents are files or subdirectories.
tools/nf_core/modules/modules_utils.py
Lines 74 to 78 in 45c7879
Command used and terminal output
$ nf-core modules bump-versions csvtk/concat
╭─────────────────────────────── Traceback (most recent call last) ────────────────────────────────╮
│ /home/dxh/others/nf-core-modules/../nf-core-tools/.venv/bin/nf-core:8 in <module> │
│ │
│ 5 from nf_core.__main__ import run_nf_core │
│ 6 if __name__ == "__main__": │
│ 7 │ sys.argv[0] = re.sub(r"(-script\.pyw|\.exe)?$", "", sys.argv[0]) │
│ ❱ 8 │ sys.exit(run_nf_core()) │
│ 9 │
│ │
│ /home/dxh/others/nf-core-tools/nf_core/__main__.py:182 in run_nf_core │
│ │
│ 179 │ │ │ log.debug(f"Could not check latest version: {e}") │
│ 180 │ │ stderr.print("\n") │
│ 181 │ # Launch the click cli │
│ ❱ 182 │ nf_core_cli(auto_envvar_prefix="NFCORE") │
│ 183 │
│ 184 │
│ 185 @tui( │
│ │
│ /home/dxh/others/nf-core-tools/.venv/lib64/python3.11/site-packages/rich_click/rich_command.py:3 │
│ 67 in __call__ │
│ │
│ 364 │ │ # Include this here because I run into a false warning │
│ 365 │ │ # in the PyCharm IDE otherwise; for some reason PyCharm doesn't │
│ 366 │ │ # seem to think RichGroups are callable. (No issues with Mypy, though.) │
│ ❱ 367 │ │ return super().__call__(*args, **kwargs) │
│ 368 │
│ 369 │
│ 370 class RichCommandCollection(CommandCollection, RichGroup): │
│ │
│ /home/dxh/others/nf-core-tools/.venv/lib64/python3.11/site-packages/click/core.py:1161 in │
│ __call__ │
│ │
│ 1158 │ │
│ 1159 │ def __call__(self, *args: t.Any, **kwargs: t.Any) -> t.Any: │
│ 1160 │ │ """Alias for :meth:`main`.""" │
│ ❱ 1161 │ │ return self.main(*args, **kwargs) │
│ 1162 │
│ 1163 │
│ 1164 class Command(BaseCommand): │
│ │
│ /home/dxh/others/nf-core-tools/.venv/lib64/python3.11/site-packages/rich_click/rich_command.py:1 │
│ 52 in main │
│ │
│ 149 │ │ try: │
│ 150 │ │ │ try: │
│ 151 │ │ │ │ with self.make_context(prog_name, args, **extra) as ctx: │
│ ❱ 152 │ │ │ │ │ rv = self.invoke(ctx) │
│ 153 │ │ │ │ │ if not standalone_mode: │
│ 154 │ │ │ │ │ │ return rv │
│ 155 │ │ │ │ │ # it's not safe to `ctx.exit(rv)` here! │
│ │
│ /home/dxh/others/nf-core-tools/.venv/lib64/python3.11/site-packages/click/core.py:1697 in invoke │
│ │
│ 1694 │ │ │ │ super().invoke(ctx) │
│ 1695 │ │ │ │ sub_ctx = cmd.make_context(cmd_name, args, parent=ctx) │
│ 1696 │ │ │ │ with sub_ctx: │
│ ❱ 1697 │ │ │ │ │ return _process_result(sub_ctx.command.invoke(sub_ctx)) │
│ 1698 │ │ │
│ 1699 │ │ # In chain mode we create the contexts step by step, but after the │
│ 1700 │ │ # base command has been invoked. Because at that point we do not │
│ │
│ /home/dxh/others/nf-core-tools/.venv/lib64/python3.11/site-packages/click/core.py:1697 in invoke │
│ │
│ 1694 │ │ │ │ super().invoke(ctx) │
│ 1695 │ │ │ │ sub_ctx = cmd.make_context(cmd_name, args, parent=ctx) │
│ 1696 │ │ │ │ with sub_ctx: │
│ ❱ 1697 │ │ │ │ │ return _process_result(sub_ctx.command.invoke(sub_ctx)) │
│ 1698 │ │ │
│ 1699 │ │ # In chain mode we create the contexts step by step, but after the │
│ 1700 │ │ # base command has been invoked. Because at that point we do not │
│ │
│ /home/dxh/others/nf-core-tools/.venv/lib64/python3.11/site-packages/click/core.py:1443 in invoke │
│ │
│ 1440 │ │ │ echo(style(message, fg="red"), err=True) │
│ 1441 │ │ │
│ 1442 │ │ if self.callback is not None: │
│ ❱ 1443 │ │ │ return ctx.invoke(self.callback, **ctx.params) │
│ 1444 │ │
│ 1445 │ def shell_complete(self, ctx: Context, incomplete: str) -> t.List["CompletionItem"]: │
│ 1446 │ │ """Return a list of completions for the incomplete value. Looks │
│ │
│ /home/dxh/others/nf-core-tools/.venv/lib64/python3.11/site-packages/click/core.py:788 in invoke │
│ │
│ 785 │ │ │
│ 786 │ │ with augment_usage_errors(__self): │
│ 787 │ │ │ with ctx: │
│ ❱ 788 │ │ │ │ return __callback(*args, **kwargs) │
│ 789 │ │
│ 790 │ def forward(__self, __cmd: "Command", *args: t.Any, **kwargs: t.Any) -> t.Any: │
│ 791 │ │ """Similar to :meth:`invoke` but fills in default keyword │
│ │
│ /home/dxh/others/nf-core-tools/.venv/lib64/python3.11/site-packages/click/decorators.py:33 in │
│ new_func │
│ │
│ 30 │ """ │
│ 31 │ │
│ 32 │ def new_func(*args: "P.args", **kwargs: "P.kwargs") -> "R": │
│ ❱ 33 │ │ return f(get_current_context(), *args, **kwargs) │
│ 34 │ │
│ 35 │ return update_wrapper(new_func, f) │
│ 36 │
│ │
│ /home/dxh/others/nf-core-tools/nf_core/__main__.py:1340 in command_modules_bump_versions │
│ │
│ 1337 │ Bump versions for one or more modules in a clone of │
│ 1338 │ the nf-core/modules repo. │
│ 1339 │ """ │
│ ❱ 1340 │ modules_bump_versions(ctx, tool, directory, all, show_all) │
│ 1341 │
│ 1342 │
│ 1343 # nf-core subworkflows click command │
│ │
│ /home/dxh/others/nf-core-tools/nf_core/commands_modules.py:352 in modules_bump_versions │
│ │
│ 349 │ │ │ ctx.obj["modules_repo_branch"], │
│ 350 │ │ │ ctx.obj["modules_repo_no_pull"], │
│ 351 │ │ ) │
│ ❱ 352 │ │ version_bumper.bump_versions(module=tool, all_modules=all, show_uptodate=show_al │
│ 353 │ except ModuleExceptionError as e: │
│ 354 │ │ log.error(e) │
│ 355 │ │ sys.exit(1) │
│ │
│ /home/dxh/others/nf-core-tools/nf_core/modules/bump_versions.py:79 in bump_versions │
│ │
│ 76 │ │ │ ) │
│ 77 │ │ │
│ 78 │ │ # Get list of all modules │
│ ❱ 79 │ │ _, nfcore_modules = nf_core.modules.modules_utils.get_installed_modules(self.dir │
│ 80 │ │ │
│ 81 │ │ # Load the .nf-core.yml config │
│ 82 │ │ _, self.tools_config = nf_core.utils.load_tools_config(self.directory) │
│ │
│ /home/dxh/others/nf-core-tools/nf_core/modules/modules_utils.py:87 in get_installed_modules │
│ │
│ 84 │ if local_modules_dir: │
│ 85 │ │ local_modules = [os.path.join(local_modules_dir, m) for m in local_modules] │
│ 86 │ │
│ ❱ 87 │ nfcore_modules = [ │
│ 88 │ │ NFCoreComponent( │
│ 89 │ │ │ m, │
│ 90 │ │ │ "nf-core/modules", │
│ │
│ /home/dxh/others/nf-core-tools/nf_core/modules/modules_utils.py:88 in <listcomp> │
│ │
│ 85 │ │ local_modules = [os.path.join(local_modules_dir, m) for m in local_modules] │
│ 86 │ │
│ 87 │ nfcore_modules = [ │
│ ❱ 88 │ │ NFCoreComponent( │
│ 89 │ │ │ m, │
│ 90 │ │ │ "nf-core/modules", │
│ 91 │ │ │ Path(nfcore_modules_dir, m), │
│ │
│ /home/dxh/others/nf-core-tools/nf_core/components/nfcore_component.py:98 in __init__ │
│ │
│ 95 │ │ │ self.test_yml = None │
│ 96 │ │ │ self.test_main_nf = None │
│ 97 │ │ │
│ ❱ 98 │ │ self.process_name: str = self._get_process_name() │
│ 99 │ │
│ 100 │ def __repr__(self) -> str: │
│ 101 │ │ return f"<NFCoreComponent {self.component_name} {self.component_dir} {self.repo_ │
│ │
│ /home/dxh/others/nf-core-tools/nf_core/components/nfcore_component.py:174 in _get_process_name │
│ │
│ 171 │ │ return included_components │
│ 172 │ │
│ 173 │ def _get_process_name(self): │
│ ❱ 174 │ │ with open(self.main_nf) as fh: │
│ 175 │ │ │ for line in fh: │
│ 176 │ │ │ │ if re.search(r"^\s*process\s*\w*\s*{", line): │
│ 177 │ │ │ │ │ return re.search(r"^\s*process\s*(\w*)\s*{.*", line).group(1) or "" │
╰──────────────────────────────────────────────────────────────────────────────────────────────────╯
NotADirectoryError: [Errno 20] Not a directory: 'modules/nf-core/cellranger/.gitignore/main.nf'System information
No response