local variable 'docker_image_name' referenced before assignment #2390
Description
Description of the bug
When i try to create a new module using nf-core tools i get an error. It doesn't happen when i try to create modules with other names such as bcftools/fakemodule or cell/phone. Looks like it can find a docker image but not a singularity image, and the evaluation of the following line:
Line 734 in e5ce6ce
leads to a set size of 0. so a few lines down the loop is never executed because the set it's looping on is empty and docker_image_name is never instantiated and singularity_image is not updated (instantiated as None earlier in the function).
I can see that the csvtk singularity image can't be found because i run the following commands in python:
package = "csvtk"
version = "0.26.0"
biocontainers_api_url = f"https://api.biocontainers.pro/ga4gh/trs/v2/tools/{package}/versions/{package}-{version}"
response = requests.get(biocontainers_api_url)
images = response.json()["images"]
[ i['image_type'] for i in images]
# ['Conda', 'Docker']
(others show ['Conda', 'Docker', 'Singularity']
Command used and terminal output
$ nf-core modules create -d . csvtk/join
,--./,-.
___ __ __ __ ___ /,-._.--~\
|\ | |__ __ / ` / \ |__) |__ } {
| \| | \__, \__/ | \ |___ \`-._,-`-,
`._,._,'
nf-core/tools version 2.9 - https://nf-co.re
INFO Repository type: modules
INFO Press enter to use default values (shown in brackets) or type your own responses. ctrl+click underlined text to
open links.
INFO Using Bioconda package: 'bioconda::csvtk=0.26.0'
╭─────────────────────────────── Traceback (most recent call last) ────────────────────────────────╮
│ /home/noronhaa/anaconda3/envs/nf-core/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/noronhaa/anaconda3/envs/nf-core/lib/python3.10/site-packages/nf_core/__main__.py:110 in │
│ run_nf_core │
│ │
│ 107 │ │ │ log.debug(f"Could not check latest version: {e}") │
│ 108 │ │ stderr.print("\n") │
│ 109 │ # Launch the click cli │
│ ❱ 110 │ nf_core_cli(auto_envvar_prefix="NFCORE") │
│ 111 │
│ 112 │
│ 113 @click.group(context_settings=dict(help_option_names=["-h", "--help"])) │
│ │
│ /home/noronhaa/anaconda3/envs/nf-core/lib/python3.10/site-packages/click/core.py:1130 in │
│ __call__ │
│ │
│ 1127 │ │
│ 1128 │ def __call__(self, *args: t.Any, **kwargs: t.Any) -> t.Any: │
│ 1129 │ │ """Alias for :meth:`main`.""" │
│ ❱ 1130 │ │ return self.main(*args, **kwargs) │
│ 1131 │
│ 1132 │
│ 1133 class Command(BaseCommand): │
│ │
│ /home/noronhaa/anaconda3/envs/nf-core/lib/python3.10/site-packages/rich_click/rich_group.py:21 │
│ in main │
│ │
│ 18 │ │
│ 19 │ def main(self, *args, standalone_mode: bool = True, **kwargs): │
│ 20 │ │ try: │
│ ❱ 21 │ │ │ rv = super().main(*args, standalone_mode=False, **kwargs) │
│ 22 │ │ │ if not standalone_mode: │
│ 23 │ │ │ │ return rv │
│ 24 │ │ except click.ClickException as e: │
│ │
│ /home/noronhaa/anaconda3/envs/nf-core/lib/python3.10/site-packages/click/core.py:1055 in main │
│ │
│ 1052 │ │ try: │
│ 1053 │ │ │ try: │
│ 1054 │ │ │ │ with self.make_context(prog_name, args, **extra) as ctx: │
│ ❱ 1055 │ │ │ │ │ rv = self.invoke(ctx) │
│ 1056 │ │ │ │ │ if not standalone_mode: │
│ 1057 │ │ │ │ │ │ return rv │
│ 1058 │ │ │ │ │ # it's not safe to `ctx.exit(rv)` here! │
│ │
│ /home/noronhaa/anaconda3/envs/nf-core/lib/python3.10/site-packages/click/core.py:1657 in invoke │
│ │
│ 1654 │ │ │ │ super().invoke(ctx) │
│ 1655 │ │ │ │ sub_ctx = cmd.make_context(cmd_name, args, parent=ctx) │
│ 1656 │ │ │ │ with sub_ctx: │
│ ❱ 1657 │ │ │ │ │ return _process_result(sub_ctx.command.invoke(sub_ctx)) │
│ 1658 │ │ │
│ 1659 │ │ # In chain mode we create the contexts step by step, but after the │
│ 1660 │ │ # base command has been invoked. Because at that point we do not │
│ │
│ /home/noronhaa/anaconda3/envs/nf-core/lib/python3.10/site-packages/click/core.py:1657 in invoke │
│ │
│ 1654 │ │ │ │ super().invoke(ctx) │
│ 1655 │ │ │ │ sub_ctx = cmd.make_context(cmd_name, args, parent=ctx) │
│ 1656 │ │ │ │ with sub_ctx: │
│ ❱ 1657 │ │ │ │ │ return _process_result(sub_ctx.command.invoke(sub_ctx)) │
│ 1658 │ │ │
│ 1659 │ │ # In chain mode we create the contexts step by step, but after the │
│ 1660 │ │ # base command has been invoked. Because at that point we do not │
│ │
│ /home/noronhaa/anaconda3/envs/nf-core/lib/python3.10/site-packages/click/core.py:1404 in invoke │
│ │
│ 1401 │ │ │ echo(style(message, fg="red"), err=True) │
│ 1402 │ │ │
│ 1403 │ │ if self.callback is not None: │
│ ❱ 1404 │ │ │ return ctx.invoke(self.callback, **ctx.params) │
│ 1405 │ │
│ 1406 │ def shell_complete(self, ctx: Context, incomplete: str) -> t.List["CompletionItem"]: │
│ 1407 │ │ """Return a list of completions for the incomplete value. Looks │
│ │
│ /home/noronhaa/anaconda3/envs/nf-core/lib/python3.10/site-packages/click/core.py:760 in invoke │
│ │
│ 757 │ │ │
│ 758 │ │ with augment_usage_errors(__self): │
│ 759 │ │ │ with ctx: │
│ ❱ 760 │ │ │ │ return __callback(*args, **kwargs) │
│ 761 │ │
│ 762 │ def forward( │
│ 763 │ │ __self, __cmd: "Command", *args: t.Any, **kwargs: t.Any # noqa: B902 │
│ │
│ /home/noronhaa/anaconda3/envs/nf-core/lib/python3.10/site-packages/click/decorators.py:26 in │
│ new_func │
│ │
│ 23 │ """ │
│ 24 │ │
│ 25 │ def new_func(*args, **kwargs): # type: ignore │
│ ❱ 26 │ │ return f(get_current_context(), *args, **kwargs) │
│ 27 │ │
│ 28 │ return update_wrapper(t.cast(F, new_func), f) │
│ 29 │
│ │
│ /home/noronhaa/anaconda3/envs/nf-core/lib/python3.10/site-packages/nf_core/__main__.py:800 in │
│ create_module │
│ │
│ 797 │ │ module_create = ModuleCreate( │
│ 798 │ │ │ dir, tool, author, label, has_meta, force, conda_name, conda_package_version │
│ 799 │ │ ) │
│ ❱ 800 │ │ module_create.create() │
│ 801 │ except UserWarning as e: │
│ 802 │ │ log.critical(e) │
│ 803 │ │ sys.exit(1) │
│ │
│ /home/noronhaa/anaconda3/envs/nf-core/lib/python3.10/site-packages/nf_core/components/create.py: │
│ 139 in create │
│ │
│ 136 │ │ │
│ 137 │ │ if self.component_type == "modules": │
│ 138 │ │ │ # Try to find a bioconda package for 'component' │
│ ❱ 139 │ │ │ self._get_bioconda_tool() │
│ 140 │ │ │
│ 141 │ │ # Prompt for GitHub username │
│ 142 │ │ self._get_username() │
│ │
│ /home/noronhaa/anaconda3/envs/nf-core/lib/python3.10/site-packages/nf_core/components/create.py: │
│ 227 in _get_bioconda_tool │
│ │
│ 224 │ │ │ │ │ │ self.tool_conda_name, version │
│ 225 │ │ │ │ │ ) │
│ 226 │ │ │ │ else: │
│ ❱ 227 │ │ │ │ │ self.docker_container, self.singularity_container = nf_core.utils.ge │
│ 228 │ │ │ │ │ │ self.component, version │
│ 229 │ │ │ │ │ ) │
│ 230 │ │ │ │ log.info(f"Using Docker container: '{self.docker_container}'") │
│ │
│ /home/noronhaa/anaconda3/envs/nf-core/lib/python3.10/site-packages/nf_core/utils.py:744 in │
│ get_biocontainer_tag │
│ │
│ 741 │ │ │ │ │ │ singularity_image = all_singularity[k]["image"] │
│ 742 │ │ │ │ │ │ current_date = date │
│ 743 │ │ │ │ │ │ docker_image_name = docker_image["image_name"].lstrip("quay.io/" │
│ ❱ 744 │ │ │ │ return docker_image_name, singularity_image["image_name"] │
│ 745 │ │ │ except TypeError: │
│ 746 │ │ │ │ raise LookupError(f"Could not find docker or singularity container for { │
│ 747 │ │ elif response.status_code != 404: │
╰──────────────────────────────────────────────────────────────────────────────────────────────────╯
UnboundLocalError: local variable 'docker_image_name' referenced before assignmentSystem information
CentOSLinux, Python 3.10, nf-core version 2.9