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allow module names with notations as in conda #961

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Merged
ewels merged 4 commits into from
Mar 24, 2021
Merged

allow module names with notations as in conda #961

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afa4a8b
Merge pull request #954 from nf-core/dev
ewels Mar 23, 2021
57fe2f8
Merge branch 'dev' of github.com:Erkison/tools into dev
Erkison Mar 24, 2021
dc9b3fd
allow module names with character notations as in conda
Erkison Mar 24, 2021
5cd47b0
request different module name on bioconda lookup fail
Erkison Mar 24, 2021
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51 changes: 35 additions & 16 deletions nf_core/modules/create.py
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Original file line number Diff line number Diff line change
Expand Up @@ -32,6 +32,7 @@ def __init__(self, directory=".", tool="", author=None, process_label=None, has_
self.has_meta = has_meta
self.force_overwrite = force

self.tool_conda_name = None
self.subtool = None
self.tool_licence = None
self.repo_type = None
Expand Down Expand Up @@ -117,26 +118,44 @@ def create(self):
self.file_paths = self.get_module_dirs()

# Try to find a bioconda package for 'tool'
try:
anaconda_response = nf_core.utils.anaconda_package(self.tool, ["bioconda"])
version = anaconda_response.get("latest_version")
if not version:
version = str(max([parse_version(v) for v in anaconda_response["versions"]]))
self.tool_licence = nf_core.utils.parse_anaconda_licence(anaconda_response, version)
self.tool_description = anaconda_response.get("summary", "")
self.tool_doc_url = anaconda_response.get("doc_url", "")
self.tool_dev_url = anaconda_response.get("dev_url", "")
self.bioconda = "bioconda::" + self.tool + "=" + version
log.info(f"Using Bioconda package: '{self.bioconda}'")
except (ValueError, LookupError) as e:
log.warning(
f"{e}\nBuilding module without tool software and meta, you will need to enter this information manually."
)
while True:
try:
if self.tool_conda_name:
anaconda_response = nf_core.utils.anaconda_package(self.tool_conda_name, ["bioconda"])
else:
anaconda_response = nf_core.utils.anaconda_package(self.tool, ["bioconda"])
version = anaconda_response.get("latest_version")
if not version:
version = str(max([parse_version(v) for v in anaconda_response["versions"]]))
self.tool_licence = nf_core.utils.parse_anaconda_licence(anaconda_response, version)
self.tool_description = anaconda_response.get("summary", "")
self.tool_doc_url = anaconda_response.get("doc_url", "")
self.tool_dev_url = anaconda_response.get("dev_url", "")
if self.tool_conda_name:
self.bioconda = "bioconda::" + self.tool_conda_name + "=" + version
else:
self.bioconda = "bioconda::" + self.tool + "=" + version
log.info(f"Using Bioconda package: '{self.bioconda}'")
break
except (ValueError, LookupError) as e:
if rich.prompt.Confirm.ask(
f"[violet]Could not find Conda dependency using the Anaconda API: '{self.tool}'. Do you want to enter a different bioconda package name?"
):
self.tool_conda_name = rich.prompt.Prompt.ask("[violet]Name of tool/subtool").strip()
continue
else:
log.warning(
f"{e}\nBuilding module without tool software and meta, you will need to enter this information manually."
)
break

# Try to get the container tag (only if bioconda package was found)
if self.bioconda:
try:
self.container_tag = nf_core.utils.get_biocontainer_tag(self.tool, version)
if self.tool_conda_name:
self.container_tag = nf_core.utils.get_biocontainer_tag(self.tool_conda_name, version)
else:
self.container_tag = nf_core.utils.get_biocontainer_tag(self.tool, version)
log.info(f"Using Docker / Singularity container with tag: '{self.container_tag}'")
except (ValueError, LookupError) as e:
log.info(f"Could not find a container tag ({e})")
Expand Down