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fix: fix assertion error in conda env file spec when applying wildcards (thanks @ddesvillechabrol) #1377

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merged 3 commits into from Feb 5, 2022
Merged

fix: fix assertion error in conda env file spec when applying wildcards (thanks @ddesvillechabrol) #1377

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1b4cb1a
fix: fix assertion error in conda env file spec when applying wildcards
johanneskoester Feb 5, 2022
5f8dda8
fix arg passing
johanneskoester Feb 5, 2022
12e4459
fix arg number
johanneskoester Feb 5, 2022
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6 changes: 3 additions & 3 deletions snakemake/deployment/conda.py
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Expand Up @@ -696,12 +696,12 @@ def __init__(self, filepath: str, rule=None):
else:
self.file = IOFile(filepath, rule=rule)

def apply_wildcards(self, wildcards):
def apply_wildcards(self, wildcards, rule):
filepath = self.file.apply_wildcards(wildcards)
if is_local_file(filepath):
# Normalize 'file:///my/path.yml' to '/my/path.yml'
filepath = parse_uri(filepath).uri_path
return CondaEnvFileSpec(filepath)
return CondaEnvFileSpec(filepath, rule)

def check(self):
self.file.check()
Expand All @@ -728,7 +728,7 @@ class CondaEnvNameSpec(CondaEnvSpec):
def __init__(self, name: str):
self.name = name

def apply_wildcards(self, wildcards):
def apply_wildcards(self, wildcards, _):
return CondaEnvNameSpec(apply_wildcards(self.name, wildcards))

def get_conda_env(self, workflow, env_dir=None, container_img=None, cleanup=None):
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4 changes: 3 additions & 1 deletion snakemake/rules.py
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Expand Up @@ -1050,7 +1050,9 @@ def expand_group(self, wildcards):
def expand_conda_env(self, wildcards):
try:
conda_env = (
self.conda_env.apply_wildcards(wildcards) if self.conda_env else None
self.conda_env.apply_wildcards(wildcards, self)
if self.conda_env
else None
)
except WildcardError as e:
raise WildcardError(
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