fix: convert conda env to string before checks (snakemake#1382)

MSamman · web-flow · commit 7a8da9fbf01a · 2022-02-09T14:40:43.000+01:00
diff --git a/snakemake/workflow.py b/snakemake/workflow.py
@@ -1484,6 +1484,9 @@ def decorate(ruleinfo):
                         rule=rule,
                     )
 
+                if isinstance(ruleinfo.conda_env, Path):
+                    ruleinfo.conda_env = str(ruleinfo.conda_env)
+
                 if (
                     ruleinfo.conda_env is not None
                     and is_conda_env_file(ruleinfo.conda_env)
diff --git a/tests/test_conda/Snakefile b/tests/test_conda/Snakefile
@@ -1,4 +1,5 @@
 shell.executable("bash")
+conda_env = Path("test-env.yaml")
 
 rule all:
     input:
@@ -19,6 +20,6 @@ rule b:
     output:
         "test{i}.out2"
     conda:
-        "test-env.yaml"
+        conda_env
     shell:
         "Tm -h > {output} || true"

Original file line number	Diff line number	Diff line change
`@@ -1484,6 +1484,9 @@ def decorate(ruleinfo):`
`1484`	`1484`	`rule=rule,`
`1485`	`1485`	`)`
`1486`	`1486`
	`1487`	`+ if isinstance(ruleinfo.conda_env, Path):`
	`1488`	`+ ruleinfo.conda_env = str(ruleinfo.conda_env)`
	`1489`	`+`
`1487`	`1490`	`if (`
`1488`	`1491`	`ruleinfo.conda_env is not None`
`1489`	`1492`	`and is_conda_env_file(ruleinfo.conda_env)`