🎨 editable workflows use .snakemake for conda envs #38

snk/cli/cli.py

@@ -54,12 +54,8 @@ def __init__(self, workflow_dir_path: Path = None) -> None:
                 self.version = self.workflow.commit
         self.options = build_dynamic_cli_options(self.snakemake_config, self.snk_config)
         self.snakefile = self._find_snakefile()
-        self.conda_prefix_dir = workflow_dir_path / ".conda"
-        if " " in str(workflow_dir_path):
-            # cannot have spaces!
-            self.singularity_prefix_dir = None
-        else:
-            self.singularity_prefix_dir = workflow_dir_path / ".singularity"
+        self.conda_prefix_dir = self.workflow.conda_prefix_dir
+        self.singularity_prefix_dir = self.workflow.singularity_prefix_dir
         self.name = self.workflow.name
         self.verbose = False
         if (

snk/main.py

@@ -192,7 +192,7 @@ def list(
     for workflow in workflows:
         if workflow.editable:
             print(
-                f'- {workflow.name} ([bold green]editable[/bold green]) -> "{workflow.path}"'
+                f'- {workflow.name} ([bold green]editable[/bold green]) -> "{workflow.path.resolve()}"'
             )
             continue
         print(f"- {workflow.name} ([bold green]{workflow.version}[/bold green])")

snk/nest.py

@@ -428,7 +428,7 @@ def create_executable(self, workflow_path: Path, name: str) -> Path:
             from snk import create_cli
             if __name__ == "__main__":
                 sys.argv[0] = re.sub(r'(-script\.pyw|\.exe)?$', '', sys.argv[0])
-                sys.exit(create_cli("{workflow_path.resolve()}"))
+                sys.exit(create_cli("{workflow_path}"))
                 
         """
         )

snk/workflow.py

@@ -35,6 +35,7 @@ def __init__(self, path: Path) -> None:
                 self.repo = None
         self.name = self.path.name
 
+
     @property
     def tag(self):
         """
@@ -43,7 +44,6 @@ def tag(self):
             str: The tag of the workflow, or None if no tag is found.
         """
         try:
-            # TODO: default to commit
             tag = self.repo.git.describe(["--tags", "--exact-match"])
         except Exception:
             tag = None
@@ -91,6 +91,28 @@ def executable(self):
         if sys.platform.startswith("win"):
             name += ".exe"
         return workflow_bin_dir / name
+
+    @property
+    def conda_prefix_dir(self):
+        """
+        Gets the conda prefix directory of the workflow.
+        Returns:
+            Path: The path to the conda prefix directory.
+        """
+        return Path(".snakemake") / "conda" if self.editable else self.path / ".conda"
+
+    @property
+    def singularity_prefix_dir(self):
+        """
+        Gets the singularity prefix directory of the workflow.
+        Returns:
+            Path: The path to the singularity prefix directory.
+        """
+        if " " in str(self.path):
+            # sigh, snakemake singularity does not support spaces in the path
+            # https://github.com/snakemake/snakemake/blob/2ecb21ba04088b9e6850447760f713784cf8b775/snakemake/deployment/singularity.py#L130C1-L131C1
+            return None
+        return Path(".snakemake") / "singularity" if self.editable else self.path / ".singularity"
 
     @property
     def editable(self):