🐛 check for mamba when creating envs

snk/cli/snakemake_workflow.py

@@ -8,6 +8,7 @@
     common,
 )
 from snakemake.persistence import Persistence
+from snk.cli.utils import check_command_available
 import os
 
 @dataclass
@@ -101,6 +102,9 @@ def create_snakemake_workflow(
             os.makedirs(workdir)
         workdir = os.path.abspath(workdir)
         os.chdir(workdir)
+
+    if check_command_available("mamba"):
+        conda_frontend = "mamba"
 
     workflow = Workflow(
         snakefile=snakefile,

snk/cli/subcommands/run.py

@@ -9,6 +9,7 @@
 from snk.cli.utils import (
     parse_config_args,
     dag_filetype_callback,
+    check_command_available
 )
 
 from snk.cli.config.config import (
@@ -409,21 +410,6 @@ def remove_resource(resource: Path):
                     remove_resource(copied_resource)
 
 
-def check_command_available(command: str):
-    """
-    Check if a command is available.
-    Args:
-      command (str): The command to check.
-    Returns:
-      bool: True if the command is available, False otherwise.
-    Examples:
-      >>> CLI.check_command_available('ls')
-    """
-    import shutil
-
-    return shutil.which(command) is not None
-
-
 def parse_config_monkeypatch(args):
     """Monkeypatch the parse_config function from snakemake."""
     import yaml

snk/cli/utils.py

@@ -12,6 +12,21 @@
 from snk.cli.options import Option
 
 
+def check_command_available(command: str):
+    """
+    Check if a command is available.
+    Args:
+      command (str): The command to check.
+    Returns:
+      bool: True if the command is available, False otherwise.
+    Examples:
+      >>> CLI.check_command_available('ls')
+    """
+    from shutil import which
+
+    return which(command) is not None
+
+
 def flatten(d, parent_key="", sep=":"):
     """
     Flattens a nested dictionary.