remove mamba special handling

galaxyproject · Dec 9, 2024 · 8d64d7e · 8d64d7e
1 parent 616fe39
commit 8d64d7e
Show file tree

Hide file tree

Showing 3 changed files with 3 additions and 34 deletions.
diff --git a/lib/galaxy/tool_util/deps/container_resolvers/mulled.py b/lib/galaxy/tool_util/deps/container_resolvers/mulled.py
@@ -738,7 +738,6 @@ def __init__(
             "namespace": namespace,
             "hash_func": self.hash_func,
             "command": "build-and-test",
-            "use_mamba": True,
         }
         self._mulled_kwds["channels"] = default_mulled_conda_channels_from_env() or self._get_config_option(
             "mulled_channels", DEFAULT_CHANNELS
@@ -789,7 +788,6 @@ def __init__(
             "namespace": "local",
             "singularity": True,
             "singularity_image_dir": self.cache_directory.path,
-            "use_mamba": True,
         }
         self.involucro_context = InvolucroContext(**self._involucro_context_kwds)
         auto_init = self._get_config_option("involucro_auto_init", True)

diff --git a/lib/galaxy/tool_util/deps/mulled/invfile.lua b/lib/galaxy/tool_util/deps/mulled/invfile.lua
@@ -42,7 +42,7 @@ end
 
 local conda_image = VAR.CONDA_IMAGE
 if conda_image == '' then
-    conda_image = 'quay.io/condaforge/mambaforge:latest'
+    conda_image = 'quay.io/condaforge/miniforge3:latest'
 end
 
 local conda_bin = VAR.CONDA_BIN

diff --git a/lib/galaxy/tool_util/deps/mulled/mulled_build.py b/lib/galaxy/tool_util/deps/mulled/mulled_build.py
@@ -211,8 +211,6 @@ def mull_targets(
     repository_template=DEFAULT_REPOSITORY_TEMPLATE,
     dry_run=False,
     conda_version=None,
-    mamba_version=None,
-    use_mamba=False,
     verbose=False,
     binds=DEFAULT_BINDS,
     rebuild=True,
@@ -303,24 +301,13 @@ def mull_targets(
 
     verbose = "--verbose" if verbose else "--quiet"
     conda_bin = "conda"
-    if use_mamba:
-        conda_bin = "mamba"
-        if mamba_version is None:
-            mamba_version = ""
     involucro_args.extend(["-set", f"CONDA_BIN={conda_bin}"])
-    if conda_version is not None or mamba_version is not None:
-        mamba_test = "true"
+    if conda_version is not None:
         specs = []
         if conda_version is not None:
             specs.append(f"conda={conda_version}")
-        if mamba_version is not None:
-            specs.append(f"mamba={mamba_version}")
-            if mamba_version == "" and not specs:
-                # If nothing but mamba without a specific version is requested,
-                # then only run conda install if mamba is not already installed.
-                mamba_test = "[ '[]' = \"$( conda list --json --full-name mamba )\" ]"
         conda_install = f"""conda install {verbose} --yes {" ".join(f"'{spec}'" for spec in specs)}"""
-        involucro_args.extend(["-set", f"PREINSTALL=if {mamba_test} ; then {conda_install} ; fi"])
+        involucro_args.extend(["-set", f"PREINSTALL={conda_install}"])
 
     involucro_args.append(command)
     if test_files:
@@ -493,18 +480,6 @@ def add_build_arguments(parser):
         default=None,
         help="Change to specified version of Conda before installing packages.",
     )
-    parser.add_argument(
-        "--mamba-version",
-        dest="mamba_version",
-        default=None,
-        help="Change to specified version of Mamba before installing packages.",
-    )
-    parser.add_argument(
-        "--use-mamba",
-        dest="use_mamba",
-        action="store_true",
-        help="Use Mamba instead of Conda for package installation.",
-    )
     parser.add_argument(
         "--oauth-token",
         dest="oauth_token",
@@ -570,10 +545,6 @@ def args_to_mull_targets_kwds(args):
         kwds["repository_template"] = args.repository_template
     if hasattr(args, "conda_version"):
         kwds["conda_version"] = args.conda_version
-    if hasattr(args, "mamba_version"):
-        kwds["mamba_version"] = args.mamba_version
-    if hasattr(args, "use_mamba"):
-        kwds["use_mamba"] = args.use_mamba
     if hasattr(args, "oauth_token"):
         kwds["oauth_token"] = args.oauth_token
     if hasattr(args, "rebuild"):