diff --git a/lib/galaxy/tool_util/deps/container_resolvers/mulled.py b/lib/galaxy/tool_util/deps/container_resolvers/mulled.py index b976662ccf6b..87e311e5a542 100644 --- 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 index 38ddc860cc3b..f7bef84d18b5 100644 --- 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 index be956c84a8b9..8efc744a78d3 100644 --- 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"): diff --git a/test/unit/tool_util/mulled/test_mulled_build.py b/test/unit/tool_util/mulled/test_mulled_build.py index eb08e531d1fa..c9c37382e470 100644 --- a/test/unit/tool_util/mulled/test_mulled_build.py +++ b/test/unit/tool_util/mulled/test_mulled_build.py @@ -30,9 +30,8 @@ def test_base_image_for_targets(target, version, base_image): assert base_image_for_targets([target], conda_context) == base_image -@pytest.mark.parametrize("use_mamba", [False, True]) @external_dependency_management -def test_mulled_build_files_cli(use_mamba: bool, tmpdir) -> None: +def test_mulled_build_files_cli(tmpdir) -> None: singularity_image_dir = tmpdir.mkdir("singularity image dir") target = build_target("zlib", version="1.2.13", build="h166bdaf_4") involucro_context = InvolucroContext(involucro_bin=os.path.join(tmpdir, "involucro")) @@ -41,7 +40,6 @@ def test_mulled_build_files_cli(use_mamba: bool, tmpdir) -> None: involucro_context=involucro_context, command="build-and-test", singularity=True, - use_mamba=use_mamba, singularity_image_dir=singularity_image_dir, ) assert exit_code == 0