Merge pull request #14770 from johanneskoester/feat/mulled-mamba-support

feat: mamba support for mulled-build

lib/galaxy/tool_util/deps/mulled/invfile.lua

@@ -42,9 +42,10 @@ end
 
 local conda_image = VAR.CONDA_IMAGE
 if conda_image == '' then
-    conda_image = 'continuumio/miniconda3:latest'
+    conda_image = 'quay.io/condaforge/mambaforge:latest'
 end
 
+local conda_bin = VAR.CONDA_BIN
 
 local singularity_image = VAR.SINGULARITY_IMAGE
 if singularity_image == '' then
@@ -87,7 +88,7 @@ inv.task('build')
     .using(conda_image)
         .withHostConfig({binds = bind_args})
         .run('/bin/sh', '-c', preinstall
-            .. 'conda install '
+            .. conda_bin .. ' install '
             .. channel_args .. ' '
             .. target_args
             .. ' --strict-channel-priority -p /usr/local --copy --yes '

lib/galaxy/tool_util/deps/mulled/mulled_build.py

@@ -197,6 +197,8 @@ 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,
@@ -284,9 +286,28 @@ def mull_targets(
         involucro_args.extend(["-set", f"USER_ID={os.getuid()}:{os.getgid()}"])
     if test:
         involucro_args.extend(["-set", f"TEST={test}"])
-    if conda_version is not None:
-        verbose = "--verbose" if verbose else "--quiet"
-        involucro_args.extend(["-set", f"PREINSTALL=conda install {verbose} --yes conda={conda_version}"])
+
+    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", "CONDA_BIN=%s" % conda_bin])
+    if conda_version is not None or mamba_version is not None:
+        mamba_test = "true"
+        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.append(command)
     if test_files:
         test_bind = []
@@ -456,6 +477,18 @@ 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",
@@ -521,6 +554,10 @@ 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"):

test/unit/tool_util/mulled/test_mulled_build.py

@@ -27,11 +27,18 @@ 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(tmpdir):
+def test_mulled_build_files_cli(use_mamba, tmpdir):
     singularity_image_dir = tmpdir.mkdir("singularity image dir")
     target = build_target("zlib")
-    mull_targets([target], command="build-and-test", singularity=True, singularity_image_dir=singularity_image_dir)
+    mull_targets(
+        [target],
+        command="build-and-test",
+        singularity=True,
+        use_mamba=use_mamba,
+        singularity_image_dir=singularity_image_dir,
+    )
     assert singularity_image_dir.join("zlib").exists()