fix mulled v2 hash generation from strings

the build information that may be contained in requirement versions is considered
as part of the version in some places of the code

- mulled container resolvers
- mulled-build-tool
- [planemo](https://github.com/galaxyproject/planemo/blob/b3e12a334e3d358ce30bf2c8c3f8d5a7a7e08136/planemo/conda.py#L116)

in others it isn't:

- mulled-hash
- mulled-build-files
- mulled_build

which are the files that use the `target_str_to_targets` function.

With this change the build info in version strings is always considered
as part of the version.

`mulled-build-files` is used in the multi-package-containers repo which
led to wrong hashes in up to approx 50 tools (check with `grep "=[^,]*=" combinations/* | wc -l`).

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

@@ -352,7 +352,7 @@ def mull_targets(
     with PrintProgress():
         ret = involucro_context.exec_command(involucro_args)
     if singularity:
-        # we can not remove this folder as it contains the image wich is owned by root
+        # we can not remove this folder as it contains the image which is owned by root
         pass
         # shutil.rmtree('./singularity_import')
     return ret
@@ -531,12 +531,7 @@ def target_str_to_targets(targets_raw):
     def parse_target(target_str):
         if "=" in target_str:
             package_name, version = target_str.split("=", 1)
-            build = None
-            if "=" in version:
-                version, build = version.split("=")
-            elif "--" in version:
-                version, build = version.split("--")
-            target = build_target(package_name, version, build)
+            target = build_target(package_name, version)
         else:
             target = build_target(target_str)
         return target
@@ -584,6 +579,8 @@ def args_to_mull_targets_kwds(args):
         kwds["singularity_image_dir"] = args.singularity_image_dir
     if hasattr(args, "invfile"):
         kwds["invfile"] = args.invfile
+    if hasattr(args, "base_image"):
+        kwds["base_image"] = args.base_image
 
     kwds["involucro_context"] = context_from_args(args)
 

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

@@ -27,6 +27,23 @@
     from galaxy.tool_util.deps.conda_util import CondaTarget
 
 
+def _mulled_build_tool(tool, args):
+    """
+    >>> import doctest
+    >>> doctest.ELLIPSIS_MARKER = '-ignore-'
+    >>> import argparse
+    >>> _mulled_build_tool("test/functional/tools/mulled_example_multi_1.xml", argparse.Namespace(dry_run=True, base_image="does-not-matter-here-but-test-is-fast", command="build", verbose=True, involucro_path="./involucro"))  # doctest: +ELLIPSIS
+    -ignore- REPO=quay.io/biocontainers/mulled-v2-8186960447c5cb2faa697666dc1e6d919ad23f3e:a6419f25efff953fc505dbd5ee734856180bb619-0 -ignore-
+    >>> _mulled_build_tool("test/functional/tools/mulled_example_multi_2.xml", argparse.Namespace(dry_run=True, base_image="does-not-matter-here-but-test-is-fast", command="build", verbose=True, involucro_path="./involucro"))  # doctest: +ELLIPSIS
+    -ignore- REPO=quay.io/biocontainers/mulled-v2-8186960447c5cb2faa697666dc1e6d919ad23f3e:8e86df67d257ce6494ae12b2c60e1b94025ea529-0 -ignore-
+    """ 
+    tool_source = get_tool_source(tool)
+    requirements, *_ = tool_source.parse_requirements_and_containers()
+    targets = requirements_to_mulled_targets(requirements)
+    kwds = args_to_mull_targets_kwds(args)
+    mull_targets(targets, **kwds)
+
+
 def main(argv=None) -> None:
     """Main entry-point for the CLI tool."""
     parser = arg_parser(argv, globals())
@@ -35,12 +52,7 @@ def main(argv=None) -> None:
     parser.add_argument("command", metavar="COMMAND", help="Command (build-and-test, build, all)")
     parser.add_argument("tool", metavar="TOOL", default=None, help="Path to tool to build mulled image for.")
     args = parser.parse_args()
-    tool_source = get_tool_source(args.tool)
-    requirements, *_ = tool_source.parse_requirements_and_containers()
-    targets = requirements_to_mulled_targets(requirements)
-    kwds = args_to_mull_targets_kwds(args)
-    mull_targets(targets, **kwds)
-
+    _mulled_build_tool(args.tool, args)
 
 def requirements_to_mulled_targets(requirements) -> List["CondaTarget"]:
     """Convert Galaxy's representation of requirements into a list of CondaTarget objects.

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

@@ -16,17 +16,29 @@
 )
 
 
+def _mulled_hash(hash, targets):
+    """
+    >>> _mulled_hash(hash="v2", targets="samtools=1.3.1,bedtools=2.26.0")
+    'mulled-v2-8186960447c5cb2faa697666dc1e6d919ad23f3e:a6419f25efff953fc505dbd5ee734856180bb619'
+    >>> _mulled_hash(hash="v2", targets="samtools=1.3.1=h9071d68_10,bedtools=2.26.0=0")
+    'mulled-v2-8186960447c5cb2faa697666dc1e6d919ad23f3e:8e86df67d257ce6494ae12b2c60e1b94025ea529'
+    """
+    targets = target_str_to_targets(targets)
+    image_name = v2_image_name if hash == "v2" else v1_image_name
+    return image_name(targets)
+
+
 def main(argv=None):
-    """Main entry-point for the CLI tool."""
+    """
+    Main entry-point for the CLI tool.
+    """
     parser = arg_parser(argv, globals())
     parser.add_argument(
         "targets", metavar="TARGETS", default=None, help="Comma-separated packages for calculating the mulled hash."
     )
     parser.add_argument("--hash", dest="hash", choices=["v1", "v2"], default="v2")
     args = parser.parse_args()
-    targets = target_str_to_targets(args.targets)
-    image_name = v2_image_name if args.hash == "v2" else v1_image_name
-    print(image_name(targets))
+    print(_mulled_hash(args.hash, args.targets))
 
 
 __all__ = ("main",)