[WIP] hash.tsv new format plus linting and auto-adding hashes

.gitignore

@@ -7,6 +7,7 @@ scripts/scramble/lib
 scripts/scramble/archives
 
 # Python virtualenv
+venv
 .venv
 .venv3
 

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

@@ -513,7 +513,7 @@ def add_single_image_arguments(parser):
     )
 
 
-def target_str_to_targets(targets_raw):
+def parse_targets(targets_raw):
     def parse_target(target_str):
         if "=" in target_str:
             package_name, version = target_str.split("=", 1)
@@ -596,7 +596,7 @@ def main(argv=None):
         "The source:dest docker syntax is respected. If relative file paths are given, files will be mounted in /source/<relative_file_path>",
     )
     args = parser.parse_args()
-    targets = target_str_to_targets(args.targets)
+    targets = parse_targets(args.targets)
     sys.exit(mull_targets(targets, **args_to_mull_targets_kwds(args)))
 
 

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

@@ -23,7 +23,7 @@
     args_to_mull_targets_kwds,
     BuildExistsException,
     mull_targets,
-    target_str_to_targets,
+    parse_targets,
 )
 
 KNOWN_FIELDS = ["targets", "image_build", "name_override", "base_image"]
@@ -101,7 +101,7 @@ def line_to_targets(line_str, line_tuple):
         len(line_parts) <= n_fields
     ), f"Too many fields in line [{line_str}], expect at most {n_fields} - targets, image build number, and name override."
     line_parts += [None] * (n_fields - len(line_parts))
-    line_parts[targets_column] = target_str_to_targets(line_parts[targets_column])
+    line_parts[targets_column] = parse_targets(line_parts[targets_column])
     return line_tuple(*line_parts)
 
 

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

@@ -9,7 +9,7 @@
 """
 
 from ._cli import arg_parser
-from .mulled_build import target_str_to_targets
+from .mulled_build import parse_targets
 from .util import (
     v1_image_name,
     v2_image_name,
@@ -24,7 +24,7 @@ def main(argv=None):
     )
     parser.add_argument("--hash", dest="hash", choices=["v1", "v2"], default="v2")
     args = parser.parse_args()
-    targets = target_str_to_targets(args.targets)
+    targets = parse_targets(args.targets)
     image_name = v2_image_name if args.hash == "v2" else v1_image_name
     print(image_name(targets))
 

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

@@ -239,6 +239,17 @@ def _simple_image_name(targets, image_build=None):
     return f"{target.package_name}{suffix}"
 
 
+def sort_build_targets(build_targets):
+    """Sort build targets by package name.
+
+    >>> ordered_targets = [Target(package_name='bioblend=1.0.0', version=None, build=None, package='bioblend=1.0.0'), Target(package_name='galaxyxml=0.4.14', version=None, build=None, package='galaxyxml=0.4.14')]
+    >>> unordered_targets = reversed(ordered_targets)
+    >>> assert ordered_targets == sort_build_targets(ordered_targets)
+    >>> assert ordered_targets == sort_build_targets(unordered_targets)
+    """
+    return sorted(build_targets, key=lambda t: t.package_name)
+
+
 def v1_image_name(targets, image_build=None, name_override=None):
     """Generate mulled hash version 1 container identifier for supplied arguments.
 
@@ -270,7 +281,7 @@ def v1_image_name(targets, image_build=None, name_override=None):
     if len(targets) == 1:
         return _simple_image_name(targets, image_build=image_build)
     else:
-        targets_order = sorted(targets, key=lambda t: t.package_name)
+        targets_order = sort_build_targets(targets)
         requirements_buffer = "\n".join(map(conda_build_target_str, targets_order))
         m = hashlib.sha1()
         m.update(requirements_buffer.encode())
@@ -318,7 +329,7 @@ def v2_image_name(targets, image_build=None, name_override=None):
     if len(targets) == 1:
         return _simple_image_name(targets, image_build=image_build)
     else:
-        targets_order = sorted(targets, key=lambda t: t.package_name)
+        targets_order = sort_build_targets(targets)
         package_name_buffer = "\n".join(map(lambda t: t.package_name, targets_order))
         package_hash = hashlib.sha1()
         package_hash.update(package_name_buffer.encode())

test/unit/tool_util/mulled/test_mulled_build.py

@@ -10,7 +10,7 @@
     DEFAULT_EXTENDED_BASE_IMAGE,
     InvolucroContext,
     mull_targets,
-    target_str_to_targets,
+    parse_targets,
 )
 from ..util import external_dependency_management
 
@@ -49,6 +49,6 @@ def test_mulled_build_files_cli(use_mamba, tmpdir):
 
 def test_target_str_to_targets():
     target_str = "samtools=1.3.1--4,bedtools=2.22"
-    targets = target_str_to_targets(target_str)
+    targets = parse_targets(target_str)
     assert (targets[0].package, targets[0].version, targets[0].build) == ("samtools", "1.3.1", "4")
     assert (targets[1].package, targets[1].version, targets[1].build) == ("bedtools", "2.22", None)

test/unit/tool_util/mulled/test_mulled_build_files.py

@@ -3,7 +3,7 @@
 import pytest
 import yaml
 
-from galaxy.tool_util.deps.mulled.mulled_build import target_str_to_targets
+from galaxy.tool_util.deps.mulled.mulled_build import parse_targets
 from galaxy.tool_util.deps.mulled.mulled_build_files import (
     FALLBACK_LINE_TUPLE,
     generate_targets,
@@ -62,7 +62,7 @@
     "content, equals", [(d[k]["content"], d[k]["equals"]) for k, d in zip(TEST_IDS, TESTCASES)], ids=TEST_IDS
 )
 def test_generate_targets(content, equals):
-    equals["targets"] = target_str_to_targets(equals["targets"])
+    equals["targets"] = parse_targets(equals["targets"])
     equals = FALLBACK_LINE_TUPLE(**equals)
     with tempfile.NamedTemporaryFile(mode="w") as tmpfile:
         tmpfile.write(content)