Restore resolution of Conda environments generated from non-lowercase package names

Fix https://github.com/galaxyproject/galaxy/issues/16435 .

test/unit/tool_util/test_conda_resolution.py

@@ -1,6 +1,8 @@
 import os.path
 import tempfile
 
+import pytest
+
 from galaxy.tool_util.deps import DependencyManager
 from galaxy.tool_util.deps.conda_util import (
     best_search_result,
@@ -9,10 +11,16 @@ from galaxy.tool_util.deps.conda_util import (
     install_conda,
     installed_conda_targets,
 )
-from galaxy.tool_util.deps.requirements import ToolRequirement
+from galaxy.tool_util.deps.requirements import (
+    ToolRequirement,
+    ToolRequirements,
+)
+from galaxy.tool_util.deps.resolvers import NullDependency
 from galaxy.tool_util.deps.resolvers.conda import (
+    CondaDependency,
     CondaDependencyResolver,
     DEFAULT_ENSURE_CHANNELS,
+    MergedCondaDependency,
 )
 from .util import external_dependency_management
 
@@ -27,27 +35,94 @@ def test_install_conda_build(tmp_path) -> None:
     assert cc.conda_build_available
 
 
-@external_dependency_management
-def test_conda_resolution(tmp_path) -> None:
-    job_dir = os.path.join(tmp_path, "000")
-    dependency_manager = DependencyManager(tmp_path)
-    resolver = CondaDependencyResolver(
+@pytest.fixture(scope="module")
+def resolver(tmp_path_factory):
+    dependency_manager = DependencyManager(tmp_path_factory.mktemp("dependencies"))
+    return CondaDependencyResolver(
         dependency_manager,
         auto_init=True,
         auto_install=True,
         use_path_exec=False,  # For the test ensure this is always a clean install
     )
+
+
+@external_dependency_management
+def test_single_package_resolution(resolver: CondaDependencyResolver) -> None:
+    # Test that a read-only resolver returns a NullDependency
     resolver.read_only = True
-    req = ToolRequirement(name="samtools", version=None, type="package")
-    dependency = resolver.resolve(req, job_directory=job_dir)
+    package_name = "eXpress"
+    req = ToolRequirement(name=package_name, version=None, type="package")
+    dependency = resolver.resolve(req)
+    assert isinstance(dependency, NullDependency)
     assert dependency.shell_commands() is None
 
+    # Test that a (fake) environment generated from a non-lowercase package name
+    # is still accepted by the resolver
+    env_path = resolver.conda_context.env_path(f"__{package_name}@_uv_")
+    os.mkdir(env_path)
+    dependency = resolver.resolve(req)
+    assert isinstance(dependency, CondaDependency)
+    assert dependency.name == package_name
+    assert dependency.version is None
+    assert dependency.exact
+    assert dependency.environment_path == env_path
+    os.rmdir(env_path)
+
+    # Test that a non-read-only resolver creates a conda environment (with a
+    # lowercase package name) and returns a CondaDependency
     resolver.read_only = False
-    req = ToolRequirement(name="samtools", version=None, type="package")
-    dependency = resolver.resolve(req, job_directory=job_dir)
+    dependency = resolver.resolve(req)
+    assert isinstance(dependency, CondaDependency)
+    assert dependency.name == package_name
+    assert dependency.version is None
+    assert dependency.exact
+    assert dependency.environment_path == resolver.conda_context.env_path(f"__{package_name.lower()}@_uv_")
     assert dependency.shell_commands() is not None
 
 
+@external_dependency_management
+def test_multi_package_resolution(resolver: CondaDependencyResolver) -> None:
+    # Test that a read-only resolver returns an empty list
+    resolver.read_only = True
+    reqs = ToolRequirements(
+        [
+            ToolRequirement(name="samtools", version=None, type="package"),
+            ToolRequirement(name="eXpress", version=None, type="package"),
+        ]
+    )
+    dependency_list = resolver.resolve_all(reqs)
+    assert dependency_list == []
+
+    # Test that a (fake) mulled environment generated from non-lowercase package
+    # names is still accepted by the resolver
+    env_path = resolver.conda_context.env_path(
+        "mulled-v1-37955d8b3667efa38f1fe42bc37b4c9a03e67a90f0055d1db9d388b2f98fe3a1"
+    )
+    os.mkdir(env_path)
+    dependency_list = resolver.resolve_all(reqs)
+    assert len(dependency_list) == 2
+    for dependency in dependency_list:
+        assert isinstance(dependency, MergedCondaDependency)
+        assert dependency.version is None
+        assert dependency.exact
+        assert dependency.environment_path == env_path
+    os.rmdir(env_path)
+
+    # Test that a non-read-only resolver creates a mulled conda environment
+    # (with a hash from lowercase package names) and returns a list of
+    # MergedCondaDependency
+    resolver.read_only = False
+    dependency_list = resolver.resolve_all(reqs)
+    assert len(dependency_list) == 2
+    for dependency in dependency_list:
+        assert isinstance(dependency, MergedCondaDependency)
+        assert dependency.version is None
+        assert dependency.exact
+        assert dependency.environment_path == resolver.conda_context.env_path(
+            "mulled-v1-f36491d362c22cdb24f7de3e1ff978a5ee02cadc8c12a12ae06bce57bbf0765c"
+        )
+
+
 @external_dependency_management
 def test_against_conda_prefix_regression() -> None:
     """Test that would fail if https://github.com/rtfd/readthedocs.org/issues/1902 regressed."""