Merge pull request #19896 from nsoranzo/release_24.0_drop_alembic-utils

mvdbeek · web-flow · commit a1418f3f301b · 2025-03-26T09:42:35.000+01:00
[24.0] Drop unused alembic-utils from galaxy-data package requirements
diff --git a/.github/workflows/api.yaml b/.github/workflows/api.yaml
@@ -5,11 +5,13 @@ on:
       - 'client/**'
       - 'doc/**'
       - 'lib/galaxy_test/selenium/**'
+      - 'packages/**'
   pull_request:
     paths-ignore:
       - 'client/**'
       - 'doc/**'
       - 'lib/galaxy_test/selenium/**'
+      - 'packages/**'
   schedule:
     # Run at midnight UTC every Tuesday
     - cron: '0 0 * * 2'
diff --git a/.github/workflows/converter_tests.yaml b/.github/workflows/converter_tests.yaml
@@ -4,10 +4,12 @@ on:
     paths-ignore:
       - 'client/**'
       - 'doc/**'
+      - 'packages/**'
   pull_request:
     paths-ignore:
       - 'client/**'
       - 'doc/**'
+      - 'packages/**'
   schedule:
     # Run at midnight UTC every Tuesday
     - cron: '0 0 * * 2'
diff --git a/.github/workflows/cwl_conformance.yaml b/.github/workflows/cwl_conformance.yaml
@@ -4,10 +4,12 @@ on:
     paths-ignore:
       - 'client/**'
       - 'doc/**'
+      - 'packages/**'
   pull_request:
     paths-ignore:
       - 'client/**'
       - 'doc/**'
+      - 'packages/**'
 env:
   GALAXY_TEST_DBURI: 'postgresql://postgres:postgres@localhost:5432/galaxy?client_encoding=utf8'
 concurrency:
diff --git a/.github/workflows/db_indexes.yaml b/.github/workflows/db_indexes.yaml
@@ -5,11 +5,13 @@ on:
       - 'client/**'
       - 'doc/**'
       - 'lib/galaxy_test/selenium/**'
+      - 'packages/**'
   pull_request:
     paths-ignore:
       - 'client/**'
       - 'doc/**'
       - 'lib/galaxy_test/selenium/**'
+      - 'packages/**'
 concurrency:
   group: ${{ github.workflow }}-${{ github.ref }}
   cancel-in-progress: true
diff --git a/.github/workflows/docs.yaml b/.github/workflows/docs.yaml
@@ -4,10 +4,12 @@ on:
     paths-ignore:
       - 'client/**'
       - 'lib/galaxy_test/selenium/**'
+      - 'packages/**'
   pull_request:
     paths-ignore:
       - 'client/**'
       - 'lib/galaxy_test/selenium/**'
+      - 'packages/**'
 concurrency:
   group: ${{ github.workflow }}-${{ github.ref }}
   cancel-in-progress: true
diff --git a/.github/workflows/first_startup.yaml b/.github/workflows/first_startup.yaml
@@ -4,10 +4,12 @@ on:
     paths-ignore:
       - 'doc/**'
       - 'lib/galaxy_test/selenium/**'
+      - 'packages/**'
   pull_request:
     paths-ignore:
       - 'doc/**'
       - 'lib/galaxy_test/selenium/**'
+      - 'packages/**'
 env:
   YARN_INSTALL_OPTS: --frozen-lockfile
 concurrency:
diff --git a/.github/workflows/framework.yaml b/.github/workflows/framework.yaml
@@ -5,11 +5,13 @@ on:
       - 'client/**'
       - 'doc/**'
       - 'lib/galaxy_test/selenium/**'
+      - 'packages/**'
   pull_request:
     paths-ignore:
       - 'client/**'
       - 'doc/**'
       - 'lib/galaxy_test/selenium/**'
+      - 'packages/**'
   schedule:
     # Run at midnight UTC every Tuesday
     - cron: '0 0 * * 2'
diff --git a/.github/workflows/integration.yaml b/.github/workflows/integration.yaml
@@ -5,11 +5,13 @@ on:
       - 'client/**'
       - 'doc/**'
       - 'lib/galaxy_test/selenium/**'
+      - 'packages/**'
   pull_request:
     paths-ignore:
       - 'client/**'
       - 'doc/**'
       - 'lib/galaxy_test/selenium/**'
+      - 'packages/**'
   schedule:
     # Run at midnight UTC every Tuesday
     - cron: '0 0 * * 2'
diff --git a/.github/workflows/integration_selenium.yaml b/.github/workflows/integration_selenium.yaml
@@ -3,9 +3,11 @@ on:
   push:
     paths-ignore:
       - 'doc/**'
+      - 'packages/**'
   pull_request:
     paths-ignore:
       - 'doc/**'
+      - 'packages/**'
   schedule:
     # Run at midnight UTC every Tuesday
     - cron: '0 0 * * 2'
diff --git a/.github/workflows/lint_openapi_schema.yml b/.github/workflows/lint_openapi_schema.yml
@@ -5,11 +5,13 @@ on:
       - 'client/**'
       - 'doc/**'
       - 'lib/galaxy_test/selenium/**'
+      - 'packages/**'
   pull_request:
     paths-ignore:
       - 'client/**'
       - 'doc/**'
       - 'lib/galaxy_test/selenium/**'
+      - 'packages/**'
 concurrency:
   group: ${{ github.workflow }}-${{ github.ref }}
   cancel-in-progress: true
diff --git a/.github/workflows/mulled.yaml b/.github/workflows/mulled.yaml
@@ -5,11 +5,13 @@ on:
       - 'client/**'
       - 'doc/**'
       - 'lib/galaxy_test/selenium/**'
+      - 'packages/**'
   pull_request:
     paths-ignore:
       - 'client/**'
       - 'doc/**'
       - 'lib/galaxy_test/selenium/**'
+      - 'packages/**'
 concurrency:
   group: ${{ github.workflow }}-${{ github.ref }}
   cancel-in-progress: true
diff --git a/.github/workflows/osx_startup.yaml b/.github/workflows/osx_startup.yaml
@@ -4,10 +4,12 @@ on:
     paths-ignore:
       - 'doc/**'
       - 'lib/galaxy_test/selenium/**'
+      - 'packages/**'
   pull_request:
     paths-ignore:
       - 'doc/**'
       - 'lib/galaxy_test/selenium/**'
+      - 'packages/**'
 concurrency:
   group: ${{ github.workflow }}-${{ github.ref }}
   cancel-in-progress: true
diff --git a/.github/workflows/performance.yaml b/.github/workflows/performance.yaml
@@ -5,11 +5,13 @@ on:
       - 'client/**'
       - 'doc/**'
       - 'lib/galaxy_test/selenium/**'
+      - 'packages/**'
   pull_request:
     paths-ignore:
       - 'client/**'
       - 'doc/**'
       - 'lib/galaxy_test/selenium/**'
+      - 'packages/**'
   schedule:
     # Run at midnight UTC every Tuesday
     - cron: '0 0 * * 2'
diff --git a/.github/workflows/publish_artifacts.yaml b/.github/workflows/publish_artifacts.yaml
@@ -1,7 +1,7 @@
 name: Publish release artifacts
 on:
-    release:
-      types: [released, prereleased]
+  release:
+    types: [released, prereleased]
 jobs:
   build-and-publish:
     if: github.repository_owner == 'galaxyproject'
diff --git a/.github/workflows/reports_startup.yaml b/.github/workflows/reports_startup.yaml
@@ -3,9 +3,11 @@ on:
   push:
     paths-ignore:
       - 'doc/**'
+      - 'packages/**'
   pull_request:
     paths-ignore:
       - 'doc/**'
+      - 'packages/**'
 env:
   YARN_INSTALL_OPTS: --frozen-lockfile
 concurrency:
diff --git a/.github/workflows/selenium.yaml b/.github/workflows/selenium.yaml
@@ -3,9 +3,11 @@ on:
   push:
     paths-ignore:
       - 'doc/**'
+      - 'packages/**'
   pull_request:
     paths-ignore:
       - 'doc/**'
+      - 'packages/**'
   schedule:
     # Run at midnight UTC every Tuesday
     - cron: '0 0 * * 2'
diff --git a/.github/workflows/toolshed.yaml b/.github/workflows/toolshed.yaml
@@ -4,10 +4,12 @@ on:
     paths-ignore:
       - 'doc/**'
       - 'lib/galaxy_test/selenium/**'
+      - 'packages/**'
   pull_request:
     paths-ignore:
       - 'doc/**'
       - 'lib/galaxy_test/selenium/**'
+      - 'packages/**'
 env:
   GALAXY_TEST_DBURI: 'postgresql://postgres:postgres@localhost:5432/galaxy?client_encoding=utf8'
   TOOL_SHED_TEST_DBURI: 'postgresql://postgres:postgres@localhost:5432/toolshed?client_encoding=utf8'
diff --git a/.github/workflows/unit-postgres.yaml b/.github/workflows/unit-postgres.yaml
@@ -5,11 +5,13 @@ on:
       - 'client/**'
       - 'doc/**'
       - 'lib/galaxy_test/selenium/**'
+      - 'packages/**'
   pull_request:
     paths-ignore:
       - 'client/**'
       - 'doc/**'
       - 'lib/galaxy_test/selenium/**'
+      - 'packages/**'
 env:
   GALAXY_TEST_DBURI: 'postgresql://postgres:postgres@localhost:5432/postgres?client_encoding=utf8'  # using postgres as the db
 concurrency:
diff --git a/.github/workflows/unit.yaml b/.github/workflows/unit.yaml
@@ -5,11 +5,13 @@ on:
       - 'client/**'
       - 'doc/**'
       - 'lib/galaxy_test/selenium/**'
+      - 'packages/**'
   pull_request:
     paths-ignore:
       - 'client/**'
       - 'doc/**'
       - 'lib/galaxy_test/selenium/**'
+      - 'packages/**'
 concurrency:
   group: ${{ github.workflow }}-${{ github.ref }}
   cancel-in-progress: true
diff --git a/lib/galaxy/tool_util/deps/conda_util.py b/lib/galaxy/tool_util/deps/conda_util.py
@@ -101,7 +101,7 @@ class CondaContext(installable.InstallableContext):
     def __init__(
         self,
         conda_prefix: Optional[str] = None,
-        conda_exec: Optional[str] = None,
+        conda_exec: Optional[Union[str, List[str]]] = None,
         shell_exec: Optional[Callable[..., int]] = None,
         debug: bool = False,
         ensure_channels: Union[str, List[str]] = "",
@@ -204,11 +204,12 @@ def conda_info(self) -> Dict[str, Any]:
 
     def is_conda_installed(self) -> bool:
         """
-        Check if conda_exec exists
+        Check if conda_info() works
         """
-        if os.path.exists(self.conda_exec):
+        try:
+            self.conda_info()
             return True
-        else:
+        except Exception:
             return False
 
     def can_install_conda(self) -> bool:
@@ -218,6 +219,7 @@ def can_install_conda(self) -> bool:
         If conda_exec equals conda_prefix/bin/conda, we can install conda if either conda_prefix
         does not exist or is empty.
         """
+        assert isinstance(self.conda_exec, str), "conda_exec is not a str"
         conda_exec = os.path.abspath(self.conda_exec)
         conda_prefix_plus_exec = os.path.abspath(os.path.join(self.conda_prefix, "bin/conda"))
         if conda_exec == conda_prefix_plus_exec:
diff --git a/lib/galaxy/tool_util/deps/container_resolvers/mulled.py b/lib/galaxy/tool_util/deps/container_resolvers/mulled.py
@@ -42,13 +42,13 @@
 )
 from ..docker_util import build_docker_images_command
 from ..mulled.mulled_build import (
-    DEFAULT_CHANNELS,
     ensure_installed,
     InvolucroContext,
     mull_targets,
 )
 from ..mulled.mulled_build_tool import requirements_to_mulled_targets
 from ..mulled.util import (
+    DEFAULT_CHANNELS,
     default_mulled_conda_channels_from_env,
     mulled_tags_for,
     split_tag,
diff --git a/lib/galaxy/tool_util/deps/dependencies.py b/lib/galaxy/tool_util/deps/dependencies.py
@@ -12,7 +12,7 @@
     ToolRequirements,
 )
 from galaxy.util import bunch
-from .mulled.mulled_build import DEFAULT_CHANNELS
+from .mulled.util import DEFAULT_CHANNELS
 
 
 class AppInfo:
diff --git a/lib/galaxy/tool_util/deps/installable.py b/lib/galaxy/tool_util/deps/installable.py
@@ -34,7 +34,7 @@ def parent_path(self):
         """Return parent path of the location the installable will be created within."""
 
 
-def ensure_installed(installable_context, install_func, auto_init):
+def ensure_installed(installable_context: InstallableContext, install_func, auto_init):
     """Make sure target is installed - handle multiple processes potentially attempting installation."""
     parent_path = installable_context.parent_path
     desc = installable_context.installable_description
diff --git a/lib/galaxy/tool_util/deps/mulled/get_tests.py b/lib/galaxy/tool_util/deps/mulled/get_tests.py
@@ -25,12 +25,17 @@
     Template = None  # type: ignore[assignment,misc]
     UndefinedError = Exception  # type: ignore[assignment,misc]
 
+from galaxy.tool_util.deps.conda_util import (
+    best_search_result,
+    CondaTarget,
+)
 from galaxy.util import (
     check_github_api_response_rate_limit,
     unicodify,
 )
 from galaxy.util.commands import argv_to_str
 from .util import (
+    CondaInDockerContext,
     get_files_from_conda_package,
     MULLED_SOCKET_TIMEOUT,
     split_container_name,
@@ -291,20 +296,19 @@ def hashed_test_search(
     targets = concatenated_targets.split(",")
     packages = [target.split("=") for target in targets]
 
+    conda_context = CondaInDockerContext(ensure_channels=[anaconda_channel])
     containers = []
-    for package in packages:
-        r = requests.get(f"https://anaconda.org/bioconda/{package[0]}/files", timeout=MULLED_SOCKET_TIMEOUT)
-        r.raise_for_status()
-        p = "-".join(package)
-        for line in r.text.split("\n"):
-            # include only linux-64 builds since that is hardcoded in get_anaconda_url and the only target for container builds
-            if p in line and "linux-64" in line:
-                build = line.split(p)[1].split(".tar.bz2")[0]
-                if build == "":
-                    containers.append(f"{package[0]}:{package[1]}")
-                else:
-                    containers.append(f"{package[0]}:{package[1]}-{build}")
-                break
+    for package_name, package_version in packages:
+        conda_target = CondaTarget(package_name, package_version)
+        # include only linux-64 builds since that is hardcoded in get_anaconda_url and the only target for container builds
+        hit, exact = best_search_result(conda_target, conda_context, platform="linux-64")
+        if not hit or not exact:
+            raise Exception(f"Could not find {conda_target}")
+        build = hit["build"]
+        if build:
+            containers.append(f"{package_name}:{package_version}--{build}")
+        else:
+            containers.append(f"{package_name}:{package_version}")
 
     for container in containers:
         tests = main_test_search(container, recipes_path, deep, anaconda_channel, github_repo)
diff --git a/lib/galaxy/tool_util/deps/mulled/mulled_build.py b/lib/galaxy/tool_util/deps/mulled/mulled_build.py
diff --git a/lib/galaxy/tool_util/deps/mulled/util.py b/lib/galaxy/tool_util/deps/mulled/util.py
diff --git a/packages/data/setup.cfg b/packages/data/setup.cfg
diff --git a/test/unit/tool_util/mulled/test_mulled_build.py b/test/unit/tool_util/mulled/test_mulled_build.py
