Replace galaxy-lib dependency with galaxy-tool-util.

galaxy-lib is now unmaintained. We're managing the decomposition of the project from inside of the core codebase to prevent drift.

Author: jmchilton

README.rst

@@ -18,8 +18,8 @@
 
 from .builder import Builder, HasReqsHints
 try:
-    from galaxy.tools.deps.requirements import ToolRequirement, ToolRequirements
-    from galaxy.tools import deps
+    from galaxy.tool_util.deps.requirements import ToolRequirement, ToolRequirements
+    from galaxy.tool_util import deps
 except ImportError:
     ToolRequirement = None  # type: ignore
     ToolRequirements = None  # type: ignore
@@ -49,25 +49,30 @@ def __init__(self, args):
             self.tool_dependency_dir = tool_dependency_dir
             self.dependency_resolvers_config_file = os.path.abspath(conf_file)
         elif conda_dependencies is not None:
-            if not tool_dependency_dir is not None:
+            if tool_dependency_dir is None:
                 tool_dependency_dir = os.path.abspath("./cwltool_deps")
             self.tool_dependency_dir = tool_dependency_dir
             self.use_tool_dependencies = True
             self.dependency_resolvers_config_file = None
         else:
             self.use_tool_dependencies = False
 
-    @property
-    def config_dict(self):  # type: () -> Dict[Text, bool]
-        return {
-            'conda_auto_install': True,
-            'conda_auto_init': True,
-        }
-
     def build_job_script(self, builder, command):
         # type: (Builder, List[str]) -> Text
         ensure_galaxy_lib_available()
-        tool_dependency_manager = deps.build_dependency_manager(self)  # type: deps.DependencyManager
+        resolution_config_dict = {
+            'use': self.use_tool_dependencies,
+            'default_base_path': self.tool_dependency_dir,
+        }
+        app_config = {
+            'conda_auto_install': True,
+            'conda_auto_init': True,
+        }
+        tool_dependency_manager = deps.build_dependency_manager(
+            app_config_dict=app_config,
+            resolution_config_dict=resolution_config_dict,
+            conf_file=self.dependency_resolvers_config_file,
+        )  # type: deps.DependencyManager
         dependencies = get_dependencies(builder)
         handle_dependencies = ""  # str
         if dependencies:
@@ -107,10 +112,11 @@ def get_container_from_software_requirements(use_biocontainers, builder):
     # type: (bool, HasReqsHints) -> Optional[Text]
     if use_biocontainers:
         ensure_galaxy_lib_available()
-        from galaxy.tools.deps.containers import ContainerRegistry, AppInfo, ToolInfo, DOCKER_CONTAINER_TYPE
+        from galaxy.tool_util.deps.dependencies import AppInfo, ToolInfo
+        from galaxy.tool_util.deps.containers import ContainerRegistry, DOCKER_CONTAINER_TYPE
         app_info = AppInfo(
             involucro_auto_init=True,
-            enable_beta_mulled_containers=True,
+            enable_mulled_containers=True,
             container_image_cache_path=".",
         )  # type: AppInfo
         container_registry = ContainerRegistry(app_info)  # type: ContainerRegistry

cwltool/software_requirements.py

@@ -80,7 +80,7 @@
       extras_require={
           ':os.name=="posix" and python_version<"3.5"': ['subprocess32 >= 3.5.0'],
           ':python_version<"3.6"': ['typing >= 3.5.3'],
-          'deps': ["galaxy-lib >= 17.09.9, <= 18.9.2 "],
+          'deps': ["galaxy-tool-util"],
           'docs': ["sphinx >= 2.2", "sphinx-rtd-theme"],
       },
       python_requires='>=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, <4',

setup.py

@@ -65,7 +65,7 @@ def __main__():
     writer = output.write
     for line_offset in line_offsets:
         seeker( line_offset )
-        writer( readliner() )
+        writer( readliner().decode("utf-8") )
     input.close()
     output.close()
     #print("Kept %i of %i total lines." % ( num_lines, total_lines ))

tests/test_deps_env/random-lines/1.0/scripts/random-lines

@@ -37,7 +37,7 @@ deps =
   py{27,35,36,37,38}-unit: pytest-xdist<1.28.0
   py{27,35,36,37,38}-unit: pytest-cov
   py{27,35,36,37,38}-unit: -rtest-requirements.txt
-  py{27,35,36,37,38}-unit: galaxy-lib
+  py{27,35,36,37,38}-unit: galaxy-tool-util
   py{27,35,36,37,38}-lint: flake8
   py{27,35,36,37,38}-bandit: bandit
   py{35,36,36,37,38}-mypy{2,3}: mypy==0.720

tox.ini

@@ -12,7 +12,7 @@ from .resolvers.tool_shed_packages import ToolShedPackageDependencyResolver as T
 log = ...  # type: Any
 CONFIG_VAL_NOT_FOUND = ...  # type: Any
 
-def build_dependency_manager(config: Any) -> DependencyManager: ...
+def build_dependency_manager(app_config_dict: Any, resolution_config_dict: Any, conf_file: Any) -> DependencyManager: ...
 
 class NullDependencyManager:
     dependency_resolvers = ...  # type: Any

typeshed/2and3/galaxy/tools/__init__.pyi renamed to typeshed/2and3/galaxy/tool_util/__init__.pyi

@@ -35,25 +35,6 @@ class ContainerRegistry:
     def __init__(self, app_info) -> None: ...
     def find_best_container_description(self, enabled_container_types, tool_info) -> ContainerDescription: ...
 
-class AppInfo:
-    galaxy_root_dir = ...  # type: Any
-    default_file_path = ...  # type: Any
-    outputs_to_working_directory = ...  # type: Any
-    container_image_cache_path = ...  # type: Any
-    library_import_dir = ...  # type: Any
-    enable_beta_mulled_containers = ...  # type: Any
-    containers_resolvers_config_file = ...  # type: Any
-    involucro_path = ...  # type: Any
-    involucro_auto_init = ...  # type: Any
-    def __init__(self, galaxy_root_dir: Optional[Any] = ..., default_file_path: Optional[Any] = ..., outputs_to_working_directory: bool = ..., container_image_cache_path: Optional[Any] = ..., library_import_dir: Optional[Any] = ..., enable_beta_mulled_containers: bool = ..., containers_resolvers_config_file: Optional[Any] = ..., involucro_path: Optional[Any] = ..., involucro_auto_init: bool = ...) -> None: ...
-
-class ToolInfo:
-    container_descriptions = ...  # type: Any
-    requirements = ...  # type: Any
-    requires_galaxy_python_environment = ...  # type: Any
-    env_pass_through = ...  # type: Any
-    def __init__(self, container_descriptions: Any = ..., requirements: Any = ..., requires_galaxy_python_environment: bool = ...) -> None: ...
-
 class JobInfo:
     working_directory = ...  # type: Any
     job_directory = ...  # type: Any

typeshed/2and3/galaxy/tools/cwl/__init__.pyi renamed to typeshed/2and3/galaxy/tool_util/cwl/__init__.pyi

@@ -0,0 +1,32 @@
+# Stubs for galaxy.tools.deps.dependencies (Python 3.4)
+#
+# NOTE: This dynamically typed stub was automatically generated by stubgen.
+
+from typing import Any, Optional
+
+class AppInfo:
+    galaxy_root_dir = ...  # type: Any
+    default_file_path = ...  # type: Any
+    outputs_to_working_directory = ...  # type: Any
+    container_image_cache_path = ...  # type: Any
+    library_import_dir = ...  # type: Any
+    enable_mulled_containers = ...  # type: Any
+    containers_resolvers_config_file = ...  # type: Any
+    involucro_path = ...  # type: Any
+    involucro_auto_init = ...  # type: Any
+    def __init__(self, galaxy_root_dir: Optional[Any] = ..., default_file_path: Optional[Any] = ..., outputs_to_working_directory: bool = ..., container_image_cache_path: Optional[Any] = ..., library_import_dir: Optional[Any] = ..., enable_mulled_containers: bool = ..., containers_resolvers_config_file: Optional[Any] = ..., involucro_path: Optional[Any] = ..., involucro_auto_init: bool = ...) -> None: ...
+
+class DependenciesDescription:
+    requirements = ...  # type: Any
+    installed_tool_dependencies = ...  # type: Any
+    def __init__(self, requirements: Any = ..., installed_tool_dependencies: Any = ...) -> None: ...
+    def to_dict(self): ...
+    @staticmethod
+    def from_dict(as_dict): ...
+
+class ToolInfo:
+    container_descriptions = ...  # type: Any
+    requirements = ...  # type: Any
+    requires_galaxy_python_environment = ...  # type: Any
+    env_pass_through = ...  # type: Any
+    def __init__(self, container_descriptions: Any = ..., requirements: Any = ..., requires_galaxy_python_environment: bool = ...) -> None: ...