Replace deprecated galaxy-lib requirement with galaxy-tool-util

MANIFEST.in

@@ -1,6 +1,5 @@
-include *.rst LICENSE
+include *.rst LICENSE *.txt
 include planemo/xml/xsd/*
-include planemo/xml/xsd/tool/*
 include planemo_ext/tool_factory_2/*
 include planemo/reports/*
 include planemo/scripts/*

docs/test_format.rst

@@ -256,7 +256,7 @@ reduce the load on the target Galaxy while checking for the status changes use t
 option where integer is the incremental increase in seconds for every request.
 
 To run tool tests against a running Galaxy, ``galaxy-tool-test`` is a script that gets installed with
-galaxy-lib and so may very well already be on your ``PATH``. Check out the options available with that
+galaxy-tool-util and so may very well already be on your ``PATH``. Check out the options available with that
 using ``galaxy-tool-test --help``.
 
 Galaxy Testing Template

planemo/commands/cmd_brew.py

@@ -1,9 +1,11 @@
 """Module describing the planemo ``brew`` command."""
 import click
-from galaxy.tools.deps import brew_exts
-from galaxy.tools.deps import brew_util
-from galaxy.tools.deps.requirements import parse_requirements_from_xml
-from galaxy.tools.loader_directory import load_tool_elements_from_path
+from galaxy.tool_util.deps import (
+    brew_exts,
+    brew_util,
+)
+from galaxy.tool_util.deps.requirements import parse_requirements_from_xml
+from galaxy.tool_util.loader_directory import load_tool_elements_from_path
 from galaxy.util import bunch
 
 from planemo import options

planemo/commands/cmd_brew_env.py

@@ -4,10 +4,12 @@
 import os
 
 import click
-from galaxy.tools.deps import brew_exts
-from galaxy.tools.deps import brew_util
-from galaxy.tools.deps.requirements import parse_requirements_from_xml
-from galaxy.tools.loader import load_tool
+from galaxy.tool_util.deps import (
+    brew_exts,
+    brew_util,
+)
+from galaxy.tool_util.deps.requirements import parse_requirements_from_xml
+from galaxy.tool_util.loader import load_tool
 from galaxy.util import bunch
 
 from planemo import options

planemo/commands/cmd_conda_env.py

@@ -2,7 +2,7 @@
 from __future__ import print_function
 
 import click
-from galaxy.tools.deps import conda_util
+from galaxy.tool_util.deps import conda_util
 
 from planemo import options
 from planemo.cli import command_function

planemo/commands/cmd_conda_init.py

@@ -1,6 +1,6 @@
 """Module describing the planemo ``conda_init`` command."""
 import click
-from galaxy.tools.deps import conda_util
+from galaxy.tool_util.deps import conda_util
 
 from planemo import options
 from planemo.cli import command_function

planemo/commands/cmd_conda_install.py

@@ -1,6 +1,6 @@
 """Module describing the planemo ``conda_install`` command."""
 import click
-from galaxy.tools.deps import conda_util
+from galaxy.tool_util.deps import conda_util
 
 from planemo import options
 from planemo.cli import command_function

planemo/commands/cmd_container_register.py

@@ -3,7 +3,11 @@
 import string
 
 import click
-from galaxy.tools.deps.mulled.util import conda_build_target_str, quay_repository, v2_image_name
+from galaxy.tool_util.deps.mulled.util import (
+    conda_build_target_str,
+    quay_repository,
+    v2_image_name,
+)
 
 from planemo import options
 from planemo.cli import command_function

planemo/commands/cmd_docker_build.py

@@ -1,7 +1,7 @@
 """Module describing the planemo ``docker_build`` command."""
 
 import click
-from galaxy.tools.deps import dockerfiles
+from galaxy.tool_util.deps import dockerfiles
 
 from planemo import options
 from planemo.cli import command_function

planemo/commands/cmd_docker_shell.py

@@ -15,10 +15,12 @@
 import os
 
 import click
-from galaxy.tools.deps import docker_util
-from galaxy.tools.deps import dockerfiles
-from galaxy.tools.deps.requirements import parse_requirements_from_xml
-from galaxy.tools.loader import load_tool
+from galaxy.tool_util.deps import (
+    docker_util,
+    dockerfiles,
+)
+from galaxy.tool_util.deps.requirements import parse_requirements_from_xml
+from galaxy.tool_util.loader import load_tool
 
 from planemo import options
 from planemo.cli import command_function

planemo/commands/cmd_mull.py

@@ -1,6 +1,6 @@
 """Module describing the planemo ``mull`` command."""
 import click
-from galaxy.tools.deps.mulled.mulled_build import mull_targets
+from galaxy.tool_util.deps.mulled.mulled_build import mull_targets
 
 from planemo import options
 from planemo.cli import command_function

planemo/commands/cmd_normalize.py

@@ -2,8 +2,8 @@
 from xml.etree import ElementTree
 
 import click
-from galaxy.tools.linters.xml_order import TAG_ORDER
-from galaxy.tools.loader import (
+from galaxy.tool_util.linters.xml_order import TAG_ORDER
+from galaxy.tool_util.loader import (
     load_tool,
     raw_tool_xml_tree,
 )

planemo/conda.py

@@ -1,6 +1,6 @@
 """Planemo specific utilities for dealing with conda.
 
-The extend Galaxy/galaxy-lib's features with planemo specific idioms.
+The extend galaxy-tool-util's features with planemo specific idioms.
 """
 
 from __future__ import absolute_import
@@ -9,7 +9,7 @@
 import os
 import threading
 
-from galaxy.tools.deps import conda_util
+from galaxy.tool_util.deps import conda_util
 
 from planemo.exit_codes import EXIT_CODE_FAILED_DEPENDENCIES, ExitCodeException
 from planemo.io import error, shell
@@ -23,7 +23,7 @@
 
 
 def build_conda_context(ctx, **kwds):
-    """Build a galaxy-lib CondaContext tailored to planemo use.
+    """Build a galaxy-tool-util CondaContext tailored to planemo use.
 
     Using planemo's common command-line/global config options.
     """

planemo/conda_lint.py

@@ -4,7 +4,7 @@
 
 from functools import wraps
 
-from galaxy.tools.deps.conda_compat import raw_metadata
+from galaxy.tool_util.deps.conda_compat import raw_metadata
 from galaxy.util import unicodify
 
 from planemo.conda_verify.recipe import (

planemo/conda_recipes.py

@@ -1,6 +1,4 @@
 """Planemo specific utilities for dealing with conda recipe generation.
-
-The extend Galaxy/galaxy-lib's features with planemo specific idioms.
 """
 
 from __future__ import absolute_import
@@ -11,13 +9,6 @@
 from planemo.bioconda_scripts import bioconductor_skeleton
 from planemo.io import info
 
-
-# from galaxy.tools.deps import conda_util
-
-# from planemo.io import shell
-# from planemo.tools import yield_tool_sources_on_paths
-
-
 # Bioconda helper functions
 
 

planemo/cwl/run.py

@@ -7,7 +7,7 @@
 import json
 import tempfile
 
-from galaxy.tools.cwl.cwltool_deps import (
+from galaxy.tool_util.cwl.cwltool_deps import (
     ensure_cwltool_available,
     main,
 )

planemo/database/factory.py

@@ -1,5 +1,5 @@
 """Create a DatabaseSource from supplied planemo configuration."""
-from galaxy.tools.deps.commands import which
+from galaxy.tool_util.deps.commands import which
 
 from .postgres import LocalPostgresDatabaseSource
 from .postgres_docker import DockerPostgresDatabaseSource

planemo/database/postgres_docker.py

@@ -1,9 +1,11 @@
 """Module describes a :class:`DatabaseSource` for managed, dockerized postgres databases."""
 import time
 
-from galaxy.tools.deps import docker_util
-from galaxy.tools.deps import dockerfiles
-from galaxy.tools.deps.commands import execute
+from galaxy.tool_util.deps import (
+    docker_util,
+    dockerfiles,
+)
+from galaxy.tool_util.deps.commands import execute
 from galaxy.util import unicodify
 
 from .interface import DatabaseSource

planemo/docker.py

@@ -5,7 +5,7 @@
 """
 from __future__ import absolute_import
 
-from galaxy.tools.deps.dockerfiles import docker_host_args
+from galaxy.tool_util.deps.dockerfiles import docker_host_args
 
 
 __all__ = (

planemo/engine/galaxy.py

@@ -4,7 +4,7 @@
 import abc
 import contextlib
 
-from galaxy.tools.verify import interactor
+from galaxy.tool_util.verify import interactor
 
 from planemo.galaxy.activity import execute
 from planemo.galaxy.config import external_galaxy_config

planemo/galaxy/activity.py

@@ -10,7 +10,7 @@
 import yaml
 from bioblend.galaxy.client import Client
 from bioblend.util import attach_file
-from galaxy.tools.cwl.util import (
+from galaxy.tool_util.cwl.util import (
     DirectoryUploadTarget,
     FileUploadTarget,
     galactic_job_json,
@@ -20,7 +20,7 @@
     path_or_uri_to_uri,
     tool_response_to_output,
 )
-from galaxy.tools.parser import get_tool_source
+from galaxy.tool_util.parser import get_tool_source
 from galaxy.util import (
     safe_makedirs,
     unicodify,

planemo/galaxy/config.py

@@ -11,8 +11,8 @@
 from tempfile import mkdtemp
 
 from galaxy.containers.docker_model import DockerVolume
-from galaxy.tools.deps import docker_util
-from galaxy.tools.deps.commands import argv_to_str
+from galaxy.tool_util.deps import docker_util
+from galaxy.tool_util.deps.commands import argv_to_str
 from pkg_resources import parse_version
 from six import (
     add_metaclass,

planemo/galaxy/profiles.py

@@ -7,7 +7,7 @@
 import os
 import shutil
 
-from galaxy.tools.deps.commands import which
+from galaxy.tool_util.deps.commands import which
 
 from planemo.config import (
     OptionSource,

planemo/galaxy/run.py

@@ -2,7 +2,7 @@
 import os
 import string
 
-from galaxy.tools.deps.commands import shell
+from galaxy.tool_util.deps.commands import shell
 from six.moves import shlex_quote
 
 from planemo.io import info, shell_join

planemo/galaxy/test/actions.py

@@ -5,7 +5,7 @@
 import os
 
 import click
-from galaxy.tools.deps.commands import shell
+from galaxy.tool_util.deps.commands import shell
 from galaxy.util import unicodify
 
 from planemo.exit_codes import (

planemo/github_util.py

@@ -3,7 +3,7 @@
 
 import os
 
-from galaxy.tools.deps.commands import which
+from galaxy.tool_util.deps.commands import which
 
 from planemo import git
 from planemo.io import (

planemo/io.py

@@ -13,8 +13,8 @@
 from xml.sax.saxutils import escape
 
 import click
-from galaxy.tools.deps import commands
-from galaxy.tools.deps.commands import download_command
+from galaxy.tool_util.deps import commands
+from galaxy.tool_util.deps.commands import download_command
 from six import (
     string_types,
     StringIO

planemo/lint.py

@@ -4,7 +4,7 @@
 import os
 
 import requests
-from galaxy.tools.lint import LintContext
+from galaxy.tool_util.lint import LintContext
 from six.moves.urllib.request import urlopen
 
 import planemo.linters.biocontainer_registered

planemo/linters/biocontainer_registered.py

@@ -1,7 +1,7 @@
 """Ensure best-practice biocontainer registered for this tool."""
 
-from galaxy.tools.deps.container_resolvers.mulled import targets_to_mulled_name
-from galaxy.tools.deps.mulled.util import build_target
+from galaxy.tool_util.deps.container_resolvers.mulled import targets_to_mulled_name
+from galaxy.tool_util.deps.mulled.util import build_target
 
 from planemo.conda import tool_source_conda_targets
 

planemo/linters/xsd.py

@@ -3,10 +3,11 @@
 import os
 import tempfile
 
+import galaxy.tool_util
+
 import planemo.lint
-from planemo.xml import XSDS_PATH
 
-TOOL_XSD = os.path.join(XSDS_PATH, "tool", "galaxy.xsd")
+TOOL_XSD = os.path.join(os.path.dirname(galaxy.tool_util.__file__), 'xsd', "galaxy.xsd")
 
 
 def lint_tool_xsd(tool_xml, lint_ctx):

planemo/mulled.py

@@ -1,17 +1,17 @@
 """Planemo specific utilities for dealing with mulled containers.
 
-The extend Galaxy/galaxy-lib's features with planemo specific idioms.
+The extend galaxy-tool-util's features with planemo specific idioms.
 """
 from __future__ import absolute_import
 
 import os
 
-from galaxy.tools.deps.mulled.mulled_build import (
+from galaxy.tool_util.deps.mulled.mulled_build import (
     DEFAULT_CHANNELS,
     ensure_installed,
     InvolucroContext,
 )
-from galaxy.tools.deps.mulled.util import build_target
+from galaxy.tool_util.deps.mulled.util import build_target
 
 from planemo.conda import collect_conda_target_lists
 from planemo.io import IS_OS_X, shell
@@ -26,7 +26,7 @@ def collect_mulled_target_lists(ctx, paths, recursive=False):
 
 
 def build_involucro_context(ctx, **kwds):
-    """Build a galaxy-lib CondaContext tailored to planemo use.
+    """Build a galaxy-tool-util InvolucroContext tailored to planemo use.
 
     Using planemo's common command-line/global config options.
     """
@@ -42,7 +42,7 @@ def build_involucro_context(ctx, **kwds):
 
 
 def build_mull_target_kwds(ctx, **kwds):
-    """Adapt Planemo's CLI and workspace configuration to galaxy-lib's mulled_build options."""
+    """Adapt Planemo's CLI and workspace configuration to galaxy-tool-util's mulled_build options."""
     involucro_context = build_involucro_context(ctx, **kwds)
     channels = kwds.get("conda_ensure_channels", ",".join(DEFAULT_CHANNELS))
     namespace = kwds.get("mulled_namespace", "biocontainers")

planemo/options.py

@@ -6,7 +6,7 @@
 import os
 
 import click
-from galaxy.tools.deps import docker_util
+from galaxy.tool_util.deps import docker_util
 
 from .config import planemo_option