diff env/lib/python3.7/site-packages/planemo/mulled.py @ 5:9b1c78e6ba9c draft default tip

"planemo upload commit 6c0a8142489327ece472c84e558c47da711a9142"
author shellac
date Mon, 01 Jun 2020 08:59:25 -0400
parents 79f47841a781
children
line wrap: on
line diff
--- a/env/lib/python3.7/site-packages/planemo/mulled.py	Thu May 14 16:47:39 2020 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,67 +0,0 @@
-"""Planemo specific utilities for dealing with mulled containers.
-
-The extend galaxy-tool-util's features with planemo specific idioms.
-"""
-from __future__ import absolute_import
-
-import os
-
-from galaxy.tool_util.deps.mulled.mulled_build import (
-    DEFAULT_CHANNELS,
-    ensure_installed,
-    InvolucroContext,
-)
-from galaxy.tool_util.deps.mulled.util import build_target
-
-from planemo.conda import collect_conda_target_lists
-from planemo.io import shell
-
-
-def conda_to_mulled_targets(conda_targets):
-    return list(map(lambda c: build_target(c.package, c.version), conda_targets))
-
-
-def collect_mulled_target_lists(ctx, paths, recursive=False):
-    return list(map(conda_to_mulled_targets, collect_conda_target_lists(ctx, paths, recursive=recursive)))
-
-
-def build_involucro_context(ctx, **kwds):
-    """Build a galaxy-tool-util InvolucroContext tailored to planemo use.
-
-    Using planemo's common command-line/global config options.
-    """
-    involucro_path_default = os.path.join(ctx.workspace, "involucro")
-    involucro_path = kwds.get("involucro_path", involucro_path_default)
-    use_planemo_shell = kwds.get("use_planemo_shell_exec", True)
-    shell_exec = shell if use_planemo_shell else None
-    involucro_context = InvolucroContext(involucro_bin=involucro_path,
-                                         shell_exec=shell_exec)
-    if not ensure_installed(involucro_context, True):
-        raise Exception("Failed to install involucro for Planemo.")
-    return involucro_context
-
-
-def build_mull_target_kwds(ctx, **kwds):
-    """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")
-    target_kwds = {
-        'involucro_context': involucro_context,
-        'channels': channels.split(","),
-        'namespace': namespace,
-        'verbose': ctx.verbose,
-    }
-
-    conda_version = kwds.get("mulled_conda_version", None)
-    if conda_version is not None:
-        target_kwds["conda_version"] = conda_version
-    return target_kwds
-
-
-__all__ = (
-    "build_involucro_context",
-    "build_mull_target_kwds",
-    "collect_mulled_target_lists",
-    "conda_to_mulled_targets",
-)