Code

Install via conda#2554

Code

Merged

blankenberg merged 58 commits intogalaxyproject:devgalaxyproject/galaxy:devfrom bxlab:install_via_condabxlab/galaxy-hackathon:install_via_condaCopy head branch name to clipboardJul 27, 2016

+519-144

Commits

Commits on Jul 22, 2016

• WIP re #39 - run dependency management during repository installation

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  bwlang

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  mvdbeek

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• Need to unnpack kwargs (ping @bwlang)

  mvdbeek

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• Move get_unique_requirements to shed_util_common

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  mvdbeek

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• Iterate over all tools in a repository

  mvdbeek

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• Fix the parsing logic

  mvdbeek

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• Be a bit more defensive about parsing requirements

  mvdbeek

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• Fix indentation

  mvdbeek

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• passed a “manual install” argument to the dependency resolve

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  bwlang

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  mvdbeek

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• Probably better not to have a fake directory here…

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  bwlang

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  mvdbeek

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• ask for tool dependency installation always.

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  bwlang

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• this view is not necessary for the current implementation

  

  bwlang

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  mvdbeek

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• strangely… we need

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  bwlang

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  mvdbeek

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• resolving style issue

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  bwlang

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  mvdbeek

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• Add api route to fetch all requirements

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  mvdbeek

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• Continue dependency resolver API routes and start work on displaying dependency status on a per repository view

  mvdbeek

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• Add first pass for displaying dependency status info

  

  bwlang

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  mvdbeek

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• Add name and version to returned dependency

  mvdbeek

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• Hack in name and version into dictified representation of Dependency instance (For NullDependency we do want to show the missing requirements)

  mvdbeek

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• add status field with icons

  

  bwlang

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  mvdbeek

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• whitespace fix

  

  bwlang

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  mvdbeek

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• Address @nsoranzo's review.

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  mvdbeek

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• Work on conda install revision

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• Fix dependency typo

  mvdbeek

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• Make api return more detailed requirements status, move tool_requirements and tool_requirements_status to Tool class

  mvdbeek

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• Use list comprehension to generate list of all requirements

  mvdbeek

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• Fix logic error in message

  mvdbeek

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• Display whether dependency is exactly resolved (check), inexactly resolved (warning) or not resolved (error)

  mvdbeek

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• Close docstring example list

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• Trigger requirement install for new install method

  mvdbeek

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• flake8 fixes

  mvdbeek

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• Add API endpoint to install (resolver) dependencies

  mvdbeek

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• Correct module description

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• Trigger dependency installation in InstallRepositoryManager

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• Add docstring to install_dependency

  mvdbeek

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• Revert manual_install mode (unncessary, better to use install_dependency)

  mvdbeek

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• Introduce installable_resolver property

  mvdbeek

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• Add install resolver dependency button

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  mvdbeek

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• Revert mako hack to always display install_tool_dependency button

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Commits on Jul 23, 2016

• Make conda verbose install check configurable

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• Only return requirements of type package (for now)

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• Use resolver.find_dep to determine dependency status

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Commits on Jul 25, 2016

• Update INDETERMINATE_DEPENDENCY use to NullDependency instance

  mvdbeek

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• Remove unused DependencyResolver view from ToolBox

  mvdbeek

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• Flake8 fix

  mvdbeek

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• Drop INDETERMINATE_DEPENDENCY alias

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• Fix NullDependency use

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  mvdbeek

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• Add api test for conda dependency resolution

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• Add more API tests for resolver dependencies

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Commits on Jul 26, 2016

• Fix syntax, return None if dependency not found

  mvdbeek

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• Revert svgwrite import, fixed in galaxyproject#2656

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• Remove reference to /tmp

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Commits on Jul 27, 2016

• Use continue instead of unused NullDependency

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• Simplify conda install logic

  mvdbeek

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• Show conda install option even when no tool_dependencies.xml is available.

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  jmchilton

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• Address @nsoranzo's review

  mvdbeek

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• Mark conda install beta and move after TS options.

  jmchilton

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• Merge remote-tracking branch 'bxlab/install_via_conda' into install_via_conda

  jmchilton

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• Merge pull request #56 from jmchilton/install_via_conda

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  martenson

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