Ephemeris is an opinionated library and set of scripts for managing the bootstrapping of Galaxy project plugins - tools, index data, and workflows.
Ephemeris is a small Python library and set of scripts for managing the bootstrapping of Galaxy plugins - tools, index data, and workflows.
- Free software: Academic Free License version 3.0
- Documentation: https://ephemeris.readthedocs.org.
- Code: https://github.com/galaxyproject/ephemeris
- Add install-tool-deps command that will install tool dependencies (thanks to @innovate-invent). Pull Request 130
- Require galaxy-tool-util instead of galaxy-lib (thanks to @nsoranzo). Pull Request 143
- Release to PyPI on tag (thanks to @mvdbeek). Pull Request 142
- Make Data library creation more robust (thanks to @erasche). Pull Request 138
- Make tool testing more robust (thanks to @mvdbeek). Pull Request 137, Pull Request 136
- fix doc building and regenerate (thanks to @martenson). Pull Request 129
- fix default for ‘parallel_tests’ typo (thanks to @martenson). Pull Request 127
- Include some additional stats for xunit reporting (thanks to @mvdbeek). Pull Request 126
- Handle timeout gracefully for UWSGI connection (thanks to @pcm32). Pull Request 123
- Update Docs for User Name (Should be Email) (thanks to @rdvelazquez). Pull Request 122
- remove the python invocation from usage examples (thanks to @martenson). Pull Request 121
- Fix crash when too_with_panel is empty (thanks to @jvanbraekel). Pull Request 120
- Test tools in parallel, with regular user permissions, without a shared filesystem (thanks to @mvdbeek). Pull Request 118
- use latest documentation dependencies to fix documentation build issue (thanks to @rhpvorderman). Pull Request 114
- Refactor shed tool functionality. Removed deprecated options from shed-tools CLI. shed-tools update now also accepts tool list, so tools in galaxy can be selectively updated. Improved algorithm leads to much faster skipping of already installed tools, which makes the installation of tools much faster on an already populated galaxy. (thanks to @rhpvorderman). Pull Request 104
- Add pytest, enable coverage testing (thanks to @rhpvorderman). Pull Request 105
- Make setup_data_libraries.py check for existence before recreation of libraries. (thanks to @Slugger70). Pull Request 103
- Catch failures on requests to the installed repo list when doing post- timeout spinning on installation in shed-tools (thanks to @natefoo). Pull Request 97
- Fix coverage reporting on codacy (thanks to @rhpvorderman). Pull Request 106
- Run-data-managers now outputs stderr of failed jobs (thanks to @rhpvorderman). Pull Request 110
- Update data managers when updating tools (thanks to @rhpvorderman). Pull Request 78, Issue 69
- Run data managers aggressive parallelization and refactoring (thanks to @rhpvorderman). Pull Request 79
- Makes publishing of imported workflows available (thanks to @pcm32). Pull Request 74
- Add option to test tools on update/install for Galaxy 18.05 (thanks to @jmchilton). Pull Request 81
- Upload 2.0 support for data library creation (thanks to @jmchilton). Pull Request 89
- Fixes to revision parsing in tools.yaml (thanks to @bgruening). Pull Request 70
- Add Codacy monitoring and badge (thanks to @jmchilton). Pull Request 73
- Fix typo in project organization document (thanks to @blankenberg). Pull Request 86
- Fix hardcoded log paths (thanks to @rhpvorderman). Pull Request 85
- Fix shed-tools update argparse handling (thanks to @rhpvorderman). Pull Request 88
- Fix a few lint issues (thanks to @jmchilton). Pull Request 90
- Many new documentation enhancements (thanks to @rhpvorderman, and others)
- rename of shed-install to shed-tools and add a new –latest and –revision argument (thanks to @rhpvorderman)
- many fixes and new tests by (thanks to @mvdbeek)
- Parallelization of run-data-managers (thanks to @rhpvorderman)
- run-data-managers now uses more advanced templating for less repetitive input yamls (thanks to @rhpvorderman)
- run-data-managers now checks if a genome index is already present before running the data manager (thanks to @rhpvorderman)
- ephemeris will now use https by default instead of http (thanks to @bgruening)
- Many new documentation enhancements (thanks to @rhpvorderman, @erasche, and others) - docs are now published to https://readthedocs.org/projects/ephemeris/.
- Fix problem with empty list options related to running data managers (thanks to @rhpvorderman).
- Enable data managers to run with API keys (thanks to @rhpvorderman).
- Add sleep command to wait for a Galaxy API to become available (thanks to @erasche).
- Preserve readable order of keys while processing tool lists (thanks to @drosofff).
- Add Python 2 and 3 testing for all scripts against galaxy-docker-stable along with various refactoring to reduce code duplication and Python 3 fixes. #36
- Add new connection options for setting up data libraries.
- Fix new run-data-managers CLI entrypoint.
- Add run-data-managers tool to trigger DM with multiple values and in order. #30
- The workflow install tool now supports a directory of workflows. #27
- enable global options in a tool yaml files, like install_resolver_dependencies: true #26
- Mention mimum required galaxy versions. #23 (thanks to @mvdbeek)
- Be more generic in determining a server time-out (thanks to @afgane).
- Get tool list entrypoint and improvements (thanks to @mvdbeek).
- Rename tool_panel_section_name to tool_panel_section_label like ansible-galaxy-tools (thanks to @nturaga).
- Add missing file tool_list.yaml.sample (thanks to @nturaga).
- More robust shed-install script, install dependencies by default, improve logging (thanks to @mvdbeek).
- Add tool generate a tool list from a Galaxy workflow file (thanks to @drosofff).
- Fix various code quality issues including adding beta support for Python 3 (thanks in part to @mvdbeek).
- Setup project, pull in scripts from ansible-galaxy-tools and adapt them for usage as a library.
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