Package: ephemeris
Ephemeris is a small Python 3 library and set of scripts for managing the
bootstrapping ofGalaxyplugins - tools, index data, and workflows.Free software: Academic Free License version 3.0Documentation:https://ephemeris.readthedocs.org.Code:https://github.com/galaxyproject/ephemerisHistory0.10.10 (2024-02-01)Use None default value where items are optional (thanks to@mvdbeek).Pull Request 2120.10.9 (2024-01-31)Fix CI tests (thanks to@mvdbeek).Pull Request 208Add black, ruff, isort and mypy (thanks to@mvdbeek).Pull Request 209Add now mandatory readthedocs config file (thanks to@nsoranzo).Pull
Request 210Enhancements to the IDC scripts (thanks to@jmchilton).Pull Request
2010.10.8 (2023-04-18)Prefer dashes instead of underscores in flags (thanks to@natefoo).Pull
Request 191Remove folder id from get_folders function call in setup-data-libraries
(thanks to@sanjaysrikakulam).Pull Request 196Standardize CLI commands on - instead of _ (thanks to@hexylena).Pull
Request 195Add partial type annotations (thanks to@mvdbeek).Pull Request 193Rename configuration option removed in tox 4.0 (thanks to@nsoranzo).Pull Request 190Set Library Permissions (thanks to@mira-miracoli).Pull Request 187delete the extra random sleep lines from sleep.py (thanks to@cat-bro).Pull Request 1710.10.7 (2021-06-08)Add option toshed-tools testfor specifying a history name (thanks to@natefoo).Pull Request 173workflow-to-tools: get tools from subworkflows (thanks to@cat-bro).Pull Request 170Add pysam and continue if test fetching errors (thanks to@mvdbeek).Pull Request 128Various updates to testing and CI infrastructure (thanks to@jmchilton).Pull Request 165Handle terminal states in wait for install (thanks to@mvdbeek).Pull Request 161Get all tools when searching for tool ids for testing
(thanks to@cat-bro).Pull Request 1590.10.6 (2020-05-04)Wait for the correct repository (thanks to@mvdbeek).Pull
Request 158Update dependencies0.10.5 (2020-02-29)Fixshed-tools test -t workflow_tools.yml(thanks to@nsoranzo).Pull
Request 155Fix installing tool dependencies from yaml list (thanks to@mvdbeek).Pull Request 154Cast exceptions to string using unicodify (thanks to@mvdbeek).Pull
Request 150Add description when creating folders with setup_data_libraries (thanks to@abretaud).Pull Request 1490.10.4 (2019-10-05)When polling for repo install status, ensure the correct revision is being
checked (thanks to@natefoo).Pull Request 146Add install_tool_deps command (thanks to@innovate-invent).Pull Request
1450.10.3 (2019-07-18)Add install-tool-deps command that will install tool dependencies
(thanks to@innovate-invent).Pull Request 130Require galaxy-tool-util instead of galaxy-lib (thanks to@nsoranzo).Pull Request 143Release to PyPI on tag (thanks to@mvdbeek).Pull Request 142Make Data library creation more robust
(thanks to@erasche).Pull Request 138Make tool testing more robust (thanks to@mvdbeek).Pull Request 137,Pull Request 1360.10.2 (2019-06-04)Fix default message check (thanks to@mvdbeek).Pull Request 1350.10.1 (2019-06-04)Fix timeout handling when installing repositories
(thanks to@mvdbeek).Pull Request 1340.10.0 (2019-05-29)fix doc building and regenerate (thanks to@martenson).Pull Request
129fix default for ‘parallel_tests’ typo (thanks to@martenson).Pull
Request 127Include some additional stats for xunit reporting (thanks to@mvdbeek).Pull Request 126Handle timeout gracefully for UWSGI connection (thanks to@pcm32).Pull
Request 123Update Docs for User Name (Should be Email) (thanks to@rdvelazquez).Pull Request 122remove the python invocation from usage examples (thanks to@martenson).Pull Request 121Fix crash when too_with_panel is empty (thanks to@jvanbraekel).Pull
Request 120Test tools in parallel, with regular user permissions, without a shared
filesystem (thanks to@mvdbeek).Pull Request 118use latest documentation dependencies to fix documentation build issue
(thanks to@rhpvorderman).Pull Request 114Refactor 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 104Addpytest, enable coverage testing (thanks to@rhpvorderman).Pull Request 105Makesetup_data_libraries.pycheck for existence before recreation of
libraries.
(thanks to@Slugger70).Pull Request 103Catch failures on requests to the installed repo list when doing post-
timeout spinning on installation inshed-tools(thanks to@natefoo).Pull Request 97Fix coverage reporting on codacy (thanks to@rhpvorderman).Pull Request 106Run-data-managers now outputs stderr of failed jobs (thanks to@rhpvorderman).Pull Request 1100.9.0 (2018-05-23)Update data managers when updating tools (thanks to@rhpvorderman).Pull Request 78,Issue 69Run data managers aggressive parallelization and refactoring (thanks to@rhpvorderman).Pull Request 79Makes publishing of imported workflows available (thanks to@pcm32).Pull Request 74Add option to test tools on update/install for Galaxy 18.05 (thanks to@jmchilton).Pull Request 81Upload 2.0 support for data library creation (thanks to@jmchilton).Pull Request 89Fixes to revision parsing in tools.yaml (thanks to@bgruening).Pull Request 70Add Codacy monitoring and badge (thanks to@jmchilton).Pull Request 73Fix typo in project organization document (thanks to@blankenberg).Pull Request 86Fix hardcoded log paths (thanks to@rhpvorderman).Pull Request 85Fixshed-toolsupdate argparse handling (thanks to@rhpvorderman).Pull Request 88Fix a few lint issues (thanks to@jmchilton).Pull Request 900.8.0 (2017-12-29)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)0.7.0 (2017-06-27)Many new documentation enhancements (thanks to @rhpvorderman, @erasche, and others) -
docs are now published tohttps://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).0.6.1 (2017-04-17)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.#360.6.0 (2017-04-10)Add new connection options for setting up data libraries.0.5.1 (2017-04-07)Fix newrun-data-managersCLI entrypoint.0.5.0 (2017-04-06)Addrun-data-managerstool to trigger DM with multiple values and in order.#30The workflow install tool now supports a directory of workflows.#27enable global options in a tool yaml files, likeinstall_resolver_dependencies: true#26Mention mimum required galaxy versions.#23(thanks to @mvdbeek)0.4.0 (2016-09-07)Be more generic in determining a server time-out (thanks to @afgane).Get tool list entrypoint and improvements (thanks to @mvdbeek).Renametool_panel_section_nametotool_panel_section_labellike
ansible-galaxy-tools (thanks to @nturaga).Add missing filetool_list.yaml.sample(thanks to @nturaga).0.3.0 (2016-08-26)More robust shed-install script, install dependencies by default, improve logging
(thanks to @mvdbeek).0.2.0 (2016-08-15)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).0.1.0 (2016-06-15)Setup project, pull in scripts fromansible-galaxy-toolsand adapt them for usage as a library.