ephemeris 0.10.9

Fix CI tests (thanks to @mvdbeek). Pull Request 208

Add black, ruff, isort and mypy (thanks to @mvdbeek). Pull Request 209

Add now mandatory readthedocs config file (thanks to @nsoranzo). Pull Request 210

Enhancements to the IDC scripts (thanks to @jmchilton). Pull Request 201

Prefer dashes instead of underscores in flags (thanks to @natefoo). Pull Request 191

Remove folder id from get_folders function call in setup-data-libraries (thanks to @sanjaysrikakulam). Pull Request 196

Standardize CLI commands on - instead of _ (thanks to @hexylena). Pull Request 195

Add partial type annotations (thanks to @mvdbeek). Pull Request 193

Rename configuration option removed in tox 4.0 (thanks to @nsoranzo). Pull Request 190

Set Library Permissions (thanks to @mira-miracoli). Pull Request 187

delete the extra random sleep lines from sleep.py (thanks to @cat-bro). Pull Request 171

Add option to shed-tools test for specifying a history name (thanks to @natefoo). Pull Request 173

workflow-to-tools: get tools from subworkflows (thanks to @cat-bro). Pull Request 170

Add pysam and continue if test fetching errors (thanks to @mvdbeek). Pull Request 128

Various updates to testing and CI infrastructure (thanks to @jmchilton). Pull Request 165

Handle terminal states in wait for install (thanks to @mvdbeek). Pull Request 161

Get all tools when searching for tool ids for testing (thanks to @cat-bro). Pull Request 159

Wait for the correct repository (thanks to @mvdbeek). Pull Request 158

Update dependencies

Fix shed-tools test -t workflow_tools.yml (thanks to @nsoranzo). Pull Request 155

Fix installing tool dependencies from yaml list (thanks to @mvdbeek). Pull Request 154

Cast exceptions to string using unicodify (thanks to @mvdbeek). Pull Request 150

Add description when creating folders with setup_data_libraries (thanks to @abretaud). Pull Request 149

When polling for repo install status, ensure the correct revision is being checked (thanks to @natefoo). Pull Request 146

Add install_tool_deps command (thanks to @innovate-invent). Pull Request 145

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 default message check (thanks to @mvdbeek). Pull Request 135

Fix timeout handling when installing repositories (thanks to @mvdbeek). Pull Request 134

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.