ephemeris

v0.10.10

Ephemeris is an opinionated library and set of scripts for managing the bootstrapping of Galaxy project plugins - tools, index data, and workflows. For more information about how to use this package see README

Latest version published 11 months ago

License: AFL-3.0

PyPI

GitHub

Package Health Score

61 / 100

security
Security review needed
popularity
Small
maintenance
Inactive
community
Active

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Popularity

Small

GitHub Stars: 27
Forks: 39
Contributors: 20

Direct Usage Popularity

Based on project statistics from the GitHub repository for the PyPI package ephemeris, we found that it has been starred 27 times.

Security

Security review needed

Security and license risk for latest version

Release Date: Feb 1, 2024
Direct Vulnerabilities: 0
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0
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Indirect Vulnerabilities: 0
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0
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License Risk: 2
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7
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All security vulnerabilities belong to production dependencies of direct and indirect packages.

License

AFL-3.0

Security Policy

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Maintenance

Inactive

Commit Frequency

Open Issues: 39
Open PR: 14
Last Release: 11 months ago
Last Commit: 11 months ago

Further analysis of the maintenance status of ephemeris based on released PyPI versions cadence, the repository activity, and other data points determined that its maintenance is Inactive.

We found that ephemeris demonstrates a positive version release cadence with at least one new version released in the past 12 months.

In the past month we didn't find any pull request activity or change in issues status has been detected for the GitHub repository.

Community

Active

Readme: Yes
Contributing.md: Yes
Code of Conduct: Yes
Contributors: 20
Funding: No

With more than 10 contributors for the ephemeris repository, this is possibly a sign for a growing and inviting community.

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Package

Python Versions Compatibility: >=3.7

Age: 9 years
Latest Release: 11 months ago
Dependencies: 8 Direct / 48 Total
Versions: 23
Maintainers: 0
Wheels: OS Independent

Not sure how to use ephemeris?

To help you get started, we've collected the most common ways that ephemeris is being used within popular public projects.

galaxyproject / ephemeris / tests / test_run_data_managers.py View on Github

def test_install_data_managers(self, start_container):  # noqa: F811 Prevent start_container unused warning.
        """Install the data_managers on galaxy"""
        container = start_container
        data_managers = [
            dict(name="data_manager_fetch_genome_dbkeys_all_fasta",
                 owner="devteam"),
            dict(name="data_manager_sam_fasta_index_builder",
                 owner="devteam"),
            dict(name="data_manager_bwa_mem_index_builder",
                 owner="devteam")
        ]
        irm = InstallRepositoryManager(container.gi)
        irm.install_repositories(data_managers)
        # Galaxy is restarted because otherwise data tables are not watched.
        container.container.exec_run("supervisorctl restart galaxy:")
        time.sleep(10)  # give time for the services to go down
        galaxy_wait(container.url)

View more ways to use ephemeris

Ephemeris is a small Python 3 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: .
Code:

History

0.10.10 (2024-02-01)

Use None default value where items are optional (thanks to @mvdbeek). Pull Request 212

0.10.9 (2024-01-31)

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

0.10.8 (2023-04-18)

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

0.10.7 (2021-06-08)

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

0.10.6 (2020-05-04)

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

0.10.5 (2020-02-29)

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

0.10.4 (2019-10-05)

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

0.10.3 (2019-07-18)

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

0.10.2 (2019-06-04)

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

0.10.1 (2019-06-04)

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

0.10.0 (2019-05-29)

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

0.9.0 (2018-05-23)

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

0.8.0 (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 to .
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. #36

0.6.0 (2017-04-10)

Add new connection options for setting up data libraries.

0.5.1 (2017-04-07)

Fix new run-data-managers CLI entrypoint.

0.5.0 (2017-04-06)

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)

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).
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).

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 from ansible-galaxy-tools and adapt them for usage as a library.

ephemeris dependencies

bioblend galaxy-tool-util galaxy-util jinja2 pysam pyyaml rich six

FAQs

What is ephemeris?

Ephemeris is an opinionated library and set of scripts for managing the bootstrapping of Galaxy project plugins - tools... Visit Snyk Advisor to see a full health score report for ephemeris, including popularity, security, maintenance & community analysis.

Is ephemeris popular?

The python package ephemeris receives a total of 3,294 weekly downloads. As such, ephemeris popularity was classified as small. Visit the popularity section on Snyk Advisor to see the full health analysis.

Is ephemeris well maintained?

We found indications that ephemeris is an Inactive project. See the full package health analysis to learn more about the package maintenance status.

Is ephemeris safe to use?

While scanning the latest version of ephemeris, we found that a security review is needed. A total of 0 vulnerabilities or license issues were detected. See the full security scan results.

Last updated on 25 December-2024, at 03:13 (UTC).

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