History¶
0.15.3 (2023-07-20)¶
Fix Pulsar consumer state after
ConnectionResetError
. Pull Request 331User auth plugins (thanks to @SergeyYakubov). Pull Request 321
0.15.2 (2023-05-02)¶
Fix Pulsar and Pulsar client reconnection to AMQP server. Pull Request 324
Reduce verbosity of timeout exception catching. Pull Request 325
0.15.1 (2023-04-13)¶
No changes, working around pypi isssue.
0.15.0 (2023-04-13)¶
Updated Galaxy+Pulsar container. Pull Request 306
Rework container execution - generalize Kubernetes execution to allow it to work without a message queue and to allow TES execution based on pydantic-tes (https://github.com/jmchilton/pydantic-tes). Pull Request 302
Add documentation and diagrams for container execution scenarios. Pull Request 302
Rework integration tests to use pytest more aggressively.
Fixes to CI to run more tests that weren’t being executed because Tox was not sending environment variables through to pytest.
Add option
amqp_key_prefix
to direct task queue naming while retaining simple default manager names and such in container scheduling deployments. Pull Request 315Various typing and CI fixes. Pull Request 312, Pull Request 319
Fixes for extra_file handling. Pull Request 318
Separate tool_stdio and job_stdio handling. Pull Request 318
Re-import MEMORY_STATEMENT.sh from Galaxy. Pull Request 297
Add support for logging to sentry. Pull Request 322
0.14.16 (2022-10-04)¶
Fix small regression related to building URLs for client action mapping.
0.14.15 (2022-10-03)¶
Fix small regressions bugs in 0.14.14 - updating runner util code was bigger swap over than it seemed.
0.14.14 (2022-10-30)¶
Bring in updated Galaxy runner util code. Pull Request 303
Fix recovering “lost” jobs where the job directory does not exist at startup/recovery time (thanks to @natefoo). Pull Request 301
Use urlencode to encode path (thanks to @mvdbeek). Pull Request 299
Support the k8s_job_ttl_secs_after_finished option as in the Galaxy Kubernetes runner (thanks to @natefoo). Pull Request 287
0.14.13 (2021-12-06)¶
Don’t pass all environment variables to jobs launched by Manager (thanks to @nsoranzo). Pull Request 295
Drop legacy job conf for Galaxy framework tests, test against
metadata_strategy: extended
(thanks to @mvdbeek). Pull Request 294
0.14.12 (2021-11-10)¶
Fixes to bring HOME and temp directory handling closer to Galaxy native runners.
Enable globbed from_work_dir outputs for remote metadata.
0.14.11 (2021-07-19)¶
Fix and test for returncode handling in certain cases. Pull Request 274
Modernize tox. Pull Request 271
0.14.10 (2021-07-17)¶
Don’t error out if annotated galaxy.json is absent. Pull Request 270
0.14.9 (2021-07-16)¶
Implement dynamic file sources abstraction for parsing files to transfer from
galaxy.json
files. Pull Request 269Use tool classes to only test remote Galaxy tools. Pull Request 266
Run Galaxy framework tests against dev and master branches of Galaxy (thanks to @mvdbeek). Pull Request 264
0.14.8 (2021-07-14)¶
Fix Galaxy composite input references. Pull Request 262
Run galaxy’s tool framework tests against this repo’s pulsar (thanks to @mvdbeek). Pull Request 259
0.14.7 (2021-07-13)¶
Accept description of tool files to transfer from Galaxy. Pull Request 261
Support globs in from_work_dir outputs (thanks to @natefoo). Pull Request 257
Fix loading the Galaxy dependency resolvers config, plus additional config directory fixes (thanks to @natefoo). Pull Request 256
0.14.6 (2021-05-24)¶
Fix for newer Galaxy tool profiles having isolated home directories.
0.14.5 (2021-04-15)¶
Potential fix for setting file actions via job destination parameters.
0.14.4 (2021-04-14)¶
Re-attempt release process - published wrong branch with 0.14.3.
0.14.3 (2021-04-13)¶
Allow transferring fewer files from Pulsar when using extended metadata with Galaxy.
0.14.2 (2021-02-15)¶
Fix the use of requests, limits, and walltime with coexecution pods. Pull Request 246
0.14.1 (2021-02-02)¶
Fix the use of named managers with coexecution pods. Pull Request 242
0.14.0 (2020-09-17)¶
fix the PyYAML “load() deprecation” warning (thanks to @gmauro). Pull Request 232
Set the DRMAA workingDirectory to the job’s working directory Pull Request 230
Fix a unicode issue and polish a bit of variables (thanks to @gmauro). Pull Request 229
Respond to MQ messages requesting status updates. Pull Request 228
Fix REST connections broken with Py3 using standard transport Issue 227 Pull Request 231
Drop Python 2.7 support in standard transport, drop Python 2.7 tests and fix Python 3.7 wheel install test, general test debugging enhancements. Pull Request 231
drop python 2.6 and add 3.7 and update the testing infrastructure to a more recent Ubuntu setup (thanks to @bgruening). Pull Request 226
Use is_alive in favour of isAlive for Python 3.9 compatibility (thanks to @tirkarthi). Issue 224 Pull Request 225
Request and register ports for Galaxy ITs when using Kubernetes. Pull Request 223
Implement killing k8s jobs. Pull Request 221
Respond to MQ messages requesting status updates. Pull Request 228
Drop python 2.6 and add 3.7 and update the testing infrastructure to a more recent Ubuntu setup (thanks to @bgruening). Pull Request 226
Add a more descriptive message in case of error parsing an external id (thanks to @gmauro). Pull Request 213
Use requests (thanks to @mvdbeek). Pull Request 216
Use is_alive in favour of isAlive for Python 3.9 compatibility (thanks to @tirkarthi). Pull Request 225
Debug connection string for AMQP. Pull Request 217
Various small Kubernetes fixes and enhancements. Pull Request 218, Pull Request 219
Improvements and fixes to container handling. Pull Request 202
Fix a typo in exception logging thanks to @erasche. Pull Request 203
Cleanup config file handling a bit by removing branch for very old Pulsar servers likely no longer supported. Pull Request 201
0.13.1 (2020-09-16)¶
Pinned all listed requirements. This is the final version of Pulsar to support Python 2.
0.13.0 (2019-06-25)¶
Various improvements and simplifications to Kubernetes job execution.
0.12.1 (2019-06-03)¶
Retry botched release that didn’t include all relevant commits.
0.12.0 (2019-06-03)¶
Revise Python Galaxy dependencies to use newer style Galaxy decomposition. galaxy-lib can no longer be installed in Pulsar’s environment, so you will likely need to rebuild your Pulsar virtualenv for this release. Pull Request 187
Add a
Dockerfile
for Pulsar with CVMFS (thanks to @nuwang and @afgane). Pull Request 166Various small improvements to Kubernetes pod execution environment. Pull Request 190
Improve readme linting. Pull Request 186
Update example docs for Condor (thanks to @bgruening). Pull Request 189
0.11.0 (2019-05-16)¶
Implement staging Galaxy metadata input files in the client. 39de377
Fix ‘amqp_ack_republish_time’ in sample (thanks to @dannon). Pull Request 185
Updated amqp_url in job_conf_sample_mq_rsync.xml (thanks to @AndreasSko). Pull Request 184
Use wildcard char for pulsar version (thanks to @VJalili). Pull Request 181
Refactor toward more structured inputs. f477bc4
Refactor toward passing objectstore identifying information around. Pull Request 180
Rework imports for new Galaxy library structure. da086c9
Revert empty input testing, it really probably should cause a failure to transfer a non-existent file. 8bd5511
Better client mapper documentation. b6278b4
0.10.0 (2019-05-06)¶
Implement support for Kubernetes two container pod jobs - staging and tool execution as separate containers in the same job’s pod. Pull Request 176, Pull Request 178
0.9.1 (2019-05-01)¶
Fix duplicate inputs being a problem when staging Galaxy files. Pull Request 175
Fix deprecated
assertEquals()
(thanks to @nsoranzo). Pull Request 173Fix a method missing problem. Pull Request 174
Sync “recent” galaxy runner util changes. Pull Request 177
0.9.0 (2019-04-12)¶
Add configuration parameter to limit stream size read from disk. Pull Request 157
Pass full job status for failed and lost jobs. Pull Request 159
Improve message handling if problems occur during job setup/staging. Pull Request 160
Rework preprocessing job state to improve restartability and reduce job loss. This change should be applied while no jobs are running. Pull Request 164
Add support for overriding config through environment variables (thanks to @nuwang). Pull Request 165
Minor docs updates (thanks to @afgane). Pull Request 170
Python 3 fixes in Pulsar client (thanks to @mvdbeek). Pull Request 172
0.8.3 (2018-02-08)¶
Create universal wheels to enable Python 3 support when installing from PyPI (thanks to @nsoranzo). Pull Request 156
0.8.1 (2018-02-08)¶
Update link for logo image. Pull Request 145
Minor error and log message typos (thanks to @blankenberg). Pull Request 146, Pull Request 153
Fixes/improvements for catching quoted tool files. Pull Request 148
Fix config sample parsing so run.sh works out of the box. Pull Request 149
0.8.0 (2017-09-21)¶
Support new features in Galaxy job running/scripting so that Pulsar respects
$GALAXY_VIRTUAL_ENV
and$PRESERVE_GALAXY_ENVIRONMENT
. Fix remote metadata in cases where the tool environment changes thepython
on$PATH
. Pull Request 137Precreate Galaxy tool outputs on the remote before executing (fixes a bug related to missing output files on stage out). Pull Request 141
Support the remote_transfer file action without setting the
jobs_directory
destination param Pull Request 136Fix invalid character in job managers documentation (thanks to @mapa17). Pull Request 130
Fix
conda_auto_*
option resolution and include a sampledependency_resolvers_conf.xml
(thanks to @mapa17). Pull Request 132Fix tox/Travis tests. Pull Request 138, Pull Request 139, Pull Request 140
Fix a bug with AMQP acknowledgement. Pull Request 143
0.7.4 (2017-02-07)¶
0.7.3 (2016-10-31)¶
Fix “AttributeError” when submitting a job as a real user. Pull Request 124, Issue 123
0.7.2 (2016-08-31)¶
Fix bug causing loops on in response to preprocessing error conditions.
0.7.1 (2016-08-29)¶
Do a release to circumvent a tool version logic error in Galaxy ( released Galaxy versions think 0.7.0 < 0.7.0.dev3).
0.7.0 (2016-08-26)¶
Update Makefile to allow release pulsar as an application and a library for Galaxy at the same time.
Small update to test scripts for TravisCI changes.
Improvements for embedded Galaxy runner. (TODO: fill this out)
Remove support for Python 2.6. 60bf962
Update docs to describe project goverance and reuse Galaxy’s Code of Conduct. 7e23d43, dc47140
Updated cluster slots detection for SLURM from Galaxy. cadfc5a
Various changes to allow usage within Galaxy as a library. ce9d4f9
Various changes to allow embedded Pulsar managers within Galaxy. ce9d4f9, d262323, 8f7c04a
Introduce a separate working and metadata directory as required for Galaxy 16.04 that requires this separation. 6f4328e
Add Tox target for Python 2.7 unit testing. d7c524e
Add
Makefile
command for setup.py develop. fd82d00
0.6.1 (2015-12-23)¶
Tweak release process that left 0.6.0 with an incorrect PyPI description page.
0.6.0 (2015-12-23)¶
Pulsar now depends on the new
galaxy-lib
Python package instead of manually synchronizing Python files across Pulsar and Galaxy.Numerous build and testing improvements.
Fixed a documentation bug in the code (thanks to @erasche). e8814ae
Remove galaxy.eggs stuff from Pulsar client (thanks to @natefoo). 00197f2
Add new logo to README (thanks to @martenson). abbba40
Implement an optional awknowledgement system on top of the message queue system (thanks to @natefoo). Pull Request 82 431088c
Documentation fixes thanks to @remimarenco. Pull Request 78, Pull Request 80
Fix project script bug introduced this cycle (thanks to @nsoranzo). 140a069
Fix config.py on Windows (thanks to @ssorgatem). Pull Request 84
Add a job manager for XSEDE jobs (thanks to @natefoo). 1017bc5
Fix pip dependency installation (thanks to @afgane) Pull Request 73
0.5.0 (2015-05-08)¶
0.4.0 (2015-04-20)¶
Python 3 support. Pull Request 62
Fix bug encountered when running
pulsar-main
andpulsar-config
commands as scripts. 9d43ae0Add
pulsar-run
script for issues commands against a Pulsar server (experimental). 3cc7f74
0.3.0 (2015-04-12)¶
Changed the name of project to Pulsar, moved to Github.
New RESTful web services interface.
SCP and Rsync file staging options added by E. Rasche. Pull Request
Allow YAML based configuration.
Support for more traditional
pip
/setup.py
-style installs.Dozens of smaller bugfixes and documentation updates.
0.2.0¶
Last version named the LWR - found on BitBucket.
Still supported in Galaxy as of 15.03 the release.
Introduced support for submitting to various queueing systems, operation as a Mesos framework, Docker support, and various other advanced deployment options.
Message queue support.
Framework for configurable file actions introduced.
0.1.0¶
Simple support for running jobs managed by the Python LWR web process.
0.0.1¶
See the original announcement and initial commit.