HISTORY.rst

History

0.15.7.dev0

0.15.6 (2024-01-15)

• Allow tus uploads to Galaxy. Pull Request 351

0.15.5 (2023-09-15)

• Add catchall OSError to recoverable exceptions (thanks to @mvdbeek). Pull Request 338

0.15.4 (2023-08-29)

• Add .readthedocs.yaml (thanks to @natefoo). Pull Request 332
• Add explicit TimeoutError catching (thanks to @mvdbeek). Pull Request 337
• Update galaxy-job-metrics requirement (thanks to @cat-bro). Pull Request 334

0.15.3 (2023-07-20)

• Fix Pulsar consumer state after ConnectionResetError. Pull Request 331
• User 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 315
• Various 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 269
• Use 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 166
• Various 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 173
• Fix 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 the python on $PATH. Pull Request 137
• Precreate 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 136
• Fix invalid character in job managers documentation (thanks to @mapa17). Pull Request 130
• Fix conda_auto_* option resolution and include a sample dependency_resolvers_conf.xml (thanks to @mapa17). Pull Request 132
• Fix 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)

• Fix Conda resolution and add a test case. 11ce744
• Style fixes for updated flake8 libraries. 93ab8a1, 3573341
• Remove unused script. 929bffa
• Fixup README. 629fdea

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
• Improve logging and comments. 38953f3, a985107, ad33cb9
• 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)

• Allow cURL downloader to resume transfers during staging in (thanks to @natefoo). 0c61bd9
• Fix to cURL downloaders status code handling (thanks to @natefoo). 86f95ce
• Fix non-wheel installs from PyPI. Issue 72
• Fix mesos imports for newer versions of mesos (thanks to @kellrott). fe3e919
• More, better logging. 2b3942d, fa2b6dc

0.4.0 (2015-04-20)

• Python 3 support. Pull Request 62
• Fix bug encountered when running pulsar-main and pulsar-config commands as scripts. 9d43ae0
• Add 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.
• https://bitbucket.org/jmchilton/lwr/branch/0.1

0.0.1

• See the original announcement and initial commit.