Code

Preparing for v2.9.0#304

Code

Merged

ksuderman merged 86 commits intomastergalaxyproject/gxabm:masterfrom devgalaxyproject/gxabm:devCopy head branch name to clipboardJul 13, 2024

+908-499

Commits

Commits on Dec 11, 2023

• Modify summarize_metrics to return a table of data rather than printing directly

  ksuderman

  committed
  60aba88

• Add --markdown option to summarize commands

  ksuderman

  committed
  b27956a

Commits on Dec 12, 2023

• Bump to dev version

  ksuderman

  committed
  228ac9f

• Finish summarize --markdown implementations

  ksuderman

  committed
  94f23e0

• Bump dev version

  ksuderman

  committed
  837b60b

• Add units to markdown table header row. Better formatting for floats

  ksuderman

  committed
  7bbafe4

• Better column formatting for markdown tables

  ksuderman

  committed
  bfe272b

• Merge pull request #243 from galaxyproject/242-results-to-markdown

  Show description for 3ce1924
  ksuderman

  authored
  3ce1924

Commits on Dec 13, 2023

• Change order that benchmarks are executed during an experiment.

  ksuderman

  committed
  61b1b29

• Add --timeout option to job.wait

  ksuderman

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  9d0eb6d

• Use --run-number to specify starting int when numbering benchmark runs

  ksuderman

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  dfb2d50

• Handle case with --run-number is not specified

  ksuderman

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  e9d0370

• Improve mardown for experiment summarize

  ksuderman

  committed
  01f624c

• Add --sort-by option to experiment.summarize

  ksuderman

  committed
  c371f14

• Merge pull request #245 from galaxyproject/244-benchmark-run-order

  Show description for 061805d
  ksuderman

  authored
  061805d

• Merge pull request #246 from galaxyproject/210-wait-timeout

  Show description for b9a62b6
  ksuderman

  authored
  b9a62b6

• Merge branch 'dev' into 169-run-number

  ksuderman

  authored
  7487c89

• Merge pull request #247 from galaxyproject/169-run-number

  Show description for 090c70b
  ksuderman

  authored
  090c70b

• Merge pull request #249 from galaxyproject/248-sort-by

  Show description for a0b4ec7
  ksuderman

  authored
  a0b4ec7

• Dev 2 version

  ksuderman

  committed
  ac90880

• Fix exception generating markdown if cell is empty

  ksuderman

  committed
  c3a5678

• Merge pull request #255 from galaxyproject/254-markdown-exceptions

  Show description for dfec3af
  ksuderman

  authored
  dfec3af

• Version dev.3

  ksuderman

  committed
  1572f11

• Dev version 4

  ksuderman

  committed
  e8940b8

Commits on Dec 14, 2023

• Add --sort-by to all summarize commands

  ksuderman

  committed
  c0086e7

• Merge pull request #256 from galaxyproject/251-summarize-sort

  Show description for 528bd44
  ksuderman

  authored
  528bd44

• Fix header for markdown tables

  ksuderman

  committed
  a253ed1

• Merge pull request #260 from galaxyproject/258-markdown-table-header

  Show description for 1a686b4
  ksuderman

  authored
  1a686b4

Commits on Dec 15, 2023

• Add invocation.show

  ksuderman

  committed
  3d627d7

• Merge pull request #262 from galaxyproject/259-invocation-show

  Show description for 0dfb4c1
  ksuderman

  authored
  0dfb4c1

• Adde help goal to the Makefile

  ksuderman

  committed
  dac22bc

• Improve history name lookup

  ksuderman

  committed
  24e327a

• Merge pull request #265 from galaxyproject/257-history-name

  Show description for 7b1a3c9
  ksuderman

  authored
  7b1a3c9

• Round up memory and runtime values if they would display zeroes

  ksuderman

  committed
  4958a7a

• Merge pull request #266 from galaxyproject/264-round-values

  Show description for b064013
  ksuderman

  authored
  b064013

• Limit the number of attempts a job will be restarted.

  ksuderman

  committed
  d0c526b

• Merge pull request #267 from galaxyproject/261-job-restarts

  Show description for 81bd807
  ksuderman

  authored
  81bd807

• Add document to menu.yml for the --sort-by option

  ksuderman

  committed
  32077fa

• Add documentation for experiment.summarize --markdown

  ksuderman

  committed
  7c2ad51

• Merge pull request #268 from galaxyproject/263-update-menu

  Show description for 1f09521
  ksuderman

  authored
  1f09521

Commits on Dec 18, 2023

• Pass env to all helm invocations

  ksuderman

  committed
  211bab9

• Add try_for method to retry api calls

  ksuderman

  committed
  3f6890a

• Fix bug handling start at value

  ksuderman

  committed
  0d00e65

• Retry invoking and waiting for invocations

  ksuderman

  committed
  382bfb3

Commits on Dec 20, 2023

• Fix run numbering range.

  ksuderman

  committed
  ab3ec5c

• Retry getting jobs list

  ksuderman

  committed
  fe6567d

Commits on Jan 19, 2024

• Use argparse in dataset.list

  ksuderman

  committed
  d078c0b

• Don't add one to the run number when generating the history name.

  ksuderman

  committed
  04763b4

• Merge pull request #271 from galaxyproject/270-run-number

  Show description for 76d15dc
  ksuderman

  authored
  76d15dc

• Bump version

  ksuderman

  committed
  1fc5c04

Commits on Jan 20, 2024

• Merge pull request #273 from galaxyproject/269-dataset-list

  Show description for 76abe10
  ksuderman

  authored
  76abe10

Commits on Jan 31, 2024

• Added code documentation.

  ksuderman

  committed
  9e62c70

• Print the starting run number after its value has been checked.

  ksuderman

  committed
  6c07eb7

• Merge pull request #276 from galaxyproject/275-run-number

  Show description for 2b6bfac
  ksuderman

  authored
  2b6bfac

• More code documentation.

  ksuderman

  committed
  29f5436

Commits on Mar 29, 2024

• Rename list methods to prevent name collisions with the list type

  ksuderman

  committed
  144ebaa

• Merge pull request #277 from galaxyproject/272-list-methods

  Show description for abfe344
  ksuderman

  authored
  abfe344

• Merge branch 'dev' into documentation

  ksuderman

  committed
  f3011b2

• Merge pull request #278 from galaxyproject/documentation

  Show description for 111fa50
  ksuderman

  authored
  111fa50

Commits on May 22, 2024

• Allow the Galaxy master API key to defined in the profile.

  ksuderman

  committed
  6efb9ce

• Add configuration as a command alias

  ksuderman

  committed
  5a85ae1

• Merge pull request #281 from galaxyproject/279-config-command

  Show description for 95008f9
  ksuderman

  authored
  95008f9

• Update year in copyright notices

  ksuderman

  committed
  1b4eeb5

• Merge pull request #282 from galaxyproject/280-copyright

  Show description for 2326217
  ksuderman

  authored
  2326217

Commits on May 24, 2024

• Update samples and cleanup unused

  nuwang

  committed
  0533f8c

• Merge pull request #284 from galaxyproject/update_samples

  Show description for dca5e0c
  ksuderman

  authored
  dca5e0c

Commits on May 28, 2024

• Add --no-tools flag for workflow import and upload

  ksuderman

  committed
  40792ca

• Merge pull request #290 from galaxyproject/85-master-api-key

  Show description for 83a53f2
  ksuderman

  authored
  83a53f2

• Merge pull request #289 from galaxyproject/288-no-tools-installed

  Show description for 1770635
  ksuderman

  authored
  1770635

Commits on May 29, 2024

• Bump dev version

  ksuderman

  committed
  88e13b8

• Update bump script

  ksuderman

  committed
  2ad1a1e

• Try to fix problems resolving dataset collection IDs

  ksuderman

  committed
  676572c

• Merge pull request #292 from galaxyproject/debugging

  Show description for 9dca47c
  ksuderman

  authored
  9dca47c

• Bump build number

  ksuderman

  committed
  fd36cd3

Commits on Jun 4, 2024

• Search for a local .abm directory before using the global directory

  ksuderman

  committed
  6bc3439

• Allow multiple datasets to be imported at once.

  ksuderman

  committed
  5e9ab17

Commits on Jun 5, 2024

• Use local .abm directory for configurations if it exists.

  ksuderman

  committed
  715098a

Commits on Jun 6, 2024

• Use gi.jobs.get_metrics(job_id) to get the metrics for a job before writing the metrics file.

  ksuderman

  committed
  774f956

• Merge pull request #299 from galaxyproject/298-replace-show-job

  Show description for 52424a9
  ksuderman

  authored
  52424a9

• Merge pull request #296 from galaxyproject/295-local-configuration

  Show description for b2c71a9
  ksuderman

  authored
  b2c71a9

Commits on Jul 13, 2024

• Allow --history to be specified by name

  ksuderman

  committed
  1a86f2f

• Document --name option when uploading/downloading datasets

  ksuderman

  committed
  6de42f9

• Update requirements

  ksuderman

  committed
  71f9aea

• Merge pull request #303 from galaxyproject/302-dataset-import-history

  Show description for 2b3e2be
  ksuderman

  authored
  2b3e2be

• Format code with Black and iSort

  ksuderman

  committed
  da7f6f4

• Merge branch 'master' into dev

  ksuderman

  authored
  24b7b5b