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Preparing for v2.9.0 #304

Merged
merged 86 commits into from
Jul 13, 2024
Merged

Preparing for v2.9.0 #304

merged 86 commits into from
Jul 13, 2024

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ksuderman
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Merging into master to prepare the 2.9.0 release.

@ksuderman
Modify summarize_metrics to return a table of data rather than printi…
60aba88 
…ng directly
@ksuderman
Add --markdown option to summarize commands
b27956a
@ksuderman
Bump to dev version
228ac9f
@ksuderman
Finish summarize --markdown implementations
94f23e0
@ksuderman
Bump dev version
837b60b
@ksuderman
Add units to markdown table header row. Better formatting for floats
7bbafe4
@ksuderman
Better column formatting for markdown tables
bfe272b
@ksuderman
Merge pull request #243 from galaxyproject/242-results-to-markdown
3ce1924 
Markdown tables
Closes #242
@ksuderman
Change order that benchmarks are executed during an experiment.
61b1b29
@ksuderman
Add --timeout option to job.wait
9d0eb6d
@ksuderman
Use --run-number to specify starting int when numbering benchmark runs
dfb2d50
@ksuderman
Handle case with --run-number is not specified
e9d0370
@ksuderman
Improve mardown for experiment summarize
01f624c
@ksuderman
Add --sort-by option to experiment.summarize
c371f14
@ksuderman
Merge pull request #245 from galaxyproject/244-benchmark-run-order
061805d 
Benchmark order
@ksuderman
Merge pull request #246 from galaxyproject/210-wait-timeout
b9a62b6 
Wait timeout
@ksuderman
Merge branch 'dev' into 169-run-number
7487c89
@ksuderman
Merge pull request #247 from galaxyproject/169-run-number
090c70b 
Run numbering
@ksuderman
Merge pull request #249 from galaxyproject/248-sort-by
a0b4ec7 
Sort experiment summarize
@ksuderman
Dev 2 version
ac90880
@ksuderman
Fix exception generating markdown if cell is empty
c3a5678
@ksuderman
Merge pull request #255 from galaxyproject/254-markdown-exceptions
dfec3af 
Markdown Exceptions
@ksuderman
Version dev.3
1572f11
@ksuderman
Dev version 4
e8940b8
@ksuderman
Add --sort-by to all summarize commands
c0086e7
@ksuderman
Merge pull request #256 from galaxyproject/251-summarize-sort
528bd44 
Sumarize sort by
@ksuderman
Fix header for markdown tables
a253ed1
@ksuderman
Merge pull request #260 from galaxyproject/258-markdown-table-header
1a686b4 
Markdown tables
@ksuderman
Add invocation.show
3d627d7
@ksuderman
Merge pull request #262 from galaxyproject/259-invocation-show
0dfb4c1 
Invocation Show
ksuderman and others added 29 commits March 29, 2024 14:09
@ksuderman
Merge branch 'dev' into documentation
f3011b2
@ksuderman
Merge pull request #278 from galaxyproject/documentation
111fa50 
Add code documentation
@ksuderman
Allow the Galaxy master API key to defined in the profile.
6efb9ce
@ksuderman
Add configuration as a command alias
5a85ae1
@ksuderman
Merge pull request #281 from galaxyproject/279-config-command
95008f9 
Configuration command
@ksuderman
Update year in copyright notices
1b4eeb5
@ksuderman
Merge pull request #282 from galaxyproject/280-copyright
2326217 
Update copyright
@nuwang
Update samples and cleanup unused
0533f8c
@ksuderman
Merge pull request #284 from galaxyproject/update_samples
dca5e0c 
Update samples and cleanup unused
@ksuderman
Add --no-tools flag for workflow import and upload
40792ca
@ksuderman
Merge pull request #290 from galaxyproject/85-master-api-key
83a53f2 
Master API key
@ksuderman
Merge pull request #289 from galaxyproject/288-no-tools-installed
1770635 
Add --no-tools flag for workflow import and upload
@ksuderman
Bump dev version
88e13b8
@ksuderman
Update bump script
2ad1a1e
@ksuderman
Try to fix problems resolving dataset collection IDs
676572c
@ksuderman
Merge pull request #292 from galaxyproject/debugging
9dca47c 
Fix dataset lookup error
@ksuderman
Bump build number
fd36cd3
@ksuderman
Search for a local .abm directory before using the global directory
6bc3439
@ksuderman
Allow multiple datasets to be imported at once.
5e9ab17
@ksuderman
Use local .abm directory for configurations if it exists.
715098a
@ksuderman
Use gi.jobs.get_metrics(job_id) to get the metrics for a job before w…
774f956 
…riting the metrics file.
@ksuderman
Merge pull request #299 from galaxyproject/298-replace-show-job
52424a9 
298 replace show job
@ksuderman
Merge pull request #296 from galaxyproject/295-local-configuration
b2c71a9 
295 local configuration
@ksuderman
Allow --history to be specified by name
1a86f2f
@ksuderman
Document --name option when uploading/downloading datasets
6de42f9
@ksuderman
Update requirements
71f9aea
@ksuderman
Merge pull request #303 from galaxyproject/302-dataset-import-history
2b3e2be 
302 dataset import history
@ksuderman
Format code with Black and iSort
da7f6f4
@ksuderman
Merge branch 'master' into dev
24b7b5b
@ksuderman ksuderman merged commit 2b1de88 into master Jul 13, 2024
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2 participants
@ksuderman @nuwang