Aug_9_2024

What's Changed

• Update pytools to 3.3.0 by @blowekamp in #479
• Specify precfect version and dask optional depenency on one line by @blowekamp in #475
• tag brt runs, update imod version by @philipmac in #481

Full Changelog: 2.1.1...2.1.2

2.1.1

What's Changed

• bumps version num in setup.py by @philipmac in #476

2.1.0

What's Changed

• process 2D 16-bit Tiffs with newstack by @blowekamp in #468
• Feature/newstack 16 bit tiff by @blowekamp in #474

May_23_2024

Sync prefect local to server version, to conform with security updates.
Minor release.

What's Changed

• adding prod UUIDs to usage.rst by @philipmac in #464
• updateing docs & prod service file by @philipmac in #465
• bump n2 version by @philipmac in #470
• default to testing in main branch by @philipmac in #471
• new dask install method by @philipmac in #473

Full Changelog: 2.0.5...2.0.6

Mar_06_2024

What's Changed

• Port workflows to Prefect2

Full Changelog: 1.2...2.0.5

Nov_16_2023

What's Changed

• Added bioformats2raw to GH build and added tests. by @mbopfNIH in #259
• Add samples of new metadata json to be produced by the pipeline by @blowekamp in #260
• Update metadata.yml for float brightness and contrast by @blowekamp in #262
• Correct legacy example for metadata by @blowekamp in #266
• Removed "shortcut" code from BRT test. by @mbopfNIH in #264
• adding explanations of file layout for spatial omics set up. by @philipmac in #267
• Update hpc.rst by @philipmac in #268
• Script to extract a czi "macro images" to a thumbnail by @blowekamp in #269
• adding illustrative example of proposed callback by @philipmac in #261
• conform to new callback format by @philipmac in #274
• init fileMetadata and imageMetadata callback elts as None by @philipmac in #283
• PR request template by @annshress in #281
• Containers by @annshress in #284
• Config modifications by @annshress in #277
• Adding new IF czi workflow by @philipmac in #299
• Add coverage comment workflow action by @annshress in #298
• Refactor large 2d flow by @annshress in #293
• Add file_share param into workflows by @annshress in #297
• Replace strings by Asset type constants by @annshress in #291
• Fix relative imports by @annshress in #304
• Register new czi workflow by @annshress in #306
• Use workers count wherever bf2raw command is used by @annshress in #310
• Addresses file share check, #309 by @annshress in #311
• Test callback structure by @annshress in #300
• bumps pytools version - new SITK goodies - closes #312 by @philipmac in #314
• Update configs for java and lrg_flow.convert by @annshress in #320
• Polish tests; Refactor and move tests by @annshress in #315
• required for registration script by @philipmac in #322
• Add pytest setup fixture to ensure .env file exists by @annshress in #290
• Refactor bf2raw command to be central/common function by @annshress in #323
• Increase tiling size (for czi files) in bf2raw by @annshress in #325
• fix up mixed tabs / spaces by @philipmac in #326
• killing off dead / commented out code - closes #302 by @philipmac in #327
• removing --scale-format-string from bioformats command by @philipmac in #331
• Fixes the removal of scale-string-format argument from bioformats2raw by @annshress in #334
• Bumps to pytools 3.0b02 by @philipmac in #337
• Fix/update brt ng metadata by @philipmac in #339
• use pytools wheel by @philipmac in #341
• Update shader parameters spec to include XYC dimensions by @blowekamp in #344
• Change locations for zarr image in single image workflows by @annshress in #345
• hardcode in XY for API by @philipmac in #350
• Mad scale by @blowekamp in #347
• Rotate label image 90 clock wise by @blowekamp in #348
• Remove redundant return statement by @annshress in #359
• prevents thumb gen for IF images by @philipmac in #360
• Return OME metadata xml file location along with ng metadata by @annshress in #361
• Add omeXml: null in fileMetadata of all results by @annshress in #368
• Use quantile based computations for CZI range by @blowekamp in #376
• Changing bioformats2raw chunk dims from 4K to 512 by @philipmac in #382

Full Changelog: 1.1.1...1.2

May_25_2023

What's Changed

• Initial version of Sphinx docs including top-level code by @mbopfNIH in #169

• Readded just the test classes to use shutil.which(), not util.Config. by @mbopfNIH in #170

• Update brt pipeline docs by @philipmac in #171

• Added docstrings and improved Sphinx docs - mostly FilePath by @mbopfNIH in #175

• Added Prefect to requirements.txt and improved docstrings by @mbopfNIH in #185

• Added utils tests; cleaned up test dir by @mbopfNIH in #189

• Added additional tests of utils.py by @mbopfNIH in #193

• PERF: Combine newstack commands which apply transforms. by @philipmac in #200

• Added pytest coverage including documentation by @mbopfNIH in #196

• Zarr format by @philipmac in #203

• Tests and Coverage upon GH Actions by @mbopfNIH in #202

• flake8 on workflow code, adds init.py to test by @philipmac in #205

• rms unused test_callback, adds .flake8 file, fixes flake8 errs by @philipmac in #208

• Fixed IMOD path issues and skipped bad dm tests by @mbopfNIH in #206

• Cleaned up errors in Sphinx docs build by @mbopfNIH in #211

• Updated the Development page of the docs. by @mbopfNIH in #212

• Added script to manually run test coverage. by @mbopfNIH in #218

• Fixed in flake8 args by @mbopfNIH in #216

• Add neuroglancer zarr asset type by @philipmac in #219

• Adding debug option to prevent removal of workdirs, closes #194 by @philipmac in #221

• Fixing Flake8 error "W605 invalid escape sequence" by @mbopfNIH in #222

• Adding MRC file for test coverage. by @mbopfNIH in #223

• Increasing test coverage; commented out dead code by @mbopfNIH in #224

• Hpc fixes by @philipmac in #233

• Released to Prod on 6/12/2023

Full Changelog: 1.0.3...1.1.0

Mar_20_2023

What's Changed

• process mrc files in 2d by @philipmac in #150
• Made some simple document changes to test if I can push. by @mbopfNIH in #156
• Determine executable paths dynamically by @mbopfNIH in #157
• Changed Config class and tests to be more platform-independent by @mbopfNIH in #159
• Adds natsort to deal with input fnames by @philipmac in #164
• clean up unneeded files in work dir (lots of interim jpgs and mrcs)
• only keep last workdir
• rm sharpen from jpeg gen

New Contributors

• @mbopfNIH made their first contribution in #156

Full Changelog: 1.0.2...1.0.3

Jan_12_2023

What's Changed

• changes BRT to single cpu, adds tag to setup, rms pytools from reqs by @philipmac in #141
• Creates Dask cluster that scales upon demand. by @philipmac in #142

Full Changelog: 1.0.1...1.0.2

Dec_19_2022

• Modifies adoc for better efficiency.
• no zip on pyramid gen
• no_api mode