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Update to 0.3.0 #15

Merged
merged 28 commits into from
Jul 12, 2024
Merged

Update to 0.3.0 #15

merged 28 commits into from
Jul 12, 2024

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kostrykin
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Essential changes:

kostrykin and others added 28 commits February 14, 2024 11:23
@kostrykin
Add missing requirement for TIFF reading
63f8d86
@kostrykin
Update README.rst
eb1bf50
@kostrykin
Add regression tests (#4)
15b834c 
* Add missing requirement for TIFF reading

* Add regression tests for BBBC039

* Fix bug in regression tests

* Add regression tests for GOWT1 datasets

* Add regression tests for NIH3T3 datasets

* Add regression tests for U2OS dataset

* Add regression tests workflow

* Update workflow

* Fix workflow

* Fix expected regression test results

* Fix workflow

* Fix workflow

* Fix workflow

* Fix workflow

* Fix workflow

* Fix workflow

* Fix workflow

* Fix workflow

* Fix workflow

* Update regressiontests.yml

* Update regressiontests.yml

* Update regressiontests.yml

* Fix workflow

* Fix workflow

* Fix workflow

* Fix workflow

* Fix workflow

* Fix workflow

* Fix workflow

* Add `SUPERDSM_INTERMEDIATE_OUTPUT` environment variable

Set `SUPERDSM_INTERMEDIATE_OUTPUT=0` to disable intermediate console output.

* Add `MKL_DEBUG_CPU_TYPE=5` to workflow

* Update regressiontests.yml

* Update regressiontests.yml

* Update regressiontests.yml

* Fix workflow

* Set workflow job timeout to 24 hours

* Fix dependency versions for reproducibility

* Fix conda channels

* Disable `use_only_tar_bz2`

* Add test example

* Pin all dependency versions

* Unset `MKL_DEBUG_CPU_TYPE=5`

* Add CPU vendor recognition

* Add more images to test task

* Add missing expected test results

* Set `MKL_DEBUG_CPU_TYPE=1` on non-AMD CPUs

* Upload artifact with results upon failure

* Unset `MKL_DEBUG_CPU_TYPE` if set to `5` on Intel CPUs

* Add  trigger

* Adapt expected results of regression tests for Intel Xeon CPU

* Activate remaining regression tests

* Fix version of `upload-artifact`

* Add debug info

* Fix

* Reenable test

* Combine regression tests into bash scripts

* Add testsuite workflow

* Update workflow name

* Add dry run for debugging

* Fix regression tests

* Add regression test results for AMD Threadripper 3970X CPU

* Do not change `MKL_DEBUG_CPU_TYPE` on Intel CPUs

* Fix regression tests expected results

* Fix expected regression test results for AMD CPU

* Fix
@dependabot @kostrykin
Bump cvxopt from 1.2.6 to 1.2.7 (#3)
fa27306 
* Bump cvxopt from 1.2.6 to 1.2.7

Bumps [cvxopt](https://github.com/cvxopt/cvxopt) from 1.2.6 to 1.2.7.
- [Release notes](https://github.com/cvxopt/cvxopt/releases)
- [Commits](cvxopt/cvxopt@1.2.6...1.2.7)

---
updated-dependencies:
- dependency-name: cvxopt
  dependency-type: direct:production
...

Signed-off-by: dependabot[bot] <[email protected]>

* Bump cvxopt version in Conda environment

---------

Signed-off-by: dependabot[bot] <[email protected]>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
Co-authored-by: Leonid Kostrykin <[email protected]>
@kostrykin
Merge branch 'develop' of github.com:kostrykin/SuperDSM into develop
62303c4
@kostrykin
Add SUPERDSM_NUM_CPUS env variable (#6)
12ab988 
* Add SUPERDSM_NUM_CPUS env variable

* Fix str to int conversion
@kostrykin
Merge branch 'develop' of github.com:kostrykin/SuperDSM into develop
5eea8ff
@kostrykin
Remove num_cpus from task files
c192b9e 
Support for `num_cpus` in task files has been removed in #6.
@kostrykin
Set SUPERDSM_NUM_CPUS=20 for regression tests (#7)
3d19328
@kostrykin
Merge branch 'develop' of github.com:kostrykin/SuperDSM into develop
f47a45e
@kostrykin
Fix workflow triggers
22391be
@kostrykin
Add blend/require-conditional-status-checks (#9)
e4908ff 
* Add blend/require-conditional-status-checks

* Add failing test to test_image.py

* Fix validate_pr.yml

* Update validate_pr.yml

* Remove failing test from f8daa37
@kostrykin
Update superdsm.io module (#10)
375accb 
* Rename `io.imwrite` to `io.imsave`

* Add `force_filetype` argument for `io.imread`

* Increase timeout for `validate_conditional_checks`

* Increase `blend/require-conditional-status-checks` timeout
@kostrykin
Add requirements.txt to CI trigger
71bc68a
@kostrykin
Switch to containerized CI using Conda (#13)
0a02a3c 
* Relax the requirement `c-blosc2=2.13.2=hb4ffafa_0` in `superdsm.yml` to just `c-blosc2=2`
* Remove BBBC039 from regression tests
@kostrykin
Remove requirements.yml from RTD installation
7a62e08
@kostrykin
Revert 7a62e08
d1cdee8
@kostrykin
Bump RTD build Python version to 3.8
a2789e6
@kostrykin
Bump RTD build Python version to 3.9
eea4fc6
@kostrykin
Add typing-extensions to RTD build
6ad57b6
@kostrykin
Fix docs/requirements.txt
9d01cc3
@kostrykin
Fix docs/requirements.txt
414503a
@kostrykin
Update the documentation (#8)
bc64b99 
* Update README.rst

* Fix typo

* Add ``Environment variables`` section to usage.rst
@kostrykin
Update usage.rst
b6738e9
@kostrykin
Update usage.rst
924e95c
@kostrykin
Add SUPERDSM_NUM_CPUS to usage.rst
a356eaf
@kostrykin
Update conf.py
67bad8a
@kostrykin
Merge branch 'master' into develop
2f78977
@kostrykin
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https://github.com/BMCV/SuperDSM/actions/runs/9904222859/job/27361182538?pr=15#step:4:48

Error: Commit Comparison contained too many files; File Count: 300

There are 1707 changed files, which cannot be handled by the blend/require-conditional-status-checks extension.

This is mostly due to the ground truth for the regression tests.

@kostrykin kostrykin merged commit e1de37a into master Jul 12, 2024
2 of 3 checks passed
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@kostrykin