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Upgrade to V1 - #437

Merged

rettigl merged 383 commits into

mainfrom

v1_feature_branch

Feb 5, 2025

Merged

Upgrade to V1#437
rettigl merged 383 commits into
mainfrom
v1_feature_branch

This pull request is big! We're only showing the most recent 250 commits

Commits on Jun 24, 2024
- enable energy offset in benchmark
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- typing fixes
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Commits on Jun 25, 2024
- apply bias offset for energy calibration in energy calibrator, and omitt from offset dict to avoid applying twice.
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- fix test
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- fix spelling in all files using Code Spell Checker
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Commits on Jun 26, 2024
- some additional spell fixes
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- Merge pull request #449 from OpenCOMPES/spelling_fixes
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- Merge remote-tracking branch 'origin/v1_feature_branch' into refactor-flashloader
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Commits on Jun 28, 2024
- remove nans from all electron channels
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  d131fe4
- use pd import, load h5 file inside df creator
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  194c874
- update comments to explain the code
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  af33740
- make review changes
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  50f7ee1
- fix tests with review comments
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- fix dropna
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Commits on Jun 30, 2024
- fix minor stuff and add test to see if exception handling works in parallel
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  b0b090d
- Merge pull request #329 from OpenCOMPES/refactor-flashloader
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  f5b9148
- fix timestamp issue in flashloader
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  118084e
- Update benchmark targets
  
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- Merge remote-tracking branch 'origin/v1_feature_branch' into energy_calibration_bias_shift
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- Merge pull request #455 from OpenCOMPES/update_benchmark_targets
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- Merge remote-tracking branch 'origin/v1_feature_branch' into energy_calibration_bias_shift
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Commits on Jul 2, 2024
- Merge remote-tracking branch 'origin/main' into v1_feature_branch
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- additional spell fixes
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  7f9422c
- change behavior of tof_binning and adc_binning to reflect actual binning factor
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- add additional ignore entries
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  84421ea
- move num_cores to "core" and use it globally
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- Merge branch 'v1_feature_branch' into energy_calibration_bias_shift
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- fix spelling
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- bump version to 0.1.10a6
  
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- Update dependencies
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Commits on Jul 3, 2024
- fix flash tests to also rune fine with defined system config
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  7687fd1
- add typing to tests, and fix issues
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Commits on Jul 4, 2024
- detect illegal keyword arguments
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- Merge remote-tracking branch 'origin/flash_test_fixes' into catch_illegal_kwds
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- add tests for illegal keyword errors
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Commits on Jul 6, 2024
- Merge pull request #465 from OpenCOMPES/flash_test_fixes
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  11d4d74
- fix group_name error
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  f6c33e6
- bring back old behavior
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  30e7447
- minor changes
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  49d93e9
- use concat for faster join
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  d830e8c
- try saving both
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  c48a6ec
- change fill section
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- parallel processing
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  88f0e9c
- change paths config to hold raw and processed keys
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  f6a45e5
- change filehandling of buffer files as it's more complicated now, and filling for both electron and pulse
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  a8632ab
- add dtype handler, make more changes to filepath handler
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Commits on Jul 7, 2024
- update methods and tests
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  e436397
- sxp test fixes
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  1b2e788
- processor test fixes
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  7ed0962
- sxp test fixes
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Commits on Jul 8, 2024
- Merge remote-tracking branch 'origin/main' into v1_feature_branch
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- Merge branch 'v1_feature_branch' into energy_calibration_bias_shift
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  989f438
- Merge branch 'v1_feature_branch' into tof_binning-as-actual-binning-values
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- Merge branch 'energy_calibration_bias_shift' into catch_illegal_kwds
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  245762a
- add further tests
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  638ed68
- fix typing
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  84f99ef
- remove 0 vals from all pulse channels
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  5b6f940
- Merge pull request #451 from OpenCOMPES/tof_binning-as-actual-binning-values
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  ecd517d
- Merge branch 'v1_feature_branch' into energy_calibration_bias_shift
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  748cb11
- update energy calibration description
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  1ef47b1
- fix Energy(TOF) view for binding energy scale
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  a017fe4
- add some more tests for mpes loader
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Commits on Jul 9, 2024
- Merge branch 'v1_feature_branch' into fix-459
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  4b682a5
- update paths
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Commits on Jul 10, 2024
- revert the benchmarking
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Commits on Jul 15, 2024
- update aux channel handling
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  2de5243
Commits on Jul 16, 2024
Commits on Jul 17, 2024
- index sorting
  zain-sohail
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  770af0d
- roll back the buffer_handler with small changes
  zain-sohail
  committed
  7944043
- fix some test issues
  zain-sohail
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  adfd335
Commits on Jul 18, 2024
- fix energy calibration and delay range
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  fbd5cbf
- Merge remote-tracking branch 'origin/v1_feature_branch' into fix-459
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- some metadata changes
  zain-sohail
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  4d35e54
- Merge branch 'fix-459' into flash-minor-changes
  zain-sohail
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  b9bef4f
- use correct lock
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  0aab5c4
- roll back to iterations
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Commits on Jul 23, 2024
- add aux alias and subchannels argument
  zain-sohail
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  d09e715
- change name and return of the run method
  zain-sohail
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  b0471f2
- Merge pull request #479 from OpenCOMPES/flash-minor-changes
  zain-sohail
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  85c1315
- Merge pull request #469 from OpenCOMPES/fix-459
  zain-sohail
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  89ba09e
- Update benchmark targets
  
  zain-sohail
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  github-actions[bot]
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Commits on Jul 25, 2024
- remove invalid channels
  zain-sohail
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  019bf40
- create exception and use it to find invalid files
  zain-sohail
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  80da01d
- Merge pull request #483 from OpenCOMPES/update_benchmark_targets
  rettigl
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- Merge remote-tracking branch 'origin/main' into v1_feature_branch
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Commits on Jul 26, 2024
- add exception when no valid files are available and fix testing
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Commits on Jul 31, 2024
- implement suggested changes
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Commits on Aug 11, 2024
- let code run even if no train channels exist
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Commits on Aug 14, 2024
- Merge remote-tracking branch 'origin/main' into v1_feature_branch
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- limit pynxtools
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Commits on Aug 16, 2024
- Merge branch 'v1_feature_branch' into remove-invalid-channels
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Commits on Aug 21, 2024
- filter out all negative pulse values as they are invalid
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  2b6f96e
- filter out in final df
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- Merge pull request #484 from OpenCOMPES/remove-invalid-channels
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Commits on Sep 19, 2024
- Merge remote-tracking branch 'origin/main' into v1_feature_branch
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  83fe946
- replace prints by logging
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  bda9e10
- fixes for new matplotlib
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  f824bad
- use base sed logger
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  fbb0af2
- add logging to mpes loader
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  469236d
- add verbosity to loader interface
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  37feca1
- add logging to delay calibrator
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  2fbae5d
- use logging in momentum calibrator
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  3292658
- use logging in energy calibrator, and further fixes
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  e3af246
- some further fixes
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  2a69836
- add function to set verbosity, and use in each class
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  79a181d
- Make verbose a private property, and add getter and setters for it, to propagate verbosity
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- Merge pull request #490 from OpenCOMPES/logging
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Commits on Oct 7, 2024
- adding this flag due to https://github.com/astral-sh/ruff/issues/5434
  
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- first pydantic model for config
  
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- without typeddict
  
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  600ef55
- remove defaults
  
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- update lock file with pydantic
  
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- nest the models
  
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- add copytool in configmodel and other attrs
  
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- update config files to conform to model
  
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- use configmodel in processor class
  
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- update modules to new config
  
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- fix some config problems
  
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- update lockfile
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Commits on Oct 11, 2024
- update poetry, limit numpy
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- update lockfile
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  a70529a
- limit dask version to <2024.8 due to bug where computation takes forwever in certain cases
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- disable dask query-planning as workaround for bugs in dask-expr
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- remove limits on python versions for tests
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Commits on Oct 12, 2024
- Merge pull request #448 from OpenCOMPES/update_dask_version
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- Merge remote-tracking branch 'origin/v1_feature_branch' into pydantic-model
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- fix tests for calibrators
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- make model fail on extra parameters
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- fix flash loader
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- fix calibrator tests again
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- fix processor tests
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- fix sxp loader
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- update notebooks
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- fix remaining tests
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Commits on Oct 13, 2024
- add config model for copy tool
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- Add further type refinements to config model
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Commits on Oct 14, 2024
- add tests for config model
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- fix remaining tutorials
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Commits on Oct 15, 2024
- fix config model tests
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- add review suggestions
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- fix reporting of energy/delay offsets
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- fix handling of nexus input files and tests
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- fix error reporting
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Commits on Oct 17, 2024
- fix sxp notebook
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Commits on Oct 21, 2024
- changes from review
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Commits on Oct 22, 2024
- Move static (#511)
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- Merge pull request #487 from OpenCOMPES/pydantic-model
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- fix benchmarks
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Commits on Nov 12, 2024
- Merge remote-tracking branch 'origin/main' into v1_feature_branch
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- update merged changes
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- update build scripts to new config model
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- move code to src folder
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- fix tests
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- update workflows
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- update tutorials
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- add config to build specs
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- fix flash build script again
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- update path to Nexus config file
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- fix tests
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- fix benchmarks
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- Merge pull request #508 from OpenCOMPES/src_layout
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- move Flash Nxmpes config
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- update build script
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- update jupyter to >v4
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- adopt figure sizes
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- change color map to default plt cycle
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- use matplotlib also for momentum correction
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- fix type error
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- fix figure sizes and font sizes
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Commits on Nov 13, 2024
- remove redundant toctree entry
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- fix config docs
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- Merge pull request #509 from OpenCOMPES/style_fixes
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Commits on Nov 21, 2024
- Merge pull request #516 from OpenCOMPES/update_jupyter
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Commits on Nov 30, 2024
- Merge remote-tracking branch 'origin/main' into v1_feature_branch
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- fix config paths
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- fix new notebooks and merging bugs
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- fix changed variable name
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Commits on Dec 3, 2024
- Merge remote-tracking branch 'origin/main' into v1_feature_branch
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Commits on Dec 19, 2024
- Merge remote-tracking branch 'origin/main' into v1_feature_branch
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- fix merge errors
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Commits on Dec 21, 2024
- move config into sed
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- fix config references
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- fix build scripts
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Commits on Dec 30, 2024
- Merge remote-tracking branch 'origin/main' into fix_src_layout
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- Merge pull request #537 from OpenCOMPES/fix_src_layout
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Commits on Jan 1, 2025
- update pyproject and workflows
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- use dynamic versioning
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- fix spelling
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- add v1 branch
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Commits on Jan 2, 2025
- update tests
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- limit photutils
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- remove 3.8 again
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- fix coverage report
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- add build step
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- try fix release
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- fix benchmark
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- fix url
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- add pypi-test url and credentials
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- fix scripts
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- remove password
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- add verbose output
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- fix docs config
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Commits on Jan 3, 2025
- publish to main pypi, and remove trigger
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- update docs
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Commits on Jan 4, 2025
- further docs fixes
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Commits on Jan 5, 2025
- Merge pull request #540 from OpenCOMPES/move_to_uv
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Commits on Jan 6, 2025
- remove empty pulses from timed dataframe, and bring back old behavior
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Commits on Jan 7, 2025
- add further exceptions for completely empty files, and exceptions
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Commits on Jan 10, 2025
- allow both timed dataframe formats
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- add back docstring
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- reformat
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- Merge pull request #546 from OpenCOMPES/flash_normalization_fixes-zain
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- fix metadata issues, and add more debug logs
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- fix lint errors
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- remove repitition
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- remove warnings
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Commits on Jan 12, 2025
- add documentation about feature
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- Merge pull request #541 from OpenCOMPES/flash_normalization_fixes
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- Merge branch 'v1_feature_branch' into flash-metadata-fixes
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- update token handling with env variables
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- update test
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- add the dotenv package
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- Merge pull request #542 from OpenCOMPES/more-broken-file-fixes
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- read write env variables without extra package, tests added
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- Merge branch 'v1_feature_branch' into flash-metadata-fixes
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Commits on Jan 13, 2025
- config error
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- Merge remote-tracking branch 'origin/main' into v1_feature_branch
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Commits on Jan 14, 2025
- use value error
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- search for .env in cwd and os env variables
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- Merge branch 'flash-metadata-fixes' of github.com:OpenCOMPES/sed into flash-metadata-fixes
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- bring back comments
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Commits on Jan 15, 2025
- Merge pull request #547 from OpenCOMPES/flash-metadata-fixes
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- Merge branch 'v1_feature_branch' into pydantic-error-handling
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Commits on Jan 16, 2025
Commits on Jan 19, 2025
- Fix release and update documentation
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Commits on Jan 20, 2025
- use user platformdir also for user config
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- Merge pull request #553 from OpenCOMPES/fix-552
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- Merge remote-tracking branch 'origin/v1_feature_branch' into config_renaming
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- add tests for system config dir
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- Merge pull request #554 from OpenCOMPES/fix-release-and-docs
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- Merge pull request #555 from OpenCOMPES/config_renaming
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Commits on Feb 5, 2025
- update workflows
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Commits

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