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243 commits

Author SHA1 Message Date
Julian Stirling
058f890c61 Update version numbers for v3 alpha2 release 2025-08-08 11:58:14 +01:00
Julian Stirling
3d7438ed2b Merge branch 'stitch-tile-size' into 'v3' 
Update to stitching 0.2

See merge request openflexure/openflexure-microscope-server!352
 2025-08-08 10:29:43 +00:00
jaknapper
f9f28b3500 Update tests 2025-08-08 10:44:03 +01:00
Julian Stirling
3a4b99df55 Apply suggestions from code review of branch faster-stage-tests 
Co-authored-by: Beth Probert <beth_probert@outlook.com>
 2025-08-08 09:32:31 +00:00
Julian Stirling
90dbb35a9e Directly call DummyStage instance during movement test for speed 2025-08-08 09:52:23 +01:00
Julian Stirling
dbdf254154 Fix CLI arg for FinalStitcher, and a docstring typo. 2025-08-07 15:20:14 +01:00
Julian Stirling
5caae613dc Apply suggestions from code review of branch yet-another-smart-scan-refactor 
Co-authored-by: Beth Probert <beth_probert@outlook.com>
 2025-08-07 13:55:47 +00:00
Julian Stirling
cd311f08bf Update stiching to differentiate bwtween stitchers that use a thread and those that block 2025-08-06 17:47:33 +01:00
Julian Stirling
f9fcdf628b Squash final todos for SmartScan refactor 2025-08-06 17:27:26 +01:00
Julian Stirling
4e9b07c78f Consolidate information into ScanData, remove ad-hoc differences for specific error in _run_scan 2025-08-06 17:27:26 +01:00
Julian Stirling
82691a6b78 Tweak error reporting in _run_scan and add a lot more testing for _run_scan 2025-08-06 17:27:26 +01:00
Julian Stirling
d7a7ac4c7d More complete testing of code that runs stitching subprocess. 2025-08-06 17:27:26 +01:00
Julian Stirling
cf74ea1351 More complete testing of code that runs stitching subprocess. 2025-08-06 17:27:26 +01:00
Julian Stirling
7569c7d6b2 Add validation checks to prevent arbitrary code execution via stitching. 2025-08-06 17:27:26 +01:00
Julian Stirling
a632ddee92 Add unit tests for generated stitching commands. 2025-08-06 17:27:26 +01:00
Julian Stirling
573fc20dec Add new tests new scan directory function and for scan data serialisation 2025-08-06 17:27:26 +01:00
Julian Stirling
73beb2b09d Merge branch 'fix-movements' into 'v3' 
Fix movements axes

Closes #498

See merge request openflexure/openflexure-microscope-server!338
 2025-08-06 15:50:08 +00:00
Julian Stirling
cbd2f9e0e3 Add check that _lock is a lock in requires_lock 2025-08-05 23:13:11 +01:00
Julian Stirling
9be9097246 Make scan directory manager thread safe 2025-08-05 23:13:11 +01:00
Julian Stirling
f3c8add398 Make axis inversion robust agains UI sending positions as strings 2025-08-05 08:30:54 +01:00
Julian Stirling
dacf219ea1 Change from axis direction set by ints to set by bools. Add a lot more tests. 2025-08-05 08:30:54 +01:00
Julian Stirling
58e3b5dcbd Start adding stage test and apply fixes to base class 2025-08-05 08:30:54 +01:00
Julian Stirling
7231e1cf5b Apply suggestions from code review of branch camera-and-bg-detect-setting-customisation 2025-08-04 22:44:40 +00:00
Julian Stirling
d994119b36 Add test to stop camera Thing APIs diverging futher without review 2025-08-01 23:08:33 +01:00
Julian Stirling
5296092b6b Fix tests now background status settings are returned as dictionaries. 2025-07-31 20:56:55 +01:00
Julian Stirling
13da56f3fd Fixes for the background detect as required by code review 2025-07-27 10:40:45 +01:00
Julian Stirling
238d022342 Apply suggestions from code review of branch bg_detect_in_camera 
Co-authored-by: Beth Probert <beth_probert@outlook.com>
 2025-07-26 16:45:06 +01:00
Julian Stirling
cc05ab4b5f Finish basic tests of background detect 2025-07-25 11:55:20 +01:00
Julian Stirling
d0b5db21ba Start adding background detect tests 2025-07-25 11:52:02 +01:00
Julian Stirling
fe1b84a922 Complete first pass (untested on hardware) of bg detect refactor. 2025-07-24 17:07:50 +01:00
Julian Stirling
c8e87577cb Add tests for new system Thing. 2025-07-15 00:14:07 +01:00
Julian Stirling
bed59c051b Merge branch 'update-setting-manager' into 'v3' 
Update setting manager

Closes #477, #343, and #475

See merge request openflexure/openflexure-microscope-server!321
 2025-07-14 16:47:41 +00:00
Julian Stirling
c9c8a89236 Merge branch 'simplify-csm-interface' into 'v3' 
Add camera-stage-mapping compliant functions to BaseStage and BaseCamera.

Closes #346 and #476

See merge request openflexure/openflexure-microscope-server!326
 2025-07-14 16:36:04 +00:00
Julian Stirling
34f8f86ef2 Apply suggestions from code review of branch update-setting-manager 
Co-authored-by: Joe Knapper <joe.knapper@glasgow.ac.uk>
Co-authored-by: Beth Probert <beth_probert@outlook.com>
 2025-07-14 17:11:54 +01:00
Julian Stirling
d3732aef2f Finish testing new version functionality in utilities. 2025-07-14 17:11:53 +01:00
Julian Stirling
ea1c1df4eb Improve testing of version strings and git hashes 2025-07-14 17:11:53 +01:00
Julian Stirling
5c1f8f2e89 Write tests for checking git hash 2025-07-14 17:11:53 +01:00
Julian Stirling
83a4b72507 Start writing tests for the version strings 2025-07-14 17:11:53 +01:00
Julian Stirling
531e5c27b2 Replace LoggingMoveWrapper with RecordedMove accepts a stage rather than an arbitrary move function 
This was needed to get the correct key word arguments
 2025-07-13 23:34:55 +01:00
Julian Stirling
fab5fdfca2 Improve log filtering and logging error handling. Adding more logging tests. 2025-07-13 15:17:11 +01:00
Julian Stirling
ea73e44b01 Start adding tests for the loging configuration. 2025-07-13 14:28:55 +01:00
Julian Stirling
7e6017f648 Get codespell passing and add it as a CI job. 2025-07-11 00:16:25 +01:00
Julian Stirling
864ca91e5c Add docstrings to all public package 2025-07-10 15:29:10 +01:00
Julian Stirling
14359e73bb Add public method docstrings. 2025-07-10 15:12:28 +01:00
Julian Stirling
a30b726b91 Class docstrings 2025-07-10 13:27:41 +01:00
Julian Stirling
2cb4003835 Add module level docstrings. 2025-07-10 09:24:50 +01:00
Julian Stirling
80beeea07b Add punctuation to docstrings 2025-07-10 09:24:50 +01:00
Julian Stirling
4dc41bb008 Single line summaries of docstrings 2025-07-10 09:24:49 +01:00
Julian Stirling
35d47fe3ed Starting docstring on the same lines as the quotations 2025-07-10 09:24:49 +01:00
Julian Stirling
be6a6ca6fe No starting docstrings with This 2025-07-10 09:24:49 +01:00