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291 commits

Author SHA1 Message Date
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
Julian Stirling
f51dae7b3a Doc strings to imperative mood 2025-07-10 09:24:49 +01:00
Julian Stirling
dceb640c77 Add documentation job to the CI. 2025-07-10 09:24:49 +01:00
Julian Stirling
a84a916719 Restructured text fixes so that pydoctor would return without an error 2025-07-09 23:59:08 +01:00
Julian Stirling
f3ec5a445a Update labthings-fastapi version in pyproject.toml 2025-07-07 15:25:16 +01:00
Julian Stirling
4e20067c68 Update json configuration and dependencies for SangaboardThing being in the repository 2025-07-02 17:27:09 +01:00
Julian Stirling
7f0745d772 Add some more scan_directories tests 2025-06-28 23:59:35 +01:00
Julian Stirling
2ce2f998fa add tests for helper classes defined by fast stack 2025-06-27 00:34:51 +01:00
Joe Knapper
378998d230 Merge branch 'jpeg-capture-in-stacking' into 'v3' 
2MP from 8MP capturing

Closes #364, #413, #298, #303, #288, #358, and #433

See merge request openflexure/openflexure-microscope-server!251
 2025-06-25 17:57:51 +00:00
Julian Stirling
0933ece63a Apply suggestions from code review of branch jpeg-capture-in-stacking 
Co-authored-by: Beth Probert <beth_probert@outlook.com>
 2025-06-25 15:39:36 +01:00
Julian Stirling
0e3f4305b5 Tidy post refactor of cameras 2025-06-23 11:26:24 +01:00
Julian Stirling
b5606984ae Consolidate the BaseCamera, CameraStub, and CameraProtocol, move StreamingPiCamera2 to this repo 2025-06-23 11:25:49 +01:00
Julian Stirling
c70b487a1f Automatically create HTML coverage report each time PyTest runs 2025-06-23 11:00:10 +01:00
Julian Stirling
c43b7cb8b4 Merge branch 'more-checkers' into 'v3' 
Enable more lint checkers

See merge request openflexure/openflexure-microscope-server!290
 2025-06-12 11:56:29 +00:00
Julian Stirling
37bb9635ad Apply 2 suggestion(s) to 2 file(s) 
Co-authored-by: Beth Probert <beth_probert@outlook.com>
 2025-06-12 10:29:54 +00:00
Julian Stirling
3019e13c80 Add commented out code check to linters 2025-06-11 23:40:49 +01:00
Julian Stirling
04832892cc Chnge docstring tester from Doc to D as Doc has no effect 2025-06-10 16:07:49 +01:00
Julian Stirling
1c54d25212 Add ruff checking for unnecessary comprehensions 2025-06-10 16:07:49 +01:00
Julian Stirling
2050c2dc7c Add return checker, needed 4 fixes 2025-06-10 16:07:48 +01:00
Julian Stirling
3f0564f253 Turning on more lint checkers, warning for cameras that ignore resolution setting 2025-06-10 16:07:48 +01:00
Julian Stirling
0457978048 Update depedencies and changelog priort to v3.0.0-alpha1 release 
Closes #398
 2025-06-09 15:39:26 +01:00
Julian Stirling
c79184a6d9 Use same version number for server and webapp, add CI check 
- Check webapp and server have same version number
- Use `genversion` on build to create javascript file with version string
from pyproject.toml
- Expose the version number in the js interface
- Correct format of current of alpha version string because javascript complains

Closes #382
 2025-06-09 12:13:15 +01:00
Julian Stirling
2aa7d0f6be Update labthings-api dep and also the version number for alpha release 2025-06-06 13:09:04 +01:00
Joe Knapper
0132813b6a update labthings-picamera to most recent release 2025-06-02 14:40:06 +00:00
jaknapper
576161e543 Import openflexure-stitching from pip, updated toml and config jsons 2025-05-20 17:54:17 +01:00
Julian Stirling
51346e45fe Update dependencies to use new OpenCV wheel compiled against numpy v2 2025-05-13 09:03:53 +01:00
Julian Stirling
2ced848695 Add functionality for testing the scan planner on a given sample shape 2025-04-14 11:27:25 +01:00
Julian Stirling
7665d45e09 Make the coverage report touch all files 2025-04-11 23:29:32 +01:00
Julian Stirling
e4cfcc76a7 Add some extra rules to ruff, also add a more complete ruff config that fails 
Over time we can enable more rules for `ruff check`
 2025-04-11 11:56:55 +01:00
Joe Knapper
d4247235e3 Merge branch 'csm-return-to-start' into 'v3' 
CSM always returns to start on error

See merge request openflexure/openflexure-microscope-server!227
 2025-04-08 12:49:38 +00:00
Joe Knapper
bf82f37c47 Dependency bump for camera_stage_mapping to 0.1.8 
Returns the errors we expect
 2025-04-08 12:09:15 +00:00
Julian Stirling
1493f51212 Purge all windows line endings and add check to formatter. 
Also changes python version in pyproject.toml as it is incorrect
 2025-04-08 10:51:26 +01:00
Julian Stirling
928d5ef300 Try pinning pydantic version as server now fails tests with error 2025-04-02 14:05:38 +01:00
Richard Bowman
e8ae496d08 Use published packages 
I've published [pre]releases on PyPI. This commit uses the mos recent releases of labthings-picamera2 and camera-stage-mapping.
 2024-12-18 14:26:15 +00:00
Richard Bowman
db11e03321 Constrain numpy < 2 
picamera2 fails to import with numpy 2.
 2024-12-18 14:23:44 +00:00
Richard Bowman
1d59cddac1 Disable pytest code quality report 
Code quality report plugin clashes with the version of pytest specced in labthings.

If we resolve this upstream, we can re-enable it.
 2024-12-03 14:19:36 +00:00
Richard Bowman
c3cd30b642 Only rebuild docker for changes 
Docker is now only rebuilt when it's changed, and on `v3`  branch.

I've also added code quality reporting for pytest.
 2024-12-03 12:54:34 +00:00
Richard Bowman
71e6d84aa4 Build docker image and run ruff/pytest 2024-12-03 12:18:45 +00:00
Richard Bowman
77794c94eb Update documentation on dependencies/dev tools 2024-12-03 11:18:24 +00:00
Richard Bowman
1e7069b375 Add more tests, speed up dummy stage 
I've sped up the stage motion, to run tests in a more reasonable time.

CSM doesn't yet calibrate in the test - I suspect debugging of capture_array
is needed.
 2024-12-03 00:16:26 +00:00
Richard Bowman
1ba799de22 Migrate to new Blob type and update imports 
This now uses the latest version of labthings-fastapi.
 2024-11-28 17:35:56 +00:00
Richard Bowman
b8ca12314c Lock labthings/picamera2 deps 
v0.0.7 of labthings includes breaking changes, we're not ready for that yet.
 2024-11-28 10:30:53 +00:00
Richard Bowman
7b584d3e64 Add labthings version constraint 2024-11-16 10:58:31 +00:00
Richard Bowman
7fb4417ebe Configuration files and other tweaks 
The OFM server can now be run in "stub" mode on
my development machine, using an OpenCV
camera feed.
 2024-08-09 02:42:32 +01:00
Richard Bowman
e3e248c46e Move server config to a config file 
Currently this is "just" a LabThings config file.
 2024-08-09 01:51:11 +01:00
Richard Bowman
3f92ed8266 Add a stub OpenCV-based camera 
This allows the server to run on a laptop, to some extent. I've not tested if this will make the whole
web app work properly.

As StreamingPiCamera2 is hardcoded in various places, this certainly doesn't make cameras totally
interchangeable - but it is a step towards that.
 2024-08-09 00:52:31 +01:00
Richard Bowman
3abddc3b39 Fix labthings dependency 
I changed the labthings package such that it will
only install the client dependencies by default.
This is now fixed by requiring the [server] extras.
In the future we might split labthings into client
and server packages.
 2024-07-18 13:17:26 +01:00
Richard Bowman
bcc13475b6 Propagate logs from camera-stage-mapping 2024-01-04 13:19:00 +00:00