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Merge branch 'prep-for-v3.0.0-alpha5' into 'v3'

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Prep for v3.0.0 alpha5

See merge request openflexure/openflexure-microscope-server!557
This commit is contained in:
Joe Knapper 2026-03-26 15:03:37 +00:00
commit 9149121d4b
5 changed files with 116 additions and 8 deletions
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110
CHANGELOG.md
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@ -1,3 +1,111 @@
# [v3.0.0-alpha5](https://gitlab.com/openflexure/openflexure-microscope-server/compare/v3.0.0-alpha4...v3.0.0-alpha5) (2026-04-08)
The fifth alpha release of the server. This release has been a huge amount of work and brings us significantly closer to a semi-stable beta release. Some highlights are:
* Move from LabThings Dependencies to ThingSlots. This has allowed for:
* Much easier communication between Things
* Static type checking
* Simpler action creation.
* Created ScanWorkflows, a backend change that allows switching scan methods. Enabling new types of scanning:
* Raster Scan
* Snake Scan
* CChip Scan (experimental, requires a configuration change to use)
* Transition front end from the end of life Vue2 to Vue3 which is in active development!
* Improvements to the simulation microscope including more simulation samples and camera options. Speeding up development.
* Improved testing, including better defined testing environments, separation of integration and unit tests, and tests passing on Windows
* OpenCV camera switching. Enabling changing between cameras in settings when in manual configuration.
* "Jogging" movement. The microscope can now move continuously when an arrow key is held.
* Improved server side UI specification. This brings us closer to "Things" being able to define their own tab, which will soon enable plugins in v3.
* A user interface for recentring and range of motion.
* Improved fallback server interface.
* Backlash correction in scanning.
* A huge number of other bug fixes and improvements.
The following merge requests have been merged into v3:
* !450 Update to be compatible with labthings-fastapi 0.0.12/0.0.13
* !451 Start to remove deps
* !452 Removing dependencies from CSM, autofocus, and stage_measure
* !453 Final dependency removals
* !454 Use new LabThingsTestEnv thoughout tests <!-- codespell:ignore thoughout -->
* !455 Type fixes
* !456 Proper integration tests
* !457 Fix (most) unit tests on Windows
* !458 Simulation Camera Improvements
* !460 Bugfix, stop saving scans into log folder
* !461 Background detector things
* !462 Implement ScanWorkflows allowing multiple scanning methods
* !464 SnakeScan as a scan planner
* !469 More workflow layers
* !465 Add raster scan, with generic typing to allow subclassed settings
* !468 Illumination Thing
* !473 HTTP API docs
* !479 Vue2-3 migration.
* !480 Tidy optional deps
* !478 Increase dz range to 400 to 3000
* !472 Manually handle out of storage and JPEG too big errors
* !485 Restore CSM stream pos to right of buttons
* !486 Add URL to wiki if Sangaboard firmware out of date
* !475 Grey out read only properties in webapp
* !484 Reduce the blur for a given z movement in simulation, to improve autofocus.
* !489 Bump ESLint from unsported version to version 9
* !483 CSM modal shows stream
* !476 Generalised Jogging
* !477 Optional options in UI property control become dropdown
* !482 Add recentre and ROM test buttons to stage settings
* !495 Add --max-warnings=0 back to eslint check. This was accidentally dropped when moving from vue-cli-service
* !490 Magnification selection in simulator by cropping canvas based on objective property
* !497 Re-enable prettier
* !496 Update release checklist from last alpha's experience
* !494 Use lt.property/setting validatiors to set numerical input range and step <!-- codespell:ignore validatiors -->
* !498 Update logging page formatting.
* !499 Use Invocation errors for expected errors.
* !500 Add a fallback page template.
* !505 Remove references to old GPU preview feature.
* !506 Webapp cleanup
* !504 Use own pagination consistently rather than vue-pagination-next
* !502 Add spellchecking for camelCase, PascalCase, and kebab-case
* !501 Scan logs
* !508 Allow 0 as a setting in the webapp
* !493 Split SmartStackParams into focus, capture, stack params
* !487 Add functionality to switch OpenCV camera without restarting the server.
* !514 Move to headless opencv
* !513 More developer documnetation <!-- codespell:ignore documnetation -->
* !510 Change pointer event names for clarity
* !509 Backlash correction in base stage class
* !517 Allow histo scans with equal dx and dy
* !516 Do less coersion for stacks now labthings validates settings. <!-- codespell:ignore coersion -->
* !519 Metadata testing
* !503 Create and mount application level data directory rather than just a scan directory
* !491 Decrease target brightness for both cameras as its pre-gamma
* !525 Align buttons in confirmation modal
* !526 Fix spellings found as codespell updates
* !518 Add limits to background detect and settling time settings
* !527 Update bug template to include table or configuration, more detail about how...
* !532 Reorder Bug.md expected and actual behaviour with correct comments
* !531 Don't tab to spinners in webapp
* !524 Improve Validation Checks
* !535 Remove uk-input from checkbox
* !530 Increase number of UI elements that can be specified in the server
* !442 Handle scan settings, then change stream, then pre-scan procedure when scanning
* !533 Stop closing seadragon when going full screen
* !529 Move more development information to the dev docs to minimise repitition and getting out of sync <!-- codespell:ignore repitition -->
* !474 CChip scan workflow
* !544 Update codespellrc to ignore ./git folder, not extension
* !545 Update camera cal instructions to look through empty area if possible
* !540 Flush more frames and use a request when doing exposure time
* !542 Close calibration with confirmation
* !546 Update path to ofm server and config file in docs
* !547 Explicit windows check before sigkill for mypy
* !536 Split up slide scan tab and create a generic action tab (attempt 2)
* !548 Word break long lines in notifications
* !552 Move from posix path to os path
* !554 Move smart stacking into a mixin so it can be re-used in other workflows <!-- codespell:ignore "re-used" -->
* !551 Sort scans by created time
* !538 Update dependency to labthings 0.1.0
# [v3.0.0-alpha4](https://gitlab.com/openflexure/openflexure-microscope-server/compare/v3.0.0-alpha3...v3.0.0-alpha4) (2025-12-15)
The fourth alpha release of the server. This release has concentrated on colour reproduction, scanning, and the structure of the web-app.
@ -58,7 +166,7 @@ The following merge requests have been merged into v3:
* !434 Improve the stability of scanning
* !438 Formalise import sorting rules and enforce
* !448 Bump required stitching version to 0.2.1
* !449 Prep for v3.0.0-alpha4
# [v3.0.0-alpha3](https://gitlab.com/openflexure/openflexure-microscope-server/compare/v3.0.0-alpha2...v3.0.0-alpha3) (2025-10-10)

6
pyproject.toml
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@ -3,7 +3,7 @@ name = "openflexure-microscope-server"
# Note that version needs to match a string stored in a unit test, and
# the package.json file in the webapp or the CI will fail.
version = "3.0.0-alpha4"
version = "3.0.0-alpha5"
authors = [
{ name="Richard Bowman", email="richard.bowman@cantab.net" },
{ name="Joel Collins" },
@ -19,10 +19,10 @@ classifiers = [
]
dependencies = [
"labthings-fastapi==0.1.0",
"sangaboard",
"sangaboard~=0.4.0",
"camera-stage-mapping ~= 0.1.10",
"opencv-python-headless ~= 4.13.0",
"openflexure-stitching[libvips]==0.2.3",
"openflexure-stitching[libvips]==0.2.4",
"pillow ~= 10.4",
"anyio ~= 4.0",
"numpy ~= 2.2",

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tests/unit_tests/test_version_strings.py
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@ -19,7 +19,7 @@ THIS_DIR = os.path.dirname(__file__)
TRUE_REPO_DIR = os.path.dirname(os.path.dirname(THIS_DIR))
# For explicit version checking.
VER_STRING = "3.0.0-alpha4"
VER_STRING = "3.0.0-alpha5"
# This is the regex provided by https://semver.org/
SEMVER_REGEX = re.compile(

4
webapp/package-lock.json generated
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@ -1,12 +1,12 @@
{
"name": "openflexure-microscope-server-ui",
"version": "3.0.0-alpha4",
"version": "3.0.0-alpha5",
"lockfileVersion": 3,
"requires": true,
"packages": {
"": {
"name": "openflexure-microscope-server-ui",
"version": "3.0.0-alpha4",
"version": "3.0.0-alpha5",
"license": "GNU General Public License v3.0 ",
"dependencies": {
"@vueuse/core": "^14.1.0",

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webapp/package.json
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{
"name": "openflexure-microscope-server-ui",
"version": "3.0.0-alpha4",
"version": "3.0.0-alpha5",
"private": true,
"description": "User interface for the OpenFlexure Microscope Server",
"author": "OpenFlexure <contact@openflexure.org> (https://www.openflexure.org)",