Merge branch 'final-v3-alpha2-things' into 'v3'

Final v3 alpha2 things

See merge request openflexure/openflexure-microscope-server!354

CHANGELOG.md

@@ -1,3 +1,80 @@
+# [v3.0.0-alpha2](https://gitlab.com/openflexure/openflexure-microscope-server/compare/v3.0.0-alpha1...v3.0.0-alpha2) (2025-08-08)
+
+This is the second alpha release the v3 server, the main focus has been higher resolution scans with more reliable focus. There have been many other changes, some highlights are:
+
+* Capture in Scanning increased from 0.5MP to 2MP
+* Using updated stitching which is significantly faster.
+* Scanning uses a "smart stacking" that camptures images until it has found the sharpest one. Removing the need to perform autofocus, and improving the focus reliability.
+* Server version is saved into image metadata
+* Improvements to settings in LabThings-FastAPI so settings persist more reliably
+* Improvements to memory management, process, and directory management during scanning
+* UI improvements including:
+  * Direct download of stitched image
+  * Stitching can be cancelled from the UI
+  * Stitch all scans button in the UI to stitch any scans that are not already stitched
+  * The log display pauses autoscroll on mouse hover
+  * More consistent updating of scan tab
+  * Better description of server version information
+* Picamera and Sangaboard code are now directly in the repository, in heriting from BaseCamera and BaseStage class. Allowing core functionality to be added to BaseStage and Base Camera.
+* Other underlying changed that will make customisation easier in the future.
+* Significantly increase in code testing
+
+The following merge requests have been merged into v3:
+
+* !290 Enable more lint checkers
+* !288 Remove numerical input spinners for x,y,z settings in Firefox
+* !295 Update issue templates
+* !298 Git ignore openflexure/ dir
+* !297 Add a timeout when shutting down the server.
+* !300 Automatically create HTML coverage report each time PyTest runs
+* !302 Correct spelling of Sangaboard
+* !303 Remove the overwriting of internal globals, requires removing future annoations <!-- codespell:ignore annoations -->
+* !251 2MP from 8MP capturing
+* !271 A stack that tests whether the sharpest image is towards the middle
+* !294 Trying to make a distinction between file directory operations for scans and scanning code
+* !308 Replace semi colon with double ampersand in package.json
+* !305 Allow downloading just the stitched image, and don't zip DZIs
+* !309 Combine uniquness and length checks <!-- codespell:ignore uniquness -->
+* !310 Remove test Thing that is is never used.
+* !312 Allow stiching to be cancelled after a scan complete
+* !311 Move SangaboardThing into repo
+* !315 Fix artifact path in CI for webapp
+* !313 Remove out of date CaptureThing from Simulation and Stub config
+* !314 Remove old unmaintained components
+* !296 Update Thing Settings and import statments for LabThings-FastAPI 0.0.10 <!-- codespell:ignore statments -->
+* !319 Python integration tests
+* !316 Stop streams to ensure that server exits gracefully.
+* !320 Better docstrings
+* !322 Update README to point at CONTRIBUTING and make contributing link to site,...
+* !324 Fix example docstring example in CONTRIBUTING.md
+* !325 Test logging
+* !326 Add camera-stage-mapping compliant functions to BaseStage and BaseCamera.
+* !321 Update setting manager
+* !323 Merge settings and system control
+* !328 Update simulation canvas to have colour so it works with background detect.
+* !330 Stitch all scans button, and refresh scan tab when closing modals
+* !327 Refactor background detect to allow switching algorithms
+* !332 Make log display pause on hover
+* !333 Bump LabThings-Fastapi to 0.0.11
+* !336 Remove zenodo scripts and job
+* !334 Stop exposure walking on camera reload, reset CCM on full calibration
+* !339 Remove auto-recentre stage
+* !340 Remove class from action button
+* !337 Report Picamera tests in CI
+* !341 Prepend images with img_
+* !343 Update .coveragerc to get 2 decimal places for coverage
+* !331 Dynamic UI for camera and background detect settings
+* !345 Change "settings" to "configure" in background detect tab
+* !346 Make scan directory manager thread safe
+* !344 Scanning in simulation
+* !338 Fix movements axes
+* !347 Pull webapp
+* !342 Break up SmartScan further so it can be tested
+* !353 Speed up `tests/test_stage.py` significantly
+* !352 Update to stitching 0.2
+
+
+
 # [v3.0.0-alpha1](https://gitlab.com/openflexure/openflexure-microscope-server/compare/v2.11.0...v3.0.0-alpha1) (2025-06-09)
 
 This is the first alpha release of an almost total overhaul of the server, and the underlying LabThings framework. Some highlights are:

change_log_helper.py

@@ -0,0 +1,62 @@
+#! /usr/bin/env python3
+
+"""Create a list of the MRs into v3 (unless specified) since the last release."""
+
+import sys
+import argparse
+
+import gitlab
+
+from gitlab.exceptions import GitlabGetError
+
+PROJECT_ID = 9238334
+
+
+def main(tag, branch: str = "v3"):
+    """Create a list of the MRs into a given branch after a tag.
+
+    :param tag: The tag the mrs should be since.
+    :param branch: The Git branch name MRs were merged into.
+    """
+    try:
+        gl = gitlab.Gitlab()
+        ofm_repo = gl.projects.get(PROJECT_ID)
+        tag_obj = ofm_repo.tags.get(tag)
+        tag_date = tag_obj.commit["committed_date"]
+        # There is no "merged_after option". So get everything updated after
+        relevant_mrs = ofm_repo.mergerequests.list(
+            state="merged",
+            target_branch=branch,
+            order_by="merged_at",
+            updated_after=tag_date,
+            get_all=True,
+        )
+        # Filter for those merged after the tagged commit.
+        for mr in reversed(relevant_mrs):
+            if mr.merged_at > tag_date:
+                print(f"* !{mr.iid} {mr.title}")
+    except GitlabGetError as e:
+        print(f"Failed contact gitlab server.\n{e}")
+        sys.exit(-1)
+
+
+if __name__ == "__main__":
+    parser = argparse.ArgumentParser(
+        description=(
+            "Get Merge requests since a specific tag to help with creating a "
+            "changelog."
+            "The response in printed to the terminal."
+            "Check the start of the list, it may have a couple of extra MRs on the "
+            "same day as the tag."
+        )
+    )
+    parser.add_argument("tag", help="The Git tag to start looking from (required)")
+    parser.add_argument(
+        "-b",
+        "--branch",
+        default="v3",
+        help="Git branch that requests were merged into (default: v3)",
+    )
+
+    args = parser.parse_args()
+    main(tag=args.tag, branch=args.branch)

pyproject.toml

@@ -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-alpha1"
+version = "3.0.0-alpha2"
 authors = [
   { name="Richard Bowman", email="richard.bowman@cantab.net" },
   { name="Joel Collins" },

tests/test_version_strings.py

@@ -19,7 +19,7 @@ THIS_DIR = os.path.dirname(__file__)
 TRUE_REPO_DIR = os.path.dirname(THIS_DIR)
 
 # For explicit version checking.
-VER_STRING = "3.0.0-alpha1"
+VER_STRING = "3.0.0-alpha2"
 
 # This is the regex provided by https://semver.org/
 SEMVER_REGEX = re.compile(

webapp/package-lock.json

@@ -1,12 +1,12 @@
 {
   "name": "openflexure-microscope-jsclient",
-  "version": "3.0.0-alpha1",
+  "version": "3.0.0-alpha2",
   "lockfileVersion": 3,
   "requires": true,
   "packages": {
     "": {
       "name": "openflexure-microscope-jsclient",
-      "version": "3.0.0-alpha1",
+      "version": "3.0.0-alpha2",
       "license": "GNU General Public License v3.0 ",
       "dependencies": {
         "material-design-icons": "^3.0",

webapp/package.json

@@ -1,6 +1,6 @@
 {
   "name": "openflexure-microscope-jsclient",
-  "version": "3.0.0-alpha1",
+  "version": "3.0.0-alpha2",
   "private": true,
   "description": "User client for the OpenFlexure Microscope Server",
   "author": "OpenFlexure <contact@openflexure.org> (https://www.openflexure.org)",