docs: update changelog for v1.5.0

Author: tifuchs

CHANGELOG.md

@@ -3,67 +3,115 @@
 This is the changelog for the software orGUI, written by Timo Fuchs
 
 
-## [1.5.0-rc.1] (2026-05-15)
-
-[532b60b](https://github.com/tifuchs/orGUI/commit/532b60bab3073ae9f0ff063a0e119aa9e9957857)...[7107429](https://github.com/tifuchs/orGUI/commit/7107429a2c81cf45d7a43ef394bb910731c09070)
-
-Release candidate for v1.5.0
-
-Adds a new command line interface mode of orGUI, which enables better scripting in headless configurations.
+## [1.5.0] (2026-06-07)
+
+[532b60b](https://github.com/tifuchs/orGUI/commit/532b60bab3073ae9f0ff063a0e119aa9e9957857)...[c574bdf](https://github.com/tifuchs/orGUI/commit/c574bdf0bd5af6fa8258d108e7355c579bfef857)
+
+This is a feature release focused on scripted/headless operation, release
+infrastructure, documentation, and several GUI and integration robustness
+fixes.
+
+orGUI now has two startup modes. The default graphical user interface is still
+the normal interactive application for inspecting images, setting reference
+reflections, adjusting ROIs, and visually checking the experiment geometry. The
+new command line interface is selected with ``--cli``, ``--nogui``, or
+``--headless`` and is intended for scripting, batch jobs, and cluster use. In
+CLI mode users can run a Python startup script with ``-i`` / ``--input`` and
+work with the preloaded ``app``, ``orgui``, and ``ub`` objects instead of
+clicking through the GUI.
+
+Scientific and analysis-impacting fixes:
+
+- Masked pixels are now excluded from rocking-scan counters and the same mask
+  handling is applied to the static background image and correction arrays used
+  in rocking integration. Results from workflows that combine rocking
+  integration with masks, static background subtraction, or correction arrays
+  should be checked against the new behavior.
+- Fixes for NumPy 2.x compatibility.
+- Reference reflection tables with image numbers outside the currently loaded
+  scan no longer crash the GUI. Invalid image numbers are reported as warnings
+  and the reflection table is updated more defensively.
+
+CLI and scripting highlights:
+
+- ``orGUI --cli`` / ``--nogui`` / ``--headless`` start the headless path, and
+  ``-i`` / ``--input`` runs a Python startup script with ``app``, ``orgui``,
+  and ``ub`` already available.
+- ``--keep-running`` keeps the application alive after a startup script and can
+  drop into the embedded shell for interactive inspection.
+- ``--cpus``, ``--logfile``, ``--errorlog``, and HDF5 file-locking options make
+  batch and cluster runs easier to control.
+- CLI runs now print progress and errors to the terminal or selected log files,
+  so batch jobs can finish or fail without waiting for a hidden dialog.
+- Batch-oriented helpers were added for static and rocking ROI workflows,
+  including support for multiple manually defined static rocking scans.
+
+Documentation:
+
+- The orGUI documentation is now available on Read the Docs:
+  <https://orgui.readthedocs.io/>.
+- End-user release notes are available in this changelog and on the Read the
+  Docs release-notes page:
+  <https://orgui.readthedocs.io/en/latest/release_notes.html>.
+
+Other user-visible changes:
+
+- Log files can be written for normal and error output.
+- Backend load errors are more verbose.
+- CHESS QM2/id4b backend examples now include the z motor in the scanned motor
+  list, and QM2 log files can be parsed for more accurate timestamps.
+- ``NUMEXPR_MAX_THREADS`` defaults to 1 when not already set, avoiding
+  oversubscription during parallel or cluster runs.
+
+Thanks to Finn Schröter (Finnjek) for the NumPy 2.x miscut fix and Bragg
+reflection image-number crash fix.
 
-The planned orGUI documentation is work in progress and a first version is now available on https://orgui.readthedocs.io/
- 
 ### Added
 
 - Add command line interface using Qt offscreen rendering and update logging ([9442123](https://github.com/tifuchs/orGUI/commit/94421236384dd5037e83a98274f2d9fe7a59d74a))
 - Add orCLI input prompt token in cli mode ([2de769a](https://github.com/tifuchs/orGUI/commit/2de769a92eb4a71f6ed5e0fca8c1879848826b5f))
 - Add batch scripting ([b1116ac](https://github.com/tifuchs/orGUI/commit/b1116ac914a8c2e3b4b6f0bc0eea3039180583ba))
 - Add Progress logging API ([0cb8246](https://github.com/tifuchs/orGUI/commit/0cb82464d5461db6ae61e21565bf1c31d722a3d0))
-- Add AGENTS.md for AI code review rules ([5df3d9d](https://github.com/tifuchs/orGUI/commit/5df3d9de9e817330dc2b412ff6056c375a89e7fd))
-- Add orGUI.py docstrings, minimal sphinx documentation ([cdc47d6](https://github.com/tifuchs/orGUI/commit/cdc47d6846ce32403c983f187f5a458b99931d2e))
-- Add .readthedocs.yaml ([b71d867](https://github.com/tifuchs/orGUI/commit/b71d86705acabd5a703314238ca2872017d0a9af))
-- Add PySide6 to docs requirements ([466e8d2](https://github.com/tifuchs/orGUI/commit/466e8d2750771f4e0b4030bd315237b961784dbe))
-- Add RTD import checker ([8fcce5b](https://github.com/tifuchs/orGUI/commit/8fcce5b7876121357cc6a97fffff121d998c47a5))
+- Add log file support ([28ffb92](https://github.com/tifuchs/orGUI/commit/28ffb928d88610f9c4a45eef7fa1fd604af6d74a))
+- Limit deltaS to a median of 1 pixel ROI center distance ([43afb8c](https://github.com/tifuchs/orGUI/commit/43afb8cfe05753d1584ae0d3b9521bc091ca743a))
+- Add multiple manual static rocking scans cli function ([7f4f5de](https://github.com/tifuchs/orGUI/commit/7f4f5de3694aae247630302f21321706f28420df))
 - Add headless CLI and batch scripting support ([9f5db10](https://github.com/tifuchs/orGUI/commit/9f5db1079b224c7c9bc04c61f118812cb1722b89))
-- Add backend and configuration pages ([5efb16e](https://github.com/tifuchs/orGUI/commit/5efb16e112520c0178ad9911da45c66f47b09a94))
-- Add project links to pyproject.toml ([9c68924](https://github.com/tifuchs/orGUI/commit/9c68924abf055c6e8be74585ee4c33da09426814))
-- Add release.yml ([6582566](https://github.com/tifuchs/orGUI/commit/6582566ce3ea10e7dc9a5182c52d00340ea0e893))
-- Add release procedure and release notes ([7107429](https://github.com/tifuchs/orGUI/commit/7107429a2c81cf45d7a43ef394bb910731c09070))
+- QM2/id4b add z motor to scanned motor list ([be77c1a](https://github.com/tifuchs/orGUI/commit/be77c1aab81be792c498b6eae15b80eed7e74a4f))
+- QM2 add log file parsing for accurate time stamps ([23bd0f7](https://github.com/tifuchs/orGUI/commit/23bd0f774cb58f5bdbb04621e3a0c4d49c725ddd))
+- Publish the first orGUI documentation set on Read the Docs ([cdc47d6](https://github.com/tifuchs/orGUI/commit/cdc47d6846ce32403c983f187f5a458b99931d2e), [b71d867](https://github.com/tifuchs/orGUI/commit/b71d86705acabd5a703314238ca2872017d0a9af), [799335c](https://github.com/tifuchs/orGUI/commit/799335c9e2f6a34b55245ecf9be3db79c7f55052), [3417b2b](https://github.com/tifuchs/orGUI/commit/3417b2b41618ba39117c0566edbdb0f21e2a40f4), [5efb16e](https://github.com/tifuchs/orGUI/commit/5efb16e112520c0178ad9911da45c66f47b09a94), [7107429](https://github.com/tifuchs/orGUI/commit/7107429a2c81cf45d7a43ef394bb910731c09070))
+- Add GitHub release workflow ([6582566](https://github.com/tifuchs/orGUI/commit/6582566ce3ea10e7dc9a5182c52d00340ea0e893))
 
 ### Changed
 
-- Log files ([28ffb92](https://github.com/tifuchs/orGUI/commit/28ffb928d88610f9c4a45eef7fa1fd604af6d74a))
-- Limit deltaS to a median of 1 pixel ROI center distance ([43afb8c](https://github.com/tifuchs/orGUI/commit/43afb8cfe05753d1584ae0d3b9521bc091ca743a))
-- Use new logging API in UBCalculator.readConfig ([c2ea4c3](https://github.com/tifuchs/orGUI/commit/c2ea4c3b0b51c9caa25f6016abe35cc56b9bd895))
-- Set number of CPUs in main.py ([b6aeda6](https://github.com/tifuchs/orGUI/commit/b6aeda64d7b1285d875c2081bc7594cd950c9afe))
-- Multiple manual static rocking scans cli function ([7f4f5de](https://github.com/tifuchs/orGUI/commit/7f4f5de3694aae247630302f21321706f28420df))
-- Expand AGENTS.md guidance for CTR stack, logging modes, and public API docs ([cf87b88](https://github.com/tifuchs/orGUI/commit/cf87b885028a4b2a0f5ee0bec0b011d3b6217ae7))
-- Safeguard CLI logging and refactor anchor ROI I/O ([c178fdc](https://github.com/tifuchs/orGUI/commit/c178fdcda1d5aa97bd72feffd48245da800fb09a))
-- Increase verbosity of backend load errors ([3df9a16](https://github.com/tifuchs/orGUI/commit/3df9a162e68a0a4bba2802c590dffd5d50eb5a08))
-- Use dispatched MessageBox logging to ensure blocking UI calls are made from main thread ([e9dc755](https://github.com/tifuchs/orGUI/commit/e9dc7558347c931cb07ca79a9005121775820f69))
-- ImagePeakFinder.calc_image_range is now besteffort, ensure message_box_dispatcher running in correct thread ([2002811](https://github.com/tifuchs/orGUI/commit/20028111fc99e30a439d984c064c006b662af2b7))
-- OrGUI startup docs, GUI screenshot and explanations ([799335c](https://github.com/tifuchs/orGUI/commit/799335c9e2f6a34b55245ecf9be3db79c7f55052))
-- Install full target on readthedocs for autodoc ([515f108](https://github.com/tifuchs/orGUI/commit/515f1080e5e91a3942070871b347034fc2bf79c9))
-- README: rephrase some paragraphs, add PyPi badge ([38293e5](https://github.com/tifuchs/orGUI/commit/38293e5b0c3696a88cd8d7ca88f15e188d4e2517))
-- QM2/id4b add z motor to scanned motor list ([be77c1a](https://github.com/tifuchs/orGUI/commit/be77c1aab81be792c498b6eae15b80eed7e74a4f))
-- QM2 add log file parsing for accurate time stamps ([23bd0f7](https://github.com/tifuchs/orGUI/commit/23bd0f774cb58f5bdbb04621e3a0c4d49c725ddd))
-- Backend and configuration pages ([3417b2b](https://github.com/tifuchs/orGUI/commit/3417b2b41618ba39117c0566edbdb0f21e2a40f4))
-- Default NUMEXPR_MAX_THREADS=1 to avoid oversubscription ([3598f0d](https://github.com/tifuchs/orGUI/commit/3598f0d149b3fa0519166d32233a088def0a3a26))
-- Specify conventional commits in AGENTS.md ([5f3d214](https://github.com/tifuchs/orGUI/commit/5f3d214ba131ffec360d42aff9cbad8e676ed38d))
+- Improve messages, progress output, and error reporting in both GUI and CLI runs ([c2ea4c3](https://github.com/tifuchs/orGUI/commit/c2ea4c3b0b51c9caa25f6016abe35cc56b9bd895), [c178fdc](https://github.com/tifuchs/orGUI/commit/c178fdcda1d5aa97bd72feffd48245da800fb09a), [3df9a16](https://github.com/tifuchs/orGUI/commit/3df9a162e68a0a4bba2802c590dffd5d50eb5a08), [e9dc755](https://github.com/tifuchs/orGUI/commit/e9dc7558347c931cb07ca79a9005121775820f69), [2002811](https://github.com/tifuchs/orGUI/commit/20028111fc99e30a439d984c064c006b662af2b7))
+- Set the number of CPUs during startup and default ``NUMEXPR_MAX_THREADS=1`` when not already configured ([b6aeda6](https://github.com/tifuchs/orGUI/commit/b6aeda64d7b1285d875c2081bc7594cd950c9afe), [3598f0d](https://github.com/tifuchs/orGUI/commit/3598f0d149b3fa0519166d32233a088def0a3a26))
+- Preserve variables created by input scripts for the GUI console ([a810dbf](https://github.com/tifuchs/orGUI/commit/a810dbfab33e4d98985de6abaf65d8180e1e5664))
+- Refactor invalid reference reflection image-number handling into warnings and add regression tests ([c574bdf](https://github.com/tifuchs/orGUI/commit/c574bdf0bd5af6fa8258d108e7355c579bfef857))
+- Expand project guidance for CTR stack, logging modes, public API docs, and conventional commits ([5df3d9d](https://github.com/tifuchs/orGUI/commit/5df3d9de9e817330dc2b412ff6056c375a89e7fd), [cf87b88](https://github.com/tifuchs/orGUI/commit/cf87b885028a4b2a0f5ee0bec0b011d3b6217ae7), [5f3d214](https://github.com/tifuchs/orGUI/commit/5f3d214ba131ffec360d42aff9cbad8e676ed38d))
 
 ### Fixed
 
 - Missing display of static ROI due to numpy 0-d array concatenation ([7654956](https://github.com/tifuchs/orGUI/commit/765495650fd09c4eca92afd4fed7630dc99209e1))
 - Restore shell init order, validate startup args, and harden integration errors ([7e9221f](https://github.com/tifuchs/orGUI/commit/7e9221fdfa8a2b2a9cde0cf9a51fc1052c0deb11))
 - Handle empty exceptions in logger, ROI I/O and UI symmetry ([991cba3](https://github.com/tifuchs/orGUI/commit/991cba39d8f37368176b951174b3d3b1016cc1c2))
 - Explicitly close database in cli mode ([5124656](https://github.com/tifuchs/orGUI/commit/5124656c09fb81188f70fc07c7bdcc80aa73a61d))
-- Apply mask to bg image and Carr ([2d22cfb](https://github.com/tifuchs/orGUI/commit/2d22cfb83635597b7beb3f11e6dae95b1c5827ef))
-- Resolve ipyconsole.pushVariables to the correct fun member ([a810dbf](https://github.com/tifuchs/orGUI/commit/a810dbfab33e4d98985de6abaf65d8180e1e5664))
+- Apply mask to bg image and Carr in rocking integration ([2d22cfb](https://github.com/tifuchs/orGUI/commit/2d22cfb83635597b7beb3f11e6dae95b1c5827ef))
 - Exclude masked pixels from rocking counters ([b5f752f](https://github.com/tifuchs/orGUI/commit/b5f752fb9986a68113193eba2f427cdb91a34d0f))
+- Resolve ipyconsole.pushVariables to the correct fun member ([a810dbf](https://github.com/tifuchs/orGUI/commit/a810dbfab33e4d98985de6abaf65d8180e1e5664))
+- Fix miscut calculation for NumPy > 2.0 ([e2538d1](https://github.com/tifuchs/orGUI/commit/e2538d13e7c6b938ec27a2016df64805935e912f))
+- Avoid crashes when Bragg reference reflections have image numbers outside the loaded scan ([9680bee](https://github.com/tifuchs/orGUI/commit/9680bee49af408c9ddd71d6d04834d46ae3502e1))
 
 ### Removed
 
-- Remove old doc from README, which is now on RTD ([147e53b](https://github.com/tifuchs/orGUI/commit/147e53b68ae31918034c29357486fce0412d2d2b))
+- Remove old doc from README, which is now on Read the Docs ([147e53b](https://github.com/tifuchs/orGUI/commit/147e53b68ae31918034c29357486fce0412d2d2b))
+
+
+## [1.5.0-rc.1] (2026-05-15)
+
+[532b60b](https://github.com/tifuchs/orGUI/commit/532b60bab3073ae9f0ff063a0e119aa9e9957857)...[7107429](https://github.com/tifuchs/orGUI/commit/7107429a2c81cf45d7a43ef394bb910731c09070)
+
+Release candidate for v1.5.0. The full user-facing release notes are included
+in the final [1.5.0](#150-2026-06-07) section above.
 
 
 ## [1.4.1] (2026-03-27)
@@ -683,7 +731,8 @@ in form of a README and a diffractometer image showing the geometry.
 - Remove old reflection spinbox edit, add toolbar buttons instead ([7854679](https://github.com/tifuchs/orGUI/commit/7854679ff96344e40fd9d88334672309f62be219))
 - Remove array index widget from ArrayTableWidget, as only 1D or 2D arrays are used ([25796e2](https://github.com/tifuchs/orGUI/commit/25796e21f103a2a6f9e4dd8544e941bd7886605d))
 
-[11.5.0-rc.1]: https://github.com/tifuchs/orGUI/compare/1.4.1..1.5.0-rc.1
+[1.5.0]: https://github.com/tifuchs/orGUI/compare/v1.4.1..v1.5.0
+[1.5.0-rc.1]: https://github.com/tifuchs/orGUI/compare/v1.4.1..v1.5.0-rc.1
 [1.4.1]: https://github.com/tifuchs/orGUI/compare/1.4.0..v1.4.1
 [1.4.0]: https://github.com/tifuchs/orGUI/compare/1.3.0..v1.4.0
 [1.3.0]: https://github.com/tifuchs/orGUI/compare/1.2.0..1.3.0

doc/source/release_notes.rst

@@ -4,14 +4,45 @@ Release Notes
 .. This file is generated by doc/generate_release_notes.py from
    CHANGELOG.md. Do not edit it by hand.
 
-1.5.0-rc.1 (2026-05-15)
------------------------
+1.5.0 (2026-06-07)
+------------------
+
+This is a feature release focused on scripted/headless operation, release infrastructure, documentation, and several GUI and integration robustness fixes.
+
+orGUI now has two startup modes. The default graphical user interface is still the normal interactive application for inspecting images, setting reference reflections, adjusting ROIs, and visually checking the experiment geometry. The new command line interface is selected with ``--cli``, ``--nogui``, or ``--headless`` and is intended for scripting, batch jobs, and cluster use. In CLI mode users can run a Python startup script with ``-i`` / ``--input`` and work with the preloaded ``app``, ``orgui``, and ``ub`` objects instead of clicking through the GUI.
+
+Scientific and analysis-impacting fixes:
+
+- Masked pixels are now excluded from rocking-scan counters and the same mask handling is applied to the static background image and correction arrays used in rocking integration. Results from workflows that combine rocking integration with masks, static background subtraction, or correction arrays should be checked against the new behavior.
+- Fixes for NumPy 2.x compatibility.
+- Reference reflection tables with image numbers outside the currently loaded scan no longer crash the GUI. Invalid image numbers are reported as warnings and the reflection table is updated more defensively.
+
+CLI and scripting highlights:
 
-Release candidate for v1.5.0
+- ``orGUI --cli`` / ``--nogui`` / ``--headless`` start the headless path, and ``-i`` / ``--input`` runs a Python startup script with ``app``, ``orgui``, and ``ub`` already available.
+- ``--keep-running`` keeps the application alive after a startup script and can drop into the embedded shell for interactive inspection.
+- ``--cpus``, ``--logfile``, ``--errorlog``, and HDF5 file-locking options make batch and cluster runs easier to control.
+- CLI runs now print progress and errors to the terminal or selected log files, so batch jobs can finish or fail without waiting for a hidden dialog.
+- Batch-oriented helpers were added for static and rocking ROI workflows, including support for multiple manually defined static rocking scans.
 
-Adds a new command line interface mode of orGUI, which enables better scripting in headless configurations.
+Documentation:
+
+- The orGUI documentation is now available on Read the Docs: <https://orgui.readthedocs.io/>.
+- End-user release notes are available in this changelog and on the Read the Docs release-notes page: <https://orgui.readthedocs.io/en/latest/release_notes.html>.
+
+Other user-visible changes:
+
+- Log files can be written for normal and error output.
+- Backend load errors are more verbose.
+- CHESS QM2/id4b backend examples now include the z motor in the scanned motor list, and QM2 log files can be parsed for more accurate timestamps.
+- ``NUMEXPR_MAX_THREADS`` defaults to 1 when not already set, avoiding oversubscription during parallel or cluster runs.
+
+Thanks to Finn Schröter (Finnjek) for the NumPy 2.x miscut fix and Bragg reflection image-number crash fix.
+
+1.5.0-rc.1 (2026-05-15)
+-----------------------
 
-The planned orGUI documentation is work in progress and a first version is now available on https://orgui.readthedocs.io/
+Release candidate for v1.5.0. The full user-facing release notes are included in the final `1.5.0 <#150-2026-06-07>`_ section above.
 
 1.4.1 (2026-03-27)
 ------------------