qplotter 1.6.0b3__tar.gz → 1.6.1__tar.gz

{qplotter-1.6.0b3 → qplotter-1.6.1}/CHANGELOG.md

@@ -2,16 +2,98 @@
 
 All notable user-facing changes are recorded here.
 
-Historical releases used GitHub source tags. The prepared split beta uses the
-PyPI distributions `qplotter` and `qplotter-native`; publication requires the
-release workflow and its validation gates. See `docs/distribution.md`.
+## 1.6.1
 
-## Unreleased
+This patch release improves live acquisition viewing and release validation.
+
+### Fixed
+
+- Restore Auto-plot in trusted live mode. Newly detected runs open automatically,
+  and enabling Auto-plot opens the newest incomplete run. Requests survive
+  selection changes and refreshes, retry while run metadata becomes available,
+  and cancel when Auto-plot is disabled, the database changes, or qPlot closes.
+- Reduce unnecessary WAL coordination overhead that could cause deferred QCoDeS
+  writes to fail with `SQLITE_BUSY` during live viewing. Existing database
+  protections remain enforced.
+- Display the main window title as `qPlot - <version>` without a duplicated
+  application-name suffix.
+- Correct editable-install validation for source checkouts without generated
+  build metadata.
+
+### Maintenance
+
+- Release the native-reader fix as `qplotter-native==1.0.1`, installed
+  automatically by the application's updated dependency pin.
+- Add a workflow to revalidate published releases against their original
+  artifacts, retaining each release's original native dependency pin.
+- Update live-reader, Auto-plot, and release-validation documentation and add
+  README badges.
+
+## 1.6.0
+
+### Highlights ###
+
+- More improvements in handling large databases and datasets.
+- Multiple heatmaps and traces can share the same plot window.
+- Program now installs as a PyPi distribution for the first time, instead of via GitHub source tags.
+- Numerous small improvements to the UI.
+- Numerous bugs found by Codex Astra have been fixed. In particular, Codex now claims to rigorously enforce the rule that the database will never be modified by `qplot`. After about 30 rounds of automated bug searches, the last two rounds uncovered no bugs.
+- To implement this database safety, the installation contains a small C extension 'qplotter-native' for reading live databases through SQLite.
+
+### Main changes since 1.5.0
+
+(Everything in this section is AI-generated)
+
+- Read supported local QCoDeS databases live without copying the whole
+  database. Main database, WAL, and rollback-journal handles remain physically
+  read-only; SQLite may update only the exact colocated SHM coordination file.
+  Reader work is bounded and cancellable.
+- Load run metadata, thumbnails, previews, and explicit plots progressively,
+  prioritising selected and visible runs. Show clearer plot-loading progress
+  and keep cancellation, database switching, and shutdown responsive.
+- Combine line traces and heatmaps in one plot, with axis-aware drag-and-drop,
+  shared appearance controls, and source annotations included in exports.
+- Add system printing, configurable heatmap display grid limits, optional saved
+  run-table columns, plot tiling, cursor precision, and version/build information
+  in Help -> About qPlot and the main window title.
+- Improve QCoDeS variable-shaped array support, missing-data handling, numerical
+  precision, native transforms, averaging, autoscaling, and live run refresh.
+  Reject drawing ranges that cannot faithfully represent recorded values.
+- Fix CSV alignment and precision, standalone-measurement exports, SVG output,
+  and PDF publication. Strengthen protection against auxiliary outputs
+  overwriting database files and against blocking special-file inputs.
+- Split the application into `qplotter` and the separately versioned
+  `qplotter-native==1.0.0`. Supported installations use prebuilt native wheels
+  without a compiler; imports and commands remain `qplot`. Release validation
+  covers CPython 3.11-3.14, Windows x64, macOS ARM64/Intel, and headless Linux
+  x86_64. Windows and macOS remain the supported desktop platforms.
+- Strengthen application/helper shutdown and settings recovery, and save
+  configuration changes transactionally.
+
+### Upgrading
+
+- Older or incompatible settings are reset to current defaults. Settings
+  migration is not supported.
+- The old `qplot` distribution and `qplotter` share imports and commands and
+  must not coexist. Prefer a fresh virtual environment, or follow the removal
+  and reinstall instructions in `docs/distribution.md`.
+- This entry is draft release text. Publication still requires the tagged
+  release workflow and all validation gates; this PR does not publish packages.
 
 ## 1.6.0b3 - Unreleased
 
 ### Added
 
+- Combine line traces and heatmaps in one plot, with axis-aware preview drops
+  and a shared Appearance dialog. Removing the original dataset promotes a
+  remaining source while retaining the plot's appearance and state.
+- Identify plotted databases, run IDs, and parameters in a shaded annotation
+  strip included in exports. A saved Show source annotation preference controls
+  visibility and is enabled by default.
+- Add saved plot-tiling and cursor-precision preferences, and limit the graph
+  font-size preference to graph text.
+- Add Help -> About qPlot with the running version, source commit and local
+  changes, plus commit and PR provenance in CI-built application packages.
 - Split pure-Python application distribution `qplotter` from native reader
   distribution `qplotter-native`, retaining the qPlot name, `qplot` imports and
   commands. Ordinary and editable application installation use prebuilt native
@@ -22,6 +104,9 @@ release workflow and its validation gates. See `docs/distribution.md`.
 
 ### Changed
 
+- Consolidate plot feedback and loading progress in the refresh toolbar, with
+  accurate initial point counts and stable cursor readouts.
+- Clarify refresh controls and incompatible-axis confirmations.
 - Load and refresh explicit plots through the trusted, physically read-only
   reader without copying the whole database. Small runs can open while a large
   run is loading, including with a single processing thread.
@@ -33,6 +118,13 @@ release workflow and its validation gates. See `docs/distribution.md`.
   exact source dimensions are not retained during downsampling. Right-align
   resolution information while keeping cursor coordinates left-aligned.
 
+### Fixed
+
+- Preserve coordinate ownership, drawing order, native transforms, and specific
+  FFT validation messages when combining or replacing plot sources.
+- Stabilize GUI test waits and release plot windows and background workers
+  during teardown.
+
 ## 1.6.0b1 - 2026-09-28
 
 ### Added

{qplotter-1.6.0b3 → qplotter-1.6.1}/CONTRIBUTING.md

@@ -52,7 +52,7 @@ Linux is exercised in headless CI; Windows and macOS are supported desktop
 platforms. See the [platform matrix](docs/distribution.md#supported-platforms).
 
 The root distribution `qplotter` is pure Python. Install the compatible
-`qplotter-native==1.0.0` platform wheel with the application in editable
+`qplotter-native==1.0.1` platform wheel with the application in editable
 mode. After the native release is on PyPI, no separate download is needed:
 
 ```console

{qplotter-1.6.0b3 → qplotter-1.6.1}/MANIFEST.in

@@ -27,6 +27,7 @@ prune src/qplotter.egg-info
 
 global-exclude .DS_Store
 global-exclude *.py[cod]
+global-exclude *.py[cod].*
 global-exclude *.dll
 global-exclude *.dylib
 global-exclude *.pyd

{qplotter-1.6.0b3 → qplotter-1.6.1}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: qplotter
-Version: 1.6.0b3
+Version: 1.6.1
 Summary: PyQt-based viewer for completed and running QCoDeS database experiments
 Author-email: Ben Wordsworth <b.wordsworth@lancaster.ac.uk>, Edward Laird <e.a.laird@lancaster.ac.uk>
 License-Expression: MIT
@@ -8,7 +8,7 @@ Project-URL: Homepage, https://github.com/lairdgrouplancaster/QCoDeS-Plotter.git
 Project-URL: Source, https://github.com/lairdgrouplancaster/QCoDeS-Plotter
 Project-URL: Issues, https://github.com/lairdgrouplancaster/QCoDeS-Plotter/issues
 Keywords: qcodes,pyqt,pyqtgraph,data-visualization,scientific-computing
-Classifier: Development Status :: 4 - Beta
+Classifier: Development Status :: 5 - Production/Stable
 Classifier: Environment :: MacOS X
 Classifier: Environment :: Win32 (MS Windows)
 Classifier: Intended Audience :: Science/Research
@@ -24,7 +24,7 @@ Classifier: Topic :: Scientific/Engineering :: Visualization
 Requires-Python: >=3.11
 Description-Content-Type: text/markdown
 License-File: LICENSE
-Requires-Dist: qplotter-native==1.0.0
+Requires-Dist: qplotter-native==1.0.1
 Requires-Dist: apsw==3.53.4.0
 Requires-Dist: jsonschema>=4.23.0
 Requires-Dist: numpy>=2.3.1
@@ -46,6 +46,11 @@ Dynamic: license-file
 # QCoDeS-Plotter
 
 [![release](https://img.shields.io/github/v/release/lairdgrouplancaster/QCoDeS-Plotter?label=release)](https://github.com/lairdgrouplancaster/QCoDeS-Plotter/releases/latest)
+[![CI](https://github.com/lairdgrouplancaster/QCoDeS-Plotter/actions/workflows/ci.yml/badge.svg?branch=main&event=push)](https://github.com/lairdgrouplancaster/QCoDeS-Plotter/actions/workflows/ci.yml)
+[![License](https://img.shields.io/github/license/lairdgrouplancaster/QCoDeS-Plotter)](LICENSE)
+[![Python](https://img.shields.io/badge/Python-3.11–3.14-blue?logo=python)](#requirements)
+[![PyPI](https://img.shields.io/pypi/v/qplotter)](https://pypi.org/project/qplotter/)
+
 [![pre-release](https://img.shields.io/github/v/release/lairdgrouplancaster/QCoDeS-Plotter?include_prereleases&label=pre-release&sort=semver)](https://github.com/lairdgrouplancaster/QCoDeS-Plotter/releases)
 
 QCoDeS-Plotter, or qPlot, is a PyQt-based data viewer for QCoDeS databases. It
@@ -116,16 +121,20 @@ fields and an unavailable detail state without starting a selected-detail
 reader or preparing an additional selected-detail snapshot. That claim applies
 only to row selection: fallback metadata and retained preview paths can still
 create private snapshots. Plot and CSV actions also acquire action-owned
-snapshots. Automatic trusted live
-previews and thumbnails are disabled until the Stage 5 scheduler and disk cache
-are implemented. See
+snapshots. Trusted live previews and thumbnails load progressively through a bounded
+scheduler and application cache. See
 [Trusted live QCoDeS reader](docs/trusted-live-reader.md).
 
 ## Packages
 
 The application distribution is `qplotter`; its Python imports and
 console commands remain `qplot`, `qplot-cfg`, and `qplot-generate-db`.
-The separately built `qplotter-native==1.0.0` supplies the protected
+Use **Help → About qPlot** to see the version in use on every platform.
+Source checkouts also show the commit and
+whether there are local changes. CI-built packages retain their build commit
+and, for pull-request builds, the PR number. Packages installed without build
+provenance still show the release number.
+The separately built `qplotter-native==1.0.1` supplies the protected
 SQLite reader through `qplot_native`. The application's exact dependency pin
 installs the compatible native wheel automatically. Both packages pin the same
 APSW/SQLite runtime, preserving trusted live reading and database protections.
@@ -143,8 +152,8 @@ source builds, and release validation.
 ## Install
 
 Install qPlot inside a supported Python virtual environment. This checkout
-prepares the first split PyPI release, application `1.6.0b3` with native `1.0.0`;
-the commands targeting these packages work after publication. Until then, use
+prepares the stable application release `1.6.1`, with native `1.0.1`.
+The installation examples below work after publication; until then, use
 validated local artifacts as described in [Distribution](docs/distribution.md).
 
 ### Prelude
@@ -174,9 +183,9 @@ For ordinary installation after a stable PyPI release is available:
 python -m pip install --only-binary=:all: qplotter
 ```
 
-For the first split beta, explicitly select the prerelease:
+To select version 1.6.1 explicitly after publication:
 ```console
-python -m pip install --only-binary=:all: qplotter==1.6.0b3
+python -m pip install --only-binary=:all: qplotter==1.6.1
 ```
 
 Both commands install the full runtime dependency set as wheels, with no C
@@ -198,7 +207,7 @@ installing the new packages:
 
 ```console
 python -m pip uninstall -y qplot qcodes-plotter qcodes-plotter-native qplotter qplotter-native
-python -m pip install --only-binary=:all: qplotter==1.6.0b3
+python -m pip install --only-binary=:all: qplotter==1.6.1
 python -m pip check
 ```
 

{qplotter-1.6.0b3 → qplotter-1.6.1}/README.md

@@ -1,6 +1,11 @@
 # QCoDeS-Plotter
 
 [![release](https://img.shields.io/github/v/release/lairdgrouplancaster/QCoDeS-Plotter?label=release)](https://github.com/lairdgrouplancaster/QCoDeS-Plotter/releases/latest)
+[![CI](https://github.com/lairdgrouplancaster/QCoDeS-Plotter/actions/workflows/ci.yml/badge.svg?branch=main&event=push)](https://github.com/lairdgrouplancaster/QCoDeS-Plotter/actions/workflows/ci.yml)
+[![License](https://img.shields.io/github/license/lairdgrouplancaster/QCoDeS-Plotter)](LICENSE)
+[![Python](https://img.shields.io/badge/Python-3.11–3.14-blue?logo=python)](#requirements)
+[![PyPI](https://img.shields.io/pypi/v/qplotter)](https://pypi.org/project/qplotter/)
+
 [![pre-release](https://img.shields.io/github/v/release/lairdgrouplancaster/QCoDeS-Plotter?include_prereleases&label=pre-release&sort=semver)](https://github.com/lairdgrouplancaster/QCoDeS-Plotter/releases)
 
 QCoDeS-Plotter, or qPlot, is a PyQt-based data viewer for QCoDeS databases. It
@@ -71,16 +76,20 @@ fields and an unavailable detail state without starting a selected-detail
 reader or preparing an additional selected-detail snapshot. That claim applies
 only to row selection: fallback metadata and retained preview paths can still
 create private snapshots. Plot and CSV actions also acquire action-owned
-snapshots. Automatic trusted live
-previews and thumbnails are disabled until the Stage 5 scheduler and disk cache
-are implemented. See
+snapshots. Trusted live previews and thumbnails load progressively through a bounded
+scheduler and application cache. See
 [Trusted live QCoDeS reader](docs/trusted-live-reader.md).
 
 ## Packages
 
 The application distribution is `qplotter`; its Python imports and
 console commands remain `qplot`, `qplot-cfg`, and `qplot-generate-db`.
-The separately built `qplotter-native==1.0.0` supplies the protected
+Use **Help → About qPlot** to see the version in use on every platform.
+Source checkouts also show the commit and
+whether there are local changes. CI-built packages retain their build commit
+and, for pull-request builds, the PR number. Packages installed without build
+provenance still show the release number.
+The separately built `qplotter-native==1.0.1` supplies the protected
 SQLite reader through `qplot_native`. The application's exact dependency pin
 installs the compatible native wheel automatically. Both packages pin the same
 APSW/SQLite runtime, preserving trusted live reading and database protections.
@@ -98,8 +107,8 @@ source builds, and release validation.
 ## Install
 
 Install qPlot inside a supported Python virtual environment. This checkout
-prepares the first split PyPI release, application `1.6.0b3` with native `1.0.0`;
-the commands targeting these packages work after publication. Until then, use
+prepares the stable application release `1.6.1`, with native `1.0.1`.
+The installation examples below work after publication; until then, use
 validated local artifacts as described in [Distribution](docs/distribution.md).
 
 ### Prelude
@@ -129,9 +138,9 @@ For ordinary installation after a stable PyPI release is available:
 python -m pip install --only-binary=:all: qplotter
 ```
 
-For the first split beta, explicitly select the prerelease:
+To select version 1.6.1 explicitly after publication:
 ```console
-python -m pip install --only-binary=:all: qplotter==1.6.0b3
+python -m pip install --only-binary=:all: qplotter==1.6.1
 ```
 
 Both commands install the full runtime dependency set as wheels, with no C
@@ -153,7 +162,7 @@ installing the new packages:
 
 ```console
 python -m pip uninstall -y qplot qcodes-plotter qcodes-plotter-native qplotter qplotter-native
-python -m pip install --only-binary=:all: qplotter==1.6.0b3
+python -m pip install --only-binary=:all: qplotter==1.6.1
 python -m pip check
 ```
 

{qplotter-1.6.0b3 → qplotter-1.6.1}/docs/architecture.md

@@ -245,8 +245,16 @@ unavailable detail state: ordinary selection starts no selected-detail worker
 and prepares no additional selected-detail snapshot. A trusted detail failure
 also does not trigger an automatic fallback copy. This is a property of the
 selection action, not the whole fallback session: fallback metadata and retained
-preview paths can still create private snapshots. Only explicit plot and CSV
-actions materialise a DataSet.
+preview paths can still create private snapshots. Fallback plot actions
+(including Auto-plot) and CSV actions can materialise a DataSet.
+
+Trusted Auto-plot owns a deduplicated queue independently of selected-detail
+and refresh requests. It submits one bounded plot-metadata request at a time,
+then uses the same asynchronous plot pipeline as manual plotting. Unavailable
+descriptions are operation-local failures that leave the reader session usable.
+Retries use bounded backoff; later run-metadata changes wake exhausted requests.
+Disabling Auto-plot, committing a database switch, closing the database, and
+shutdown cancel the queue. Source identity checks still guard publication.
 
 Stage 5A's `trusted_work_scheduler.py` owns the exact derived priority key
 `(run tier, work kind, stable run index)` without materialising one task per

{qplotter-1.6.0b3 → qplotter-1.6.1}/docs/distribution.md

@@ -29,11 +29,15 @@ virtual environment with:
 python -m pip install --only-binary=:all: qplotter
 ```
 
-The first prepared application release is the beta `1.6.0b3`, with exact native
-dependency `1.0.0`. Once published, install that prerelease explicitly:
+The current development target is the stable application release `1.6.1`,
+with exact native dependency `1.0.1`. Existing candidate tags do not establish
+that publication succeeded. Preparing a PR does not publish either package.
+
+The prepared stable application release is `1.6.1`, with exact native
+dependency `1.0.1`. Once published, install that release explicitly:
 
 ```console
-python -m pip install --only-binary=:all: qplotter==1.6.0b3
+python -m pip install --only-binary=:all: qplotter==1.6.1
 ```
 
 The earlier `native-and-app/v1.6.0b2` candidate did not pass its complete hosted
@@ -55,7 +59,7 @@ wheel paths from this revision's validated artifacts together. For example,
 on Windows x64 (replace the application version when appropriate):
 
 ```console
-python -m pip install --only-binary=:all: dist/qplotter_native-1.0.0-cp311-abi3-win_amd64.whl dist/qplotter-1.6.0b3-py3-none-any.whl
+python -m pip install --only-binary=:all: dist/qplotter_native-1.0.1-cp311-abi3-win_amd64.whl dist/qplotter-1.6.1-py3-none-any.whl
 ```
 
 Use your platform's native filename on macOS/Linux. Never mix artifacts from
@@ -87,7 +91,7 @@ application names before installing the replacement:
 
 ```console
 python -m pip uninstall -y qplot qcodes-plotter qcodes-plotter-native qplotter qplotter-native
-python -m pip install --only-binary=:all: qplotter==1.6.0b3
+python -m pip install --only-binary=:all: qplotter==1.6.1
 python -m pip check
 python -c "from importlib.metadata import packages_distributions; p = packages_distributions(); assert set(p['qplot']) == {'qplotter'}; assert set(p['qplot_native']) == {'qplotter-native'}"
 ```
@@ -217,7 +221,7 @@ wheels must build the extension from source.
 
 The native wheel contains the `cp311-abi3` extension
 `qplot_native._trusted_vfs_native` and is platform-specific. The application
-wheel is `py3-none-any`. The application requires exactly native version 1.0.0;
+wheel is `py3-none-any`. The application requires exactly native version 1.0.1;
 both distributions pin APSW 3.53.4.0. Keep these dependencies, the validator's
 pins, and the Python/native SQLite 3.53.4 and source-ID checks coordinated.
 The reader also rejects an incompatible native distribution version, SQLite
@@ -395,8 +399,8 @@ application version from `pyproject.toml`:
 
 | Tag | Native handling | PyPI uploads |
 | --- | --- | --- |
-| `native-and-app/v1.6.0b3` | Build/validate native `1.0.0` at this revision | Native wheels first, then application wheel/sdist |
-| `v1.6.0b4` (example later version) | Fetch/validate the application's exact published native pin | Application wheel/sdist only |
+| `native-and-app/v1.6.1` | Build/validate native `1.0.1` at this revision, if unpublished | Native wheels first, then application wheel/sdist |
+| `v1.6.1` | Fetch/validate the application's exact published native pin | Application wheel/sdist only |
 
 The workflow calls the entire CI workflow at the tagged revision. Failure of
 any build, static check, source-distribution suite, database-protection suite,
@@ -428,9 +432,9 @@ After application publication and byte verification, `public-installations`
 runs on all four platforms and every advertised CPython version (3.11–3.14).
 Each entry creates two fresh environments outside the original checkout.
 The ordinary path runs `python -m pip install --only-binary=:all:
-qplotter==1.6.0b3` against the public PyPI index with all runtime dependencies.
+qplotter==1.6.1` against the public PyPI index with all runtime dependencies.
 The editable path fetches the exact tested commit into a fresh checkout and
-installs `.[dev]` with `qplotter-native==1.0.0` resolved from public PyPI.
+installs `.[dev]` with `qplotter-native==1.0.1` resolved from public PyPI.
 Neither path installs a local release wheel; the validated artifacts are only
 comparison receipts for the pip report and installed-file hashes. All runtime
 and development dependencies must resolve to public wheels. Both paths disable
@@ -440,7 +444,10 @@ protections. Editable acceptance additionally observes a Python edit without
 reinstalling and checks that the native binary's bytes, identity and timestamp
 remain unchanged. Windows uses the standard-user wrapper for both paths.
 Publication is irreversible; failures in these post-publication checks must
-be reported and fixed in a new release, rather than described as acceptance.
+be reported. Changes to published package contents require a new release.
+A defect confined to the validation tools can instead be corrected and the
+existing release rechecked as described below; the failed original run remains
+part of the release record.
 
 ### One-time account configuration
 
@@ -484,10 +491,13 @@ and [pending-publisher instructions](https://docs.pypi.org/trusted-publishers/cr
    release version before tagging; never move a published tag. If migrating
    from token publishing, revoke/remove the old upload tokens/secrets.
 
-### First release commands
+### Paired release commands
+
+Version 1.6.1 includes native-reader changes, so release native 1.0.1 with
+the paired tag below. Keep the already published native 1.0.0 unchanged.
 
 Complete the account setup and merge the reviewed packaging/release changes
-to `main`. With application `1.6.0b3` and native `1.0.0`, use the configured
+to `main`. With application `1.6.1` and native `1.0.1`, use the configured
 Git remote/credentials:
 
 ```console
@@ -495,8 +505,8 @@ git fetch origin
 git switch main
 git pull --ff-only origin main
 python scripts/validate_distribution.py --check-clean
-git tag -a native-and-app/v1.6.0b3 -m "qPlot 1.6.0b3 with native reader 1.0.0"
-git push origin refs/tags/native-and-app/v1.6.0b3
+git tag -a native-and-app/v1.6.1 -m "qPlot 1.6.1 with native reader 1.0.1"
+git push origin refs/tags/native-and-app/v1.6.1
 ```
 
 Use the activated project venv for Python; on macOS set
@@ -537,6 +547,35 @@ the application remains blocked. Once the complete native release is verified,
 an application-only tag for the still-unpublished application version can also
 recover a failed paired release after a new validation run.
 
+### Recheck an existing published release
+
+If post-publication acceptance fails because of a validation-tool defect,
+fix and review the tools, then merge them to `main`. Do not move the release
+tag or rerun a successful publication job. In GitHub Actions, select
+**Revalidate published qPlot release**, then **Run workflow**, using branch
+`main`. Supply the original release tag and publication workflow run ID.
+For the 1.6.0 resource-inventory correction these are `v1.6.0` and
+`38429734516`.
+
+This manual workflow uses the corrected tools from `main`, but checks out
+the original release source separately. It checks the native package version
+pinned by that original source while retaining the tools' supported APSW/SQLite
+ABI checks. It downloads the `qplot-release` artifact from the original
+publication run, verifies its tag, commit, run ID,
+and hashes, and checks the published PyPI bytes against those receipts. The
+artifact must still be available; a missing/expired receipt is a failed gate,
+not permission to substitute a new build. The receipts are comparison inputs;
+ordinary and editable dependencies are still installed from public PyPI.
+All four platforms and CPython 3.11-3.14 run both installation paths, including
+GUI startup and the trusted live reader/database-protection smokes. Windows
+runs unprivileged. The workflow has only read permissions and no publishing
+jobs or deployment approvals.
+
+Wait for all 16 matrix jobs to pass before reporting corrected acceptance.
+Link both the original publication run and the new validation run in the
+release notes. If any failure requires an application or native package change,
+use a new package version and the normal release workflow.
+
 ### Local and hosted results
 
 Local tests and actionlint validate release configuration and failure gates.

{qplotter-1.6.0b3 → qplotter-1.6.1}/docs/trusted-live-reader.md

@@ -265,8 +265,19 @@ proof handles, actual SQLite handles, source pathnames, rollback-journal absence
 and active SHM bindings. Only after that succeeds may page reads reuse pathname
 proofs until operation cleanup. Every page read still validates the retained and
 actual handle identities and their physically read-only permissions, before and
-after delegation. Other callbacks, including SHM mapping/locking, retain their
-full existing checks. Newly opened or promoted WAL handles are fully validated.
+after delegation. SHM mapping and newly opened or promoted WAL handles retain
+their full checks. SHM locks and memory barriers use the binding already proved
+by mapping and operation-boundary validation, without filesystem calls inside
+SQLite's WAL critical sections. Unlocks are forwarded even after a latched
+validation error, allowing SQLite to release its coordination locks on cleanup.
+
+SQLite reads the two WAL-index header copies around `xShmBarrier`. Filesystem
+checks in that callback widen the race with a commit and can force even a
+read-only connection to acquire `WAL_WRITE_LOCK` to retry the header. Checks
+after acquisition or before release then prolong that lock, causing a QCoDeS
+deferred read-to-write upgrade to fail with `SQLITE_BUSY`. The native callbacks
+retain the platform memory fence and real SHM locking, including legitimate
+WAL-index recovery; they neither suppress locks nor bypass them.
 
 Cleanup disables pathname reuse and performs full native validation before any
 materialised result is published, including error, deadline and cancellation
@@ -279,6 +290,11 @@ transaction. Reads outside the explicit finite scope retain per-read path checks
 Native audit counters include `read_path_reused`, `read_validation_ns` and
 `read_io_ns`. The timings separate page-read validation from the delegated OS VFS
 read, not total SQL or IPC time, and never govern safety checks or deadlines.
+`shm_write_lock_attempts`, `shm_write_lock_acquired`, `shm_write_lock_ns` and
+`shm_write_lock_max_ns` expose transient WAL write-lock contention. The durations
+run from successful acquisition return through successful release return; these
+diagnostics do not control locking. A read-only connection can legitimately
+acquire this lock to coordinate the writable WAL index.
 `scripts/profile_trusted_reads.py DATABASE RUN_ID` profiles finite 65,536-row
 intervals through the pinned reader and checks protected-file sizes/timestamps.
 It does not clear OS caches or modify the selected database. Use the actual plot

{qplotter-1.6.0b3 → qplotter-1.6.1}/docs/user-guide.md

@@ -315,6 +315,8 @@ Common actions:
 * `Options -> Preferences...` edits common theme, plot mouse mode, default
   load location, preview, refresh, confirmation, and runtime settings. On
   macOS this appears as `qPlot -> Preferences...`.
+  In Appearance, `Cursor significant figures` controls the x, y, and z
+  coordinate readouts, including snapped trace values (1–17; default 6).
   Use `Restore Defaults` in that dialog to reset the shown preferences without
   leaving the dialog.
 * `Options -> Reset All Settings...` resets all qPlot settings to their
@@ -327,9 +329,14 @@ Common actions:
   on macOS and `Ctrl+Q` on Windows and Linux.
 * The refresh interval controls how often qPlot checks for new runs. Set it to
   `0.0 s` to disable automatic checks.
-* `Auto-plot` retains its existing behavior for snapshot fallback sessions.
-  Trusted live Stage 4 does not materialise an action-owned plot dataset
-  automatically; use an explicit plot action instead.
+* `Auto-plot` opens every newly detected run, including runs already complete,
+  in both trusted live and snapshot fallback sessions. Enabling it also opens
+  the newest incomplete run already listed. Trusted live requests use the
+  asynchronous reader and survive selection changes and subsequent refreshes.
+  An empty plot waits for its first data. Missing descriptions are retried with
+  backoff (eight attempts); after that, a run metadata change wakes the request,
+  or you can open it manually. Disabling Auto-plot, changing databases, or
+  quitting cancels pending automatic requests.
 
 Where a legacy preview is available, its double-click and context-menu actions
 can still request a plot or export. Trusted live sessions do not generate those
@@ -364,15 +371,34 @@ snapshot and materialises the QCoDeS dataset. Merely loading, selecting, or
 scrolling a trusted live database does not do this work or copy the database.
 
 Plot windows may appear before their data has finished loading. Check the plot
-window status bar; unless qPlot stops responding or shows an error, wait for the
+window refresh toolbar; unless qPlot stops responding or shows an error, wait for the
 load to complete.
 
 ## Plot Windows
 
-Each plot window has plot controls, a status bar, optional toolbars, and dock
-panels. Toolbars and dock panels can be shown or hidden from `View -> Toolbars`,
+Each plot window has plot controls, optional toolbars, and dock
+panels. Toolbars and dock panels can be shown or hidden from `View -> Panels and toolbars`,
 by right-clicking a toolbar or panel, or with keyboard shortcuts.
 
+Above the plot, qPlot identifies the displayed sources, for example
+`Databasename: 9 (Signal); 10-12 (Current); 6-8, 11, 12 (Voltage)`.
+Run IDs are grouped by parameter label, with ranges for three or more
+consecutive IDs. Each database has its own line. Hidden or fully transparent
+traces and heatmaps are omitted. This annotation is included in plot images,
+SVGs, PDFs, and printing.
+The annotation uses a shaded strip with a bold database name. In
+`Preferences -> Appearance`, `Show source annotation` controls its visibility
+in all plots and exports. It is enabled by default. Hiding it also removes
+the space reserved for the strip.
+
+The `Refresh and status` toolbar is visible by default, including for completed
+runs. Its right-hand side shows the latest status message until another
+message or loading progress replaces it. During loading it shows a progress
+bar for the current stage, elapsed time, and the stage number. Hover over
+progress for the stage name and detailed counts, or over a shortened status
+message to read it in full. Empty-data and error explanations also appear in
+the plot area.
+
 Common plot controls:
 
 * Mouse wheel over the plot: zoom.
@@ -387,8 +413,9 @@ Common plot controls:
   linear and base-10 logarithmic scaling. Non-positive values are omitted.
 * Right-drag on the plot, or scroll over an axis, to fast scale an axis.
 * The bottom toolbar shows cursor coordinates and array indices.
-* The left panel controls assigned axes and plot-specific options.
-* The right `Operations` panel applies data operations during refresh, after
+* Use `Swap X/Y` in the Appearance dialog to exchange the plotted axes.
+* Cut windows have a `Cut controls` panel for the cut direction and position.
+* The right `Data operations` panel applies data operations during refresh, after
   data is loaded from the database.
 
 ### Line Plots
@@ -455,7 +482,7 @@ Color-scale controls:
 
 ### Data Operations
 
-Plot windows can apply operations during refresh from the `Operations` panel.
+Plot windows can apply operations during refresh from the `Data operations` panel.
 The available operations depend on the plot type.
 
 Common operations:
@@ -565,10 +592,10 @@ Plot-window shortcuts:
 | `Ctrl+C` / `Cmd+C` | Copy the plot image to the clipboard using the selected copy format/resolution |
 | `Ctrl+E` | Export the plot |
 | `Ctrl+P` / `Cmd+P` | Print the visible plot area |
-| `Ctrl+Alt+R` | Show or hide the refresh toolbar |
-| `Ctrl+Alt+C` | Show or hide the coordinate toolbar |
-| `Ctrl+Alt+A` | Show or hide the axis control panel |
-| `Ctrl+Alt+O` | Show or hide the operations dock |
+| `Ctrl+Alt+R` | Show or hide the refresh and status toolbar |
+| `Ctrl+Alt+C` | Show or hide the coordinates toolbar |
+| `Ctrl+Alt+A` | Show or hide Cut controls in a cut window |
+| `Ctrl+Alt+O` | Show or hide the data operations panel |
 | `S` | Snap the 1D coordinate readout to the nearest trace point |
 
 Heatmap shortcuts:

{qplotter-1.6.0b3 → qplotter-1.6.1}/pyproject.toml

@@ -4,7 +4,7 @@ build-backend = "setuptools.build_meta"
 
 [project]
 name = "qplotter"
-version = "1.6.0b3"
+version = "1.6.1"
 description = "PyQt-based viewer for completed and running QCoDeS database experiments"
 readme = "README.md"
 authors = [{name="Ben Wordsworth", email="b.wordsworth@lancaster.ac.uk"},{name="Edward Laird", email="e.a.laird@lancaster.ac.uk"}]
@@ -12,7 +12,7 @@ license = "MIT"
 requires-python = ">=3.11"
 keywords = ["qcodes", "pyqt", "pyqtgraph", "data-visualization", "scientific-computing"]
 classifiers = [
-    "Development Status :: 4 - Beta",
+    "Development Status :: 5 - Production/Stable",
     "Environment :: MacOS X",
     "Environment :: Win32 (MS Windows)",
     "Intended Audience :: Science/Research",
@@ -27,7 +27,7 @@ classifiers = [
     "Topic :: Scientific/Engineering :: Visualization",
 ]
 dependencies = [
-    "qplotter-native==1.0.0",
+    "qplotter-native==1.0.1",
     "apsw==3.53.4.0",
     "jsonschema>=4.23.0",
     "numpy>=2.3.1",
@@ -148,6 +148,10 @@ files = [
     "src/qplot/windows/_dataset_handle.py",
     "src/qplot/windows/_dragdrop.py",
     "src/qplot/windows/_help.py",
+    "src/qplot/windows/_mixed_plots.py",
+    "src/qplot/windows/_mixed_appearance.py",
+    "src/qplot/windows/_plot_source_promotion.py",
+    "src/qplot/windows/_plot_data_viewbox.py",
     "src/qplot/windows/_native_averaging.py",
     "src/qplot/windows/_native_transforms.py",
     "src/qplot/windows/_plot1d_snap.py",
@@ -157,6 +161,7 @@ files = [
     "src/qplot/windows/_plot2d_layers.py",
     "src/qplot/windows/_plot2d_sweeps.py",
     "src/qplot/windows/_plot_axis_scaling.py",
+    "src/qplot/windows/_plot_drop_axes.py",
     "src/qplot/windows/_plot_export.py",
     "src/qplot/windows/_plot_feedback.py",
     "src/qplot/windows/_plot_marquee.py",