release: release Pylake v1.6.0

changelog.md

@@ -1,39 +1,39 @@
 # Changelog
 
-## v1.6.0 | t.b.d.
+## v1.6.0 | 2025-01-09
 
 #### New features
 
-* Added model to correct for bead-bead coupling when using active calibration deep in bulk with two beads. See [`tutorial`](https://lumicks-pylake.readthedocs.io/en/latest/tutorial/force_calibration.html#active-calibration-with-two-beads-far-away-from-the-surface) and [`theory`](https://lumicks-pylake.readthedocs.io/en/latest/theory/force_calibration/active.html#bead-bead-coupling) for more information.
-* Added option to highlight a region on a time plot using [`Slice.highlight_time_range()`](https://lumicks-pylake.readthedocs.io/en/latest/_api/lumicks.pylake.channel.Slice.html#lumicks.pylake.channel.Slice.highlight_time_range). For more information see the [`tutorial`](https://lumicks-pylake.readthedocs.io/en/latest/tutorial/file.html#highlight-time-range).
-* Added `__array__` to [`Slice`](https://lumicks-pylake.readthedocs.io/en/latest/_api/lumicks.pylake.channel.Slice.html). This allows passing slices directly to `numpy` functions such as `np.mean()`or `np.sum()`.
-* Added parameter `allow_overwrite` to [`lk.download_from_doi()`](https://lumicks-pylake.readthedocs.io/en/latest/_api/lumicks.pylake.download_from_doi.html#lumicks.pylake.download_from_doi) to allow re-downloading only those files where the checksum does not match.
+* Calibration results and parameters are now accessible via properties which are listed when items are printed. See [calibration results](https://lumicks-pylake.readthedocs.io/en/v1.6.0/_api/lumicks.pylake.force_calibration.power_spectrum_calibration.CalibrationResults.html) and [calibration item](https://lumicks-pylake.readthedocs.io/en/v1.6.0/_api/lumicks.pylake.calibration.ForceCalibrationItem.html) API documentation for more information.
+* Added property `diode_calibration` to access the diode calibration model, and `trap_power` to access the used trap power in [calibration item](https://lumicks-pylake.readthedocs.io/en/v1.6.0/_api/lumicks.pylake.calibration.ForceCalibrationItem.html). See the new [tutorial](https://lumicks-pylake.readthedocs.io/en/v1.6.0/tutorial/force_calibration/diode_model.html) and [theory](https://lumicks-pylake.readthedocs.io/en/v1.6.0/theory/force_calibration/diode.html) for more information.
+* Added model to correct for bead-bead coupling when using active calibration deep in bulk with two beads. See [tutorial](https://lumicks-pylake.readthedocs.io/en/v1.6.0/tutorial/force_calibration/index.html), [theory](https://lumicks-pylake.readthedocs.io/en/v1.6.0/theory/force_calibration/active.html#bead-bead-coupling) and [example](https://lumicks-pylake.readthedocs.io/en/v1.6.0/examples/bead_coupling/coupling.html) for more information.
+* Added option to highlight a region on a time plot using [`Slice.highlight_time_range()`](https://lumicks-pylake.readthedocs.io/en/v1.6.0/_api/lumicks.pylake.channel.Slice.html#lumicks.pylake.channel.Slice.highlight_time_range). For more information see the [tutorial](https://lumicks-pylake.readthedocs.io/en/v1.6.0/tutorial/file.html#highlighting).
+* Added `__array__` to [`Slice`](https://lumicks-pylake.readthedocs.io/en/v1.6.0/_api/lumicks.pylake.channel.Slice.html). This allows passing slices directly to `numpy` functions such as `np.mean()`or `np.sum()`.
+* Added parameter `allow_overwrite` to [`lk.download_from_doi()`](https://lumicks-pylake.readthedocs.io/en/v1.6.0/_api/lumicks.pylake.download_from_doi.html#lumicks.pylake.download_from_doi) to allow re-downloading only those files where the checksum does not match.
 * Added force calibration information to channels accessed directly via the square bracket notation (e.g. `file["Force HF"]["Force 1x"].calibration`).
-* Calibration results and parameters are now accessible via properties which are listed when items are printed. See [calibration results](https://lumicks-pylake.readthedocs.io/en/latest/_api/lumicks.pylake.force_calibration.power_spectrum_calibration.CalibrationResults.html) and [calibration item](https://lumicks-pylake.readthedocs.io/en/latest/_api/lumicks.pylake.calibration.ForceCalibrationItem.html) API documentation for more information.
-* Added `applied_at` property to a [calibration item](https://lumicks-pylake.readthedocs.io/en/latest/_api/lumicks.pylake.calibration.ForceCalibrationItem.html) obtained from a force slice. This property returns the timestamp in nanoseconds at which the force calibration was applied.
-* Added property `diode_calibration` to access diode calibration model, and `trap_power` to access the used trap power in [calibration item](https://lumicks-pylake.readthedocs.io/en/latest/_api/lumicks.pylake.calibration.ForceCalibrationItem.html).
-* Added parameter `titles` to customize title of each subplot in [`Kymo.plot_with_channels()`](https://lumicks-pylake.readthedocs.io/en/latest/_api/lumicks.pylake.kymo.Kymo.html#lumicks.pylake.kymo.Kymo.plot_with_channels).
-* Added [`KymoTrack.sample_from_channel()`](https://lumicks-pylake.readthedocs.io/en/latest/_api/lumicks.pylake.kymotracker.kymotrack.KymoTrack.html#lumicks.pylake.kymotracker.kymotrack.KymoTrack.sample_from_channel) to downsample channel data to the time points of a kymotrack.
-* Added support for file names with spaces in [`lk.download_from_doi()`](https://lumicks-pylake.readthedocs.io/en/latest/_api/lumicks.pylake.download_from_doi.html#lumicks.pylake.download_from_doi).
-* Show the ranges that were excluded from a power spectrum or calibration fit by passing `show_excluded=True` to [`PowerSpectrum.plot()`](https://lumicks-pylake.readthedocs.io/en/latest/_api/lumicks.pylake.force_calibration.power_spectrum.PowerSpectrum.html#lumicks.pylake.force_calibration.power_spectrum.PowerSpectrum.plot) or [`CalibrationResults.plot()`](https://lumicks-pylake.readthedocs.io/en/latest/_api/lumicks.pylake.force_calibration.power_spectrum_calibration.CalibrationResults.html#lumicks.pylake.force_calibration.power_spectrum_calibration.CalibrationResults.plot).
-* Plot the active calibration peak for a calibration result using `show_active_peak=True` with [`CalibrationResults.plot()`](https://lumicks-pylake.readthedocs.io/en/latest/_api/lumicks.pylake.force_calibration.power_spectrum_calibration.CalibrationResults.html#lumicks.pylake.force_calibration.power_spectrum_calibration.CalibrationResults.plot).
-* Added function to import a [`KymoTrackGroup`](https://lumicks-pylake.readthedocs.io/en/latest/_api/lumicks.pylake.kymotracker.kymotrack.KymoTrackGroup.html) from a `CSV` file using [`load_tracks`](https://lumicks-pylake.readthedocs.io/en/latest/_api/lumicks.pylake.load_tracks.html).
-* Added function to load tracks into the kymotracker widget using [`KymoWidgetGreedy.load_tracks()`](https://lumicks-pylake.readthedocs.io/en/latest/_api/lumicks.pylake.KymoWidgetGreedy.html#lumicks.pylake.KymoWidgetGreedy.load_tracks).
+* Added `applied_at` property to a [calibration item](https://lumicks-pylake.readthedocs.io/en/v1.6.0/_api/lumicks.pylake.calibration.ForceCalibrationItem.html) obtained from a force slice. This property returns the timestamp in nanoseconds at which the force calibration was applied.
+* Added parameter `titles` to customize the title of each subplot in [`Kymo.plot_with_channels()`](https://lumicks-pylake.readthedocs.io/en/v1.6.0/_api/lumicks.pylake.kymo.Kymo.html#lumicks.pylake.kymo.Kymo.plot_with_channels).
+* Added [`KymoTrack.sample_from_channel()`](https://lumicks-pylake.readthedocs.io/en/v1.6.0/_api/lumicks.pylake.kymotracker.kymotrack.KymoTrack.html#lumicks.pylake.kymotracker.kymotrack.KymoTrack.sample_from_channel) to downsample channel data to the time points of a kymotrack.
+* Added support for file names with spaces in [`lk.download_from_doi()`](https://lumicks-pylake.readthedocs.io/en/v1.6.0/_api/lumicks.pylake.download_from_doi.html#lumicks.pylake.download_from_doi).
+* Show the ranges that were excluded from a power spectrum or calibration fit by passing `show_excluded=True` to [`PowerSpectrum.plot()`](https://lumicks-pylake.readthedocs.io/en/v1.6.0/_api/lumicks.pylake.force_calibration.power_spectrum.PowerSpectrum.html#lumicks.pylake.force_calibration.power_spectrum.PowerSpectrum.plot) or [`CalibrationResults.plot()`](https://lumicks-pylake.readthedocs.io/en/v1.6.0/_api/lumicks.pylake.force_calibration.power_spectrum_calibration.CalibrationResults.html#lumicks.pylake.force_calibration.power_spectrum_calibration.CalibrationResults.plot).
+* Plot the active calibration peak for a calibration result using `show_active_peak=True` with [`CalibrationResults.plot()`](https://lumicks-pylake.readthedocs.io/en/v1.6.0/_api/lumicks.pylake.force_calibration.power_spectrum_calibration.CalibrationResults.html#lumicks.pylake.force_calibration.power_spectrum_calibration.CalibrationResults.plot).
+* Added function to import a [`KymoTrackGroup`](https://lumicks-pylake.readthedocs.io/en/v1.6.0/_api/lumicks.pylake.kymotracker.kymotrack.KymoTrackGroup.html) from a `CSV` file using [`load_tracks`](https://lumicks-pylake.readthedocs.io/en/v1.6.0/_api/lumicks.pylake.load_tracks.html).
+* Added function to load tracks into the kymotracker widget using [`KymoWidgetGreedy.load_tracks()`](https://lumicks-pylake.readthedocs.io/en/v1.6.0/_api/lumicks.pylake.KymoWidgetGreedy.html#lumicks.pylake.KymoWidgetGreedy.load_tracks).
 
 #### Improvements
 
 * Added improved printing of calibration items under `channel.calibration` providing a more convenient overview of the items associated with a `Slice`.
 * Added improved printing of calibrations performed with `Pylake`.
-* Improved error message that includes the name of the model when trying to access a model that was not added in an [`FdFit`](https://lumicks-pylake.readthedocs.io/en/latest/_api/lumicks.pylake.FdFit.html) using angular brackets.
-* Allow customizing the minimum step size during step size determination for [`DwelltimeModel.profile_likelihood()`](https://lumicks-pylake.readthedocs.io/en/latest/_api/lumicks.pylake.DwelltimeModel.html#lumicks.pylake.DwelltimeModel.profile_likelihood) and choose a more sensible default. Also ensured that the warning only gets emitted at most once per direction.
+* Improved [`FdFit`](https://lumicks-pylake.readthedocs.io/en/v1.6.0/_api/lumicks.pylake.FdFit.html) error message that includes the name of the model when trying to access a model that was not added in an [`FdFit`](https://lumicks-pylake.readthedocs.io/en/v1.6.0/_api/lumicks.pylake.FdFit.html) using angular brackets.
+* Allow customizing the minimum step size during step size determination for [`DwelltimeModel.profile_likelihood()`](https://lumicks-pylake.readthedocs.io/en/v1.6.0/_api/lumicks.pylake.DwelltimeModel.html#lumicks.pylake.DwelltimeModel.profile_likelihood) and set a more sensible default. Also ensured that the warning only gets emitted at most once per direction.
 
 #### Bug fixes
 
-* Ensure that operators such as (e.g. `+`, `-`, `/`) work on [`Slice`](https://lumicks-pylake.readthedocs.io/en/latest/_api/lumicks.pylake.channel.Slice.html) with all types that are convertible to scalars. Previously these failed with zero dimensional numpy arrays and other convertible objects.
-* Fixed a bug where bead edge determination could fail with an unhandled exception during background estimation. This raised a `np.linalg.LinAlgError` when determining the background failed rather than the expected `RuntimeError`. In this case, a simple median is used as a fallback option.
-* Fix a bug to ensure that [`lk.GaussianMixtureModel`](https://lumicks-pylake.readthedocs.io/en/latest/_api/lumicks.pylake.GaussianMixtureModel.html) can also be used with a single state.
 * Fixed bug that prevented opening the force distance widgets when using them with the `widget` backend on `matplotlib >= 3.9.0`.
-* Prevent near `0/0` during fitting when components of a [`DwelltimeModel`](https://lumicks-pylake.readthedocs.io/en/latest/_api/lumicks.pylake.DwelltimeModel.html) are near zero. Note that these only occurred during the computation of the model derivatives during the fitting procedure and should not impact the model simulation itself.
+* Ensure that operators such as (e.g. `+`, `-`, `/`) work on [`Slice`](https://lumicks-pylake.readthedocs.io/en/v1.6.0/_api/lumicks.pylake.channel.Slice.html) with all types that are convertible to scalars. Previously these failed with zero dimensional numpy arrays and other convertible objects.
+* Fixed a bug where bead edge determination could fail with an unhandled exception during background estimation. This raised a `np.linalg.LinAlgError` when determining the background failed rather than the expected `RuntimeError`. In this case, a simple median is used as a fallback option.
+* Fixed a bug to ensure that [`lk.GaussianMixtureModel`](https://lumicks-pylake.readthedocs.io/en/v1.6.0/_api/lumicks.pylake.GaussianMixtureModel.html) can also be used with a single state.
+* Fixed a bug that could result in a near `0/0` during fitting when components of a [`DwelltimeModel`](https://lumicks-pylake.readthedocs.io/en/v1.6.0/_api/lumicks.pylake.DwelltimeModel.html) are near zero. Note that these only occurred during the computation of the model derivatives during the fitting procedure and should not impact the model simulation itself.
 
 ## v1.5.3 | 2024-10-29
 

docs/theory/force_calibration/fitting.rst

@@ -56,8 +56,10 @@ frequency :cite:`berg2004power`.
 
 .. math::
 
+    \begin{eqnarray}
     \bar{f} &= \frac{1}{n_b} \sum_{f \in \mathrm{block}} f\\
     \bar{P}_\mathrm{meas} &= \frac{1}{n_b} \sum_{f \in \mathrm{block}} P_\mathrm{meas}(f)
+    \end{eqnarray}
 
 Setting the number of points per block too low results in a bias from insufficient averaging :cite:`berg2004power`.
 Insufficient averaging would result in an overestimation of the force response :math:`R_f` and an

docs/whatsnew/1.6.0/1_6_0.rst

@@ -3,7 +3,7 @@ Pylake 1.6.0
 
 .. only:: html
 
-Here is a sneak preview of features that will likely be in Pylake `v1.6.0`.
+Here is an overview of features that were released in Pylake `v1.6.0`.
 
 New example notebooks
 ---------------------

lumicks/pylake/__about__.py

@@ -1,9 +1,9 @@
 __title__ = "lumicks.pylake"
-__version__ = "1.5.3"
+__version__ = "1.6.0"
 __summary__ = "Bluelake data analysis tools"
 __url__ = "https://github.com/lumicks/pylake"
 
 __author__ = "Lumicks B.V."
-__copyright__ = "2024, " + __author__
+__copyright__ = "2025, " + __author__
 __email__ = "[email protected]"
 __license__ = "Apache 2.0"

pyproject.toml

@@ -25,7 +25,7 @@ classifiers=[
     "Programming Language :: Python :: Implementation :: CPython",
 ]
 dependencies = [
-    "pytest>=3.5",
+    "pytest>=7.4",
     "h5py>=3.4, <4",
     "numpy>=1.24",  # 1.24 is needed for dtype in vstack/hstack (Dec 18th, 2022)
     "scipy>=1.9, <2",  # 1.9.0 needed for lazy imports (July 29th, 2022)

release.md

@@ -13,10 +13,10 @@ Within the Pylake repo dir:
   - Update the date of the new release.
   - Review the changelog entries. Make sure everything is clear and informative for users.
   - Consider grouping some related entries if it makes sense.
-- Bump the version number in `./pyproject.toml`.
+- Bump the version number in `__about__.py`.
 - Commit changes with message "release: release Pylake v<X.YY.Z>".
 - Check whether any dependencies of Pylake have changed and check if required packages do exist on anaconda:
-  - `git diff v<previous_release_version_number> setup.py` to check changed dependencies.
+  - `git diff v<previous_release_version_number> pyproject.toml` to check changed dependencies.
   - Check availability of package versions on [anaconda](https://anaconda.org/) in the channel `anaconda` and `conda-forge`.
 - Run `pytest` with `pytest --runpreflight --runslow ./lumicks/pylake` and verify that all tests pass (none may be skipped).
 - Build the docs (see `docs/readme.md`) and verify that they build without warnings.