From 1f55beae3e65088eeb2c98601389b3fefb8bf52a Mon Sep 17 00:00:00 2001 From: Joep Vanlier Date: Tue, 28 May 2024 11:14:40 +0200 Subject: [PATCH] release: release Pylake v1.5.0 --- changelog.md | 23 +++++++++++------------ lumicks/pylake/__about__.py | 2 +- 2 files changed, 12 insertions(+), 13 deletions(-) diff --git a/changelog.md b/changelog.md index 0cbcfff39..98d2557d4 100644 --- a/changelog.md +++ b/changelog.md @@ -1,32 +1,31 @@ # Changelog -## v1.5.0 | t.b.d. +## v1.5.0 | 2024-05-28 #### New features * Support Python `3.12`, dropped support for `3.9`. -* Added [`Kymo.plot_with_channels()`](https://lumicks-pylake.readthedocs.io/en/latest/_api/lumicks.pylake.kymo.Kymo.html#lumicks.pylake.kymo.Kymo.plot_with_channels) for plotting a kymograph with corresponding channel data. For more information, please refer to the [kymograph tutorial](https://lumicks-pylake.readthedocs.io/en/latest/tutorial/kymographs.html#correlating-with-channel-data). -* Added option to disable downsampling channel data to frame rates with correlated plots ([`ImageStack.plot_correlated()`](https://lumicks-pylake.readthedocs.io/en/latest/_api/lumicks.pylake.ImageStack.html#lumicks.pylake.ImageStack.plot_correlated), [`Scan.plot_correlated()`](https://lumicks-pylake.readthedocs.io/en/latest/_api/lumicks.pylake.Scan.html#lumicks.pylake.Scan.plot_correlated)) and exported videos ([`ImageStack.export_video()`](https://lumicks-pylake.readthedocs.io/en/latest/_api/lumicks.pylake.ImageStack.html#lumicks.pylake.ImageStack.export_video), [`Scan.export_video()`](https://lumicks-pylake.readthedocs.io/en/latest/_api/lumicks.pylake.Scan.html#lumicks.pylake.Scan.export_video)) using `downsample_to_frames=False`. +* Added [`Kymo.plot_with_channels()`](https://lumicks-pylake.readthedocs.io/en/v1.5.0/_api/lumicks.pylake.kymo.Kymo.html#lumicks.pylake.kymo.Kymo.plot_with_channels) for plotting a kymograph with corresponding channel data. For more information, please refer to the [kymograph tutorial](https://lumicks-pylake.readthedocs.io/en/v1.5.0/tutorial/kymographs.html#correlating-with-channel-data). +* Added option to disable downsampling channel data to frame rates with correlated plots ([`ImageStack.plot_correlated()`](https://lumicks-pylake.readthedocs.io/en/v1.5.0/_api/lumicks.pylake.ImageStack.html#lumicks.pylake.ImageStack.plot_correlated), [`Scan.plot_correlated()`](https://lumicks-pylake.readthedocs.io/en/v1.5.0/_api/lumicks.pylake.scan.Scan.html#lumicks.pylake.scan.Scan.plot_correlated)) and exported videos ([`ImageStack.export_video()`](https://lumicks-pylake.readthedocs.io/en/v1.5.0/_api/lumicks.pylake.ImageStack.html#lumicks.pylake.ImageStack.export_video), [`Scan.export_video()`](https://lumicks-pylake.readthedocs.io/en/v1.5.0/_api/lumicks.pylake.scan.Scan.html#lumicks.pylake.scan.Scan.export_video)) using `downsample_to_frames=False`. * Added `err_kappa` and `err_Rd` to force calibration results. These contain error estimates for the calibration constants propagated from the fitting errors. -* Added support for loading two-color `TIF` files with [`ImageStack`](https://lumicks-pylake.readthedocs.io/en/latest/_api/lumicks.pylake.ImageStack.html#lumicks.pylake.ImageStack). -* Made ([`CalibrationResults`](https://lumicks-pylake.readthedocs.io/en/latest/_api/lumicks.pylake.force_calibration.power_spectrum_calibration.CalibrationResults.html#calibrationresults)) callable to evaluate the fitted model power spectral density at the specified frequencies. -* Added `fitted_params` field to ([`CalibrationResults`](https://lumicks-pylake.readthedocs.io/en/latest/_api/lumicks.pylake.force_calibration.power_spectrum_calibration.CalibrationResults.html#calibrationresults)) for convenience. -* Allow accessing FdFit model defaults through key access notation (i.e. `model["m/Lc"]`). +* Added support for loading two-color `TIF` files with [`ImageStack`](https://lumicks-pylake.readthedocs.io/en/v1.5.0/_api/lumicks.pylake.ImageStack.html#lumicks.pylake.ImageStack). +* Made ([`CalibrationResults`](https://lumicks-pylake.readthedocs.io/en/v1.5.0/_api/lumicks.pylake.force_calibration.power_spectrum_calibration.CalibrationResults.html#calibrationresults)) callable to evaluate the fitted model power spectral density at the specified frequencies. +* Added `fitted_params` field to ([`CalibrationResults`](https://lumicks-pylake.readthedocs.io/en/v1.5.0/_api/lumicks.pylake.force_calibration.power_spectrum_calibration.CalibrationResults.html#calibrationresults)) for convenience. +* Allow accessing [`Model`](https://lumicks-pylake.readthedocs.io/en/v1.5.0/_api/lumicks.pylake.fitting.model.Model.html) default parameters for a force-distance model by key (i.e. `model["m/Lc"]`). #### Improvements -* Added error message when parameters are passed to [`lk.parameter_trace()`](https://lumicks-pylake.readthedocs.io/en/latest/_api/lumicks.pylake.parameter_trace.html) that do not have the required attributes. -* Warn when parameter estimates are hitting the fitting bounds when using [`lk.parameter_trace()`](https://lumicks-pylake.readthedocs.io/en/latest/_api/lumicks.pylake.parameter_trace.html). -* Added `err_kappa` and `err_Rd` to force calibration results. These contain error estimates for the calibration constants propagated from the fitting errors. +* Added error message when parameters are passed to [`lk.parameter_trace()`](https://lumicks-pylake.readthedocs.io/en/v1.5.0/_api/lumicks.pylake.parameter_trace.html) that do not have the required attributes. +* Warn when parameter estimates are hitting the fitting bounds when using [`lk.parameter_trace()`](https://lumicks-pylake.readthedocs.io/en/v1.5.0/_api/lumicks.pylake.parameter_trace.html). #### Other changes -* Switch to notebook v7 with `ipympl`. See https://blog.jupyter.org/announcing-jupyter-notebook-7-8d6d66126dcf for more information. Note that this means that you have to have to invoke `%matplotlib widget` in notebooks where you previously used `%matplotlib notebook`. +* Switch to notebook v7 with `ipympl`. Note that this means that you have to have to invoke `%matplotlib widget` in notebooks where you previously used `%matplotlib notebook`. See the jupyter [notebook 7 announcement](https://blog.jupyter.org/announcing-jupyter-notebook-7-8d6d66126dcf) for more information. #### Bug fixes * Fixed statistical backing returning an incorrect value. -* Fixed bug where the `start_frame` parameter was being ignored when exporting a movie with [`ImageStack.export_video()`](https://lumicks-pylake.readthedocs.io/en/latest/_api/lumicks.pylake.ImageStack.html#lumicks.pylake.ImageStack.export_video) and [`Scan.export_video()`](https://lumicks-pylake.readthedocs.io/en/latest/_api/lumicks.pylake.scan.Scan.html#lumicks.pylake.scan.Scan.export_video). This bug was introduced in Pylake `v1.3.0`. +* Fixed bug where the `start_frame` parameter was being ignored when exporting a movie with [`ImageStack.export_video()`](https://lumicks-pylake.readthedocs.io/en/v1.5.0/_api/lumicks.pylake.ImageStack.html#lumicks.pylake.ImageStack.export_video) and [`Scan.export_video()`](https://lumicks-pylake.readthedocs.io/en/v1.5.0/_api/lumicks.pylake.scan.Scan.html#lumicks.pylake.scan.Scan.export_video). This bug was introduced in Pylake `v1.3.0`. ## v1.4.0 | 2024-02-28 diff --git a/lumicks/pylake/__about__.py b/lumicks/pylake/__about__.py index d942adfd8..f13009f48 100644 --- a/lumicks/pylake/__about__.py +++ b/lumicks/pylake/__about__.py @@ -1,5 +1,5 @@ __title__ = "lumicks.pylake" -__version__ = "1.4.0" +__version__ = "1.5.0" __summary__ = "Bluelake data analysis tools" __url__ = "https://github.com/lumicks/pylake"