release: release Pylake v1.1.0

changelog.md

@@ -1,26 +1,26 @@
 # Changelog
 
-## v1.1.0 | t.b.d.
+## v1.1.0 | 2023-05-17
 
 #### New features
 
-* Added [`DwelltimeModel.profile_likelihood()`](https://lumicks-pylake.readthedocs.io/en/latest/_api/lumicks.pylake.DwelltimeModel.html#lumicks.pylake.DwelltimeModel.profile_likelihood) for calculating profile likelihoods for dwell time analysis. These can be used to determine confidence intervals and assess whether the model has too many parameters (i.e., if a model with fewer components would be sufficient).
+* Enabled adding [`KymoTrackGroup`](https://lumicks-pylake.readthedocs.io/en/v1.1.0/_api/lumicks.pylake.kymotracker.kymotrack.KymoTrackGroup.html) instances with tracks from different source kymographs. *Note that certain features (e.g., [`KymoTrackGroup.ensemble_msd()`](https://lumicks-pylake.readthedocs.io/en/v1.1.0/_api/lumicks.pylake.kymotracker.kymotrack.KymoTrackGroup.html#lumicks.pylake.kymotracker.kymotrack.KymoTrackGroup.ensemble_msd) and `KymoTrackGroup.ensemble_diffusion("ols")`) require that all source kymographs have the same pixel size and scan line times.* See the [kymotracking tutorial](https://lumicks-pylake.readthedocs.io/en/v1.1.0/tutorial/kymotracking.html#global-analysis) for more information.
+* Added [`DwelltimeModel.profile_likelihood()`](https://lumicks-pylake.readthedocs.io/en/v1.1.0/_api/lumicks.pylake.DwelltimeModel.html#lumicks.pylake.DwelltimeModel.profile_likelihood) for calculating profile likelihoods for dwell time analysis. These can be used to determine confidence intervals and assess whether the model has too many parameters (i.e., if a model with fewer components would be sufficient). See the [population dynamics tutorial](https://lumicks-pylake.readthedocs.io/en/v1.1.0/tutorial/population_dynamics.html#profile-likelihood-based-confidence-intervals) for more information.
 * Added functionality to split tracks in the Kymotracking widget.
-* Added functionality to provide minimum and maximum observation times per data point to `DwelltimeModel` and `DwelltimeBootstrap`.
-* Enabled adding `KymoTrackGroup`s with tracks from different source kymographs. *Note that certain features (e.g., `KymoTrackGroup.ensemble_msd()` and `KymoTrackGroup.ensemble_diffusion("ols")`) require that all source kymographs have the same pixel size and scan line times.*
+* Added functionality to provide minimum and maximum observation times per data point to [`DwelltimeModel`](https://lumicks-pylake.readthedocs.io/en/v1.1.0/_api/lumicks.pylake.DwelltimeModel.html) and [`DwelltimeBootstrap`](https://lumicks-pylake.readthedocs.io/en/v1.1.0/_api/lumicks.pylake.population.dwelltime.DwelltimeBootstrap.html).
 
 #### Bug fixes
 
-* Fixed bug that could lead to mutability of `Kymo` and `Scan` through `.get_image()` or `.timestamps`. This bug was introduced in `0.7.2`. Grabbing a single color image from a `Scan` or `Kymo` using `.get_image()` returns a reference to an internal image cache. This numpy array was write-able and modifying data in the returned image would result in future calls to `.get_image()` returning the modified data rather than the original `Kymo` or `Scan` image. Timestamps obtained from `.timestamps` were similarly affected. These arrays are now returned non-writeable.
-* Fixed a bug that would round the center of the window to the incorrect pixel when using `KymoTrack.sample_from_image()`. Pixels are defined with their origin at the center of the pixel, whereas this function incorrectly assumed that the origin was on the edge of the pixel. The effects of this bug are larger for small windows. For backward compatibility this bugfix is not enabled by default. To enable the bugfix specify `correct_origin=True` as a keyword argument to the method.
+* Fixed a bug that would round the center of the window to the incorrect pixel when using [`KymoTrack.sample_from_image()`](https://lumicks-pylake.readthedocs.io/en/v1.1.0/_api/lumicks.pylake.kymotracker.kymotrack.KymoTrack.html#lumicks.pylake.kymotracker.kymotrack.KymoTrack.sample_from_image). Pixels are defined with their origin at the center of the pixel, whereas this function incorrectly assumed that the origin was on the edge of the pixel. The effects of this bug are larger for small windows. For backward compatibility this bugfix is not enabled by default. To enable the bugfix specify `correct_origin=True` as a keyword argument to the method.
+* Fixed bug that could lead to mutability of [`Kymo`](https://lumicks-pylake.readthedocs.io/en/v1.1.0/_api/lumicks.pylake.kymo.Kymo.html) and [`Scan`](https://lumicks-pylake.readthedocs.io/en/v1.1.0/_api/lumicks.pylake.scan.Scan.html) through `.get_image()` or `.timestamps`. This bug was introduced in `0.7.2`. Grabbing a single color image from a [`Scan`](https://lumicks-pylake.readthedocs.io/en/v1.1.0/_api/lumicks.pylake.scan.Scan.html) or [`Kymo`](https://lumicks-pylake.readthedocs.io/en/v1.1.0/_api/lumicks.pylake.kymo.Kymo.html) using `.get_image()` returns a reference to an internal image cache. This numpy array was write-able and modifying data in the returned image would result in future calls to `.get_image()` returning the modified data rather than the original [`Kymo`](https://lumicks-pylake.readthedocs.io/en/v1.1.0/_api/lumicks.pylake.kymo.Kymo.html) or [`Scan`](https://lumicks-pylake.readthedocs.io/en/v1.1.0/_api/lumicks.pylake.scan.Scan.html) image. Timestamps obtained from `.timestamps` were similarly affected. These arrays are now returned non-writeable.
 * Fixed a bug where we passed a `SampleFormat` tag while saving to `tiff` using `tifffile`. However, `tifffile` infers the `SampleFormat` automatically from the datatype of the `numpy` array it is passed. This produced warnings on the latest version of `tifffile` when running the benchmark.
-* Ensure that the probability density returns zero outside its support for `DwelltimeModel.pdf()`. Prior to this change, non-zero values would be returned outside the observation limits of the dwelltime model.
-* Fixed a bug where `DwelltimeModel.hist()` produces one less bin than requested with `n_bins`.
-* Fixed a bug where `lk.dsdna_ewlc_odijk_distance()` erroneously returned a model where force is the dependent variable rather than distance. This bug was introduced in `0.13.2`. Note that `lk.ewlc_odijk_distance()` was unaffected. It was specifically the convenience function with DNA parameters that was affected.
+* Ensure that the probability density returns zero outside its support for [`DwelltimeModel.pdf()`](https://lumicks-pylake.readthedocs.io/en/v1.1.0/_api/lumicks.pylake.DwelltimeModel.html#lumicks.pylake.DwelltimeModel.pdf). Prior to this change, non-zero values would be returned outside the observation limits of the dwelltime model.
+* Fixed a bug where [`DwelltimeModel.hist()`](https://lumicks-pylake.readthedocs.io/en/v1.1.0/_api/lumicks.pylake.DwelltimeModel.html#lumicks.pylake.DwelltimeModel.hist) produces one less bin than requested with `n_bins`.
+* Fixed a bug where [`lk.dsdna_ewlc_odijk_distance()`](https://lumicks-pylake.readthedocs.io/en/v1.1.0/_api/lumicks.pylake.dsdna_ewlc_odijk_distance.html) erroneously returned a model where force is the dependent variable rather than distance. This bug was introduced in `0.13.2`. Note that [`lk.ewlc_odijk_distance()`](https://lumicks-pylake.readthedocs.io/en/v1.1.0/_api/lumicks.pylake.ewlc_odijk_distance.html) was unaffected. It was specifically the convenience function with DNA parameters that was affected.
 
 #### Improvements
 
-* Improve API description of the channel data in a default `FdCurve`.
+* Improve API description of the channel data in a default [`FdCurve`](https://lumicks-pylake.readthedocs.io/en/v1.1.0/_api/lumicks.pylake.fdcurve.FdCurve.html).
 * Improved fitting performance dwell time analyses by implementing analytic gradient.
 * Added lower and upper bounds when fitting dwell time models. This prevents numerical issues that occur when approaching these extremes. Prior to this change, over-parameterized models could encounter numerical issues due to divisions by (near) zero. After this change, amplitudes are constrained to stay between `1e-9` and `1.0 - 1e-9`, while lifetimes are constrained to remain between `1e-8` and `1e8`.
 * Provided better initial guess for dwell time models with three or more components. Prior to this change, the dwelltime models involving three components or more would get an initial guess with an average lifetime beyond the mean of the observations.

docs/api.rst

@@ -77,10 +77,12 @@ FD Fitting
     ewlc_marko_siggia_distance
     ewlc_odijk_force
     ewlc_odijk_distance
+    dsdna_ewlc_odijk_distance
     twlc_force
     twlc_distance
     efjc_force
     efjc_distance
+    ssdna_efjc_distance
 
 
 Kymotracking

lumicks/pylake/__about__.py

@@ -1,5 +1,5 @@
 __title__ = "lumicks.pylake"
-__version__ = "1.0.0"
+__version__ = "1.1.0"
 __summary__ = "Bluelake data analysis tools"
 __url__ = "https://github.com/lumicks/pylake"