From 993b3dcbdf78c552cb39d67cedf270f98e98af4f Mon Sep 17 00:00:00 2001 From: Yan Wong Date: Sat, 6 Jan 2024 12:23:16 +0000 Subject: [PATCH] Tidy CHANGELOG for 0.1.6 --- CHANGELOG.md | 27 +++++++++++++++++++-------- 1 file changed, 19 insertions(+), 8 deletions(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index 122984ec..1859f213 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -1,6 +1,6 @@ # Changelog -## [0.1.6] - ****-**-** +## [0.1.6] - 2024-01-07 **Breaking changes** @@ -8,9 +8,10 @@ individuals, populations, or sites, aiming to change the tree sequence tables as little as possible. -- Not strictly breaking, as not in the published API, but the "normalize" flag - in `get_dates` and the internal `normalize` terminology is changed to - `standardize` to better reflect the fact that the maximum (not sum) is one. +- `get_dates` (previously undocumented) has been removed, as posteriors can be + obtained using `return_posterior`. The `normalize` terminology previously used + in `get_dates` is changed to `standardize` to better reflect the fact that the + maximum (not sum) is one, and exposed via the `outside_standardize` parameter. - The `Ne` argument to `date` has been deprecated (although it is still in the API for backward compatibility). The equivalent argument @@ -27,6 +28,9 @@ atomically over time points, so `start_time` and `end_time` have been replaced by a single key `time`. +- The `return_posteriors=True` option with `method="maximization"` is no + longer accepted (previously simply returned `None`) + - Python 3.7 is no longer supported. **Features** @@ -34,8 +38,9 @@ - A new continuous-time method, `"variational_gamma"` has been introduced, which uses an iterative expectation propagation approach. Tests show this increases accuracy, especially at older times. A Laplace approximation and damping are - used to ensure numerical stability. Future releases may switch to using this - as the default method. + used to ensure numerical stability. After testing, the node priors used in this + method are based on a global mixture prior, which can be refined during iteration. + Future releases may switch to using this as the default method. - Priors may be calculated using a piecewise-constant effective population trajectory, which is implemented in the `demography.PopulationSizeHistory` class. The @@ -44,14 +49,20 @@ - Added support and wheels for Python 3.11 +- The `.date()` function is now a wrapper for the individual dating methods + (accessible using `tsdate.core.dating_methods`), which can be called independently. + (e.g. `tsdate.inside_outside(...)`). This makes it easier to document method-specific + options. The API docs have been revised accordingly. Provenance is now saved with the + name of the method used as the celled command, rather than `"command": "date"`. + **Bugfixes** - The returned posteriors when `return_posteriors=True` now return actual probabilities (scaled so that they sum to one) rather than standardized "probabilities" whose maximum value is one. -- The population size is saved in provenance metadata when possible (e.g. if it is - a single number) +- The population size is saved in provenance metadata (as a dictionary if + it is a `PopulationSizeHistory` instance) - `preprocess_ts` always records provenance as being from the `preprocess_ts` command, even if no gaps are removed. The command now has a (rarely used)