--------------------------------------------- lines 6-253 of file: xrst/whats_new/2025.xrst --------------------------------------------- {xrst_begin 2025} {xrst_spell mm dd py pdf relrisk rcond subprocess dismodat toml conda pyproject setuptools sqlite unix cee xam } Release Notes for 2025 ###################### mm-dd ***** 11-28 ===== In the documentation, change 'child rate' to 'child rate effect' because these are not really rates, but rather random effects on rates. This is explained in the csv fit :ref:`csv.fit@Input Files@child_rate.csv@value_prior` 11-15 ===== Fix documentation for :ref:`csv.predict@Input Files@option_predict.csv@float_precision` . To be more specific, the comments about the no effect rates were moved to the :ref:`csv.predict@Input Files@option_predict.csv@plot` documentation. 10-17 ===== The at_cascade `example/no_ode_xam.py` was passing a list for the `dismod_at.plot_rate_fit` *rate_set* argument. This made a test crash using a newer version of dismod_at and has been fixed. 10-15 ===== The problem with the optimization perturbation was introduced by commit c802cee on 08-21 and was fixed on 10-11 (see below). The csv.fit default value for these parameters was set to 0 and as been corrected to be backward compatible to before the change on 08-21; see :ref:`csv.fit@Input Files@option_fit.csv@perturb_optimization_scale` and :ref:`csv.fit@Input Files@option_fit.csv@perturb_optimization_start` . 10-14 ===== The version number for dismod_at and at_cascade was added at the beginning of each log table in the data base for each fit. One way to view this is in the log.csv file that is created when :ref:`csv.predict@Input Files@option_predict.csv@db2csv` is true in the csv.predict option file. 10-11 ===== The :ref:`option_all_table@perturb_optimization_scale` and :ref:`option_all_table@perturb_optimization_scale` options were not working. This was a bug in :ref:`fit_one_job-name` . This has been fixed. In addition these options were added to :ref:`csv.fit@Input Files@option_fit.csv` in a way that is backward compatible. 09-26 ===== Add the csv.predict option :ref:`csv.predict@Input Files@option_predict.csv@descendant_std_factor` ; see the :ref:`csv.predict_descend-name` example. 09-23 ===== Both descendent and descendant were spread throughout the documentation and at_cascade source code. The spelling descendent was changed to descendant to be consistent While this included moving `job_descendent` to :ref:`job_descendant-name` , it did not change the :ref:`csv.fit-name` of :ref:`csv.predict-name` API . 08-23 ===== Some of the python sqlite3 connections were not being closed. The corresponding variable just dropped out of scope. Dropping out of scope freed the corresponding resources on Unix but not on Windows. This has been fixed (all the connections are closed). 08-22 ===== Switch the pip build back end from setuptools to hatchling ( see `pyproject.toml` ) . This fixes the install of at_cascade on conda (and maybe other systems). 08-21 ===== Complete the subprocess wish list item; i.e. use `dismod_at.db2csv_command(database)` instead of `dismodat.py database db2csv` . 08-01 ===== Add :ref:`csv.predict@Input Files@option_predict.csv@number_sample_predict` to the option_fit.csv file. This requires dismod_at-2025.7.31 or later. 07-09 ===== Add the :ref:`csv.diphtheria-name` example. 07-08 ===== Add the subprocess wish list item. 07-07 ===== The value of the random effects used to create :ref:`csv.predict@Output Files@tru_predict.csv` where not correct when there was a non-zero covariate multiplier. This has been fixed. 07-05 ===== Add the ``censor_asymptotic`` *sample_method* to the :ref:`option_all table` and the :ref:`option_fit.csv file` . 06-05 ===== #. Add the following wish list items: :ref:`wish_list@csv.fit@Child Job Priors` , :ref:`wish_list@csv.fit@predict_goal.csv` . #. The name of the new option asymptotic_rcond_lower was miss spelled one place in the csv.fit.py source code. This made it impossible to use and has been fixed. 06-03 ===== #. Add the csv.fit :ref:`csv.fit@Input Files@option_fit.csv@asymptotic_rcond_lower` option. #. Add the :ref:`csv.fit@Input Files@option_fit.csv@child_prior_dage` and :ref:`csv.fit@Input Files@option_fit.csv@child_prior_dtime` options to the csv interface; for example, see :ref:`csv.dage_prior-name` . This also added the :ref:`option_all_table@shift_prior_dage` and :ref:`option_all_table@shift_prior_dtime` options in the option all table. #. Remove white space from the header in the :ref:`csv.no_data@data_in.csv` file in the no_data.py example. Also improve the discussion of the :ref:`csv.no_data@option_fit.csv` file for this example. #. Discuss a :ref:`create_shift_db@Problem` with the current method used to create child job priors. 05-18 ===== Add a discussion child job shifted priors under :ref:`create_shift_db@Theory` in the :ref:`create_shift_db-title` section 05-11 ===== Add discussion of the :ref:`csv.no_data@Negative Log Likelihood` and the how it relates to the :ref:`csv.fit@Output Files@sam_predict.csv` file. 05-10 ===== The special case where there is no data at the root (node, sex) pair used to cause at_cascade to abort. This has been changed so that the no data case can be used to better understand how the priors work; see :ref:`csv.no_data-name` . Note the this requires a special case when :ref:`fit_one_job@run_job_id` is zero. 02-06 ===== Add the *max_fit_parent* option to the :ref:`option_all table` and the :ref:`option_fit.csv file` . 01-15 ===== Start the 2025 stable versions of at_cascade; see the new :ref:`at_cascade@Versions` table. A release for 2025 has the stable version 2025.0.\ *number* where *number* is the release number. Only bug fixes, not new features, are added between release numbers. This change has broken old web links to the at_cascade documentation. An old link of the form | |tab| ``https://at-cascade.readthedocs.io/``\ *html_file_name* has the following form in the latest documentation: | |tab| ``https://at-cascade.readthedocs.io/latest/``\ *html_file_name* and the following for in the 2025 stable documentation: | |tab| ``https://at-cascade.readthedocs.io/stable-2025/``\ *html_file_name* 01-13 ===== #. Add :ref:`csv.fit@Input Files@option_fit.csv@child_prior_std_factor_mulcov` to the option_fit csv file and :ref:`option_all_table@shift_prior_std_factor_mulcov` to the option_all table. #. The computation of the standard deviation for the child priors was using one degree of freedom. This is not correct because we know the true mean of the samples; i.e., the fit value (the number of degrees of freedom should be zero). This has been fixed and the child prior standard deviations that are a factor of :math:`\sqrt{(N-1)/N}` smaller where N is the number of samples. #. There was a bug in :ref:`fit_one_process-name` . It sometimes returned on the main branch before all the other processes had finished. This has been fixed. It was found by repeated running of the `example/relrisk.py` test which uses a large value for :ref:`option_all_table@max_number_cpu` . 01-12 ===== The test/csv/fit.py and test/csv/sample_fail.py tests were failing on some systems; see `pull request 29 `_ . The failures have has been fixed by not expecting the plot_data.pdf file to exist for (node, sex) pairs that have only one data point. {xrst_end 2025}