Releases | Open Source Science

Changelog

Fix deploy.yml by @stephanmg in https://github.com/ICB-DCM/pyABC/pull/642
Fix issue https://github.com/ICB-DCM/pyABC/pull/644
Preparation for release 0.12.16 by @stephanmg in https://github.com/ICB-DCM/pyABC/pull/646
Fix tests after migration to PEtab v2.

Full Changelog: https://github.com/ICB-DCM/pyABC/compare/v0.12.15...v0.12.16

Scientific Software - Peer-reviewed - Python
Published by stephanmg 9 months ago

pyABC - pyABC 0.12.15

General:

Minor improvements in the documentation
Minor bug fixes in dependencies
Minor bug fixed in general
Dropping support of python 3.9
Adding support for python 3.12

Scientific Software - Peer-reviewed - Python
Published by arrjon over 1 year ago

pyABC - pyABC 0.12.14

Visualization:

Selected plotly versions of matplotlib visualizations

General:

Added functionality to evaluate the model using boundary values of parameter

Scientific Software - Peer-reviewed - Python
Published by stephanmg over 2 years ago

pyABC - Release 0.12.13

Bugfix release for pyABC's visserver.

Scientific Software - Peer-reviewed - Python
Published by stephanmg over 2 years ago

pyABC - pyABC 0.12.12

Visualization:

Dash-based visualization server (#581)

Scientific Software - Peer-reviewed - Python
Published by yannikschaelte over 2 years ago

pyABC - pyABC 0.12.11

Fixes (https://github.com/ICB-DCM/pyABC/pull/608)

Fix petab test suite (different name resolution)
Fix LocalTransition (pandas -> numpy argument)
Fix sklearn intersphinx

Scientific Software - Peer-reviewed - Python
Published by yannikschaelte over 2 years ago

pyABC - pyABC 0.12.10

General:

Update to Python 3.11, drop Python 3.8 support
Turn simple files into submodules for cleaner import
Fix dask sampler (change default pickling and use global function that it can pickle)

Documentation:

Configure readthedocs build environment
Refactor API docs (add [+]; easier navigation)
Correct scipy intersphinx link
Add docstrings to submodules

Minor fixes:

Flake8 fixes of dict creation from key+value
Fix imports from correct submodule in external submodule
Fix package versions in migration test

Visualization:

Contour plots as a direct alternative to kernel density heat maps and histograms (#597)
Fix column renaming in visserver

Scientific Software - Peer-reviewed - Python
Published by yannikschaelte almost 3 years ago

pyABC - pyABC 0.12.9

Minor:

Improve documentation of p-norm (#592)
Update citation to JOSS
Temporarily fixate sqlalchemy version
Update pre-commit hooks (all #596)

Scientific Software - Peer-reviewed - Python
Published by yannikschaelte almost 3 years ago

pyABC - pyABC 0.12.8

Fix look-ahead implementation in case of biased proposals (#568)

Minor:

Remove boteh in test env as distributed #7227 got fixed
Remove obsolete two gaussians test
Fix Mixin random seed (set it via /dev/urandom)
Update viserver to bokeh >= 3.0.1 (different import of TabPanel, Tabs) (all #589)
Fix sqlalchemy warning "SAWarning: TypeDecorator BytesStorage() will not produce a cache key" (#590)

Scientific Software - Peer-reviewed - Python
Published by yannikschaelte over 3 years ago

pyABC - pyABC 0.12.7

Ignore B027 empty method in an abstract base class
Refactor EPSMixin
Fix EPSMixin for ConcurrentFutureSampler
Temporarily add bokeh to test due to dask error

Scientific Software - Peer-reviewed - Python
Published by yannikschaelte over 3 years ago

pyABC - pyABC 0.12.6

Add JOSS paper of version 0.12.5
Update Julia reference DiffEqJump -> JumpProcesses (name change)
Unfix jinja2
Update flake8 dependencies after new issues

Scientific Software - Peer-reviewed - Python
Published by yannikschaelte over 3 years ago

pyABC - pyABC 0.12.5

Minor:

Document outdated Google Colab version (Python 3.7)

Scientific Software - Peer-reviewed - Python
Published by yannikschaelte over 3 years ago

pyABC - pyABC 0.12.4

Minor:

Move near-zero population weight to warning (#563)
Improve test installation instructions; fix for updates of flake8-print and black (#567)

Scientific Software - Peer-reviewed - Python
Published by yannikschaelte almost 4 years ago

pyABC - pyABC 0.12.3

Document custom priors (#559)

Scientific Software - Peer-reviewed - Python
Published by yannikschaelte almost 4 years ago

pyABC - pyABC 0.12.2

Update citation hints, add logo license (#554)

Scientific Software - Peer-reviewed - Python
Published by yannikschaelte almost 4 years ago

pyABC - pyABC 0.12.1

Fix double logging in grid search

Scientific Software - Peer-reviewed - Python
Published by yannikschaelte almost 4 years ago

pyABC - pyABC 0.12.0

Major changes compared to 0.11.0:

New features:

Add Silk acceptance rate curve based optimal threshold scheme (#539)
Interface Copasi model simulators via BasiCO (thanks to Frank Bergmann) (#531)
Interface simulators in the Julia language via pyjulia (#514)
Add Wasserstein and Sliced Wasserstein optimal transport distances (#500)
Finalize sensitivity weighted distance functions using inverse regression models and augmented regression targets (#478, 484)

Technical changes:

Support python>=3.8 (#543)

Internals:

Automatic code formatting via black, isort, and nbqa (#506, #508, #544)

Random:

The logo is pink (#549)

Scientific Software - Peer-reviewed - Python
Published by yannikschaelte almost 4 years ago

pyABC - pyABC 0.11.12

Add Silk acceptance rate curve based optimal threshold scheme (#539)
Fix Julia version in tests (#542)
Apply nbqa black and isort to notebooks (#544)
Update to stable tox
Require python>=3.8 (#543)

Scientific Software - Peer-reviewed - Python
Published by yannikschaelte about 4 years ago

pyABC - pyABC 0.11.11

Implement color grouping by summary statistics and parameters in sankey plots (#536)

Scientific Software - Peer-reviewed - Python
Published by yannikschaelte about 4 years ago

pyABC - pyABC 0.11.10

Add BasiCO-Copasi model interface (thanks to Frank Bergmann) (#531)
CI: Run Amici without sensitivity calculation (#533)

Scientific Software - Peer-reviewed - Python
Published by yannikschaelte about 4 years ago

pyABC - pyABC 0.11.9

Allow pickling of AMICI models (#527)
Remove external handler cleanup as not used (#529)
Allow timeout of external handlers (#530)

Scientific Software - Peer-reviewed - Python
Published by yannikschaelte about 4 years ago

pyABC - pyABC 0.11.8

Interface Julia simulators via pyjulia (#514)
Refactor PCA distance, add tests (#518)
Remove pyarrow as hard dependency for pandas storage (#523)
Hierarchically structure examples, update "Parameter Inference" introduction (#524)
Add minimum epsilon difference stopping condition (#525)

Scientific Software - Peer-reviewed - Python
Published by yannikschaelte about 4 years ago

pyABC - pyABC 0.11.7

Decompose ABCSMC.run for easier outer loop (#510)

Scientific Software - Peer-reviewed - Python
Published by yannikschaelte over 4 years ago

pyABC - pyABC 0.11.6

Unfix sphinx version for documentation (#509)
Streamline function wrapper objects (#511)
Remove rpy2 warning upon import of pyabc.external (#512)
Move ot distance to scipy due to bug in pot 0.8.0 (#512)

Scientific Software - Peer-reviewed - Python
Published by yannikschaelte over 4 years ago

pyABC - pyABC 0.11.5

Regularly scheduled CI (#504)
Fix Dask for Windows (#503)
Apply the uncompromising Python code formatter black (#506)
Apply automatic import sorting via isort (#508)

Scientific Software - Peer-reviewed - Python
Published by yannikschaelte over 4 years ago

pyABC - pyABC 0.11.4

Implement Wasserstein and Sliced Wasserstein distances (#500)
Add env variable to bound population size in tests (#501)

Scientific Software - Peer-reviewed - Python
Published by yannikschaelte over 4 years ago

pyABC - pyABC 0.11.3

Update to amici 0.11.19 for scaled residual support (#491)
Add links for online execution of notebooks on Google Colab and nbviewer (#492)
Tests: Fix early stopping test for first generation (#494)

Scientific Software - Peer-reviewed - Python
Published by yannikschaelte over 4 years ago

pyABC - pyABC 0.11.2

Remove codacy due to excessive permission requests
Tidy up example titles

Scientific Software - Peer-reviewed - Python
Published by yannikschaelte over 4 years ago

pyABC - pyABC 0.11.1

Summary statistics:

Allow transformed parameters as regression targets via ParTrafo (#478)
Add Sankey flow plot (#484)
Add "informative" notebook to document regression-based summary statistics and weights (#484)

Sampler:

Speed up redis done-list checking by atomic operations (#482)

Scientific Software - Peer-reviewed - Python
Published by yannikschaelte over 4 years ago

This release brings, besides many bug fixes and smaller improvements, in particular outlier-robust and flexible adaptive distance functions working with any inputs. Further, a preliminary framework for semi-automatic summary statistics learning is provided (fully documented implementation planned for 0.12.0).

Diverse:

Shorten date-time log (#456)
Add look-ahead example notebook (#461)
Fix decoration of plot_acceptance_rates_trajectory (#465)
Hot-fix redis clean-up (#475)

Semi-automatic summary statistics and robust sample weighting (#429) ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Breaking changes:

API of the (Adaptive)PNormDistance was altered substantially to allow cutom definition of update indices.
Internal weighting of samples (should not affect users).

Semi-automatic summary statistics:

Implement (Adaptive)PNormDistance with the ability to learn summary statistics from simulations.
Add sumstat submodule for generic mappings (id, trafos), and especially a PredictorSumstat summary statistic that can make use of Predictor objects.
Add subsetting routines that allow restricting predictor model training samples.
Add predictor submodule with generic Predictor class and concrete implementations including linear regression, Lasso, Gaussian Process, Neural Network.
Add InfoWeightedPNormDistance that allows using predictor models to weight data not only by scale, but also by information content.

Outlier-robust adaptive distances:

Update documentation towards robust distances.
Add section in the corresponding notebook.
Implement PCMAD outlier correction scheme.

Changes to internal sample weighting:

Do not normalize weights of in-memory particles by model; this allows to more easily use the sampling weights and the list of particles for adaptive components (e.g. distance functions)
Normalization of population to 1 is applied on sample level in the sampler wrapper function
In the database, normalization is still by sample to not break old db support; would be nicer to also there only normalize by total sum -- requires a db update though.

Changes to internal object instruction from samples:

Pass sample instead of weightedsumstats to distance function. This is because thus the distance can choose on its own what it wants -- all or only accepted particles; distances; weights; parameters; summary statistics.

Visualization:

Function to plot adaptive distance weights from log file.

Scientific Software - Peer-reviewed - Python
Published by yannikschaelte over 4 years ago

pyABC - pyABC 0.10.16

Allow color customization for plot_credible_intervals plots (#414)
pyABC logo to grey to fit with both black and white backgrounds (#453)
Add style set to global figure parameters, enabling dark mode (#454)

Scientific Software - Peer-reviewed - Python
Published by yannikschaelte almost 5 years ago

pyABC - pyABC 0.10.15

Sampler:

Allow redis dynamical sampler to only wait for relevant particles after a generatio, giving a speed-up without drawbacks (#448)
Add option to limit number of delayed look-ahead samples to limit memory usage (#428)

Logging:

Standardize output of floats (#450)
Use hierarchical logging (ABC.Submodule) (#417)

General:

Refactor: Remove deprecated nr_samples_per_parameter, internal simplifications (#422)
Tidy up and minimize dependencies (#436, #441)
External: Remove simulation files after collecting results (#434)
Make feather/pyarrow dependency optional for older hardware (#442)

Documentation:

Add description of JupyterHub to documentation (#439)

CI:

Test webserver basic functionality
Rerun stochastically failing tests (all #436)
Test whether dataframe storage routines work properly (#442)

Scientific Software - Peer-reviewed - Python
Published by yannikschaelte almost 5 years ago

pyABC - pyABC 0.10.14

General:

Speed up parameter handling (30% internal speed-up) (#387)
Streamline testing via tox and pre-commit hooks, add flake8 config file (#408)
Update to python 3.9 (#411)
Extract PEtab bounds and nominal parameters (#416)
Allow specifying parameter names in density plots (#416)
Normalize look-ahead sampling by subpopulation ESS (#418, #421)

Documentation:

Update contribution and issue guidelines (#408)
Add example on yaml2sbml usage (#416)
Clean up user docs on parallelization and storage (#419)

Fixes:

Fix redis for later started workers (#410)
Fix PEtab parameter scale import, support all PEtab prior distributions (#413)

Database:

Add database migration scheme based on alembic (#419)
Store proposal ids, increment database version to 0 (#419)

Scientific Software - Peer-reviewed - Python
Published by yannikschaelte almost 5 years ago

pyABC - pyABC 0.10.13

Update branch name master -> main in agreement with https://github.com/github/renaming (#406).
Notebook improvements:
- Add ground truth to noise notebook.
- Rename notebook "quickstart" -> "model_selection".
- Split notebook tests in 2, extend, reduce test matrix (python 3.7).
Improve output at the beginning and end (e.g. no end_time at beginning; show duration).
Add walltime plots (plot_total_walltime, plot_walltime, plot_eps_walltime).
Make sure ABCSMC.run() is always properly finished (sampler, history) by a wrapper (all #401).
Redis sampler with look-ahead mode:
- Fix insufficient logging of look-ahead samples.
- Log all accepted particles.
Add plot_lookahead_... plots for look-ahead mode diagnostics.
Add global figure parameter settings for pyABC (all #405).

Scientific Software - Peer-reviewed - Python
Published by yannikschaelte about 5 years ago

pyABC - pyABC 0.10.12

Check components for their adaptivity for correct application of look-ahead mode (#397).

Scientific Software - Peer-reviewed - Python
Published by yannikschaelte about 5 years ago

pyABC - pyABC 0.10.11

Require pandas >= 1.2.0 for PEtab.

Scientific Software - Peer-reviewed - Python
Published by yannikschaelte about 5 years ago

pyABC - pyABC 0.10.10

Uniquely identify redis runs via a uuid.
Secure proper termination of processes for redis and dask (all #338).
Rework redis sampler, implement a look-ahead mode for pre-defined (#338) and adaptive algorithms (#374) for near-perfect parallel efficiency.
Allow subprocessing in multiprocessed redis workers (#377).
Add a static-scheduling redis sampler (#379).
Check whether epsilon is nan before sampling (#382).
Remove useless IdentityFakeDistance (#390).

Scientific Software - Peer-reviewed - Python
Published by yannikschaelte about 5 years ago

pyABC - pyABC 0.10.9

0.10.9 (2020-11-28) * Add stopping criterion for total walltime (#370).

0.10.8 (2020-11-27) (forgotten to release :seenoevil: ) * Allow to normalize acceptance rate plots by ESS (#346). * Add a list of pyABC references (#348). * Update to petabtests 0.0.0a5 (#362). * Add stopping criterion for total number of samples (#364). * Remove dill dependency, thus fixing a cloudpickle error, and run selected tests also with python 3.7 (#367).

Scientific Software - Peer-reviewed - Python
Published by yannikschaelte about 5 years ago

pyABC - pyABC 0.10.7

Move progress usage to attribute level (#336).
Add check for whether redis is up already (#337).
Add a self-tuned finite-space discrete transition (#341).

Scientific Software - Peer-reviewed - Python
Published by yannikschaelte over 5 years ago

pyABC - pyABC 0.10.6

Refactor and modularize ABCSMC inference module (#333).
Make fast random choice function robust across dimensions (#333).

Scientific Software - Peer-reviewed - Python
Published by yannikschaelte over 5 years ago

pyABC - pyABC 0.10.5

Remove bkcharts dependency (#328).
Add optional progress bar to various samplers (#330).
Refactor package metadata (#330).
Refactor CI build, add code quality tests (#331).
Add warning when many zero-prior samples are generated (#331).

Scientific Software - Peer-reviewed - Python
Published by yannikschaelte over 5 years ago

pyABC - pyABC 0.10.4

Refactor __all__ imports and docs API build (#312).
Fix json export of aggregated adaptive distances (#316).
Apply additional flake8 checks on code quality (#317).
Assert model input is of type pyabc.Parameter (#318).
Extend noise notebook to estimated noise parameters (#319).
Implement optional pickling for multicore samplers; add MacOS pipeline tests (#320).

Scientific Software - Peer-reviewed - Python
Published by yannikschaelte over 5 years ago

pyABC - pyABC 0.10.3

Speed up multivariate normal multiple sampling (#299).
Set default value for OMPNUMTHREADS=1, stops warnings (#299).
Base default number of parallel cores on PYABCNUMPROCS (#309).
Update all notebooks to the latest numpy/scipy (#310).

Scientific Software - Peer-reviewed - Python
Published by yannikschaelte almost 6 years ago

pyABC - pyABC 0.10.2

Update CI test system: latest Ubuntu, python 3.8, simplify R build (#296).
Add weights logging to adaptive distances (#295).
Migrate CI tests to GitHub Actions for speed-up, reliability and maintainability (#297, #298).

Scientific Software - Peer-reviewed - Python
Published by yannikschaelte almost 6 years ago

pyABC - pyABC 0.10.1

Allow separate calibration population sizes, slightly reformulate PopulationStrategy class (#278).
Allow specifying initial weights for adaptive distances, then without sampling from the prior (#279).
Check PEtab test suite in tests (#281).

Scientific Software - Peer-reviewed - Python
Published by yannikschaelte almost 6 years ago

pyABC - pyABC 0.10.0

Exact inference via stochastic acceptor finalized and tested (developed throughout the 0.9 series).
Support basic PEtab functionality using AMICI ODE simulations (#268).
Various error fixes (#265, #267).
Log number of processes used by multiprocessing samplers (#263).
Implement pyabc.acceptor.ScaledPDFNorm (#269).
Implement list population size (#274, #276).
On history loading, automatically find an id of a successful run (#273).

Scientific Software - Peer-reviewed - Python
Published by yannikschaelte about 6 years ago

pyABC - pyABC 0.9.26

Add optional check whether database is non-existent, to detect typos.
Set lower bound in 1-dim KDEs to <= 0 to not wrongly display near-uniform distributions. (both #257)
Implement redis password protection for sampler and manage routine (#256).
Make samplers available in global namespace (#249).
Implement ListTemperature (#248).
Allow plotting the relative ESS (#245).
Allow resampling of weighted particles (#244).
Fix ABCSMC.load with rpy2 (#242).

Scientific Software - Peer-reviewed - Python
Published by yannikschaelte about 6 years ago

pyABC - pyABC 0.9.25

Add summary statistics callback plot function (#231).
Add possibility to log employed norms in StochasticAcceptor (#231) and temperature proposals in Temperature (#232).
Implement optional early stopping in the MulticoreEvalParallelSampler and the SingleCoreSampler, when a maximum simulation number is exceeded (default behavior untouched).
Log stopping reason in ABCSMC.run (all #236).
Implement Poisson (#237) and negative binomial (#239) stochastic kernels.
Enable password protection for Redis sampler (#238).
Fix scipy deprecations (#234, #241).

Scientific Software - Peer-reviewed - Python
Published by yannikschaelte about 6 years ago

pyABC - pyABC 0.9.24

In ABCSMC.run, allow a default infinite number of iterations, and log the ESS in each iteration.
Reformulate exponential temperature decay, allowing for a fixed number of iterations or fixed ratios.
Solve acceptance rate temperature match in log space for numeric stability.
Perform temperation of likelihood ratio in log space for numeric stability (all #221).
Fix wrong maximum density value in binomial kernel.
Allow not fixing the final temperature to 1 (all #223).
Allow passing id to history directly (#225).
Pass additional arguments to Acceptor.update.
Give optional min_rate argument to AcceptanceRateScheme (all #226).
In plot functions, add parameter specifying the reference value color (#227).

Scientific Software - Peer-reviewed - Python
Published by yannikschaelte about 6 years ago