fitgrid - 0.5.3

Maintenance release

• Add Python 3.9 conda package support
• Switch Action CI from daily to weekly
• Patch gallery doc for matplotlib update

Scientific Software - Peer-reviewed - Jupyter Notebook
Published by turbach about 4 years ago

fitgrid - 0.5.2

Maintenance release, no functional changes.

• Update CI, Installation docs, and Contributing docs for revised strict channel priority semantics in mamba release 0.15.0
• Add bug report template for Issues

Scientific Software - Peer-reviewed - Jupyter Notebook
Published by turbach almost 5 years ago

fitgrid - 0.5.1

Maintenance release, no functional changes

Continuous integration and deployment

• Update CI with mamba/boa and CI for breaking changes in dependencies
• Deprecate PyPI package uploads

Docs with thanks to @sappelhoff and @AJQuinn

• Update user installation instructions in sphinx docs for mamba, conda, no pip
• Add Contributing section to sphinx docs for developers
• Added intersphinx links, numerous corrections, fixes, references, to the docs

Scientific Software - Peer-reviewed - Jupyter Notebook
Published by turbach almost 5 years ago

fitgrid - 0.5.0

• Code updates for pymer4 0.7.1 (conda package) and lme4::lmer 0.22 warnings
• Switch CI from TravisCI to Actions
• Undo stale python 3.6 pinned conda package dependencies
• Add conda packages for python 3.7, 3.8

Scientific Software - Peer-reviewed - Jupyter Notebook
Published by turbach about 5 years ago

fitgrid - 0.4.11

bug fix for #173 fitgrid default time and epoch_id values changed to time and epoch_id align with mkpy and spudtr

Scientific Software - Peer-reviewed - Jupyter Notebook
Published by turbach almost 6 years ago

fitgrid - 0.4.10

Pinned pandas below 0.1.0 b.c. rpy2 breaks, so no LMER

Known bugs: #173

Scientific Software - Peer-reviewed - Jupyter Notebook
Published by turbach over 6 years ago

fitgrid - 0.4.9

Patched pytests to report discrepancies between fitgrd.lmer() results for different versions of r-lme4 and r-matrix and fail on potentially serious deviations.

Scientific Software - Peer-reviewed - Jupyter Notebook
Published by turbach over 6 years ago

fitgrid - 0.4.8

version bump

Scientific Software - Peer-reviewed - Jupyter Notebook
Published by turbach over 6 years ago

fitgrid - 0.4.7

bump release for Zenodo

Scientific Software - Peer-reviewed - Jupyter Notebook
Published by turbach over 6 years ago

fitgrid - 0.4.6

Maintanence release to sync PyPI and Anaconda Cloud package distribution vN.N.N

Scientific Software - Peer-reviewed - Jupyter Notebook
Published by turbach over 6 years ago

fitgrid - 0.4.5

Maintenance release. Updated TravisCI to

• run pytests a conda created environment
• deploy each github release vN.N.N to PyPI

Scientific Software - Peer-reviewed - Jupyter Notebook
Published by turbach over 6 years ago

fitgrid - 0.4.4

Relaxed nearly all the package version pinning for the conda environment

Cleaned up AIC plotting and lm diagnostics in fitgrid.utils.summary

Scientific Software - Peer-reviewed - Jupyter Notebook
Published by turbach over 6 years ago

fitgrid - 0.4.3

fitgrid 0.4.3 pins conda env tomro-base and versioned r-lme4, r-lmertest for reproducibility.

Scientific Software - Peer-reviewed - Jupyter Notebook
Published by turbach almost 7 years ago

fitgrid - 0.4.0

UI: convenience wrappers for statsmodels OLS diagnostics, tuned up utils.summary AICmin delta plotting

closes #144, #145

Scientific Software - Peer-reviewed - Jupyter Notebook
Published by turbach about 7 years ago

fitgrid - 0.3.0

• added fitgrid.utils.summary functions to fit and summarize sets of models, plot betas and AICs

• juggled and expanded docs

Scientific Software - Peer-reviewed - Jupyter Notebook
Published by turbach about 7 years ago

fitgrid - 0.2.2

Bug fixes

• Saving in fit_lmers() (TPU)

Other

• A number of clarifications in the docs (thanks Anna!)
• Added fitgrid.__version__

Scientific Software - Peer-reviewed - Jupyter Notebook
Published by andportnoy about 7 years ago

fitgrid - 0.2.1

Features

• add Feather file reader
• add VIF calculator for OLS

Bug fixes

• add missing dependencies to setup.py
• improve dir(grid) behavior

Other

• massive refactor, move away from using constants to using parameters
• update docs to reflect refactor
• make the tutorial into a notebook
• add design matrix checker, which is a first step towards eliminating redundant model fitting
• update conda channel from aportnoy to kutaslab

Scientific Software - Peer-reviewed - Jupyter Notebook
Published by andportnoy over 7 years ago

fitgrid - 0.2.0

Major refactor in this release.

Features

• Add DFBETAS calculator routine for lmer models

Other

• major refactor, model fitters now top level functions, so fitgrid.lm instead of epochs.lm, add LMFitGrid and LmerFitGrid, subclasses of FitGrid
• Travis environment updates
• expand docs, add page with installation instructions, add page with miscellaneous details of how things are done
• skip single thread context manager tests on Travis, see #86

Scientific Software - Peer-reviewed - Jupyter Notebook
Published by andportnoy over 7 years ago

fitgrid - 0.1.8

Bug fixes

• utils package added to distribution, was missing because no __init__.py

Scientific Software - Peer-reviewed - Jupyter Notebook
Published by andportnoy over 7 years ago

fitgrid - 0.1.7

Bug fixes

• set correct evaluation environment for patsy in lm

Scientific Software - Peer-reviewed - Jupyter Notebook
Published by andportnoy over 7 years ago

fitgrid - 0.1.6

Installation

bash conda install -c aportnoy fitgrid or bash pip install -U fitgrid

Features

• new lmer fitting routine that allows for visual model comparison based on AIC
• grids can now be saved to files and loaded from files using grid.save and fitgrid.load_grid
• additional parameters now available in epochs.lmer: REML/ML, confidence interval types, etc.

Bug fixes

• exorbitant memory usage slightly mitigated by removing a number of attributes from lmer fit objects
• missing lmer correctness tests now added

Other

• fitgrid is now available from conda: run conda install -c aportnoy fitgrid
• Travis tests are now run using conda
• slight structure reorganization

Scientific Software - Peer-reviewed - Jupyter Notebook
Published by andportnoy over 7 years ago

fitgrid - 0.1.5

Bug fixes

• fix stupid bug where lmer did not use specified channels

Scientific Software - Peer-reviewed - Jupyter Notebook
Published by andportnoy over 7 years ago

fitgrid - 0.1.4

Bug fixes

• add option to plot legend separately in plot_betas, otherwise we fail miserably with many betas
• guard against duplicate channels in Epochs and FitGrid's, also when slicing FitGrid's
• fix issue with plot_betas used on a grid with a single channel
• add colorscale to plot_betas

Scientific Software - Peer-reviewed - Jupyter Notebook
Published by andportnoy over 7 years ago

fitgrid - 0.1.3

Features

• Add multicore processing, made possible by making NumPy single-threaded
• Add support for full linear mixed models using lme4, replacing statsmodels

Bug fixes

• Use all channels by default in run_model
• Fix formatting of duplicate epoch indices error message

Other

• Model running is now done sample by sample instead of channel by channel
• Correctness tests for lm added

Scientific Software - Peer-reviewed - Jupyter Notebook
Published by andportnoy over 7 years ago

fitgrid - 0.1.2

Features

• Add support for mixed models to the extent allowed by statsmodels
• Add Epochs.distances, a function assigning distances from the "mean epoch" to all epochs. This allows for preliminary outlier rejection.

Bug fixes

• Fix bad _snapshots access using get_group (#38)

Other

• Private Epochs attributes are prefixed with _ to get them out of the way of the user.
• Refactor LHS and RHS validation (DRY).

Scientific Software - Peer-reviewed - Jupyter Notebook
Published by andportnoy over 7 years ago

fitgrid - 0.1.1

Features

• Helpful message on duplicate indices (suggested by Melissa)
• run_model function in Epochs allowing for running arbitrary models
• One shot R^2 plot with marginal subplots
• Averages plotted negative up by default to respect the convention
• Add correct epoch id resolution for returned dataframes, this matters when we get bare arrays from statsmodels
• Both Epochs and FitGrid are channel aware (have a channels attribute tracking what channels they have)

Bug fixes

• Font sizes for the plots are changed using context managers so the changes are contained
• table inside epochs is now a copy not a reference to the original
• Use Agg matplotlib backend to prevent fatal erros when $DISPLAY is not set
• Copy when creating smaller grids on slicing

Other

• Add API reference to docs
• Trimmed down dependencies
• Better test coverage
• Clearer example in demo notebook

Scientific Software - Peer-reviewed - Jupyter Notebook
Published by andportnoy over 7 years ago