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Recent Releases of beiwe-forest

beiwe-forest - Release 1.0

What's Changed

  • Add get_path function for calculating routes by @GeorgeEfstathiadis in https://github.com/onnela-lab/forest/pull/41
  • Added getbasicpath and bounding_box by @GeorgeEfstathiadis in https://github.com/onnela-lab/forest/pull/42
  • Add support for static type checking using mypy by @hackdna in https://github.com/onnela-lab/forest/pull/44
  • Added Person class for trajectory simulation by @GeorgeEfstathiadis in https://github.com/onnela-lab/forest/pull/43
  • Add code style checking using flake8 by @hackdna in https://github.com/onnela-lab/forest/pull/45
  • Update generating trajectories and adding tests in Bonsai by @GeorgeEfstathiadis in https://github.com/onnela-lab/forest/pull/46
  • Bonsai genalltraj by @GeorgeEfstathiadis in https://github.com/onnela-lab/forest/pull/47
  • Added 3 functions to prepare trajectories format by @GeorgeEfstathiadis in https://github.com/onnela-lab/forest/pull/48
  • Added process_attributes function by @GeorgeEfstathiadis in https://github.com/onnela-lab/forest/pull/49
  • Bonsai simgpsdata by @GeorgeEfstathiadis in https://github.com/onnela-lab/forest/pull/52
  • Added transformpointto_circle by @GeorgeEfstathiadis in https://github.com/onnela-lab/forest/pull/54
  • added getnearbylocations function by @GeorgeEfstathiadis in https://github.com/onnela-lab/forest/pull/57
  • Fix assertion error in testgetpath_distance by @GeorgeEfstathiadis in https://github.com/onnela-lab/forest/pull/62
  • Upgrade develop branch to Python 3.8 by @hackdna in https://github.com/onnela-lab/forest/pull/63
  • gps_summaries places of interest feature by @GeorgeEfstathiadis in https://github.com/onnela-lab/forest/pull/60
  • Update gps quality check for better readability by @GeorgeEfstathiadis in https://github.com/onnela-lab/forest/pull/67
  • Fix traj2stats warnings in testing by @GeorgeEfstathiadis in https://github.com/onnela-lab/forest/pull/66
  • Update gpsstatsmain for new features by @GeorgeEfstathiadis in https://github.com/onnela-lab/forest/pull/69
  • Update README by @GeorgeEfstathiadis in https://github.com/onnela-lab/forest/pull/70
  • check for remaining quota and valid api key in ORS by @GeorgeEfstathiadis in https://github.com/onnela-lab/forest/pull/73
  • Bonsai tests cleanup by @hackdna in https://github.com/onnela-lab/forest/pull/76
  • change assert statement of test on gen_pause by @GeorgeEfstathiadis in https://github.com/onnela-lab/forest/pull/77
  • change overpass request to POST from GET by @GeorgeEfstathiadis in https://github.com/onnela-lab/forest/pull/75
  • Add dictionary to store transformed polygons by @GeorgeEfstathiadis in https://github.com/onnela-lab/forest/pull/79
  • Update forest_usage.ipynb by @dbbhuang in https://github.com/onnela-lab/forest/pull/82
  • Provide default values to all text and call variables by @hackdna in https://github.com/onnela-lab/forest/pull/80
  • Fix survey timings by @clementzach in https://github.com/onnela-lab/forest/pull/90
  • Remove unused file events.json by @hackdna in https://github.com/onnela-lab/forest/pull/95
  • Update Sycamore Readme by @clementzach in https://github.com/onnela-lab/forest/pull/94
  • Fix Deprecation Warning in Bonsai by @clementzach in https://github.com/onnela-lab/forest/pull/97
  • Read survey answers by @clementzach in https://github.com/onnela-lab/forest/pull/96
  • Fix poplar deprecation by @clementzach in https://github.com/onnela-lab/forest/pull/102
  • GitHub wiki to Read the Docs migration by @hackdna in https://github.com/onnela-lab/forest/pull/104
  • Add instructions on how to build the documentation by @hackdna in https://github.com/onnela-lab/forest/pull/106
  • validate that something is a directory before counting it as an ID by @clementzach in https://github.com/onnela-lab/forest/pull/103
  • Changed rounding to 3 decimal places instead of 4 by @clementzach in https://github.com/onnela-lab/forest/pull/107
  • Removing sycamore README because it is redundant with other files by @clementzach in https://github.com/onnela-lab/forest/pull/110
  • Sycamore submits fix by @clementzach in https://github.com/onnela-lab/forest/pull/109
  • Sycamore Android Radio Answers from config by @clementzach in https://github.com/onnela-lab/forest/pull/111
  • Fixed bug in forest.poplar.legacy.commonfuncs.readdata by @clementzach in https://github.com/onnela-lab/forest/pull/113
  • change link to README to direct to documentation by @clementzach in https://github.com/onnela-lab/forest/pull/116
  • Change default argument in computesurveystats by @clementzach in https://github.com/onnela-lab/forest/pull/117
  • add question index columns to survey answers lines by @clementzach in https://github.com/onnela-lab/forest/pull/120
  • Fix sycamore submit line by @clementzach in https://github.com/onnela-lab/forest/pull/121
  • Raise error if timezonefinder returns None by @GeorgeEfstathiadis in https://github.com/onnela-lab/forest/pull/126
  • Fix bug in OpenStreetMaps locator code that showed if place of interest not in nearby locations of a pause by @martakarass in https://github.com/onnela-lab/forest/pull/125
  • Sycamore tableau function by @clementzach in https://github.com/onnela-lab/forest/pull/119
  • Fixes to Oak_1 by @MStraczkiewicz in https://github.com/onnela-lab/forest/pull/132
  • Audio submits by @clementzach in https://github.com/onnela-lab/forest/pull/134
  • Treat survey openings on Android and iOS the same by @clementzach in https://github.com/onnela-lab/forest/pull/137
  • change NOANSWERSELECTED to np.nan by @clementzach in https://github.com/onnela-lab/forest/pull/138
  • adding creator information to doc Working with Forest on AWS by @martakarass in https://github.com/onnela-lab/forest/pull/140
  • adding new documentation md file: Accessing and decrypting Beiwe data by @martakarass in https://github.com/onnela-lab/forest/pull/141
  • add check for empty GPS data loaded by @GeorgeEfstathiadis in https://github.com/onnela-lab/forest/pull/146
  • HTTPError timing out for OSM API calls by @GeorgeEfstathiadis in https://github.com/onnela-lab/forest/pull/143
  • Converted summary statistics for distances in jasmine to km by @GeorgeEfstathiadis in https://github.com/onnela-lab/forest/pull/142
  • Get distance from ORS API when available by @GeorgeEfstathiadis in https://github.com/onnela-lab/forest/pull/145
  • fix jasmine bug when no missing data in gps trajectories by @GeorgeEfstathiadis in https://github.com/onnela-lab/forest/pull/152
  • jasmine osm summary statistic by @GeorgeEfstathiadis in https://github.com/onnela-lab/forest/pull/151
  • Docs jasmine missing vars by @GeorgeEfstathiadis in https://github.com/onnela-lab/forest/pull/149
  • Docs add bonsai tree by @GeorgeEfstathiadis in https://github.com/onnela-lab/forest/pull/148
  • Jasmine few gps files by @GeorgeEfstathiadis in https://github.com/onnela-lab/forest/pull/150
  • add new parameter osmtags in getnearby_locations by @GeorgeEfstathiadis in https://github.com/onnela-lab/forest/pull/153
  • New feature by @MStraczkiewicz in https://github.com/onnela-lab/forest/pull/147
  • added 3hr, 6hr and 12hr windows for GPS summary stats by @GeorgeEfstathiadis in https://github.com/onnela-lab/forest/pull/154
  • Willow hoursplit by @GeorgeEfstathiadis in https://github.com/onnela-lab/forest/pull/155
  • Oak hoursplit by @GeorgeEfstathiadis in https://github.com/onnela-lab/forest/pull/156
  • Add duration of audio surveys to sycamore by @clementzach in https://github.com/onnela-lab/forest/pull/139
  • Sycamore Documentation updates by @clementzach in https://github.com/onnela-lab/forest/pull/158
  • Sycamore documentation round 2 by @clementzach in https://github.com/onnela-lab/forest/pull/159
  • Jasmine update docs by @GeorgeEfstathiadis in https://github.com/onnela-lab/forest/pull/160
  • Update forest tutorial with mano, venv and forest updates by @GeorgeEfstathiadis in https://github.com/onnela-lab/forest/pull/161
  • More documentation updates by @clementzach in https://github.com/onnela-lab/forest/pull/162
  • fix negative entropy when 1 significant place by @GeorgeEfstathiadis in https://github.com/onnela-lab/forest/pull/163
  • import mano.sync fix on tutorial by @GeorgeEfstathiadis in https://github.com/onnela-lab/forest/pull/165
  • Revert "More documentation updates" by @joannakennedyharvard in https://github.com/onnela-lab/forest/pull/164
  • don't iterate over None in sycamore.common.parse_surveys by @clementzach in https://github.com/onnela-lab/forest/pull/168
  • Jasmine readme bug by @GeorgeEfstathiadis in https://github.com/onnela-lab/forest/pull/170
  • Style and document simulatelogdata module by @GeorgeEfstathiadis in https://github.com/onnela-lab/forest/pull/171
  • Poplar clean modules by @GeorgeEfstathiadis in https://github.com/onnela-lab/forest/pull/173
  • Jasmine clean data2mobmat by @GeorgeEfstathiadis in https://github.com/onnela-lab/forest/pull/174
  • Update frequency parameter in Oak docs by @GeorgeEfstathiadis in https://github.com/onnela-lab/forest/pull/176
  • sort file_list by @GeorgeEfstathiadis in https://github.com/onnela-lab/forest/pull/182
  • Bug in row calculation in data2mobmat by @GeorgeEfstathiadis in https://github.com/onnela-lab/forest/pull/183
  • remove vectorized version of greatcircledist by @GeorgeEfstathiadis in https://github.com/onnela-lab/forest/pull/181
  • Jasmine clean mobmat2traj by @GeorgeEfstathiadis in https://github.com/onnela-lab/forest/pull/184
  • fix docstring returns in preprocess_bout by @GeorgeEfstathiadis in https://github.com/onnela-lab/forest/pull/187
  • Use logging by @GeorgeEfstathiadis in https://github.com/onnela-lab/forest/pull/186
  • Jasmine clean sogp gps module by @GeorgeEfstathiadis in https://github.com/onnela-lab/forest/pull/188
  • Willow clean log stats by @GeorgeEfstathiadis in https://github.com/onnela-lab/forest/pull/192
  • clean functions and write docstrings for poplar/legacy by @GeorgeEfstathiadis in https://github.com/onnela-lab/forest/pull/193
  • fix dimensions of array concaat by @GeorgeEfstathiadis in https://github.com/onnela-lab/forest/pull/196
  • Sycamore clean by @GeorgeEfstathiadis in https://github.com/onnela-lab/forest/pull/194
  • fix imputation code to not mix up x/y and times by @clementzach in https://github.com/onnela-lab/forest/pull/197
  • Interp overflow fix by @muschellij2 in https://github.com/onnela-lab/forest/pull/191
  • add checks for coordinates out of range by @GeorgeEfstathiadis in https://github.com/onnela-lab/forest/pull/198
  • Typo in calculate_position argument in Jasmine by @GeorgeEfstathiadis in https://github.com/onnela-lab/forest/pull/199
  • Willow add numuniqindividualscallor_text by @clementzach in https://github.com/onnela-lab/forest/pull/200
  • sycamore.md documentation update by @joannakennedyharvard in https://github.com/onnela-lab/forest/pull/202
  • Fix docs breaking - willow.md by @GeorgeEfstathiadis in https://github.com/onnela-lab/forest/pull/204
  • update jasmine function docs by @GeorgeEfstathiadis in https://github.com/onnela-lab/forest/pull/203
  • Oak: add timezone info if start or end date are None by @GeorgeEfstathiadis in https://github.com/onnela-lab/forest/pull/207
  • Jasmine physical cyrcadian rhythm by @GeorgeEfstathiadis in https://github.com/onnela-lab/forest/pull/205
  • Typo flight instead of pause in jasmine docs by @GeorgeEfstathiadis in https://github.com/onnela-lab/forest/pull/209
  • Add style checking for tests by @hackdna in https://github.com/onnela-lab/forest/pull/212
  • Mypy update and PEP484 fixes by @hackdna in https://github.com/onnela-lab/forest/pull/213
  • oak.md documentation update by @joannakennedyharvard in https://github.com/onnela-lab/forest/pull/206
  • Bug when mix of filetypes in oak processing by @GeorgeEfstathiadis in https://github.com/onnela-lab/forest/pull/215
  • Oak optimize by @GeorgeEfstathiadis in https://github.com/onnela-lab/forest/pull/214
  • Update index.md by @joannakennedyharvard in https://github.com/onnela-lab/forest/pull/218
  • Oak refactor run by @GeorgeEfstathiadis in https://github.com/onnela-lab/forest/pull/216
  • Jasmine - Add more tests for summary values by @GeorgeEfstathiadis in https://github.com/onnela-lab/forest/pull/221
  • Update testlogstats.py by @clementzach in https://github.com/onnela-lab/forest/pull/223
  • Remove deprecation warning for Sycamore by @clementzach in https://github.com/onnela-lab/forest/pull/222
  • Oak - Minute level analysis by @GeorgeEfstathiadis in https://github.com/onnela-lab/forest/pull/220
  • Oak fixes zc by @clementzach in https://github.com/onnela-lab/forest/pull/224
  • Oak bug preprocess dates by @GeorgeEfstathiadis in https://github.com/onnela-lab/forest/pull/225
  • Avoid using the root logger by @hackdna in https://github.com/onnela-lab/forest/pull/229
  • Additional frequency names by @GeorgeEfstathiadis in https://github.com/onnela-lab/forest/pull/227
  • Add check for length of input in preprocess_bout by @GeorgeEfstathiadis in https://github.com/onnela-lab/forest/pull/235
  • Add check if no new pauses to concatenate by @GeorgeEfstathiadis in https://github.com/onnela-lab/forest/pull/238
  • Raise error if no data with lower accuracy than limit by @GeorgeEfstathiadis in https://github.com/onnela-lab/forest/pull/237
  • Add checks for empty elements in imputation by @GeorgeEfstathiadis in https://github.com/onnela-lab/forest/pull/236
  • Beiwe taskrunner by @biblicabeebli in https://github.com/onnela-lab/forest/pull/228
  • Jasmine updates by @clementzach in https://github.com/onnela-lab/forest/pull/241
  • Bug when empty row doesn't have correct number of NAs by @GeorgeEfstathiadis in https://github.com/onnela-lab/forest/pull/242
  • Oak: RuntimeWarnings for large numbers overflowing by @GeorgeEfstathiadis in https://github.com/onnela-lab/forest/pull/243
  • Upgrade to Python 3.11 by @hackdna in https://github.com/onnela-lab/forest/pull/248
  • Jasmine - solve bug with saving locations visited log by @GeorgeEfstathiadis in https://github.com/onnela-lab/forest/pull/249
  • Replace interp2d with RegularGridInterpolator by @hackdna in https://github.com/onnela-lab/forest/pull/253
  • Don't check against empty timings array by @clementzach in https://github.com/onnela-lab/forest/pull/250
  • Oak warnings by @GeorgeEfstathiadis in https://github.com/onnela-lab/forest/pull/257
  • Address DeprecationWarning in Bonsai by @hackdna in https://github.com/onnela-lab/forest/pull/260
  • Bonsai: Warning on pd.concat with empty df by @GeorgeEfstathiadis in https://github.com/onnela-lab/forest/pull/262
  • Address FutureWarnings in Sycamore by @hackdna in https://github.com/onnela-lab/forest/pull/264
  • Fail pytest on warnings by @hackdna in https://github.com/onnela-lab/forest/pull/265
  • Update units in jasmine docs by @GeorgeEfstathiadis in https://github.com/onnela-lab/forest/pull/266
  • Update jasmine.md low data by @jprince127 in https://github.com/onnela-lab/forest/pull/268
  • Bug at smoothtempends in jasmine by @GeorgeEfstathiadis in https://github.com/onnela-lab/forest/pull/280
  • Comments in mobmat2traj are reversed on the definition of status by @GeorgeEfstathiadis in https://github.com/onnela-lab/forest/pull/282
  • Mypy fixes by @hackdna in https://github.com/onnela-lab/forest/pull/286
  • Upgrade to Python 3.12 by @hackdna in https://github.com/onnela-lab/forest/pull/288
  • Modify identifypeaksin_cwt alpha beta filtering by @GeorgeEfstathiadis in https://github.com/onnela-lab/forest/pull/291

New Contributors

  • @dbbhuang made their first contribution in https://github.com/onnela-lab/forest/pull/82
  • @martakarass made their first contribution in https://github.com/onnela-lab/forest/pull/125
  • @MStraczkiewicz made their first contribution in https://github.com/onnela-lab/forest/pull/132
  • @joannakennedyharvard made their first contribution in https://github.com/onnela-lab/forest/pull/164
  • @muschellij2 made their first contribution in https://github.com/onnela-lab/forest/pull/191
  • @jprince127 made their first contribution in https://github.com/onnela-lab/forest/pull/268

Full Changelog: https://github.com/onnela-lab/forest/compare/v0.2...v1.0

- Python
Published by hackdna 8 months ago

beiwe-forest - Release 0.2

What's Changed

  • General bug fixes by @alvinsiu in https://github.com/onnela-lab/forest/pull/5
  • Update README.md by @GreysonL in https://github.com/onnela-lab/forest/pull/8
  • fix typo by @jflournoy in https://github.com/onnela-lab/forest/pull/7
  • Merge from master by @patricknnamdi in https://github.com/onnela-lab/forest/pull/9
  • Develop by @GreysonL in https://github.com/onnela-lab/forest/pull/12
  • Update README.md by @debeuker in https://github.com/onnela-lab/forest/pull/10
  • Update README.md by @debeuker in https://github.com/onnela-lab/forest/pull/15
  • initialize bonsai by @debeuker in https://github.com/onnela-lab/forest/pull/16
  • Added reproducible examples to README file by @debeuker in https://github.com/onnela-lab/forest/pull/17
  • Updated readme with some links by @debeuker in https://github.com/onnela-lab/forest/pull/18
  • Add sycamore to master branch by @nponarul in https://github.com/onnela-lab/forest/pull/19
  • Develop by @GreysonL in https://github.com/onnela-lab/forest/pull/21
  • Updated answer timing logic by @nponarul in https://github.com/onnela-lab/forest/pull/20
  • Update traj2stats.py by @GreysonL in https://github.com/onnela-lab/forest/pull/22
  • Adding events.json to prevent sycamore.functions warning by @nponarul in https://github.com/onnela-lab/forest/pull/25
  • Update README.md by @debeuker in https://github.com/onnela-lab/forest/pull/24
  • Update README.md by @debeuker in https://github.com/onnela-lab/forest/pull/23
  • Updated relative importing in sycamore by @nponarul in https://github.com/onnela-lab/forest/pull/26
  • Removed the logger module and fixed several bugs by @GreysonL in https://github.com/onnela-lab/forest/pull/27
  • Develop by @GreysonL in https://github.com/onnela-lab/forest/pull/28
  • Add a basic gitignore file by @hackdna in https://github.com/onnela-lab/forest/pull/30
  • Update commonfuncs.py to skip audiorecordings by @debeuker in https://github.com/onnela-lab/forest/pull/29
  • Compare output of summary API with output of Forest by @hackdna in https://github.com/onnela-lab/forest/pull/31
  • Add a script to run Willow algorithm by @hackdna in https://github.com/onnela-lab/forest/pull/32
  • Add a script to run Jasmine algorithm by @hackdna in https://github.com/onnela-lab/forest/pull/33
  • Fix comparison of missing values by @hackdna in https://github.com/onnela-lab/forest/pull/34
  • Add CI prototype using GitHub Actions by @hackdna in https://github.com/onnela-lab/forest/pull/37
  • Sycamore: added summary of completed surveys table by @nponarul in https://github.com/onnela-lab/forest/pull/36
  • Apply PEP 8 to setup, utils, and tests by @hackdna in https://github.com/onnela-lab/forest/pull/39
  • Updated survey instance logic by @nponarul in https://github.com/onnela-lab/forest/pull/53
  • Eli/jasmine quality threshold by @biblicabeebli in https://github.com/onnela-lab/forest/pull/58
  • Add tutorial by @clementzach in https://github.com/onnela-lab/forest/pull/71

New Contributors

  • @alvinsiu made their first contribution in https://github.com/onnela-lab/forest/pull/5
  • @jflournoy made their first contribution in https://github.com/onnela-lab/forest/pull/7
  • @patricknnamdi made their first contribution in https://github.com/onnela-lab/forest/pull/9
  • @nponarul made their first contribution in https://github.com/onnela-lab/forest/pull/19

Full Changelog: https://github.com/onnela-lab/forest/compare/v0.1.1...v0.2

- Python
Published by hackdna about 1 year ago

beiwe-forest - Release 0.1.1

What's Changed

  • Packaging by @debeuker in https://github.com/onnela-lab/forest/pull/2
  • delete dated code by @GreysonL in https://github.com/onnela-lab/forest/pull/3

Full Changelog: https://github.com/onnela-lab/forest/compare/v0.1...v0.1.1

- Python
Published by hackdna about 1 year ago

beiwe-forest - Release 0.1

Initial release: Jasmine, Poplar, and Willow.

Full Changelog: https://github.com/onnela-lab/forest/commits/v0.1

- Python
Published by hackdna about 1 year ago