Abil: A Python package for the interpolation of aquatic biogeochemical datasets - v25.09.23

Abil.py

Aquatic Biogeochemical Interpolation Library in Python

What's Changed

• Improve tests by @nanophyto in https://github.com/nanophyto/Abil/pull/286
• Fix deps pip install by @nanophyto in https://github.com/nanophyto/Abil/pull/288

Full Changelog: https://github.com/nanophyto/Abil/compare/v25.09.18...v25.09.23

- Python
Published by nanophyto 8 months ago

Abil: A Python package for the interpolation of aquatic biogeochemical datasets - v25.09.18

Abil.py

Aquatic Biogeochemical Interpolation Library in Python

What's Changed

• 275 joss reference check by @nicola-wiseman in https://github.com/nanophyto/Abil/pull/280
• Dimension agnostic integration by @nanophyto in https://github.com/nanophyto/Abil/pull/282
• Dimension agnostic merge_obs by @nanophyto in https://github.com/nanophyto/Abil/pull/283
• unit test instruction by @ruiying-ocean in https://github.com/nanophyto/Abil/pull/285
• Add ref to applications by @nanophyto in https://github.com/nanophyto/Abil/pull/287
• Update documentation with real examples by @nanophyto in https://github.com/nanophyto/Abil/pull/277
• python code style/hygene by @ljwolf in https://github.com/nanophyto/Abil/pull/281

New Contributors

• @ruiying-ocean made their first contribution in https://github.com/nanophyto/Abil/pull/285

Full Changelog: https://github.com/nanophyto/Abil/compare/v25.08.06...v25.09.18

- Python
Published by nanophyto 9 months ago

Abil: A Python package for the interpolation of aquatic biogeochemical datasets - v25.08.06

What's Changed

• 265 need cutpoint output from aoa by @nicola-wiseman in https://github.com/nanophyto/Abil/pull/266
• Aoa pseudos by @nanophyto in https://github.com/nanophyto/Abil/pull/264
• Now includes Zenodo hook

Full Changelog: https://github.com/nanophyto/Abil/compare/v25.08.04...v25.08.06

- Python
Published by nanophyto 10 months ago

Abil: A Python package for the interpolation of aquatic biogeochemical datasets - v25.08.04

What's Changed

• Add notes on AOA values to post.py and analyze.py by @nicola-wiseman in https://github.com/nanophyto/Abil/pull/251
• JOSS paper final draft by @nanophyto in https://github.com/nanophyto/Abil/pull/252
• Tidying by @nanophyto in https://github.com/nanophyto/Abil/pull/253
• Joss rendering by @nanophyto in https://github.com/nanophyto/Abil/pull/254
• Update Singularity.sif by @nicola-wiseman in https://github.com/nanophyto/Abil/pull/257
• Fix DOIs by @nanophyto in https://github.com/nanophyto/Abil/pull/258
• return dissimilarity indices in AOA function for downstream usage by @ljwolf in https://github.com/nanophyto/Abil/pull/262
• Mask out nan values for AOA calculation, and add back in at the end by @ljwolf in https://github.com/nanophyto/Abil/pull/263

Full Changelog: https://github.com/nanophyto/Abil/compare/v25.05.01...v25.08.04

- Python
Published by nanophyto 10 months ago

Abil: A Python package for the interpolation of aquatic biogeochemical datasets - v25.05.01

What's Changed

• remove debugging print statements from predict and unifiedtreeor_bag by @nicola-wiseman in https://github.com/nanophyto/Abil/pull/247
• add option for aoa to run on specific targets by @nicola-wiseman in https://github.com/nanophyto/Abil/pull/248

Full Changelog: https://github.com/nanophyto/Abil/compare/v24.04.14...v25.05.01

- Python
Published by nicola-wiseman about 1 year ago

Abil: A Python package for the interpolation of aquatic biogeochemical datasets - v25.04.14

What's Changed

• Fix target labeling of performance.csv output and update version by @nicola-wiseman in https://github.com/nanophyto/Abil/pull/242

Full Changelog: https://github.com/nanophyto/Abil/compare/v25.04.01...v24.04.14

- Python
Published by nicola-wiseman about 1 year ago

Abil: A Python package for the interpolation of aquatic biogeochemical datasets - v25.04.01

What's Changed

• bag the xgboost estimators right at the end during uncertainty quantification by @ljwolf in https://github.com/nanophyto/Abil/pull/239

Full Changelog: https://github.com/nanophyto/Abil/compare/v25.03.31...v25.04.01

- Python
Published by nanophyto about 1 year ago

Abil: A Python package for the interpolation of aquatic biogeochemical datasets - v25.03.31

What's Changed

• Use predict() for mean and add weighted ensemble members by @nanophyto in https://github.com/nanophyto/Abil/pull/228
• add presampled fields to integrated totals by @nicola-wiseman in https://github.com/nanophyto/Abil/pull/236
• Fix booster preds by @nanophyto in https://github.com/nanophyto/Abil/pull/234

Full Changelog: https://github.com/nanophyto/Abil/compare/v25.03.12...v25.03.31

- Python
Published by nanophyto about 1 year ago

Abil: A Python package for the interpolation of aquatic biogeochemical datasets - v25.03.12

What's Changed

• Minor doc fixes by @nanophyto in https://github.com/nanophyto/Abil/pull/220
• Update hpc documentation by @nicola-wiseman in https://github.com/nanophyto/Abil/pull/214
• Remove pathin deprecated mentions and hardcode regscoring and clf_scoring by @nicola-wiseman in https://github.com/nanophyto/Abil/pull/218
• Removing default csv export in test.py by @nicola-wiseman in https://github.com/nanophyto/Abil/pull/217
• add OS specific instructions for building singularity containers by @nicola-wiseman in https://github.com/nanophyto/Abil/pull/223
• update to file for wiseman2024 .py files as test case by @nicola-wiseman in https://github.com/nanophyto/Abil/pull/224
• Set refit in GridSearchCV to True by @nicola-wiseman in https://github.com/nanophyto/Abil/pull/226

Full Changelog: https://github.com/nanophyto/Abil/compare/v25.03.10...v25.03.12

- Python
Published by nanophyto about 1 year ago

Abil: A Python package for the interpolation of aquatic biogeochemical datasets - v25.03.10

What's Changed

• BUG: use median() instead of std() when reporting median by @ljwolf in https://github.com/nanophyto/Abil/pull/212
• fixes np import in unifiedtreeor_bag.py by @nanophyto in https://github.com/nanophyto/Abil/pull/215

Full Changelog: https://github.com/nanophyto/Abil/compare/v25.03.06...v25.03.10

- Python
Published by nanophyto about 1 year ago

Abil: A Python package for the interpolation of aquatic biogeochemical datasets - v25.03.06

What's Changed

• adds post processing for resampled dataset model output
• add data chunking during predict to reduce RAM usage
• fixes issue with dimensions being stored as integers
• moves functions to make them picklable for use with loky backend

Full Changelog: https://github.com/nanophyto/Abil/compare/v25.02.25...v25.03.06

- Python
Published by nicola-wiseman about 1 year ago

Abil: A Python package for the interpolation of aquatic biogeochemical datasets - v25.02.25

What's Changed

• update documentation by @nanophyto in https://github.com/nanophyto/Abil/pull/177

Full Changelog: https://github.com/nanophyto/Abil/compare/v25.02.24...v25.02.25

- Python
Published by nanophyto over 1 year ago

Abil: A Python package for the interpolation of aquatic biogeochemical datasets - v25.02.24

What's Changed

• Changes how datasets are concatenated during post by @nanophyto in https://github.com/nanophyto/Abil/pull/195
• Updates parallel prediction to create a tmp folder in "." by @nanophyto in https://github.com/nanophyto/Abil/pull/196
• Fixes ds export by @nanophyto in https://github.com/nanophyto/Abil/pull/200

Full Changelog: https://github.com/nanophyto/Abil/compare/v25.02.19...v25.02.24

- Python
Published by nanophyto over 1 year ago

Abil: A Python package for the interpolation of aquatic biogeochemical datasets - v25.02.19

What's Changed

• Fix ZIR prediction over heterogeneous outputs by @ljwolf in https://github.com/nanophyto/Abil/pull/189

Full Changelog: https://github.com/nanophyto/Abil/compare/v25.02.17...v.25.02.19

- Python
Published by nanophyto over 1 year ago

Abil: A Python package for the interpolation of aquatic biogeochemical datasets - v25.02.17

What's Changed

• Merge main updates to docs by @nanophyto in https://github.com/nanophyto/Abil/pull/51
• Only test Python 3.11 during CI by @nanophyto in https://github.com/nanophyto/Abil/pull/85
• add local tests by @nanophyto in https://github.com/nanophyto/Abil/pull/84
• add monthly_integration by @nicola-wiseman in https://github.com/nanophyto/Abil/pull/83
• update post.py use xarray for merge_env by @nicola-wiseman in https://github.com/nanophyto/Abil/pull/86
• merge wiseman2024_updates by @nicola-wiseman in https://github.com/nanophyto/Abil/pull/88
• add pre.py by @nicola-wiseman in https://github.com/nanophyto/Abil/pull/90
• Cross val errors by @nanophyto in https://github.com/nanophyto/Abil/pull/93
• Revert "Cross val errors" by @nanophyto in https://github.com/nanophyto/Abil/pull/96
• Revert "Cross val errors" by @nanophyto in https://github.com/nanophyto/Abil/pull/97
• add raw env_data preprocessing by @nicola-wiseman in https://github.com/nanophyto/Abil/pull/100
• Wiseman2024 updates by @nicola-wiseman in https://github.com/nanophyto/Abil/pull/101
• merge main updates by @nicola-wiseman in https://github.com/nanophyto/Abil/pull/107
• Wiseman2024 updates by @nicola-wiseman in https://github.com/nanophyto/Abil/pull/108
• 104 update mld in env data by @nicola-wiseman in https://github.com/nanophyto/Abil/pull/109
• update with main by @nicola-wiseman in https://github.com/nanophyto/Abil/pull/110
• Remove classifiers by @nanophyto in https://github.com/nanophyto/Abil/pull/114
• Remove package build by @nanophyto in https://github.com/nanophyto/Abil/pull/115
• add yml export to post init by @nicola-wiseman in https://github.com/nanophyto/Abil/pull/116
• remove tau by @nicola-wiseman in https://github.com/nanophyto/Abil/pull/118
• Remove mapie by @nanophyto in https://github.com/nanophyto/Abil/pull/117
• Update docs branch with latest main changes by @nanophyto in https://github.com/nanophyto/Abil/pull/120
• replace np.arraysplit with indices call and then create dfsections … by @nicola-wiseman in https://github.com/nanophyto/Abil/pull/121
• 47 scikit bio is broken by @nicola-wiseman in https://github.com/nanophyto/Abil/pull/122
• 111 non posix path support by @nicola-wiseman in https://github.com/nanophyto/Abil/pull/124
• avoid d.rename(inplace=True) by @nicola-wiseman in https://github.com/nanophyto/Abil/pull/130
• update yml to have more reasonable rf clf hyperparams by @nanophyto in https://github.com/nanophyto/Abil/pull/132
• update yml to have more reasonable rf clf hyperparams (#132) by @nicola-wiseman in https://github.com/nanophyto/Abil/pull/134
• 131 hyperparameter values not exported correctly by @nicola-wiseman in https://github.com/nanophyto/Abil/pull/135
• 129 mtrain refractor by @nicola-wiseman in https://github.com/nanophyto/Abil/pull/138
• remove MLP support by @nicola-wiseman in https://github.com/nanophyto/Abil/pull/139
• Remove hpc arg by @nanophyto in https://github.com/nanophyto/Abil/pull/142
• Refactor merge param and merge performance by @nanophyto in https://github.com/nanophyto/Abil/pull/144
• add refactor changes to docstrings branch by @nicola-wiseman in https://github.com/nanophyto/Abil/pull/145
• 137 update docstrings by @nicola-wiseman in https://github.com/nanophyto/Abil/pull/148
• Merge main to wiseman2024_updates by @nicola-wiseman in https://github.com/nanophyto/Abil/pull/149
• Wiseman2024 updates by @nicola-wiseman in https://github.com/nanophyto/Abil/pull/150
• Fix predictions issue by @nanophyto in https://github.com/nanophyto/Abil/pull/153
• Fix predictions issue in devries2024 branch by @nanophyto in https://github.com/nanophyto/Abil/pull/155
• adds datatype argument to post by @nanophyto in https://github.com/nanophyto/Abil/pull/158
• main updates -> devries2024 branch by @nanophyto in https://github.com/nanophyto/Abil/pull/159
• Fix dist exclude by @nanophyto in https://github.com/nanophyto/Abil/pull/160
• new main updates -> devries2024 by @nanophyto in https://github.com/nanophyto/Abil/pull/162
• Remove verbose hyperparam specs by @nanophyto in https://github.com/nanophyto/Abil/pull/164
• updates by @nanophyto in https://github.com/nanophyto/Abil/pull/165
• post updates by @nanophyto in https://github.com/nanophyto/Abil/pull/166
• improve upsampling such that the presences are not randomly replaced by @nanophyto in https://github.com/nanophyto/Abil/pull/167
• 137 update docstrings by @nicola-wiseman in https://github.com/nanophyto/Abil/pull/172
• Add initial version of docs by @nanophyto in https://github.com/nanophyto/Abil/pull/175
• Revert "Add initial version of docs" by @nanophyto in https://github.com/nanophyto/Abil/pull/176
• Add the area of applicability estimation by @ljwolf in https://github.com/nanophyto/Abil/pull/170
• Using XGBoost trees for summary stats by @nanophyto in https://github.com/nanophyto/Abil/pull/105

Full Changelog: https://github.com/nanophyto/Abil/compare/v.0.0.10...v25.02.17

- Python
Published by ljwolf over 1 year ago

Abil: A Python package for the interpolation of aquatic biogeochemical datasets - v0.0.10

Fixes a MAPIE dependency

- Python
Published by nanophyto over 1 year ago

Abil: A Python package for the interpolation of aquatic biogeochemical datasets - v0.0.9

New version now support parallel prediction.

Other features:

• 2-phase zero-inflated models
• Model prediction intervals (MAPIE)
• Presence/Absence and continuous data
• Random Forest, XGBoost, Bagged KNN, and MultiLayer Perceptrons
• Automatic feature scaling and one-hot-encoding
• Hyperparameter tuning and cross-validation
• SLURM and Singularity scripts

- Python
Published by nanophyto about 2 years ago