2.0.0

This is the 2.0.0 release of pyrealm - this release has moved to trunk-based development from develop. Some previous releases (including the last stable release of 1.0.0) were made using git flow releases from main.

What's Changed

• Soil moisture stress factors by David Orme (@davidorme) in #67
• Documentation updates for new soil moisture by David Orme (@davidorme) in #68
• Version 0.10.0 release by David Orme (@davidorme) in #73
• Merge 0.10.0 release branch back into develop by David Orme (@davidorme) in #74
• Handling np.nan in pyrealm.pmodel.subdaily.memory_effect by David Orme (@davidorme) in #78
• Release 0.10.1 by David Orme (@davidorme) in #79
• Merge release/0.10.1 back into develop. by David Orme (@davidorme) in #80
• added license file by Marion (@MarionBWeinzierl) in #86
• Fixing pre-commit issues and updating pre-commit config by David Orme (@davidorme) in #93
• Added draft CITATION.cff by David Orme (@davidorme) in #88
• Improved README and new CONTRIBUTING by David Orme (@davidorme) in #91
• Fix doctests by David Orme (@davidorme) in #92
• Adds minimum example to README by David Orme (@davidorme) in #97
• Update pre-commit hooks by @github-actions[bot] in #99
• Extend python versions covered to include Python 3.11 by David Orme (@davidorme) in #102
• Update pre-commit hooks by @github-actions[bot] in #103
• Update of water density and viscosity functions by David Orme (@davidorme) in #100
• Add docstrings to tests by David Orme (@davidorme) in #104
• Adding coverage reports by David Orme (@davidorme) in #105
• Fixing PR incompatibility pileup. by David Orme (@davidorme) in #106
• Added coverage report output step to GA pytest step by David Orme (@davidorme) in #107
• Update pre-commit hooks by @github-actions[bot] in #109
• 56 check requirements and ensure that these are consistent between pyprojecttoml and poetry by Marion (@MarionBWeinzierl) in #111
• Updated README and code of conduct. by David Orme (@davidorme) in #113
• Update pre-commit hooks by @github-actions[bot] in #114
• Update reference links to use alp style. by David Orme (@davidorme) in #115
• Building out better structured data package of golden outputs and example data. by David Orme (@davidorme) in #108
• Bad syntax in developers.md by David Orme (@davidorme) in #116
• Profiling by Dr Alexander Smith (@a-smith-github) in #85
• Update pre-commit hooks by @github-actions[bot] in #118
• Update pre-commit hooks by @github-actions[bot] in #137
• Split pmodel file by Marion (@MarionBWeinzierl) in #136
• Update pre-commit hooks by @github-actions[bot] in #138
• Update pre-commit hooks by @github-actions[bot] in #148
• Update CONTRIBUTING.md by @tztsai in #146
• Updating the information on generating profiling call graph by Surbhi Goel (@surbhigoel77) in #147
• Split the tests directory into unit and regression by Surbhi Goel (@surbhigoel77) in #151
• Update pre-commit hooks by @github-actions[bot] in #155
• Add profiling to CI workflow by @tztsai in #156
• Update pyproject.toml by @tztsai in #154
• Update pre-commit hooks by @github-actions[bot] in #157
• Create core module by Marion (@MarionBWeinzierl) in #139
• Update pre-commit hooks by @github-actions[bot] in #160
• Add small dataset for profiling by @tztsai in #149
• Implementation of SPLASH 1.0 in pyrealm by David Orme (@davidorme) in #69
• hotfix test_evap.py by @tztsai in #171
• Let flake8 ignore E203 by @tztsai in #176
• Add unit tests for splash by @tztsai in #170
• Draft implementation of new OptimalChi structure by David Orme (@davidorme) in #172
• Update to the latest versions of checkout and setup-python actions by @tztsai in #180
• Fixing missing attribute docstrings in core.calendar by David Orme (@davidorme) in #182
• Profiling of the Splash module by @tztsai in #181
• New subdaily pmodel implementation by David Orme (@davidorme) in #183
• Add code to generate SPLASH golden datasets by David Orme (@davidorme) in #185
• Allowing incomplete days by David Orme (@davidorme) in #194
• Remove outdated FastSlowPModel by David Orme (@davidorme) in #199
• Fix time handling in Splash by @tztsai in #186
• Handle NaNs when calculating max difference in Splash.estimate_initial_soil_moisture by @tztsai in #193
• Use a function eval_poly for polynomial evaluation by @tztsai in #187
• Update profiling/report.py and its documentation by @tztsai in #188
• Setup trusted publishing by David Orme (@davidorme) in #200
• Fix for RTD build environment by David Orme (@davidorme) in #204
• Remove support for Python 3.9 by David Orme (@davidorme) in #202
• Fixing profiling issues by David Orme (@davidorme) in #208
• Fixing profile workflow by David Orme (@davidorme) in #211
• Python version bug in pyrealm_profiling.yaml by David Orme (@davidorme) in #214
• Add unit tests by Surbhi Goel (@surbhigoel77) in #153
• [pre-commit.ci] pre-commit autoupdate by pre-commit.ci (@pre-commit-ci)[bot] in #221
• Switched to pre-commit.ci by David Orme (@davidorme) in #218
• Scaling profiling datasets by David Orme (@davidorme) in #216
• Updating development docs by David Orme (@davidorme) in #212
• [pre-commit.ci] pre-commit autoupdate by pre-commit.ci (@pre-commit-ci)[bot] in #228
• Fixing profiling and comparing profiling implementations by David Orme (@davidorme) in #225
• Baseline data and code for two leaf model by David Orme (@davidorme) in #240
• Simplify the jupyter kernelspec setup by David Orme (@davidorme) in #247
• Rebuild of QA chain using ruff by David Orme (@davidorme) in #220
• [pre-commit.ci] pre-commit autoupdate by pre-commit.ci (@pre-commit-ci)[bot] in #243
• 248 numpy 2 0 migration by James Emberton (@j-emberton) in #251
• Updated module import in pmodel unit tests by Surbhi Goel (@surbhigoel77) in #250
• [pre-commit.ci] pre-commit autoupdate by pre-commit.ci (@pre-commit-ci)[bot] in #249
• Merging release 1.0.0 changes back into develop by David Orme (@davidorme) in #252
• [pre-commit.ci] pre-commit autoupdate by pre-commit.ci (@pre-commit-ci)[bot] in #253
• [pre-commit.ci] pre-commit autoupdate by pre-commit.ci (@pre-commit-ci)[bot] in #260
• Fix copyright date by James Emberton (@j-emberton) in #255
• Updating xarray by David Orme (@davidorme) in #258
• [pre-commit.ci] pre-commit autoupdate by pre-commit.ci (@pre-commit-ci)[bot] in #265
• Allow P Models to accept an array of kphio values by David Orme (@davidorme) in #263
• [pre-commit.ci] pre-commit autoupdate by pre-commit.ci (@pre-commit-ci)[bot] in #268
• [pre-commit.ci] pre-commit autoupdate by pre-commit.ci (@pre-commit-ci)[bot] in #273
• [pre-commit.ci] pre-commit autoupdate by pre-commit.ci (@pre-commit-ci)[bot] in #275
• Initial draft of new quantum yield module by David Orme (@davidorme) in #267
• Implementation of Flora and PlantFunctionalType by David Orme (@davidorme) in #277
• [pre-commit.ci] pre-commit autoupdate by pre-commit.ci (@pre-commit-ci)[bot] in #280
• Implementation of Community object init and factory methods. by David Orme (@davidorme) in #282
• Fixed incorrect yield value in TModelConst and updated regression tests by David Orme (@davidorme) in #283
• Complete implementation of T model functions by David Orme (@davidorme) in #285
• [pre-commit.ci] pre-commit autoupdate by pre-commit.ci (@pre-commit-ci)[bot] in #287
• Replace use of pandas in pyrealm.demography by David Orme (@davidorme) in #292
• Implementation of the canopy model by David Orme (@davidorme) in #288
• Add Flora helper methods by David Orme (@davidorme) in #296
• Revert "Add Flora helper methods" by David Orme (@davidorme) in #299
• Update traits data structures by David Orme (@davidorme) in #300
• Minor updates to T Model functions and testing by David Orme (@davidorme) in #303
• Add StemAllometry class by David Orme (@davidorme) in #306
• Add StemAllocation class by David Orme (@davidorme) in #308
• Update canopy profile branch with stem allocation changes. by David Orme (@davidorme) in #310
• Add CrownProfile class by David Orme (@davidorme) in #311
• [pre-commit.ci] pre-commit autoupdate by pre-commit.ci (@pre-commit-ci)[bot] in #294
• Add user docs demonstrating demography traits and crown properties by David Orme (@davidorme) in #313
• Fix notebook code formatting by David Orme (@davidorme) in #330
• Move pyrealm_build_data documentation into an autodoc style setup by David Orme (@davidorme) in #331
• [pre-commit.ci] pre-commit autoupdate by pre-commit.ci (@pre-commit-ci)[bot] in #320
• Fastslow initval by Surbhi Goel (@surbhigoel77) in #190
• Revise and document functionality of canopy and crown by David Orme (@davidorme) in #328
• Calculate canopy light extinction and interception by David Orme (@davidorme) in #318
• Updating and systematising NDArray typing by David Orme (@davidorme) in #335
• Revise cohort structure inside community by David Orme (@davidorme) in #340
• Group internal attributes in canopy into data classes by David Orme (@davidorme) in #341
• [pre-commit.ci] pre-commit autoupdate by pre-commit.ci (@pre-commit-ci)[bot] in #339
• Shared base classes for demography classes by David Orme (@davidorme) in #338
• 236 develop pyrealmcoresolar function radiation calc library by James Emberton (@j-emberton) in #237
• Fix bug in profiling code and create profiling CI by Marion (@MarionBWeinzierl) in #346
• Review validation and shapes in demography by David Orme (@davidorme) in #342
• [pre-commit.ci] pre-commit autoupdate by pre-commit.ci (@pre-commit-ci)[bot] in #343
• Upgrade upload-artifact version by Marion (@MarionBWeinzierl) in #357
• Manual/semi-automatic performance regression checking by Marion (@MarionBWeinzierl) in #356
• [pre-commit.ci] pre-commit autoupdate by pre-commit.ci (@pre-commit-ci)[bot] in #355
• Adding regression test data for phenology by David Orme (@davidorme) in #360
• Updating mypy in poetry to version 1 by David Orme (@davidorme) in #365
• [pre-commit.ci] pre-commit autoupdate by pre-commit.ci (@pre-commit-ci)[bot] in #363
• Remove outdated T Model module by David Orme (@davidorme) in #370
• Fix pyrealm typo in readme by James Emberton (@j-emberton) in #362
• Add a migration guide by David Orme (@davidorme) in #371
• Add the logo by David Orme (@davidorme) in #373
• Move to 2.0.0 RC 1 by David Orme (@davidorme) in #375
• [pre-commit.ci] pre-commit autoupdate by pre-commit.ci (@pre-commit-ci)[bot] in #377
• Added mm/m2 to moles, tests, fixed docs by David Orme (@davidorme) in #379
• Convert JmaxLimitation to a registry of subclasses by David Orme (@davidorme) in #393
• Fixing formatting in QuantumYieldABC by David Orme (@davidorme) in #398
• Implementation of Arrhenius methods by David Orme (@davidorme) in #389
• [pre-commit.ci] pre-commit autoupdate by pre-commit.ci (@pre-commit-ci)[bot] in #381
• Make summarize_attrs use non-mutable tuple as attrs argument by David Orme (@davidorme) in #404
• Adding convert_water_mm_to_moles and calculate_water_molar_volume by David Orme (@davidorme) in #400
• New BoundsChecker implementation by David Orme (@davidorme) in #409
• [pre-commit.ci] pre-commit autoupdate by pre-commit.ci (@pre-commit-ci)[bot] in #411
• New PModelEnvironment implementation by David Orme (@davidorme) in #412
• [pre-commit.ci] pre-commit autoupdate by pre-commit.ci (@pre-commit-ci)[bot] in #417
• Aligning PModel and Subdaily PModel by David Orme (@davidorme) in #401
• Update poetry to version 2.0 by David Orme (@davidorme) in #421
• Develop the AcclimationModel class by David Orme (@davidorme) in #418
• Actually use the new AcclimationModel by David Orme (@davidorme) in #424
• Update docs to new P Model API by David Orme (@davidorme) in #426
• Removing old PModel implementations by David Orme (@davidorme) in #427
• [pre-commit.ci] pre-commit autoupdate by pre-commit.ci (@pre-commit-ci)[bot] in #428
• Swap pmodel.functions over to use tk as needed by David Orme (@davidorme) in #431
• Update default values for phi0 by David Orme (@davidorme) in #432
• Arrhenius class should have simpler signature and __init__ by David Orme (@davidorme) in #434
• Rework PModelConsts and usage in functions by David Orme (@davidorme) in #435
• [pre-commit.ci] pre-commit autoupdate by pre-commit.ci (@pre-commit-ci)[bot] in #437
• Revise the migration guide and changes doc by David Orme (@davidorme) in #440
• Revise the P Model documentation by David Orme (@davidorme) in #441
• Replacing np.allclose by David Orme (@davidorme) in #382
• [pre-commit.ci] pre-commit autoupdate by pre-commit.ci (@pre-commit-ci)[bot] in #444
• New version of the P Model architecture by David Orme (@davidorme) in #442
• Update two leaf irradiance to V2.0.0 by David Orme (@davidorme) in #445
• Adding two leaf irradience model by James Emberton (@j-emberton) in #245
• [pre-commit.ci] pre-commit autoupdate by pre-commit.ci (@pre-commit-ci)[bot] in #447
• Updated golden dataset for phenology module by David Orme (@davidorme) in #448
• Doc updates for 2.0.0 by David Orme (@davidorme) in #450
• Revise P Model attributes by David Orme (@davidorme) in #452
• [pre-commit.ci] pre-commit autoupdate by pre-commit.ci (@pre-commit-ci)[bot] in #457
• Rework of pyrealm.core.solar and downstream changes. by David Orme (@davidorme) in #456
• Interim experimental markup implementation by David Orme (@davidorme) in #454
• Adding fortnightly model to phenology golden dataset by David Orme (@davidorme) in #465
• 459 review two leaf model by David Orme (@davidorme) in #462
• Adopt changed data and scripts from #448 by Marion (@MarionBWeinzierl) in #460
• [pre-commit.ci] pre-commit autoupdate by pre-commit.ci (@pre-commit-ci)[bot] in #466
• Example usage page for two leaf two stream model by David Orme (@davidorme) in #470
• Marking experimental classes by David Orme (@davidorme) in #473
• Update documentation T model by arne-scheire (@arne-exe) in #472
• Adding plant reproductive tissue respiration and turnover by Sally Matson (@sallymatson) in #461
• Regression tests for FaparLimitation class by Marion (@MarionBWeinzierl) in #443
• [pre-commit.ci] pre-commit autoupdate by pre-commit.ci (@pre-commit-ci)[bot] in #474
• Unpinning numpy 2.2, updating pyproject.toml for 2.0.0-rc.2 by David Orme (@davidorme) in #475
• [pre-commit.ci] pre-commit autoupdate by pre-commit.ci (@pre-commit-ci)[bot] in #477
• Moving potential_gpp calculation outside StemAllocation by David Orme (@davidorme) in #480
• Updating CohortMethods to handle a count attribute in subclasses by David Orme (@davidorme) in #481
• Changes and version bump for 2.0.0-rc.3 by David Orme (@davidorme) in #483
• Implement from_subdailypmodel for FaparLimitation by Marion (@MarionBWeinzierl) in #468
• [pre-commit.ci] pre-commit autoupdate by pre-commit.ci (@pre-commit-ci)[bot] in #484
• Profiling v2.0.0-rc.3 by Sam Avis (@sjavis) in #487
• [pre-commit.ci] pre-commit autoupdate by pre-commit.ci (@pre-commit-ci)[bot] in #489
• 488 profiling docs by Sam Avis (@sjavis) in #491
• Add subdaily check by Marion (@MarionBWeinzierl) in #485
• Improve the annual value calculator by David Orme (@davidorme) in #492
• [pre-commit.ci] pre-commit autoupdate by pre-commit.ci (@pre-commit-ci)[bot] in #493
• [pre-commit.ci] pre-commit autoupdate by pre-commit.ci (@pre-commit-ci)[bot] in #495
• Extend the AnnualValueCalculator by David Orme (@davidorme) in #499
• [pre-commit.ci] pre-commit autoupdate by pre-commit.ci (@pre-commit-ci)[bot] in #500
• Remove syntax warnings by David Orme (@davidorme) in #505
• Annual fAPAR_max and LAI_max by Marion (@MarionBWeinzierl) in #403
• Fixing errors in canopy calculation by David Orme (@davidorme) in #503
• PR 503 - part two. by David Orme (@davidorme) in #515
• Update for release 2.0.0-rc.4 by David Orme (@davidorme) in #517
• Adding community fAPAR to code objects and into docs by David Orme (@davidorme) in #520
• [pre-commit.ci] pre-commit autoupdate by pre-commit.ci (@pre-commit-ci)[bot] in #523
• Adding UUIDs to cohorts by David Orme (@davidorme) in #522
• Fixing behaviour of T Model with zero DBH values by David Orme (@davidorme) in #525
• [pre-commit.ci] pre-commit autoupdate by pre-commit.ci (@pre-commit-ci)[bot] in #528
• Add phenology_const to FaparLimitation method arguments by David Orme (@davidorme) in #529
• Update docstrings in phenology by David Orme (@davidorme) in #530
• Remove unused functions in phenology by David Orme (@davidorme) in #531
• [pre-commit.ci] pre-commit autoupdate by pre-commit.ci (@pre-commit-ci)[bot] in #532
• Getting started for users by Marion (@MarionBWeinzierl) in #518
• Add a glossary by David Orme (@davidorme) in #527
• Extend FaparLimitation to include the $m$ parameter by David Orme (@davidorme) in #533
• [pre-commit.ci] pre-commit autoupdate by pre-commit.ci (@pre-commit-ci)[bot] in #536
• [pre-commit.ci] pre-commit autoupdate by pre-commit.ci (@pre-commit-ci)[bot] in #538
• Broadcastable array inputs by Sam Avis (@sjavis) in #496
• Adopt SPEC0 by David Orme (@davidorme) in #540
• [pre-commit.ci] pre-commit autoupdate by pre-commit.ci (@pre-commit-ci)[bot] in #541
• [pre-commit.ci] pre-commit autoupdate by pre-commit.ci (@pre-commit-ci)[bot] in #544
• [pre-commit.ci] pre-commit autoupdate by pre-commit.ci (@pre-commit-ci)[bot] in #546
• Add array inputs page to documentation by Sam Avis (@sjavis) in #548
• Updating docs to release 2.0.0 by David Orme (@davidorme) in #549

New Contributors

• Marion (@MarionBWeinzierl) made their first contribution in #86
• Dr Alexander Smith (@a-smith-github) made their first contribution in #85
• @tztsai made their first contribution in #146
• Surbhi Goel (@surbhigoel77) made their first contribution in #147
• pre-commit.ci (@pre-commit-ci)[bot] made their first contribution in #221
• James Emberton (@j-emberton) made their first contribution in #251
• arne-scheire (@arne-exe) made their first contribution in #472
• Sally Matson (@sallymatson) made their first contribution in #461
• Sam Avis (@sjavis) made their first contribution in #487

Full Changelog: 0.9.0...v2.0.0