Release v1.0.0a8 January 2025

What's Changed

• 681 setup skipped improperly by @sallymatson in #682
• Csvxlsx file reader by @sallymatson in #664
• Bump the production-dependencies group with 2 updates by @dependabot in #683
• Bump the development-dependencies group with 2 updates by @dependabot in #684
• Bump abatilo/actions-poetry from 3.0.2 to 4.0.0 by @dependabot in #685
• [pre-commit.ci] pre-commit autoupdate by @pre-commit-ci in #689
• Windows specific getting started instructions by @jacobcook1995 in #678
• Update package version ready for 0.1.1 alpha release 8 by @jacobcook1995 in #691

Full Changelog: v0.1.1a7_2025_02_15...v0.1.1a8_2025_01_21

Release v1.0.0a7 January 2025

What's Changed

• Bump abatilo/actions-poetry from 2.3.0 to 3.0.0 by @dependabot in #555
• Bump pytest-cov from 3.0.0 to 5.0.0 by @dependabot in #557
• Bump actions/upload-artifact from 3 to 4 by @dependabot in #554
• Add animal consumption of litter by @jacobcook1995 in #566
• Bump jupyterlab from 4.2.3 to 4.2.5 by @dependabot in #560
• [pre-commit.ci] pre-commit autoupdate by @pre-commit-ci in #542
• Add waste from herbivore mechanical inefficiencies to the litter by @jacobcook1995 in #577
• Bump pint from 0.24.1 to 0.24.3 by @dependabot in #571
• Bump ipython from 8.26.0 to 8.27.0 by @dependabot in #572
• Bump types-jsonschema from 4.22.0.20240610 to 4.23.0.20240813 by @dependabot in #573
• Updating example data formats to consistent NetCDF4 by @davidorme in #586
• [pre-commit.ci] pre-commit autoupdate by @pre-commit-ci in #576
• Execution order based on variables by @dalonsoa in #548
• Added automerge github workflow by @jacobcook1995 in #584
• Bump autodocsumm from 0.2.12 to 0.2.13 by @dependabot in #574
• Stop bots from running codecov upload step in CI by @davidorme in #590
• Bump tqdm from 4.66.4 to 4.66.5 by @dependabot in #580
• Bump mypy from 1.10.1 to 1.11.2 by @dependabot in #579
• Bump ipykernel from 6.29.4 to 6.29.5 by @dependabot in #578
• Added handling of herbivory waste products to the litter model by @jacobcook1995 in #583
• Bump tomli from 2.0.1 to 2.0.2 by @dependabot in #594
• Bump pre-commit from 3.8.0 to 4.0.1 by @dependabot in #595
• Bump matplotlib from 3.9.0 to 3.9.2 by @dependabot in #597
• Bump sphinx-rtd-theme from 2.0.0 to 3.0.1 by @dependabot in #598
• Bump ipython from 8.27.0 to 8.28.0 by @dependabot in #596
• Try and group dependabot PRs by @davidorme in #592
• Bump dask from 2023.12.1 to 2024.9.1 in the production-dependencies group by @dependabot in #599
• Bump pytest from 7.4.4 to 8.3.3 by @dependabot in #575
• Bump sphinxcontrib-mermaid from 0.9.2 to 1.0.0 by @dependabot in #601
• Bump mdformat-frontmatter from 0.4.1 to 2.0.8 in the development-dependencies group across 1 directory by @dependabot in #603
• Bump sphinx from 7.4.7 to 8.1.3 by @dependabot in #602
• Revert "Bump sphinx from 7.4.7 to 8.1.3" by @davidorme in #604
• Adding jupytext to pre commit to apply black to myst notebook code by @davidorme in #607
• Bump dask from 2024.9.1 to 2024.10.0 in the production-dependencies group by @dependabot in #608
• Bump sphinx from 7.4.7 to 8.1.3 by @dependabot in #610
• Bump the development-dependencies group with 2 updates by @dependabot in #609
• Revert "Bump sphinx from 7.4.7 to 8.1.3" by @davidorme in #611
• Litter model theory and implementation docs by @jacobcook1995 in #593
• Bump the production-dependencies group with 2 updates by @dependabot in #613
• Bump the development-dependencies group with 4 updates by @dependabot in #614
• Bump abatilo/actions-poetry from 3.0.0 to 3.0.1 by @dependabot in #617
• Bump the production-dependencies group with 2 updates by @dependabot in #618
• Bump the development-dependencies group with 3 updates by @dependabot in #619
• Adding nitrogen mineralisation by @jacobcook1995 in #616
• Bump the production-dependencies group with 3 updates by @dependabot in #620
• Bump hypothesis from 6.116.0 to 6.118.4 in the development-dependencies group by @dependabot in #621
• Bump the production-dependencies group with 2 updates by @dependabot in #622
• Bump sphinx-rtd-theme from 3.0.1 to 3.0.2 in the sphinx group by @dependabot in #624
• Bump the development-dependencies group with 2 updates by @dependabot in #623
• Bump codecov/codecov-action from 4 to 5 by @dependabot in #625
• Bump xarray from 2024.10.0 to 2024.11.0 in the production-dependencies group by @dependabot in #626
• Bump the development-dependencies group with 3 updates by @dependabot in #627
• Bump the production-dependencies group with 2 updates by @dependabot in #629
• Bump the development-dependencies group with 3 updates by @dependabot in #630
• Animal - Feature/multi grid no community by @TaranRallings in #538
• Animal - Feature/multi grid occupancy by @TaranRallings in #530
• Added nitrogen limitation for microbial growth by @jacobcook1995 in #628
• Bump dask from 2024.11.2 to 2024.12.0 in the production-dependencies group by @dependabot in #632
• Bump the development-dependencies group with 4 updates by @dependabot in #633
• Animal docs update by @TaranRallings in #634
• Adds support for static models by @dalonsoa in #373
• Bump numpy from 2.1.3 to 2.2.0 in the production-dependencies group by @dependabot in #639
• Bump the development-dependencies group with 3 updates by @dependabot in #640
• Revert "Bump numpy from 2.1.3 to 2.2.0 in the production-dependencies group" by @davidorme in #641
• Adding pyrealm by @davidorme in #638
• [pre-commit.ci] pre-commit autoupdate by @pre-commit-ci in #612
• 642 abiotic simple model add simple wind profile by @vgro in #643
• Bump dask from 2024.12.0 to 2024.12.1 in the production-dependencies group by @dependabot in #644
• [pre-commit.ci] pre-commit autoupdate by @pre-commit-ci in #646
• Bump the development-dependencies group across 1 directory with 7 updates by @dependabot in #647
• Bump the production-dependencies group with 2 updates by @dependabot in #650
• Bump mypy from 1.14.0 to 1.14.1 in the development-dependencies group by @dependabot in #651
• Bump abatilo/actions-poetry from 3.0.1 to 4.0.0 by @depend...

Release v1.0.0a6 September 2024

What's Changed

• Release branch 0.1.1a5 by @jacobcook1995 in #550
• Add phosphorus to litter model by @jacobcook1995 in #539
• Improving how excrement and carcass decay is handled by @jacobcook1995 in #562
• Update tutorial documentation to mention need to delete old files by @jacobcook1995 in #551
• Bump xarray from 2024.6.0 to 2024.9.0 by @dependabot in #565
• Bump mdformat-tables from 0.4.1 to 1.0.0 by @dependabot in #558
• Bump pre-commit/action from 3.0.0 to 3.0.1 by @dependabot in #552
• Bump softprops/action-gh-release from 1 to 2 by @dependabot in #553
• Bump hypothesis from 6.104.1 to 6.112.1 by @dependabot in #564
• Bump version number for September 2024 develop release by @davidorme in #569

New Contributors

• @dependabot made their first contribution in #565

Full Changelog: v0.1.1a5...v0.1.1a6_2024_09_24

Release v0.1.1 alpha 5

What's Changed

• Feature/abiotic tools by @vgro in #340
• Feature/wind profiles by @vgro in #350
• Feature/energy balance init by @vgro in #357
• Feature/initialise for first timestep by @vgro in #362
• Feature/soil absorption by @vgro in #377
• Adding new BaseModel structure into the abiotic model. by @davidorme in #382
• Feature/use abiotic tools by @vgro in #386
• Publish version 0.1.0a0 by @davidorme in #401
• Fixing up PyPI issues in 0.1.0a0 by @davidorme in #404
• Feature/calculate conductivities by @vgro in #406
• Set up new trusted publication workflow by @davidorme in #408
• np.mean error fixed by @vgro in #414
• Feature/animal module - The Madingley Foraging Update by @TaranRallings in #410
• [pre-commit.ci] pre-commit autoupdate by @pre-commit-ci in #409
• Feature - Feeding Animals into Data by @TaranRallings in #415
• Soil moisture units to mm in data object by @vgro in #420
• Feature/revised wind model by @vgro in #418
• Feature/juvenile dispersal - Adding juvenile dispersal to the Animal Module by @TaranRallings in #419
• Adding non-predation mortality and semelparity to the Animal Module. by @TaranRallings in #422
• Feature/add radiation input by @vgro in #423
• Feature/test ragged arrays by @vgro in #424
• [pre-commit.ci] pre-commit autoupdate by @pre-commit-ci in #417
• Add the demo run to the website pages by @davidorme in #428
• Simplify the jupyter kernelspec setup by @davidorme in #429
• Feature/fixes for variables pr by @vgro in #430
• Update QA tool chain and add Python 3.12 by @davidorme in #433
• 434 soil temperature not returned correctly by @vgro in #435
• Rename 'animals' model to 'animal' by @davidorme in #439
• [pre-commit.ci] pre-commit autoupdate by @pre-commit-ci in #440
• Variables 1 vgro by @vgro in #431
• Fixing Hydrology model to work with LayerStructure by @davidorme in #445
• LayerStructure updates for abiotic_simple by @davidorme in #448
• Indirect development in animals by @TaranRallings in #450
• Initial draft of abiotic model changes for new LayerStructure by @davidorme in #449
• Amending vertical layer structure by @davidorme in #441
• Update PULL_REQUEST_TEMPLATE.md by @vgro in #456
• Turning on single-threaded handling in dask by @davidorme in #457
• [pre-commit.ci] pre-commit autoupdate by @pre-commit-ci in #443
• Add more functionality into LayerStructure. by @davidorme in #452
• Revised animal excretion by @TaranRallings in #460
• Setup for the documentation review by @davidorme in #455
• Updated TODOs across animal module code. by @TaranRallings in #475
• abiotic and hydrology models overview updated by @vgro in #476
• [pre-commit.ci] pre-commit autoupdate by @pre-commit-ci in #478
• Adopt extended LayerStructure functionality by @davidorme in #459
• Adding a microbial necromass pool by @jacobcook1995 in #477
• Removed a handful of now defunct constants and methods. by @TaranRallings in #482
• Update ve theory by @vgro in #481
• Updating to numpy 2.0.0 by @davidorme in #454
• Animal model description in module_overview.md by @TaranRallings in #497
• [pre-commit.ci] pre-commit autoupdate by @pre-commit-ci in #503
• Landing page links by @davidorme in #502
• Add abiotic documentation by @vgro in #500
• reference links added by @vgro in #505
• Update contributor docs by @davidorme in #499
• 507 add more theory to the theory by @vgro in #508
• 506 implementation of abiotic simple model docs by @vgro in #515
• Add variables setup by @dalonsoa in #388
• Direct input from plant model to the litter model by @jacobcook1995 in #509
• Review the implementation section of the docs by @davidorme in #516
• [pre-commit.ci] pre-commit autoupdate by @pre-commit-ci in #520
• 519 review abiotic simple and hydrology docstrings to match updated documentation by @vgro in #521
• 490 hydrology docs on implementation by @vgro in #518
• abiotic model preliminary implementation by @vgro in #523
• climate recipes deleted and note on pre-processing in implementation by @vgro in #526
• 532 litter model should average abiotic quantities over relevant soil layers by @jacobcook1995 in #534
• [pre-commit.ci] pre-commit autoupdate by @pre-commit-ci in #527
• Added tracking of litter nitrogen by @jacobcook1995 in #531
• [pre-commit.ci] pre-commit autoupdate by @pre-commit-ci in #537
• Move setup step to init in Abiotic and AbioticSimple models by @dalonsoa in #524
• Release branch 0.1.1a5 by @jacobcook1995 in #550

Full Changelog: test_publish2...v0.1.1a5

Test Publish 2

test_publish2

Hopefully only one release job, hopefully codecov gets the token

Test

test_publish

Broken pyproject.toml - no idea how

First pre-alpha release

This is a first pre-alpha release of the virtual-ecosystem package. The patch and alpha component of the version number reflect changes to the codebase from the first PR to the release branch main to get the PyPI details set up correctly and displaying nicely.

What's Changed

Basically everything, since this is the first release.

• Updated notes on Jupyter notebook settings. Fixes #6 by @davidorme in #8
• Added details required to setup git flow by @jacobcook1995 in #7
• Changing to DavidAnson/markdownlint with igorshubovych/markdownlint-cli by @davidorme in #14
• Feature/sphinx setup and tidy by @davidorme in #15
• Merging file structure change into soil docs feature branch by @jacobcook1995 in #16
• Feature/soil docs by @jacobcook1995 in #17
• Create CODE_OF_CONDUCT.md by @TaranRallings in #40
• Update issue templates by @vgro in #38
• Fixing broken links and typos in README. Closes #35 by @davidorme in #41
• Added a dependabout config by @davidorme in #45
• Fixing outstanding pre-commit issues, mostly markdown. by @davidorme in #47
• Pointing pytest at the test directory only by @davidorme in #48
• Add VS code settings.json file by @alexdewar in #42
• add CI system by @robewers01 in #43
• Adds a PULL_REQUEST_TEMPLATE and accompanying CHANGELOG file by @TaranRallings in #46
• Delete check-links.yml by @dalonsoa in #50
• Added a first draft of CONTRIBUTING.md by @davidorme in #44
• Getting rid of the check links by @dalonsoa in #54
• added export_geojson docstring by @TaranRallings in #55
• Moved _feature function to top level by @robewers01 in #51
• Update ci.yml by @robewers01 in #56
• Add flake8-docstrings by @dalonsoa in #52
• Fix coverage report by @dalonsoa in #53
• Update pre-commit hooks by @github-actions in #57
• [pre-commit.ci] pre-commit autoupdate by @pre-commit-ci in #58
• Core test by @vgro in #59
• Update pre-commit hooks by @github-actions in #62
• Feature/ci 3.9 by @jacobcook1995 in #67
• Adding design notes on core data setup and configuration by @davidorme in #65
• [pre-commit.ci] pre-commit autoupdate by @pre-commit-ci in #72
• Removed no longer necessary pre-commit update workflow by @jacobcook1995 in #73
• Restructure of grid creation code by @davidorme in #69
• Feature/extend ci by @davidorme in #76
• Basic config system by @jacobcook1995 in #78
• [pre-commit.ci] pre-commit autoupdate by @pre-commit-ci in #81
• [pre-commit.ci] pre-commit autoupdate by @pre-commit-ci in #82
• Strict requirement for type hinting by @jacobcook1995 in #83
• Fixed mutable default argument problem by @jacobcook1995 in #86
• Feature/strict optional by @jacobcook1995 in #89
• Feature/version fixup by @davidorme in #92
• Getting the docs building on ReadTheDocs by @davidorme in #94
• Updated grid implementation by @davidorme in #84
• Feature/default config by @jacobcook1995 in #93
• Create LICENSE by @robewers01 in #109
• Basic definition and initialisation of models by @jacobcook1995 in #106
• Update to CI by @jacobcook1995 in #110
• [pre-commit.ci] pre-commit autoupdate by @pre-commit-ci in #114
• Draft high level function to setup and run simulation by @jacobcook1995 in #112
• Update README.md by @dalonsoa in #111
• [pre-commit.ci] pre-commit autoupdate by @pre-commit-ci in #118
• Bug/fix rtd yaml by @davidorme in #119
• updated abiotic module summary by @vgro in #120
• Improved module docstrings by @jacobcook1995 in #115
• Added basic entry point by @jacobcook1995 in #117
• [pre-commit.ci] pre-commit autoupdate by @pre-commit-ci in #123
• Main timing loop by @jacobcook1995 in #121
• Command line documentation by @jacobcook1995 in #127
• Converted Data from UserDict to thin wrapper around xarray.Dataset by @davidorme in #131
• [pre-commit.ci] pre-commit autoupdate by @pre-commit-ci in #132
• Update to axis validation in data system by @davidorme in #133
• [pre-commit.ci] pre-commit autoupdate by @pre-commit-ci in #137
• [pre-commit.ci] pre-commit autoupdate by @pre-commit-ci in #138
• data_preprocessing ERA5 and CDS examples by @vgro in #139
• [pre-commit.ci] pre-commit autoupdate by @pre-commit-ci in #141
• Added xarray dataset accessor to record axis validation by @davidorme in #136
• Solve issue with documentation not rendering properly by @dalonsoa in #145
• Unpinning CI python versions as no longer needed by @jacobcook1995 in #146
• Patch to fix isort issue in pre-commit by @davidorme in #156
• First draft of the data loading system by @davidorme in #122
• How to set up new model documentation by @jacobcook1995 in #152
• Updated documentation notes and example docstring style by @davidorme in #157
• Update API docstrings and automodule structure by @davidorme in #159
• Removing log_and_raise by @davidorme in #158
• Minimal carbon pool model by @jacobcook1995 in #134
• First draft of supplementary classes for dummy_animal_module by @TaranRallings in #153
• Feature/abiotic model by @vgro in #165
• [pre-commit.ci] pre-commit autoupdate by @pre-commit-ci in #164
• Remove unnecessary critical messages in model.py scripts by @jacobcook1995 in https:/...