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 https://github.com/ImperialCollegeLondon/virtual_ecosystem/pull/8
* Added details required to setup git flow by jacobcook1995 in https://github.com/ImperialCollegeLondon/virtual_ecosystem/pull/7
* Changing to DavidAnson/markdownlint with igorshubovych/markdownlint-cli by davidorme in https://github.com/ImperialCollegeLondon/virtual_ecosystem/pull/14
* Feature/sphinx setup and tidy by davidorme in https://github.com/ImperialCollegeLondon/virtual_ecosystem/pull/15
* Merging file structure change into soil docs feature branch by jacobcook1995 in https://github.com/ImperialCollegeLondon/virtual_ecosystem/pull/16
* Feature/soil docs by jacobcook1995 in https://github.com/ImperialCollegeLondon/virtual_ecosystem/pull/17
* Create CODE_OF_CONDUCT.md by TaranRallings in https://github.com/ImperialCollegeLondon/virtual_ecosystem/pull/40
* Update issue templates by vgro in https://github.com/ImperialCollegeLondon/virtual_ecosystem/pull/38
* Fixing broken links and typos in README. Closes 35 by davidorme in https://github.com/ImperialCollegeLondon/virtual_ecosystem/pull/41
* Added a dependabout config by davidorme in https://github.com/ImperialCollegeLondon/virtual_ecosystem/pull/45
* Fixing outstanding pre-commit issues, mostly markdown. by davidorme in https://github.com/ImperialCollegeLondon/virtual_ecosystem/pull/47
* Pointing pytest at the test directory only by davidorme in https://github.com/ImperialCollegeLondon/virtual_ecosystem/pull/48
* Add VS code settings.json file by alexdewar in https://github.com/ImperialCollegeLondon/virtual_ecosystem/pull/42
* add CI system by robewers01 in https://github.com/ImperialCollegeLondon/virtual_ecosystem/pull/43
* Adds a PULL_REQUEST_TEMPLATE and accompanying CHANGELOG file by TaranRallings in https://github.com/ImperialCollegeLondon/virtual_ecosystem/pull/46
* Delete check-links.yml by dalonsoa in https://github.com/ImperialCollegeLondon/virtual_ecosystem/pull/50
* Added a first draft of CONTRIBUTING.md by davidorme in https://github.com/ImperialCollegeLondon/virtual_ecosystem/pull/44
* Getting rid of the check links by dalonsoa in https://github.com/ImperialCollegeLondon/virtual_ecosystem/pull/54
* added export_geojson docstring by TaranRallings in https://github.com/ImperialCollegeLondon/virtual_ecosystem/pull/55
* Moved _feature function to top level by robewers01 in https://github.com/ImperialCollegeLondon/virtual_ecosystem/pull/51
* Update ci.yml by robewers01 in https://github.com/ImperialCollegeLondon/virtual_ecosystem/pull/56
* Add flake8-docstrings by dalonsoa in https://github.com/ImperialCollegeLondon/virtual_ecosystem/pull/52
* Fix coverage report by dalonsoa in https://github.com/ImperialCollegeLondon/virtual_ecosystem/pull/53
* Update pre-commit hooks by github-actions in https://github.com/ImperialCollegeLondon/virtual_ecosystem/pull/57
* [pre-commit.ci] pre-commit autoupdate by pre-commit-ci in https://github.com/ImperialCollegeLondon/virtual_ecosystem/pull/58
* Core test by vgro in https://github.com/ImperialCollegeLondon/virtual_ecosystem/pull/59
* Update pre-commit hooks by github-actions in https://github.com/ImperialCollegeLondon/virtual_ecosystem/pull/62
* Feature/ci 3.9 by jacobcook1995 in https://github.com/ImperialCollegeLondon/virtual_ecosystem/pull/67
* Adding design notes on core data setup and configuration by davidorme in https://github.com/ImperialCollegeLondon/virtual_ecosystem/pull/65
* [pre-commit.ci] pre-commit autoupdate by pre-commit-ci in https://github.com/ImperialCollegeLondon/virtual_ecosystem/pull/72
* Removed no longer necessary pre-commit update workflow by jacobcook1995 in https://github.com/ImperialCollegeLondon/virtual_ecosystem/pull/73
* Restructure of grid creation code by davidorme in https://github.com/ImperialCollegeLondon/virtual_ecosystem/pull/69
* Feature/extend ci by davidorme in https://github.com/ImperialCollegeLondon/virtual_ecosystem/pull/76
* Basic config system by jacobcook1995 in https://github.com/ImperialCollegeLondon/virtual_ecosystem/pull/78
* [pre-commit.ci] pre-commit autoupdate by pre-commit-ci in https://github.com/ImperialCollegeLondon/virtual_ecosystem/pull/81
* [pre-commit.ci] pre-commit autoupdate by pre-commit-ci in https://github.com/ImperialCollegeLondon/virtual_ecosystem/pull/82
* Strict requirement for type hinting by jacobcook1995 in https://github.com/ImperialCollegeLondon/virtual_ecosystem/pull/83
* Fixed mutable default argument problem by jacobcook1995 in https://github.com/ImperialCollegeLondon/virtual_ecosystem/pull/86
* Feature/strict optional by jacobcook1995 in https://github.com/ImperialCollegeLondon/virtual_ecosystem/pull/89
* Feature/version fixup by davidorme in https://github.com/ImperialCollegeLondon/virtual_ecosystem/pull/92
* Getting the docs building on ReadTheDocs by davidorme in https://github.com/ImperialCollegeLondon/virtual_ecosystem/pull/94
* Updated grid implementation by davidorme in https://github.com/ImperialCollegeLondon/virtual_ecosystem/pull/84
* Feature/default config by jacobcook1995 in https://github.com/ImperialCollegeLondon/virtual_ecosystem/pull/93
* Create LICENSE by robewers01 in https://github.com/ImperialCollegeLondon/virtual_ecosystem/pull/109
* Basic definition and initialisation of models by jacobcook1995 in https://github.com/ImperialCollegeLondon/virtual_ecosystem/pull/106
* Update to CI by jacobcook1995 in https://github.com/ImperialCollegeLondon/virtual_ecosystem/pull/110
* [pre-commit.ci] pre-commit autoupdate by pre-commit-ci in https://github.com/ImperialCollegeLondon/virtual_ecosystem/pull/114
* Draft high level function to setup and run simulation by jacobcook1995 in https://github.com/ImperialCollegeLondon/virtual_ecosystem/pull/112
* Update README.md by dalonsoa in https://github.com/ImperialCollegeLondon/virtual_ecosystem/pull/111
* [pre-commit.ci] pre-commit autoupdate by pre-commit-ci in https://github.com/ImperialCollegeLondon/virtual_ecosystem/pull/118
* Bug/fix rtd yaml by davidorme in https://github.com/ImperialCollegeLondon/virtual_ecosystem/pull/119
* updated abiotic module summary by vgro in https://github.com/ImperialCollegeLondon/virtual_ecosystem/pull/120
* Improved module docstrings by jacobcook1995 in https://github.com/ImperialCollegeLondon/virtual_ecosystem/pull/115
* Added basic entry point by jacobcook1995 in https://github.com/ImperialCollegeLondon/virtual_ecosystem/pull/117
* [pre-commit.ci] pre-commit autoupdate by pre-commit-ci in https://github.com/ImperialCollegeLondon/virtual_ecosystem/pull/123
* Main timing loop by jacobcook1995 in https://github.com/ImperialCollegeLondon/virtual_ecosystem/pull/121
* Command line documentation by jacobcook1995 in https://github.com/ImperialCollegeLondon/virtual_ecosystem/pull/127
* Converted Data from UserDict to thin wrapper around xarray.Dataset by davidorme in https://github.com/ImperialCollegeLondon/virtual_ecosystem/pull/131
* [pre-commit.ci] pre-commit autoupdate by pre-commit-ci in https://github.com/ImperialCollegeLondon/virtual_ecosystem/pull/132
* Update to axis validation in data system by davidorme in https://github.com/ImperialCollegeLondon/virtual_ecosystem/pull/133
* [pre-commit.ci] pre-commit autoupdate by pre-commit-ci in https://github.com/ImperialCollegeLondon/virtual_ecosystem/pull/137
* [pre-commit.ci] pre-commit autoupdate by pre-commit-ci in https://github.com/ImperialCollegeLondon/virtual_ecosystem/pull/138
* data_preprocessing ERA5 and CDS examples by vgro in https://github.com/ImperialCollegeLondon/virtual_ecosystem/pull/139
* [pre-commit.ci] pre-commit autoupdate by pre-commit-ci in https://github.com/ImperialCollegeLondon/virtual_ecosystem/pull/141
* Added xarray dataset accessor to record axis validation by davidorme in https://github.com/ImperialCollegeLondon/virtual_ecosystem/pull/136
* Solve issue with documentation not rendering properly by dalonsoa in https://github.com/ImperialCollegeLondon/virtual_ecosystem/pull/145
* Unpinning CI python versions as no longer needed by jacobcook1995 in https://github.com/ImperialCollegeLondon/virtual_ecosystem/pull/146
* Patch to fix `isort` issue in `pre-commit` by davidorme in https://github.com/ImperialCollegeLondon/virtual_ecosystem/pull/156
* First draft of the data loading system by davidorme in https://github.com/ImperialCollegeLondon/virtual_ecosystem/pull/122
* How to set up new model documentation by jacobcook1995 in https://github.com/ImperialCollegeLondon/virtual_ecosystem/pull/152
* Updated documentation notes and example docstring style by davidorme in https://github.com/ImperialCollegeLondon/virtual_ecosystem/pull/157
* Update API docstrings and automodule structure by davidorme in https://github.com/ImperialCollegeLondon/virtual_ecosystem/pull/159
* Removing `log_and_raise` by davidorme in https://github.com/ImperialCollegeLondon/virtual_ecosystem/pull/158
* Minimal carbon pool model by jacobcook1995 in https://github.com/ImperialCollegeLondon/virtual_ecosystem/pull/134
* First draft of supplementary classes for dummy_animal_module by TaranRallings in https://github.com/ImperialCollegeLondon/virtual_ecosystem/pull/153
* Feature/abiotic model by vgro in https://github.com/ImperialCollegeLondon/virtual_ecosystem/pull/165
* [pre-commit.ci] pre-commit autoupdate by pre-commit-ci in https://github.com/ImperialCollegeLondon/virtual_ecosystem/pull/164
* Remove unnecessary critical messages in model.py scripts by jacobcook1995 in https://github.com/ImperialCollegeLondon/virtual_ecosystem/pull/169
* Fixes the `precommit` issue with `mypy` dependencies by davidorme in https://github.com/ImperialCollegeLondon/virtual_ecosystem/pull/175
* Feature/split testing by jacobcook1995 in https://github.com/ImperialCollegeLondon/virtual_ecosystem/pull/174
* API links updated to new model names by vgro in https://github.com/ImperialCollegeLondon/virtual_ecosystem/pull/177
* Feature/radiation dummy 2 by vgro in https://github.com/ImperialCollegeLondon/virtual_ecosystem/pull/179
* Feature/model autodiscovery by davidorme in https://github.com/ImperialCollegeLondon/virtual_ecosystem/pull/173
* Added docs build check to the CI by jacobcook1995 in https://github.com/ImperialCollegeLondon/virtual_ecosystem/pull/181
* Feature/dummy animal - AnimalModel by TaranRallings in https://github.com/ImperialCollegeLondon/virtual_ecosystem/pull/171
* Make a `Data` object part of the `BaseModel.__init__` by davidorme in https://github.com/ImperialCollegeLondon/virtual_ecosystem/pull/176
* Switched to using a consistent key format for citations by jacobcook1995 in https://github.com/ImperialCollegeLondon/virtual_ecosystem/pull/184
* Pull already-reviewed changes from feature/animal module into develop. by TaranRallings in https://github.com/ImperialCollegeLondon/virtual_ecosystem/pull/182
* Feature/wind dummy by vgro in https://github.com/ImperialCollegeLondon/virtual_ecosystem/pull/183
* abiotic_tools introduced by vgro in https://github.com/ImperialCollegeLondon/virtual_ecosystem/pull/186
* Feature/animal module - First implementation of AnimalCohort class by TaranRallings in https://github.com/ImperialCollegeLondon/virtual_ecosystem/pull/185
* Change SoilModel to use the data object by jacobcook1995 in https://github.com/ImperialCollegeLondon/virtual_ecosystem/pull/187
* Feature/co2 dummy by vgro in https://github.com/ImperialCollegeLondon/virtual_ecosystem/pull/193
* Added utility function to extract model specific timing details by jacobcook1995 in https://github.com/ImperialCollegeLondon/virtual_ecosystem/pull/189
* Feature/animal module - Basic AnimalCohort functions by TaranRallings in https://github.com/ImperialCollegeLondon/virtual_ecosystem/pull/192
* Numerical integration of the soil module by jacobcook1995 in https://github.com/ImperialCollegeLondon/virtual_ecosystem/pull/191
* Basic data output functionality by jacobcook1995 in https://github.com/ImperialCollegeLondon/virtual_ecosystem/pull/194
* Documentation for main simulation flow by jacobcook1995 in https://github.com/ImperialCollegeLondon/virtual_ecosystem/pull/195
* Remove usage of `pip install codecov` from CI action by jacobcook1995 in https://github.com/ImperialCollegeLondon/virtual_ecosystem/pull/200
* Extend carbon pool from 2 to 3 pools by jacobcook1995 in https://github.com/ImperialCollegeLondon/virtual_ecosystem/pull/206
* Feature/data object toml by vgro in https://github.com/ImperialCollegeLondon/virtual_ecosystem/pull/201
* Update config module to use a class by davidorme in https://github.com/ImperialCollegeLondon/virtual_ecosystem/pull/212
* Factory method for Grid by davidorme in https://github.com/ImperialCollegeLondon/virtual_ecosystem/pull/214
* Feature/update climate data recipe by vgro in https://github.com/ImperialCollegeLondon/virtual_ecosystem/pull/217
* Introduce common update time step and timescale bounds for all models by jacobcook1995 in https://github.com/ImperialCollegeLondon/virtual_ecosystem/pull/211
* Fixs for `pint` problem in docs build action by jacobcook1995 in https://github.com/ImperialCollegeLondon/virtual_ecosystem/pull/218
* Feature/abiotic simple model by vgro in https://github.com/ImperialCollegeLondon/virtual_ecosystem/pull/219
* updated for dummy model and ERA5 land by vgro in https://github.com/ImperialCollegeLondon/virtual_ecosystem/pull/220
* Feature/Animal_Module: Basic dispersal function and tracking of cohort positions on grid. by TaranRallings in https://github.com/ImperialCollegeLondon/virtual_ecosystem/pull/198
* Feature/update module overview by vgro in https://github.com/ImperialCollegeLondon/virtual_ecosystem/pull/224
* Feature/simple regression by vgro in https://github.com/ImperialCollegeLondon/virtual_ecosystem/pull/221
* Updated defaults for core config options to match dummy data by jacobcook1995 in https://github.com/ImperialCollegeLondon/virtual_ecosystem/pull/226
* Use abiotic soil layers correctly in soil model by jacobcook1995 in https://github.com/ImperialCollegeLondon/virtual_ecosystem/pull/225
* Added setup step to main function flow by jacobcook1995 in https://github.com/ImperialCollegeLondon/virtual_ecosystem/pull/227
* Feature/data recipes section by vgro in https://github.com/ImperialCollegeLondon/virtual_ecosystem/pull/228
* Add recipe for generating dummy soil data by jacobcook1995 in https://github.com/ImperialCollegeLondon/virtual_ecosystem/pull/229
* Feature/animal module - Ectothermic metabolism by TaranRallings in https://github.com/ImperialCollegeLondon/virtual_ecosystem/pull/230
* Various bug fixes to allow `vr_run` to work with `soil` and `abiotic_simple` models by jacobcook1995 in https://github.com/ImperialCollegeLondon/virtual_ecosystem/pull/236
* Feature/separate hydrology by vgro in https://github.com/ImperialCollegeLondon/virtual_ecosystem/pull/243
* bugfix log interpolation by vgro in https://github.com/ImperialCollegeLondon/virtual_ecosystem/pull/244
* Forced module order to be fixed based on config input by jacobcook1995 in https://github.com/ImperialCollegeLondon/virtual_ecosystem/pull/245
* Remove soil model specific function to update data object by jacobcook1995 in https://github.com/ImperialCollegeLondon/virtual_ecosystem/pull/246
* Continuous output of the `data` object by jacobcook1995 in https://github.com/ImperialCollegeLondon/virtual_ecosystem/pull/237
* atmosperic pressure unit correction by vgro in https://github.com/ImperialCollegeLondon/virtual_ecosystem/pull/250
* Fix dask warning about saving "layer_roles" as an object by jacobcook1995 in https://github.com/ImperialCollegeLondon/virtual_ecosystem/pull/251
* Updated poetry to latest versions by jacobcook1995 in https://github.com/ImperialCollegeLondon/virtual_ecosystem/pull/252
* Adding a particulate organic matter pool by jacobcook1995 in https://github.com/ImperialCollegeLondon/virtual_ecosystem/pull/253
* Feature/correct dummy climate by vgro in https://github.com/ImperialCollegeLondon/virtual_ecosystem/pull/254
* fix time_index by vgro in https://github.com/ImperialCollegeLondon/virtual_ecosystem/pull/255
* Feature/vertical water flow by vgro in https://github.com/ImperialCollegeLondon/virtual_ecosystem/pull/257
* System to allow constants to be altered based on configuration by jacobcook1995 in https://github.com/ImperialCollegeLondon/virtual_ecosystem/pull/258
* Feature/update hydrology constants by vgro in https://github.com/ImperialCollegeLondon/virtual_ecosystem/pull/260
* Change soil constants to use new system by jacobcook1995 in https://github.com/ImperialCollegeLondon/virtual_ecosystem/pull/261
* Feature/add streamflow by vgro in https://github.com/ImperialCollegeLondon/virtual_ecosystem/pull/262
* soil depth correction by vgro in https://github.com/ImperialCollegeLondon/virtual_ecosystem/pull/263
* Allow setting params with command-line arguments by alexdewar in https://github.com/ImperialCollegeLondon/virtual_ecosystem/pull/267
* Adding a litter model by jacobcook1995 in https://github.com/ImperialCollegeLondon/virtual_ecosystem/pull/268
* Treat paths in config files as relative to config dir by alexdewar in https://github.com/ImperialCollegeLondon/virtual_ecosystem/pull/269
* Add example data by alexdewar in https://github.com/ImperialCollegeLondon/virtual_ecosystem/pull/279
* Fix dependance of some tests on local filesystem by jacobcook1995 in https://github.com/ImperialCollegeLondon/virtual_ecosystem/pull/275
* Connect litter pools to soil pools by jacobcook1995 in https://github.com/ImperialCollegeLondon/virtual_ecosystem/pull/281
* Feature/animal module - Foraging functions by TaranRallings in https://github.com/ImperialCollegeLondon/virtual_ecosystem/pull/248
* Systematise various output file parameters by alexdewar in https://github.com/ImperialCollegeLondon/virtual_ecosystem/pull/280
* Feature/update hydro model by vgro in https://github.com/ImperialCollegeLondon/virtual_ecosystem/pull/283
* Added three more litter pools to litter model by jacobcook1995 in https://github.com/ImperialCollegeLondon/virtual_ecosystem/pull/285
* Feature/animal module by TaranRallings in https://github.com/ImperialCollegeLondon/virtual_ecosystem/pull/284
* Fix unified path merge bug by alexdewar in https://github.com/ImperialCollegeLondon/virtual_ecosystem/pull/286
* Revert "Fix unified path merge bug" by alexdewar in https://github.com/ImperialCollegeLondon/virtual_ecosystem/pull/289
* Fix path merge bug, take 2 by alexdewar in https://github.com/ImperialCollegeLondon/virtual_ecosystem/pull/290
* Remove `--merge` command-line option and replace with config option by alexdewar in https://github.com/ImperialCollegeLondon/virtual_ecosystem/pull/292
* Fix: Correctly merge configs recursively by alexdewar in https://github.com/ImperialCollegeLondon/virtual_ecosystem/pull/291
* Linking animal excretion to the litter model by jacobcook1995 in https://github.com/ImperialCollegeLondon/virtual_ecosystem/pull/287
* Feature/animal module - A Miscellanea by TaranRallings in https://github.com/ImperialCollegeLondon/virtual_ecosystem/pull/300
* Add carcass to litter flow by jacobcook1995 in https://github.com/ImperialCollegeLondon/virtual_ecosystem/pull/298
* updated to include hydro and abiotic_simple by vgro in https://github.com/ImperialCollegeLondon/virtual_ecosystem/pull/299
* Feature/horizontal flow by vgro in https://github.com/ImperialCollegeLondon/virtual_ecosystem/pull/293
* Add a constants registry by jacobcook1995 in https://github.com/ImperialCollegeLondon/virtual_ecosystem/pull/295
* Initial plants model draft by davidorme in https://github.com/ImperialCollegeLondon/virtual_ecosystem/pull/296
* Adding canopy functionality to draft PlantsModel by davidorme in https://github.com/ImperialCollegeLondon/virtual_ecosystem/pull/303
* Add litter chemistry to the litter model by jacobcook1995 in https://github.com/ImperialCollegeLondon/virtual_ecosystem/pull/306
* Update soil depth configuration by davidorme in https://github.com/ImperialCollegeLondon/virtual_ecosystem/pull/309
* Update typing of `config` arguments. by davidorme in https://github.com/ImperialCollegeLondon/virtual_ecosystem/pull/310
* Feature/plants model by davidorme in https://github.com/ImperialCollegeLondon/virtual_ecosystem/pull/312
* Feature/intercept by vgro in https://github.com/ImperialCollegeLondon/virtual_ecosystem/pull/315
* Update `vr_run_cli` by davidorme in https://github.com/ImperialCollegeLondon/virtual_ecosystem/pull/314
* Feature/animal vr run integration by TaranRallings in https://github.com/ImperialCollegeLondon/virtual_ecosystem/pull/311
* old abiotic model deleted, docs updated by vgro in https://github.com/ImperialCollegeLondon/virtual_ecosystem/pull/317
* soil evaporation constraint by vgro in https://github.com/ImperialCollegeLondon/virtual_ecosystem/pull/318
* Feature/matric potential by vgro in https://github.com/ImperialCollegeLondon/virtual_ecosystem/pull/320
* Feature/rainfall stochasticity by vgro in https://github.com/ImperialCollegeLondon/virtual_ecosystem/pull/319
* Feature/bypass flow by vgro in https://github.com/ImperialCollegeLondon/virtual_ecosystem/pull/321
* soil moist to matric potential moved from litter by vgro in https://github.com/ImperialCollegeLondon/virtual_ecosystem/pull/326
* Feature/adjust surface evaporation by vgro in https://github.com/ImperialCollegeLondon/virtual_ecosystem/pull/327
* Feature/plants model by davidorme in https://github.com/ImperialCollegeLondon/virtual_ecosystem/pull/322
* Remove old temperature and moisture dependance by jacobcook1995 in https://github.com/ImperialCollegeLondon/virtual_ecosystem/pull/325
* Feature/groundwater flow by vgro in https://github.com/ImperialCollegeLondon/virtual_ecosystem/pull/329
* Moving to a single registry and importing on request not automatically by davidorme in https://github.com/ImperialCollegeLondon/virtual_ecosystem/pull/323
* Better handling of file loggers in testing by davidorme in https://github.com/ImperialCollegeLondon/virtual_ecosystem/pull/332
* Configurable system for setting model execution sequence by davidorme in https://github.com/ImperialCollegeLondon/virtual_ecosystem/pull/336
* Alter schema structure to use a cleaner model set definition by davidorme in https://github.com/ImperialCollegeLondon/virtual_ecosystem/pull/337
* Feature/animal module - Energy to Mass Conversion by TaranRallings in https://github.com/ImperialCollegeLondon/virtual_ecosystem/pull/338
* Animal Module constants rework by TaranRallings in https://github.com/ImperialCollegeLondon/virtual_ecosystem/pull/343
* Add soil enzymes to model by jacobcook1995 in https://github.com/ImperialCollegeLondon/virtual_ecosystem/pull/341
* Feature/vertical flow average by vgro in https://github.com/ImperialCollegeLondon/virtual_ecosystem/pull/351
* Plants model integration into full `vr_run` by davidorme in https://github.com/ImperialCollegeLondon/virtual_ecosystem/pull/352
* Changed `open_mfdataset` call to use `lock=False` to fix `vr_run` halt by jacobcook1995 in https://github.com/ImperialCollegeLondon/virtual_ecosystem/pull/355
* Remove Python 3.9 by davidorme in https://github.com/ImperialCollegeLondon/virtual_ecosystem/pull/356
* Feature/update example data code by vgro in https://github.com/ImperialCollegeLondon/virtual_ecosystem/pull/339
* Refactor BaseModel by davidorme in https://github.com/ImperialCollegeLondon/virtual_ecosystem/pull/365
* Adopting the new BaseModel structure in the model files. by davidorme in https://github.com/ImperialCollegeLondon/virtual_ecosystem/pull/375
* Adding automodule hooks for plants model to docs by davidorme in https://github.com/ImperialCollegeLondon/virtual_ecosystem/pull/380
* Defining the CoreComponents, LayerStructure and ModelTiming classes by davidorme in https://github.com/ImperialCollegeLondon/virtual_ecosystem/pull/374
* Fixing broken tests by davidorme in https://github.com/ImperialCollegeLondon/virtual_ecosystem/pull/393
* Updating GitHub Actions to new Node20 versions by davidorme in https://github.com/ImperialCollegeLondon/virtual_ecosystem/pull/384
* Make `map_xy_to_cell_indexing` less objectionable to mypy by davidorme in https://github.com/ImperialCollegeLondon/virtual_ecosystem/pull/395
* [pre-commit.ci] pre-commit autoupdate by pre-commit-ci in https://github.com/ImperialCollegeLondon/virtual_ecosystem/pull/387
* Renaming the package by davidorme in https://github.com/ImperialCollegeLondon/virtual_ecosystem/pull/392
* Fix RTD builds by davidorme in https://github.com/ImperialCollegeLondon/virtual_ecosystem/pull/398
* Adding explicit ipykernel install step to RTD by davidorme in https://github.com/ImperialCollegeLondon/virtual_ecosystem/pull/400
* Add progress option to `ve_run` by davidorme in https://github.com/ImperialCollegeLondon/virtual_ecosystem/pull/403
* Publish version `0.1.0a0` by davidorme in https://github.com/ImperialCollegeLondon/virtual_ecosystem/pull/401
* Fixing up PyPI issues in `0.1.0a0` by davidorme in https://github.com/ImperialCollegeLondon/virtual_ecosystem/pull/404
New Contributors
* jacobcook1995 made their first contribution in https://github.com/ImperialCollegeLondon/virtual_ecosystem/pull/7
* TaranRallings made their first contribution in https://github.com/ImperialCollegeLondon/virtual_ecosystem/pull/40
* alexdewar made their first contribution in https://github.com/ImperialCollegeLondon/virtual_ecosystem/pull/42
* robewers01 made their first contribution in https://github.com/ImperialCollegeLondon/virtual_ecosystem/pull/43
* dalonsoa made their first contribution in https://github.com/ImperialCollegeLondon/virtual_ecosystem/pull/50
* github-actions made their first contribution in https://github.com/ImperialCollegeLondon/virtual_ecosystem/pull/57
* pre-commit-ci made their first contribution in https://github.com/ImperialCollegeLondon/virtual_ecosystem/pull/58
**Full Changelog**: https://github.com/ImperialCollegeLondon/virtual_ecosystem/commits/v0.1.1a4