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 #169
• Fixes the precommit issue with mypy dependencies by @davidorme in #175
• Feature/split testing by @jacobcook1995 in #174
• API links updated to new model names by @vgro in #177
• Feature/radiation dummy 2 by @vgro in #179
• Feature/model autodiscovery by @davidorme in #173
• Added docs build check to the CI by @jacobcook1995 in #181
• Feature/dummy animal - AnimalModel by @TaranRallings in #171
• Make a Data object part of the BaseModel.__init__ by @davidorme in #176
• Switched to using a consistent key format for citations by @jacobcook1995 in #184
• Pull already-reviewed changes from feature/animal module into develop. by @TaranRallings in #182
• Feature/wind dummy by @vgro in #183
• abiotic_tools introduced by @vgro in #186
• Feature/animal module - First implementation of AnimalCohort class by @TaranRallings in #185
• Change SoilModel to use the data object by @jacobcook1995 in #187
• Feature/co2 dummy by @vgro in #193
• Added utility function to extract model specific timing details by @jacobcook1995 in #189
• Feature/animal module - Basic AnimalCohort functions by @TaranRallings in #192
• Numerical integration of the soil module by @jacobcook1995 in #191
• Basic data output functionality by @jacobcook1995 in #194
• Documentation for main simulation flow by @jacobcook1995 in #195
• Remove usage of pip install codecov from CI action by @jacobcook1995 in #200
• Extend carbon pool from 2 to 3 pools by @jacobcook1995 in #206
• Feature/data object toml by @vgro in #201
• Update config module to use a class by @davidorme in #212
• Factory method for Grid by @davidorme in #214
• Feature/update climate data recipe by @vgro in #217
• Introduce common update time step and timescale bounds for all models by @jacobcook1995 in #211
• Fixs for pint problem in docs build action by @jacobcook1995 in #218
• Feature/abiotic simple model by @vgro in #219
• updated for dummy model and ERA5 land by @vgro in #220
• Feature/Animal_Module: Basic dispersal function and tracking of cohort positions on grid. by @TaranRallings in #198
• Feature/update module overview by @vgro in #224
• Feature/simple regression by @vgro in #221
• Updated defaults for core config options to match dummy data by @jacobcook1995 in #226
• Use abiotic soil layers correctly in soil model by @jacobcook1995 in #225
• Added setup step to main function flow by @jacobcook1995 in #227
• Feature/data recipes section by @vgro in #228
• Add recipe for generating dummy soil data by @jacobcook1995 in #229
• Feature/animal module - Ectothermic metabolism by @TaranRallings in #230
• Various bug fixes to allow vr_run to work with soil and abiotic_simple models by @jacobcook1995 in #236
• Feature/separate hydrology by @vgro in #243
• bugfix log interpolation by @vgro in #244
• Forced module order to be fixed based on config input by @jacobcook1995 in #245
• Remove soil model specific function to update data object by @jacobcook1995 in #246
• Continuous output of the data object by @jacobcook1995 in #237
• atmosperic pressure unit correction by @vgro in #250
• Fix dask warning about saving "layer_roles" as an object by @jacobcook1995 in #251
• Updated poetry to latest versions by @jacobcook1995 in #252
• Adding a particulate organic matter pool by @jacobcook1995 in #253
• Feature/correct dummy climate by @vgro in #254
• fix time_index by @vgro in #255
• Feature/vertical water flow by @vgro in #257
• System to allow constants to be altered based on configuration by @jacobcook1995 in #258
• Feature/update hydrology constants by @vgro in #260
• Change soil constants to use new system by @jacobcook1995 in #261
• Feature/add streamflow by @vgro in #262
• soil depth correction by @vgro in #263
• Allow setting params with command-line arguments by @alexdewar in #267
• Adding a litter model by @jacobcook1995 in #268
• Treat paths in config files as relative to config dir by @alexdewar in #269
• Add example data by @alexdewar in #279
• Fix dependance of some tests on local filesystem by @jacobcook1995 in #275
• Connect litter pools to soil pools by @jacobcook1995 in #281
• Feature/animal module - Foraging functions by @TaranRallings in #248
• Systematise various output file parameters by @alexdewar in #280
• Feature/update hydro model by @vgro in #283
• Added three more litter pools to litter model by @jacobcook1995 in #285
• Feature/animal module by @TaranRallings in #284
• Fix unified path merge bug by @alexdewar in #286
• Revert "Fix unified path merge bug" by @alexdewar in #289
• Fix path merge bug, take 2 by @alexdewar in #290
• Remove --merge command-line option and replace with config option by @alexdewar in #292
• Fix: Correctly merge configs recursively by @alexdewar in #291
• Linking animal excretion to the litter model by @jacobcook1995 in #287
• Feature/animal module - A Miscellanea by @TaranRallings in #300
• Add carcass to litter flow by @jacobcook1995 in #298
• updated to include hydro and abiotic_simple by @vgro in #299
• Feature/horizontal flow by @vgro in #293
• Add a constants registry by @jacobcook1995 in #295
• Initial plants model draft by @davidorme in #296
• Adding canopy functionality to draft PlantsModel by @davidorme in #303
• Add litter chemistry to the litter model by @jacobcook1995 in #306
• Update soil depth configuration by @davidorme in #309
• Update typing of config arguments. by @davidorme in #310
• Feature/plants model by @davidorme in #312
• Feature/intercept by @vgro in #315
• Update vr_run_cli by @davidorme in #314
• Feature/animal vr run integration by @TaranRallings in #311
• old abiotic model deleted, docs updated by @vgro in #317
• soil evaporation constraint by @vgro in #318
• Feature/matric potential by @vgro in #320
• Feature/rainfall stochasticity by @vgro in #319
• Feature/bypass flow by @vgro in #321
• soil moist to matric potential moved from litter by @vgro in #326
• Feature/adjust surface evaporation by @vgro in #327
• Feature/plants model by @davidorme in #322
• Remove old temperature and moisture dependance by @jacobcook1995 in #325
• Feature/groundwater flow by @vgro in #329
• Moving to a single registry and importing on request not automatically by @davidorme in #323
• Better handling of file loggers in testing by @davidorme in #332
• Configurable system for setting model execution sequence by @davidorme in #336
• Alter schema structure to use a cleaner model set definition by @davidorme in #337
• Feature/animal module - Energy to Mass Conversion by @TaranRallings in #338
• Animal Module constants rework by @TaranRallings in #343
• Add soil enzymes to model by @jacobcook1995 in #341
• Feature/vertical flow average by @vgro in #351
• Plants model integration into full vr_run by @davidorme in #352
• Changed open_mfdataset call to use lock=False to fix vr_run halt by @jacobcook1995 in #355
• Remove Python 3.9 by @davidorme in #356
• Feature/update example data code by @vgro in #339
• Refactor BaseModel by @davidorme in #365
• Adopting the new BaseModel structure in the model files. by @davidorme in #375
• Adding automodule hooks for plants model to docs by @davidorme in #380
• Defining the CoreComponents, LayerStructure and ModelTiming classes by @davidorme in #374
• Fixing broken tests by @davidorme in #393
• Updating GitHub Actions to new Node20 versions by @davidorme in #384
• Make map_xy_to_cell_indexing less objectionable to mypy by @davidorme in #395
• [pre-commit.ci] pre-commit autoupdate by @pre-commit-ci in #387
• Renaming the package by @davidorme in #392
• Fix RTD builds by @davidorme in #398
• Adding explicit ipykernel install step to RTD by @davidorme in #400
• Add progress option to ve_run by @davidorme in #403
• Publish version 0.1.0a0 by @davidorme in #401
• Fixing up PyPI issues in 0.1.0a0 by @davidorme in #404

New Contributors

• @jacobcook1995 made their first contribution in #7
• @TaranRallings made their first contribution in #40
• @alexdewar made their first contribution in #42
• @robewers01 made their first contribution in #43
• @dalonsoa made their first contribution in #50
• @github-actions made their first contribution in #57
• @pre-commit-ci made their first contribution in #58

Full Changelog: https://github.com/ImperialCollegeLondon/virtual_ecosystem/commits/v0.1.1a4