Merge branch 'main' into claireh93/pre-release

CONTRIBUTING.md

@@ -4,7 +4,6 @@ Thanks for contributing to EcoSISTEM.jl! Please read the below on how best to ma
 
 ## Pull Request Process
 
-
 1. Please branch from within boydorr/EcoSISTEM.jl
 
    - Please **don't** fork this repository to your own github.com/username or other organisation.
@@ -27,6 +26,6 @@ Following the first release of the package, all subsequent merges to `main` shou
 
 By contributing to this project (e.g. by submitting a pull request or providing advice on code), you agree - unless simultaneously and expressly stated otherwise - that your contribution may be included in the source code of the project and published under the following copyright licenses:
 
-[GNU GPL-3.0 (or any later version)](LICENSE.md) with a special exception to allow distribution under the [2-Clause BSD License](https://opensource.org/licenses/BSD-2-Clause) if the package as a whole is rereleased under that license.
+[GNU GPL-3.0 (or any later version)](LICENSE.md) with a special exception to allow distribution under the [2-Clause BSD License](https://opensource.org/licenses/BSD-2-Clause) if the package as a whole is rereleased under that license (such a decision can only be made by the lead developers of the package - currently Claire Harris and Richard Reeve).
 
 and that the contribution was created in whole or in part by you and you have the right to submit it under the open source license indicated above.

Project.toml

@@ -44,34 +44,34 @@ UUIDs = "cf7118a7-6976-5b1a-9a39-7adc72f591a4"
 Unitful = "1986cc42-f94f-5a68-af5c-568840ba703d"
 
 [compat]
-ArchGDAL = "0.6.0"
+ArchGDAL = "0.6"
 AxisArrays = "0.4.3"
 Calculus = "0.4.1, 0.5"
-Compat = "2.2.1"
-DataFrames = "0.21.8"
+Compat = "2.2.1, 3"
+DataFrames = "0.21.8, 0.22"
 Distributions = "0.24.15"
 Diversity = "0.5.3"
 EcoBase = "0.1.3"
 Feather = "0.5.7"
 HCubature = "1.5.0"
-IndexedTables = "0.12.6, 1.0"
+IndexedTables = "0.12.6, 0.13, 1"
 Interpolations = "0.13.1"
-JLD = "0.10.0"
-JuliaDB = "0.13.0"
+JLD = "0.10, 0.11, 0.12"
+JuliaDB = "0.13"
 MPI = "0.17.2"
 Measures = "0.3.1"
 Missings = "0.4.5"
 NetCDF = "0.11.3"
 OnlineStats = "1.5.8"
-Optim = "0.18.1, 1.3"
+Optim = "0.18, 0.19, 0.20, 0.21, 0.22, 1"
 Phylo = "0.4.18"
-Plots = "0.28.4"
+Plots = "0.28.4, 0.29, 1"
 RCall = "0.13.10"
-RecipesBase = "0.7.0"
-Requires = "1.1.3"
-SpatialEcology = "0.9.7"
-StatsBase = "0.32.2"
-Unitful = "1.7.0"
+RecipesBase = "0.7, 0.8, 1"
+Requires = "1"
+SpatialEcology = "0.9"
+StatsBase = "0.32.2, 0.33"
+Unitful = "1.7"
 
 [extras]
 MPI = "da04e1cc-30fd-572f-bb4f-1f8673147195"

README.md

@@ -1,12 +1,12 @@
 # EcoSISTEM
-[![][docs-main-img]][docs-main-url] [![][docs-dev-img]][docs-dev-url]
 
+[![main docs][docs-main-img]][docs-main-url] [![dev docs][docs-dev-img]][docs-dev-url]
 
-[![][actions-img]][actions-url] [![][codecov-img]][codecov-url]
+[![build tests][actions-img]][actions-url] [![codecov][codecov-img]][codecov-url]
 
-*Package for running dynamic ecosystem simulations*
+## Package for running dynamic ecosystem simulations
 
-## Summary
+### Summary
 
 **EcoSISTEM** (Ecosystem Simulation through Integrated Species-Trait Environment Modelling) is a [Julia](http://www.julialang.org) package that
 provides functionality for simulating species undergoing dynamic
@@ -23,12 +23,17 @@ There are substantial changes to the package introduced through the [`dev`][dev-
 This package is in beta now, so please raise an issue if you find any problems. For more information on how to contribute, please read [our contributing guidelines](CONTRIBUTING.md).
 
 [paper-url]: https://arxiv.org/abs/1911.12257
+
 [docs-main-img]: https://img.shields.io/badge/docs-main-blue.svg
 [docs-main-url]: https://boydorr.github.io/EcoSISTEM.jl/main/
+
 [docs-dev-img]: https://img.shields.io/badge/docs-dev-blue.svg
 [docs-dev-url]: https://boydorr.github.io/EcoSISTEM.jl/dev/
+
 [actions-img]: https://github.com/boydorr/EcoSISTEM.jl/actions/workflows/testing.yaml/badge.svg?branch=main
 [actions-url]: https://github.com/boydorr/EcoSISTEM.jl/actions
+
 [codecov-img]: https://codecov.io/gh/boydorr/EcoSISTEM.jl/branch/main/graph/badge.svg
 [codecov-url]: https://codecov.io/gh/boydorr/EcoSISTEM.jl?branch=main
+
 [dev-url]: https://github.com/boydorr/EcoSISTEM.jl/tree/dev