Merge pull request #404 from ImperialCollegeLondon/release/0.1.0

Fixing up PyPI issues in `0.1.0a0`

Author: davidorme

.gitignore

@@ -133,3 +133,7 @@ dmypy.json
 
 # Mac DS Store files
 .DS_Store
+
+# PYPI credentials
+.pypirc
+

README.md

@@ -22,12 +22,12 @@ Foundation to Professor Robert Ewers:
 * [NOMIS project summary](https://nomisfoundation.ch/research-projects/a-virtual-rainforest-for-understanding-the-stability-resilience-and-sustainability-of-complex-ecosystems/)
 
 <!-- markdownlint-disable-next-line  MD033 MD013-->
-[<img alt="NOMIS logo" src="docs/source/_static/images/logo-nomis-822-by-321.png" width=250>](https://nomisfoundation.ch)
+[<img alt="NOMIS logo" src="https://github.com/ImperialCollegeLondon/virtual_ecosystem/blob/c94cef61d997764442d7beb9ac2eaedae71cfad1/docs/source/_static/images/logo-nomis-822-by-321.png?raw=true" width=250>](https://nomisfoundation.ch)
 
 The research is based at Imperial College London:
 
 <!-- markdownlint-disable-next-line  MD033 MD013-->
-[<img alt="Imperial logo" src="docs/source/_static/images/IMP_ML_1CS_4CP_CLEAR-SPACE.png" width=250>](https://imperial.ac.uk)
+[<img alt="Imperial logo" src="https://github.com/ImperialCollegeLondon/virtual_ecosystem/blob/c94cef61d997764442d7beb9ac2eaedae71cfad1/docs/source/_static/images/IMP_ML_1CS_4CP_CLEAR-SPACE.png?raw=true" width=250>](https://imperial.ac.uk)
 
 ## Project Team
 

pyproject.toml

@@ -1,71 +1,86 @@
 [tool.poetry]
-name = "virtual_ecosystem"
-version = "0.1.1a0"
-description = """The package simulates the abiotic, soil, animal and plant components of an ecosystem."""
 authors = [
-    "Rob Ewers <[email protected]>",
-    "David Orme <[email protected]>",
-    "Jacob Cook <[email protected]>",
-    "Vivienne Groner <[email protected]>",
-    "Taran Rallings <[email protected]>",
-    "Olivia Daniel <[email protected]>",
+  "Rob Ewers <[email protected]>",
+  "David Orme <[email protected]>",
+  "Jacob Cook <[email protected]>",
+  "Vivienne Groner <[email protected]>",
+  "Taran Rallings <[email protected]>",
+  "Olivia Daniel <[email protected]>",
+  "Jaideep Joshi <[email protected]>",
+  "Anna Rallings <[email protected]>",
+  "Priyanga Amarasekare <[email protected]>",
+  "Diego Alonso Alvarez <[email protected]>",
+  "Alex Dewar <[email protected]>",
+]
+classifiers = [
+  "Development Status :: 2 - Pre-Alpha",
+  "Intended Audience :: Science/Research",
+  "License :: OSI Approved :: BSD License",
+  "Topic :: Scientific/Engineering",
 ]
+description = """An holistic ecosystem simulation model."""
+homepage = "https://virtual-ecosystem.readthedocs.io/"
+license = "BSD-3-Clause"
+name = "virtual_ecosystem"
+readme = "README.md"
+repository = "https://github.com/ImperialCollegeLondon/virtual_ecosystem"
+version = "0.1.1a4"
 
 [tool.poetry.scripts]
 ve_run = "virtual_ecosystem.entry_points:ve_run_cli"
 
 [tool.poetry.dependencies]
-python = ">=3.10,<3.12"
-numpy = "^1.23.0"
-tomli = { version = "^2.0.1", python = "<3.11" }
-dpath = "^2.0.6"
-tomli-w = "^1.0.0"
-scipy = "^1.9.0"
-jsonschema = "^4.14.0"
 Shapely = "^1.8.4"
-pint = "^0.20.1"
-xarray = "^2024.02.0"
 dask = "^2023.6.0"
+dpath = "^2.0.6"
+jsonschema = "^4.14.0"
 netcdf4 = "^1.6.5"
+numpy = "^1.23.0"
+pint = "^0.20.1"
+python = ">=3.10,<3.12"
+scipy = "^1.9.0"
+tomli = {version = "^2.0.1", python = "<3.11"}
+tomli-w = "^1.0.0"
 tqdm = "^4.66.2"
+xarray = "^2024.02.0"
 
 [tool.poetry.group.types.dependencies]
-types-jsonschema = "^4.16.1"
 types-dataclasses = "^0.6.6"
+types-jsonschema = "^4.16.1"
 types-tqdm = "^4.66.0.20240106"
 
 [tool.poetry.group.test.dependencies]
+hypothesis = "^6.54.2"
 pytest = "^7.1.2"
 pytest-cov = "^3.0.0"
 pytest-datadir = "^1.4.1"
 pytest-flake8 = "^1.1.1"
-pytest-mypy = "^0.10.3"
 pytest-mock = "^3.8.1"
-hypothesis = "^6.54.2"
+pytest-mypy = "^0.10.3"
 
 [tool.poetry.group.devenv.dependencies]
 black = "^22.6.0"
 flake8 = "^4.0.1"
-mypy = "^1.5.1"
-pre-commit = "^2.19.0"
+flake8-docstrings = "^1.6.0"
+ipykernel = "^6.15.0"
+ipython = "^8.4.0"
 isort = "^5.12.0"
+matplotlib = "^3.5.2"
 mdformat = "^0.7.14"
 mdformat_frontmatter = "^0.4.1"
 mdformat_tables = "^0.4.1"
-flake8-docstrings = "^1.6.0"
-ipython = "^8.4.0"
-ipykernel = "^6.15.0"
-matplotlib = "^3.5.2"
+mypy = "^1.5.1"
+pre-commit = "^2.19.0"
 
 [tool.poetry.group.docs.dependencies]
-sphinx = "^7.0.0"
-sphinxcontrib-bibtex = "^2.4.2"
-myst-nb = "^1.0.0"
-sphinx-rtd-theme = "^1.0.0"
 autodocsumm = "^0.2.8"
+myst-nb = "^1.0.0"
 pydocstyle = "^6.1.1"
+sphinx = "^7.0.0"
+sphinx-rtd-theme = "^1.0.0"
+sphinxcontrib-bibtex = "^2.4.2"
 sphinxcontrib-mermaid = "^0.9.2"
 
 [build-system]
-requires = ["poetry-core>=1.2.0"]
 build-backend = "poetry.core.masonry.api"
+requires = ["poetry-core>=1.2.0"]