Port infrastructure to pyproject.toml (#29)

* Switch to pyproject.toml

* Fix syntax errors

* New requirements files

* Point to new requirements file

* Add dill requirement

* Add __init__.py

* Update install instructions

* Minor requested changes, rebuiding requirements files

.github/workflows/ci.yml

@@ -13,6 +13,6 @@ jobs:
       with:
         python-version: 3.10.9
     - name: Install and build
-      run: pip install .
+      run: pip install -r requirements-dev.txt
     - name: Run tests
       run: pytest

README.md

@@ -20,7 +20,7 @@ with arcs, and create simulations.
 
 You can access our documentation below or at [https://imperialcollegelondon.github.io/wsi](https://barneydobson.github.io/wsi).
 
-*Requires*: Python 3 (tested on versions >=3.7), [tqdm](https://tqdm.github.io/), [PyYAML](https://pyyaml.org/)
+*Requires*: Python 3 (tested on versions >=3.7), [tqdm](https://tqdm.github.io/), [PyYAML](https://pyyaml.org/), [dill](https://dill.readthedocs.io/en/latest/)
 
 *Optional requirements to run demos*: [Pandas](https://pandas.pydata.org/), [GeoPandas](https://geopandas.org/en/stable/), [Matplotlib](https://matplotlib.org/), [Shapely](https://shapely.readthedocs.io/en/stable/manual.html)
 
@@ -52,37 +52,27 @@ and consists of:
 8. [Coverage](https://barneydobson.github.io/wsi/coverage/)
 
 ## Installation
-Create and activate new conda environment
-```
-conda create --name wsimod python=3.10
-conda activate wsimod
-```
-
-Install a GUI if you like
-```
-conda install spyder -c conda-forge
-```
 
 Install WSIMOD directly from GitHub
 ```
-pip install https://github.com/barneydobson/wsi/archive/refs/heads/main.zip
+pip install https://github.com/ImperialCollegeLondon/wsi/archive/refs/heads/main.zip
 ```
 
 Use `[demos]` to include the demos and tutorials.
 ```
-pip install https://github.com/barneydobson/wsi/archive/refs/heads/main.zip
+pip install https://github.com/ImperialCollegeLondon/wsi/archive/refs/heads/main.zip
 pip install wsimod[demos]
 ```
 
-If you want to make changes WSIMOD you can download/clone this folder, navigate to it, and run:
+If you want to make changes to WSIMOD you can download/clone this folder, navigate to it, and run:
 ```
-python setup.py develop
+pip install -e .[dev]
 ```
 
 or (with demos)
 
 ```
-python setup.py develop easy_install "wsimod[demos]"
+pip install -e .[dev,demos]
 ```
 
 ## How to cite WSIMOD

pyproject.toml

@@ -0,0 +1,51 @@
+[build-system]
+requires = ["setuptools", "setuptools-scm"]
+build-backend = "setuptools.build_meta"
+
+[tool.setuptools.packages.find]
+exclude = ["htmlcov"] # Exclude the coverage report file from setuptools package finder
+
+[project]
+name = "wsimod"
+description = "WSIMOD is for simulating water quality and quantity"
+readme = "README.md"
+version = "0.2.0"
+license = {file = "LICENSE"}
+authors = [
+    { name = "Barnaby Dobson", email = "[email protected]" },
+    { name = "Imperial College London RSE Team", email = "[email protected]" }
+]
+requires-python = ">=3.9"
+dependencies = [
+    "PyYAML",
+    "tqdm",
+    "dill"
+]
+
+[project.optional-dependencies]
+dev = [
+    "pytest"
+]
+
+demos = [
+    "pandas==1.5.2",
+    "geopandas",
+    "matplotlib",
+    "shapely"
+]
+
+doc = [
+    "mkdocs",
+    "mkdocstrings[python]",
+    "mkdocs-material",
+    "mkdocs-autorefs",
+    "mkdocs-bibtex",
+    "mkdocs-coverage",
+    "mkdocs-jupyter",
+    "mkdocs-material-extensions",
+    "pypandoc",
+    "wsimod[demos]"
+]
+
+[tool.pytest.ini_options]
+addopts = "-v -p no:warnings"

requirements-demos.txt

@@ -0,0 +1,82 @@
+#
+# This file is autogenerated by pip-compile with Python 3.11
+# by the following command:
+#
+#    pip-compile --extra=demos --output-file=requirements-demos.txt
+#
+attrs==23.1.0
+    # via fiona
+certifi==2023.7.22
+    # via
+    #   fiona
+    #   pyproj
+click==8.1.7
+    # via
+    #   click-plugins
+    #   cligj
+    #   fiona
+click-plugins==1.1.1
+    # via fiona
+cligj==0.7.2
+    # via fiona
+colorama==0.4.6
+    # via
+    #   click
+    #   tqdm
+contourpy==1.1.1
+    # via matplotlib
+cycler==0.12.1
+    # via matplotlib
+dill==0.3.7
+    # via wsimod (pyproject.toml)
+fiona==1.9.5
+    # via geopandas
+fonttools==4.43.1
+    # via matplotlib
+geopandas==0.14.0
+    # via wsimod (pyproject.toml)
+kiwisolver==1.4.5
+    # via matplotlib
+matplotlib==3.8.1
+    # via wsimod (pyproject.toml)
+numpy==1.26.1
+    # via
+    #   contourpy
+    #   matplotlib
+    #   pandas
+    #   shapely
+packaging==23.2
+    # via
+    #   geopandas
+    #   matplotlib
+pandas==1.5.2
+    # via
+    #   geopandas
+    #   wsimod (pyproject.toml)
+pillow==10.1.0
+    # via matplotlib
+pyparsing==3.1.1
+    # via matplotlib
+pyproj==3.6.1
+    # via geopandas
+python-dateutil==2.8.2
+    # via
+    #   matplotlib
+    #   pandas
+pytz==2023.3.post1
+    # via pandas
+pyyaml==6.0.1
+    # via wsimod (pyproject.toml)
+shapely==2.0.2
+    # via
+    #   geopandas
+    #   wsimod (pyproject.toml)
+six==1.16.0
+    # via
+    #   fiona
+    #   python-dateutil
+tqdm==4.66.1
+    # via wsimod (pyproject.toml)
+
+# The following packages are considered to be unsafe in a requirements file:
+# setuptools

requirements-dev.txt

@@ -0,0 +1,24 @@
+#
+# This file is autogenerated by pip-compile with Python 3.11
+# by the following command:
+#
+#    pip-compile --extra=dev --output-file=requirements-dev.txt
+#
+colorama==0.4.6
+    # via
+    #   pytest
+    #   tqdm
+dill==0.3.7
+    # via wsimod (pyproject.toml)
+iniconfig==2.0.0
+    # via pytest
+packaging==23.2
+    # via pytest
+pluggy==1.3.0
+    # via pytest
+pytest==7.4.3
+    # via wsimod (pyproject.toml)
+pyyaml==6.0.1
+    # via wsimod (pyproject.toml)
+tqdm==4.66.1
+    # via wsimod (pyproject.toml)