update to use pyproject.toml; update workflows and docs to use

.github/pull_request_template.md

@@ -10,7 +10,7 @@
 
 ## :white_check_mark: Checklist before requesting a review
 (See the contributing guide for more details on these steps.)
-- [ ] I have installed developer dependencies with `pip install -r requirements/requirements.dev.txt` and running `pre-commit install` (or alternatively, manually running `ruff format` before commiting)
+- [ ] I have installed developer dependencies with `pip install .[dev]` and running `pre-commit install` (or alternatively, manually running `ruff format` before commiting)
 
 If changing or adding source code:
 - [ ] tests are included and are passing (run `pytest`).

.github/workflows/docs.yml

@@ -14,9 +14,7 @@ jobs:
             - name: "Upgrade pip"
               run: pip install --upgrade pip
             - name: "Install dependencies"
-              run: pip install -r requirements/requirements.txt
-            - name: "Install jupyterbook"
-              run: pip install -r requirements/requirements.docs.txt
+              run: pip install .[docs]
             - name: "Run jupyterbook"
               run: jupyter-book build docs --all
             - name: "Deploy"

.github/workflows/publish.yml

@@ -31,11 +31,10 @@ jobs:
       - name: Install dependencies
         run: |
           python -m pip install --upgrade pip
-          pip install -U setuptools wheel twine
+          pip install -U setuptools wheel twine build
 
       - name: Build and publish
-        run: |
-          python setup.py sdist bdist_wheel
+        run: python -m build 
 
       - name: Publish distribution 📦 to PyPI
         uses: pypa/gh-action-pypi-publish@release/v1

.github/workflows/tests.yml

@@ -28,8 +28,8 @@ jobs:
     - name: Install dependencies
       run: |
         python -m pip install --upgrade pip
-        pip install -r requirements/requirements.txt
-        pip install -r requirements/requirements.dev.txt
+        pip install .[dev,testing]
+        pip install tox-gh-actions
     - name: Test with tox
       run: tox
     - name: Run coveralls

CONTRIBUTING.md

@@ -96,7 +96,7 @@ command to edit previous commit messages, combine multiple commits into one, or
 commits that are no longer necessary.
 
 Make sure you're using the developer dependencies.
-If you're working locally on the source code, *before* commiting, please run `pip install -r requirements/requirements.dev.txt` to install some useful dependencies just for development.
+If you're working locally on the source code, *before* commiting, please run `pip install .[dev]` to install some useful dependencies just for development.
 This includes `pre-commit` and `ruff` which are used to check and format your code style when you run `git commit`, so that you don't have to.
 
 Using pre-commit:
@@ -151,7 +151,7 @@ One easy way to contribute to the documentation is to provide feedback in [this
 
 Another way to contribute is to directly edit or add to the documentation and open a PR:
 * Follow all the forking instructions above
-* Install the documentation requirements: `pip install -r requirements/requirements.docs.txt`
+* Install the documentation requirements: `pip install deepsensor[docs]`
 * Option A: Editing a markdown file
   * Simply make your edits!
 * Option B: Editing a jupyter notebook file

README.md

@@ -85,8 +85,7 @@ over the US. First, pip install the package. In this case we will use the PyTorc
 want GPU support).
 
 ```bash
-pip install deepsensor
-pip install torch
+pip install deepsensor[torch]
 ```
 
 We can go from imports to predictions with a trained model in less than 30 lines of code!

docs/getting-started/installation.md

@@ -37,6 +37,14 @@ This method will create a `DeepSensor` directory on your machine which will cont
   ```bash
   pip install -v -e .
   ```
+
+```{note}
+If you intend on contributing to the source code of DeepSensor, install DeepSensor with its development dependencies using
+````{bash}
+pip install -v -e .[dev]
+````
+```
+
 ## Install PyTorch or TensorFlow
 
 The next step, if you intend to use any of DeepSensor's deep learning modelling functionality,
@@ -60,3 +68,11 @@ To install `pytorch` via pip:
 ```bash
 pip install torch
 ```
+
+To install DeepSensor as well as a deep learning library at the same time use:
+
+```bash
+pip install deepsensor[tf]    # for tensorflow and tensorflow_probability
+# or
+pip install deepsensor[torch] # for pytorch
+```

pyproject.toml

@@ -1,3 +1,75 @@
+[build-system]
+requires = ["setuptools>=61"]
+build-backend = "setuptools.build_meta"
+
+[project]
+name = "deepsensor"
+version = "0.4.2"
+authors = [
+    {name = "Tom R. Andersson", email="[email protected]"},
+]
+description = "A Python package for modelling xarray and pandas data with neural processes."
+readme = "README.md"
+license = {text="MIT"}
+classifiers = [
+    "Programming Language :: Python :: 3",
+    "Operating System :: OS Independent"
+]
+requires-python = ">=3.8"
+dependencies = [
+    "backends",
+    "backends-matrix",
+    "dask",
+    "distributed",
+    "gcsfs",
+    "matplotlib",
+    "neuralprocesses>=0.2.7",
+    "numpy",
+    "pandas",
+    "pooch",
+    "pyshp",
+    "seaborn",
+    "tqdm",
+    "xarray",
+    "zarr"
+]
+
+[tool.setuptools]
+packages = ["deepsensor"]
+
+[project.urls]
+Source = "https://github.com/alan-turing-institute/deepsensor"
+Bug_Tracker = "https://github.com/alan-turing-institute/deepsensor/issues"
+
+[project.optional-dependencies]
+torch = ["torch>=2"]
+tf = ["tensorflow", "tensorflow_probability[tf]"]
+dev = [
+    "coveralls",
+    "parameterized",
+    "pre-commit",
+    "pytest",
+    "ruff",
+]
+docs = [
+    "jupyter-book",
+    "matplotlib",
+    "numpy",
+]
+testing = [
+    "mypy",
+    "parameterized",
+    "pytest",
+    "pytest-cov",
+    "tox",
+]
+rioxarray = [
+    "rioxarray"
+]
+
+[tool.setuptools.package-data]
+deepsensor = ["py.typed"]
+
 [tool.pytest.ini_options]
 addopts = "--cov=deepsensor"
 testpaths = [

tox.ini

@@ -15,7 +15,6 @@ python =
 setenv =
     PYTHONPATH = {toxinidir}
 deps =
-    -r{toxinidir}/requirements/requirements.txt
-    -r{toxinidir}/requirements/requirements.dev.txt
+    .[tf,torch,testing]
 commands =
     pytest --basetemp={envtmpdir}