Add publish workflow, install prettier hook and run it

.editorconfig

@@ -0,0 +1,21 @@
+root = true
+
+[*]
+charset = utf-8
+insert_final_newline = true
+trim_trailing_whitespace = true
+indent_style = space
+indent_size = 4
+max_line_length = 88
+
+[*.md]
+indent_size = 2
+
+[*.yaml]
+indent_size = 2
+
+[*.yml]
+indent_size = 2
+
+[Makefile]
+indent_style = tab

.github/workflows/ci.yml

@@ -15,19 +15,19 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        os: [ ubuntu-latest, windows-latest, macos-latest]
-        python-version: [ "3.9", "3.10", "3.11" ]
+        os: [ubuntu-latest, windows-latest, macos-latest]
+        python-version: ["3.9", "3.10", "3.11"]
 
     steps:
-    - uses: actions/checkout@v4
-    - uses: actions/setup-python@v4
-      with:
-        python-version: ${{ matrix.python-version }}
+      - uses: actions/checkout@v4
+      - uses: actions/setup-python@v4
+        with:
+          python-version: ${{ matrix.python-version }}
 
-    - name: Install and build
-      run: |
-        python -m pip install -r requirements-dev.txt
-        python -m pip install .
+      - name: Install and build
+        run: |
+          python -m pip install -r requirements-dev.txt
+          python -m pip install .
 
-    - name: Run tests
-      run: python -m pytest
+      - name: Run tests
+        run: python -m pytest

.github/workflows/publish.yml

@@ -0,0 +1,64 @@
+on: [release]
+
+jobs:
+  test:
+    uses: ./.github/workflows/ci.yml
+
+  build-wheel:
+    needs: test
+    name: Build source distribution
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+
+      - name: Build sdist
+        run: |
+          python -m pip install --upgrade build
+          python -m build
+
+      - uses: actions/upload-artifact@v3
+        with:
+          path: dist/wsimod
+
+  publish-TestPyPI:
+    needs: build-wheel
+    name: Publish WSIMOD to TestPyPI
+    runs-on: ubuntu-latest
+    permissions:
+      id-token: write
+
+    steps:
+      - name: Download sdist artifact
+        uses: actions/download-artifact@v3
+        with:
+          name: artifact
+          path: dist
+
+      - name: Display structure of downloaded files
+        run: ls -R dist
+
+      - name: Publish package distributions to TestPyPI
+        uses: pypa/gh-action-pypi-publish@release/v1
+        with:
+          repository-url: https://test.pypi.org/legacy/
+          skip-existing: true
+
+  publish-PyPI:
+    needs: publish-TestPyPI
+    name: Publish WSIMOD to PyPI
+    runs-on: ubuntu-latest
+    permissions:
+      id-token: write
+
+    steps:
+      - name: Download sdist artifact
+        uses: actions/download-artifact@v3
+        with:
+          name: artifact
+          path: dist
+
+      - name: Display structure of downloaded files
+        run: ls -R dist
+
+      - name: Publish package distributions to PyPI
+        uses: pypa/gh-action-pypi-publish@release/v1

.pre-commit-config.yaml

@@ -9,7 +9,7 @@ repos:
     hooks:
       - id: black
   - repo: https://github.com/astral-sh/ruff-pre-commit
-    rev: 'v0.1.3'
+    rev: "v0.1.3"
     hooks:
       - id: ruff
         args: [--fix, --exit-non-zero-on-fix]
@@ -21,4 +21,8 @@ repos:
     rev: v0.37.0
     hooks:
       - id: markdownlint
-        args: ["--disable", "MD013", "MD033", "--"]
+        args: ["--disable", "MD013", "MD033", "--"]
+  - repo: https://github.com/pre-commit/mirrors-prettier
+    rev: v3.1.0
+    hooks:
+      - id: prettier

.zenodo.json

@@ -1,14 +1,14 @@
 {
-    "description": "Release following the JOSS review process", 
+    "description": "Release following the JOSS review process",
     "license": {
         "id": "bsd-3-clause",
         "title": "BSD 3-Clause License",
         "url": "https://opensource.org/licenses/BSD-3-Clause"
-    }, 
-    "title": "Water Systems Integrated Modelling framework, WSIMOD: A Python package for integrated modelling of water quality and quantity across the water cycle", 
-    "version": "0.3_joss_reviewed", 
-    "upload_type": "software", 
-    "publication_date": "2023-02-21", 
+    },
+    "title": "Water Systems Integrated Modelling framework, WSIMOD: A Python package for integrated modelling of water quality and quantity across the water cycle",
+    "version": "0.3_joss_reviewed",
+    "upload_type": "software",
+    "publication_date": "2023-02-21",
     "creators": [
         {
             "name": "Dobson, Barnaby",

README.md

@@ -20,9 +20,9 @@ with arcs, and create simulations.
 
 You can access our documentation below or at [https://imperialcollegelondon.github.io/wsi](https://imperialcollegelondon.github.io/wsi).
 
-*Requires*: Python 3 (tested on versions >=3.7), [tqdm](https://tqdm.github.io/), [PyYAML](https://pyyaml.org/), [dill](https://dill.readthedocs.io/en/latest/)
+_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)
+_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)
 
 Please consider [contributing](./docs/CONTRIBUTING.md) and note the [code of conduct](./docs/CODE_OF_CONDUCT.md)
 
@@ -84,13 +84,13 @@ pip install -e .[dev,demos]
 
 If you would like to use our software, please cite it using the following:
 
- > Dobson, B., Liu, L. and Mijic, A. (2023)
- ‘Water Systems Integrated Modelling framework, WSIMOD: A Python package for integrated modelling of water quality and quantity across the water cycle’,
- Journal of Open Source Software.
- The Open Journal,
- 8(83),
- p. 4996.
- doi: 10.21105/joss.04996.
+> Dobson, B., Liu, L. and Mijic, A. (2023)
+> ‘Water Systems Integrated Modelling framework, WSIMOD: A Python package for integrated modelling of water quality and quantity across the water cycle’,
+> Journal of Open Source Software.
+> The Open Journal,
+> 8(83),
+> p. 4996.
+> doi: 10.21105/joss.04996.
 
 Find the bibtex citation below:
 

docker-compose.yaml

@@ -1,4 +1,4 @@
-version: '3'
+version: "3"
 services:
   wsimod:
     build: .

docs/CODE_OF_CONDUCT.md

@@ -1,4 +1,3 @@
-
 # Contributor Covenant Code of Conduct
 
 ## Our Pledge
@@ -18,23 +17,23 @@ diverse, inclusive, and healthy community.
 Examples of behavior that contributes to a positive environment for our
 community include:
 
-* Demonstrating empathy and kindness toward other people
-* Being respectful of differing opinions, viewpoints, and experiences
-* Giving and gracefully accepting constructive feedback
-* Accepting responsibility and apologizing to those affected by our mistakes,
+- Demonstrating empathy and kindness toward other people
+- Being respectful of differing opinions, viewpoints, and experiences
+- Giving and gracefully accepting constructive feedback
+- Accepting responsibility and apologizing to those affected by our mistakes,
   and learning from the experience
-* Focusing on what is best not just for us as individuals, but for the overall
+- Focusing on what is best not just for us as individuals, but for the overall
   community
 
 Examples of unacceptable behavior include:
 
-* The use of sexualized language or imagery, and sexual attention or advances of
+- The use of sexualized language or imagery, and sexual attention or advances of
   any kind
-* Trolling, insulting or derogatory comments, and personal or political attacks
-* Public or private harassment
-* Publishing others' private information, such as a physical or email address,
+- Trolling, insulting or derogatory comments, and personal or political attacks
+- Public or private harassment
+- Publishing others' private information, such as a physical or email address,
   without their explicit permission
-* Other conduct which could reasonably be considered inappropriate in a
+- Other conduct which could reasonably be considered inappropriate in a
   professional setting
 
 ## Enforcement Responsibilities