Merge branch 'EAPD-DRB:main' into main

.github/ISSUE_TEMPLATE.md

@@ -0,0 +1,7 @@
+Thanks for filing an issue! Please remove any top-level headers that do not apply.
+
+# Problem or Error
+Please characterize the problem concisely and precisely. You may want to include error message output, other terminal output, your environment characteristics, and a way to replicate the issue. Let us know what solutions you have tried.
+
+# Question
+Please ask the question with clear context and any potential answer directions you can think of.

.github/PULL_REQUEST_TEMPLATE.md

@@ -0,0 +1,16 @@
+Thanks for contributing! Please remove any top-level sections that do not apply to your changes.
+
+- [ ] `make format` and `make documentation` has been run. (You may also want to run `make test`.)
+
+## What's changed
+
+Description of the changes here.
+
+# Bug fix
+
+- [ ] Continuous integration test added
+- [ ] Continuous integration test passing
+
+## What this fixes and how it's fixed
+
+Description of how this fix works goes here. Link any issues this PR fixes.

.github/workflows/build_and_test.yml

@@ -0,0 +1,47 @@
+name: Build and test [Python 3.9, 3.10]
+
+on: [push, pull_request]
+
+jobs:
+  build:
+    runs-on: ${{ matrix.os }}
+    strategy:
+      matrix:
+        os: [ubuntu-latest, macos-latest]
+        python-version: ["3.9", "3.10"]
+
+    steps:
+      - name: Checkout
+        uses: actions/checkout@v4
+        with:
+          persist-credentials: false
+
+      - name: Setup Miniconda using Python ${{ matrix.python-version }}
+        uses: conda-incubator/setup-miniconda@v2
+        with:
+          miniforge-variant: Mambaforge
+          auto-update-conda: true
+          activate-environment: ogzaf-dev
+          environment-file: environment.yml
+          python-version: ${{ matrix.python-version }}
+          auto-activate-base: false
+
+      - name: Build
+        shell: bash -l {0}
+        run: |
+          pip install -e .
+          pip install pytest-cov
+          pip install pytest-pycodestyle
+      - name: Test
+        shell: bash -l {0}
+        working-directory: ./
+        run: |
+          pytest -m 'not local' --cov=./ --cov-report=xml
+      - name: Upload coverage to Codecov
+        uses: codecov/codecov-action@v3
+        with:
+          files: ./coverage.xml
+          flags: unittests
+          name: codecov-umbrella
+          fail_ci_if_error: true
+          verbose: true

.github/workflows/check_format.yml

@@ -0,0 +1,14 @@
+name: Check code formatting
+
+on: [push, pull_request]
+
+jobs:
+  lint:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+      - uses: actions/setup-python@v4
+      - uses: psf/black@stable
+        with:
+          options: "-l 79 --check"
+          src: "."

.github/workflows/deploy_docs.yml

@@ -0,0 +1,39 @@
+name: Build and Deploy Jupyter Book documentation
+on:
+  push:
+    branches:
+      - main
+jobs:
+  build-and-deploy:
+    if: github.repository == 'EAPD-DRB/OG-ZAF'
+    runs-on: ubuntu-latest
+    steps:
+      - name: Checkout
+        uses: actions/checkout@v4
+        with:
+          persist-credentials: false
+
+      - name: Setup Miniconda
+        uses: conda-incubator/setup-miniconda@v2
+        with:
+          miniforge-variant: Mambaforge
+          activate-environment: ogzaf-dev
+          environment-file: environment.yml
+          python-version: "3.10"
+          auto-activate-base: false
+
+      - name: Build # Build Jupyter Book
+        shell: bash -l {0}
+        run: |
+          pip install jupyter-book>=0.11.3
+          pip install sphinxcontrib-bibtex>=2.0.0
+          pip install -e .
+          python -m ipykernel install --user --name=ogzaf-dev
+          jb build ./docs/book
+
+      - name: Deploy
+        uses: JamesIves/github-pages-deploy-action@releases/v4
+        with:
+          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+          BRANCH: gh-pages # The branch the action should deploy to.
+          FOLDER: docs/book/_build/html # The folder the action should deploy.

.github/workflows/docs_check.yml

@@ -0,0 +1,29 @@
+name: Check that docs build
+on: [push, pull_request]
+
+jobs:
+  build:
+    runs-on: ubuntu-latest
+    steps:
+      - name: Checkout
+        uses: actions/checkout@v4
+        with:
+          persist-credentials: false
+
+      - name: Setup Miniconda
+        uses: conda-incubator/setup-miniconda@v2
+        with:
+          miniforge-variant: Mambaforge
+          activate-environment: ogzaf-dev
+          environment-file: environment.yml
+          python-version: "3.10"
+          auto-activate-base: false
+
+      - name: Build # Build Jupyter Book
+        shell: bash -l {0}
+        run: |
+          pip install jupyter-book>=0.11.3
+          pip install sphinxcontrib-bibtex>=2.0.0
+          pip install -e .
+          python -m ipykernel install --user --name=ogzaf-dev
+          jb build ./docs/book

.github/workflows/publish_to_pypi.yml

@@ -0,0 +1,30 @@
+name: Publish package to PyPI
+
+on:
+  push:
+    branches:
+      - main
+
+jobs:
+  deploy:
+    name: Publish to PyPI
+    if: github.repository == 'EAPD-DRB/OG-ZAF'
+    runs-on: ubuntu-latest
+    steps:
+      - name: Checkout repo
+        uses: actions/checkout@v4
+      - name: Setup Python
+        uses: actions/setup-python@v4
+        with:
+          python-version: "3.10"
+      - name: Build package
+        shell: bash -l {0}
+        run: |
+          pip install wheel
+          python setup.py sdist bdist_wheel
+      - name: Publish a Python distribution to PyPI
+        uses: pypa/gh-action-pypi-publish@release/v1
+        with:
+          user: __token__
+          password: ${{ secrets.PYPI }}
+          skip_existing: true

.gitignore

@@ -38,8 +38,9 @@ envs/
 *dask-worker-space*
 .ipynb_checkpoints*
 */__pycache__/*
+*.coverage*
+*coverage.xml*
 docs/book/_build/*
-docs/build*
-examples/OG-ZAF_example_plots/*
-examples/ogzaf_example_output.csv
-examples/OG-ZAF-Example/*
+*/OG-ZAF_example_plots/*
+*ogzaf_example_output.csv
+*/OG-ZAF-Example/*

CHANGELOG.md

@@ -0,0 +1,27 @@
+# Changelog
+
+All notable changes to this project will be documented in this file.
+
+The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/),
+and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
+
+## [0.0.1] - 2023-10-30 8:00:00
+
+### Added
+
+- Adds CI tests `check_format.yml`, `build_and_test.yml`, `docs_build.yml`, `deploy_docs.yml`, `publish_to_pypi.yml`
+- Adds `/tests/` directory with test files in it
+- Added `Makefile`
+- Updated `environment.yml` and `setup.py`
+- Updated `pyproject.toml`
+- Updates the `README.md`
+
+## [0.0.0] - 2022-10-15 12:00:00
+
+### Added
+
+- This version is a pre-release alpha. The example run script OG-ZAF/examples/run_og_zaf.py runs, but the model is not currently calibrated to represent the South African economy and population.
+
+
+
+[0.0.1]: https://github.com/EAPD-DRB/OG-ZAF/compare/v0.0.0...v0.0.1

LICENSE

@@ -0,0 +1,121 @@
+Creative Commons Legal Code
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MANIFEST.in

@@ -0,0 +1,5 @@
+include ogzaf/data/demographic/un_zaf_deaths.csv
+include ogzaf/data/demographic/un_zaf_fert.csv
+include ogzaf/data/demographic/un_zaf_infmort.csv
+include ogzaf/data/demographic/un_zaf_mort.csv
+include ogzaf/data/demographic/un_zaf_pop.csv