Merge pull request #1 from jdebacker/initial_files

Initial files

.github/ISSUE_TEMPLATE.md

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+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

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+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

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+name: Build and test
+on:
+  push:
+    paths:
+      - '**.yml'
+      - '**.toml'
+      - '**.ini'
+      - '**.py'
+      - '**.json'
+      - '**.csv'
+      - '**.pkl'
+  pull_request:
+    paths:
+      - '**.yml'
+      - '**.toml'
+      - '**.ini'
+      - '**.py'
+      - '**.json'
+      - '**.csv'
+      - '**.pkl'
+jobs:
+  build:
+    runs-on: ${{ matrix.os }}
+    strategy:
+      matrix:
+        os: [ubuntu-latest, macos-latest, windows-latest]
+        python-version: ["3.10", "3.11"]
+
+    steps:
+      - name: Checkout
+        uses: actions/checkout@v4
+        with:
+          persist-credentials: false
+
+      - name: Setup Miniconda using Python ${{ matrix.python-version }}
+        uses: conda-incubator/setup-miniconda@v3
+        with:
+          miniforge-variant: Mambaforge
+          auto-update-conda: true
+          activate-environment: ogidn-dev
+          environment-file: environment.yml
+          python-version: ${{ matrix.python-version }}
+          auto-activate-base: false
+
+      - name: Build
+        shell: bash -l {0}
+        run: |
+          pip install -e .
+      - name: Test
+        shell: bash -l {0}
+        working-directory: ./
+        run: |
+          python -m pytest -m 'not local' --cov=./ --cov-report=xml
+      - name: Upload coverage to Codecov
+        if: matrix.os == 'ubuntu-latest' && contains(github.repository, 'EAPD-DRB/OG-IDN')
+        uses: codecov/codecov-action@v4
+        with:
+          files: ./coverage.xml
+          flags: unittests
+          name: codecov-umbrella
+          token: ${{ secrets.CODECOV_TOKEN }}
+          fail_ci_if_error: true
+          verbose: true

.github/workflows/check_format.yml

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+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

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+name: Build and Deploy Jupyter Book documentation
+on:
+  push:
+    branches:
+      - main
+    paths:
+      - './docs/**.png'
+      - './docs/book/content/calibration/images/**.png'
+      - './docs/README.md'
+      - './docs/book/**.yml'
+      - './docs/book/**.bib'
+      - '**.md'
+      - './docs/book/content/api/**.rst'
+      - './ogidn/**.py'
+jobs:
+  build-and-deploy:
+    if: github.repository == 'EAPD-DRB/OG-IDN'
+    runs-on: ubuntu-latest
+    steps:
+      - name: Checkout
+        uses: actions/checkout@v4
+        with:
+          persist-credentials: false
+
+      - name: Setup Miniconda
+        uses: conda-incubator/setup-miniconda@v3
+        with:
+          miniforge-variant: Mambaforge
+          activate-environment: ogidn-dev
+          environment-file: environment.yml
+          python-version: "3.11"
+          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=ogidn-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

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+name: Check that docs build
+on:
+  pull_request:
+    paths:
+      - './docs/**.png'
+      - './docs/book/content/calibration/images/**.png'
+      - './docs/README.md'
+      - './docs/book/**.yml'
+      - './docs/book/**.bib'
+      - '**.md'
+      - './docs/book/content/api/**.rst'
+      - './ogidn/**.py'
+
+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@v3
+        with:
+          miniforge-variant: Mambaforge
+          activate-environment: ogidn-dev
+          environment-file: environment.yml
+          python-version: "3.11"
+          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=ogidn-dev
+          jb build ./docs/book

.github/workflows/publish_to_pypi.yml

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+name: Publish package to PyPI
+
+on:
+  push:
+    branches:
+      - main
+
+jobs:
+  deploy:
+    name: Publish to PyPI
+    if: github.repository == 'EAPD-DRB/OG-IDN'
+    runs-on: ubuntu-latest
+    steps:
+      - name: Checkout repo
+        uses: actions/checkout@v4
+      - name: Setup Python
+        uses: actions/setup-python@v4
+        with:
+          python-version: "3.11"
+      - 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

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+*.pyc
+MANIFEST
+build/*
+dist/*
+*.cache/
+.coverage
+.coveragerc
+htmlcov/*
+*.aux
+*.bbl
+*.blg
+*.fdb_latexmk
+*.idx
+*.ilg
+*.ind
+*.lof
+*.log
+*.lot
+*.out
+*.pdfsync
+*.synctex.gz
+*.toc
+*.swp
+*.asv
+*.nav
+*.snm
+*.gz
+*.bib.bak
+*.fls
+*.m~
+*.sublime*
+*.DS_Store*
+*puf.csv
+*tax_func_loop_inputs_large.pkl
+*/OUTPUT/*
+envs/
+*.egg-info/
+*dask-worker-space*
+.ipynb_checkpoints*
+*/__pycache__/*
+*.coverage*
+*coverage.xml*
+docs/book/_build/*
+*/OG-ZAF_example_plots/*
+*ogzaf_example_output.csv
+*/OG-ZAF-Example/*

CHANGELOG.md

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+# 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).
+
+
+## [0.0.0] - 2024-06-20 12:00:00
+
+### Added
+
+- This version is a pre-release alpha. The example run script OG-IDN/examples/run_og_idn.py runs, but the model is not currently calibrated to represent the Indonesian economy and population.
+