inital repository setup

.github/CODEOWNERS

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+# default owners
+* @albrja @hussain-jafari @patricktnast @rmudambi @stevebachmeier

.github/pull_request_template.md

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+## Title: Summary, imperative, start upper case, don't end with a period
+<!-- Ideally, <=50 chars. 50 chars is here..: -->
+
+### Description
+<!-- For use in commit message, wrap at 72 chars. 72 chars is here: -->
+- *Category*: <!-- one of bugfix, data artifact, implementation, observers,
+                   post-processing, refactor, revert, test, release, other/misc -->
+- *JIRA issue*: https://jira.ihme.washington.edu/browse/MIC-XYZ
+- *Research reference*: <!--Link to research documentation for code -->
+
+### Changes and notes
+<!-- 
+Change description – why, what, anything unexplained by the above.
+Include guidance to reviewers if changes are complex.
+--> 
+
+### Verification and Testing
+<!--
+Details on how code was verified. Consider: plots, images, (small) csv files.
+-->
+

.github/workflows/build.yml

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+# -----------------------------------------------------------------------------
+#   - invoked on push, pull_request, or manual trigger
+#   - test under all supported versions of Python (python_versions.json)
+# -----------------------------------------------------------------------------
+name: build
+on: [push, pull_request, workflow_dispatch]
+
+jobs:
+  get-python-versions:
+    runs-on: ubuntu-latest
+    steps:
+      - name: Checkout code
+        uses: actions/checkout@v2
+      - name: Install jq
+        run: sudo apt-get install jq
+      - name: Get Python versions
+        id: set-matrix
+        run: |
+          echo "MATRIX_RESULT=$(jq -c . python_versions.json)" >> $GITHUB_ENV
+    outputs:
+      matrix: ${{ env.MATRIX_RESULT }}
+  build:
+    needs: get-python-versions
+    runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        python-version: ${{ fromJSON(needs.get-python-versions.outputs.matrix) }}
+    defaults:
+      run:
+        shell: bash -l {0}
+    steps:
+      - uses: actions/checkout@v2
+      - name: Set up Python
+        uses: actions/setup-python@v2
+        with:
+          python-version: ${{ matrix.python-version }}
+      - name: get upstream branch name
+        run: |
+          if "${{ github.event_name == 'pull_request' }}" ; then
+            echo "branch_name=${GITHUB_HEAD_REF}" >> $GITHUB_ENV
+          else
+            echo "branch_name=${GITHUB_REF_NAME}" >> $GITHUB_ENV
+          fi
+      - name: check for upstream vivarium
+        run: |
+          if git ls-remote --exit-code --heads https://github.com/ihmeuw/vivarium.git ${branch_name} == "0"; then
+            echo "upstream_exist=true" >> $GITHUB_ENV
+          else
+            echo "upstream_exist=false" >> $GITHUB_ENV
+          fi
+      - name: check for upstream vivarium_public_health
+        run: |
+          if git ls-remote --exit-code --heads https://github.com/ihmeuw/vivarium_public_health.git ${branch_name} == "0"; then
+            echo "upstream_exist=true" >> $GITHUB_ENV
+          else
+            echo "upstream_exist=false" >> $GITHUB_ENV
+          fi
+      - name: check for upstream vivarium_inputs
+        run: |
+          if git ls-remote --exit-code --heads https://github.com/ihmeuw/vivarium_inputs.git ${branch_name} == "0"; then
+            echo "upstream_exist=true" >> $GITHUB_ENV
+          else
+            echo "upstream_exist=false" >> $GITHUB_ENV
+          fi
+      - name: print environment values
+        run: |
+          cat $GITHUB_ENV
+      - name: Update pip
+        run: |
+          python -m pip install --upgrade pip
+      - name: Retrieve upstream vivarium
+        if: env.upstream_vivarium_exist == 'true'
+        run: |
+          echo "Cloning vivarium upstream branch: ${GITHUB_HEAD_REF}"
+          git clone --branch=${GITHUB_HEAD_REF} https://github.com/ihmeuw/vivarium.git
+          pushd vivarium
+          pip install .
+          popd
+      - name: Retrieve upstream vivarium_public_health
+        if: env.upstream_vivarium_public_health_exist == 'true'
+        run: |
+          echo "Cloning vivarium_public_health upstream branch: ${GITHUB_HEAD_REF}"
+          git clone --branch=${GITHUB_HEAD_REF} https://github.com/ihmeuw/vivarium_public_health.git
+          pushd vivarium_public_health
+          pip install .
+          popd
+      - name: Retrieve upstream vivarium_inputs
+        if: env.upstream_vivarium_inputs_exist == 'true'
+        run: |
+          echo "Cloning upstream vivarium_inputs branch: ${GITHUB_HEAD_REF}"
+          git clone --branch=${GITHUB_HEAD_REF} https://github.com/ihmeuw/vivarium_inputs.git
+          pushd vivarium_inputs
+          pip install .
+          popd
+      - name: Install dependencies
+        run: |
+          pip install .[test]
+      - name: Lint
+        run: |
+          pip install black==22.3.0 isort
+          black . --check -v
+          isort . --check -v
+      - name: Test
+        run: |
+          pytest ./tests

.github/workflows/update_readme.yml

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+# -----------------------------------------------------------------------------
+#   - invoked on push to any branch
+# -----------------------------------------------------------------------------
+name: update README
+on: push
+
+jobs:
+    update-readme:
+    runs-on: ubuntu-latest
+    steps:
+        - name: Checkout code
+        uses: actions/checkout@v2
+        - name: Set up Python
+        uses: actions/setup-python@v2
+        with:
+            python-version: 3.11
+        - name: Update README
+        run: |
+            pip install packaging
+            python update_readme.py
+        - name: Commit and push changes
+        run: |
+            git config --local user.email "[email protected]"
+            git config --local user.name "github-actions"
+            git diff --quiet && git diff --staged --quiet || (
+            git add README.rst
+            git commit -am "update README with supported Python versions"
+            git pull --rebase origin ${{ github.ref_name }}
+            git push origin ${{ github.ref_name }}
+            )
+        env:
+            GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}

.gitignore

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+# Byte-compiled / optimized / DLL files
+__pycache__/
+*.py[cod]
+*$py.class
+
+# C extensions
+*.so
+
+# Distribution / packaging
+.Python
+build/
+develop-eggs/
+dist/
+downloads/
+eggs/
+.eggs/
+lib/
+lib64/
+parts/
+sdist/
+var/
+wheels/
+pip-wheel-metadata/
+share/python-wheels/
+*.egg-info/
+.installed.cfg
+*.egg
+MANIFEST
+
+# PyInstaller
+#  Usually these files are written by a python script from a template
+#  before PyInstaller builds the exe, so as to inject date/other infos into it.
+*.manifest
+*.spec
+
+# Installer logs
+pip-log.txt
+pip-delete-this-directory.txt
+
+# Unit test / coverage reports
+htmlcov/
+.tox/
+.nox/
+.coverage
+.coverage.*
+.cache
+nosetests.xml
+coverage.xml
+*.cover
+.hypothesis/
+.pytest_cache/
+
+# Translations
+*.mo
+*.pot
+
+# Django stuff:
+*.log
+local_settings.py
+db.sqlite3
+db.sqlite3-journal
+
+# Flask stuff:
+instance/
+.webassets-cache
+
+# Scrapy stuff:
+.scrapy
+
+# Sphinx documentation
+docs/_build/
+
+# PyBuilder
+target/
+
+# Jupyter Notebook
+.ipynb_checkpoints
+
+# IPython
+profile_default/
+ipython_config.py
+
+# pyenv
+.python-version
+
+# pipenv
+#   According to pypa/pipenv#598, it is recommended to include Pipfile.lock in version control.
+#   However, in case of collaboration, if having platform-specific dependencies or dependencies
+#   having no cross-platform support, pipenv may install dependencies that don't work, or not
+#   install all needed dependencies.
+#Pipfile.lock
+
+# celery beat schedule file
+celerybeat-schedule
+
+# SageMath parsed files
+*.sage.py
+
+# Environments
+.env
+.venv
+env/
+venv/
+ENV/
+env.bak/
+venv.bak/
+
+# Spyder project settings
+.spyderproject
+.spyproject
+
+# Rope project settings
+.ropeproject
+
+# mkdocs documentation
+/site
+
+# mypy
+.mypy_cache/
+.dmypy.json
+dmypy.json
+
+# Pyre type checker
+.pyre/
+
+# Pycharm project settings
+.idea/
+
+# Version file
+src/*/_version.py

.zenodo.json

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+{
+    "license": "BSD-3-Clause",
+    "title": "ihmeuw/vivarium_sodium_reduction: Archival release",
+    "upload_type": "software",
+    "creators": [
+//        {
+//            "orcid": "0000-0000-0000-0000",
+//            "affiliation": "Institute for Health Metrics and Evaluation",
+//            "name": "TODO: Add authors names, affiliation, and orcid (if applicable) to `creators` array"
+//        }
+    ],
+    "access_right": "open",
+    "description": "<p>TODO: add description (e.g., Archival release of simulation software.)</p>"
+}

CHANGELOG.rst

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+**v0.0.0 - mm/dd/yy**
+
+ - Initial release

LICENSE

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+BSD 3-Clause License
+
+Copyright 2022 Institute for Health Metrics and Evaluation
+All rights reserved
+
+Redistribution and use in source and binary forms, with or without
+modification, are permitted provided that the following conditions are met:
+
+1. Redistributions of source code must retain the above copyright notice, this
+   list of conditions and the following disclaimer.
+
+2. Redistributions in binary form must reproduce the above copyright notice,
+   this list of conditions and the following disclaimer in the documentation
+   and/or other materials provided with the distribution.
+
+3. Neither the name of the copyright holder nor the names of its
+   contributors may be used to endorse or promote products derived from
+   this software without specific prior written permission.
+
+THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
+DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE
+FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
+DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
+SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
+CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
+OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
+OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.

MANIFEST.in

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+include LICENSE
+include README.rst
+
+recursive-include src/vivarium_sodium_reduction *.py *.yaml *.ipynb
+recursive-include tests *.py *txt *.yaml