First commit

.github/CODEOWNERS

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+# All changes to PL
+* @gvegayoncdc
+
+# Anything under pipeline should pass to
+pipeline/ @natemcintosh

.github/ISSUE_TEMPLATE/development_task.md

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+---
+name: Multisignal Renewal Dev Task Template
+about: A template for writing specs following Multisignal Renewal project standards
+title: ''
+labels: ["development task"]
+assignees: ''
+---
+
+This template should be used as an outline. It may not be necessary to fill out every section. Delete this block of text and fill in anything in brackets.
+
+Make sure you follow the project's standards specified in [this adr doc](https://github.com/cdcent/cfa-multisignal-renewal/blob/main/ADR/model/development_standards.md) (private link)
+
+## Goal
+
+[1-3 sentence summary of the issue or feature request. E.g. "We want to be able to ..."]
+
+## Context
+
+[Short paragraph describing how the issue arose and constraints imposed by the existing code architecture]
+
+## Required features
+
+- [Describe each thing you need the code to do to achieve the goal]
+- [Example 1: Use a config to set input and output paths]
+- [Example 2: Read in some-dataset and output some-transformed-dataset]
+- etc...
+
+## Specifications
+
+[A checklist to keep track of details for each feature. At least one specification per feature is recommended. Edit the example below:]
+
+- [ ] EX2: A function that reads data from the `some-api` API and returns the dataset
+- [ ] EX2: Another function that inputs the dataset, performs $x$ transform, and outputs $y$
+- [ ] EX1: A script that runs the workflow from a config
+- [ ] All functions should follow PEP8 package conventions with blah, blah, blah
+- [ ] The workflow should run in the VAP from `directory`
+- [ ] All functions should have associated unit tests
+- [ ] etc. etc.
+
+## Out of scope
+
+- [Things out of scope from this issue/PR]
+
+## Related documents
+
+- [Link to related scripts, functions, issues, PRs, conversations, datasets, etc.]

.github/unused_templates/bug_report.md

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+---
+name: Bug report
+about: Create a report to help us improve
+title: ''
+labels: ''
+assignees: ''
+
+---
+
+**Describe the bug**
+A clear and concise description of what the bug is.
+
+**To Reproduce**
+Steps to reproduce the behavior:
+1. Go to '...'
+2. Click on '....'
+3. Scroll down to '....'
+4. See error
+
+**Expected behavior**
+A clear and concise description of what you expected to happen.
+
+**Screenshots**
+If applicable, add screenshots to help explain your problem.
+
+**Desktop (please complete the following information):**
+ - OS: [e.g. iOS]
+ - Browser [e.g. chrome, safari]
+ - Version [e.g. 22]
+
+**Smartphone (please complete the following information):**
+ - Device: [e.g. iPhone6]
+ - OS: [e.g. iOS8.1]
+ - Browser [e.g. stock browser, safari]
+ - Version [e.g. 22]
+
+**Additional context**
+Add any other context about the problem here.

.github/unused_templates/feature_request.md

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+---
+name: Feature request
+about: Suggest an idea for this project
+title: ''
+labels: ''
+assignees: ''
+
+---
+
+**Is your feature request related to a problem? Please describe.**
+A clear and concise description of what the problem is. Ex. I'm always frustrated when [...]
+
+**Describe the solution you'd like**
+A clear and concise description of what you want to happen.
+
+**Describe alternatives you've considered**
+A clear and concise description of any alternative solutions or features you've considered.
+
+**Additional context**
+Add any other context or screenshots about the feature request here.

.github/unused_templates/scientific-improvement.md

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+---
+name: Scientific improvement
+about: Suggest a way to improve an existing tool or pipeline
+title: ''
+labels: ''
+assignees: ''
+
+---
+
+## Describe the improvement that needs to be made
+(e.g. update a parameter estimate, tweak the prior, modify the model)
+
+## Provide links to references to methods or data sources
+
+## Describe the changes expected to the model's outputs
+
+## Suggest new tests that will need to be implemented

.github/workflows/pre-commit.yaml

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+name: pre-commit
+
+on:
+  pull_request:
+  push:
+    branches: [main]
+
+jobs:
+  pre-commit:
+    runs-on: ubuntu-latest
+    steps:
+    - uses: actions/checkout@v4
+    - uses: actions/setup-python@v5
+      with:
+        python-version: "3.12"
+    - uses: pre-commit/[email protected]

.github/workflows/test_model.yaml

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+name: installation and testing model
+
+on:
+  pull_request:
+  push:
+    branches: [main]
+
+jobs:
+  install-and-test:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+      - uses: actions/setup-python@v5
+        with:
+          python-version: "3.12"
+      - name: cache poetry
+        uses: actions/cache@v4
+        with:
+          path: ~/.local
+          key: ${{ runner.os }}-poetry
+      - name: install poetry
+        run: pip install poetry
+      - name: install package
+        run: poetry install -C model
+      - name: run tests
+        run: poetry run -C model pytest model

.github/workflows/test_pipeline.yaml

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+name: installation and testing pipeline
+
+on:
+  pull_request:
+  push:
+    branches: [main]
+
+jobs:
+  install-and-test:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+      - uses: actions/setup-python@v5
+        with:
+          python-version: "3.12"
+      - name: cache poetry
+        uses: actions/cache@v4
+        with:
+          path: ~/.local
+          key: ${{ runner.os }}-poetry
+      - name: install poetry
+        run: pip install poetry
+      - name: install package
+        run: poetry install -C pipeline
+      - name: run tests
+        run: poetry run -C pipeline pytest pipeline