feat: 🎉 Project setup (WIP)

.copier-answers.yml

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+# Changes here will be overwritten by Copier
+_commit: 1.2.6
+_src_path: gh:pawamoy/copier-pdm
+author_email: bernardo@impulsogov.org
+author_fullname: Bernardo Chrispim Baron
+author_username: bcbernardo
+copyright_date: '2024'
+copyright_holder: ImpulsoGov
+copyright_holder_email: contato@impulsogov.org
+copyright_license: MIT License
+insiders: false
+project_description: A stochastic model of the natural history and effects of vaccination
+    and screening in the progression of Human Papillomavirus infections and cervical
+    precancer lesions and invasive cancers.
+project_name: HPV Progression Model
+python_package_command_line_name: hpv-model
+python_package_distribution_name: hpv_progression_model
+python_package_import_name: hpv_progression_model
+repository_name: hpv-progression-model
+repository_namespace: ImpulsoGov
+repository_provider: github.com
+

.github/FUNDING.yml

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+github: bcbernardo
+ko_fi: bcbernardo
+custom:
+- https://www.paypal.me/bcbernardo

.github/ISSUE_TEMPLATE/bug_report.md

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+---
+name: Bug report
+about: Create a bug report to help us improve.
+title: "bug: "
+labels: unconfirmed
+assignees: [pawamoy]
+---
+
+### Description of the bug
+<!-- Please provide a clear and concise description of what the bug is. -->
+
+### To Reproduce
+<!-- Please provide a Minimal Reproducible Example (MRE) if possible.
+     Try to boil down the problem to a few lines of code.
+     Your code should run by simply copying and pasting it.
+
+     Example:
+
+     ```
+     git clone https://github.com/username/repro
+     cd repro
+     python -m venv .venv
+     . .venv/bin/activate
+     pip install -r requirements.txt
+     ...  # command or code showing the issue
+     ```
+-->
+
+```
+WRITE MRE / INSTRUCTIONS HERE
+```
+
+### Full traceback
+<!-- Please provide the full error message / traceback if any, by pasting it in the code block below.
+     No snapshots! -->
+
+<details><summary>Full traceback</summary>
+
+```python
+PASTE TRACEBACK HERE
+```
+
+</details>
+
+### Expected behavior
+<!-- Please provide a clear and concise description of what you expected to happen. -->
+
+### Environment information
+<!-- Please run the following command in your repository and paste its output below it,
+     redacting sensitive information. -->
+
+```bash
+hpv-model --debug-info  # | xclip -selection clipboard
+```
+
+PASTE OUTPUT HERE
+
+### Additional context
+<!-- Add any other relevant context about the problem here,
+     like links to other issues or pull requests, snapshots, etc.
+-->

.github/ISSUE_TEMPLATE/config.yml

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+blank_issues_enabled: false
+contact_links:
+- name: I have a question / I need help
+  url: https://github.com/ImpulsoGov/hpv-progression-model/discussions/new?category=q-a
+  about: Ask and answer questions in the Discussions tab.

.github/ISSUE_TEMPLATE/feature_request.md

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+---
+name: Feature request
+about: Suggest an idea for this project.
+title: "feature: "
+labels: feature
+assignees: pawamoy
+---
+
+### 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 snapshots about the feature request here. -->

.github/workflows/ci.yml

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+name: ci
+
+on:
+  push:
+  pull_request:
+    branches:
+    - main
+
+defaults:
+  run:
+    shell: bash
+
+env:
+  LANG: en_US.utf-8
+  LC_ALL: en_US.utf-8
+  PYTHONIOENCODING: UTF-8
+
+jobs:
+
+  quality:
+
+    runs-on: ubuntu-latest
+
+    steps:
+    - name: Checkout
+      uses: actions/checkout@v4
+
+    - name: Fetch all tags
+      run: git fetch --depth=1 --tags
+
+    - name: Set up PDM
+      uses: pdm-project/setup-pdm@v4
+      with:
+        python-version: "3.8"
+
+    - name: Resolving dependencies
+      run: pdm lock -v --no-cross-platform -G ci-quality
+
+    - name: Install dependencies
+      run: pdm install -G ci-quality
+
+    - name: Check if the documentation builds correctly
+      run: pdm run duty check-docs
+
+    - name: Check the code quality
+      run: pdm run duty check-quality
+
+    - name: Check if the code is correctly typed
+      run: pdm run duty check-types
+
+    - name: Check for vulnerabilities in dependencies
+      run: pdm run duty check-dependencies
+
+    - name: Check for breaking changes in the API
+      run: pdm run duty check-api
+
+  tests:
+
+    strategy:
+      max-parallel: 4
+      matrix:
+        os:
+        - ubuntu-latest
+        - macos-latest
+        - windows-latest
+        python-version:
+        - "3.8"
+        - "3.9"
+        - "3.10"
+        - "3.11"
+        - "3.12"
+    runs-on: ${{ matrix.os }}
+    continue-on-error: ${{ matrix.python-version == '3.12' }}
+
+    steps:
+    - name: Checkout
+      uses: actions/checkout@v4
+
+    - name: Set up PDM
+      uses: pdm-project/setup-pdm@v4
+      with:
+        python-version: ${{ matrix.python-version }}
+        allow-python-prereleases: true
+
+    - name: Resolving dependencies
+      run: pdm lock -v --no-cross-platform -G ci-tests
+
+    - name: Install dependencies
+      run: pdm install --no-editable -G ci-tests
+
+    - name: Run the test suite
+      run: pdm run duty test

.github/workflows/release.yml

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+name: release
+
+on: push
+permissions:
+  contents: write
+
+jobs:
+  release:
+    runs-on: ubuntu-latest
+    if: startsWith(github.ref, 'refs/tags/')
+    steps:
+    - name: Checkout
+      uses: actions/checkout@v4
+    - name: Fetch all tags
+      run: git fetch --depth=1 --tags
+    - name: Setup Python
+      uses: actions/setup-python@v4
+    - name: Install git-changelog
+      run: pip install git-changelog
+    - name: Prepare release notes
+      run: git-changelog --release-notes > release-notes.md
+    - name: Create release
+      uses: softprops/action-gh-release@v1
+      with:
+        body_path: release-notes.md

.gitignore

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+.idea/
+.vscode/
+__pycache__/
+*.py[cod]
+dist/
+*.egg-info/
+build/
+htmlcov/
+.coverage*
+pip-wheel-metadata/
+.pytest_cache/
+.mypy_cache/
+site/
+pdm.lock
+pdm.toml
+.pdm-plugins/
+.pdm-python
+__pypackages__/
+.venv/
+.cache/

.gitpod.dockerfile

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+FROM gitpod/workspace-full
+USER gitpod
+ENV PIP_USER=no
+RUN pip3 install pipx; \
+    pipx install pdm; \
+    pipx ensurepath

.gitpod.yml

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+vscode:
+  extensions:
+  - ms-python.python
+
+image:
+  file: .gitpod.dockerfile
+
+ports:
+- port: 8000
+  onOpen: notify
+
+tasks:
+- init: make setup

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](http://keepachangelog.com/en/1.0.0/)
+and this project adheres to [Semantic Versioning](http://semver.org/spec/v2.0.0.html).
+
+<!-- insertion marker -->

LICENSE

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+MIT License
+
+Copyright (c) 2024 ImpulsoGov
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.

Makefile

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+.DEFAULT_GOAL := help
+SHELL := bash
+DUTY := $(if $(VIRTUAL_ENV),,pdm run) duty
+export PDM_MULTIRUN_VERSIONS ?= 3.8 3.9 3.10 3.11 3.12
+export PDM_MULTIRUN_USE_VENVS ?= $(if $(shell pdm config python.use_venv | grep True),1,0)
+
+args = $(foreach a,$($(subst -,_,$1)_args),$(if $(value $a),$a="$($a)"))
+check_quality_args = files
+docs_args = host port
+release_args = version
+test_args = match
+
+BASIC_DUTIES = \
+	changelog \
+	check-api \
+	check-dependencies \
+	clean \
+	coverage \
+	docs \
+	docs-deploy \
+	format \
+	release \
+	vscode
+
+QUALITY_DUTIES = \
+	check-quality \
+	check-docs \
+	check-types \
+	test
+
+.PHONY: help
+help:
+	@$(DUTY) --list
+
+.PHONY: lock
+lock:
+	@pdm lock -G:all
+
+.PHONY: setup
+setup:
+	@bash scripts/setup.sh
+
+.PHONY: check
+check:
+	@pdm multirun duty check-quality check-types check-docs
+	@$(DUTY) check-dependencies check-api
+
+.PHONY: $(BASIC_DUTIES)
+$(BASIC_DUTIES):
+	@$(DUTY) $@ $(call args,$@)
+
+.PHONY: $(QUALITY_DUTIES)
+$(QUALITY_DUTIES):
+	@pdm multirun duty $@ $(call args,$@)

README.md

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+# HPV Progression Model
+
+[![ci](https://github.com/ImpulsoGov/hpv-progression-model/workflows/ci/badge.svg)](https://github.com/ImpulsoGov/hpv-progression-model/actions?query=workflow%3Aci)
+[![documentation](https://img.shields.io/badge/docs-mkdocs%20material-blue.svg?style=flat)](https://ImpulsoGov.github.io/hpv-progression-model/)
+[![pypi version](https://img.shields.io/pypi/v/hpv_progression_model.svg)](https://pypi.org/project/hpv_progression_model/)
+
+A stochastic model of the natural history and effects of vaccination and screening in the progression of Human Papillomavirus infections and cervical precancer lesions and invasive cancers.
+
+## Requirements
+
+- Python 3.11+
+
+## Installation
+
+With `pip`:
+
+```bash
+pip install git+https://github.com/ImpulsoGov/hpv-progression-model.git
+```
+
+With [`pipx`](https://github.com/pipxproject/pipx):
+
+```bash
+python3 -m pip install --user pipx
+pipx install git+https://github.com/ImpulsoGov/hpv-progression-model.git
+```
+
+## Getting started
+

config/black.toml

@@ -0,0 +1,3 @@
+[tool.black]
+line-length = 120
+exclude = "tests/fixtures"