Merge pull request #1

Add initial structure

.github/workflows/docs.yml

@@ -0,0 +1,39 @@
+# This pipeline builds the documentation.
+name: docs
+
+on:
+  push:
+    branches: [ main ]
+
+permissions:
+  contents: write
+
+jobs:
+  deploy:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v3
+      - name: Set up Python
+        uses: actions/setup-python@v4
+        with:
+          python-version: "3.10"
+          cache: "pip"
+      - name: Install Poetry
+        uses: snok/install-poetry@v1
+        with:
+          virtualenvs-create: true
+          virtualenvs-in-project: true
+          version: "1.5.1"
+      - name: Cache dependencies
+        id: cache-deps
+        uses: actions/cache@v2
+        with:
+          path: .venv
+          key: pydeps-${{ hashFiles('**/poetry.lock') }}
+      - name: Install the dependencies
+        run: poetry install --no-interaction --no-root --with dev
+        if: steps.cache-deps.outputs.cache-hit != 'true'
+      - name: Install the module
+        run: poetry install --with dev --no-interaction
+      - name: Generate the documentation
+        run: poetry run mkdocs gh-deploy --force

.github/workflows/test.yml

@@ -0,0 +1,53 @@
+# This pipeline checks whether the package
+# installs properly, passes unit tests and whether
+# the code formatting is right.
+name: build
+
+on:
+  push:
+    branches: [ main ]
+  pull_request:
+    branches: [ main ]
+
+jobs:
+  build:
+    runs-on: ubuntu-latest
+    strategy:
+      fail-fast: true
+      matrix:
+        python-version: ["3.10"]
+        poetry-version: ["1.3.2"]
+
+    steps:
+      - uses: actions/checkout@v3
+      - name: Run black formatting check
+        uses: psf/black@stable
+      - name: Set up Python ${{ matrix.python-version }}
+        uses: actions/setup-python@v4
+        with:
+          python-version: ${{ matrix.python-version }}
+          cache: "pip"
+      - name: Install Poetry
+        uses: snok/install-poetry@v1
+        with:  
+          virtualenvs-create: true
+          virtualenvs-in-project: true
+          version: ${{ matrix.poetry-version }}
+      - name: Cache dependencies
+        id: cache-deps
+        uses: actions/cache@v2
+        with:
+          path: .venv
+          key: pydeps-${{ hashFiles('**/poetry.lock') }}
+      - name: Install the dependencies
+        run: poetry install --no-interaction --no-root --with dev
+        if: steps.cache-deps.outputs.cache-hit != 'true'
+      - name: Install the module
+        run: poetry install --with dev --no-interaction
+      - name: Run unit tests
+        run: poetry run pytest
+      - name: Run Ruff
+        run: poetry run ruff check .
+      - name: Run Pyright (type checking)
+        run: poetry run pyright
+

.gitignore

@@ -1,3 +1,20 @@
+# Notebooks by default should not be uploaded (use Quarto Markdown as an alternative)
+*.nb
+*.ipynb
+
+# Data and plots
+*.csv
+*.jpg
+*.jpeg
+*.npy
+*.npz
+*.pdf
+*.png
+*.zip
+
+# Poetry lock file
+poetry.lock
+
 # Byte-compiled / optimized / DLL files
 __pycache__/
 *.py[cod]

.pre-commit-config.yaml

@@ -0,0 +1,18 @@
+repos:
+  - repo: https://github.com/psf/black
+    rev: 23.1.0
+    hooks:
+      - id: black
+  - repo: https://github.com/charliermarsh/ruff-pre-commit
+    rev: 'v0.0.245'
+    hooks:
+      - id: ruff
+        args: [--fix, --exit-non-zero-on-fix]
+  - repo: local
+    hooks:
+      - id: pyright
+        name: pyright
+        entry: poetry run pyright
+        language: node
+        pass_filenames: true
+        types: [python]

README.md

@@ -1,2 +1,37 @@
-# covvfit-
-fitness estimates of SARS-CoV-2 variants
+[![Project Status: WIP – Initial development is in progress, but there has not yet been a stable, usable release suitable for the public.](https://www.repostatus.org/badges/latest/wip.svg)](https://www.repostatus.org/#wip)
+[![build](https://github.com/cbg-ethz/covvfit/actions/workflows/test.yml/badge.svg?branch=main)](https://github.com/cbg-ethz/covvfit/actions/workflows/test.yml)
+[![Ruff](https://img.shields.io/endpoint?url=https://raw.githubusercontent.com/charliermarsh/ruff/main/assets/badge/v2.json)](https://github.com/charliermarsh/ruff)
+[![Code style: black](https://img.shields.io/badge/code%20style-black-000000.svg)](https://github.com/psf/black)
+
+
+# covvfit
+Fitness estimates of SARS-CoV-2 variants.
+
+  - **Documentation:** [https://cbg-ethz.github.io/covvfit](https://cbg-ethz.github.io/covvfit)
+  - **Source code:** [https://github.com/cbg-ethz/covvfit](https://github.com/cbg-ethz/covvfit)
+  - **Bug reports:** [https://github.com/cbg-ethz/covvfit/issues](https://github.com/cbg-ethz/covvfit/issues)
+
+
+## Installation
+
+### Developers
+Create a new environment, e.g., using [Micromamba](https://mamba.readthedocs.io/en/latest/user_guide/micromamba.html):
+```bash
+$ micromamba create -n covvfit -c conda-forge python=3.10
+```
+
+Then, install the package. 
+
+For a machine where development happens it comes with developer utilities:
+
+```bash
+$ pip install poetry
+$ poetry install --with dev
+$ pre-commit install
+```
+
+## See Also
+
+  - [V-pipe](https://cbg-ethz.github.io/V-pipe/): a bioinformatics pipeline for viral sequencing data.
+  - [cojac](https://github.com/cbg-ethz/cojac): command-line tools for the analysis of co-occurrence of mutations on amplicons.
+

docs/index.md

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+../README.md

mkdocs.yml

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+site_name: Inference of SARS-Cov-2 variant fitness
+
+theme:
+  name: "material"
+  features:
+    - navigation.tabs
+    - navigation.sections
+    - toc.integrate
+    - search.suggest
+    - search.highlight
+    - content.tabs.link
+    - content.code.annotation
+    - content.code.copy
+  language: en
+  palette:
+    - scheme: default
+      toggle:
+        icon: material/toggle-switch-off-outline 
+        name: Switch to dark mode
+      primary: teal
+      accent: purple 
+    - scheme: slate 
+      toggle:
+        icon: material/toggle-switch
+        name: Switch to light mode    
+      primary: teal
+      accent: lime
+
+plugins:
+  - search
+  - mkdocstrings:
+      default_handler: python
+      handlers:
+        python:
+          options:
+            show_source: false
+            show_root_heading: true
+
+nav:
+  - Documentation: index.md
+  - API Reference: api.md
+
+repo_name: covvfit
+repo_url: https://github.com/cbg-ethz/covvfit
+
+watch:
+  - src/covvfit

pyproject.toml

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+[tool.poetry]
+name = "covvfit"
+version = "0.1.0"
+description = ""
+authors = ["David Dreifuss <[email protected]>", "Paweł Czyż <[email protected]>"]
+readme = "README.md"
+packages = [{include = "covvfit", from = "src"}]
+
+[tool.poetry.dependencies]
+python = ">=3.10,<3.12"
+numpy = "^1.25"
+matplotlib = "^3.8.0"
+pymc = "^5.9.1"
+scipy = "^1.11.3"
+
+
+[tool.poetry.group.dev.dependencies]
+pytest = "^7.4.3"
+ruff = "^0.1.3"
+black = "^23.10.1"
+pre-commit = "^3.5.0"
+pyright = "^1.1.333"
+
+[build-system]
+requires = ["poetry-core"]
+build-backend = "poetry.core.masonry.api"

src/covvfit/__init__.py

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+VERSION = "0.1.0"

tests/test_installed.py

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+import covvfit
+
+
+def test_imports() -> None:
+    assert isinstance(covvfit.VERSION, str)