Initial commit

.github/PULL_REQUEST_TEMPLATE.md

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+<!--
+# TODO: If you're a maintainer of this repo, open `.github/PULL_REQUEST_TEMPLATE.md`, replace <NAME> with the repo name, and remove this line.
+
+Many thanks for contributing to Arcadia-Science/<NAME>!
+
+Please fill in the appropriate checklist below (delete whatever is not relevant).
+These are the most common things requested on pull requests (PRs).
+-->
+
+## PR checklist
+
+- [ ] Tag the issue(s) or milestones this PR fixes (e.g. `Fixes #123, Resolves #456`).
+- [ ] Describe the changes you've made.
+- [ ] Describe any tests you have conducted to confirm that your changes behave as expected.
+- [ ] If you've added new software dependencies, make sure that those dependencies are included in the appropriate `conda` environments.
+- [ ] If you've added new functionality, make sure that the documentation is updated accordingly.
+- [ ] If you encountered bugs or features that you won't address, but should be addressed eventually, create new issues for them.

.github/workflows/lint.yml

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+name: lint
+
+on:
+  push:
+    branches:
+      - main
+  pull_request:
+    branches:
+      - main
+
+jobs:
+  lint:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v3
+
+      - name: Install Python
+        uses: actions/setup-python@v4
+        with:
+          python-version: "3.12"
+
+      - name: Install test dependencies
+        run: |
+          python -m pip install --upgrade pip
+          pip install pre-commit==3.5.0 ruff==0.4.8
+
+      - name: Run Ruff
+        run: ruff check --output-format=github .
+
+      - name: Run Ruff formatter
+        run: ruff format --check .

.gitignore

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+# packages installed in editable mode
+envs/src/**
+
+# Snakemake-related folders and files
+.snakemake/
+/input/
+/output/
+/demo/output/
+/demo/input/
+/logs
+
+# Byte-compiled / optimized / DLL files
+__pycache__/
+*.py[cod]
+*$py.class
+
+# C extensions
+*.so
+
+# Distribution / packaging
+.Python
+env/
+build/
+develop-eggs/
+dist/
+downloads/
+eggs/
+.eggs/
+lib64/
+parts/
+sdist/
+var/
+*.egg-info/
+.installed.cfg
+*.egg
+
+# Installer logs
+pip-log.txt
+pip-delete-this-directory.txt
+
+# Unit test / coverage reports
+htmlcov/
+.tox/
+.coverage
+.coverage.*
+.cache
+nosetests.xml
+coverage.xml
+*,cover
+.hypothesis/
+.napari_cache
+
+# Translations
+*.mo
+*.pot
+
+# Sphinx documentation
+docs/_build/
+
+# MkDocs documentation
+/site/
+
+# PyBuilder
+target/
+
+# Pycharm and VSCode
+.idea/
+venv/
+
+# Jupyter notebook checkpoints
+.ipynb_checkpoints
+
+# pyenv
+.python-version
+
+# OS
+.DS_Store
+
+# written by setuptools_scm
+**/_version.py
+
+# Nextflow related folders and files
+.nextflow*
+work/

.pre-commit-config.yaml

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+exclude: (examples/|demo/|dev/|input/|output/)
+repos:
+  - repo: https://github.com/pre-commit/pre-commit-hooks
+    rev: v4.1.0
+    hooks:
+      - id: check-yaml
+      - id: check-toml
+      - id: check-json
+      - id: check-case-conflict
+      - id: check-merge-conflict
+      - id: check-symlinks
+      - id: debug-statements
+      - id: trailing-whitespace
+      - id: mixed-line-ending
+      - id: end-of-file-fixer
+      - id: requirements-txt-fixer
+
+  - repo: https://github.com/astral-sh/ruff-pre-commit
+    rev: v0.4.8
+    hooks:
+      - id: ruff
+        types_or: [ python, pyi, jupyter ]
+        args: [--fix]
+      - id: ruff-format
+        types_or: [ python, pyi, jupyter ]

.vscode/extensions.json

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+{
+  // See http://go.microsoft.com/fwlink/?LinkId=827846
+  // for the documentation about the extensions.json format
+  "recommendations": ["charliermarsh.ruff"]
+}

LICENSE

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+MIT License
+
+Copyright (c) 2024 Arcadia Science
+
+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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+.PHONY: lint
+lint:
+	ruff check --exit-zero .
+
+.PHONY: format
+format:
+	ruff check --fix .
+	ruff format .
+
+.PHONY: pre-commit
+pre-commit:
+	pre-commit run --all-files

README.md

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+# TODO: Replace with the name of the repo
+
+[![run with conda](https://img.shields.io/badge/run%20with-conda-3EB049?labelColor=000000&logo=anaconda)](https://docs.conda.io/projects/miniconda/en/latest/)
+
+Note: Analysis repo names should be prefixed with the year (ie `2024-noveltree-analysis`)
+
+## Purpose
+
+TODO: Briefly describe the core analyses performed in the repository and the motivation behind them.
+
+## Installation and Setup
+
+This repository uses conda to manage software environments and installations. You can find operating system-specific instructions for installing miniconda [here](https://docs.conda.io/projects/miniconda/en/latest/). After installing conda and [mamba](https://mamba.readthedocs.io/en/latest/), run the following command to create the pipeline run environment.
+
+```{bash}
+TODO: Replace <NAME> with the name of your environment
+mamba env create -n <NAME> --file envs/dev.yml
+conda activate <NAME>
+```
+
+<details><summary>Developer Notes (click to expand/collapse)</summary>
+
+1. Install your pre-commit hooks:
+
+    ```{bash}
+    pre-commit install
+    ```
+
+    This installs the pre-commit hooks defined in your config (`./.pre-commit-config.yaml`).
+
+2. Export your conda environment before sharing:
+
+    As your project develops, the number of dependencies in your environment may increase. Whenever you install new dependencies (using either `pip install` or `mamba install`), you should update the environment file using the following command.
+
+    ```{bash}
+    conda env export --from-history --no-builds > envs/dev.yml
+    ```
+
+    `--from-history` only exports packages that were explicitly added by you (e.g., the packages you installed with `pip` or `mamba`) and `--no-builds` removes build specification from the exported packages to increase portability between different platforms.
+</details>
+
+## Data
+
+TODO: Add details about the description of input / output data and links to Zenodo depositions, if applicable.
+
+## Overview
+
+### Description of the folder structure
+
+### Methods
+
+TODO: Include a brief, step-wise overview of analyses performed.
+
+> Example:
+>
+> 1.  Download scripts using `download.ipynb`.
+> 2.  Preprocess using `./preprocessing.sh -a data/`
+> 3.  Run Snakemake pipeline `snakemake --snakefile Snakefile`
+> 4.  Generate figures using `pub/make_figures.ipynb`.
+
+### Compute Specifications
+
+TODO: Describe what compute resources were used to run the analysis. For example, you could list the operating system, number of cores, RAM, and storage space.
+
+## Contributing
+
+See how we recognize [feedback and contributions to our code](https://github.com/Arcadia-Science/arcadia-software-handbook/blob/main/guides-and-standards/guide-credit-for-contributions.md).
+
+---
+## For Developers
+
+This section contains information for developers who are working off of this template. Please adjust or edit this section as appropriate when you're ready to share your repo.
+
+### GitHub templates
+This template uses GitHub templates to provide checklists when making new pull requests. These templates are stored in the [.github/](./.github/) directory.
+
+### VSCode
+This template includes recommendations to VSCode users for extensions, particularly the `ruff` linter. These recommendations are stored in `.vscode/extensions.json`. When you open the repository in VSCode, you should see a prompt to install the recommended extensions.
+
+### `.gitignore`
+This template uses a `.gitignore` file to prevent certain files from being committed to the repository.
+
+### `pyproject.toml`
+`pyproject.toml` is a configuration file to specify your project's metadata and to set the behavior of other tools such as linters, type checkers etc. You can learn more [here](https://packaging.python.org/en/latest/guides/writing-pyproject-toml/)
+
+### Linting
+This template automates linting and formatting using GitHub Actions and the `ruff` linter. When you push changes to your repository, GitHub will automatically run the linter and report any errors, blocking merges until they are resolved.

envs/dev.yml

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+channels:
+  - conda-forge
+  - bioconda
+  - defaults
+dependencies:
+  - jupyter=1.0.0
+  - pip=23.2.1
+  - pre-commit=3.5.0
+  - python=3.12.0
+  - ruff=0.4.8

pyproject.toml

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+[project]
+name = "TODO: Tool name"
+description = "TODO: Tool description"
+version = "0.0.0"
+readme = "README.md"
+requires-python = ">=3.12"
+license = { file = "LICENSE" }
+
+
+[tool.ruff]
+# The directories to consider when resolving first- vs. third-party imports
+src = ["."]
+
+line-length = 100
+indent-width = 4
+
+# run ruff on jupyter notebooks (this is not enabled by default)
+extend-include = ["*.ipynb"]
+
+[tool.ruff.lint.per-file-ignores]
+# ignore star and unused imports
+"__init__.py" = ["F403", "F405"]
+
+[tool.ruff.lint]
+select = [
+    # flake8-bugbear
+    "B",
+    # pycodestyle error
+    "E",
+    # pyflakes
+    "F",
+    # isort
+    "I",
+    # pyupgrade
+    "UP",
+    # pycodestyle warning
+    "W",
+]
+
+# rule codes to ignore
+ignore = []
+
+# Allows fix for all enabled rules when `--fix` is provided
+fixable = ["ALL"]
+unfixable = []
+
+[tool.ruff.format]
+# Like Black, use double quotes, indent with spaces, and respect trailing commas
+quote-style = "double"
+indent-style = "space"
+skip-magic-trailing-comma = false
+line-ending = "auto"
+
+[tool.ruff.lint.isort]
+order-by-type = true
+no-lines-before = ["future", "standard-library"]