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update on-release-main workflow with modern permissions
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‎.github/workflows/on-release-main.yml‎

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types: [published]
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jobs:
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set-version:
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runs-on: ubuntu-24.04
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steps:
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- uses: actions/checkout@v4
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- name: Export tag
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id: vars
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run: echo tag=${GITHUB_REF#refs/*/} >> $GITHUB_OUTPUT
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if: ${{ github.event_name == 'release' }}
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- name: Update project version
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run: |
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sed -i "s/^version = \".*\"/version = \"$RELEASE_VERSION\"/" pyproject.toml
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env:
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RELEASE_VERSION: ${{ steps.vars.outputs.tag }}
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if: ${{ github.event_name == 'release' }}
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- name: Upload updated pyproject.toml
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uses: actions/upload-artifact@v4
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with:
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name: pyproject-toml
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path: pyproject.toml
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publish:
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runs-on: ubuntu-latest
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needs: [set-version]
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permissions:
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id-token: write
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contents: write
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steps:
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- name: Check out
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uses: actions/checkout@v4
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run: uv build
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- name: Publish package
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# Requires trusted publisher configuration at pypi
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# No environment tokens required
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run: uv publish
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env:
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UV_PUBLISH_TOKEN: ${{ secrets.PYPI_TOKEN }}
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deploy-docs:
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needs: publish
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runs-on: ubuntu-latest
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permissions:
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contents: write
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steps:
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- name: Check out
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uses: actions/checkout@v4

‎.gitignore‎

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__marimo__/
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__pycache__/
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__pypackages__/

‎orig2/Makefile‎

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# Makefile for Python project
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.DELETE_ON_ERROR:
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.PHONY: FORCE
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.PRECIOUS:
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.SUFFIXES:
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ifeq ("","$(shell command -v zsh)")
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$(error "zsh not found; you must install zsh first")
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endif
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SHELL:=zsh -eu -o pipefail -o null_glob
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SELF:=$(firstword $(MAKEFILE_LIST))
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VE_DIR:=.venv
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PY_VERSION:=3.13
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SRC_DIRS:=src
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TEST_DIRS:=tests
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DOC_TESTS:=${SRC_DIRS} # ./README.md
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############################################################################
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#= BASIC USAGE
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default: help
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#=> help -- display this help message
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help:
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@sbin/makefile-extract-documentation "${SELF}"
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############################################################################
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#= SETUP, INSTALLATION, PACKAGING
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#=> devready: create venv, install prerequisites, install pkg in develop mode
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.PHONY: devready
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devready:
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make ${VE_DIR} && source ${VE_DIR}/bin/activate && make develop
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@echo '#################################################################################'
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@echo '### Do not forget to `source ${VE_DIR}/bin/activate` to use this environment ###'
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@echo '#################################################################################'
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#=> venv: make a Python 3 virtual environment
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${VE_DIR}:
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uv venv --python ${PY_VERSION} $@
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#=> develop: install package in develop mode
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.PHONY: develop
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develop:
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uv sync --extra dev --extra tests
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pre-commit install
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#=> install: install package
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.PHONY: install
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install:
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uv sync
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#=> build: make sdist and wheel
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.PHONY: build
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build: %:
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python -m build
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############################################################################
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#= TESTING
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# see test configuration in setup.cfg
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#=> test: execute tests
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#=> test-code: test code (including embedded doctests)
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#=> test-docs: test example code in docs
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.PHONY: test test-code test-docs
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test:
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pytest --cov ${SRC_DIRS}
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test-code:
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pytest ${TEST_DIRS}
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test-docs:
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pytest ${DOC_TESTS}
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stest:
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pytest -vvv -s -k ${t}
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test-%:
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pytest -m '$*' ${TEST_DIRS}
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#=> tox -- run all tox tests
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tox:
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uvx tox
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#=> cqa: execute code quality tests
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cqa:
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uvx ruff format --check
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uvx ruff check
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############################################################################
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#= UTILITY TARGETS
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#=> reformat: reformat code
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.PHONY: reformat
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reformat:
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uvx ruff check --fix
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uvx ruff format
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#=> docs -- make sphinx docs
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.PHONY: docs
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docs: develop
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# RTD makes json. Build here to ensure that it works.
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make -C docs html json
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############################################################################
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#= CLEANUP
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#=> clean: remove temporary and backup files
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.PHONY: clean
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clean:
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rm -frv **/*~ **/*.bak
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-make -C docs $@
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-make -C examples $@
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#=> cleaner: remove files and directories that are easily rebuilt
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.PHONY: cleaner
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cleaner: clean
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rm -frv .cache build dist docs/_build
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rm -frv **/__pycache__
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rm -frv **/*.egg-info
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rm -frv **/*.pyc
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rm -frv **/*.orig
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rm -frv **/*.rej
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-make -C docs $@
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-make -C examples $@
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#=> cleanest: remove files and directories that are more expensive to rebuild
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.PHONY: cleanest
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cleanest: cleaner
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rm -frv .eggs .tox venv
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-make -C docs $@
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-make -C examples $@
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#=> distclean: remove untracked files and other detritus
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.PHONY: distclean
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distclean: cleanest
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git clean -df
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############################################################################
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#= Repo renamer
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#=> rename: rename files and substitute content for new repo name
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.PHONY: rename
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rename:
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./sbin/rename-package
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## <LICENSE>
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## Copyright 2023 Source Code Committers
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##
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## Licensed under the Apache License, Version 2.0 (the "License");
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## you may not use this file except in compliance with the License.
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## You may obtain a copy of the License at
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##
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## http://www.apache.org/licenses/LICENSE-2.0
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##
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## Unless required by applicable law or agreed to in writing, software
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## distributed under the License is distributed on an "AS IS" BASIS,
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## WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
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## See the License for the specific language governing permissions and
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## limitations under the License.
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## </LICENSE>

‎orig2/README.md‎

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# biocommons.example Test Package
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[![codecov](https://codecov.io/gh/biocommons/biocommons.example/graph/badge.svg?token=CCUMQQV5R6)](https://codecov.io/gh/biocommons/biocommons.example)
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---
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This repo provides a template for biocommons Python packages. Here's how to use it:
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1. Click the [Use this template](https://github.com/biocommons/example/generate)
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button. Name the new repo like "biocommons.something".
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1. Clone your repo locally.
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1. In the repo, type `make rename`. The new name will be chosen based on the repo name.
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1. Remove this header.
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1. Commit and push.
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Delete this section in your generated template.
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---
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## Installation
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To install from pypi: ```pip install biocommons.example```
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## Developer Setup
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### Prerequisites
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- [GNU make](https://www.gnu.org/software/make/): Current mechanism for consistent invocation of developer tools.
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- Mac: [Install brew](https://brew.sh/), then [install make](https://formulae.brew.sh/formula/make)
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- Ubuntu: `sudo apt install make`
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- [uv](https://docs.astral.sh/uv/): An extremely fast Python package and project manager, written in Rust.
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- All platforms: See the [uv installation instructions](https://docs.astral.sh/uv/getting-started/installation/).
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- [zsh](https://www.zsh.org/): Shell used by the Makefile
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- Mac: included by default
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- Ubuntu: `sudo apt install zsh`
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### One-time developer setup
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Create a Python virtual environment and install dependencies:
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make devready
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### Development
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Activate your environment:
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source venv/bin/activate
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Code reformatting:
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make reformat
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Test:
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make test # for current environment
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make tox # for all supported versions
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Build:
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git tag 0.0.0
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make build
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Try it:
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$ python3 -m biocommons.example
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Marvin says:
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There's only one life-form as intelligent as me within thirty parsecs...
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$ marvin-quote
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Marvin says:
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You think you've got problems? What are you supposed to do if you...
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$ ipython
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>>> from biocommons.example import __version__, get_quote_from_marvin
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>>> __version__
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'0.1.dev8+gd5519a8.d20211123'
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>>> get_quote()
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"The first ten million years were the worst, ...
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# Features
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## Code structure and features
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* Modern pyproject.toml with setuptools
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* Versioning based on git tag (only)
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* Easy development setup
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* Support for namespaces
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* Testing with coverage using pytest; tests may be in `tests/`, embedded in the package, and in doc strings
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* Examples for logging and package data
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* Command-line with argument parsing with argparse
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## DevOps
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* Quality tools: Code linting and reformatting with Ruff
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* GitHub Actions for testing and packaging

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