From 62c861d85f01e5e5e343dfa59a0b184de260e132 Mon Sep 17 00:00:00 2001
From: Jonathan Chang <me@jonathanchang.org>
Date: Mon, 6 Jan 2025 11:38:11 -0800
Subject: [PATCH 1/5] Update for poetry 2.0

---
 Dockerfile     |   1 +
 poetry.lock    | 298 +++----------------------------------------------
 pyproject.toml |  57 ++++++----
 3 files changed, 52 insertions(+), 304 deletions(-)

diff --git a/Dockerfile b/Dockerfile
index d3bb8ce..43ba2f0 100644
--- a/Dockerfile
+++ b/Dockerfile
@@ -30,6 +30,7 @@ RUN apt-get update \
   && pypy3.10 get-pip.py \
   && pypy3.10 get-poetry.py \
   && cd tact \
+  && poetry self add poetry-plugin-export \
   && poetry export -f requirements.txt -o requirements.txt --without-hashes --only main \
   && pypy3.10 -mpip install -r requirements.txt --compile . \
   && cd .. \
diff --git a/poetry.lock b/poetry.lock
index 440047c..fc6ef8c 100644
--- a/poetry.lock
+++ b/poetry.lock
@@ -1,32 +1,4 @@
-# This file is automatically @generated by Poetry 1.8.5 and should not be changed by hand.
-
-[[package]]
-name = "atomicwrites"
-version = "1.4.0"
-description = "Atomic file writes."
-optional = false
-python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*"
-files = [
-    {file = "atomicwrites-1.4.0-py2.py3-none-any.whl", hash = "sha256:6d1784dea7c0c8d4a5172b6c620f40b6e4cbfdf96d783691f2e1302a7b88e197"},
-    {file = "atomicwrites-1.4.0.tar.gz", hash = "sha256:ae70396ad1a434f9c7046fd2dd196fc04b12f9e91ffb859164193be8b6168a7a"},
-]
-
-[[package]]
-name = "attrs"
-version = "21.4.0"
-description = "Classes Without Boilerplate"
-optional = false
-python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, !=3.4.*"
-files = [
-    {file = "attrs-21.4.0-py2.py3-none-any.whl", hash = "sha256:2d27e3784d7a565d36ab851fe94887c5eccd6a463168875832a1be79c82828b4"},
-    {file = "attrs-21.4.0.tar.gz", hash = "sha256:626ba8234211db98e869df76230a137c4c40a12d72445c45d5f5b716f076e2fd"},
-]
-
-[package.extras]
-dev = ["cloudpickle", "coverage[toml] (>=5.0.2)", "furo", "hypothesis", "mypy", "pre-commit", "pympler", "pytest (>=4.3.0)", "pytest-mypy-plugins", "six", "sphinx", "sphinx-notfound-page", "zope.interface"]
-docs = ["furo", "sphinx", "sphinx-notfound-page", "zope.interface"]
-tests = ["cloudpickle", "coverage[toml] (>=5.0.2)", "hypothesis", "mypy", "pympler", "pytest (>=4.3.0)", "pytest-mypy-plugins", "six", "zope.interface"]
-tests-no-zope = ["cloudpickle", "coverage[toml] (>=5.0.2)", "hypothesis", "mypy", "pympler", "pytest (>=4.3.0)", "pytest-mypy-plugins", "six"]
+# This file is automatically @generated by Poetry 2.0.0 and should not be changed by hand.
 
 [[package]]
 name = "click"
@@ -34,6 +6,7 @@ version = "8.1.7"
 description = "Composable command line interface toolkit"
 optional = false
 python-versions = ">=3.7"
+groups = ["main"]
 files = [
     {file = "click-8.1.7-py3-none-any.whl", hash = "sha256:ae74fb96c20a0277a1d615f1e4d73c8414f5a98db8b799a7931d1582f3390c28"},
     {file = "click-8.1.7.tar.gz", hash = "sha256:ca9853ad459e787e2192211578cc907e7594e294c7ccc834310722b41b9ca6de"},
@@ -48,70 +21,20 @@ version = "0.4.4"
 description = "Cross-platform colored terminal text."
 optional = false
 python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, !=3.4.*"
+groups = ["main"]
+markers = "platform_system == \"Windows\""
 files = [
     {file = "colorama-0.4.4-py2.py3-none-any.whl", hash = "sha256:9f47eda37229f68eee03b24b9748937c7dc3868f906e8ba69fbcbdd3bc5dc3e2"},
     {file = "colorama-0.4.4.tar.gz", hash = "sha256:5941b2b48a20143d2267e95b1c2a7603ce057ee39fd88e7329b0c292aa16869b"},
 ]
 
-[[package]]
-name = "coverage"
-version = "6.3.2"
-description = "Code coverage measurement for Python"
-optional = false
-python-versions = ">=3.7"
-files = [
-    {file = "coverage-6.3.2-cp310-cp310-macosx_10_9_x86_64.whl", hash = "sha256:9b27d894748475fa858f9597c0ee1d4829f44683f3813633aaf94b19cb5453cf"},
-    {file = "coverage-6.3.2-cp310-cp310-macosx_11_0_arm64.whl", hash = "sha256:37d1141ad6b2466a7b53a22e08fe76994c2d35a5b6b469590424a9953155afac"},
-    {file = "coverage-6.3.2-cp310-cp310-manylinux_2_17_aarch64.manylinux2014_aarch64.whl", hash = "sha256:f9987b0354b06d4df0f4d3e0ec1ae76d7ce7cbca9a2f98c25041eb79eec766f1"},
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-    {file = "coverage-6.3.2-cp310-cp310-manylinux_2_5_x86_64.manylinux1_x86_64.manylinux_2_17_x86_64.manylinux2014_x86_64.whl", hash = "sha256:4dd8bafa458b5c7d061540f1ee9f18025a68e2d8471b3e858a9dad47c8d41903"},
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-    {file = "coverage-6.3.2-cp39-cp39-musllinux_1_1_x86_64.whl", hash = "sha256:5ca5aeb4344b30d0bec47481536b8ba1181d50dbe783b0e4ad03c95dc1296684"},
-    {file = "coverage-6.3.2-cp39-cp39-win32.whl", hash = "sha256:f5fa5803f47e095d7ad8443d28b01d48c0359484fec1b9d8606d0e3282084bc4"},
-    {file = "coverage-6.3.2-cp39-cp39-win_amd64.whl", hash = "sha256:9548f10d8be799551eb3a9c74bbf2b4934ddb330e08a73320123c07f95cc2d92"},
-    {file = "coverage-6.3.2-pp36.pp37.pp38-none-any.whl", hash = "sha256:18d520c6860515a771708937d2f78f63cc47ab3b80cb78e86573b0a760161faf"},
-    {file = "coverage-6.3.2.tar.gz", hash = "sha256:03e2a7826086b91ef345ff18742ee9fc47a6839ccd517061ef8fa1976e652ce9"},
-]
-
-[package.extras]
-toml = ["tomli"]
-
 [[package]]
 name = "dendropy"
 version = "5.0.1"
 description = "A Python library for phylogenetics and phylogenetic computing: reading, writing, simulation, processing and manipulation of phylogenetic trees (phylogenies) and characters."
 optional = false
 python-versions = ">=3.6"
+groups = ["main"]
 files = [
     {file = "DendroPy-5.0.1-py3-none-any.whl", hash = "sha256:20066d300e65517119f885baf1061717bbb68cbb5190e611f3ff8b558e20cbc6"},
     {file = "DendroPy-5.0.1.tar.gz", hash = "sha256:f2815e7649a6fe2924ff3fdf00a660c948dc6f3316e303b8b022f74cc75ca42e"},
@@ -120,70 +43,13 @@ files = [
 [package.dependencies]
 setuptools = "*"
 
-[[package]]
-name = "hypothesis"
-version = "6.37.2"
-description = "A library for property-based testing"
-optional = false
-python-versions = ">=3.7"
-files = [
-    {file = "hypothesis-6.37.2-py3-none-any.whl", hash = "sha256:1c1777ccd3074fcca768d7594a284a41501c99843089d37e3235d38319e3f217"},
-    {file = "hypothesis-6.37.2.tar.gz", hash = "sha256:79321035b9174ffa506d724ca5e8af375d7bf532c80e4f602bd433792c527e6c"},
-]
-
-[package.dependencies]
-attrs = ">=19.2.0"
-sortedcontainers = ">=2.1.0,<3.0.0"
-
-[package.extras]
-all = ["backports.zoneinfo (>=0.2.1)", "black (>=19.10b0)", "click (>=7.0)", "django (>=2.2)", "dpcontracts (>=0.4)", "importlib-metadata (>=3.6)", "lark-parser (>=0.6.5)", "libcst (>=0.3.16)", "numpy (>=1.9.0)", "pandas (>=0.25)", "pytest (>=4.6)", "python-dateutil (>=1.4)", "pytz (>=2014.1)", "redis (>=3.0.0)", "rich (>=9.0.0)", "tzdata (>=2021.5)"]
-cli = ["black (>=19.10b0)", "click (>=7.0)", "rich (>=9.0.0)"]
-codemods = ["libcst (>=0.3.16)"]
-dateutil = ["python-dateutil (>=1.4)"]
-django = ["django (>=2.2)"]
-dpcontracts = ["dpcontracts (>=0.4)"]
-ghostwriter = ["black (>=19.10b0)"]
-lark = ["lark-parser (>=0.6.5)"]
-numpy = ["numpy (>=1.9.0)"]
-pandas = ["pandas (>=0.25)"]
-pytest = ["pytest (>=4.6)"]
-pytz = ["pytz (>=2014.1)"]
-redis = ["redis (>=3.0.0)"]
-zoneinfo = ["backports.zoneinfo (>=0.2.1)", "tzdata (>=2021.5)"]
-
-[[package]]
-name = "iniconfig"
-version = "1.1.1"
-description = "iniconfig: brain-dead simple config-ini parsing"
-optional = false
-python-versions = "*"
-files = [
-    {file = "iniconfig-1.1.1-py2.py3-none-any.whl", hash = "sha256:011e24c64b7f47f6ebd835bb12a743f2fbe9a26d4cecaa7f53bc4f35ee9da8b3"},
-    {file = "iniconfig-1.1.1.tar.gz", hash = "sha256:bc3af051d7d14b2ee5ef9969666def0cd1a000e121eaea580d4a313df4b37f32"},
-]
-
-[[package]]
-name = "mock"
-version = "4.0.3"
-description = "Rolling backport of unittest.mock for all Pythons"
-optional = false
-python-versions = ">=3.6"
-files = [
-    {file = "mock-4.0.3-py3-none-any.whl", hash = "sha256:122fcb64ee37cfad5b3f48d7a7d51875d7031aaf3d8be7c42e2bee25044eee62"},
-    {file = "mock-4.0.3.tar.gz", hash = "sha256:7d3fbbde18228f4ff2f1f119a45cdffa458b4c0dee32eb4d2bb2f82554bac7bc"},
-]
-
-[package.extras]
-build = ["blurb", "twine", "wheel"]
-docs = ["sphinx"]
-test = ["pytest (<5.4)", "pytest-cov"]
-
 [[package]]
 name = "numpy"
 version = "2.2.0"
 description = "Fundamental package for array computing in Python"
 optional = false
 python-versions = ">=3.10"
+groups = ["main"]
 files = [
     {file = "numpy-2.2.0-cp310-cp310-macosx_10_9_x86_64.whl", hash = "sha256:1e25507d85da11ff5066269d0bd25d06e0a0f2e908415534f3e603d2a78e4ffa"},
     {file = "numpy-2.2.0-cp310-cp310-macosx_11_0_arm64.whl", hash = "sha256:a62eb442011776e4036af5c8b1a00b706c5bc02dc15eb5344b0c750428c94219"},
@@ -242,41 +108,13 @@ files = [
     {file = "numpy-2.2.0.tar.gz", hash = "sha256:140dd80ff8981a583a60980be1a655068f8adebf7a45a06a6858c873fcdcd4a0"},
 ]
 
-[[package]]
-name = "packaging"
-version = "21.3"
-description = "Core utilities for Python packages"
-optional = false
-python-versions = ">=3.6"
-files = [
-    {file = "packaging-21.3-py3-none-any.whl", hash = "sha256:ef103e05f519cdc783ae24ea4e2e0f508a9c99b2d4969652eed6a2e1ea5bd522"},
-    {file = "packaging-21.3.tar.gz", hash = "sha256:dd47c42927d89ab911e606518907cc2d3a1f38bbd026385970643f9c5b8ecfeb"},
-]
-
-[package.dependencies]
-pyparsing = ">=2.0.2,<3.0.5 || >3.0.5"
-
-[[package]]
-name = "pluggy"
-version = "1.0.0"
-description = "plugin and hook calling mechanisms for python"
-optional = false
-python-versions = ">=3.6"
-files = [
-    {file = "pluggy-1.0.0-py2.py3-none-any.whl", hash = "sha256:74134bbf457f031a36d68416e1509f34bd5ccc019f0bcc952c7b909d06b37bd3"},
-    {file = "pluggy-1.0.0.tar.gz", hash = "sha256:4224373bacce55f955a878bf9cfa763c1e360858e330072059e10bad68531159"},
-]
-
-[package.extras]
-dev = ["pre-commit", "tox"]
-testing = ["pytest", "pytest-benchmark"]
-
 [[package]]
 name = "portion"
 version = "2.6.0"
 description = "Python data structure and operations for intervals"
 optional = false
 python-versions = "~=3.8"
+groups = ["main"]
 files = [
     {file = "portion-2.6.0-py3-none-any.whl", hash = "sha256:9132580df989b1985dae1caa3070b768f2a3360b40c89c59daa4acc7e6674dc4"},
     {file = "portion-2.6.0.tar.gz", hash = "sha256:6fb538b57a92058f0edd360667694448aa3fc028ab97e41e3091359d14ba4dd5"},
@@ -288,124 +126,13 @@ sortedcontainers = ">=2.2,<3.0"
 [package.extras]
 test = ["black (>=21.8b)", "coverage (>=6.0,<7.0)", "pytest (>=7.0,<8.0)"]
 
-[[package]]
-name = "py"
-version = "1.11.0"
-description = "library with cross-python path, ini-parsing, io, code, log facilities"
-optional = false
-python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, !=3.4.*"
-files = [
-    {file = "py-1.11.0-py2.py3-none-any.whl", hash = "sha256:607c53218732647dff4acdfcd50cb62615cedf612e72d1724fb1a0cc6405b378"},
-    {file = "py-1.11.0.tar.gz", hash = "sha256:51c75c4126074b472f746a24399ad32f6053d1b34b68d2fa41e558e6f4a98719"},
-]
-
-[[package]]
-name = "py-cpuinfo"
-version = "8.0.0"
-description = "Get CPU info with pure Python 2 & 3"
-optional = false
-python-versions = "*"
-files = [
-    {file = "py-cpuinfo-8.0.0.tar.gz", hash = "sha256:5f269be0e08e33fd959de96b34cd4aeeeacac014dd8305f70eb28d06de2345c5"},
-]
-
-[[package]]
-name = "pyparsing"
-version = "3.0.7"
-description = "Python parsing module"
-optional = false
-python-versions = ">=3.6"
-files = [
-    {file = "pyparsing-3.0.7-py3-none-any.whl", hash = "sha256:a6c06a88f252e6c322f65faf8f418b16213b51bdfaece0524c1c1bc30c63c484"},
-    {file = "pyparsing-3.0.7.tar.gz", hash = "sha256:18ee9022775d270c55187733956460083db60b37d0d0fb357445f3094eed3eea"},
-]
-
-[package.extras]
-diagrams = ["jinja2", "railroad-diagrams"]
-
-[[package]]
-name = "pytest"
-version = "6.2.5"
-description = "pytest: simple powerful testing with Python"
-optional = false
-python-versions = ">=3.6"
-files = [
-    {file = "pytest-6.2.5-py3-none-any.whl", hash = "sha256:7310f8d27bc79ced999e760ca304d69f6ba6c6649c0b60fb0e04a4a77cacc134"},
-    {file = "pytest-6.2.5.tar.gz", hash = "sha256:131b36680866a76e6781d13f101efb86cf674ebb9762eb70d3082b6f29889e89"},
-]
-
-[package.dependencies]
-atomicwrites = {version = ">=1.0", markers = "sys_platform == \"win32\""}
-attrs = ">=19.2.0"
-colorama = {version = "*", markers = "sys_platform == \"win32\""}
-iniconfig = "*"
-packaging = "*"
-pluggy = ">=0.12,<2.0"
-py = ">=1.8.2"
-toml = "*"
-
-[package.extras]
-testing = ["argcomplete", "hypothesis (>=3.56)", "mock", "nose", "requests", "xmlschema"]
-
-[[package]]
-name = "pytest-benchmark"
-version = "3.4.1"
-description = "A ``pytest`` fixture for benchmarking code. It will group the tests into rounds that are calibrated to the chosen timer."
-optional = false
-python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, !=3.4.*"
-files = [
-    {file = "pytest-benchmark-3.4.1.tar.gz", hash = "sha256:40e263f912de5a81d891619032983557d62a3d85843f9a9f30b98baea0cd7b47"},
-    {file = "pytest_benchmark-3.4.1-py2.py3-none-any.whl", hash = "sha256:36d2b08c4882f6f997fd3126a3d6dfd70f3249cde178ed8bbc0b73db7c20f809"},
-]
-
-[package.dependencies]
-py-cpuinfo = "*"
-pytest = ">=3.8"
-
-[package.extras]
-aspect = ["aspectlib"]
-elasticsearch = ["elasticsearch"]
-histogram = ["pygal", "pygaljs"]
-
-[[package]]
-name = "pytest-console-scripts"
-version = "1.2.2"
-description = "Pytest plugin for testing console scripts"
-optional = false
-python-versions = "*"
-files = [
-    {file = "pytest-console-scripts-1.2.2.tar.gz", hash = "sha256:caeaaaf57f3a99e4482127e8a18467a1cfd49c92f4b37e5578d0bc40bf1b3394"},
-]
-
-[package.dependencies]
-mock = ">=2.0.0"
-pytest = ">=4.0.0"
-
-[[package]]
-name = "pytest-cov"
-version = "2.12.1"
-description = "Pytest plugin for measuring coverage."
-optional = false
-python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, !=3.4.*"
-files = [
-    {file = "pytest-cov-2.12.1.tar.gz", hash = "sha256:261ceeb8c227b726249b376b8526b600f38667ee314f910353fa318caa01f4d7"},
-    {file = "pytest_cov-2.12.1-py2.py3-none-any.whl", hash = "sha256:261bb9e47e65bd099c89c3edf92972865210c36813f80ede5277dceb77a4a62a"},
-]
-
-[package.dependencies]
-coverage = ">=5.2.1"
-pytest = ">=4.6"
-toml = "*"
-
-[package.extras]
-testing = ["fields", "hunter", "process-tests", "pytest-xdist", "six", "virtualenv"]
-
 [[package]]
 name = "scipy"
 version = "1.14.1"
 description = "Fundamental algorithms for scientific computing in Python"
 optional = false
 python-versions = ">=3.10"
+groups = ["main"]
 files = [
     {file = "scipy-1.14.1-cp310-cp310-macosx_10_13_x86_64.whl", hash = "sha256:b28d2ca4add7ac16ae8bb6632a3c86e4b9e4d52d3e34267f6e1b0c1f8d87e389"},
     {file = "scipy-1.14.1-cp310-cp310-macosx_12_0_arm64.whl", hash = "sha256:d0d2821003174de06b69e58cef2316a6622b60ee613121199cb2852a873f8cf3"},
@@ -456,6 +183,7 @@ version = "75.6.0"
 description = "Easily download, build, install, upgrade, and uninstall Python packages"
 optional = false
 python-versions = ">=3.9"
+groups = ["main"]
 files = [
     {file = "setuptools-75.6.0-py3-none-any.whl", hash = "sha256:ce74b49e8f7110f9bf04883b730f4765b774ef3ef28f722cce7c273d253aaf7d"},
     {file = "setuptools-75.6.0.tar.gz", hash = "sha256:8199222558df7c86216af4f84c30e9b34a61d8ba19366cc914424cdbd28252f6"},
@@ -476,6 +204,7 @@ version = "2.4.0"
 description = "Sorted Containers -- Sorted List, Sorted Dict, Sorted Set"
 optional = false
 python-versions = "*"
+groups = ["main"]
 files = [
     {file = "sortedcontainers-2.4.0-py2.py3-none-any.whl", hash = "sha256:a163dcaede0f1c021485e957a39245190e74249897e2ae4b2aa38595db237ee0"},
     {file = "sortedcontainers-2.4.0.tar.gz", hash = "sha256:25caa5a06cc30b6b83d11423433f65d1f9d76c4c6a0c90e3379eaa43b9bfdb88"},
@@ -487,12 +216,13 @@ version = "0.10.2"
 description = "Python Library for Tom's Obvious, Minimal Language"
 optional = false
 python-versions = ">=2.6, !=3.0.*, !=3.1.*, !=3.2.*"
+groups = ["main"]
 files = [
     {file = "toml-0.10.2-py2.py3-none-any.whl", hash = "sha256:806143ae5bfb6a3c6e736a764057db0e6a0e05e338b5630894a5f779cabb4f9b"},
     {file = "toml-0.10.2.tar.gz", hash = "sha256:b3bda1d108d5dd99f4a20d24d9c348e91c4db7ab1b749200bded2f839ccbe68f"},
 ]
 
 [metadata]
-lock-version = "2.0"
-python-versions = ">= 3.10, < 3.14"
-content-hash = "9fe5436f6152c4b33988659bcbdef911d77579b6ce1b9408da7d4bf48984f03b"
+lock-version = "2.1"
+python-versions = ">=3.10,<4"
+content-hash = "2f25614503c14ddfee2095224b1a03ec7cccb92c75a11607caa19a6c0b465bb2"
diff --git a/pyproject.toml b/pyproject.toml
index bb786d5..eba8ec5 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -1,12 +1,44 @@
-[tool.poetry]
+[project]
 name = "tact"
 version = "0.6.0"
 description = "Taxonomic addition for complete trees: Adds tips to a backbone phylogeny using taxonomy simulated with birth-death models"
-authors = ["Jonathan Chang <me@jonathanchang.org>"]
+authors = [
+    { name = "Jonathan Chang", email = "me@jonathanchang.org" },
+    { name = "Dan Rabosky", email = "drabosky@umich.edu" },
+    { name = "Michael Alfaro", email = "michaelalfaro@ucla.edu" },
+]
+maintainers = [
+    { name = "Jonathan Chang", email = "me@jonathanchang.org" },
+]
 license = "MIT"
 readme = "README.md"
-repository = "https://github.com/jonchang/tact"
+requires-python = ">=3.10,<4"
+dynamic = ["classifiers"]
+dependencies = [
+    "scipy>=1.13",
+    "numpy>=2.2",
+    "click>=7,<9",
+    "DendroPy>=4.5,<6.0",
+    "portion>=2.2",
+    "toml>=0.10",
+]
+
+[project.urls]
 homepage = "https://tact.jonathanchang.org"
+repository = "https://github.com/jonchang/tact"
+documentation = "https://tact.jonathanchang.org"
+issue = "https://github.com/jonchang/tact/issues"
+changelog = "https://tact.jonathanchang.org/news/"
+sponsor = "https://github.com/sponsors/jonchang"
+
+[project.scripts]
+tact_add_taxa = "tact.cli_add_taxa:main"
+tact_add_config = "tact.cli_add_toml:main"
+tact_build_taxonomic_tree = "tact.cli_taxonomy:main"
+tact_check_results = "tact.cli_check_trees:main"
+
+
+[tool.poetry]
 include = ["examples"]
 classifiers = [
     "Development Status :: 5 - Production/Stable",
@@ -15,32 +47,17 @@ classifiers = [
     "Topic :: Scientific/Engineering :: Bio-Informatics"
 ]
 
-[tool.poetry.dependencies]
-python = ">= 3.10, < 3.14"
-scipy = ">=1.13"
-numpy = ">=2.2"
-click = ">=7,<9"
-DendroPy = ">=4.5,<6.0"
-portion = "^2.2"
-toml = "^0.10"
-
-[tool.poetry.dev-dependencies]
+[poetry.group.dev.dependencies]
 pytest = "^6.2"
 pytest-cov = "^2.12"
 pytest-benchmark = "^3.4"
 pytest-console-scripts = "^1.2"
 hypothesis = "^6.14"
 
-[tool.poetry.scripts]
-tact_add_taxa = "tact.cli_add_taxa:main"
-tact_add_config = "tact.cli_add_toml:main"
-tact_build_taxonomic_tree = "tact.cli_taxonomy:main"
-tact_check_results = "tact.cli_check_trees:main"
-
 [tool.black]
 line-length = 118
 target-version = ['py38', 'py39', 'py310', 'py311']
 
 [build-system]
-requires = ["poetry_core"]
+requires = ["poetry_core>=2.0"]
 build-backend = "poetry.core.masonry.api"

From 47b830b57e97eb1f175d790f69da0ee982c15a8d Mon Sep 17 00:00:00 2001
From: Jonathan Chang <me@jonathanchang.org>
Date: Mon, 6 Jan 2025 11:47:52 -0800
Subject: [PATCH 2/5] Also install dev dependencies when testing

---
 .github/workflows/pythonpackage.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/pythonpackage.yml b/.github/workflows/pythonpackage.yml
index bfd2dbe..4803b9b 100644
--- a/.github/workflows/pythonpackage.yml
+++ b/.github/workflows/pythonpackage.yml
@@ -45,7 +45,7 @@ jobs:
           echo $gitd
           echo $poetryv
       - name: Install package
-        run: poetry install -v
+        run: poetry install -v --with=dev
       - name: Lint with flake8
         run: |
           pip install flake8

From 3574985a5e3bcde83336f685dc76264f53e349fe Mon Sep 17 00:00:00 2001
From: Jonathan Chang <me@jonathanchang.org>
Date: Mon, 6 Jan 2025 11:52:10 -0800
Subject: [PATCH 3/5] updates

---
 .github/workflows/pythonpackage.yml | 6 +++++-
 1 file changed, 5 insertions(+), 1 deletion(-)

diff --git a/.github/workflows/pythonpackage.yml b/.github/workflows/pythonpackage.yml
index 4803b9b..3d3b8d2 100644
--- a/.github/workflows/pythonpackage.yml
+++ b/.github/workflows/pythonpackage.yml
@@ -44,7 +44,7 @@ jobs:
           poetryv=$(echo v$(poetry version | cut -d ' ' -f2))
           echo $gitd
           echo $poetryv
-      - name: Install package
+      - name: Install package for testing
         run: poetry install -v --with=dev
       - name: Lint with flake8
         run: |
@@ -57,6 +57,10 @@ jobs:
             --max-line-length=127 --statistics
       - name: Test with pytest
         run: poetry run pytest --script-launch-mode=subprocess
+      - name: Reinstall package for production
+        run: |
+          poetry env list --full-path | xargs rm -rf
+          poetry install -v --only=main
       - name: Build distribution package
         id: build
         run: |

From 9ddc20ad5ba284fdafd62d32e8df464ba72f925f Mon Sep 17 00:00:00 2001
From: Jonathan Chang <me@jonathanchang.org>
Date: Mon, 6 Jan 2025 14:48:56 -0800
Subject: [PATCH 4/5] tweak dep specifiers

---
 .github/workflows/pythonpackage.yml |   2 +-
 poetry.lock                         | 321 +++++++++++++++++++++++++++-
 pyproject.toml                      |  16 +-
 3 files changed, 329 insertions(+), 10 deletions(-)

diff --git a/.github/workflows/pythonpackage.yml b/.github/workflows/pythonpackage.yml
index 3d3b8d2..0b4e120 100644
--- a/.github/workflows/pythonpackage.yml
+++ b/.github/workflows/pythonpackage.yml
@@ -33,7 +33,7 @@ jobs:
           python-version: ${{ matrix.python-version }}
       - name: Install dependencies
         run: |
-          pip install poetry
+          pipx install 'poetry>=2'
       - name: Check tags
         if: startsWith(github.event.ref, 'refs/tags')
         id: tag
diff --git a/poetry.lock b/poetry.lock
index fc6ef8c..ca37730 100644
--- a/poetry.lock
+++ b/poetry.lock
@@ -1,5 +1,38 @@
 # This file is automatically @generated by Poetry 2.0.0 and should not be changed by hand.
 
+[[package]]
+name = "atomicwrites"
+version = "1.4.1"
+description = "Atomic file writes."
+optional = true
+python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*"
+groups = ["main"]
+markers = "extra == \"dev\" and sys_platform == \"win32\""
+files = [
+    {file = "atomicwrites-1.4.1.tar.gz", hash = "sha256:81b2c9071a49367a7f770170e5eec8cb66567cfbbc8c73d20ce5ca4a8d71cf11"},
+]
+
+[[package]]
+name = "attrs"
+version = "24.3.0"
+description = "Classes Without Boilerplate"
+optional = true
+python-versions = ">=3.8"
+groups = ["main"]
+markers = "extra == \"dev\""
+files = [
+    {file = "attrs-24.3.0-py3-none-any.whl", hash = "sha256:ac96cd038792094f438ad1f6ff80837353805ac950cd2aa0e0625ef19850c308"},
+    {file = "attrs-24.3.0.tar.gz", hash = "sha256:8f5c07333d543103541ba7be0e2ce16eeee8130cb0b3f9238ab904ce1e85baff"},
+]
+
+[package.extras]
+benchmark = ["cloudpickle", "hypothesis", "mypy (>=1.11.1)", "pympler", "pytest (>=4.3.0)", "pytest-codspeed", "pytest-mypy-plugins", "pytest-xdist[psutil]"]
+cov = ["cloudpickle", "coverage[toml] (>=5.3)", "hypothesis", "mypy (>=1.11.1)", "pympler", "pytest (>=4.3.0)", "pytest-mypy-plugins", "pytest-xdist[psutil]"]
+dev = ["cloudpickle", "hypothesis", "mypy (>=1.11.1)", "pre-commit-uv", "pympler", "pytest (>=4.3.0)", "pytest-mypy-plugins", "pytest-xdist[psutil]"]
+docs = ["cogapp", "furo", "myst-parser", "sphinx", "sphinx-notfound-page", "sphinxcontrib-towncrier", "towncrier (<24.7)"]
+tests = ["cloudpickle", "hypothesis", "mypy (>=1.11.1)", "pympler", "pytest (>=4.3.0)", "pytest-mypy-plugins", "pytest-xdist[psutil]"]
+tests-mypy = ["mypy (>=1.11.1)", "pytest-mypy-plugins"]
+
 [[package]]
 name = "click"
 version = "8.1.7"
@@ -22,12 +55,88 @@ description = "Cross-platform colored terminal text."
 optional = false
 python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, !=3.4.*"
 groups = ["main"]
-markers = "platform_system == \"Windows\""
+markers = "extra == \"dev\" and sys_platform == \"win32\" or platform_system == \"Windows\""
 files = [
     {file = "colorama-0.4.4-py2.py3-none-any.whl", hash = "sha256:9f47eda37229f68eee03b24b9748937c7dc3868f906e8ba69fbcbdd3bc5dc3e2"},
     {file = "colorama-0.4.4.tar.gz", hash = "sha256:5941b2b48a20143d2267e95b1c2a7603ce057ee39fd88e7329b0c292aa16869b"},
 ]
 
+[[package]]
+name = "coverage"
+version = "7.6.10"
+description = "Code coverage measurement for Python"
+optional = true
+python-versions = ">=3.9"
+groups = ["main"]
+markers = "extra == \"dev\""
+files = [
+    {file = "coverage-7.6.10-cp310-cp310-macosx_10_9_x86_64.whl", hash = "sha256:5c912978f7fbf47ef99cec50c4401340436d200d41d714c7a4766f377c5b7b78"},
+    {file = "coverage-7.6.10-cp310-cp310-macosx_11_0_arm64.whl", hash = "sha256:a01ec4af7dfeb96ff0078ad9a48810bb0cc8abcb0115180c6013a6b26237626c"},
+    {file = "coverage-7.6.10-cp310-cp310-manylinux_2_17_aarch64.manylinux2014_aarch64.whl", hash = "sha256:a3b204c11e2b2d883946fe1d97f89403aa1811df28ce0447439178cc7463448a"},
+    {file = "coverage-7.6.10-cp310-cp310-manylinux_2_5_i686.manylinux1_i686.manylinux_2_17_i686.manylinux2014_i686.whl", hash = "sha256:32ee6d8491fcfc82652a37109f69dee9a830e9379166cb73c16d8dc5c2915165"},
+    {file = "coverage-7.6.10-cp310-cp310-manylinux_2_5_x86_64.manylinux1_x86_64.manylinux_2_17_x86_64.manylinux2014_x86_64.whl", hash = "sha256:675cefc4c06e3b4c876b85bfb7c59c5e2218167bbd4da5075cbe3b5790a28988"},
+    {file = "coverage-7.6.10-cp310-cp310-musllinux_1_2_aarch64.whl", hash = "sha256:f4f620668dbc6f5e909a0946a877310fb3d57aea8198bde792aae369ee1c23b5"},
+    {file = "coverage-7.6.10-cp310-cp310-musllinux_1_2_i686.whl", hash = "sha256:4eea95ef275de7abaef630c9b2c002ffbc01918b726a39f5a4353916ec72d2f3"},
+    {file = "coverage-7.6.10-cp310-cp310-musllinux_1_2_x86_64.whl", hash = "sha256:e2f0280519e42b0a17550072861e0bc8a80a0870de260f9796157d3fca2733c5"},
+    {file = "coverage-7.6.10-cp310-cp310-win32.whl", hash = "sha256:bc67deb76bc3717f22e765ab3e07ee9c7a5e26b9019ca19a3b063d9f4b874244"},
+    {file = "coverage-7.6.10-cp310-cp310-win_amd64.whl", hash = "sha256:0f460286cb94036455e703c66988851d970fdfd8acc2a1122ab7f4f904e4029e"},
+    {file = "coverage-7.6.10-cp311-cp311-macosx_10_9_x86_64.whl", hash = "sha256:ea3c8f04b3e4af80e17bab607c386a830ffc2fb88a5484e1df756478cf70d1d3"},
+    {file = "coverage-7.6.10-cp311-cp311-macosx_11_0_arm64.whl", hash = "sha256:507a20fc863cae1d5720797761b42d2d87a04b3e5aeb682ef3b7332e90598f43"},
+    {file = "coverage-7.6.10-cp311-cp311-manylinux_2_17_aarch64.manylinux2014_aarch64.whl", hash = "sha256:d37a84878285b903c0fe21ac8794c6dab58150e9359f1aaebbeddd6412d53132"},
+    {file = "coverage-7.6.10-cp311-cp311-manylinux_2_5_i686.manylinux1_i686.manylinux_2_17_i686.manylinux2014_i686.whl", hash = "sha256:a534738b47b0de1995f85f582d983d94031dffb48ab86c95bdf88dc62212142f"},
+    {file = "coverage-7.6.10-cp311-cp311-manylinux_2_5_x86_64.manylinux1_x86_64.manylinux_2_17_x86_64.manylinux2014_x86_64.whl", hash = "sha256:0d7a2bf79378d8fb8afaa994f91bfd8215134f8631d27eba3e0e2c13546ce994"},
+    {file = "coverage-7.6.10-cp311-cp311-musllinux_1_2_aarch64.whl", hash = "sha256:6713ba4b4ebc330f3def51df1d5d38fad60b66720948112f114968feb52d3f99"},
+    {file = "coverage-7.6.10-cp311-cp311-musllinux_1_2_i686.whl", hash = "sha256:ab32947f481f7e8c763fa2c92fd9f44eeb143e7610c4ca9ecd6a36adab4081bd"},
+    {file = "coverage-7.6.10-cp311-cp311-musllinux_1_2_x86_64.whl", hash = "sha256:7bbd8c8f1b115b892e34ba66a097b915d3871db7ce0e6b9901f462ff3a975377"},
+    {file = "coverage-7.6.10-cp311-cp311-win32.whl", hash = "sha256:299e91b274c5c9cdb64cbdf1b3e4a8fe538a7a86acdd08fae52301b28ba297f8"},
+    {file = "coverage-7.6.10-cp311-cp311-win_amd64.whl", hash = "sha256:489a01f94aa581dbd961f306e37d75d4ba16104bbfa2b0edb21d29b73be83609"},
+    {file = "coverage-7.6.10-cp312-cp312-macosx_10_13_x86_64.whl", hash = "sha256:27c6e64726b307782fa5cbe531e7647aee385a29b2107cd87ba7c0105a5d3853"},
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+    {file = "coverage-7.6.10-cp39-cp39-win_amd64.whl", hash = "sha256:457574f4599d2b00f7f637a0700a6422243b3565509457b2dbd3f50703e11f59"},
+    {file = "coverage-7.6.10-pp39.pp310-none-any.whl", hash = "sha256:fd34e7b3405f0cc7ab03d54a334c17a9e802897580d964bd8c2001f4b9fd488f"},
+    {file = "coverage-7.6.10.tar.gz", hash = "sha256:7fb105327c8f8f0682e29843e2ff96af9dcbe5bab8eeb4b398c6a33a16d80a23"},
+]
+
+[package.extras]
+toml = ["tomli"]
+
 [[package]]
 name = "dendropy"
 version = "5.0.1"
@@ -43,6 +152,70 @@ files = [
 [package.dependencies]
 setuptools = "*"
 
+[[package]]
+name = "exceptiongroup"
+version = "1.2.2"
+description = "Backport of PEP 654 (exception groups)"
+optional = true
+python-versions = ">=3.7"
+groups = ["main"]
+markers = "extra == \"dev\" and python_version < \"3.11\""
+files = [
+    {file = "exceptiongroup-1.2.2-py3-none-any.whl", hash = "sha256:3111b9d131c238bec2f8f516e123e14ba243563fb135d3fe885990585aa7795b"},
+    {file = "exceptiongroup-1.2.2.tar.gz", hash = "sha256:47c2edf7c6738fafb49fd34290706d1a1a2f4d1c6df275526b62cbb4aa5393cc"},
+]
+
+[package.extras]
+test = ["pytest (>=6)"]
+
+[[package]]
+name = "hypothesis"
+version = "6.123.4"
+description = "A library for property-based testing"
+optional = true
+python-versions = ">=3.9"
+groups = ["main"]
+markers = "extra == \"dev\""
+files = [
+    {file = "hypothesis-6.123.4-py3-none-any.whl", hash = "sha256:3cdd4c7ecd53c4da9a76faf391c3f5af3722f68ed9bc31b7961f4b47ac6d4b19"},
+    {file = "hypothesis-6.123.4.tar.gz", hash = "sha256:99648fbf1c373ba33390c3f49d5069a2aa00f39e9bd569823f99943bbec01a69"},
+]
+
+[package.dependencies]
+attrs = ">=22.2.0"
+exceptiongroup = {version = ">=1.0.0", markers = "python_version < \"3.11\""}
+sortedcontainers = ">=2.1.0,<3.0.0"
+
+[package.extras]
+all = ["black (>=19.10b0)", "click (>=7.0)", "crosshair-tool (>=0.0.81)", "django (>=4.2)", "dpcontracts (>=0.4)", "hypothesis-crosshair (>=0.0.18)", "lark (>=0.10.1)", "libcst (>=0.3.16)", "numpy (>=1.19.3)", "pandas (>=1.1)", "pytest (>=4.6)", "python-dateutil (>=1.4)", "pytz (>=2014.1)", "redis (>=3.0.0)", "rich (>=9.0.0)", "tzdata (>=2024.2)"]
+cli = ["black (>=19.10b0)", "click (>=7.0)", "rich (>=9.0.0)"]
+codemods = ["libcst (>=0.3.16)"]
+crosshair = ["crosshair-tool (>=0.0.81)", "hypothesis-crosshair (>=0.0.18)"]
+dateutil = ["python-dateutil (>=1.4)"]
+django = ["django (>=4.2)"]
+dpcontracts = ["dpcontracts (>=0.4)"]
+ghostwriter = ["black (>=19.10b0)"]
+lark = ["lark (>=0.10.1)"]
+numpy = ["numpy (>=1.19.3)"]
+pandas = ["pandas (>=1.1)"]
+pytest = ["pytest (>=4.6)"]
+pytz = ["pytz (>=2014.1)"]
+redis = ["redis (>=3.0.0)"]
+zoneinfo = ["tzdata (>=2024.2)"]
+
+[[package]]
+name = "iniconfig"
+version = "2.0.0"
+description = "brain-dead simple config-ini parsing"
+optional = true
+python-versions = ">=3.7"
+groups = ["main"]
+markers = "extra == \"dev\""
+files = [
+    {file = "iniconfig-2.0.0-py3-none-any.whl", hash = "sha256:b6a85871a79d2e3b22d2d1b94ac2824226a63c6b741c88f7ae975f18b6778374"},
+    {file = "iniconfig-2.0.0.tar.gz", hash = "sha256:2d91e135bf72d31a410b17c16da610a82cb55f6b0477d1a902134b24a455b8b3"},
+]
+
 [[package]]
 name = "numpy"
 version = "2.2.0"
@@ -108,6 +281,36 @@ files = [
     {file = "numpy-2.2.0.tar.gz", hash = "sha256:140dd80ff8981a583a60980be1a655068f8adebf7a45a06a6858c873fcdcd4a0"},
 ]
 
+[[package]]
+name = "packaging"
+version = "24.2"
+description = "Core utilities for Python packages"
+optional = true
+python-versions = ">=3.8"
+groups = ["main"]
+markers = "extra == \"dev\""
+files = [
+    {file = "packaging-24.2-py3-none-any.whl", hash = "sha256:09abb1bccd265c01f4a3aa3f7a7db064b36514d2cba19a2f694fe6150451a759"},
+    {file = "packaging-24.2.tar.gz", hash = "sha256:c228a6dc5e932d346bc5739379109d49e8853dd8223571c7c5b55260edc0b97f"},
+]
+
+[[package]]
+name = "pluggy"
+version = "1.5.0"
+description = "plugin and hook calling mechanisms for python"
+optional = true
+python-versions = ">=3.8"
+groups = ["main"]
+markers = "extra == \"dev\""
+files = [
+    {file = "pluggy-1.5.0-py3-none-any.whl", hash = "sha256:44e1ad92c8ca002de6377e165f3e0f1be63266ab4d554740532335b9d75ea669"},
+    {file = "pluggy-1.5.0.tar.gz", hash = "sha256:2cffa88e94fdc978c4c574f15f9e59b7f4201d439195c3715ca9e2486f1d0cf1"},
+]
+
+[package.extras]
+dev = ["pre-commit", "tox"]
+testing = ["pytest", "pytest-benchmark"]
+
 [[package]]
 name = "portion"
 version = "2.6.0"
@@ -126,6 +329,117 @@ sortedcontainers = ">=2.2,<3.0"
 [package.extras]
 test = ["black (>=21.8b)", "coverage (>=6.0,<7.0)", "pytest (>=7.0,<8.0)"]
 
+[[package]]
+name = "py"
+version = "1.11.0"
+description = "library with cross-python path, ini-parsing, io, code, log facilities"
+optional = true
+python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, !=3.4.*"
+groups = ["main"]
+markers = "extra == \"dev\""
+files = [
+    {file = "py-1.11.0-py2.py3-none-any.whl", hash = "sha256:607c53218732647dff4acdfcd50cb62615cedf612e72d1724fb1a0cc6405b378"},
+    {file = "py-1.11.0.tar.gz", hash = "sha256:51c75c4126074b472f746a24399ad32f6053d1b34b68d2fa41e558e6f4a98719"},
+]
+
+[[package]]
+name = "py-cpuinfo"
+version = "9.0.0"
+description = "Get CPU info with pure Python"
+optional = true
+python-versions = "*"
+groups = ["main"]
+markers = "extra == \"dev\""
+files = [
+    {file = "py-cpuinfo-9.0.0.tar.gz", hash = "sha256:3cdbbf3fac90dc6f118bfd64384f309edeadd902d7c8fb17f02ffa1fc3f49690"},
+    {file = "py_cpuinfo-9.0.0-py3-none-any.whl", hash = "sha256:859625bc251f64e21f077d099d4162689c762b5d6a4c3c97553d56241c9674d5"},
+]
+
+[[package]]
+name = "pytest"
+version = "6.2.5"
+description = "pytest: simple powerful testing with Python"
+optional = true
+python-versions = ">=3.6"
+groups = ["main"]
+markers = "extra == \"dev\""
+files = [
+    {file = "pytest-6.2.5-py3-none-any.whl", hash = "sha256:7310f8d27bc79ced999e760ca304d69f6ba6c6649c0b60fb0e04a4a77cacc134"},
+    {file = "pytest-6.2.5.tar.gz", hash = "sha256:131b36680866a76e6781d13f101efb86cf674ebb9762eb70d3082b6f29889e89"},
+]
+
+[package.dependencies]
+atomicwrites = {version = ">=1.0", markers = "sys_platform == \"win32\""}
+attrs = ">=19.2.0"
+colorama = {version = "*", markers = "sys_platform == \"win32\""}
+iniconfig = "*"
+packaging = "*"
+pluggy = ">=0.12,<2.0"
+py = ">=1.8.2"
+toml = "*"
+
+[package.extras]
+testing = ["argcomplete", "hypothesis (>=3.56)", "mock", "nose", "requests", "xmlschema"]
+
+[[package]]
+name = "pytest-benchmark"
+version = "3.4.1"
+description = "A ``pytest`` fixture for benchmarking code. It will group the tests into rounds that are calibrated to the chosen timer."
+optional = true
+python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, !=3.4.*"
+groups = ["main"]
+markers = "extra == \"dev\""
+files = [
+    {file = "pytest-benchmark-3.4.1.tar.gz", hash = "sha256:40e263f912de5a81d891619032983557d62a3d85843f9a9f30b98baea0cd7b47"},
+    {file = "pytest_benchmark-3.4.1-py2.py3-none-any.whl", hash = "sha256:36d2b08c4882f6f997fd3126a3d6dfd70f3249cde178ed8bbc0b73db7c20f809"},
+]
+
+[package.dependencies]
+py-cpuinfo = "*"
+pytest = ">=3.8"
+
+[package.extras]
+aspect = ["aspectlib"]
+elasticsearch = ["elasticsearch"]
+histogram = ["pygal", "pygaljs"]
+
+[[package]]
+name = "pytest-console-scripts"
+version = "1.4.1"
+description = "Pytest plugin for testing console scripts"
+optional = true
+python-versions = ">=3.8"
+groups = ["main"]
+markers = "extra == \"dev\""
+files = [
+    {file = "pytest-console-scripts-1.4.1.tar.gz", hash = "sha256:5a826ed84cc0afa202eb9e44381d7d762f7bdda8e0c23f9f79a7f1f44cf4a895"},
+    {file = "pytest_console_scripts-1.4.1-py3-none-any.whl", hash = "sha256:ad860a951a90eca4bd3bd1159b8f5428633ba4ea01abd5c9526b67a95f65437a"},
+]
+
+[package.dependencies]
+pytest = ">=4.0.0"
+
+[[package]]
+name = "pytest-cov"
+version = "2.12.1"
+description = "Pytest plugin for measuring coverage."
+optional = true
+python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, !=3.4.*"
+groups = ["main"]
+markers = "extra == \"dev\""
+files = [
+    {file = "pytest-cov-2.12.1.tar.gz", hash = "sha256:261ceeb8c227b726249b376b8526b600f38667ee314f910353fa318caa01f4d7"},
+    {file = "pytest_cov-2.12.1-py2.py3-none-any.whl", hash = "sha256:261bb9e47e65bd099c89c3edf92972865210c36813f80ede5277dceb77a4a62a"},
+]
+
+[package.dependencies]
+coverage = ">=5.2.1"
+pytest = ">=4.6"
+toml = "*"
+
+[package.extras]
+testing = ["fields", "hunter", "process-tests", "pytest-xdist", "six", "virtualenv"]
+
 [[package]]
 name = "scipy"
 version = "1.14.1"
@@ -222,7 +536,10 @@ files = [
     {file = "toml-0.10.2.tar.gz", hash = "sha256:b3bda1d108d5dd99f4a20d24d9c348e91c4db7ab1b749200bded2f839ccbe68f"},
 ]
 
+[extras]
+dev = ["hypothesis", "pytest", "pytest-benchmark", "pytest-console-scripts", "pytest-cov"]
+
 [metadata]
 lock-version = "2.1"
 python-versions = ">=3.10,<4"
-content-hash = "2f25614503c14ddfee2095224b1a03ec7cccb92c75a11607caa19a6c0b465bb2"
+content-hash = "a587c459a5cebb3eb272078094d0d5ba87522fa1a3482576a250872e60db2aa7"
diff --git a/pyproject.toml b/pyproject.toml
index eba8ec5..bd614cd 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -23,6 +23,15 @@ dependencies = [
     "toml>=0.10",
 ]
 
+[project.optional-dependencies]
+dev = [
+    "pytest~=6.2",
+    "pytest-cov~=2.12",
+    "pytest-benchmark~=3.4",
+    "pytest-console-scripts~=1.2",
+    "hypothesis~=6.14",
+]
+
 [project.urls]
 homepage = "https://tact.jonathanchang.org"
 repository = "https://github.com/jonchang/tact"
@@ -47,13 +56,6 @@ classifiers = [
     "Topic :: Scientific/Engineering :: Bio-Informatics"
 ]
 
-[poetry.group.dev.dependencies]
-pytest = "^6.2"
-pytest-cov = "^2.12"
-pytest-benchmark = "^3.4"
-pytest-console-scripts = "^1.2"
-hypothesis = "^6.14"
-
 [tool.black]
 line-length = 118
 target-version = ['py38', 'py39', 'py310', 'py311']

From 0bd5c7fa251ba4acbfbbb1f0469a3b21d3f38cf9 Mon Sep 17 00:00:00 2001
From: Jonathan Chang <me@jonathanchang.org>
Date: Mon, 6 Jan 2025 14:51:06 -0800
Subject: [PATCH 5/5] fix cmds

---
 .github/workflows/pythonpackage.yml | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/.github/workflows/pythonpackage.yml b/.github/workflows/pythonpackage.yml
index 0b4e120..1e35018 100644
--- a/.github/workflows/pythonpackage.yml
+++ b/.github/workflows/pythonpackage.yml
@@ -45,10 +45,10 @@ jobs:
           echo $gitd
           echo $poetryv
       - name: Install package for testing
-        run: poetry install -v --with=dev
+        run: poetry install -v --all-extras
       - name: Lint with flake8
         run: |
-          pip install flake8
+          pipx install flake8
           # stop the build if there are Python syntax errors or undefined names
           flake8 . --count --select=E9,F63,F7,F82 --show-source --statistics
           # exit-zero treats all errors as warnings
@@ -60,7 +60,7 @@ jobs:
       - name: Reinstall package for production
         run: |
           poetry env list --full-path | xargs rm -rf
-          poetry install -v --only=main
+          poetry install -v
       - name: Build distribution package
         id: build
         run: |