From dd41ee6dae64ca29cb95c7641bc7b7da37de1f1d Mon Sep 17 00:00:00 2001
From: Ben Jeffery <ben.jeffery@bdi.ox.ac.uk>
Date: Sun, 7 Sep 2025 23:03:44 +0100
Subject: [PATCH] Pyproject reqs

---
 .circleci/config.yml       |  6 ++-
 .github/workflows/docs.yml |  4 +-
 docs/requirements.txt      | 22 ---------
 pyproject.toml             | 96 ++++++++++++++++++++++++++++++++++++--
 requirements.txt           | 20 --------
 5 files changed, 99 insertions(+), 49 deletions(-)
 delete mode 100644 docs/requirements.txt
 delete mode 100644 requirements.txt

diff --git a/.circleci/config.yml b/.circleci/config.yml
index 3bb5663d..52565d84 100644
--- a/.circleci/config.yml
+++ b/.circleci/config.yml
@@ -20,7 +20,11 @@ jobs:
       - run:
           name: install dependencies
           command: |
-              pip install -r requirements.txt --user
+              # Install uv for dependency management
+              pip install --user uv
+              # Install dependencies from pyproject.toml
+              uv pip install --system -r pyproject.toml --extra test --extra dev
+              pyenv rehash
       - run:
           name: Lint Python
           command: |
diff --git a/.github/workflows/docs.yml b/.github/workflows/docs.yml
index 990be4dc..d6bba304 100644
--- a/.github/workflows/docs.yml
+++ b/.github/workflows/docs.yml
@@ -8,6 +8,4 @@ on:
   merge_group:
 jobs:
   Docs:
-    uses: tskit-dev/.github/.github/workflows/docs-build-template.yml@main
-    with:
-      requirements-path: docs/requirements.txt
+    uses: tskit-dev/.github/.github/workflows/docs-build-template.yml@v1
diff --git a/docs/requirements.txt b/docs/requirements.txt
deleted file mode 100644
index ba651abb..00000000
--- a/docs/requirements.txt
+++ /dev/null
@@ -1,22 +0,0 @@
-appdirs
-demesdraw
-attrs
-matplotlib
-mpmath
-numba
-pandas
-scipy>=1.13.0
-stdpopsim==0.3.0
-tsinfer
-tskit
-tqdm
-jupyter-book==1.0.4.post1
-sphinx-issues==5.0.0
-sphinx-argparse==0.5.2
-sphinxcontrib-bibtex
-humanize==4.12.1
-tqdm==4.67.1
-daiquiri
-msprime==1.3.3
-ipywidgets==8.1.5
-sphinx-book-theme #Unpinned to allow easy updating.
diff --git a/pyproject.toml b/pyproject.toml
index 6c6e4526..7a70ba5e 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -3,10 +3,100 @@ requires = [
     "setuptools>=42",
     "setuptools_scm",
     "wheel",
-    "oldest-supported-numpy"
+    "oldest-supported-numpy",
 ]
-
 build-backend = "setuptools.build_meta"
 
+[project]
+name = "tsdate"
+dynamic = [
+    "version",
+]
+authors = [
+    { name = "tsdate Developers", email = "admin@tskit.dev" },
+]
+description = "Infer tree sequence node times"
+readme = "README.md"
+requires-python = ">=3.8"
+classifiers = [
+    "Development Status :: 4 - Beta",
+    "Intended Audience :: Developers",
+    "License :: OSI Approved :: MIT License",
+    "Programming Language :: Python :: 3",
+    "Programming Language :: Python :: 3.8",
+    "Programming Language :: Python :: 3.9",
+    "Programming Language :: Python :: 3.10",
+    "Programming Language :: Python :: 3.11",
+    "Programming Language :: Python :: 3.12",
+]
+dependencies = [
+    "tskit>=0.6.0",
+    "tsinfer>=0.3.0",
+    "numpy",
+    "tqdm",
+    "daiquiri",
+    "scipy>=1.13.0",
+    "numba>=0.58.1",
+    "appdirs",
+    "setuptools>=45",
+]
+
+[project.license]
+text = "MIT"
+
+[project.optional-dependencies]
+test = [
+    "pytest==8.4.2",
+    "pytest-xdist==3.8.0",
+    "pytest-cov==6.3.0",
+    "msprime==1.3.4",
+    "mpmath==1.3.0",
+    "numdifftools==0.9.41",
+    "matplotlib==3.10.6",
+]
+docs = [
+    "demesdraw==0.4.0",
+    "attrs==25.3.0",
+    "matplotlib==3.10.6",
+    "mpmath==1.3.0",
+    "numba==0.61.2",
+    "pandas==2.3.2",
+    "stdpopsim==0.3.0",
+    "tsinfer==0.4.1",
+    "tskit==0.6.4",
+    "jupyter-book==1.0.4.post1",
+    "sphinx-issues==5.0.1",
+    "sphinx-argparse==0.5.2",
+    "sphinxcontrib-bibtex==2.6.5",
+    "humanize==4.13.0",
+    "msprime==1.3.4",
+    "ipywidgets==8.1.7",
+    "sphinx-book-theme==1.1.4",
+]
+dev = [
+    "ruff",
+    "pre-commit",
+    "pytest",
+    "pytest-xdist",
+    "pytest-cov",
+    "msprime",
+    "mpmath",
+    "numdifftools",
+    "matplotlib",
+    "twine",
+    "build",
+    "demesdraw",
+    "attrs",
+    "pandas",
+    "stdpopsim",
+    "jupyter-book",
+    "sphinx-issues",
+    "sphinx-argparse",
+    "sphinxcontrib-bibtex",
+    "humanize",
+    "ipywidgets",
+    "sphinx-book-theme",
+]
+
 [tool.setuptools_scm]
-write_to = "tsdate/_version.py"
\ No newline at end of file
+write_to = "tsdate/_version.py"
diff --git a/requirements.txt b/requirements.txt
deleted file mode 100644
index 4dd62e86..00000000
--- a/requirements.txt
+++ /dev/null
@@ -1,20 +0,0 @@
-tskit>=0.6.0
-tsinfer>=0.3.0
-ruff
-numpy
-tqdm
-daiquiri
-msprime>=1.3.2
-scipy>=1.13.0
-numba>=0.58.1
-appdirs
-pre-commit
-pytest
-pytest-xdist
-pytest-cov
-mpmath
-numdifftools
-setuptools>=45
-matplotlib
-twine
-build