Move requiremets to pyproject

.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: |

.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

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"
+write_to = "tsdate/_version.py"