replace requirements files with uv.lock (#1353)

* update docs
* explicit pin of build-system

Author: molpopgen

.github/workflows/black.yml

@@ -26,11 +26,16 @@ jobs:
         uses: actions/checkout@v4
         with:
           submodules: true
+      - name: Install the latest version of uv
+        uses: astral-sh/setup-uv@v5
+        with:
+          version: "latest"
+          python-version: ${{ matrix.python }}
       - name: Install black
         run: |
-          python -m pip install black=="24.10.0"
+          uv sync --only-group format
       - name: Validate code
         run: |
-          find . -name '*.py'|grep -v headers|grep -v demes-spec|xargs python -m black --check
+          find fwdpy11 tests tests_with_cpp examples -name '*.py' | grep -v headers | grep -v demes-spec | xargs python -m black --check
 
 

.github/workflows/docs.yml

@@ -56,10 +56,6 @@ jobs:
         run: |
           sudo apt install --fix-missing -y libgsl-dev cmake 
 
-      - name: Install Python dependencies
-        run: |
-          uv pip install -r requirements/CI_${{ matrix.python-version }}.txt
-
       - name: rustc version
         run: |
             rustc --version
@@ -68,9 +64,9 @@ jobs:
         run: |
             cbindgen --version
 
-      - name: Build module
+      - name: uv sync
         run: |
-            uv pip install -e .
+          uv sync -p ${{ matrix.python-version }} --locked --group build --group doc --no-dev
 
       - name: Build the docs
         working-directory: doc

.github/workflows/macos_CI.yml

@@ -52,7 +52,11 @@ jobs:
 
       - name: Install Python dependencies
         run: |
-          uv pip install -r requirements/CI_${{ matrix.python }}.txt
+          # We need to build the C++ test suite, etc., so
+          # we don't let uv install the project (b/c the other
+          # stuff isn't built in that case)
+          uv sync -p ${{ matrix.python }} --no-install-project --frozen --group build
+
       - name: Build extension module
         run: |
           cmake -S. -Bbuild -DCMAKE_BUILD_TYPE=Release -DBUILD_PYTHON_UNIT_TESTS=ON -DDISABLE_LTO=ON

.github/workflows/ubuntu.yml

@@ -89,9 +89,12 @@ jobs:
         run: |
           python --version
 
-      - name: Install pip dependencies
+      - name: Install python dependencies
         run: |
-          uv pip install -r requirements/CI_${{ matrix.python }}.txt
+          # We need to build the C++ test suite, etc., so
+          # we don't let uv install the project (b/c the other
+          # stuff isn't built in that case)
+          uv sync -p ${{ matrix.python }} --no-install-project --frozen --group build
 
       # Need#   ed so that we don't affect building any pip dependencies with these flags
       - name: Set CPPFLAGS for C++ builds

doc/misc/developersguide.md

@@ -36,16 +36,14 @@ The C++ test suite requires:
 :::{warning}
 `conda` users **must** install all of these dependencies using that system, including the compilers!
 See [here](https://docs.conda.io/projects/conda-build/en/latest/resources/compiler-tools.html) for info about `conda` compilers for Linux and for macOS.
-
-The `requirements/` folder of the source code repository contains a list of minimal `conda` dependencies that we use for CI.
 :::
 
 #### Python
 
 To reproduce the environments that we use for CI and deployment:
 
 ```sh
-python3 -m pip install -r requirements/development.txt
+uv sync --no-install-package --all-groups
 ```
 
 ```{note}

pyproject.toml

@@ -1,8 +1,8 @@
 [build-system]
 # We need setup.cfg support, which setuptools indtroduced in 30.3.0.
 requires = [
-    "scikit-build-core>=0.3.3",
-    "setuptools_scm>=8",
+    "scikit-build-core==0.11.1",
+    "setuptools_scm==7.1.0",
     "pybind11[global]==2.12.0",
     "numpy >= 2.0"
 ]
@@ -31,6 +31,49 @@ dependencies = [
 ]
 requires-python = ">=3.10, <3.14"
 
+[dependency-groups]
+# NOTE: we are doing a very odd hack here!
+# uv does NOT currently support locking build dependencies
+# so we add it as a dependency group and force it.
+# The PROBLEM is that we have TWO places to modify
+# things in the future.
+build = [
+    "scikit-build-core==0.11.1",
+    "setuptools_scm==7.1.0",
+    "pybind11[global]==2.12.0",
+    "numpy >= 2.0"
+]
+format = [
+    "black==24.10.0"
+]
+lint = [
+    "flake8",
+    "flake8-bugbear",
+]
+dev = [
+#below are for building package
+#and running tests
+    "pytest",
+    "pytest-xdist",
+    "hypothesis==6.56.4",
+    "msprime ~= 1.3.0",
+    "build",
+    "twine",
+]
+
+doc = [
+    "jupyter-book~=0.15.1",
+    "pydata-sphinx-theme==0.13.1",
+    "matplotlib",
+    "msprime",
+    "pandas",
+# pyarrow will be a requirement of pandas soon.
+# right now, not having it raises a warning
+    "pyarrow",
+    "sphinx-issues",
+    "demesdraw~=0.4.0",
+]
+
 [project.scripts]
 fwdpy11 = "fwdpy11.__main__:main"
 
@@ -69,3 +112,8 @@ before-all = "./deployment/linux_wheels/cibuildwheel.sh"
 archs = "x86_64"
 # skip = "pp* *musllinux*"
 
+[tool.uv]
+required-environments = [
+    "sys_platform == 'darwin' and implementation_name == 'cpython'",
+    "sys_platform == 'linux' and implementation_name == 'cpython'",
+]