From 2df313bec00174ddca440adbf34031db11400711 Mon Sep 17 00:00:00 2001
From: MilesCranmer <miles.cranmer@gmail.com>
Date: Fri, 29 Nov 2024 20:36:21 +0000
Subject: [PATCH] deps: create optional deps under `dev`

---
 .github/workflows/CI.yml               | 18 +++----------
 .github/workflows/CI_Windows.yml       |  3 +--
 .github/workflows/CI_large_nightly.yml |  3 +--
 .github/workflows/CI_mac.yml           |  7 +-----
 pyproject.toml                         | 35 ++++++++++++++------------
 5 files changed, 25 insertions(+), 41 deletions(-)

diff --git a/.github/workflows/CI.yml b/.github/workflows/CI.yml
index a454345ae..9d1428541 100644
--- a/.github/workflows/CI.yml
+++ b/.github/workflows/CI.yml
@@ -58,26 +58,18 @@ jobs:
       - name: "Install PySR"
         run: |
             python -m pip install --upgrade pip
-            pip install .
+            pip install '.[dev]'
             python -c 'import pysr'
       - name: "Assert Julia version"
         if: ${{ matrix.julia-version != '1'}}
         run: python3 -c "from pysr import jl; assert jl.VERSION.major == jl.seval('v\"${{ matrix.julia-version }}\"').major; assert jl.VERSION.minor == jl.seval('v\"${{ matrix.julia-version }}\"').minor"
-      - name: "Install test dependencies"
-        run: pip install coverage coveralls pytest nbval
       - name: "Set up coverage for subprocesses"
         run: echo 'import coverage; coverage.process_startup()' > "${{ github.workspace }}/sitecustomize.py"
       - name: "Run tests"
         run: coverage run -m pysr test main,cli,startup
-      - name: "Install JAX"
-        run: pip install jax jaxlib # (optional import)
-        if: ${{ matrix.test-id == 'main' }}
       - name: "Run JAX tests"
         run: coverage run --append -m pysr test jax
         if: ${{ matrix.test-id == 'main' }}
-      - name: "Install Torch"
-        run: pip install torch # (optional import)
-        if: ${{ matrix.test-id == 'main' }}
       - name: "Run Torch tests"
         run: coverage run --append -m pysr test torch
         if: ${{ matrix.test-id == 'main' }}
@@ -105,7 +97,7 @@ jobs:
       - name: "Install PySR"
         run: |
             python -m pip install --upgrade pip
-            pip install .
+            pip install '.[dev]'
       - name: "Run development test"
         run: PYSR_TEST_JULIA_VERSION=${{ matrix.julia-version }} PYSR_TEST_PYTHON_VERSION=${{ matrix.python-version }} python -m pysr test dev
 
@@ -189,11 +181,7 @@ jobs:
       - name: "Install PySR and all dependencies"
         run: |
             python -m pip install --upgrade pip
-            pip install .
-            pip install mypy
-      - name: "Install additional dependencies"
-        run: python -m pip install jax jaxlib torch
-        if: ${{ matrix.python-version != '3.9' }}
+            pip install '.[dev]'
       - name: "Run mypy"
         run: python -m mypy --install-types --non-interactive pysr
         if: ${{ matrix.python-version != '3.9' }}
diff --git a/.github/workflows/CI_Windows.yml b/.github/workflows/CI_Windows.yml
index f66644342..a62b7af6e 100644
--- a/.github/workflows/CI_Windows.yml
+++ b/.github/workflows/CI_Windows.yml
@@ -46,8 +46,7 @@ jobs:
       - name: "Install PySR"
         run: |
             python -m pip install --upgrade pip
-            pip install pytest nbval "numpy<2.0.0"
-            pip install .
+            pip install '.[dev]'
             python -c 'import pysr'
       - name: "Run tests"
         run: |
diff --git a/.github/workflows/CI_large_nightly.yml b/.github/workflows/CI_large_nightly.yml
index af00eb8c4..369d4bf47 100644
--- a/.github/workflows/CI_large_nightly.yml
+++ b/.github/workflows/CI_large_nightly.yml
@@ -40,8 +40,7 @@ jobs:
       - name: "Install PySR"
         run: |
             python -m pip install --upgrade pip
-            pip install pytest nbval
-            pip install .
+            pip install '.[dev]'
             python -c 'import pysr'
       - name: "Assert Julia version"
         if: ${{ matrix.julia-version != '1'}}
diff --git a/.github/workflows/CI_mac.yml b/.github/workflows/CI_mac.yml
index fab20425c..68a940ee3 100644
--- a/.github/workflows/CI_mac.yml
+++ b/.github/workflows/CI_mac.yml
@@ -46,17 +46,12 @@ jobs:
       - name: "Install PySR"
         run: |
             python -m pip install --upgrade pip
-            pip install pytest nbval
-            pip install .
+            pip install '.[dev]'
             python -c 'import pysr'
       - name: "Run tests"
         run: |
             python -m pysr test main,cli,startup
-      - name: "Install JAX"
-        run: pip install jax jaxlib # (optional import)
       - name: "Run JAX tests"
         run: python -m pysr test jax
-      - name: "Install Torch"
-        run: pip install torch # (optional import)
       - name: "Run Torch tests"
         run: python -m pysr test torch
diff --git a/pyproject.toml b/pyproject.toml
index 724e5c0e6..42518283a 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -28,6 +28,25 @@ dependencies = [
     "typing-extensions>=4.0.0,<5.0.0",
 ]
 
+[project.optional-dependencies]
+dev = [
+    "beartype>=0.19,<0.20",
+    "coverage>=7,<8",
+    "coveralls>=4,<5",
+    "ipykernel>=6,<7",
+    "ipython>=8,<9",
+    "jax[cpu]>=0.4,<0.5",
+    "jupyter>=1,<2",
+    "mypy>=1,<2",
+    "nbval>=0.11,<0.12",
+    "pandas-stubs",
+    "pre-commit>=3.7,<5",
+    "pytest>=8,<9",
+    "torch>=2,<3",
+    "types-openpyxl",
+    "types-pytz",
+]
+
 [tool.setuptools]
 packages = ["pysr", "pysr._cli", "pysr.test"]
 include-package-data = false
@@ -38,19 +57,3 @@ dependencies = {file = "requirements.txt"}
 
 [tool.isort]
 profile = "black"
-
-[tool.rye]
-dev-dependencies = [
-    "pre-commit>=3.7.0",
-    "ipython>=8.23.0",
-    "ipykernel>=6.29.4",
-    "mypy>=1.10.0",
-    "jax[cpu]>=0.4.26",
-    "torch>=2.3.0",
-    "pandas-stubs>=2.2.1.240316",
-    "types-pytz>=2024.1.0.20240417",
-    "types-openpyxl>=3.1.0.20240428",
-    "coverage>=7.5.3",
-    "pytest>=8.3.3",
-    "nbval>=0.11.0",
-]