Merge branch 'master' of https://github.com/MilesCranmer/PySR

MilesCranmer · Dec 31, 2024 · 1c7e43d · 1c7e43d
2 parents da7d620 + fc32e76
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diff --git a/.github/workflows/CI.yml b/.github/workflows/CI.yml
@@ -14,6 +14,9 @@ on:
     paths:
       - '**'
 
+permissions:
+  contents: write
+
 jobs:
   test:
     runs-on: ${{ matrix.os }}
@@ -30,8 +33,8 @@ jobs:
         os: [ubuntu-latest]
         test-id: [main]
         include:
-          - julia-version: '1.6'
-            python-version: '3.8'
+          - julia-version: '1.10'
+            python-version: '3.10'
             os: ubuntu-latest
             test-id: include
           - julia-version: '1'
@@ -58,26 +61,18 @@ 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: ${{ matrix.test-id == 'main' }}
@@ -103,15 +98,15 @@ jobs:
         julia-version: ['1']
         include:
           - os: ubuntu-latest
-            python-version: '3.8'
-            julia-version: '1.6'
+            python-version: '3.10'
+            julia-version: '1.10'
     steps:
       - uses: actions/checkout@v4
       - uses: actions/setup-python@v5
       - name: "Install PySR"
         run: |
             python -m pip install --upgrade pip
-            pip install .
+            pip install '.[dev]'
       - name: "Run development test"
         run: PYSR_TEST_JULIA_VERSION=${{ matrix.julia-version }} PYSR_TEST_PYTHON_VERSION=${{ matrix.python-version }} python -m pysr test dev
 
@@ -137,7 +132,7 @@ jobs:
       - name: "Set up Conda"
         uses: conda-incubator/setup-miniconda@v3
         with:
-          miniforge-variant: Mambaforge
+          miniforge-variant: Miniforge3
           miniforge-version: latest
           auto-activate-base: true
           python-version: ${{ matrix.python-version }}
@@ -182,7 +177,7 @@ jobs:
       matrix:
         python-version:
           - '3.12'
-          - '3.8'
+          - '3.10'
         os: ['ubuntu-latest']
 
     steps:
@@ -195,14 +190,37 @@ 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 paddlepaddle
-        if: ${{ matrix.python-version != '3.8' }}
+            pip install '.[dev]'
       - name: "Run mypy"
         run: python -m mypy --install-types --non-interactive pysr
-        if: ${{ matrix.python-version != '3.8' }}
+        if: ${{ matrix.python-version != '3.10' }}
       - name: "Run compatible mypy"
         run: python -m mypy --ignore-missing-imports pysr
-        if: ${{ matrix.python-version == '3.8' }}
+        if: ${{ matrix.python-version == '3.10' }}
+
+  beartype:
+    name: Test with beartype
+    runs-on: ubuntu-latest
+    defaults:
+      run:
+        shell: bash -l {0}
+    env:
+      PYSR_USE_BEARTYPE: "1"
+    strategy:
+      matrix:
+        python-version: ['3.12']
+        os: ['ubuntu-latest']
+
+    steps:
+      - uses: actions/checkout@v4
+      - name: "Set up Python"
+        uses: actions/setup-python@v5
+        with:
+          python-version: ${{ matrix.python-version }}
+          cache: pip
+      - name: "Install PySR and all dependencies"
+        run: |
+            python -m pip install --upgrade pip
+            pip install '.[dev]'
+      - name: "Run tests"
+        run: python -m pysr test main,jax,torch
diff --git 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_apptainer.yml b/.github/workflows/CI_apptainer.yml
@@ -31,10 +31,10 @@ jobs:
         with:
             apptainer-version: 1.3.0
       - name: Build apptainer
-        run: apptainer build --notest pysr.sif Apptainer.def
+        run: sudo apptainer build --notest pysr.sif Apptainer.def
       - name: Test apptainer
         run: |
           TMPDIR=$(mktemp -d)
           cp pysr.sif $TMPDIR
           cd $TMPDIR
-          apptainer test ./pysr.sif
+          sudo apptainer test ./pysr.sif
diff --git a/.github/workflows/CI_conda_forge.yml b/.github/workflows/CI_conda_forge.yml
@@ -20,28 +20,28 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        python-version: ['3.9', '3.10', '3.11', '3.12']
+        python-version: ['3.10', '3.11', '3.12']
         os: ['ubuntu-latest']
         use-mamba: [true, false]
         include:
-          - python-version: 3.9
+          - python-version: '3.10'
             os: 'windows-latest'
             use-mamba: true
-          - python-version: 3.12
+          - python-version: '3.12'
             os: 'windows-latest'
             use-mamba: true
-          - python-version: 3.9
+          - python-version: '3.10'
             os: 'macos-latest'
             use-mamba: true
-          - python-version: 3.12
+          - python-version: '3.12'
             os: 'macos-latest'
             use-mamba: true
 
     steps:
       - name: "Set up Conda"
         uses: conda-incubator/setup-miniconda@v3
         with:
-          miniforge-variant: Mambaforge
+          miniforge-variant: Miniforge3
           miniforge-version: latest
           auto-activate-base: true
           python-version: ${{ matrix.python-version }}

diff --git a/.github/workflows/CI_docker_large_nightly.yml b/.github/workflows/CI_docker_large_nightly.yml
@@ -18,8 +18,8 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        julia-version: ['1.6', '1']
-        python-version: ['3.8', '3.12']
+        julia-version: ['1.10', '1']
+        python-version: ['3.10', '3.12']
         os: [ubuntu-latest]
         arch: ['linux/amd64', 'linux/arm64']
 

diff --git a/.github/workflows/CI_large_nightly.yml b/.github/workflows/CI_large_nightly.yml
@@ -23,8 +23,8 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        julia-version: ['1.6', '1.8', '1.10']
-        python-version: ['3.8', '3.10', '3.12']
+        julia-version: ['1.10', '1']
+        python-version: ['3.10', '3.12']
         os: [ubuntu-latest, macos-latest, windows-latest]
 
     steps:
@@ -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
@@ -46,18 +46,13 @@ 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
       - name: "Install Paddle"

diff --git a/.github/workflows/docs.yml b/.github/workflows/docs.yml
@@ -25,13 +25,26 @@ jobs:
       - name: "Set up Python"
         uses: actions/setup-python@v5
         with:
-          python-version: 3.9
+          python-version: 3.12
           cache: pip
       - name: "Install packages for docs building"
         run: pip install -r docs/requirements.txt
       - name: "Install PySR"
         run: pip install . && python -c 'import pysr'
       - name: "Build API docs"
         run: cd docs && ./gen_docs.sh
-      - name: "Deploy documentation"
+      - name: "Deploy documentation to primary repository"
         run: mkdocs gh-deploy --force
+      - name: "Deploy documentation to secondary repository"
+        env:
+          DEPLOY_KEY: ${{ secrets.DAMTP_DEPLOY_KEY }}
+        run: |
+          # Set up SSH key for authentication
+          mkdir -p ~/.ssh
+          echo "$DEPLOY_KEY" > ~/.ssh/id_rsa
+          chmod 600 ~/.ssh/id_rsa
+          ssh-keyscan github.com >> ~/.ssh/known_hosts
+
+          git checkout gh-pages
+          git remote add secondary [email protected]:ai-damtp-cam-ac-uk/pysr.git
+          git push secondary gh-pages --force
diff --git a/.gitignore b/.gitignore
@@ -25,3 +25,5 @@ site
 venv
 requirements-dev.lock
 requirements.lock
+outputs
+.mypy_cache
diff --git a/Apptainer.def b/Apptainer.def
@@ -1,10 +1,10 @@
 # Build an Apptainer SIF file containing a working copy of PySR and its prereqs
 Bootstrap: docker
-From: julia:1.10.4-bullseye
+From: julia:1.11.1-bullseye
 Stage: jl
 
 Bootstrap: docker
-From: python:3.12-bullseye
+From: python:3.12.6-bullseye
 Stage: runtime
 
 %environment
@@ -19,7 +19,6 @@ Stage: runtime
 	/usr/local/julia /usr/local/julia
 
 %files
-	./requirements.txt /pysr/requirements.txt
 	./pyproject.toml /pysr/pyproject.toml
 	./setup.py /pysr/setup.py
 	./pysr /pysr/pysr

diff --git a/CONTRIBUTORS.md b/CONTRIBUTORS.md
@@ -6,7 +6,7 @@ In this guide you will get an overview of the contribution workflow from opening
 
 ## New contributor guide
 
-To get an overview of the project, read PySR's [README](README.md). The [PySR docs](https://astroautomata.com/PySR/) give additional information.
+To get an overview of the project, read PySR's [README](README.md). The [PySR docs](https://ai.damtp.cam.ac.uk/pysr/) give additional information.
 Here are some resources to help you get started with open source contributions in general:
 
 - [Finding ways to contribute to open source on GitHub](https://docs.github.com/en/get-started/exploring-projects-on-github/finding-ways-to-contribute-to-open-source-on-github)
@@ -39,7 +39,7 @@ Scan through our [existing issues](https://github.com/MilesCranmer/PySR/issues)
 2. Create a working branch and start with your changes!
 
 3. (Optional) If you would like to make changes to PySR itself, skip to step 4. However, if you are interested in making changes to the _symbolic regression code_ itself,
-check out the [guide](https://astroautomata.com/PySR/backend/) on modifying a custom SymbolicRegression.jl library.
+check out the [guide](https://ai.damtp.cam.ac.uk/pysr/backend/) on modifying a custom SymbolicRegression.jl library.
 In this case, you might instead be interested in making suggestions to the [SymbolicRegression.jl](http://github.com/MilesCranmer/SymbolicRegression.jl) library.
 
 4. You can install your local version of PySR with `python setup.py install`, and run tests with `python -m pysr test main`.

diff --git a/Dockerfile b/Dockerfile
@@ -1,8 +1,8 @@
 # This builds a dockerfile containing a working copy of PySR
 # with all pre-requisites installed.
 
-ARG JLVERSION=1.10.4
-ARG PYVERSION=3.12.2
+ARG JLVERSION=1.11.1
+ARG PYVERSION=3.12.6
 ARG BASE_IMAGE=bullseye
 
 FROM julia:${JLVERSION}-${BASE_IMAGE} AS jl
@@ -17,10 +17,6 @@ RUN pip install --no-cache-dir ipython matplotlib
 
 WORKDIR /pysr
 
-# Caches install (https://stackoverflow.com/questions/25305788/how-to-avoid-reinstalling-packages-when-building-docker-image-for-python-project)
-ADD ./requirements.txt /pysr/requirements.txt
-RUN pip3 install --no-cache-dir -r /pysr/requirements.txt
-
 # Install PySR:
 # We do a minimal copy so it doesn't need to rerun at every file change:
 ADD ./pyproject.toml /pysr/pyproject.toml

diff --git a/README.md b/README.md
@@ -11,7 +11,7 @@ https://github.com/MilesCranmer/PySR/assets/7593028/c8511a49-b408-488f-8f18-b174
 
 | **Docs** | **Forums** | **Paper** | **colab demo** |
 |:---:|:---:|:---:|:---:|
-|[![Documentation](https://github.com/MilesCranmer/PySR/actions/workflows/docs.yml/badge.svg)](https://astroautomata.com/PySR/)|[![Discussions](https://img.shields.io/badge/discussions-github-informational)](https://github.com/MilesCranmer/PySR/discussions)|[![Paper](https://img.shields.io/badge/arXiv-2305.01582-b31b1b)](https://arxiv.org/abs/2305.01582)|[![Colab](https://img.shields.io/badge/colab-notebook-yellow)](https://colab.research.google.com/github/MilesCranmer/PySR/blob/master/examples/pysr_demo.ipynb)|
+|[![Documentation](https://github.com/MilesCranmer/PySR/actions/workflows/docs.yml/badge.svg)](https://ai.damtp.cam.ac.uk/pysr/)|[![Discussions](https://img.shields.io/badge/discussions-github-informational)](https://github.com/MilesCranmer/PySR/discussions)|[![Paper](https://img.shields.io/badge/arXiv-2305.01582-b31b1b)](https://arxiv.org/abs/2305.01582)|[![Colab](https://img.shields.io/badge/colab-notebook-yellow)](https://colab.research.google.com/github/MilesCranmer/PySR/blob/master/examples/pysr_demo.ipynb)|
 
 | **pip** | **conda** | **Stats** |
 | :---: | :---: | :---: |
@@ -20,14 +20,14 @@ https://github.com/MilesCranmer/PySR/assets/7593028/c8511a49-b408-488f-8f18-b174
 </div>
 
 If you find PySR useful, please cite the paper [arXiv:2305.01582](https://arxiv.org/abs/2305.01582).
-If you've finished a project with PySR, please submit a PR to showcase your work on the [research showcase page](https://astroautomata.com/PySR/papers)!
+If you've finished a project with PySR, please submit a PR to showcase your work on the [research showcase page](https://ai.damtp.cam.ac.uk/pysr/papers)!
 
 **Contents**:
 
 - [Why PySR?](#why-pysr)
 - [Installation](#installation)
 - [Quickstart](#quickstart)
-- [→ Documentation](https://astroautomata.com/PySR)
+- [→ Documentation](https://ai.damtp.cam.ac.uk/PySR)
 - [Contributors](#contributors-)
 
 <div align="center">
@@ -178,6 +178,7 @@ PySR's main interface is in the style of scikit-learn:
 from pysr import PySRRegressor
 
 model = PySRRegressor(
+    maxsize=20,
     niterations=40,  # < Increase me for better results
     binary_operators=["+", "*"],
     unary_operators=[
@@ -254,22 +255,21 @@ model = PySRRegressor.from_file("hall_of_fame.2022-08-10_100832.281.pkl")
 
 There are several other useful features such as denoising (e.g., `denoise=True`),
 feature selection (e.g., `select_k_features=3`).
-For examples of these and other features, see the [examples page](https://astroautomata.com/PySR/examples).
-For a detailed look at more options, see the [options page](https://astroautomata.com/PySR/options).
-You can also see the full API at [this page](https://astroautomata.com/PySR/api).
-There are also tips for tuning PySR on [this page](https://astroautomata.com/PySR/tuning).
+For examples of these and other features, see the [examples page](https://ai.damtp.cam.ac.uk/pysr/examples).
+For a detailed look at more options, see the [options page](https://ai.damtp.cam.ac.uk/pysr/options).
+You can also see the full API at [this page](https://ai.damtp.cam.ac.uk/pysr/api).
+There are also tips for tuning PySR on [this page](https://ai.damtp.cam.ac.uk/pysr/tuning).
 
 ### Detailed Example
 
 The following code makes use of as many PySR features as possible.
 Note that is just a demonstration of features and you should not use this example as-is.
-For details on what each parameter does, check out the [API page](https://astroautomata.com/PySR/api/).
+For details on what each parameter does, check out the [API page](https://ai.damtp.cam.ac.uk/pysr/api/).
 
 ```python
 model = PySRRegressor(
-    procs=4,
     populations=8,
-    # ^ 2 populations per core, so one is always running.
+    # ^ Assuming we have 4 cores, this means 2 populations per core, so one is always running.
     population_size=50,
     # ^ Slightly larger populations, for greater diversity.
     ncycles_per_iteration=500,