Merge pull request #748 from MilesCranmer/release-v1-beta

Update to 1.0 backend

Author: MilesCranmer

.github/workflows/CI.yml

@@ -30,8 +30,8 @@ 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 +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: ${{ matrix.test-id == 'main' }}
@@ -97,15 +89,15 @@ jobs:
         julia-version: ['1']
         include:
           - os: ubuntu-latest
-            python-version: '3.8'
-            julia-version: '1.6'
+            python-version: '3.10'
+            julia-version: '1.10'
     steps:
       - uses: actions/checkout@v4
       - uses: actions/setup-python@v5
       - name: "Install PySR"
         run: |
             python -m pip install --upgrade pip
-            pip install .
+            pip install '.[dev]'
       - name: "Run development test"
         run: PYSR_TEST_JULIA_VERSION=${{ matrix.julia-version }} PYSR_TEST_PYTHON_VERSION=${{ matrix.python-version }} python -m pysr test dev
 
@@ -131,7 +123,7 @@ 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 }}
@@ -176,7 +168,7 @@ jobs:
       matrix:
         python-version:
           - '3.12'
-          - '3.8'
+          - '3.10'
         os: ['ubuntu-latest']
 
     steps:
@@ -189,14 +181,37 @@ 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
-        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

.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: |

.github/workflows/CI_conda_forge.yml

@@ -20,17 +20,17 @@ 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
             os: 'windows-latest'
             use-mamba: true
-          - python-version: 3.9
+          - python-version: 3.10
             os: 'macos-latest'
             use-mamba: true
           - python-version: 3.12

.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']
 

.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'}}

.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

.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

.gitignore

@@ -25,3 +25,5 @@ site
 venv
 requirements-dev.lock
 requirements.lock
+outputs
+.mypy_cache

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

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`.