(BREAKING) Rewrite Julia interface with PyJulia -> JuliaCall; other changes

.coveragerc

@@ -0,0 +1,4 @@
+[run]
+omit =
+    */test/*
+source = pysr

.github/workflows/CI.yml

@@ -24,6 +24,8 @@ jobs:
   test:
     runs-on: ${{ matrix.os }}
     timeout-minutes: 60
+    env:
+      COVERAGE_PROCESS_START: "${{ github.workspace }}/.coveragerc"
     defaults:
       run:
         shell: bash
@@ -38,6 +40,10 @@ jobs:
             python-version: '3.7'
             os: ubuntu-latest
             test-id: include
+          - julia-version: '1'
+            python-version: '3.12'
+            os: ubuntu-latest
+            test-id: include
 
     steps:
       - uses: actions/checkout@v4
@@ -58,44 +64,56 @@ jobs:
       - name: "Install PySR"
         run: |
             python -m pip install --upgrade pip
-            pip install -r requirements.txt
-            python setup.py install
-            python -m pysr install
-      - name: "Install Coverage tool"
-        run: pip install coverage coveralls
+            pip install .
+            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 --source=pysr --omit='*/test/*,*/feynman_problems.py' -m pysr.test main
-            coverage run --append --source=pysr --omit='*/test/*,*/feynman_problems.py' -m pysr.test cli
+        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 --source=pysr --omit='*/test/*,*/feynman_problems.py' -m pysr.test jax
+        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 --source=pysr --omit='*/test/*,*/feynman_problems.py' -m pysr.test torch
+        run: coverage run --append -m pysr test torch
         if: ${{ matrix.test-id == 'main' }}
-      - name: "Run custom env tests"
-        run: coverage run --append --source=pysr --omit='*/test/*,*/feynman_problems.py' -m pysr.test env
       - name: "Coveralls"
         env:
           GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
           COVERALLS_FLAG_NAME: test-${{ matrix.julia-version }}-${{ matrix.python-version }}
           COVERALLS_PARALLEL: true
         run: coveralls --service=github
 
-  incremental_install:
-    runs-on: ubuntu-latest
+  dev_install:
+    runs-on: ${{ matrix.os }}
+    strategy:
+      matrix:
+        os: ['ubuntu-latest']
+        python-version: ['3.11']
+        julia-version: ['1']
+        include:
+          - os: ubuntu-latest
+            python-version: '3.7'
+            julia-version: '1.6'
     steps:
       - uses: actions/checkout@v4
-      - name: "Build incremental install"
-        run: docker build -t pysr -f pysr/test/incremental_install_simulator.dockerfile .
-      - name: "Test incremental install"
-        run: docker run --rm pysr /bin/bash -l -c 'python3 -m pysr.test main && python3 -m pysr.test env'
+      - uses: actions/setup-python@v5
+      - name: "Install PySR"
+        run: |
+            python -m pip install --upgrade pip
+            pip install .
+      - name: "Run development test"
+        run: PYSR_TEST_JULIA_VERSION=${{ matrix.julia-version }} PYSR_TEST_PYTHON_VERSION=${{ matrix.python-version }} python -m pysr test dev
 
   conda_test:
     runs-on: ${{ matrix.os }}
@@ -133,9 +151,9 @@ jobs:
       - name: "Install PySR"
         run: |
             python3 -m pip install .
-            python3 -m pysr install
+            python3 -c 'import pysr'
       - name: "Run tests"
-        run: cd /tmp && python -m pysr.test main
+        run: cd /tmp && python -m pysr test main
 
   coveralls:
     name: Indicate completion to coveralls.io
@@ -177,9 +195,8 @@ jobs:
       - name: "Install PySR and all dependencies"
         run: |
             python -m pip install --upgrade pip
-            python -m pip install -r requirements.txt
-            python -m pip install mypy
-            python -m pip install .
+            pip install .
+            pip install mypy
       - name: "Install additional dependencies"
         run: python -m pip install jax jaxlib torch
         if: ${{ matrix.python-version != '3.7' }}

.github/workflows/CI_Windows.yml

@@ -52,16 +52,13 @@ jobs:
       - name: "Install PySR"
         run: |
             python -m pip install --upgrade pip
-            pip install -r requirements.txt
-            python setup.py install
-            python -m pysr install
+            pip install pytest nbval
+            pip install .
+            python -c 'import pysr'
       - name: "Run tests"
         run: |
-            python -m pysr.test main
-            python -m pysr.test cli
+            python -m pysr test main,cli,startup
       - name: "Install Torch"
         run: pip install torch # (optional import)
       - name: "Run Torch tests"
-        run: python -m pysr.test torch
-      - name: "Run custom env tests"
-        run: python -m pysr.test env
+        run: python -m pysr test torch

.github/workflows/CI_conda_forge.yml

@@ -40,4 +40,6 @@ jobs:
         run: conda activate pysr-test && conda install pysr
         if: ${{ !matrix.use-mamba }}
       - name: "Run tests"
-        run: python -m pysr.test main
+        run: |
+          pip install pytest nbval
+          python -m pysr test main,startup

.github/workflows/CI_docker.yml

@@ -37,4 +37,4 @@ jobs:
       - name: Build docker
         run: docker build --platform=${{ matrix.arch }} -t pysr .
       - name: Test docker
-        run: docker run --platform=${{ matrix.arch }} --rm pysr /bin/bash -c 'python3 -m pysr.test main && python3 -m pysr.test cli && python3 -m pysr.test env'
+        run: docker run --platform=${{ matrix.arch }} --rm pysr /bin/bash -c 'pip install pytest nbval && python3 -m pysr test main,cli,startup'

.github/workflows/CI_docker_large_nightly.yml

@@ -33,4 +33,4 @@ jobs:
       - name: Build docker
         run: docker build --platform=${{ matrix.arch }} -t pysr --build-arg JLVERSION=${{ matrix.julia-version }} --build-arg PYVERSION=${{ matrix.python-version }} .
       - name: Test docker
-        run: docker run --platform=${{ matrix.arch }} --rm pysr /bin/bash -c 'python3 -m pysr.test main && python3 -m pysr.test cli && python3 -m pysr.test env'
+        run: docker run --platform=${{ matrix.arch }} --rm pysr /bin/bash -c 'pip install pytest nbval && python3 -m pysr test main,cli,startup'

.github/workflows/CI_large_nightly.yml

@@ -40,13 +40,11 @@ jobs:
       - name: "Install PySR"
         run: |
             python -m pip install --upgrade pip
-            pip install -r requirements.txt
-            python setup.py install
-            python -m pysr install
+            pip install pytest nbval
+            pip install .
+            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: "Run tests"
-        run: |
-            python -m pysr.test main
-            python -m pysr.test cli
-      - name: "Run new env test"
-        run: python -m pysr.test env
-        if: ${{ !(matrix.os == 'windows-latest' && matrix.python-version == '3.7') }}
+        run: python -m pysr test main,cli,startup

.github/workflows/CI_mac.yml

@@ -52,20 +52,17 @@ jobs:
       - name: "Install PySR"
         run: |
             python -m pip install --upgrade pip
-            pip install -r requirements.txt
-            python setup.py install
-            python -m pysr install
+            pip install pytest nbval
+            pip install .
+            python -c 'import pysr'
       - name: "Run tests"
         run: |
-            python -m pysr.test main
-            python -m pysr.test cli
+            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
+        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: "Run custom env tests"
-        run: python -m pysr.test env
+        run: python -m pysr test torch

.pre-commit-config.yaml

@@ -13,11 +13,13 @@ repos:
     hooks:
       - id: black
       - id: black-jupyter
+        exclude: pysr/test/test_nb.ipynb
   # Stripping notebooks
   - repo: https://github.com/kynan/nbstripout
     rev: 0.6.1
     hooks:
       - id: nbstripout
+        exclude: pysr/test/test_nb.ipynb
   # Unused imports
   - repo: https://github.com/hadialqattan/pycln
     rev: "v2.4.0"

CONTRIBUTORS.md

@@ -42,7 +42,7 @@ Scan through our [existing issues](https://github.com/MilesCranmer/PySR/issues)
 check out the [guide](https://astroautomata.com/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`.
+4. You can install your local version of PySR with `python setup.py install`, and run tests with `python -m pysr test main`.
 
 ### Commit your update
 

Dockerfile

@@ -13,22 +13,23 @@ COPY --from=jl /usr/local/julia /usr/local/julia
 ENV PATH="/usr/local/julia/bin:${PATH}"
 
 # Install IPython and other useful libraries:
-RUN pip install ipython matplotlib
+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 -r /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
 ADD ./setup.py /pysr/setup.py
-ADD ./pysr/ /pysr/pysr/
-RUN pip3 install .
+ADD ./pysr /pysr/pysr
+RUN pip3 install --no-cache-dir .
 
 # Install Julia pre-requisites:
-RUN python3 -m pysr install
+RUN python3 -c 'import pysr'
 
 # metainformation
 LABEL org.opencontainers.image.authors = "Miles Cranmer"

README.md

@@ -27,10 +27,6 @@ If you've finished a project with PySR, please submit a PR to showcase your work
 - [Contributors](#contributors-)
 - [Why PySR?](#why-pysr)
 - [Installation](#installation)
-  - [pip](#pip)
-  - [conda](#conda)
-  - [docker](#docker-build)
-  - [Troubleshooting](#troubleshooting)
 - [Quickstart](#quickstart)
 - [→ Documentation](https://astroautomata.com/PySR)
 
@@ -129,48 +125,31 @@ an explicit and powerful way to interpret deep neural networks.
 
 ## Installation
 
-| [pip](#pip) | [conda](#conda) | [docker](#docker-build) |
-|:---:|:---:|:---:|
-| Everywhere (recommended) | Linux and Intel-based macOS | Everywhere (if all else fails) |
+### Pip
 
----
-
-### pip
+You can install PySR with pip:
 
-1. [Install Julia](https://julialang.org/downloads/)
-    - Alternatively, my personal preference is to use [juliaup](https://github.com/JuliaLang/juliaup#installation), which performs this automatically.
-2. Then, run:
 ```bash
-pip3 install -U pysr
+pip install pysr
 ```
-3. Finally, to install Julia dependencies:
-```bash
-python3 -m pysr install
-```
-> (Alternatively, from within Python, you can call `import pysr; pysr.install()`)
 
----
+Julia dependencies will be installed at first import.
 
-### conda
+### Conda
 
-The PySR build in conda includes all required dependencies, so you can install it by simply running:
+Similarly, with conda:
 
 ```bash
 conda install -c conda-forge pysr
 ```
 
-from within your target conda environment.
 
-However, note that the conda install does not support precompilation of Julia libraries, so the
-start time may be slightly slower as the JIT-compilation will be running.
-(Once the compilation finishes, there will not be a performance difference though.)
-
----
+### Docker
 
-### docker build
+You can also use the `Dockerfile` to install PySR in a docker container
 
 1. Clone this repo.
-2. In the repo, run the build command with:
+2. Within the repo's directory, build the docker container:
 ```bash
 docker build -t pysr .
 ```
@@ -185,11 +164,7 @@ For more details, see the [docker section](#docker).
 
 ### Troubleshooting
 
-Common issues tend to be related to Python not finding Julia.
-To debug this, try running `python3 -c 'import os; print(os.environ["PATH"])'`.
-If none of these folders contain your Julia binary, then you need to add Julia's `bin` folder to your `PATH` environment variable.
-
-Another issue you might run into can result in a hard crash at import with
+One issue you might run into can result in a hard crash at import with
 a message like "`GLIBCXX_...` not found". This is due to another one of the Python dependencies
 loading an incorrect `libstdc++` library. To fix this, you should modify your
 `LD_LIBRARY_PATH` variable to reference the Julia libraries. For example, if the Julia
@@ -202,7 +177,6 @@ export LD_LIBRARY_PATH=$HOME/.julia/juliaup/julia-1.10.0+0.x64.linux.gnu/lib/jul
 
 to your `.bashrc` or `.zshrc` file.
 
-**Running PySR on macOS with an M1 processor:** you should use the pip version, and make sure to get the Julia binary for ARM/M-series processors.
 
 ## Quickstart
 
@@ -240,7 +214,7 @@ model = PySRRegressor(
     ],
     extra_sympy_mappings={"inv": lambda x: 1 / x},
     # ^ Define operator for SymPy as well
-    loss="loss(prediction, target) = (prediction - target)^2",
+    elementwise_loss="loss(prediction, target) = (prediction - target)^2",
     # ^ Custom loss function (julia syntax)
 )
 ```
@@ -323,7 +297,7 @@ model = PySRRegressor(
     # ^ 2 populations per core, so one is always running.
     population_size=50,
     # ^ Slightly larger populations, for greater diversity.
-    ncyclesperiteration=500,
+    ncycles_per_iteration=500,
     # ^ Generations between migrations.
     niterations=10000000,  # Run forever
     early_stop_condition=(