Merge ceeb420 into 9a56c67

.github/workflows/CI.yml

@@ -61,6 +61,7 @@ jobs:
             python -m pip install --upgrade pip
             pip install -r requirements.txt
             python setup.py install
+            python -c 'import pysr; pysr.install()'
       - name: "Install Coverage tool"
         run: pip install coverage coveralls
       - name: "Run tests"

.github/workflows/CI_Windows.yml

@@ -61,6 +61,7 @@ jobs:
             python -m pip install --upgrade pip
             pip install -r requirements.txt
             python setup.py install
+            python -c 'import pysr; pysr.install()'
       - name: "Run tests"
         run: python -m unittest test.test
         shell: bash

.github/workflows/CI_conda.yml

@@ -0,0 +1,76 @@
+name: CI_conda
+# This tests whether conda, a statically-linked libpython, works
+# with PySR.
+
+on:
+  push:
+    branches:
+      - '*'
+    paths:
+      - 'test/**'
+      - 'pysr/**'
+      - '.github/workflows/**'
+      - 'setup.py'
+      - 'Project.toml'
+  pull_request:
+    branches:
+      - '*'
+    paths:
+      - 'test/**'
+      - 'pysr/**'
+      - '.github/workflows/**'
+      - 'setup.py'
+      - 'Project.toml'
+
+jobs:
+  test:
+    runs-on: ${{ matrix.os }}
+    strategy:
+      matrix:
+        julia-version: ['1.7.1']
+        python-version: ['3.9']
+        os: ['ubuntu-latest']
+
+    steps:
+      - uses: actions/checkout@v1.0.0
+      - name: "Set up Julia"
+        uses: julia-actions/setup-julia@v1.6.0
+        with:
+          version: ${{ matrix.julia-version }}
+      - name: "Change package server"
+        shell: bash
+        env:
+            JULIA_PKG_SERVER: ""
+        run: |
+            julia -e 'using Pkg; Pkg.Registry.add("General")'
+      - name: "Cache dependencies"
+        uses: actions/cache@v1 # Thanks FromFile.jl
+        env:
+          cache-name: cache-artifacts
+        with:
+          path: ~/.julia/artifacts
+          key: ${{ runner.os }}-build-${{ env.cache-name }}-${{ hashFiles('**/Project.toml') }}
+          restore-keys: |
+            ${{ runner.os }}-build-${{ env.cache-name }}-
+            ${{ runner.os }}-build-
+            ${{ runner.os }}-
+      - name: "Set up Conda"
+        uses: conda-incubator/setup-miniconda@v2
+        with:
+          miniforge-variant: Mambaforge
+          miniforge-version: latest
+          auto-activate-base: true
+          python-version: ${{ matrix.python-version }}
+          activate-environment: test
+          environment-file: environment.yml
+      - name: "Install PySR"
+        run: |
+            python3 -m pip install .
+            python3 -c 'import pysr; pysr.install()'
+        shell: bash -l {0}
+      - name: "Ensure that static libpython warning appears"
+        run: python3 test/test_static_libpython_warning.py
+        shell: bash -l {0}
+      - name: "Run tests"
+        run: python3 -m unittest discover -s test
+        shell: bash -l {0}

.github/workflows/CI_mac.yml

@@ -61,6 +61,7 @@ jobs:
             python -m pip install --upgrade pip
             pip install -r requirements.txt
             python setup.py install
+            python -c 'import pysr; pysr.install()'
       - name: "Run tests"
         run: python -m unittest test.test
         shell: bash

.gitignore

@@ -12,3 +12,6 @@ dist
 *.pyproj
 *.sln
 pysr/.vs/
+pysr.egg-info
+Manifest.toml
+workflow

Dockerfile

@@ -1,30 +1,44 @@
 # This builds a dockerfile containing a working copy of PySR
 # with all pre-requisites installed.
 
-
 ARG VERSION=latest
+
 FROM julia:$VERSION
 
 RUN apt-get update && apt-get upgrade -y && apt-get install -y \
-    build-essential python3 python3-dev python3-pip python3-setuptools \
-    vim git wget curl \
+    make build-essential libssl-dev zlib1g-dev \
+    libbz2-dev libreadline-dev libsqlite3-dev wget curl llvm \
+    libncursesw5-dev xz-utils tk-dev libxml2-dev libxmlsec1-dev libffi-dev liblzma-dev \
+    vim git \
     && apt-get clean \
     && rm -rf /var/lib/apt/lists/*
 
 WORKDIR /pysr
 
+# Install PyEnv to switch Python to dynamically linked version:
+RUN curl https://pyenv.run | bash
+ENV PATH="/root/.pyenv/bin:$PATH"
+
+ENV PYTHON_VERSION="3.9.10"
+RUN PYTHON_CONFIGURE_OPTS="--enable-shared" pyenv install ${PYTHON_VERSION}
+ENV PATH="/root/.pyenv/versions/${PYTHON_VERSION}/bin:$PATH"
+
+# Install IPython and other useful libraries:
+RUN pip install ipython jupyter matplotlib
+
 # 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
 
 # Install PySR:
-ADD . /pysr/
+# We do a minimal copy so it doesn't need to rerun at every file change:
+ADD ./setup.py /pysr/setup.py
+ADD ./README.md /pysr/README.md
+Add ./Project.toml /pysr/Project.toml
+ADD ./pysr/ /pysr/pysr/
 RUN pip3 install .
 
 # Install Julia pre-requisites:
-RUN julia -e 'using Pkg; Pkg.add("SymbolicRegression")'
-
-# Install IPython and other useful libraries:
-RUN pip3 install ipython jupyter matplotlib
+RUN python3 -c 'import pysr; pysr.install()'
 
-CMD ["bash"]
+CMD ["bash"]

Project.toml

@@ -2,5 +2,5 @@
 SymbolicRegression = "8254be44-1295-4e6a-a16d-46603ac705cb"
 
 [compat]
-SymbolicRegression = "0.6.10"
+SymbolicRegression = "0.6.18"
 julia = "1.5"

README.md

@@ -62,11 +62,14 @@ and [linux](https://julialang.org/downloads/platform/#linux_and_freebsd).
 
 You can install PySR with:
 ```bash
-pip install pysr
+pip3 install pysr
+python3 -c 'import pysr; pysr.install()'
 ```
+The second line will install and update the required Julia packages, including
+`PyCall.jl`.
 
-The first launch will automatically install the Julia packages
-required. Most common issues at this stage are solved
+
+Most common issues at this stage are solved
 by [tweaking the Julia package server](https://github.com/MilesCranmer/PySR/issues/27).
 to use up-to-date packages.
 
@@ -121,6 +124,10 @@ which gives:
 x0**2 + 2.000016*cos(x3) - 1.9999845
 ```
 
+The second and additional calls of `pysr` will be significantly
+faster in startup time, since the first call to Julia will compile
+and cache functions from the symbolic regression backend.
+
 One can also use `best_tex` to get the LaTeX form,
 or `best_callable` to get a function you can call.
 This uses a score which balances complexity and error;

docs/start.md

@@ -7,20 +7,14 @@ Install Julia - see [downloads](https://julialang.org/downloads/), and
 then instructions for [mac](https://julialang.org/downloads/platform/#macos)
 and [linux](https://julialang.org/downloads/platform/#linux_and_freebsd).
 (Don't use the `conda-forge` version; it doesn't seem to work properly.)
-Then, at the command line,
-install the `Optim` and `SpecialFunctions` packages via:
 
+You can install PySR with:
 ```bash
-julia -e 'import Pkg; Pkg.add("Optim"); Pkg.add("SpecialFunctions")'
-```
-
-For python, you need to have Python 3, numpy, sympy, and pandas installed.
-
-You can install this package from PyPI with:
-
-```bash
-pip install pysr
+pip3 install pysr
+python3 -c 'import pysr; pysr.install()'
 ```
+The second line will install and update the required Julia packages, including
+`PyCall.jl`.
 
 ## Quickstart
 
@@ -48,6 +42,10 @@ which gives:
 x0**2 + 2.000016*cos(x3) - 1.9999845
 ```
 
+The second and additional calls of `pysr` will be significantly
+faster in startup time, since the first call to Julia will compile
+and cache functions from the symbolic regression backend.
+
 One can also use `best_tex` to get the LaTeX form,
 or `best_callable` to get a function you can call.
 This uses a score which balances complexity and error;

environment.yml

@@ -0,0 +1,14 @@
+name: test
+channels:
+  - conda-forge
+  - defaults
+dependencies:
+  - python=3.9
+  - sympy
+  - pandas
+  - numpy
+  - scikit-learn
+  - setuptools
+  - pip
+  - pip:
+    - julia

pysr/__init__.py

@@ -1,4 +1,13 @@
-from .sr import pysr, get_hof, best, best_tex, best_callable, best_row
+from .sr import (
+    pysr,
+    get_hof,
+    best,
+    best_tex,
+    best_callable,
+    best_row,
+    install,
+    silence_julia_warning,
+)
 from .feynman_problems import Problem, FeynmanProblem
 from .export_jax import sympy2jax
 from .export_torch import sympy2torch

pysr/feynman_problems.py

@@ -1,6 +1,5 @@
 import numpy as np
 import csv
-import traceback
 from .sr import pysr, best
 from pathlib import Path
 from functools import partial
@@ -80,20 +79,14 @@ def mk_problems(first=100, gen=False, dp=500, data_dir=FEYNMAN_DATASET):
     """
     ret = []
     with open(data_dir) as csvfile:
-        ind = 0
         reader = csv.DictReader(csvfile)
         for i, row in enumerate(reader):
-            if ind > first:
+            if i > first:
                 break
             if row["Filename"] == "":
                 continue
-            try:
-                p = FeynmanProblem(row, gen=gen, dp=dp)
-                ret.append(p)
-            except Exception as e:
-                traceback.print_exc()
-                print(f"FAILED ON ROW {i} with {e}")
-            ind += 1
+            p = FeynmanProblem(row, gen=gen, dp=dp)
+            ret.append(p)
     return ret