Self-repairing incremental installs

.github/workflows/CI.yml

@@ -78,6 +78,15 @@ jobs:
           COVERALLS_PARALLEL: true
         run: coveralls --service=github
 
+  incremental_install:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v2
+      - 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'
+
   conda_test:
     runs-on: ${{ matrix.os }}
     defaults:

pysr/julia_helpers.py

@@ -81,7 +81,20 @@ def install(julia_project=None, quiet=False, precompile=None):  # pragma: no cov
     if precompile == False:
         os.environ["JULIA_PKG_PRECOMPILE_AUTO"] = "0"
 
-    julia.install(quiet=quiet)
+    try:
+        julia.install(quiet=quiet)
+    except julia.tools.PyCallInstallError:
+        # Attempt to reset PyCall.jl's build:
+        subprocess.run(
+            [
+                "julia",
+                "-e",
+                f'ENV["PYTHON"] = "{sys.executable}"; import Pkg; Pkg.build("PyCall")',
+            ],
+        )
+        # Try installing again:
+        julia.install(quiet=quiet)
+
     Main, init_log = init_julia(julia_project, quiet=quiet, return_aux=True)
     io_arg = _get_io_arg(quiet)
 

pysr/test/incremental_install_simulator.dockerfile

@@ -0,0 +1,52 @@
+# This dockerfile simulates a user installation that first
+# builds PySR for Python 3.9, and then upgrades to Python 3.10.
+# Normally this would cause an error when installing PyCall, so we want to
+# ensure that PySR can automatically patch things.
+FROM debian:bullseye-slim
+
+ENV DEBIAN_FRONTEND=noninteractive
+
+# Install juliaup and pyenv:
+RUN apt-get update && apt-get install -y curl git build-essential \
+    libssl-dev zlib1g-dev libbz2-dev libreadline-dev libsqlite3-dev \
+    libncurses5-dev libncursesw5-dev xz-utils libffi-dev liblzma-dev && \
+    apt-get clean && \
+    rm -rf /var/lib/apt/lists/*
+
+# Install juliaup:
+RUN curl -fsSL https://install.julialang.org | sh -s -- -y
+
+# Install pyenv:
+RUN curl -fsSL curl https://pyenv.run | sh && \
+    echo 'export PATH="/root/.pyenv/bin:$PATH"' >> ~/.bashrc && \
+    echo 'export PYENV_ROOT="$HOME/.pyenv"' >> ~/.bashrc && \
+    echo 'eval "$(pyenv init -)"' >> ~/.bashrc && \
+    echo 'eval "$(pyenv virtualenv-init -)"' >> ~/.bashrc
+
+# Default to using bash -l:
+SHELL ["/bin/bash", "-l", "-c"]
+
+RUN juliaup add 1.8 && juliaup default 1.8
+RUN pyenv install 3.9.2 && pyenv global 3.9.2
+RUN python3 -m pip install --upgrade pip
+
+# Get PySR source:
+WORKDIR /pysr
+ADD ./requirements.txt /pysr/requirements.txt
+RUN python3 -m pip install -r /pysr/requirements.txt
+
+ADD ./setup.py /pysr/setup.py
+ADD ./pysr/ /pysr/pysr/
+
+# First install of PySR:
+RUN python3 -m pip install .
+RUN python3 -m pysr install
+
+# Change Python version:
+RUN pyenv install 3.10 && pyenv global 3.10 && pyenv uninstall -f 3.9.2
+RUN python3 -m pip install --upgrade pip
+
+# Second install of PySR:
+RUN python3 -m pip install .
+RUN rm -r ~/.julia/environments/pysr-0.14.2
+RUN python3 -m pysr install