Merge branch 'master' into recurrence

.github/workflows/CI_apptainer.yml

@@ -0,0 +1,40 @@
+name: Apptainer
+
+on:
+  push:
+    branches:
+      - 'master'
+    paths:
+      - '**'
+    tags:
+      - 'v*.*.*'
+  pull_request:
+    branches:
+      - 'master'
+    paths:
+      - '**'
+
+jobs:
+  test:
+    runs-on: ${{ matrix.os }}
+    timeout-minutes: 60
+    defaults:
+      run:
+        shell: bash
+    strategy:
+      matrix:
+        os: [ubuntu-latest]
+
+    steps:
+      - uses: actions/checkout@v4
+      - uses: eWaterCycle/setup-apptainer@v2
+        with:
+            apptainer-version: 1.3.0
+      - name: Build apptainer
+        run: apptainer build --notest pysr.sif Apptainer.def
+      - name: Test apptainer
+        run: |
+          TMPDIR=$(mktemp -d)
+          cp pysr.sif $TMPDIR
+          cd $TMPDIR
+          apptainer test ./pysr.sif

Apptainer.def

@@ -0,0 +1,55 @@
+# Build an Apptainer SIF file containing a working copy of PySR and its prereqs
+Bootstrap: docker
+From: julia:1.10.4-bullseye
+Stage: jl
+
+Bootstrap: docker
+From: python:3.12-bullseye
+Stage: runtime
+
+%environment
+	# Use the container Julia binary
+	export PATH="/usr/local/julia/bin:$PATH"
+
+	# Create a stacked environment for additional Julia packages
+	export JULIA_DEPOT_PATH="$HOME/.pysr:/pysr/depot:$JULIA_DEPOT_PATH"
+	export JULIA_LOAD_PATH="$HOME/.pysr:/pysr:$JULIA_LOAD_PATH"
+
+%files from jl
+	/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
+
+%post
+	# Ensure we don't use the local pysr commands:
+	cd $(mktemp -d)
+
+	export PATH="/usr/local/julia/bin:$PATH"
+
+	# Install IPython and other useful libraries:
+	pip3 install --no-cache-dir ipython matplotlib pytest nbval
+	# Install PySR and requirements:
+	pip3 install --no-cache-dir /pysr
+
+	# Put the Julia dependencies in /pysr/depot
+	mkdir /pysr/depot
+	export JULIA_DEPOT_PATH="/pysr/depot"
+
+	# And set a specific environment for Julia dependencies
+	mkdir /pysr/env
+	export PYTHON_JULIAPKG_PROJECT="/pysr/env"
+
+	# Pull in all the Julia dependencies
+	python3 -c 'import pysr; pysr.load_all_packages()'
+
+%test
+	python3 -m pysr test main,cli,startup
+
+%runscript
+	# Start ipython when the container is executed
+	[ ! -d $HOME/.pysr ] && mkdir $HOME/.pysr
+	PYTHONPATH=/pysr ipython

README.md

@@ -83,8 +83,12 @@ Similarly, with conda:
 conda install -c conda-forge pysr
 ```
 
+<details>
+<summary>
 
-### Dockerfile
+### Docker
+
+</summary>
 
 You can also use the `Dockerfile` to install PySR in a docker container
 
@@ -100,23 +104,31 @@ docker run -it --rm pysr ipython
 
 For more details, see the [docker section](#docker).
 
----
+</details>
 
-### Troubleshooting
+<details>
+<summary>
 
-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
-version of `libstdc++.so` is located in `$HOME/.julia/juliaup/julia-1.10.0+0.x64.linux.gnu/lib/julia/`
-(which likely differs on your system!), you could add:
+### Apptainer
 
+</summary>
+
+If you are using PySR on a cluster where you do not have root access,
+you can use [Apptainer](https://apptainer.org/) to build a container
+instead of Docker. The `Apptainer.def` file is analogous to the `Dockerfile`,
+and can be built with:
+
+```bash
+apptainer build --notest pysr.sif Apptainer.def
 ```
-export LD_LIBRARY_PATH=$HOME/.julia/juliaup/julia-1.10.0+0.x64.linux.gnu/lib/julia/:$LD_LIBRARY_PATH
-```
 
-to your `.bashrc` or `.zshrc` file.
+and launched with
+
+```bash
+apptainer run pysr.sif
+```
 
+</details>
 
 ## Quickstart
 

environment.yml

@@ -7,5 +7,5 @@ dependencies:
   - pandas>=0.21.0,<3.0.0
   - numpy>=1.20.0,<2.0.0
   - scikit-learn>=1.0.0,<2.0.0
-  - pyjuliacall>=0.9.15,<0.10.0
+  - pyjuliacall>=0.9.21,<0.9.22
   - click>=7.0.0,<9.0.0

pyproject.toml

@@ -4,7 +4,7 @@ build-backend = "setuptools.build_meta"
 
 [project]
 name = "pysr"
-version = "0.19.3"
+version = "0.19.4"
 authors = [
     {name = "Miles Cranmer", email = "[email protected]"},
 ]

pysr/julia_extensions.py

@@ -40,6 +40,7 @@ def isinstalled(uuid_s: str):
 def load_package(package_name: str, uuid_s: str) -> None:
     if not isinstalled(uuid_s):
         Pkg.add(name=package_name, uuid=uuid_s)
+        Pkg.resolve()
 
     # TODO: Protect against loading the same symbol from two packages,
     #       maybe with a @gensym here.

pysr/test/test_startup.py

@@ -134,6 +134,8 @@ def test_notebook(self):
             self.skipTest("Julia version too old")
         if platform.system() == "Windows":
             self.skipTest("Notebook test incompatible with Windows")
+        if not os.access(Path(__file__).parent, os.W_OK):
+            self.skipTest("Read-only file system")
 
         notebook_file = Path(__file__).parent / "test_nb.ipynb"
         sanitize_file = Path(__file__).parent / "nb_sanitize.cfg"