Merge pull request #687 from wkharold/apptainer

Apptainer definition file for PySR

.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

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"