Update environment.yml

.binder/apt.txt

@@ -0,0 +1,11 @@
+# .binder/apt.txt
+# System packages for Binder
+build-essential
+gcc
+g++
+gfortran
+libblas-dev
+liblapack-dev
+vim
+htop
+

.binder/environment.yml

@@ -0,0 +1,49 @@
+# .binder/environment.yml
+# Conda environment for Binder deployment
+# Updated: December 18, 2024
+
+name: skilmpy-binder
+channels:
+  - conda-forge
+  - defaults
+
+dependencies:
+  # Python 3.14+ when available, fallback to 3.11+
+  - python=3.11
+
+  # Core scientific computing
+  - numpy=2.0
+  - scipy>=1.14
+  - pandas>=2.2
+  - matplotlib>=3.8
+  - seaborn>=0.13
+
+  # Jupyter ecosystem
+  - jupyterlab>=4.0
+  - jupyter>=1.0
+  - ipywidgets>=8.0
+  - voila>=0.5
+
+  # Visualization
+  - plotly>=5.17
+  - bokeh>=3.3
+
+  # Performance tools
+  - numba>=0.59
+  - cython>=3.0
+
+  # Development tools
+  - git
+  - pip
+
+  # Install via pip for latest versions
+  - pip:
+    - polars>=1.0.0
+    - lark>=1.2.0
+    - ply>=3.11
+    - sympy>=1.13
+    - joblib>=1.4
+    - memory-profiler
+    - line-profiler
+    - git+https://github.com/dhard/skILMpy.git
+

.binder/postBuild

@@ -0,0 +1,161 @@
+# .binder/postBuild
+#!/bin/bash
+# Post-build script for Binder setup
+
+set -euo pipefail
+
+echo "Setting up skILMpy for Binder..."
+
+# Configure environment for optimal performance
+export PYTHONGIL=0
+export OMP_NUM_THREADS=1
+export MKL_NUM_THREADS=1
+
+# Install skILMpy in development mode
+pip install -e ".[jupyter,performance]"
+
+# Configure skILMpy for interactive use
+python -c "
+import ilmpy
+try:
+    ilmpy.configure_for_hpc()
+    print('skILMpy configured successfully')
+except Exception as e:
+    print(f'Configuration warning: {e}')
+"
+
+# Install additional Jupyter extensions
+jupyter labextension install @jupyter-widgets/jupyterlab-manager --no-build
+jupyter labextension install plotlywidget --no-build
+jupyter labextension install jupyterlab-plotly --no-build
+jupyter lab build --dev-build=False --minimize=True
+
+# Set up example notebooks
+mkdir -p examples/binder
+cp examples/quickstart.ipynb examples/binder/
+cp examples/benchmarks.ipynb examples/binder/
+
+# Create a welcome notebook
+cat > examples/binder/Welcome.ipynb << 'EOF'
+{
+ "cells": [
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "# Welcome to skILMpy 3.0! 🚀\n",
+    "\n",
+    "This is an interactive environment for exploring Smith-Kirby Iterated Learning Models.\n",
+    "\n",
+    "## Quick Start\n",
+    "\n",
+    "1. **[Quickstart Tutorial](quickstart.ipynb)** - Learn the basics in 10 minutes\n",
+    "2. **[Performance Benchmarks](benchmarks.ipynb)** - See the speed improvements\n",
+    "3. **[Research Examples](../research_examples/)** - Real-world applications\n",
+    "\n",
+    "## Try It Now!\n",
+    "\n",
+    "Run a simple simulation:"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "import ilmpy\n",
+    "from ilmpy.argument_parser import ModernILM_Parser\n",
+    "from ilmpy.learners import OptimizedAssociationMatrixLearner\n",
+    "\n",
+    "# Parse signal and meaning spaces\n",
+    "parser = ModernILM_Parser()\n",
+    "signal_space, meaning_space = parser.parse(\"[bp].[ao] (4).(3)\")\n",
+    "\n",
+    "print(f\"Signal space: {len(signal_space.signals())} signals\")\n",
+    "print(f\"Meaning space: {len(meaning_space.meanings())} meanings\")\n",
+    "print(f\"Signals: {signal_space.signals()[:10]}\")\n",
+    "print(f\"Meanings: {meaning_space.meanings()[:10]}\")"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "# Create and run a simple simulation\n",
+    "observables = ilmpy.create_observables(\n",
+    "    show_compositionality=True,\n",
+    "    show_accuracy=True,\n",
+    "    precision=4\n",
+    ")\n",
+    "\n",
+    "learner = OptimizedAssociationMatrixLearner(\n",
+    "    meaning_space, signal_space,\n",
+    "    alpha=1.0, beta=0.0, gamma=-1.0, delta=0.0,\n",
+    "    observables=observables\n",
+    ")\n",
+    "\n",
+    "# Run 5 generations\n",
+    "for generation in range(5):\n",
+    "    print(f\"\\nGeneration {generation}:\")\n",
+    "    child = learner.spawn()\n",
+    "    lessons = learner.teach(10)\n",
+    "    child.learn(lessons)\n",
+    "    \n",
+    "    # Print statistics\n",
+    "    comp = child.compute_compositionality()\n",
+    "    acc = child.compute_accuracy()\n",
+    "    print(f\"  Compositionality: {comp:.4f}\")\n",
+    "    print(f\"  Accuracy: {acc:.4f}\")\n",
+    "    \n",
+    "    learner = child\n",
+    "\n",
+    "print(\"\\nSimulation complete! 🎉\")"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "## Next Steps\n",
+    "\n",
+    "- Explore the other notebooks for more advanced examples\n",
+    "- Try different signal and meaning space configurations\n",
+    "- Experiment with the model parameters (alpha, beta, gamma, delta)\n",
+    "- Check out the [GitHub repository](https://github.com/dhard/skILMpy) for full documentation\n",
+    "\n",
+    "Happy modeling! 🧬🔬"
+   ]
+  }
+ ],
+ "metadata": {
+  "kernelspec": {
+   "display_name": "Python 3",
+   "language": "python",
+   "name": "python3"
+  },
+  "language_info": {
+   "codemirror_mode": {
+    "name": "ipython",
+    "version": 3
+   },
+   "file_extension": ".py",
+   "mimetype": "text/x-python",
+   "name": "python",
+   "nbconvert_exporter": "python",
+   "pygments_lexer": "ipython3",
+   "version": "3.11.0"
+  }
+ },
+ "nbformat": 4,
+ "nbformat_minor": 4
+}
+EOF
+
+echo "Binder setup complete!"
+
+# Set default working directory
+echo 'cd $HOME' >> ~/.bashrc
+

.binder/start

@@ -0,0 +1,5 @@
+# .binder/start
+#!/bin/bash
+# Custom start script for Binder
+
+exec "$@"

.gitignore

@@ -1,18 +1,9 @@
-# Byte-compiled / optimized / DLL files
+# Python
 __pycache__/
 *.py[cod]
 *$py.class
-
-# emacs
-*~
-#*#
-
-# C extensions
 *.so
-
-# Distribution / packaging
 .Python
-env/
 build/
 develop-eggs/
 dist/
@@ -24,43 +15,54 @@ lib64/
 parts/
 sdist/
 var/
+wheels/
 *.egg-info/
 .installed.cfg
 *.egg
 
-# PyInstaller
-#  Usually these files are written by a python script from a template
-#  before PyInstaller builds the exe, so as to inject date/other infos into it.
-*.manifest
-*.spec
+# Virtual environments
+venv/
+env/
+ENV/
+
+# IDEs
+.vscode/
+.idea/
+*.swp
+*.swo
 
-# Installer logs
-pip-log.txt
-pip-delete-this-directory.txt
+# OS
+.DS_Store
+Thumbs.db
 
-# Unit test / coverage reports
+# Project specific
+results/
+data/private/
+*.log
+*.prof
+*.stats
+
+# Jupyter
+.ipynb_checkpoints/
+*.ipynb_backup
+
+# Docker
+.dockerignore
+
+# Coverage
 htmlcov/
-.tox/
 .coverage
-.coverage.*
-.cache
-nosetests.xml
 coverage.xml
-*,cover
-.hypothesis/
-
-# Translations
-*.mo
-*.pot
-
-# Django stuff:
-*.log
 
-# Sphinx documentation
-docs/_build/
+# MyPy
+.mypy_cache/
+.dmypy.json
+dmypy.json
 
-# PyBuilder
-target/
+# PLY parser files
+*parsetab.py
+parser.out
 
-#Ipython Notebook
-.ipynb_checkpoints
+# Temporary files
+tmp/
+temp/