Add development docker

Dockerfile.dev

@@ -0,0 +1,41 @@
+FROM continuumio/miniconda3
+
+# Install build essentials and clean up
+RUN apt-get update --quiet \
+  && apt-get install -y --no-install-recommends --quiet build-essential \
+  && apt-get clean \
+  && rm -rf /var/lib/apt/lists/*
+
+# Update conda, install packages, and clean up
+RUN conda update conda --yes --quiet \
+  && conda install python=3.5 pip numpy scipy pandas --yes --quiet \
+  && conda clean --yes --all \
+  && hash -r
+
+# Get the requirements files (seperate from the main body)
+COPY requirements.txt requirements_dev.txt /reqs/
+
+# Install requirements and clean up
+RUN pip --no-cache-dir install -r /reqs/requirements.txt \
+  && pip --no-cache-dir install -r /reqs/requirements_dev.txt \
+  && pip install jupyter jupyterlab \
+  && rm -rf /root/.cache \
+  && rm -rf /reqs
+
+# Manually install GPflow and clean up
+RUN git clone --depth=1 --branch=0.4.0 https://github.com/GPflow/GPflow.git \
+  && cd GPflow \
+  && python setup.py install \
+  && rm -rf /GPflow
+
+# Output scrubber for jupyter
+ADD scripts/jupyter_output.py /
+
+RUN jupyter notebook --generate-config \
+  && cat /jupyter_output.py >> /root/.jupyter/jupyter_notebook_config.py \
+  && rm /jupyter_output.py
+
+WORKDIR /code
+
+CMD python setup.py develop \
+  && jupyter lab --ip="0.0.0.0" --no-browser --allow-root

Makefile

@@ -3,7 +3,7 @@
 help:
 	@grep -E '^[a-zA-Z_-]+:.*?## .*$$' $(MAKEFILE_LIST) | sort | awk 'BEGIN {FS = ":.*?## "}; {printf "\033[36m%-30s\033[0m %s\n", $$1, $$2}'
 
-doc: ## Build documentation (docs/_build/html/index.html) 
+doc: ## Build documentation (docs/_build/html/index.html)
 	cd docs && $(MAKE) html
 
 coverage: ## Construct coverage (htmlcov/index.html)
@@ -16,6 +16,10 @@ test: docker ## Test the docker images
 	docker run safe_learning_py2 make test-local
 	docker run safe_learning_py3 make test-local
 
+dev: ## Mount current code as volume and run jupyterlab for development
+	docker build -f Dockerfile.dev -t safe_learning_dev .
+	docker run -p 8888:8888 -v $(shell pwd):/code safe_learning_dev
+
 docker: ## Build the docker images
 	docker build -f Dockerfile.python2 -t safe_learning_py2 .
 	docker build -f Dockerfile.python3 -t safe_learning_py3 .

examples/1d_discrete.ipynb

@@ -3,15 +3,13 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "metadata": {
-    "collapsed": true
-   },
+   "metadata": {},
    "outputs": [],
    "source": [
     "from __future__ import division, print_function\n",
     "\n",
     "import tensorflow as tf\n",
-    "import GPflow\n",
+    "import gpflow\n",
     "import numpy as np\n",
     "import matplotlib.pyplot as plt\n",
     "from future.builtins import *\n",
@@ -72,8 +70,8 @@
     "# Mean dynamics\n",
     "mean_function = safe_learning.LinearSystem((0.25, 0.), name='mean_dynamics')\n",
     "\n",
-    "kernel = (GPflow.kernels.Matern32(1, lengthscales=1, variance=0.4**2, active_dims=[0])\n",
-    "          * GPflow.kernels.Linear(1, active_dims=[0]))\n",
+    "kernel = (gpflow.kernels.Matern32(1, lengthscales=1, variance=0.4**2, active_dims=[0])\n",
+    "          * gpflow.kernels.Linear(1, active_dims=[0]))\n",
     "\n",
     "gp = safe_learning.GPRCached(np.empty((0, 2), dtype=safe_learning.config.np_dtype),\n",
     "                    np.empty((0, 1), dtype=safe_learning.config.np_dtype),\n",
@@ -122,9 +120,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "metadata": {
-    "collapsed": true
-   },
+   "metadata": {},
    "outputs": [],
    "source": [
     "# lyapunov_function = safe_learning.QuadraticFunction(np.array([[1]]))\n",
@@ -178,9 +174,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "metadata": {
-    "collapsed": true
-   },
+   "metadata": {},
    "outputs": [],
    "source": [
     "lyapunov.initial_safe_set = np.abs(lyapunov.discretization.all_points.squeeze()) < 0.2"
@@ -197,9 +191,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "metadata": {
-    "collapsed": true
-   },
+   "metadata": {},
    "outputs": [],
    "source": [
     "grid = lyapunov.discretization.all_points\n",
@@ -239,9 +231,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "metadata": {
-    "collapsed": true
-   },
+   "metadata": {},
    "outputs": [],
    "source": [
     "# Update the GP model a couple of times\n",
@@ -301,21 +291,21 @@
  "metadata": {
   "anaconda-cloud": {},
   "kernelspec": {
-   "display_name": "Python 2",
+   "display_name": "Python 3",
    "language": "python",
-   "name": "python2"
+   "name": "python3"
   },
   "language_info": {
    "codemirror_mode": {
     "name": "ipython",
-    "version": 2
+    "version": 3
    },
    "file_extension": ".py",
    "mimetype": "text/x-python",
    "name": "python",
    "nbconvert_exporter": "python",
-   "pygments_lexer": "ipython2",
-   "version": "2.7.13"
+   "pygments_lexer": "ipython3",
+   "version": "3.5.4"
   }
  },
  "nbformat": 4,

scripts/jupyter_output.py

@@ -0,0 +1,16 @@
+def scrub_output_pre_save(model, **kwargs):
+    """scrub output before saving notebooks"""
+    # only run on notebooks
+    if model['type'] != 'notebook':
+        return
+    # only run on nbformat v4
+    if model['content']['nbformat'] != 4:
+        return
+
+    for cell in model['content']['cells']:
+        if cell['cell_type'] != 'code':
+            continue
+        cell['outputs'] = []
+        cell['execution_count'] = None
+
+c.FileContentsManager.pre_save_hook = scrub_output_pre_save