Merge pull request #15 from SD2E/from-ubuntu

Fixes #14 and #13

CHANGELOG.md

@@ -2,6 +2,22 @@
 
 All notable changes to this project are to be documented in this file.
 
+## Version 0.3.3
+
+ - Added hub https://github.com/github/hub
+ - Create persistent environments
+   - `conda create -y -p $LOCAL_ENVS/tabsAreGreat python=2.7 ipykernel 'scipy==0.16.0'`
+ - Discover persistent environments
+   - `conda env list`
+ - Create a new kernel
+   - `$LOCAL_ENVS/tabsAreGreat/bin/python -m ipykernel install --prefix $JUPYTER_WORK --name tabsAreGreat --display-name "tabs are great"`
+   - Refresh main page
+ - Added ML modules
+   - Tensorflow 1.6
+   - Theano
+   - Keras
+ - Optimized image size by starting from ubuntu base
+
 ## Version 0.3.1
 
  - Added `PYTHONUSERBASE` variable, which points at `tacc-work/jupyter_packages`, and allows for persistent local pip installs

CONTRIBUTING.md

@@ -56,13 +56,13 @@ git checkout -b myFeature development
 Please add any external example or configuration files in a descriptive folder in
 
 ```
-images/custom/
+images/sd2e/
 ```
 
 and add a new section at the end of the main `Dockerfile` in
 
 ```
-images/custom/Dockerfile
+images/sd2e/Dockerfile
 ```
 
 for your code immediately **before** the permissiosn section.

Makefile

@@ -1,4 +1,3 @@
-.ONESHELL:
 .PHONY: build test docker help stage release clean
 ifndef VERBOSE
 .SILENT: build test docker help stage release clean
@@ -9,98 +8,99 @@ all: help
 
 .PHONY: help
 help:
-	echo "\nUsage: make [action] [target]\n"
-	echo "Actions:"
-	echo " - build   - build docker images locally"
-	echo " - test    - test images locally"
-	echo " - stage   - push images to staging environment"
-	echo " - release - push images to production environment\n"
-	echo "Targets:"
-	echo " - base - Recipe in images/base"
-	echo " - sd2e - Recipe in images/custom which is where all community software should belong"
+
+	echo "\nUsage: make [action] [target]\n" && \
+	echo "Actions:" && \
+	echo " - build   - build docker images locally" && \
+	echo " - test    - test images locally" && \
+	echo " - stage   - push images to staging environment" && \
+	echo " - release - push images to production environment\n" && \
+	echo "Targets:" && \
+	echo " - base - Recipe in images/base" && \
+	echo " - sd2e - Recipe in images/sd2e which is where all community software should belong" && \
 	echo " - singularity - Image for running on TACC HPC\n"
 
 # Make sure image targets are not used as make targets
 %:
 	@:
 
 docker:
-	docker info > /dev/null 2> /dev/null
-	if [ ! $$? -eq 0 ]; then
-		echo "\n[ERROR] Could not communicate with docker daemon. You may need to run with sudo.\n"
-		exit 1
+	docker info 1> /dev/null 2> /dev/null && \
+	if [ ! $$? -eq 0 ]; then \
+		echo "\n[ERROR] Could not communicate with docker daemon. You may need to run with sudo.\n"; \
+		exit 1; \
 	fi
 
 build: docker
-	TARGET=$(filter-out $@,$(MAKECMDGOALS))
-	case $${TARGET} in
-	base)
-		build/build_jupyteruser.sh build images/base
-		;;
-	sd2e)
-		build/build_jupyteruser.sh build images/custom
-		;;
-	singularity)
-		build/build_jupyteruser.sh build images/singularity
-		;;
-	*)
-		$(MAKE) help
-		;;
+	TARGET=$(filter-out $@,$(MAKECMDGOALS)) && \
+	case $${TARGET} in \
+	base) \
+		build/build_jupyteruser.sh build images/base; \
+		;; \
+	sd2e) \
+		build/build_jupyteruser.sh build images/sd2e; \
+		;; \
+	singularity) \
+		build/build_jupyteruser.sh build images/singularity; \
+		;; \
+	*) \
+		$(MAKE) help; \
+		;; \
 	esac
 
 test: docker
-	TARGET=$(filter-out $@,$(MAKECMDGOALS))
-	case $$TARGET in
-	base)
-		build/build_jupyteruser.sh test images/base
-		;;
-	sd2e)
-		build/build_jupyteruser.sh test images/custom
-		;;
-	singularity)
-		build/build_jupyteruser.sh test images/singularity
-		;;
-	*)
-		$(MAKE) help
-		;;
+	TARGET=$(filter-out $@,$(MAKECMDGOALS)) && \
+	case $$TARGET in \
+	base) \
+		build/build_jupyteruser.sh test images/base; \
+		;; \
+	sd2e) \
+		build/build_jupyteruser.sh test images/sd2e; \
+		;; \
+	singularity) \
+		build/build_jupyteruser.sh test images/singularity; \
+		;; \
+	*) \
+		$(MAKE) help; \
+		;; \
 	esac
 
 stage: docker
-	TARGET=$(filter-out $@,$(MAKECMDGOALS))
-	case $$TARGET in
-	base)
-		build/build_jupyteruser.sh stage images/base
-		;;
-	sd2e)
-		build/build_jupyteruser.sh stage images/custom
-		;;
-	singularity)
-		build/build_jupyteruser.sh stage images/singularity
-		;;
-	*)
-		$(MAKE) help
-		;;
+	TARGET=$(filter-out $@,$(MAKECMDGOALS)) && \
+	case $$TARGET in \
+	base) \
+		build/build_jupyteruser.sh stage images/base; \
+		;; \
+	sd2e) \
+		build/build_jupyteruser.sh stage images/sd2e; \
+		;; \
+	singularity) \
+		build/build_jupyteruser.sh stage images/singularity; \
+		;; \
+	*) \
+		$(MAKE) help; \
+		;; \
 	esac
 
 release: docker
-	TARGET=$(filter-out $@,$(MAKECMDGOALS))
-	case $$TARGET in
-	base)
-		build/build_jupyteruser.sh release images/base
-		;;
-	sd2e)
-		build/build_jupyteruser.sh release images/custom
-		;;
-	singularity)
-		build/build_jupyteruser.sh release images/singularity
-		;;
-	*)
-		$(MAKE) help
-		;;
+	TARGET=$(filter-out $@,$(MAKECMDGOALS)) && \
+	case $$TARGET in \
+	base) \
+		build/build_jupyteruser.sh release images/base; \
+		;; \
+	sd2e) \
+		build/build_jupyteruser.sh release images/sd2e; \
+		;; \
+	singularity) \
+		build/build_jupyteruser.sh release images/singularity; \
+		;; \
+	*) \
+		$(MAKE) help; \
+		;; \
 	esac
 
 clean: docker
-	TARGET=$(filter-out $@,$(MAKECMDGOALS))
-	build/build_jupyteruser.sh clean images/singularity
-	build/build_jupyteruser.sh clean images/custom
+	TARGET=$(filter-out $@,$(MAKECMDGOALS)) && \
+	build/build_jupyteruser.sh clean images/singularity && \
+	build/build_jupyteruser.sh clean images/sd2e && \
 	build/build_jupyteruser.sh clean images/base

README.md

@@ -4,6 +4,7 @@
 
 * Jupyter Notebook \(v5.2.0\)server
 * Conda Python 3.4.x and Python 2.7.x environments
+  * Custom environments and kernels now supported through `Advanced Jupyter.ipynb` notebook
 * Pre-installed python packages (highlights)
   * pandas
   * matplotlib 2.1.2
@@ -16,6 +17,7 @@
 * Plotly, igraph, networkx, graphviz for graphs and plots
 * MIT's [Open Probabilistic Programming Stack](http://probcomp.org/)
 * [Common Lisp kernel and stack](http://www.sbcl.org/)
+  * v1.4.6 Now installed as binary
 * Bioconda and Bioconductor
 * BioPython
 * Git

TESTING.md

@@ -1,5 +1,5 @@
 # Testing out your changes
 
-After you've added software or updated configurations at `images/custom`, you can and should test in a local instance of Jupyter Notebooks. We've made this really easy for you. You can either leverage the extensive Makefile support for building and testing an updated user image, or manually drive the process.
+After you've added software or updated configurations at `images/sd2e`, you can and should test in a local instance of Jupyter Notebooks. We've made this really easy for you. You can either leverage the extensive Makefile support for building and testing an updated user image, or manually drive the process.
 
 *Before you issue a PR, you must have tested locally*

VERSION

@@ -1 +1 @@
-0.3.1
+0.3.3

build/build_jupyteruser.sh

@@ -94,7 +94,8 @@ function testImage {
 		EIP=$(dig +short myip.opendns.com @resolver1.opendns.com)
 		ed "Local Address: http://localhost:8888"
 		ed "External Address: http://${EIP}:8888"
-		ed "docker run --rm -p 8888:8888 ${IMG}:${VERSION} start-notebook.sh"
+		# Added -u flag to test as non-existent user
+		ed "docker run -u 1337 --rm -p 8888:8888 ${IMG}:${VERSION} start-notebook.sh"
 		docker run --rm -p 8888:8888 ${IMG}:${VERSION} start-notebook.sh
 		if [ ! $? -eq 0 ]; then
 			ee "Notebook could not launch"
@@ -153,7 +154,7 @@ function pushImage {
 	fi
 }
 
-helpStr="Usage: $0 option target\n\nAutomating the build and deploy process for taccsciapps images\n\nPlease specify an option and target\n\nOptions:\n - build\n - test\n - push\n - all\n\nTargets:\n - images/base\n - images/custom"
+helpStr="Usage: $0 option target\n\nAutomating the build and deploy process for taccsciapps images\n\nPlease specify an option and target\n\nOptions:\n - build\n - test\n - push\n - all\n\nTargets:\n - images/base\n - images/sd2e"
 
 # Make sure enough arguments were used
 if [ ! $# -eq 2 ]; then