From e360f7db9c645d84a4f89051e230c40434aa1640 Mon Sep 17 00:00:00 2001
From: Shaun C Read <shaun.c.read@gmail.com>
Date: Thu, 28 Mar 2019 16:54:34 +0000
Subject: [PATCH 1/9] testing?

---
 .travis.yml | 17 +++++++++++++++++
 install.sh  | 44 ++++++++++++++++++++++++++++++--------------
 2 files changed, 47 insertions(+), 14 deletions(-)
 create mode 100644 .travis.yml

diff --git a/.travis.yml b/.travis.yml
new file mode 100644
index 0000000..0dc4608
--- /dev/null
+++ b/.travis.yml
@@ -0,0 +1,17 @@
+language: python
+python:
+  - "2.7"
+  - "3.7"
+
+os:
+  - linux
+  - osx
+sudo: required
+
+
+install:
+  - chmod +x install.sh
+
+script:
+  - ./install.sh y "$(python -c "import sys; print('.'.join(map(str, sys.version_info[:2])))")" username uhppc00 y "$HOME" y "me@me.com" firstname lastname y $HOME y
+  - python ~/.jupyter/jupyter_notebook_config.py
diff --git a/install.sh b/install.sh
index b4f217c..9ccd55f 100644
--- a/install.sh
+++ b/install.sh
@@ -1,7 +1,23 @@
 #!/bin/bash
-
 set -e
 
+install_conda="$1"; shift
+version="$1"; shift
+username="$1"; shift
+pcname="$1"; shift
+do_jupyter="$1"; shift
+notebook_dir="$1"; shift
+personal_git="$1"; shift
+git_email="$1"; shift
+firstname="$1"; shift
+lastname="$1"; shift
+code_review="$1"; shift
+review_dir="$1"; shift
+keys="$1"; shift
+
+email="$git_email"
+
+
 SCRIPTPATH="$( cd "$(dirname "$0")" ; pwd -P )"
 cd "$SCRIPTPATH"
 
@@ -15,7 +31,7 @@ touch "$HOME/.bashrc"
 touch "$HOME/.tcshrc"
 
 if [ ! -d "$HOME/.bash-git-prompt/" ]; then
-  git clone https://github.com/magicmonty/bash-git-prompt.git ~/.bash-git-prompt --depth=1
+  git clone https://github.com/magicmonty/bash-git-prompt.git ~/.bash-git-prompt --depth=1 || echo already installed
   cp "$SCRIPTPATH/Single_line_Minimalist_notime.bgptheme" ~/.bash-git-prompt/
 fi
 
@@ -31,12 +47,12 @@ else
 	# 	read install_conda
 	# else
 	echo -n "Install miniconda for personal use (you can choose where later)? [y/n]"
-	read -r install_conda
-	# fi
+	if [ -z ${install_conda+x} ]; then read -r install_conda; else echo "$install_conda"; fi
+	
 
     if [[ $install_conda = 'y' ]]; then
     	echo -n "Which python should I use as your default? 2 or 3:"
-    	read -r version
+    	if [ -z ${version+x} ]; then read -r version; else echo "$version"; fi
 	    unameOut="$(uname -s)"
 		case "${unameOut}" in
 		    Linux*)    
@@ -93,11 +109,11 @@ fi
 
 herts_string="source $SCRIPTPATH/herts.sh"
 echo -n "What is your work username?"
-read -r username 
+if [ -z ${username+x} ]; then read -r username; else echo "$username"; fi
 echo "setenv UHUSERNAME $username" >> ~/.tcshrc
 echo "export UHUSERNAME=$username" >> ~/.bashrc
 echo -n "What is your work pc name (something like uhppc60)?"
-read -r pcname
+if [ -z ${pcname+x} ]; then read -r pcname; else echo "$pcname"; fi
 echo "setenv UHPCNAME $pcname" >> ~/.tcshrc
 echo "export UHPCNAME=$pcname" >> ~/.bashrc
 
@@ -133,7 +149,7 @@ if jupyter --version; then
 	hostname="$(echo "$HOSTNAME" || cat /proc/sys/kernel/hostname || echo '')"
 	if [[ "$hostname" == *"uhppc"* ]]; then
 		echo -n "You are on a university machine, shall I setup jupyter remote access?[y/n]"
-		read -r do_jupyter
+		if [ -z ${do_jupyter+x} ]; then read -r do_jupyter; else echo "$do_jupyter"; fi
 		if [[ $do_jupyter = 'y' ]]; then
 			mkdir "$HOME/certficates" || echo "certficates folder exists, skipping"
 			mkdir "$HOME/certficates/jupyter" || echo "certficates folder exists, skipping"
@@ -144,7 +160,7 @@ if jupyter --version; then
 			echo "c.NotebookApp.open_browser = False" >> "$HOME/.jupyter/jupyter_notebook_config.py"
 			echo "c.NotebookApp.port = 9999" >> "$HOME/.jupyter/jupyter_notebook_config.py"
 			echo -n "In what absolute directory shall Jupyter start its notebooks?"
-			read -r notebook_dir
+			if [ -z ${notebook_dir+x} ]; then read -r notebook_dir; else echo "$notebook_dir"; fi
 			echo "c.NotebookApp.notebook_dir = $notebook_dir" >> "$HOME/.jupyter/jupyter_notebook_config.py"
 			chmod +x jupyter_autostart.sh
 			echo "bash $SCRIPTPATH/jupyter_autostart.sh" >> "$HOME/.login"
@@ -157,7 +173,7 @@ else
 fi
 
 echo -n "Shall I personalise git to your github username?[y/n] "
-read -r personal_git
+if [ -z ${personal_git+x} ]; then read -r personal_git; else echo "$personal_git"; fi
 if [[ $personal_git == 'y' ]]; then
 	echo -n "Github email: "
 	read -r git_email
@@ -173,10 +189,10 @@ fi
 
 if [[ ! -f "$HOME/.ssh/id_rsa.pub" ]]; then 
 	echo -n "Shall I add a new ssh key for passwordless ssh?[y/n] "
-	read -r keys
+	if [ -z ${keys+x} ]; then read -r keys; else echo "$keys"; fi
 	if [[ -n $keys ]]; then
 		echo -n "What is your email? (this should be the same one you used with github) "
-		read -r email
+		if [ -z ${email+x} ]; then read -r email; else echo "$email"; fi
 		ssh-keygen -t rsa -b 4096 -C "$email" -f "$HOME/.ssh/id_rsa.pub"
 		eval "$(ssh-agent -s)" || echo agent already started
 		ssh-add "$HOME/.ssh/id_rsa"
@@ -190,13 +206,13 @@ if [[ ! -f "$HOME/.ssh/id_rsa.pub" ]]; then
 fi
 
 echo -n "Shall I install code-review.sh?[y/n] "
-read -r code_review
+if [ -z ${code_review+x} ]; then read -r code_review; else echo "$code_review"; fi
 if [[ $code_review == 'y' ]]; then
 	git clone https://github.com/herts-astrostudents/code-review.sh "$HOME/code-review.sh" || echo "already installed"
 	chmod +x "$HOME/code-review.sh/code-review.sh"
 	"$HOME/code-review.sh/code-review.sh" install
 	echo -n "Where shall I put the code-review repository where you will fill in tasks? "
-	read -r review_dir
+	if [ -z ${review_dir+x} ]; then read -r review_dir; else echo "$review_dir"; fi
 	git clone https://github.com/herts-astrostudents/code-review "$review_dir/code-review" || echo "already installed"
 fi
 

From 303f7fc0c5ec7ec795cd723605a28586355b3cb1 Mon Sep 17 00:00:00 2001
From: Shaun C Read <shaun.c.read@gmail.com>
Date: Thu, 28 Mar 2019 17:03:58 +0000
Subject: [PATCH 2/9] test.sh

---
 .travis.yml | 4 ++--
 README.md   | 2 ++
 test.sh     | 6 ++++++
 3 files changed, 10 insertions(+), 2 deletions(-)
 create mode 100644 test.sh

diff --git a/.travis.yml b/.travis.yml
index 0dc4608..f531853 100644
--- a/.travis.yml
+++ b/.travis.yml
@@ -11,7 +11,7 @@ sudo: required
 
 install:
   - chmod +x install.sh
+  - chmod +x test.sh
 
 script:
-  - ./install.sh y "$(python -c "import sys; print('.'.join(map(str, sys.version_info[:2])))")" username uhppc00 y "$HOME" y "me@me.com" firstname lastname y $HOME y
-  - python ~/.jupyter/jupyter_notebook_config.py
+  - ./test.sh
\ No newline at end of file
diff --git a/README.md b/README.md
index 0e7b8c8..b860d5a 100644
--- a/README.md
+++ b/README.md
@@ -1,3 +1,5 @@
+[![Build Status](https://travis-ci.com/herts-astrostudents/bash-scripts.svg?branch=master)](https://travis-ci.com/herts-astrostudents/bash-scripts)
+
 # bash-scripts
 Useful scripts: install with: `git clone https://github.com/herts-astrostudents/bash-scripts.git ~/.bash-scripts && cd ~/.bash-scripts && bash ./install.sh`
 
diff --git a/test.sh b/test.sh
new file mode 100644
index 0000000..95aaee5
--- /dev/null
+++ b/test.sh
@@ -0,0 +1,6 @@
+#!/bin/bash
+set -e
+
+./install.sh y "$(python -c "import sys; print('.'.join(map(str, sys.version_info[:2])))")" username uhppc00 y "$HOME" y "me@me.com" firstname lastname y $HOME y
+python ~/.jupyter/jupyter_notebook_config.py
+source ~/.bashrc

From 871823dd60a367df12750577cd59f288f8566338 Mon Sep 17 00:00:00 2001
From: Shaun C Read <shaun.c.read@gmail.com>
Date: Fri, 29 Mar 2019 10:24:07 +0000
Subject: [PATCH 3/9] python version should be 2/3

---
 install.sh | 1 +
 1 file changed, 1 insertion(+)

diff --git a/install.sh b/install.sh
index 9ccd55f..79854d4 100644
--- a/install.sh
+++ b/install.sh
@@ -53,6 +53,7 @@ else
     if [[ $install_conda = 'y' ]]; then
     	echo -n "Which python should I use as your default? 2 or 3:"
     	if [ -z ${version+x} ]; then read -r version; else echo "$version"; fi
+	    version="$(echo $version | head -c 1)"
 	    unameOut="$(uname -s)"
 		case "${unameOut}" in
 		    Linux*)    

From 4c72176733d9d260016a1fbad58aa60ee1d0cd6e Mon Sep 17 00:00:00 2001
From: Shaun C Read <shaun.c.read@gmail.com>
Date: Fri, 29 Mar 2019 10:31:25 +0000
Subject: [PATCH 4/9] auto install conda

---
 install.sh | 9 ++++++---
 test.sh    | 2 +-
 2 files changed, 7 insertions(+), 4 deletions(-)

diff --git a/install.sh b/install.sh
index 79854d4..764b369 100644
--- a/install.sh
+++ b/install.sh
@@ -48,9 +48,8 @@ else
 	# else
 	echo -n "Install miniconda for personal use (you can choose where later)? [y/n]"
 	if [ -z ${install_conda+x} ]; then read -r install_conda; else echo "$install_conda"; fi
-	
 
-    if [[ $install_conda = 'y' ]]; then
+    if [[ $install_conda = *"y"* ]]; then
     	echo -n "Which python should I use as your default? 2 or 3:"
     	if [ -z ${version+x} ]; then read -r version; else echo "$version"; fi
 	    version="$(echo $version | head -c 1)"
@@ -80,7 +79,11 @@ else
 		fi
 		wget "https://repo.continuum.io/miniconda/$fname"
 		chmod +x "$fname"
-		sh "$fname"
+		if [[ "$install_conda" = "yes-silent" ]]; then
+			bash "$fname" -b -p "$HOME/miniconda"
+		else
+			sh "$fname"
+		fi
 		eval "$(register-python-argcomplete conda)"
 		conda install jupyter
 		conda_dir="$(dirname $(dirname $(which conda)))"
diff --git a/test.sh b/test.sh
index 95aaee5..c171fff 100644
--- a/test.sh
+++ b/test.sh
@@ -1,6 +1,6 @@
 #!/bin/bash
 set -e
 
-./install.sh y "$(python -c "import sys; print('.'.join(map(str, sys.version_info[:2])))")" username uhppc00 y "$HOME" y "me@me.com" firstname lastname y $HOME y
+./install.sh yes-silent "$(python -c "import sys; print('.'.join(map(str, sys.version_info[:2])))")" username uhppc00 y "$HOME" y "me@me.com" firstname lastname y $HOME y
 python ~/.jupyter/jupyter_notebook_config.py
 source ~/.bashrc

From 56d959a991af49bbeb17b979b1ae093b14119109 Mon Sep 17 00:00:00 2001
From: Shaun C Read <shaun.c.read@gmail.com>
Date: Fri, 29 Mar 2019 11:10:23 +0000
Subject: [PATCH 5/9] source conda

---
 install.sh | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/install.sh b/install.sh
index 764b369..86a0347 100644
--- a/install.sh
+++ b/install.sh
@@ -81,6 +81,8 @@ else
 		chmod +x "$fname"
 		if [[ "$install_conda" = "yes-silent" ]]; then
 			bash "$fname" -b -p "$HOME/miniconda"
+			echo 'export PATH="$HOME/miniconda/bin:$PATH"' >> ~/.bashrc
+			source ~/.bashrc
 		else
 			sh "$fname"
 		fi

From 1a0689200e97051bd8190ba3ce4c304e5679f9e3 Mon Sep 17 00:00:00 2001
From: Shaun C Read <shaun.c.read@gmail.com>
Date: Fri, 29 Mar 2019 11:16:00 +0000
Subject: [PATCH 6/9] echo path

---
 install.sh | 7 +++++--
 1 file changed, 5 insertions(+), 2 deletions(-)

diff --git a/install.sh b/install.sh
index 86a0347..c1d94a2 100644
--- a/install.sh
+++ b/install.sh
@@ -80,8 +80,11 @@ else
 		wget "https://repo.continuum.io/miniconda/$fname"
 		chmod +x "$fname"
 		if [[ "$install_conda" = "yes-silent" ]]; then
-			bash "$fname" -b -p "$HOME/miniconda"
-			echo 'export PATH="$HOME/miniconda/bin:$PATH"' >> ~/.bashrc
+			prefix="$HOME/miniconda"
+			bash "$fname" -b -p $prefix
+			echo export PATH='$HOME'"$prefix/bin:"'$PATH' >> ~/.bashrc
+			ls -alt $prefix
+			echo $PATH
 			source ~/.bashrc
 		else
 			sh "$fname"

From 8fbca1062ebd8303b2941bdae28b6d8d933b9f9b Mon Sep 17 00:00:00 2001
From: Shaun C Read <shaun.c.read@gmail.com>
Date: Fri, 29 Mar 2019 11:50:04 +0000
Subject: [PATCH 7/9] testing

---
 install.sh | 8 ++++----
 1 file changed, 4 insertions(+), 4 deletions(-)

diff --git a/install.sh b/install.sh
index c1d94a2..ff9fe3a 100644
--- a/install.sh
+++ b/install.sh
@@ -83,9 +83,9 @@ else
 			prefix="$HOME/miniconda"
 			bash "$fname" -b -p $prefix
 			echo export PATH='$HOME'"$prefix/bin:"'$PATH' >> ~/.bashrc
-			ls -alt $prefix
-			echo $PATH
 			source ~/.bashrc
+			ls -alt $prefix/bin
+			echo $PATH
 		else
 			sh "$fname"
 		fi
@@ -93,10 +93,10 @@ else
 		conda install jupyter
 		conda_dir="$(dirname $(dirname $(which conda)))"
 		echo "source $conda_dir/etc/profile.d/conda.csh" >> ~/.tcshrc
-		echo "conda activate" >> ~/.bashrc
-		echo "conda activate" >> ~/.tcshrc
 		echo "unsetenv PYTHONPATH" >> ~/.tcshrc
 		echo "unset PYTHONPATH" >> ~/.bashrc
+		echo "conda activate" >> ~/.bashrc
+		echo "conda activate" >> ~/.tcshrc
 		echo "Conda has been installed and the base environment activated by default"
 		echo "You will need to source your tcshrc/bashrc files to make these changes now"
 		echo

From 57428a2d2c4bee1e2e00e11cef61b66c15d3ad05 Mon Sep 17 00:00:00 2001
From: Shaun C Read <shaun.c.read@gmail.com>
Date: Fri, 29 Mar 2019 11:54:26 +0000
Subject: [PATCH 8/9] reorder

---
 install.sh | 14 +++++++++-----
 1 file changed, 9 insertions(+), 5 deletions(-)

diff --git a/install.sh b/install.sh
index ff9fe3a..6f8d23f 100644
--- a/install.sh
+++ b/install.sh
@@ -83,20 +83,24 @@ else
 			prefix="$HOME/miniconda"
 			bash "$fname" -b -p $prefix
 			echo export PATH='$HOME'"$prefix/bin:"'$PATH' >> ~/.bashrc
-			source ~/.bashrc
-			ls -alt $prefix/bin
-			echo $PATH
 		else
 			sh "$fname"
 		fi
-		eval "$(register-python-argcomplete conda)"
-		conda install jupyter
 		conda_dir="$(dirname $(dirname $(which conda)))"
 		echo "source $conda_dir/etc/profile.d/conda.csh" >> ~/.tcshrc
 		echo "unsetenv PYTHONPATH" >> ~/.tcshrc
 		echo "unset PYTHONPATH" >> ~/.bashrc
 		echo "conda activate" >> ~/.bashrc
 		echo "conda activate" >> ~/.tcshrc
+
+		source ~/.bashrc
+		ls -alt $prefix/bin
+		echo $PATH
+		pip install argcomplete
+		activate-global-python-argcomplete
+		eval "$(register-python-argcomplete conda)"
+		conda install jupyter
+
 		echo "Conda has been installed and the base environment activated by default"
 		echo "You will need to source your tcshrc/bashrc files to make these changes now"
 		echo

From 34455e3c27fd89e63de6f4afab382f32e3e1d975 Mon Sep 17 00:00:00 2001
From: Shaun C Read <shaun.c.read@gmail.com>
Date: Fri, 29 Mar 2019 11:56:53 +0000
Subject: [PATCH 9/9] source again

---
 install.sh | 1 +
 1 file changed, 1 insertion(+)

diff --git a/install.sh b/install.sh
index 6f8d23f..56f0eec 100644
--- a/install.sh
+++ b/install.sh
@@ -86,6 +86,7 @@ else
 		else
 			sh "$fname"
 		fi
+		source ~/.bashrc
 		conda_dir="$(dirname $(dirname $(which conda)))"
 		echo "source $conda_dir/etc/profile.d/conda.csh" >> ~/.tcshrc
 		echo "unsetenv PYTHONPATH" >> ~/.tcshrc