Ref #numpygh-182, fixes #numpygh-217 review comments addressed

Cleanup of README, 80char line

Cleanup of README, 80char line

Author: shaloo

scripts/fetch-ehtim.sh

@@ -0,0 +1,138 @@
+# NumPy Dependency Chart generator Scripts 
+
+## Overview
+
+Typically, you only need to run the top level script **redraw-numpy-dep-charts.sh.**
+
+Here is how these scripts are organized:
+
+* **Top level script:**  redraw-numpy-dep-charts.sh
+* **Helper scripts:** These scripts are used by **redraw-numpy-dep-charts.sh**
+and should be run in the suggested order below:
+
+1. fetch-numpydeppkg.sh
+2. gen-numpy-dep-graph.sh
+3. cleanup-numpydeppkg.sh
+
+If you run the helper scripts, make sure you run them in this order to generate graphs in specified output directory.
+
+Usage details of each script are listed in the section below.
+
+----
+
+## Script: redraw-numpy-dep-charts.sh
+
+### Use Case:
+
+NumPy case studies refers to ehtim, gwpy and PyCBC packages.  For each of these,
+we have created NumPy dependency graphs.  You can redraw all these three graphs
+in one go (obtain 3 png files) in the specified output directory. If you wish
+to add a new package and also refresh existing charts, you can edit the script
+and update three arrays:
+
+* *pkgarray:* List of packages for which numpy dependency chart is to be generated
+* *pkgurl:* List of github urls from where pkg sources can be git cloned
+* *pkgsetup:* Dirname (not path) of the top level dir in pkg source that contains
+  requirements.txt file used to pip install the package in a virtualenv.
+  The package is uninstalled as part of cleanup after graphs is generated.
+
+#### Usage
+
+redraw-numpy-dep-charts.sh **outputdir**
+
+*outputdir:* The output directory is an optional parameter.
+
+If no output directory is specified, the graphs (.png files) of all the packages
+listed in pkgarray variable are generated in the current directory from where 
+the script is run.
+
+**Pre-requisites:**
+
+The following software packages must be installed on the system where you are running this bash script:  git, python3, pip3, virtualenv.
+
+----
+
+## Script: fetch-numpydeppkg.sh
+
+### Use Case:
+
+This script is one of the helper scripts used by **redraw-numpy-dep-charts.sh**
+script. Its sole purpose is to download the package for which numpy dependency
+graph is to be generated and install it in a virtual environment, setup the 
+directory structure which can be used by other helper script 
+**gen-numpy-dep-graph.sh** to generate the graph.  This script is paired with
+**cleanup-numpydeppkg.sh** script for uninstalling and removing scratch data.
+
+#### Usage
+
+fetch-numpydeppkg.sh **package_name scratchdir git_url reqfile_parentdir**
+
+*package_name:*  Name of the package (as in pip registry) that will be fetched.
+
+*scratchdir:* local directory where the package contents will be fetched.
+
+*git_url:*  Full git url required for git cloning.
+
+*reqfile_parentdir:*  This is the name (not path) of the root directory of package that contains requirements.txt file
+
+----
+
+## Script: gen-numpy-dep-graph.sh
+
+### Use Case:
+
+This is a helper script used by **redraw-numpy-dep-charts.sh** script. Its sole
+purpose is to use the pre-installed pkg in a local virtual environment by
+the script **fetch-numpydeppkg.sh** (or manually installed locally) and use them
+to run graphviz, dot and other utilities for creating NumPy dependency chart
+as png files for the pkg.  It assumes that packages is pre-installed and does
+not clean up any pre-installed packages.  In case a user has the package 
+pre-installed and would like to simply generate NumPy dependency chart, this script can be used.
+
+#### Usage:
+
+gen-numpy-dep-graph.sh **package_name scratchdir output_graphdir highlight_color (optional)**
+
+*package_name:* Name of the package (as in pip registry) for which NumPy dependency graph is to be generated.
+
+*scratchdir:* local directory where the package contents reside, the same directory as input to the fetch-numpydeppkg.sh where package_name was fetched by that script.
+
+*output_graphdir:* directory pathname where generated graphs in png format will be stored.
+
+highlight_color:* color understood by dot language.  Default is cyan.  Other
+acceptable colors are red, blue.  For a complete list see:
+
+* https://www.graphviz.org/doc/info/lang.html
+* https://www.graphviz.org/doc/info/colors.html
+
+**Pre-requisite:**
+
+Please note, **gen-numpy-dep-graph** script needs the virtualenv directory
+that was activated and used for package deployment a priori say by
+**fetch-numpydeppkg.sh** script or manually by user.  It is assumed that the 
+scratchdir comprises of two top level directories - virtualenv dir and another
+dir with package_name sources that are git cloned or a local copy of the same.
+
+----
+
+##Script: cleanup-numpydeppkg.sh
+
+### Use Case:
+
+This is a helper script used by **redraw-numpy-dep-charts.sh** script. Its sole
+purpose is to cleanup all the packages that were installed by
+**fetch-numpydeppkg.sh** script executed prior to running cleanup script. It
+ also removes the scratch directory contents related to virtualenv setup and
+package sources that were installed by **fetch-numpydeppkg.sh** script. If you
+have not used **fetch-numpydeppkg** script then you do not need to run the cleanup script.
+
+#### Usage:
+
+*package_name:*  Name of the package (as in pip registry) that will be uninstalled.
+
+*scratchdir:* local directory where the package contents were earlier fetched by
+**fetch-numpydeppkg.sh** script.
+
+*reqfile_parentdir:*  This is the name (not path) of the root directory of
+package that contains requirements.txt file. This is needed to uninstall all
+package dependencies that were installed as part of fetching and setting up of package by **fetch-numpydeppkg.sh** script.

scripts/numpy-ehtim-dep-graph.sh

@@ -30,6 +30,9 @@ cleanup_pkg() {
 
   $workingdir/env-${pkgname}/bin/pip3 uninstall -y -r $workingdir/numpy_${pkgname}_dep/$setupdir/requirements.txt
 
+  \rm -rf $workingdir/env-${pkgname}
+  \rm -rf $workingdir/numpy_${pkgname}_dep
+
   return 0
 }
 

scripts/pkgdepchart/README.md

@@ -5,6 +5,8 @@
 
 set -ue
 
+scriptdir="$( cd "$( dirname "${BASH_SOURCE[0]}" )" >/dev/null 2>&1 && pwd )"
+
 curdir=`pwd`
 outputdir=$curdir
 
@@ -40,6 +42,7 @@ declare -a pkgurl=("https://github.com/achael/eht-imaging.git"
                    "https://github.com/gwpy/gwpy.git"
                    "https://github.com/gwastro/pycbc.git")
 declare -a pkgsetup=("eht-imaging" "gwpy" "pycbc")
+
 highlightcolor="cyan"
 
 #numpkg=${#pkgarray[@]}
@@ -52,8 +55,8 @@ do
     echo "and using $workingdir as scratch"
 
     mkdir $workingdir/${pkgarray[$index]} $workingdir/${pkgarray[$index]}/graphdir
-    ./scripts/fetch-numpydeppkg.sh ${pkgarray[$index]} $workingdir/${pkgarray[$index]} ${pkgurl[$index]} ${pkgsetup[$index]}
-    ./scripts/gen-numpy-dep-graph.sh ${pkgarray[$index]} $workingdir/${pkgarray[$index]} $workingdir/${pkgarray[$index]}/numpy_${pkgarray[$index]}_dep/${pkgsetup[$index]} $workingdir/${pkgarray[$index]}/graphdir/ $highlightcolor
+    ${scriptdir}/fetch-numpydeppkg.sh ${pkgarray[$index]} $workingdir/${pkgarray[$index]} ${pkgurl[$index]} ${pkgsetup[$index]}
+    ${scriptdir}/gen-numpy-dep-graph.sh ${pkgarray[$index]} $workingdir/${pkgarray[$index]} $workingdir/${pkgarray[$index]}/numpy_${pkgarray[$index]}_dep/${pkgsetup[$index]} $workingdir/${pkgarray[$index]}/graphdir/ $highlightcolor
     if ! [ -f $workingdir/${pkgarray[$index]}/graphdir/numpy-clean-color.png ]
     then
         echo "Error: Graph for ${pkgarray[$index]} failed! Exiting."
@@ -66,7 +69,7 @@ done
 for index in "${!pkgarray[@]}" ;
 do
     echo "Uninstalling ${pkgarray[$index]}....."
-    ./scripts/cleanup-numpydeppkg.sh ${pkgarray[$index]} $workingdir/${pkgarray[$index]} ${pkgsetup[$index]}
+    ${scriptdir}/cleanup-numpydeppkg.sh ${pkgarray[$index]} $workingdir/${pkgarray[$index]} ${pkgsetup[$index]}
 done
 
 echo "Cleaning up scratch dir: $workingdir..........."