Qbox minor issues 18664 (#18665)

* qbox: install to correct directory structure

* qbox: Have qb executable put in bin rather than src subdir

* qbox: Fix python script shebangs to use python from path

* qbox: Add dependencies on gnuplot, python2 for utilities

* qbox: fix flake8 issue

* qbox: Add $prefix/util to PATH

var/spack/repos/builtin/packages/qbox/package.py

@@ -43,6 +43,11 @@ class Qbox(MakefilePackage):
     depends_on('scalapack')
     depends_on('fftw')
     depends_on('xerces-c')
+    depends_on('python@:2.999', type='run')
+    depends_on('gnuplot', type='run')
+
+    # Change /usr/bin/python shebangs to /usr/bin/env python
+    patch('qbox-python-shebang-path.patch')
 
     build_directory = 'src'
 
@@ -64,9 +69,12 @@ def edit(self, spec, prefix):
             ))))
         filter_file('$(TARGET)', 'spack', 'src/Makefile', string=True)
 
+    def setup_run_environment(self, env):
+        env.prepend_path('PATH', self.prefix.util)
+
     def install(self, spec, prefix):
-        mkdir(prefix.src)
+        mkdir(prefix.bin)
-        install('src/qb', prefix.src)
+        install('src/qb', prefix.bin)
-        install_tree('test', prefix)
+        install_tree('test', prefix.test)
-        install_tree('xml', prefix)
+        install_tree('xml', prefix.xml)
-        install_tree('util', prefix)
+        install_tree('util', prefix.util)

var/spack/repos/builtin/packages/qbox/qbox-python-shebang-path.patch

@@ -0,0 +1,108 @@
+diff -Nuar spack-src/util/qbox_angle.py spack-src.patched/util/qbox_angle.py
+--- spack-src/util/qbox_angle.py	2016-07-05 00:43:50.000000000 -0400
++++ spack-src.patched/util/qbox_angle.py	2020-09-11 17:48:34.381997541 -0400
+@@ -1,4 +1,4 @@
+-#!/usr/bin/python
++#!/usr/bin/env python
+ # qbox_angle.py
+ # extract angle defined by three atoms from Qbox output
+ # use: qbox_angle.py name1 name2 name3 file.r
+diff -Nuar spack-src/util/qbox_distance.py spack-src.patched/util/qbox_distance.py
+--- spack-src/util/qbox_distance.py	2016-07-05 00:43:50.000000000 -0400
++++ spack-src.patched/util/qbox_distance.py	2020-09-11 17:48:40.733188691 -0400
+@@ -1,4 +1,4 @@
+-#!/usr/bin/python
++#!/usr/bin/env python
+ # qbox_distance.py
+ # extract distance between two atoms from Qbox output
+ # use: qbox_distance.py name1 name2 file.r
+diff -Nuar spack-src/util/qbox_dos.py spack-src.patched/util/qbox_dos.py
+--- spack-src/util/qbox_dos.py	2014-01-10 15:39:02.000000000 -0500
++++ spack-src.patched/util/qbox_dos.py	2020-09-11 17:48:46.141351461 -0400
+@@ -1,4 +1,4 @@
+-#!/usr/bin/python
++#!/usr/bin/env python
+ # qbox_dos.py: extract electronic DOS from Qbox output
+ # generate DOS plot in gnuplot format
+ # use: qbox_dos.py [-last] emin emax width file.r
+diff -Nuar spack-src/util/qbox_eig.py spack-src.patched/util/qbox_eig.py
+--- spack-src/util/qbox_eig.py	2016-09-06 19:47:51.000000000 -0400
++++ spack-src.patched/util/qbox_eig.py	2020-09-11 17:49:00.811792982 -0400
+@@ -1,4 +1,4 @@
+-#!/usr/bin/python
++#!/usr/bin/env python
+ # qbox_eig.py: extract eigenvalues from Qbox output
+ # use: qbox_eig.py kpoint n ispin file.r
+ # extracts eigenvalue n at (ispin,kpoint)
+diff -Nuar spack-src/util/qbox_maxforce.py spack-src.patched/util/qbox_maxforce.py
+--- spack-src/util/qbox_maxforce.py	2016-09-06 19:47:51.000000000 -0400
++++ spack-src.patched/util/qbox_maxforce.py	2020-09-11 17:49:05.763942033 -0400
+@@ -1,4 +1,4 @@
+-#!/usr/bin/python
++#!/usr/bin/env python
+ # Copyright 2016 The Regents of the University of California
+ # This file is part of Qbox
+ #
+diff -Nuar spack-src/util/qbox_msd.py spack-src.patched/util/qbox_msd.py
+--- spack-src/util/qbox_msd.py	2014-04-24 16:30:49.000000000 -0400
++++ spack-src.patched/util/qbox_msd.py	2020-09-11 17:49:11.751122219 -0400
+@@ -1,4 +1,4 @@
+-#!/usr/bin/python
++#!/usr/bin/env python
+ # qbox_msd.py: compute mean-square displacement in an MD simulation
+ # generate plot of <r^2>(t) in gnuplot format
+ # use: qbox_msd.py species file.r [file.r ...]
+diff -Nuar spack-src/util/qbox_repair_h2o.py spack-src.patched/util/qbox_repair_h2o.py
+--- spack-src/util/qbox_repair_h2o.py	2013-12-05 15:28:06.000000000 -0500
++++ spack-src.patched/util/qbox_repair_h2o.py	2020-09-11 17:49:16.467264160 -0400
+@@ -1,4 +1,4 @@
+-#!/usr/bin/python
++#!/usr/bin/env python
+ # qbox_repair_h2o.py: repair broken h2o molecules in a Qbox sys file
+ # move hydrogen atoms across periodic boundaries to repair molecules
+ # use: qbox_repair_h2o.py file.sys
+diff -Nuar spack-src/util/qbox_torsion.py spack-src.patched/util/qbox_torsion.py
+--- spack-src/util/qbox_torsion.py	2017-03-10 14:46:12.000000000 -0500
++++ spack-src.patched/util/qbox_torsion.py	2020-09-11 17:49:21.469414705 -0400
+@@ -1,4 +1,4 @@
+-#!/usr/bin/python
++#!/usr/bin/env python
+ # qbox_torsion.py
+ # extract torsion angle defined by four atoms from Qbox output
+ # use: qbox_torsion.py name1 name2 name3 name4 file.r
+diff -Nuar spack-src/util/qbox_xyz.py spack-src.patched/util/qbox_xyz.py
+--- spack-src/util/qbox_xyz.py	2016-05-31 13:23:45.000000000 -0400
++++ spack-src.patched/util/qbox_xyz.py	2020-09-11 17:49:26.550567625 -0400
+@@ -1,4 +1,4 @@
+-#!/usr/bin/python
++#!/usr/bin/env python
+ # Copyright 2016 The Regents of the University of California
+ # This file is part of Qbox
+ #
+diff -Nuar spack-src/util/qso2qbox.py spack-src.patched/util/qso2qbox.py
+--- spack-src/util/qso2qbox.py	2016-05-31 13:23:45.000000000 -0400
++++ spack-src.patched/util/qso2qbox.py	2020-09-11 17:49:31.049703037 -0400
+@@ -1,4 +1,4 @@
+-#!/usr/bin/python
++#!/usr/bin/env python
+ # Convert <atomset> elements from quantum-simulation.org (QSO) format 
+ # to Qbox input file
+ # use: qso2qbox.py [-last] {file|URL}
+diff -Nuar spack-src/util/qso2qe.py spack-src.patched/util/qso2qe.py
+--- spack-src/util/qso2qe.py	2016-05-31 13:23:45.000000000 -0400
++++ spack-src.patched/util/qso2qe.py	2020-09-11 17:49:36.099855027 -0400
+@@ -1,4 +1,4 @@
+-#!/usr/bin/python
++#!/usr/bin/env python
+ # Convert from quantum-simulation.org format to QuantumEspresso input format
+ # use: env ECUT=ecut qso2qe.py [-last] {file|URL}
+ 
+diff -Nuar spack-src/util/qso.py spack-src.patched/util/qso.py
+--- spack-src/util/qso.py	2016-05-31 13:23:45.000000000 -0400
++++ spack-src.patched/util/qso.py	2020-09-11 17:49:42.412045000 -0400
+@@ -1,4 +1,4 @@
+-#!/usr/bin/python
++#!/usr/bin/env python
+ import xml.sax
+ # quantum-simulation.org (QSO) definitions
+ class Atom: