gnu: bam: Build with python3.

* gnu/packages/build-tools.scm (bam)[source]: Add patch.
[native-inputs]: Remove python-2; add python-minimal-wrapper.
* gnu/packages/patches/bam-python3-compat.patch: New file.
* gnu/local.mk (dist_patch_DATA): Register it.

Change-Id: Iec960101e148b7b71caf737cccdb5b762477a545

2 files changed, 294 insertions, 2 deletions

diff --git a/gnu/packages/build-tools.scm b/gnu/packages/build-tools.scm
index 813760f8455..5e401dbd846 100644
--- a/gnu/packages/build-tools.scm
+++ b/gnu/packages/build-tools.scm
@@ -196,7 +196,8 @@ according to the system capabilities and the user-selected options.")
               (file-name (git-file-name name version))
               (sha256
                (base32
-                "13br735ig7lygvzyfd15fc2rdygrqm503j6xj5xkrl1r7w2wipq6"))))
+                "13br735ig7lygvzyfd15fc2rdygrqm503j6xj5xkrl1r7w2wipq6"))
+              (patches (search-patches "bam-python3-compat.patch"))))
     (build-system gnu-build-system)
     (arguments
      `(#:make-flags `(,(string-append "CC=" ,(cc-for-target))
@@ -207,7 +208,7 @@ according to the system capabilities and the user-selected options.")
        (modify-phases %standard-phases
          (delete 'configure))))
     (native-inputs
-     `(("python" ,python-2)))
+     (list python-minimal-wrapper))
     (inputs
      (list lua))
     (home-page "https://matricks.github.io/bam/")
diff --git a/gnu/packages/patches/bam-python3-compat.patch b/gnu/packages/patches/bam-python3-compat.patch
new file mode 100644
index 00000000000..81d56a3e2ff
--- /dev/null
+++ b/gnu/packages/patches/bam-python3-compat.patch
@@ -0,0 +1,291 @@
+This patch is taken from the upstream repository
+
+From b937572d157e660af98e224523ffb3fe5810ed2c Mon Sep 17 00:00:00 2001
+Message-ID: <b937572d157e660af98e224523ffb3fe5810ed2c.1776087342.git.efraim@flashner.co.il>
+From: Felix Geyer <debfx@fobos.de>
+Date: Fri, 30 Aug 2019 19:08:35 +0200
+Subject: [PATCH] Port scripts to Python 3
+
+Compatibility with Python 2 is preserved.
+---
+ scripts/gendocs.py |  2 +-
+ scripts/test.py    | 67 +++++++++++++++++++++++-----------------------
+ scripts/tinydoc.py | 23 ++++++++--------
+ 3 files changed, 47 insertions(+), 45 deletions(-)
+
+diff --git a/scripts/gendocs.py b/scripts/gendocs.py
+index c9f206e..ba872c4 100644
+--- a/scripts/gendocs.py
++++ b/scripts/gendocs.py
+@@ -29,6 +29,6 @@ root.nodes += [ParseTextFile(Node("License"), "license.txt", True)]
+ 
+ # render files
+ for o in outputs:
+-       o.file = file(o.output_name(), "w")
++       o.file = open(o.output_name(), "w")
+        o.render(root)
+        o.file.close()
+diff --git a/scripts/test.py b/scripts/test.py
+index accc26c..bbc9c7d 100755
+--- a/scripts/test.py
++++ b/scripts/test.py
+@@ -1,5 +1,6 @@
+ #!/usr/bin/env python
+ 
++from __future__ import print_function
+ import os, sys, shutil, subprocess
+ 
+ extra_bam_flags = ""
+@@ -36,8 +37,8 @@ def copytree(src, dst):
+                                copytree(srcname, dstname)
+                        else:
+                                shutil.copy2(srcname, dstname)
+-               except (IOError, os.error), why:
+-                       print "Can't copy %s to %s: %s" % (`srcname`, `dstname`, str(why))
++               except (IOError, os.error) as why:
++                       print("Can't copy '%s' to '%s': %s" % (srcname, dstname, str(why)))
+ 
+ 
+ def run_bam(testname, flags):
+@@ -45,7 +46,7 @@ def run_bam(testname, flags):
+        olddir = os.getcwd()
+        os.chdir(output_path+"/"+testname)
+        
+-       p = subprocess.Popen(bam+" "+flags, stdout=subprocess.PIPE, shell=True, stderr=subprocess.STDOUT)
++       p = subprocess.Popen(bam+" "+flags, stdout=subprocess.PIPE, shell=True, stderr=subprocess.STDOUT, universal_newlines=True)
+        report = p.stdout.readlines()
+        p.wait()
+        ret = p.returncode
+@@ -64,8 +65,8 @@ def test(name, moreflags="", should_fail=0):
+        os.chdir(output_path+"/"+name)
+        cmdline = bam+" -t -v "+extra_bam_flags+" " + moreflags
+        
+-       print name + ":",
+-       p = subprocess.Popen(cmdline, stdout=subprocess.PIPE, shell=True, stderr=subprocess.STDOUT)
++       print(name + ":", end=" ")
++       p = subprocess.Popen(cmdline, stdout=subprocess.PIPE, shell=True, stderr=subprocess.STDOUT, universal_newlines=True)
+        report = p.stdout.readlines()
+        p.wait()
+        ret = p.returncode
+@@ -73,50 +74,50 @@ def test(name, moreflags="", should_fail=0):
+        os.chdir(olddir)
+        
+        if (should_fail and not ret) or (not should_fail and ret):
+-               print " FAILED!"
++               print(" FAILED!")
+                for l in report:
+-                       print "\t", l,
++                       print("\t", l, end=" ")
+                failed_tests += [name + "(returned %d)" % ret]
+        else:
+-               print " ok"
++               print(" ok")
+ 
+ def difftest(name, flags1, flags2):
+        global failed_tests
+        if len(tests) and not name in tests:
+                return
+        testname = "difftest: %s '%s' vs '%s': "%(name, flags1, flags2)
+-       print testname,
++       print(testname, end=" ")
+        ret1, report1 = run_bam(name, flags1)
+        ret2, report2 = run_bam(name, flags2)
+        
+        if ret1:
+-               print "FAILED! '%s' returned %d" %(flags1, ret1)
++               print("FAILED! '%s' returned %d" %(flags1, ret1))
+                failed_tests += [testname]
+                return
+        
+        if ret2:
+-               print "FAILED! '%s' returned %d" %(flags2, ret2)
++               print("FAILED! '%s' returned %d" %(flags2, ret2))
+                failed_tests += [testname]
+                return
+        
+        if len(report1) != len(report2):
+-               print "FAILED! %d lines vs %d lines" % (len(report1), len(report2))
++               print("FAILED! %d lines vs %d lines" % (len(report1), len(report2)))
+                failed_tests += [testname]
+                return
+        
+        failed = 0
+-       for i in xrange(0, len(report1)):
++       for i in range(0, len(report1)):
+                if report1[i] != report2[i]:
+                        if not failed:
+-                               print "FAILED!"
+-                       print "1:", report1[i].strip()
+-                       print "2:", report2[i].strip()
++                               print("FAILED!")
++                       print("1:", report1[i].strip())
++                       print("2:", report2[i].strip())
+                        failed += 1
+                        
+        if failed:
+                failed_tests += [testname]
+        else:
+-               print "ok"
++               print("ok")
+ 
+ def unittests():
+        global failed_tests
+@@ -129,7 +130,7 @@ def unittests():
+        
+        tests = []
+        state = 0
+-       for line in file('src/base.lua'):
++       for line in open('src/base.lua'):
+                if state == 0:
+                        if "@UNITTESTS" in line:
+                                state = 1
+@@ -157,16 +158,16 @@ def unittests():
+        os.chdir(output_path+"/unit")
+        
+        for test in tests:
+-               f = file("bam.lua", "w")
++               f = open("bam.lua", "w")
+                if test.catch != None:
+-                       print >>f, "print(\"CATCH:\", %s)"%(test.line)
++                       print("print(\"CATCH:\", %s)"%(test.line), file=f)
+                else:
+-                       print >>f, test.line
+-               print >>f, 'DefaultTarget(PseudoTarget("Test"))'
++                       print(test.line, file=f)
++               print('DefaultTarget(PseudoTarget("Test"))', file=f)
+                f.close()
+ 
+-               print  "%s:"%(test.line),
+-               p = subprocess.Popen(bam + " --dry", stdout=subprocess.PIPE, shell=True, stderr=subprocess.STDOUT)
++               print("%s:"%(test.line), end=" ")
++               p = subprocess.Popen(bam + " --dry", stdout=subprocess.PIPE, shell=True, stderr=subprocess.STDOUT, universal_newlines=True)
+                report = p.stdout.readlines()
+                p.wait()
+                ret = p.returncode
+@@ -174,7 +175,7 @@ def unittests():
+                failed = False
+                if ret != test.err:
+                        failed = True
+-                       print "FAILED! error %d != %d" % (test.err, ret)
++                       print("FAILED! error %d != %d" % (test.err, ret))
+                
+                if test.catch != None:
+                        found = False
+@@ -185,7 +186,7 @@ def unittests():
+                                        if catched == test.catch:
+                                                found = True
+                                        else:
+-                                               print "FAILED! catch '%s' != '%s'" % (test.catch, catched)
++                                               print("FAILED! catch '%s' != '%s'" % (test.catch, catched))
+                                                
+                        if not found:
+                                failed = True
+@@ -198,16 +199,16 @@ def unittests():
+                        
+                        if not found:
+                                failed = True
+-                               print "FAILED! could not find '%s' in output" % (test.find)
++                               print("FAILED! could not find '%s' in output" % (test.find))
+                if failed or verbose:
+                        if failed:
+                                failed_tests += [test.line]
+                        else:
+-                               print "",
++                               print("", end=" ")
+                        for l in report:
+-                               print "\t", l.rstrip()
++                               print("\t", l.rstrip())
+                else:
+-                       print "ok"
++                       print("ok")
+                        
+ 
+        os.chdir(olddir)
+@@ -246,11 +247,11 @@ test("multipleoutput")
+ test("missingoutput", "", 1)
+ 
+ if len(failed_tests):
+-       print "FAILED TESTS:"
++       print("FAILED TESTS:")
+        for t in failed_tests:
+-               print "\t"+t
++               print("\t"+t)
+        sys.exit(1)
+ else:
+-       print "ALL TESTS PASSED!"
++       print("ALL TESTS PASSED!")
+        sys.exit(0)
+ 
+diff --git a/scripts/tinydoc.py b/scripts/tinydoc.py
+index 536a74f..6557cf8 100644
+--- a/scripts/tinydoc.py
++++ b/scripts/tinydoc.py
+@@ -1,4 +1,5 @@
+ 
++from __future__ import print_function
+ import re, time
+ 
+ class Node:
+@@ -47,20 +48,20 @@ class Output:
+        
+        def render_node_index(self, cur):
+                if len(cur.index):
+-                       print >>self.file, self.index_node_begin(cur)
++                       print(self.index_node_begin(cur), file=self.file)
+                for node in cur.nodes:
+                        self.render_node_index(node)
+                if len(cur.index):
+-                       print >>self.file, self.index_node_end(cur)
++                       print(self.index_node_end(cur), file=self.file)
+        def render_node(self, cur):
+                if len(cur.index):
+-                       print >>self.file, self.format_header(cur)
+-                       print >>self.file, self.format_body(cur)
++                       print(self.format_header(cur), file=self.file)
++                       print(self.format_body(cur), file=self.file)
+                for node in cur.nodes:
+                        self.render_node(node)
+                        
+        def index_nodes(self, cur, index=""):
+-               for i in xrange(0, len(cur.nodes)):
++               for i in range(0, len(cur.nodes)):
+                        if len(index):
+                                cur.nodes[i].index = index + "." + str(i+1)
+                        else:
+@@ -73,14 +74,14 @@ class Output:
+                
+        def render(self, rootnode):
+                self.index_nodes(rootnode)
+-               print >>self.file, self.render_begin()
++               print(self.render_begin(), file=self.file)
+                
+-               print >>self.file, self.index_begin()
++               print(self.index_begin(), file=self.file)
+                self.render_node_index(rootnode)
+-               print >>self.file, self.index_end()
++               print(self.index_end(), file=self.file)
+                
+                self.render_node(rootnode)
+-               print >>self.file, self.render_end()
++               print(self.render_end(), file=self.file)
+ 
+ class HTMLOutput(Output):
+        def render_begin(self):
+@@ -225,7 +226,7 @@ class HTMLOutput(Output):
+ 
+ def ParseTextFile(rootnode, filename, addbr=False):
+        group = rootnode
+-       for line in file(filename):
++       for line in open(filename):
+                if group_tag in line:
+                        group_name = line.split(group_tag)[-1].split(end_tag)[0].strip()
+                        group = Node(group_name)
+@@ -244,7 +245,7 @@ def ParseFile(rootnode, filename):
+        # 2 = outputting function decl
+        state = 0
+        group = rootnode
+-       for line in file(filename):
++       for line in open(filename):
+                if state == 0:
+                        if group_tag in line:
+                                group_name = line.split(group_tag)[-1].split(end_tag)[0].strip()