Commit 216ad6fe authored by Andreas Tille's avatar Andreas Tille
Browse files

Fix opening of text file; replace scons calls by calls to Debian packaged scons.

parent f3f79c56

debian/patches/2to3.patch

+64 −11
Original line number Diff line number Diff line
@@ -333,6 +333,32 @@ Last-Update: Thu, 12 Dec 2019 15:41:47 +0100 
         numpy_error = True

 

     if not numpy_error:

@@ -234,9 +234,9 @@ if env['BUILD_PDB2PKA']:

         compile_targets.append(algorithms_pyc)

 

         if os.name == 'nt':

-            alg_msvs_env = env.Clone(MSVSBUILDCOM='cd .. && '+pythonBin+' scons/scons.py algorithms DEBUG=True',

-                                     MSVSCLEANCOM='cd .. && '+pythonBin+' scons/scons.py -c algorithms',

-                                     MSVSREBUILDCOM='cd .. && '+pythonBin+' scons/scons.py -c algorithms && '+pythonBin+' scons/scons.py algorithms DEBUG=True')

+            alg_msvs_env = env.Clone(MSVSBUILDCOM='cd .. && scons algorithms DEBUG=True',

+                                     MSVSCLEANCOM='cd .. && scons -c algorithms',

+                                     MSVSREBUILDCOM='cd .. && scons -c algorithms && scons algorithms DEBUG=True')

 

             algorithms_project = alg_msvs_env.MSVSProject(target = 'msvs/Algorithms' + env['MSVSPROJECTSUFFIX'],

                                                           auto_build_solution=0,

@@ -259,9 +259,9 @@ if env['BUILD_PDB2PKA']:

         compile_targets.append(pmc_pyc)

 

         if os.name == 'nt':

-            pmc_msvs_env = env.Clone(MSVSBUILDCOM='cd .. && '+pythonBin+' scons/scons.py pmc_mult DEBUG=True'+build_swig,

-                                     MSVSCLEANCOM='cd .. && '+pythonBin+' scons/scons.py -c pmc_mult',

-                                     MSVSREBUILDCOM='cd .. && '+pythonBin+' scons/scons.py -c pmc_mult && '+pythonBin+' scons/scons.py pmc_mult DEBUG=True'+build_swig)

+            pmc_msvs_env = env.Clone(MSVSBUILDCOM='cd .. && scons pmc_mult DEBUG=True'+build_swig,

+                                     MSVSCLEANCOM='cd .. && scons -c pmc_mult',

+                                     MSVSREBUILDCOM='cd .. && scons -c pmc_mult && scons pmc_mult DEBUG=True'+build_swig)

 

             pmc_mult_project = pmc_msvs_env.MSVSProject(target = 'msvs/pMC_mult' + env['MSVSPROJECTSUFFIX'],

                                                         auto_build_solution=0,

@@ -285,65 +285,65 @@ SConscript('SConscript-install.py', expo

 SConscript('SConscript-error.py')
@@ -385,7 +411,7 @@ Last-Update: Thu, 12 Dec 2019 15:41:47 +0100 
-        print

-        print 'Run "python scons/scons.py" to build pdb2pqr.'

+        print()

+        print('Run "python3 scons/scons.py" to build pdb2pqr.')

+        print('Run "scons" to build pdb2pqr.')

 

-    print

-    print 'The preferred way to configure the build is by editing the file', config_file
@@ -396,13 +422,13 @@ Last-Update: Thu, 12 Dec 2019 15:41:47 +0100 
+    print('The preferred way to configure the build is by editing the file', config_file)

+    print()

+    print('Run scons with the python3 that you intend to use with pdb2pqr.')

+    print('For example: "/usr/bin/python3 scons/scons.py" will setup pdb2pqr to be run with /usr/bin/python3')

+    print('For example: "scons" will setup pdb2pqr to be run with Debian default Python3 interpreter')

 

     if 'install' not in target_list:

-        print

-        print 'Run "python scons/scons.py install" to install pdb2pqr in', env['PREFIX']

+        print()

+        print('Run "python3 scons/scons.py install" to install pdb2pqr in', env['PREFIX'])

+        print('Run "scons install" to install pdb2pqr in', env['PREFIX'])

 

-    print

-    print 'Run "python scons/scons.py basic-test" for a basic functionality test'
@@ -418,16 +444,16 @@ Last-Update: Thu, 12 Dec 2019 15:41:47 +0100 
-    print 'VS project generation is not well supported in scons. Resulting projects should build using NMAKE but cannot be used for debugging.'

-    print 'The resulting projects will need to modified to use VS natively to compile the code or debug.'

+    print()

+    print('Run "python3 scons/scons.py basic-test" for a basic functionality test')

+    print('Run "python3 scons/scons.py advanced-test" for a single test of ligand and PROPKA support. Requires numpy and PDB2PKA support compiled.')

+    print('Run "python3 scons/scons.py complete-test" for a complete test of all functionality EXCEPT PDB2PKA. Requires numpy and PDB2PKA support compiled.')

+    print('Run "python3 scons/scons.py pdb2pka-test" for a test of PDB2PKA functionality.')

+    print('Run "scons basic-test" for a basic functionality test')

+    print('Run "scons advanced-test" for a single test of ligand and PROPKA support. Requires numpy and PDB2PKA support compiled.')

+    print('Run "scons complete-test" for a complete test of all functionality EXCEPT PDB2PKA. Requires numpy and PDB2PKA support compiled.')

+    print('Run "scons pdb2pka-test" for a test of PDB2PKA functionality.')

+    print('    Requires numpy, PDB2PKA support compiled AND the APBS python3 libraries compiled and installed in the pdb2pka directory.')

+

+    print()

+    print('To setup a web service create a symbolic link to', env['PREFIX'], 'that enables you to view', env['URL'],'after running "scons/scons.py install"')

+    print('To setup a web service create a symbolic link to', env['PREFIX'], 'that enables you to view', env['URL'],'after running "scons install"')

+    print()

+    print('Run "python3 scons/scons.py msvs" to build Visual Studio projects for the Algorithms and pMC_mult modules.')

+    print('Run "scons msvs" to build Visual Studio projects for the Algorithms and pMC_mult modules.')

+    print('VS project generation is not well supported in scons. Resulting projects should build using NMAKE but cannot be used for debugging.')

+    print('The resulting projects will need to modified to use VS natively to compile the code or debug.')
@@ -8468,7 +8494,18 @@ Last-Update: Thu, 12 Dec 2019 15:41:47 +0100 
 

     put('pdb2pqr.tgz', '~/')

     with settings(warn_only=True):

@@ -114,7 +114,7 @@ def deploy():

@@ -106,15 +106,15 @@ def deploy():

 

     with cd('~/tmp/'):

         run('tar -zxvf ~/pdb2pqr.tgz')

-        run(python+' scons/scons.py')

+        run('scons')

 

         if run_tests:

-            run(python+' scons/scons.py -j 4 pdb2pka-test')

-            run(python+' scons/scons.py -j 4 complete-test')

+            run('scons -j 4 pdb2pka-test')

+            run('scons -j 4 complete-test')

 

 

 def install_on_deployed():
@@ -8477,6 +8514,17 @@ Last-Update: Thu, 12 Dec 2019 15:41:47 +0100 
 

     with settings(warn_only=True):

         with cd('~/www/pdb2pqr'):

@@ -147,8 +147,8 @@ def install_on_deployed():

 #             configopts += ' PREFIX=/Users/d3k084/www/pdb2pqr/'

 #             configopts += ' URL=http://PT24098/d3k084/pdb2pqr'

 

-        run(python+' scons/scons.py ' + configopts)

-        run(python+' scons/scons.py install ' + configopts)

+        run('scons ' + configopts)

+        run('scons install ' + configopts)

 

 def build_binary_from_deploy():

     create_dist_folder()

@@ -190,11 +190,11 @@ def linux_bin_cross_platform_test():

 @runs_once

 def build_windows():
@@ -13658,7 +13706,12 @@ Last-Update: Thu, 12 Dec 2019 15:41:47 +0100 
             if callable(v):

                 d[k] = env.subst(v())

             elif SCons.Util.is_String(v):

@@ -112,21 +112,21 @@ def CopySubAction(targetfile, sourcefile

@@ -108,25 +108,25 @@ def CopySubAction(targetfile, sourcefile

     1.2345 etc.

     """

     try:

-        f = open(sourcefile, 'rb')

+        f = open(sourcefile, 'r')

         contents = f.read()

         f.close()

     except: