Don't hardcode /usr/bin/python

Determine the shebang for bin/cryptosite at make time (so that it will work with either Python 2 or Python 3). Use sys.executable in Python code rather than /usr/bin/python so that we respect the configured Python version.
salilab · Oct 14, 2019 · ae9cbb3 · ae9cbb3
1 parent bde9fb3
commit ae9cbb3
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Showing 16 changed files with 36 additions and 20 deletions.
diff --git a/Makefile b/Makefile
@@ -1,13 +1,19 @@
 include Makefile.include
 
-.PHONY: install test
+.PHONY: install test bin clean
 
-install:
+bin:
+	${MAKE} -C bin
+
+clean:
+	${MAKE} -C bin clean
+
+install: bin
 	${MAKE} -C data install
 	${MAKE} -C data/ligands install
 	${MAKE} -C bin install
 	${MAKE} -C lib/cryptosite install
 	${MAKE} -C lib/cryptosite/config install
 
-test:
+test: bin
 	nosetests --processes=-1 test
diff --git a/Makefile.include b/Makefile.include
@@ -1,5 +1,6 @@
 PREFIX=/usr/local
 DATADIR=${PREFIX}/share/data/cryptosite
 BINDIR=${PREFIX}/bin
+PYTHON=python
 PYTHONDIR=${PREFIX}/python
 UNIPROT=/usr/share/databases/uniprot
diff --git a/bin/.gitignore b/bin/.gitignore
@@ -0,0 +1 @@
+cryptosite
diff --git a/bin/Makefile b/bin/Makefile
@@ -1,11 +1,17 @@
 include ../Makefile.include
 
-.PHONY: install
+.PHONY: install clean
+
+cryptosite: cryptosite.in
+	FULL_PYTHON=`which ${PYTHON}`; sed -e "s^#!.*^#!$$FULL_PYTHON^" $< > $@ && chmod a+x $@
 
 FILES=${BINDIR}/cryptosite
 
 install: ${FILES}
 
+clean:
+	rm -f cryptosite
+
 ${BINDIR}/%: %
 	@if [ ! -d ${BINDIR} ]; then mkdir -p ${BINDIR}; fi
 	install $< $@
diff --git a/bin/cryptosite → bin/cryptosite.in b/bin/cryptosite → bin/cryptosite.in
diff --git a/doc/installation.rst b/doc/installation.rst
@@ -63,6 +63,8 @@ will get all of these dependencies.
 Building
 ========
 
+Use ``make PYTHON=python3`` or ``make PYTHON=python2`` to build the library
+(depending on which version of Python you want to use).
 Use ``make test`` to test the library, and ``make install`` to install it.
 In most cases you will need to tell ``make`` where to install (if running on
 a Linux cluster, CryptoSite will need to be installed on a network-accessible

diff --git a/test/test_am_bmi.py b/test/test_am_bmi.py
@@ -15,7 +15,7 @@ def test_bad(self):
         for args in (['x'],):
             out = utils.check_output(['cryptosite', 'am_bmi'] + args,
                                      stderr=subprocess.STDOUT, retcode=2)
-            out = utils.check_output(['python', '-m',
+            out = utils.check_output([sys.executable, '-m',
                                      'cryptosite.am_bmi'] + args,
                                      stderr=subprocess.STDOUT, retcode=2)
 

diff --git a/test/test_analysis.py b/test/test_analysis.py
@@ -26,7 +26,7 @@ def test_bad(self):
         for args in ([],):
             out = utils.check_output(['cryptosite', 'analysis'] + args,
                                      stderr=subprocess.STDOUT, retcode=2)
-            out = utils.check_output(['python', '-m',
+            out = utils.check_output([sys.executable, '-m',
                                      'cryptosite.analysis'] + args,
                                      stderr=subprocess.STDOUT, retcode=2)
 

diff --git a/test/test_chimera.py b/test/test_chimera.py
@@ -17,7 +17,7 @@ def test_bad(self):
         for args in ([], ['x'] * 4):
             out = utils.check_output(['cryptosite', 'chimera'] + args,
                                      stderr=subprocess.STDOUT, retcode=2)
-            out = utils.check_output(['python', '-m',
+            out = utils.check_output([sys.executable, '-m',
                                      'cryptosite.chimera'] + args,
                                      stderr=subprocess.STDOUT, retcode=2)
 

diff --git a/test/test_gather.py b/test/test_gather.py
@@ -17,7 +17,7 @@ def test_bad(self):
         for args in ([], ['x'] * 4):
             out = utils.check_output(['cryptosite', 'gather'] + args,
                                      stderr=subprocess.STDOUT, retcode=2)
-            out = utils.check_output(['python', '-m',
+            out = utils.check_output([sys.executable, '-m',
                                      'cryptosite.gather'] + args,
                                      stderr=subprocess.STDOUT, retcode=2)
 

diff --git a/test/test_patch_mapper.py b/test/test_patch_mapper.py
@@ -18,24 +18,24 @@ def mock_patch_dock_lig_score():
     os.mkdir(subdir)
     fname = os.path.join(subdir, 'patch_dock.Linux')
     with open(fname, 'w') as fh:
-        fh.write("""#!/usr/bin/env python
+        fh.write("""#!%s
 with open('ligands.ids') as fh:
     ligands = [l.rstrip('\\r\\n') for l in fh.readlines()]
 for i, lig in enumerate(ligands):
-    with open('test.pdb%d.res' % i, 'w') as fh:
+    with open('test.pdb%%d.res' %% i, 'w') as fh:
         fh.write("receptorPdb     (Str)   test.pdb\\n")
-        fh.write("ligandPdb     (Str)   %s\\n" % lig)
+        fh.write("ligandPdb     (Str)   %%s\\n" %% lig)
         fh.write(" # | score | pen.  | Area    | as1   | as2   | as12  | ACE     | hydroph | Energy  |cluster| dist. || Ligand Transformation\\n")
         if i == 13:
             fh.write("   1 |   684 | -0.61 |   72.40 |     0 |     0 |     0 |  -63.66 |    0.00 |    0.00 |     0 | 0.00 || -0.21078 -0.07140 0.71339 1.12228 -7.44875 0.86045\\n")
         fh.write("Best Rmsd Result: 100000000.00 rank -1\\n")
         fh.write("Best Rank Result: 100000000.00 rank 100000\\n")
-""")
+""" % sys.executable)
     os.chmod(fname, 0o755)
 
     fname = os.path.join(subdir, 'ligand_score_multiple')
     with open(fname, 'w') as fh:
-        fh.write("""#!/usr/bin/env python
+        fh.write("""#!%s
 import sys, os
 pdb, ligand, trans = sys.argv[1:]
 if not os.path.exists(pdb) or not os.path.exists(ligand):
@@ -45,7 +45,7 @@ def mock_patch_dock_lig_score():
 with open('mol2_score.res', 'w') as fh:
     if tr:
         fh.write("Score for ISB.pdb trans 0 is -0.41\\n")
-""")
+""" % sys.executable)
     os.chmod(fname, 0o755)
 
     oldpath = os.environ['PATH']

diff --git a/test/test_pockets.py b/test/test_pockets.py
@@ -16,7 +16,7 @@ def test_bad(self):
         for args in (['x'],):
             out = utils.check_output(['cryptosite', 'pockets'] + args,
                                      stderr=subprocess.STDOUT, retcode=2)
-            out = utils.check_output(['python', '-m',
+            out = utils.check_output([sys.executable, '-m',
                                      'cryptosite.pockets'] + args,
                                      stderr=subprocess.STDOUT, retcode=2)
 

diff --git a/test/test_predict.py b/test/test_predict.py
@@ -41,7 +41,7 @@ def test_bad(self):
         for args in (['x', 'y'], []):
             out = utils.check_output(['cryptosite', 'predict'] + args,
                                      stderr=subprocess.STDOUT, retcode=2)
-            out = utils.check_output(['python', '-m',
+            out = utils.check_output([sys.executable, '-m',
                                      'cryptosite.predict'] + args,
                                      stderr=subprocess.STDOUT, retcode=2)
 

diff --git a/test/test_seq_conservation.py b/test/test_seq_conservation.py
@@ -17,7 +17,7 @@ def mock_usearch():
     os.mkdir(subdir)
     fname = os.path.join(subdir, 'usearch')
     with open(fname, 'w') as fh:
-        fh.write("""#!/usr/bin/env python
+        fh.write("""#!%s
 import sys
 outf = sys.argv[4]
 with open(outf, 'w') as fh:
@@ -31,7 +31,7 @@ def mock_usearch():
                          'EX70_12567', '*\\n']))
     fh.write('\\t'.join(['H', '1', '292', '98.2', '+', '0', '0', '292M',
                          'AH70_12410', 'EX70_12567\\n']))
-""")
+""" % sys.executable)
     os.chmod(fname, 0o755)
 
     oldpath = os.environ['PATH']

diff --git a/test/test_setup.py b/test/test_setup.py
@@ -43,7 +43,7 @@ def test_bad(self):
         for args in (['x'], ['x']*3):
             out = utils.check_output(['cryptosite', 'setup'] + args,
                                      stderr=subprocess.STDOUT, retcode=2)
-            out = utils.check_output(['python', '-m',
+            out = utils.check_output([sys.executable, '-m',
                                      'cryptosite.setup'] + args,
                                      stderr=subprocess.STDOUT, retcode=2)
 

diff --git a/test/test_soap.py b/test/test_soap.py
@@ -35,7 +35,7 @@ def test_bad(self):
         for args in (['x'],):
             out = utils.check_output(['cryptosite', 'soap'] + args,
                                      stderr=subprocess.STDOUT, retcode=2)
-            out = utils.check_output(['python', '-m',
+            out = utils.check_output([sys.executable, '-m',
                                      'cryptosite.soap'] + args,
                                      stderr=subprocess.STDOUT, retcode=2)