Pull request for #26: Allow CL arguments to be passed (#46)

* #26 Adds CL argument capabilities

* #26 Small edit

* #26 Updates unit tests

* #26 Updates readme to note mock requirement

README.md

@@ -11,6 +11,8 @@ This repository contains the following GSLab Python libraries:
 
 Information about each of these packages is available in its internal documentation. 
 
+Note: In order to run the unit tests, `mock` (version 2.0.0 or higher) needs to be installed.
+
 Installation
 ------------
 To install this repository's Python libraries, run the `setup.py` script at its root

gslab_scons/builders/build_python.py

@@ -24,8 +24,9 @@ def build_python(target, source, env):
     target_dir  = os.path.dirname(target_file)
     misc.check_code_extension(source_file, 'python')
     log_file    = target_dir + '/sconscript.log'
+    cl_arg      = misc.command_line_arg(env)
 
-    os.system('python %s > %s' % (source_file, log_file))
+    os.system('python %s %s > %s' % (source_file, cl_arg, log_file))
 
     end_time   =  misc.current_time()    
     log_timestamp(start_time, end_time, log_file)

gslab_scons/builders/build_r.py

@@ -24,8 +24,11 @@ def build_r(target, source, env):
     target_dir  = os.path.dirname(target_file)
     misc.check_code_extension(source_file, 'r')
     log_file    = target_dir + '/sconscript.log'
-
-    os.system('R CMD BATCH --no-save %s %s' % (source_file, log_file))
+
+    cl_arg      = misc.command_line_arg(env)
+    if cl_arg != '':
+        cl_arg = "'--args %s'" % cl_arg
+    os.system("R CMD BATCH --no-save %s %s %s" % (cl_arg, source_file, log_file))
 
     end_time   =  misc.current_time()    
     log_timestamp(start_time, end_time, log_file)

gslab_scons/builders/build_stata.py

@@ -24,7 +24,8 @@ def build_stata(target, source, env):
     (By default, SCons will try to find each flavour). 
     '''
     start_time =  misc.current_time()
-
+    cl_arg     = misc.command_line_arg(env)
+
     source       = misc.make_list_if_string(source)
     target       = misc.make_list_if_string(target)
     source_file  = str(source[0])
@@ -38,15 +39,15 @@ def build_stata(target, source, env):
     user_flavor  = env['user_flavor']  
     if user_flavor is not None:
         if misc.is_unix():
-            command = misc.stata_command_unix(user_flavor)
+            command = misc.stata_command_unix(user_flavor, cl_arg)
         elif platform == 'win32':
-            command = misc.stata_command_win(user_flavor)
+            command = misc.stata_command_win(user_flavor, cl_arg)
     else:
         flavors = ['stata-mp', 'stata-se', 'stata']
         if misc.is_unix():
             for flavor in flavors:
                 if misc.is_in_path(flavor):
-                    command = misc.stata_command_unix(flavor)
+                    command = misc.stata_command_unix(flavor, cl_arg)
                     break
         elif platform == 'win32':
             try:
@@ -58,7 +59,7 @@ def build_stata(target, source, env):
                     flavors = [f.replace('.exe', '-64.exe') for f in flavors]
                 for flavor in flavors:
                     if misc.is_in_path(flavor):
-                        command = misc.stata_command_win(flavor)
+                        command = misc.stata_command_win(flavor, cl_arg)
                         break
 
     try:

gslab_scons/misc.py

@@ -20,8 +20,14 @@ def check_lfs():
             raise LFSError('''Either Git LFS is not installed or your Git LFS settings need to be updated. 
                   Please install Git LFS or run 'git lfs install --force' if prompted above.''')
 
+def command_line_arg(env):
+    try:
+        cl_arg = env['CL_ARG']
+    except KeyError:
+        cl_arg = ''
+    return cl_arg
 
-def stata_command_unix(flavor):
+def stata_command_unix(flavor, cl_arg):
     '''
     This function returns the appropriate Stata command for a user's 
     Unix platform.
@@ -30,16 +36,16 @@ def stata_command_unix(flavor):
                'linux' : '-b',
                'linux2': '-b'}
     option  = options[platform]
-    command = flavor + ' ' + option + ' %s ' # %s will take filename later
+    command = flavor + ' ' + option + ' %s ' + cl_arg # %s will take filename later
     return command
 
 
-def stata_command_win(flavor):
+def stata_command_win(flavor, cl_arg):
     '''
     This function returns the appropriate Stata command for a user's 
     Windows platform.
     '''
-    command  = flavor + ' /e do' + ' %s ' # %s will take filename later
+    command  = flavor + ' /e do' + ' %s ' + cl_arg # %s will take filename later
     return command
 
 

gslab_scons/tests/input/R_test_script.R

@@ -1,3 +1,6 @@
+args = commandArgs(trailingOnly = TRUE)
+cat(args[1])
+
 NCols=5
 NRows=5 
 x<-matrix(runif(NCols*NRows), ncol=NCols)

gslab_scons/tests/input/python_test_script.py

@@ -1,12 +1,13 @@
 #! /usr/bin/env python
-import argparse, pdb
+import sys
 
-parser = argparse.ArgumentParser()    
-parser.add_argument('-i', dest='input', nargs='+')
-args = parser.parse_args()
-
-if args.input:
-    message = args.input
+try:
+	arg = sys.argv[1]
+except:
+	arg = ''
+
+if arg != '':
+    message = arg
 else:
     message = 'Test Output \n'
 output_name = 'output.txt'

gslab_scons/tests/input/stata_test_script.do

@@ -6,7 +6,9 @@ preliminaries
 set obs 10
 gen var1 = _n
 
-save_data ../output/stata1.dta, key(var1) log(../output/data_file_manifest.log) replace
+di `1`
+
+save ../output/stata`1`.dta, replace
 save_data ../output/stata2.dta, key(var1) log(../output/data_file_manifest.log) replace
 save_data ../output/stata.csv, key(var1) outsheet log(../output/data_file_manifest.log) replace
 save_data ../output/stata.txt, key(var1) outsheet log(../output/data_file_manifest.log) replace

gslab_scons/tests/log/make.log

@@ -2,14 +2,17 @@ test_bad_extension (test_build_lyx.test_build_lyx)
 Test that build_lyx() recognises an inappropriate file extension ... ok
 test_default (test_build_lyx.test_build_lyx) ... ok
 test_bad_extension (test_build_python.testbuild_python) ... ok
+test_clarg (test_build_python.testbuild_python) ... ok
 test_default (test_build_python.testbuild_python) ... ok
 test_bad_extension (test_build_r.testbuild_r)
 Test that build_r() recognises an inappropriate file extension ... ok
+test_clarg (test_build_r.testbuild_r) ... ok
 test_default (test_build_r.testbuild_r) ... ok
 test_bad_extension (test_build_stata.testbuild_stata) ... ok
 test_bad_user_executable (test_build_stata.testbuild_stata) ... ok
+test_clarg (test_build_stata.testbuild_stata) ... ok
 test_default (test_build_stata.testbuild_stata) ... ok
-test_user_executable_unix (test_build_stata.testbuild_stata) ... skipped 'skipped test_user_executable_unix because on a windows machine'
+test_user_executable_unix (test_build_stata.testbuild_stata) ... ok
 test_default (test_build_tables.test_build_tables) ... ok
 test_default_string_target (test_build_tables.test_build_tables) ... ok
 test_target_extension (test_build_tables.test_build_tables)
@@ -20,11 +23,12 @@ test_start_log (test_log.test_log) ... ok
 test_check_code_extension (test_misc.test_misc)
 Unit tests for check_code_extension() ... ok
 test_check_lfs (test_misc.test_misc) ... ok
+test_command_line_arg (test_misc.test_misc) ... ok
 test_current_time (test_misc.test_misc)
 Test that current_time() prints times in the expected format ... ok
 test_is_64_windows (test_misc.test_misc) ... ok
-test_is_exe (test_misc.test_misc) ... skipped 'skipped test_is_exe because on a windows machine'
-test_is_in_path (test_misc.test_misc) ... skipped 'skipped test_is_in_path because on a windows machine'
+test_is_exe (test_misc.test_misc) ... ok
+test_is_in_path (test_misc.test_misc) ... ok
 test_is_unix (test_misc.test_misc) ... ok
 test_make_list_if_string (test_misc.test_misc) ... ok
 test_stata_command_unix (test_misc.test_misc) ... ok
@@ -40,6 +44,6 @@ test_upload_asset_bad_file (test_release_tools.TestReleaseTools) ... ok
 test_upload_asset_standard (test_release_tools.TestReleaseTools) ... ok
 
 ----------------------------------------------------------------------
-Ran 34 tests in 24.886s
+Ran 38 tests in 55.880s
 
-OK (skipped=4)
+OK (skipped=1)

gslab_scons/tests/test_build_python.py

@@ -16,15 +16,23 @@ def setUp(self):
             os.mkdir('../build/')
 
     def test_default(self):
-        env = ''
+        env = {}
         build_python('../build/py.py', './input/python_test_script.py', env)
         logfile_data = open('../build/sconscript.log', 'rU').read()
         self.assertIn('Log created:', logfile_data)
         if os.path.isfile('../build/sconscript.log'):
             os.remove('../build/sconscript.log')
-
+
+    def test_clarg(self):
+        env = {'CL_ARG' : 'COMMANDLINE'}
+        build_python('../build/py.py', './input/python_test_script.py', env)
+        logfile_data = open('output.txt', 'rU').read()
+        self.assertIn('COMMANDLINE', logfile_data)
+        if os.path.isfile('../build/sconscript.log'):
+            os.remove('../build/sconscript.log')
+
     def test_bad_extension(self):
-        env = ''
+        env = {}
         with self.assertRaises(BadExtensionError):
             build_python('../build/py.py', 
                          ['bad', './input/python_test_script.py'], 

gslab_scons/tests/test_build_r.py

@@ -21,16 +21,24 @@ def setUp(self):
             os.mkdir('../build/')
 
     def test_default(self):
-        env = ''
+        env = {}
         build_r('../build/r.rds', './input/R_test_script.R', env)
         logfile_data = open('../build/sconscript.log', 'rU').read()
         self.assertIn('Log created:', logfile_data)
         if os.path.isfile('../build/sconscript.log'):
             os.remove('../build/sconscript.log')
 
+    def test_clarg(self):
+        env = {'CL_ARG' : 'COMMANDLINE'}
+        build_r('../build/r.rds', './input/R_test_script.R', env)
+        logfile_data = open('../build/sconscript.log', 'rU').read()
+        self.assertIn('COMMANDLINE', logfile_data)
+        if os.path.isfile('../build/sconscript.log'):
+            os.remove('../build/sconscript.log')
+
     def test_bad_extension(self):
         '''Test that build_r() recognises an inappropriate file extension'''
-        env = ''
+        env = {}
         with self.assertRaises(BadExtensionError):
             build_r('../build/r.rds', ['bad', './input/R_test_script.R'], env)
 

gslab_scons/tests/test_build_stata.py

@@ -29,7 +29,15 @@ def test_default(self):
         self.assertIn('Log created:', logfile_data)
         if os.path.isfile('./build/sconscript.log'):
             os.remove('./build/sconscript.log')
-
+
+    def test_clarg(self):
+        env = {'user_flavor' : None, 'CL_ARG' : 'COMMANDLINE'}
+        build_stata('./build/stata.dta', './input/stata_test_script.do', env)
+        logfile_data = open('./build/sconscript.log', 'rU').read()
+        self.assertIn('COMMANDLINE', logfile_data)
+        if os.path.isfile('./build/sconscript.log'):
+            os.remove('./build/sconscript.log')
+
     @unittest.skipIf(sys.platform.startswith("win"), 
     "skipped test_user_executable_unix because on a windows machine")
     def test_user_executable_unix(self):

gslab_scons/tests/test_misc.py

@@ -22,25 +22,31 @@ def test_check_lfs(self):
     @unittest.skipIf(sys.platform.startswith("win"), 
         "skipped test_stata_command_unix because on a windows machine")
     def test_stata_command_unix(self):
-    	output = misc.stata_command_unix('flavor')
+        cl_arg = 'test'
+    	output = misc.stata_command_unix('flavor', cl_arg)
     	if sys.platform == 'darwin':
     		option = '-e'
     	else:
     		option = '-b'
-    	self.assertEqual(output, 'flavor %s' % (option) + ' %s ')
+    	self.assertEqual(output, 'flavor %s' % (option) + ' %s ' + cl_arg)
 
     @unittest.skipUnless(sys.platform.startswith("win"), 
         "skipped test_stata_command_win because on a unix machine")
     def test_stata_command_win(self):
-    	output = misc.stata_command_win('flavor')
-    	self.assertEqual(output, 'flavor %s' % ('/e do') + ' %s ')
+        cl_arg = 'test'
+    	output = misc.stata_command_win('flavor', cl_arg)
+    	self.assertEqual(output, 'flavor %s' % ('/e do') + ' %s ' + cl_arg)
 
     def test_is_unix(self):
     	self.assertEqual(misc.is_unix(), not sys.platform.startswith("win"))
 
     def test_is_64_windows(self):
     	pass
 
+    def test_command_line_arg(self):
+        self.assertEqual(misc.command_line_arg({'test' : ''}), '')
+        self.assertEqual(misc.command_line_arg({'CL_ARG' : 'Test'}), 'Test')
+
     @unittest.skipIf(sys.platform.startswith("win"), 
     "skipped test_is_in_path because on a windows machine")
     def test_is_in_path(self):