Merge branch 'master' of github.com:RNAer/burrito

.travis.yml

@@ -5,7 +5,7 @@ python:
   - "3.3"
   - "3.4"
 install:
-  - pip install nose pep8 flake8 coveralls
+  - pip install nose flake8 coveralls
   - pip install .
 script:
   - nosetests --with-coverage

CHANGELOG.md

@@ -1,6 +1,10 @@
 # burrito changelog
 
-## Version 0.9.0-dev (changes since 0.9.0 release go here)
+## Version 0.9.1-dev (changes since 0.9.1 go here)
+
+## Version 0.9.1 (2015-05-22)
+
+* Updated default temporary directory from ``/tmp`` to python's ``tempfile.gettempdir()``. This should address many of the issues with temporary files being written to ``/tmp``, which sometimes doesn't exist, doesn't provide a lot of storage, or is not shared across cluster nodes. It is still possible that individual burrito fillings (i.e., ``CommandLineApplication`` derived classes) can hard code ``/tmp``, so care should be taken when writing those derived classes to avoid that.
 
 ## Version 0.9.0 (2014-08-04)
 

burrito/__init__.py

@@ -6,4 +6,4 @@
 # The full license is in the file LICENSE, distributed with this software.
 # ----------------------------------------------------------------------------
 
-__version__ = "0.9.0-dev"
+__version__ = "0.9.1-dev"

burrito/tests/test_util.py

@@ -460,10 +460,11 @@ def test_base_command(self):
         # because parameters are printed in arbitrary order
         app.Parameters['-F'].on('junk.txt')
         app.Parameters['--duh'].on()
-        self.assertTrue(app.BaseCommand ==
-                        'cd "/tmp/"; /tmp/CLAppTester.py -F "junk.txt" --duh'
-                        or app.BaseCommand ==
-                        'cd "/tmp/"; /tmp/CLAppTester.py --duh -F "junk.txt"')
+        self.assertTrue(
+            app.BaseCommand ==
+            'cd "/tmp/"; /tmp/CLAppTester.py -F "junk.txt" --duh' or
+            app.BaseCommand ==
+            'cd "/tmp/"; /tmp/CLAppTester.py --duh -F "junk.txt"')
         # Space in _command
         app = CLAppTester_space_in_command()
         self.assertEqual(app.BaseCommand,
@@ -760,7 +761,7 @@ def test_TmpDir(self):
         self.assertEqual(app.InputHandler, '_input_as_string')
         assert not app.SuppressStderr
         # TmpDir is what we expect
-        self.assertEqual(app.TmpDir, '/tmp/tmp2')
+        self.assertEqual(app.TmpDir, '/tmp/tmp2/')
         # test_command
         self.assertEqual(app.BaseCommand,
                          'cd "/tmp/"; /tmp/CLAppTester.py -F "p_file.txt"')
@@ -788,7 +789,7 @@ def test_TmpDir_w_space(self):
         self.assertEqual(app.InputHandler, '_input_as_string')
         assert not app.SuppressStderr
         # TmpDir is what we expect
-        self.assertEqual(app.TmpDir, '/tmp/tmp space')
+        self.assertEqual(app.TmpDir, '/tmp/tmp space/')
         # test_command
         self.assertEqual(app.BaseCommand,
                          'cd "/tmp/"; /tmp/CLAppTester.py -F "p_file.txt"')
@@ -893,7 +894,7 @@ def test_getTmpFilename_non_default(self):
         """TmpFilename handles alt tmp_dir, prefix and suffix properly"""
         app = CLAppTester()
         obs = app.getTmpFilename(include_class_id=False)
-        self.assertTrue(obs.startswith('/tmp/tmp'))
+        self.assertTrue(obs.startswith(app.TmpDir + 'tmp'))
         self.assertTrue(obs.endswith('.txt'))
 
         obs = app.getTmpFilename(tmp_dir="/tmp/blah", prefix="app_ctl_test",
@@ -908,9 +909,9 @@ def test_getTmpFilename_defaults_to_no_class_id(self):
         # set the default to False if they change it for testing purposes
         app = CLAppTester()
         self.assertFalse(app.getTmpFilename().
-                         startswith('/tmp/tmpCLAppTester'))
+                         startswith(app.TmpDir + 'tmpCLAppTester'))
         self.assertTrue(app.getTmpFilename(include_class_id=True).
-                        startswith('/tmp/tmpCLAppTester'))
+                        startswith(app.TmpDir + 'tmpCLAppTester'))
 
     def test_input_as_path(self):
         """CLAppTester: _input_as_path casts data to FilePath"""
@@ -991,33 +992,33 @@ def test_getTmpFilename(self):
         obs = app.getTmpFilename(include_class_id=True)
         # leaving the strings in this statement so it's clear where the
         # expected length comes from
-        self.assertEqual(len(obs), len(app.TmpDir) + len('/') + app.TmpNameLen
-                         + len('tmp') + len('CLAppTester') + len('.txt'))
+        self.assertEqual(len(obs), len(app.TmpDir) + app.TmpNameLen +
+                         len('tmp') + len('CLAppTester') + len('.txt'))
         assert obs.startswith(app.TmpDir)
         chars = set(obs[18:])
         assert len(chars) > 1
 
         obs = app.getTmpFilename(include_class_id=False)
         # leaving the strings in this statement so it's clear where the
         # expected length comes from
-        self.assertEqual(len(obs), len(app.TmpDir) + len('/') + app.TmpNameLen
-                         + len('tmp') + len('.txt'))
+        self.assertEqual(len(obs), len(app.TmpDir) + app.TmpNameLen +
+                         len('tmp') + len('.txt'))
         assert obs.startswith(app.TmpDir)
 
     def test_getTmpFilename_prefix_suffix_result_constructor(self):
         """TmpFilename: result has correct prefix, suffix, type"""
         app = CLAppTester()
         obs = app.getTmpFilename(prefix='blah', include_class_id=False)
-        self.assertTrue(obs.startswith('/tmp/blah'))
+        self.assertTrue(obs.startswith(app.TmpDir + 'blah'))
         obs = app.getTmpFilename(suffix='.blah', include_class_id=False)
         self.assertTrue(obs.endswith('.blah'))
         # Prefix defaults to not include the class name
         obs = app.getTmpFilename(include_class_id=False)
-        self.assertFalse(obs.startswith('/tmp/tmpCLAppTester'))
+        self.assertFalse(obs.startswith(app.TmpDir + 'tmpCLAppTester'))
         self.assertTrue(obs.endswith('.txt'))
         # including class id functions correctly
         obs = app.getTmpFilename(include_class_id=True)
-        self.assertTrue(obs.startswith('/tmp/tmpCLAppTester'))
+        self.assertTrue(obs.startswith(app.TmpDir + 'tmpCLAppTester'))
         self.assertTrue(obs.endswith('.txt'))
 
         # result as FilePath
@@ -1064,8 +1065,8 @@ def test_get_tmp_filename(self):
         # leaving the strings in this statement so it's clear where the
         # expected length comes from
         self.assertEqual(len(obs),
-                         len(self.tmp_dir) + len('/') + self.tmp_name_len
-                         + len('tmp') + len('.txt'))
+                         len(self.tmp_dir) + len('/') + self.tmp_name_len +
+                         len('tmp') + len('.txt'))
         self.assertTrue(obs.startswith(self.tmp_dir))
 
         # different results on different calls
@@ -1075,8 +1076,8 @@ def test_get_tmp_filename(self):
         # leaving the strings in this statement so it's clear where the
         # expected length comes from
         self.assertEqual(len(obs),
-                         len(self.tmp_dir) + len('/') + self.tmp_name_len
-                         + len('tmp') + len('.txt'))
+                         len(self.tmp_dir) + len('/') + self.tmp_name_len +
+                         len('tmp') + len('.txt'))
         assert obs.startswith(self.tmp_dir)
 
     def test_get_tmp_filename_prefix_suffix_constructor(self):

burrito/util.py

@@ -169,7 +169,7 @@ class CommandLineApplication(Application):
     _working_dir = None
 
     def __init__(self, params=None, InputHandler=None, SuppressStderr=None,
-                 SuppressStdout=None, WorkingDir=None, TmpDir='/tmp',
+                 SuppressStdout=None, WorkingDir=None, TmpDir=gettempdir(),
                  TmpNameLen=20, HALT_EXEC=False):
         """ Initialize the CommandLineApplication object
 
@@ -192,8 +192,7 @@ def __init__(self, params=None, InputHandler=None, SuppressStderr=None,
                 running the script doesn't have write access to the current
                 working directory
                 WARNING: WorkingDir MUST be an absolute path!
-            TmpDir: the directory where temp files will be created, /tmp
-                by default
+            TmpDir: the directory where temp files will be created
             TmpNameLen: the length of the temp file name
             HALT_EXEC: if True, raises exception w/ command output just
             before execution, doesn't clean up temp files. Default False.
@@ -219,6 +218,8 @@ def __init__(self, params=None, InputHandler=None, SuppressStderr=None,
         else:
             working_dir = self._working_dir or getcwd()
         self.WorkingDir = FilePath(working_dir)
+        if not TmpDir.endswith("/"):
+            TmpDir += "/"
         self.TmpDir = FilePath(TmpDir)
         self.TmpNameLen = TmpNameLen
         self.HaltExec = HALT_EXEC
@@ -496,11 +497,11 @@ def _get_result_paths(self, data):
         """
         return {}
 
-    def getTmpFilename(self, tmp_dir="/tmp", prefix='tmp', suffix='.txt',
+    def getTmpFilename(self, tmp_dir=None, prefix='tmp', suffix='.txt',
                        include_class_id=False, result_constructor=FilePath):
         """ Return a temp filename
 
-            tmp_dir: path for temp file
+            tmp_dir: directory where temporary files will be stored
             prefix: text to append to start of file name
             suffix: text to append to end of file name
             include_class_id: if True, will append a class identifier (built
@@ -746,14 +747,13 @@ def get_tmp_filename(tmp_dir=gettempdir(), prefix="tmp", suffix=".txt",
                      result_constructor=FilePath):
     """ Generate a temporary filename and return as a FilePath object
 
-        tmp_dir: the directory to house the tmp_filename (default: '/tmp')
-        prefix: string to append to beginning of filename (default: 'tmp')
+        tmp_dir: the directory to house the tmp_filename
+        prefix: string to append to beginning of filename
             Note: It is very useful to have prefix be descriptive of the
             process which is creating the temporary file. For example, if
             your temp file will be used to build a temporary blast database,
             you might pass prefix=TempBlastDB
         suffix: the suffix to be appended to the temp filename
-            (default '.txt')
         result_constructor: the constructor used to build the result filename
             (default: cogent.app.parameters.FilePath). Note that joining
             FilePath objects with one another or with strings, you must use

setup.py

@@ -8,10 +8,10 @@
 # The full license is in the file LICENSE, distributed with this software.
 # ----------------------------------------------------------------------------
 
-__version__ = "0.9.0-dev"
-
 from setuptools import find_packages, setup
 
+__version__ = "0.9.1-dev"
+
 classes = """
     Development Status :: 5 - Production/Stable
     Intended Audience :: Developers
@@ -50,6 +50,6 @@
       test_suite='nose.collector',
       packages=find_packages(),
       install_requires=['future'],
-      extras_require={'test': ["nose >= 0.10.1", "pep8", "flake8",
+      extras_require={'test': ["nose >= 0.10.1", "flake8",
                                "coveralls"]},
       classifiers=classifiers)