From: Ananthu C V Date: Sun, 8 Mar 2026 11:17:36 +0100 Subject: use raw strings to avoid syntax warnings Last-Update: 2024-12-05 --- doc/conf.py | 2 +- ruffus/cmdline.py | 6 ++--- ruffus/combinatorics.py | 2 +- ruffus/parse_old_style_ruffus.py | 6 ++--- ruffus/proxy_logger.py | 4 ++-- ruffus/ruffus_utility.py | 2 +- ruffus/test/test_combinatorics.py | 28 +++++++++++------------ ruffus/test/test_file_name_parameters.py | 14 ++++++------ ruffus/test/test_newstyle_combinatorics.py | 28 +++++++++++------------ ruffus/test/test_newstyle_regex_error_messages.py | 20 ++++++++-------- ruffus/test/test_regex_error_messages.py | 20 ++++++++-------- ruffus/test/test_ruffus_utility.py | 2 +- 12 files changed, 67 insertions(+), 67 deletions(-) diff --git a/doc/conf.py b/doc/conf.py index 0b9cea2..37bf632 100644 --- a/doc/conf.py +++ b/doc/conf.py @@ -65,7 +65,7 @@ copyright = u'2009-2019 cgat-developers' version=ruffus.ruffus_version.__version #major.minor[.patch[.sub]] # The full version, without betaincluding alpha/beta/rc tags. import re -release = re.subn("([\d\.]+).*", r"\1", version)[0] +release = re.subn(r"([\d\.]+).*", r"\1", version)[0] print(version, release) diff --git a/ruffus/cmdline.py b/ruffus/cmdline.py index 46d39bc..6928035 100644 --- a/ruffus/cmdline.py +++ b/ruffus/cmdline.py @@ -665,7 +665,7 @@ def get_extra_options_appropriate_for_command(appropriate_option_names, extra_op # _________________________________________________________________________________________ def handle_verbose(options): - """ + r""" raw options.verbose is a list of specifiers '+' : i.e. --verbose. This just increases the current verbosity value by 1 '\d+' : e.g. --verbose 6. This (re)sets the verbosity value @@ -704,8 +704,8 @@ def handle_verbose(options): # # Each verbosity specifier can be # '+' : i.e. --verbose. This just increases the current verbosity value by 1 - # '\d+' : e.g. --verbose 6. This (re)sets the verbosity value - # '\d+:\d+' : e.g. --verbose 7:-5 The second number is the verbose_abbreviated_path + # r'\d+' : e.g. --verbose 6. This (re)sets the verbosity value + # r'\d+:\d+' : e.g. --verbose 7:-5 The second number is the verbose_abbreviated_path # for vv in options.verbose: mm = match_regex.match(vv) diff --git a/ruffus/combinatorics.py b/ruffus/combinatorics.py index 2aeed35..b2f2826 100644 --- a/ruffus/combinatorics.py +++ b/ruffus/combinatorics.py @@ -23,7 +23,7 @@ # OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN # THE SOFTWARE. ################################################################################# -""" +r""" ******************************************** :mod:`ruffus.combinatorics` -- Overview diff --git a/ruffus/parse_old_style_ruffus.py b/ruffus/parse_old_style_ruffus.py index 8559c72..6ad84b8 100755 --- a/ruffus/parse_old_style_ruffus.py +++ b/ruffus/parse_old_style_ruffus.py @@ -175,7 +175,7 @@ if __name__ == '__main__': # 88888888888888888888888888888888888888888888888888888888888888888888888888888888888888888 -func_re = re.compile("^\s*def.*\(") +func_re = re.compile(r"^\s*def.*\(") def get_decorators(line_num, decorated_lines, all_lines): @@ -192,8 +192,8 @@ def get_decorators(line_num, decorated_lines, all_lines): raise Exception("Unterminated decorators %s" % (decorated_lines,)) -decorator_re = re.compile("^\s*@") -no_white_space_re = re.compile("^[^#\s]") +decorator_re = re.compile(r"^\s*@") +no_white_space_re = re.compile(r"^[^#\s]") if __name__ == '__main__': line_num = 1 last_decorated_line_num = 1 diff --git a/ruffus/proxy_logger.py b/ruffus/proxy_logger.py index 539ed9f..0b4830a 100644 --- a/ruffus/proxy_logger.py +++ b/ruffus/proxy_logger.py @@ -23,7 +23,7 @@ # OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN # THE SOFTWARE. ################################################################################# -""" +r""" **************************************************************************** Create proxy for logging for use with multiprocessing **************************************************************************** @@ -320,7 +320,7 @@ class LoggingManager(multiprocessing.managers.SyncManager): def make_shared_logger_and_proxy(logger_factory, logger_name, args): - """ + r""" Make a `logging `_ object called "\ ``logger_name``\ " by calling ``logger_factory``\ (``args``\ ) diff --git a/ruffus/ruffus_utility.py b/ruffus/ruffus_utility.py index 168c196..30c8af9 100644 --- a/ruffus/ruffus_utility.py +++ b/ruffus/ruffus_utility.py @@ -499,7 +499,7 @@ def regex_matches_as_dict(test_str, compiled_regex): # # _________________________________________________________________________________________ def path_decomposition_regex_match(test_str, compiled_regex): - """ + r""" Returns a dictionary identifying the components of a file path. This includes both the components of a path: diff --git a/ruffus/test/test_combinatorics.py b/ruffus/test/test_combinatorics.py index 6b3e198..ef3245c 100755 --- a/ruffus/test/test_combinatorics.py +++ b/ruffus/test/test_combinatorics.py @@ -385,10 +385,10 @@ class TestCombinatorics(unittest.TestCase): pipeline_printout(s, [check_product_merged_task], verbose=5, wrap_width=10000, pipeline="main") self.assertTrue(re.search('Job needs update:.*Missing files.*' - '\[.*{tempdir}/a_name.tmp1, ' + r'\[.*{tempdir}/a_name.tmp1, ' '.*{tempdir}/e_name.tmp1, ' '.*{tempdir}/h_name.tmp1, ' - '.*{tempdir}/a_name.e_name.h_name.tmp2\]'.format(tempdir=tempdir), s.getvalue(), re.DOTALL)) + r'.*{tempdir}/a_name.e_name.h_name.tmp2\]'.format(tempdir=tempdir), s.getvalue(), re.DOTALL)) def test_product_run(self): """Run product""" @@ -460,9 +460,9 @@ class TestCombinatorics(unittest.TestCase): pipeline_printout(s, [check_combinations2_merged_task], verbose=5, wrap_width=10000, pipeline="main") self.assertTrue(re.search('Job needs update:.*Missing files.*' - '\[.*{tempdir}/a_name.tmp1, ' + r'\[.*{tempdir}/a_name.tmp1, ' '.*{tempdir}/b_name.tmp1, ' - '.*{tempdir}/a_name.b_name.tmp2\]'.format(tempdir=tempdir), s.getvalue(), re.DOTALL)) + r'.*{tempdir}/a_name.b_name.tmp2\]'.format(tempdir=tempdir), s.getvalue(), re.DOTALL)) def test_combinations2_run(self): """Run product""" @@ -486,10 +486,10 @@ class TestCombinatorics(unittest.TestCase): pipeline_printout(s, [check_combinations3_merged_task], verbose=5, wrap_width=10000, pipeline="main") self.assertTrue(re.search( - '\[.*{tempdir}/a_name.tmp1, ' + r'\[.*{tempdir}/a_name.tmp1, ' '.*{tempdir}/b_name.tmp1, ' '.*{tempdir}/c_name.tmp1, ' - '.*{tempdir}/a_name.b_name.c_name.tmp2\]'.format(tempdir=tempdir), s.getvalue())) + r'.*{tempdir}/a_name.b_name.c_name.tmp2\]'.format(tempdir=tempdir), s.getvalue())) def test_combinations3_run(self): """Run product""" @@ -513,9 +513,9 @@ class TestCombinatorics(unittest.TestCase): s = StringIO() pipeline_printout(s, [check_permutations2_merged_task], verbose=5, wrap_width=10000, pipeline="main") - self.assertTrue(re.search('\[.*{tempdir}/a_name.tmp1, ' + self.assertTrue(re.search(r'\[.*{tempdir}/a_name.tmp1, ' '.*{tempdir}/b_name.tmp1, ' - '.*{tempdir}/a_name.b_name.tmp2\]'.format(tempdir=tempdir), s.getvalue())) + r'.*{tempdir}/a_name.b_name.tmp2\]'.format(tempdir=tempdir), s.getvalue())) def test_permutations2_run(self): """Run product""" @@ -538,10 +538,10 @@ class TestCombinatorics(unittest.TestCase): s = StringIO() pipeline_printout(s, [check_permutations3_merged_task], verbose=5, wrap_width=10000, pipeline="main") - self.assertTrue(re.search('\[.*{tempdir}/a_name.tmp1, ' + self.assertTrue(re.search(r'\[.*{tempdir}/a_name.tmp1, ' '.*{tempdir}/b_name.tmp1, ' '.*{tempdir}/c_name.tmp1, ' - '.*{tempdir}/a_name.b_name.c_name.tmp2\]'.format(tempdir=tempdir), s.getvalue())) + r'.*{tempdir}/a_name.b_name.c_name.tmp2\]'.format(tempdir=tempdir), s.getvalue())) def test_permutations3_run(self): """Run product""" @@ -565,9 +565,9 @@ class TestCombinatorics(unittest.TestCase): s = StringIO() pipeline_printout(s, [check_combinations_with_replacement2_merged_task], verbose=5, wrap_width=10000, pipeline="main") - self.assertTrue(re.search('\[.*{tempdir}/a_name.tmp1, ' + self.assertTrue(re.search(r'\[.*{tempdir}/a_name.tmp1, ' '.*{tempdir}/b_name.tmp1, ' - '.*{tempdir}/a_name.b_name.tmp2\]'.format(tempdir=tempdir), s.getvalue())) + r'.*{tempdir}/a_name.b_name.tmp2\]'.format(tempdir=tempdir), s.getvalue())) def test_combinations_with_replacement2_run(self): """Run product""" @@ -590,10 +590,10 @@ class TestCombinatorics(unittest.TestCase): s = StringIO() pipeline_printout(s, [check_combinations_with_replacement3_merged_task], verbose=5, wrap_width=10000, pipeline="main") - self.assertTrue(re.search('\[.*{tempdir}/a_name.tmp1, ' + self.assertTrue(re.search(r'\[.*{tempdir}/a_name.tmp1, ' '.*{tempdir}/b_name.tmp1, ' '.*{tempdir}/c_name.tmp1, ' - '.*{tempdir}/a_name.b_name.c_name.tmp2\]'.format(tempdir=tempdir), s.getvalue())) + r'.*{tempdir}/a_name.b_name.c_name.tmp2\]'.format(tempdir=tempdir), s.getvalue())) def test_combinations_with_replacement3_run(self): """Run product""" diff --git a/ruffus/test/test_file_name_parameters.py b/ruffus/test/test_file_name_parameters.py index e805a6a..22cf06a 100755 --- a/ruffus/test/test_file_name_parameters.py +++ b/ruffus/test/test_file_name_parameters.py @@ -797,7 +797,7 @@ class Test_transform_param_factory(unittest.TestCase): # simple 1 input, 1 output # unnamed_args = [tempdir + "/*.test", - task.formatter("/(?P\w+).test$"), + task.formatter(r"/(?P\w+).test$"), ["{path[0]}/{name[0]}.output1{ext[0]}", "{path[0]}/{name[0]}.output2"], "{path[0]}/{name[0]}.output3"] expected_results = [ ('DIR/f0.test', ['DIR/f0.output1.test', @@ -1589,9 +1589,9 @@ class Test_product_param_factory(unittest.TestCase): # simple 1 input, 1 output # args = [[tempdir + "/a.test1", tempdir + "/b.test1"], - task.formatter("(?:.+/)?(?P\w+)\.(.+)"), + task.formatter(r"(?:.+/)?(?P\w+)\.(.+)"), [tempdir + "/c.test2", tempdir + "/d.test2", tempdir + "/e.ignore"], - task.formatter("(?:.+/)?(?P\w+)\.(test2)"), + task.formatter(r"(?:.+/)?(?P\w+)\.(test2)"), r"{path[0][0]}/{ID[0][0]}.{1[1][0]}.output"] expected_result = [ (('DIR/a.test1', 'DIR/c.test2'), 'DIR/a.c.output'), @@ -1630,9 +1630,9 @@ class Test_product_param_factory(unittest.TestCase): # (replace) inputs # # - paths = self.do_task_product([tempdir + "/a.test1", tempdir + "/b.test1"], task.formatter("(?:.+/)?(?P\w+)\.(.+)"), + paths = self.do_task_product([tempdir + "/a.test1", tempdir + "/b.test1"], task.formatter(r"(?:.+/)?(?P\w+)\.(.+)"), [tempdir + "/c.test2", tempdir + "/d.test2", tempdir + - "/e.ignore"], task.formatter("(?:.+/)?(?P\w+)\.(test2)"), + "/e.ignore"], task.formatter(r"(?:.+/)?(?P\w+)\.(test2)"), task.inputs( ("{path[0][0]}/{basename[0][0]}.testwhat1", "{path[1][0]}/{basename[1][0]}.testwhat2")), r"{path[0][0]}/{ID[0][0]}.{1[1][0]}.output") @@ -1649,9 +1649,9 @@ class Test_product_param_factory(unittest.TestCase): # add inputs # # - paths = self.do_task_product([tempdir + "/a.test1", tempdir + "/b.test1"], task.formatter("(?:.+/)?(?P\w+)\.(.+)"), + paths = self.do_task_product([tempdir + "/a.test1", tempdir + "/b.test1"], task.formatter(r"(?:.+/)?(?P\w+)\.(.+)"), [tempdir + "/c.test2", tempdir + "/d.test2", tempdir + - "/e.ignore"], task.formatter("(?:.+/)?(?P\w+)\.(test2)"), + "/e.ignore"], task.formatter(r"(?:.+/)?(?P\w+)\.(test2)"), add_inputs( "{path[0][0]}/{basename[0][0]}.testwhat1", "{path[1][0]}/{basename[1][0]}.testwhat2", ), r"{path[0][0]}/{ID[0][0]}.{1[1][0]}.output") diff --git a/ruffus/test/test_newstyle_combinatorics.py b/ruffus/test/test_newstyle_combinatorics.py index 35af678..713e92a 100755 --- a/ruffus/test/test_newstyle_combinatorics.py +++ b/ruffus/test/test_newstyle_combinatorics.py @@ -397,10 +397,10 @@ class TestCombinatorics(unittest.TestCase): test_pipeline2.printout( s, [check_product_merged_task], verbose=5, wrap_width=10000) self.assertTrue(re.search('Job needs update:.*Missing files.*' - '\[.*{tempdir}/a_name.tmp1, ' + r'\[.*{tempdir}/a_name.tmp1, ' '.*{tempdir}/e_name.tmp1, ' '.*{tempdir}/h_name.tmp1, ' - '.*{tempdir}/a_name.e_name.h_name.tmp2\]'.format(tempdir=tempdir), s.getvalue(), re.DOTALL)) + r'.*{tempdir}/a_name.e_name.h_name.tmp2\]'.format(tempdir=tempdir), s.getvalue(), re.DOTALL)) def test_product_run(self): """Run product""" @@ -471,9 +471,9 @@ class TestCombinatorics(unittest.TestCase): test_pipeline1.printout( s, [check_combinations2_merged_task], verbose=5, wrap_width=10000) self.assertTrue(re.search('Job needs update:.*Missing files.*' - '\[.*{tempdir}/a_name.tmp1, ' + r'\[.*{tempdir}/a_name.tmp1, ' '.*{tempdir}/b_name.tmp1, ' - '.*{tempdir}/a_name.b_name.tmp2\]'.format(tempdir=tempdir), s.getvalue(), re.DOTALL)) + r'.*{tempdir}/a_name.b_name.tmp2\]'.format(tempdir=tempdir), s.getvalue(), re.DOTALL)) def test_combinations2_run(self): """Run product""" @@ -497,10 +497,10 @@ class TestCombinatorics(unittest.TestCase): test_pipeline2.printout( s, [check_combinations3_merged_task], verbose=5, wrap_width=10000) self.assertTrue(re.search( - '\[.*{tempdir}/a_name.tmp1, ' + r'\[.*{tempdir}/a_name.tmp1, ' '.*{tempdir}/b_name.tmp1, ' '.*{tempdir}/c_name.tmp1, ' - '.*{tempdir}/a_name.b_name.c_name.tmp2\]'.format(tempdir=tempdir), s.getvalue())) + r'.*{tempdir}/a_name.b_name.c_name.tmp2\]'.format(tempdir=tempdir), s.getvalue())) def test_combinations3_run(self): """Run product""" @@ -524,9 +524,9 @@ class TestCombinatorics(unittest.TestCase): s = StringIO() test_pipeline2.printout( s, [check_permutations2_merged_task], verbose=5, wrap_width=10000) - self.assertTrue(re.search('\[.*{tempdir}/a_name.tmp1, ' + self.assertTrue(re.search(r'\[.*{tempdir}/a_name.tmp1, ' '.*{tempdir}/b_name.tmp1, ' - '.*{tempdir}/a_name.b_name.tmp2\]'.format(tempdir=tempdir), s.getvalue())) + r'.*{tempdir}/a_name.b_name.tmp2\]'.format(tempdir=tempdir), s.getvalue())) def test_permutations2_run(self): """Run product""" @@ -549,10 +549,10 @@ class TestCombinatorics(unittest.TestCase): s = StringIO() test_pipeline2.printout( s, [check_permutations3_merged_task], verbose=5, wrap_width=10000) - self.assertTrue(re.search('\[.*{tempdir}/a_name.tmp1, ' + self.assertTrue(re.search(r'\[.*{tempdir}/a_name.tmp1, ' '.*{tempdir}/b_name.tmp1, ' '.*{tempdir}/c_name.tmp1, ' - '.*{tempdir}/a_name.b_name.c_name.tmp2\]'.format(tempdir=tempdir), s.getvalue())) + r'.*{tempdir}/a_name.b_name.c_name.tmp2\]'.format(tempdir=tempdir), s.getvalue())) def test_permutations3_run(self): """Run product""" @@ -576,9 +576,9 @@ class TestCombinatorics(unittest.TestCase): s = StringIO() test_pipeline2.printout( s, [check_combinations_with_replacement2_merged_task], verbose=5, wrap_width=10000) - self.assertTrue(re.search('\[.*{tempdir}/a_name.tmp1, ' + self.assertTrue(re.search(r'\[.*{tempdir}/a_name.tmp1, ' '.*{tempdir}/b_name.tmp1, ' - '.*{tempdir}/a_name.b_name.tmp2\]'.format(tempdir=tempdir), s.getvalue())) + r'.*{tempdir}/a_name.b_name.tmp2\]'.format(tempdir=tempdir), s.getvalue())) def test_combinations_with_replacement2_run(self): """Run product""" @@ -601,10 +601,10 @@ class TestCombinatorics(unittest.TestCase): s = StringIO() test_pipeline2.printout( s, [check_combinations_with_replacement3_merged_task], verbose=5, wrap_width=10000) - self.assertTrue(re.search('\[.*{tempdir}/a_name.tmp1, ' + self.assertTrue(re.search(r'\[.*{tempdir}/a_name.tmp1, ' '.*{tempdir}/b_name.tmp1, ' '.*{tempdir}/c_name.tmp1, ' - '.*{tempdir}/a_name.b_name.c_name.tmp2\]'.format(tempdir=tempdir), s.getvalue())) + r'.*{tempdir}/a_name.b_name.c_name.tmp2\]'.format(tempdir=tempdir), s.getvalue())) def test_combinations_with_replacement3_run(self): """Run product""" diff --git a/ruffus/test/test_newstyle_regex_error_messages.py b/ruffus/test/test_newstyle_regex_error_messages.py index a10cfa7..b1e7446 100755 --- a/ruffus/test/test_newstyle_regex_error_messages.py +++ b/ruffus/test/test_newstyle_regex_error_messages.py @@ -307,7 +307,7 @@ class Test_regex_error_messages(unittest.TestCase): test_pipeline.printout(s, [check_regex_task], verbose=5, wrap_width=10000) self.assertTrue(re.search( - 'Missing files.*\[{tempdir}/a_name.tmp1, {tempdir}/a_name.tmp2'.format(tempdir=tempdir), s.getvalue(), re.DOTALL)) + r'Missing files.*\[{tempdir}/a_name.tmp1, {tempdir}/a_name.tmp2'.format(tempdir=tempdir), s.getvalue(), re.DOTALL)) def test_regex_run(self): """Run transform(...,regex()...)""" @@ -349,7 +349,7 @@ class Test_regex_error_messages(unittest.TestCase): test_pipeline.printout( s, [check_suffix_task], verbose=5, wrap_width=10000) self.assertTrue(re.search( - 'Missing files.*\[{tempdir}/a_name.tmp1, {tempdir}/a_name.tmp2'.format(tempdir=tempdir), s.getvalue(), re.DOTALL)) + r'Missing files.*\[{tempdir}/a_name.tmp1, {tempdir}/a_name.tmp2'.format(tempdir=tempdir), s.getvalue(), re.DOTALL)) def test_suffix_run(self): """Run transform(...,suffix()...)""" @@ -367,12 +367,12 @@ class Test_regex_error_messages(unittest.TestCase): cleanup_tmpdir() s = StringIO() self.assertRaisesRegex(fatal_error_input_file_does_not_match, - "File '.*?' does not match regex\('.*?'\) and pattern '.*?':\n.*invalid group reference", + r"File '.*?' does not match regex\('.*?'\) and pattern '.*?':\n.*invalid group reference", pipeline_printout, s, [check_suffix_unmatched_task], verbose=3) self.assertRaisesRegex(RethrownJobError, - "File '.*?' does not match regex\('.*?'\) and pattern '.*?':\n.*invalid group reference", + r"File '.*?' does not match regex\('.*?'\) and pattern '.*?':\n.*invalid group reference", test_pipeline.run, [check_suffix_unmatched_task], verbose=0, multiprocess=parallelism) @@ -406,12 +406,12 @@ class Test_regex_error_messages(unittest.TestCase): cleanup_tmpdir() s = StringIO() self.assertRaisesRegex(fatal_error_input_file_does_not_match, - "File '.*?' does not match regex\('.*?'\) and pattern '.*?':\n.*unknown group name", + r"File '.*?' does not match regex\('.*?'\) and pattern '.*?':\n.*unknown group name", test_pipeline.printout, s, [check_regex_misspelt_capture_error_task], verbose=3) self.assertRaisesRegex(RethrownJobError, - "File '.*?' does not match regex\('.*?'\) and pattern '.*?':\n.*unknown group name", + r"File '.*?' does not match regex\('.*?'\) and pattern '.*?':\n.*unknown group name", test_pipeline.run, [check_regex_misspelt_capture_error_task], verbose=0) @@ -423,12 +423,12 @@ class Test_regex_error_messages(unittest.TestCase): cleanup_tmpdir() s = StringIO() self.assertRaisesRegex(fatal_error_input_file_does_not_match, - "File '.*?' does not match regex\('.*?'\) and pattern '.*?':\n.*unknown group name", + r"File '.*?' does not match regex\('.*?'\) and pattern '.*?':\n.*unknown group name", test_pipeline.printout, s, [check_regex_misspelt_capture2_error_task], verbose=3) self.assertRaisesRegex(RethrownJobError, - "File '.*?' does not match regex\('.*?'\) and pattern '.*?':\n.*unknown group name", + r"File '.*?' does not match regex\('.*?'\) and pattern '.*?':\n.*unknown group name", test_pipeline.run, [check_regex_misspelt_capture2_error_task], verbose=0, multiprocess=parallelism) @@ -441,12 +441,12 @@ class Test_regex_error_messages(unittest.TestCase): cleanup_tmpdir() s = StringIO() self.assertRaisesRegex(fatal_error_input_file_does_not_match, - "File '.*?' does not match regex\('.*?'\) and pattern '.*?':\n.*invalid group reference", + r"File '.*?' does not match regex\('.*?'\) and pattern '.*?':\n.*invalid group reference", test_pipeline.printout, s, [check_regex_out_of_range_regex_reference_error_task], verbose=3) self.assertRaisesRegex(RethrownJobError, - "File '.*?' does not match regex\('.*?'\) and pattern '.*?':\n.*invalid group reference", + r"File '.*?' does not match regex\('.*?'\) and pattern '.*?':\n.*invalid group reference", test_pipeline.run, [check_regex_out_of_range_regex_reference_error_task], verbose=0, multiprocess=parallelism) diff --git a/ruffus/test/test_regex_error_messages.py b/ruffus/test/test_regex_error_messages.py index b744aae..012e896 100755 --- a/ruffus/test/test_regex_error_messages.py +++ b/ruffus/test/test_regex_error_messages.py @@ -299,7 +299,7 @@ class Test_regex_error_messages(unittest.TestCase): pipeline_printout(s, [check_regex_task], verbose=5, wrap_width=10000, pipeline="main") self.assertTrue(re.search( - 'Missing files.*\[{tempdir}a_name.tmp1, {tempdir}a_name.tmp2'.format(tempdir=tempdir), s.getvalue(), re.DOTALL)) + r'Missing files.*\[{tempdir}a_name.tmp1, {tempdir}a_name.tmp2'.format(tempdir=tempdir), s.getvalue(), re.DOTALL)) def test_regex_run(self): """Run transform(...,regex()...)""" @@ -341,7 +341,7 @@ class Test_regex_error_messages(unittest.TestCase): pipeline_printout(s, [check_suffix_task], verbose=5, wrap_width=10000, pipeline="main") self.assertTrue(re.search( - 'Missing files.*\[{tempdir}a_name.tmp1, {tempdir}a_name.tmp2'.format(tempdir=tempdir), s.getvalue(), re.DOTALL)) + r'Missing files.*\[{tempdir}a_name.tmp1, {tempdir}a_name.tmp2'.format(tempdir=tempdir), s.getvalue(), re.DOTALL)) def test_suffix_run(self): """Run transform(...,suffix()...)""" @@ -359,12 +359,12 @@ class Test_regex_error_messages(unittest.TestCase): cleanup_tmpdir() s = StringIO() self.assertRaisesRegex(fatal_error_input_file_does_not_match, - "File '.*?' does not match regex\('.*?'\) and pattern '.*?':\n.*invalid group reference", + r"File '.*?' does not match regex\('.*?'\) and pattern '.*?':\n.*invalid group reference", pipeline_printout, s, [check_suffix_unmatched_task], verbose=3) self.assertRaisesRegex(RethrownJobError, - "File '.*?' does not match regex\('.*?'\) and pattern '.*?':\n.*invalid group reference", + r"File '.*?' does not match regex\('.*?'\) and pattern '.*?':\n.*invalid group reference", pipeline_run, [check_suffix_unmatched_task], verbose=0, multiprocess=parallelism) @@ -398,12 +398,12 @@ class Test_regex_error_messages(unittest.TestCase): cleanup_tmpdir() s = StringIO() self.assertRaisesRegex(fatal_error_input_file_does_not_match, - "File '.*?' does not match regex\('.*?'\) and pattern '.*?':\n.*unknown group name", + r"File '.*?' does not match regex\('.*?'\) and pattern '.*?':\n.*unknown group name", pipeline_printout, s, [check_regex_misspelt_capture_error_task], verbose=3) self.assertRaisesRegex(RethrownJobError, - "File '.*?' does not match regex\('.*?'\) and pattern '.*?':\n.*unknown group name", + r"File '.*?' does not match regex\('.*?'\) and pattern '.*?':\n.*unknown group name", pipeline_run, [check_regex_misspelt_capture_error_task], verbose=0) @@ -415,12 +415,12 @@ class Test_regex_error_messages(unittest.TestCase): cleanup_tmpdir() s = StringIO() self.assertRaisesRegex(fatal_error_input_file_does_not_match, - "File '.*?' does not match regex\('.*?'\) and pattern '.*?':\n.*unknown group name", + r"File '.*?' does not match regex\('.*?'\) and pattern '.*?':\n.*unknown group name", pipeline_printout, s, [check_regex_misspelt_capture2_error_task], verbose=3) self.assertRaisesRegex(RethrownJobError, - "File '.*?' does not match regex\('.*?'\) and pattern '.*?':\n.*unknown group name", + r"File '.*?' does not match regex\('.*?'\) and pattern '.*?':\n.*unknown group name", pipeline_run, [check_regex_misspelt_capture2_error_task], verbose=0, multiprocess=parallelism) @@ -433,12 +433,12 @@ class Test_regex_error_messages(unittest.TestCase): cleanup_tmpdir() s = StringIO() self.assertRaisesRegex(fatal_error_input_file_does_not_match, - "File '.*?' does not match regex\('.*?'\) and pattern '.*?':\n.*invalid group reference", + r"File '.*?' does not match regex\('.*?'\) and pattern '.*?':\n.*invalid group reference", pipeline_printout, s, [check_regex_out_of_range_regex_reference_error_task], verbose=3) self.assertRaisesRegex(RethrownJobError, - "File '.*?' does not match regex\('.*?'\) and pattern '.*?':\n.*invalid group reference", + r"File '.*?' does not match regex\('.*?'\) and pattern '.*?':\n.*invalid group reference", pipeline_run, [check_regex_out_of_range_regex_reference_error_task], verbose=0, multiprocess=parallelism) diff --git a/ruffus/test/test_ruffus_utility.py b/ruffus/test/test_ruffus_utility.py index 1f640cd..61269b1 100755 --- a/ruffus/test/test_ruffus_utility.py +++ b/ruffus/test/test_ruffus_utility.py @@ -508,7 +508,7 @@ class Test_expand_nested_tasks_or_globs(unittest.TestCase): class Test_regex_replace (unittest.TestCase): def helper(self, data, result): - regex_str = "([a-z]+)\.([a-z]+)\.([a-z]+)\.([a-z]+)" + regex_str = r"([a-z]+)\.([a-z]+)\.([a-z]+)\.([a-z]+)" try_result = regex_replace("aaa.bbb.ccc.aaa", regex_str, re.compile(regex_str),