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Commit b20a29fa authored by Bienchen's avatar Bienchen
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Made description mandatory

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core/doc/helper.rst
+ 2
− 2
View file @ b20a29fa
......@@ -53,7 +53,7 @@ File Tests
(fh, fn) = tempfile.mkstemp(suffix='.pdb')
os.close(fh)
p = pm3argparse.PM3ArgumentParser()
p = pm3argparse.PM3ArgumentParser('Dummy')
p.add_argument('file', type=str)
opts = p.Parse([fn])
......@@ -71,7 +71,7 @@ File Tests
from promod3.core import helper
from promod3.core import pm3argparse
p = pm3argparse.PM3ArgumentParser()
p = pm3argparse.PM3ArgumentParser(__doc__)
p.add_argument('file', type=str)
opts = p.Parse()
......
core/pymod/core/pm3argparse.py
+ 5
− 5
View file @ b20a29fa
......@@ -63,10 +63,14 @@ class PM3ArgumentParser(argparse.ArgumentParser):
:type: :class:`bool`
"""
def __init__(self, action=True, description=None):
def __init__(self, description, action=True):
"""
Create a new instance of :class:`~pm3argparse.PM3ArgumentParser`.
:param description: Help text for this script, handed down to
|descattr|_ of |argpinit|_.
:type description: :class:`str`
:param action: Indicates if the calling script is a |project| action.
This influences |progattr|_ of
:class:`~argparse.ArgumentParser` by clipping of the
......@@ -75,10 +79,6 @@ class PM3ArgumentParser(argparse.ArgumentParser):
:class:`~argparse.ArgumentParser` kicks in.
:type action: :class:`bool`
:param description: Help text for this script, handed down to
|descattr|_ of |argpinit|_.
:type description: :class:`str`
:returns: :class:`argparse.ArgumentParser`.
"""
prog = None
......
core/tests/test_pm3argparse.py
+ 23
− 17
View file @ b20a29fa
"""
Testing our own little argument parser.
"""
import unittest
import ost
from promod3.core import pm3argparse
......@@ -30,7 +34,7 @@ class PM3ArgParseTests(unittest.TestCase):
ost.PopLogSink()
def testUnrecognisedArguments(self):
parser = pm3argparse.PM3ArgumentParser(action=False)
parser = pm3argparse.PM3ArgumentParser(__doc__, action=False)
with self.assertRaises(SystemExit) as ecd:
parser.Parse(['-x'])
self.assertEqual(ecd.exception.code, 2)
......@@ -40,22 +44,24 @@ class PM3ArgParseTests(unittest.TestCase):
'arguments: -x'])
def testActionSwitch(self):
parser = pm3argparse.PM3ArgumentParser(action=False)
parser = pm3argparse.PM3ArgumentParser(__doc__, action=False)
with self.assertRaises(SystemExit) as ecd:
parser.Parse(['--help'])
self.assertEqual(ecd.exception.code, 0)
self.assertEqual(self.log.messages['SCRIPT'],
['usage: test_pm3argparse.py [-h]\n\noptional '+
['usage: test_pm3argparse.py [-h]\n\nTesting our '+
'own little argument parser.\n\noptional '+
'arguments:\n -h, --help show this help message '+
'and exit'])
self.log.messages = dict()
parser = pm3argparse.PM3ArgumentParser(action=True)
parser = pm3argparse.PM3ArgumentParser(__doc__, action=True)
with self.assertRaises(SystemExit) as ecd:
parser.Parse(['--help'])
self.assertEqual(ecd.exception.code, 0)
self.assertEqual(self.log.messages['SCRIPT'],
['usage: t_pm3argparse.py [-h]\n\noptional '+
['usage: t_pm3argparse.py [-h]\n\nTesting our own '+
'little argument parser.\n\noptional '+
'arguments:\n -h, --help show this help message '+
'and exit'])
......@@ -74,7 +80,7 @@ class PM3ArgParseTests(unittest.TestCase):
def testAddAlignemntNoTrgPfx(self):
# checking that we fail on missing 'trg:' prefix for arguments of
# --fasta
parser = pm3argparse.PM3ArgumentParser(action=False)
parser = pm3argparse.PM3ArgumentParser(__doc__, action=False)
parser.AddAlignment()
parser.AssembleParser()
with self.assertRaises(SystemExit) as ecd:
......@@ -88,7 +94,7 @@ class PM3ArgParseTests(unittest.TestCase):
def testAddAlignemntEmptyTrgPfx(self):
# checking that we fail on empty 'trg:' prefix for arguments of
# --fasta
parser = pm3argparse.PM3ArgumentParser(action=False)
parser = pm3argparse.PM3ArgumentParser(__doc__, action=False)
parser.AddAlignment()
parser.AssembleParser()
with self.assertRaises(SystemExit) as ecd:
......@@ -101,7 +107,7 @@ class PM3ArgParseTests(unittest.TestCase):
def testAddAlignemntSwapTrgPfx(self):
# checking that we fail on empty 'trg:' prefix for arguments of
# --fasta
parser = pm3argparse.PM3ArgumentParser(action=False)
parser = pm3argparse.PM3ArgumentParser(__doc__, action=False)
parser.AddAlignment()
parser.AssembleParser()
with self.assertRaises(SystemExit) as ecd:
......@@ -113,7 +119,7 @@ class PM3ArgParseTests(unittest.TestCase):
def testAddAlignmentNoFile(self):
# check that we throw an error if a non-exisiting file is given
parser = pm3argparse.PM3ArgumentParser(action=False)
parser = pm3argparse.PM3ArgumentParser(__doc__, action=False)
parser.AddAlignment()
parser.AssembleParser()
with self.assertRaises(SystemExit) as ecd:
......@@ -124,7 +130,7 @@ class PM3ArgParseTests(unittest.TestCase):
def testAddAlignmentEmpty(self):
# we want to fail if we get an empty FastA file
parser = pm3argparse.PM3ArgumentParser(action=False)
parser = pm3argparse.PM3ArgumentParser(__doc__, action=False)
parser.AddAlignment()
parser.AssembleParser()
with self.assertRaises(SystemExit) as ecd:
......@@ -135,7 +141,7 @@ class PM3ArgParseTests(unittest.TestCase):
"wrong format: data/fasta/alignment.fas")
def testAddAlignmentToMany(self):
parser = pm3argparse.PM3ArgumentParser(action=False)
parser = pm3argparse.PM3ArgumentParser(__doc__, action=False)
parser.AddAlignment()
parser.AssembleParser()
with self.assertRaises(SystemExit) as ecd:
......@@ -146,7 +152,7 @@ class PM3ArgParseTests(unittest.TestCase):
"more than 2 sequences.")
def testAddAlignmentMissingTargetName(self):
parser = pm3argparse.PM3ArgumentParser(action=False)
parser = pm3argparse.PM3ArgumentParser(__doc__, action=False)
parser.AddAlignment()
parser.AssembleParser()
with self.assertRaises(SystemExit) as ecd:
......@@ -157,7 +163,7 @@ class PM3ArgParseTests(unittest.TestCase):
"found in the alignment.")
def testAddAlignmentDifferentSeqLens(self):
parser = pm3argparse.PM3ArgumentParser(action=False)
parser = pm3argparse.PM3ArgumentParser(__doc__, action=False)
parser.AddAlignment()
parser.AssembleParser()
with self.assertRaises(SystemExit) as ecd:
......@@ -168,7 +174,7 @@ class PM3ArgParseTests(unittest.TestCase):
"alignment have different length.")
def testAddAlignmentGzipIn(self):
parser = pm3argparse.PM3ArgumentParser(action=False)
parser = pm3argparse.PM3ArgumentParser(__doc__, action=False)
parser.AddAlignment()
parser.AssembleParser()
opts = parser.Parse(['--fasta', 'trg:target',
......@@ -197,7 +203,7 @@ class PM3ArgParseTests(unittest.TestCase):
'YHQMTAPLIGYYYYSKEAEAGNTKYAKVDGTKPV---AEVRADLEK\n')
def testAddAlignmentSwitchSeqs(self):
parser = pm3argparse.PM3ArgumentParser(action=False)
parser = pm3argparse.PM3ArgumentParser(__doc__, action=False)
parser.AddAlignment()
parser.AssembleParser()
opts = parser.Parse(['--fasta', 'trg:target',
......@@ -209,7 +215,7 @@ class PM3ArgParseTests(unittest.TestCase):
'DDQEETVRKRLVEYHQMTAPLL--YYYYKEAEAGNTKYAKVDGTKPVAEV'+
'RADLEKILG')
parser = pm3argparse.PM3ArgumentParser(action=False)
parser = pm3argparse.PM3ArgumentParser(__doc__, action=False)
parser.AddAlignment()
parser.AssembleParser()
opts = parser.Parse(['--fasta', 'trg:target',
......@@ -222,7 +228,7 @@ class PM3ArgParseTests(unittest.TestCase):
'RADLEKILG')
def testAddAlignment(self):
parser = pm3argparse.PM3ArgumentParser(action=False)
parser = pm3argparse.PM3ArgumentParser(__doc__, action=False)
parser.AddAlignment()
parser.AssembleParser()
opts = parser.Parse(['--fasta', 'trg:target',
......
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