8000 change library name from pycwl to cwlgen · phenoflow/python-cwlgen@eafe4e7 · GitHub
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khillionkhillion
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change library name from pycwl to cwlgen
1 parent ae53090 commit eafe4e7

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3 files changed

+25
-25
lines changed

3 files changed

+25
-25
lines changed

‎examples/example.py

Lines changed: 9 additions & 9 deletions
Original file line numberDiff line numberDiff line change
@@ -6,38 +6,38 @@
66
## Creation : 12-30-2016
77

88
'''
9-
Example of usage of the pycwl library
9+
Example of usage of the cwlgen library
1010
'''
1111

1212
########### Import ###########
1313

14-
import pycwl
14+
import cwlgen
1515

1616
if __name__ == "__main__":
1717

1818
# Create a tool
19-
cwl_tool = pycwl.CommandLineTool(tool_id='my_tool', label='my_tool is magic',\
19+
cwl_tool = cwlgen.CommandLineTool(tool_id='my_tool', label='my_tool is magic',\
2020
base_command='run_my_tool')
2121

2222
# Add documentation
2323
cwl_tool.doc = "Magic is no magic without secrets..."
2424

2525
# Add 2 inputs
26-
input_1_binding = pycwl.CommandLineBinding(position=1)
27-
input_1 = pycwl.CommandInputParameter('config_file', param_type='File',\
26+
input_1_binding = cwlgen.CommandLineBinding(position=1)
27+
input_1 = cwlgen.CommandInputParameter('config_file', param_type='File',\
2828
input_binding=input_1_binding,\
2929
doc='config file',\
3030
param_format='http://edamontology.org/format_2330')
3131
cwl_tool.inputs.append(input_1)
32-
input_2_binding = pycwl.CommandLineBinding(prefix='-t')
33-
input_2 = pycwl.CommandInputParameter('threads', param_type='int',\
32+
input_2_binding = cwlgen.CommandLineBinding(prefix='-t')
33+
input_2 = cwlgen.CommandInputParameter('threads', param_type='int',\
3434
input_binding=input_2_binding,\
3535
doc='number of threads')
3636
cwl_tool.inputs.append(input_2)
3737

3838
# Add 1 output
39-
output_1_binding = pycwl.CommandOutputBinding(glob='counts.txt')
40-
output_1 = pycwl.CommandOutputParameter('result_file', param_type='File',\
39+
output_1_binding = cwlgen.CommandOutputBinding(glob='counts.txt')
40+
output_1 = cwlgen.CommandOutputParameter('result_file', param_type='File',\
4141
output_binding=output_1_binding,\
4242
param_format='http://edamontology.org/format_2330',\
4343
doc='magic results')

‎setup.py

Lines changed: 1 addition & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -7,7 +7,7 @@
77
author_email='kehillio@pasteur.fr and hmenager@pasteur.fr',
88
keywords = ['cwl'],
99
install_requires=['six', 'ruamel.yaml'],
10-
packages=["pycwl"],
10+
packages=["cwlgen"],
1111
classifiers=[
1212
'Development Status :: 3 - Alpha',
1313
'Topic :: Scientific/Engineering :: Bio-Informatics',

‎test/test_unit_pycwl.py

Lines changed: 15 additions & 15 deletions
Original file line numberDiff line numberDiff line change
@@ -6,7 +6,7 @@
66
## Creation : 01-02-2017
77

88
'''
9-
Unit tests for pycwl library
9+
Unit tests for cwlgen library
1010
'''
1111

1212
########### Import ###########
@@ -17,7 +17,7 @@
1717
import unittest
1818

1919
# External libraries
20-
import pycwl
20+
import cwlgen
2121

2222
# Class and Objects
2323

@@ -30,7 +30,7 @@
3030
class TestCommandLineTool(unittest.TestCase):
3131

3232
def setUp(self):
33-
self.cwl = pycwl.CommandLineTool(tool_id='an_id', label='a description '+\
33+
self.cwl = cwlgen.CommandLineTool(tool_id='an_id', label='a description '+\
3434
'with spaces.', base_command='a_command')
3535

3636
def test_init(self):
@@ -55,9 +55,9 @@ def test_full_export(self):
5555
tmp_file = 'test_full_export.tmp'
5656
expected_file = os.path.dirname(__file__) + '/test_full_export.cwl'
5757
self.cwl.doc = "documentation"
58-
an_input = pycwl.CommandInputParameter('an_in_id', param_type='File')
58+
an_input = cwlgen.CommandInputParameter('an_in_id', param_type='File')
5959
self.cwl.inputs.append(an_input)
60-
an_output = pycwl.CommandOutputParameter('an_out_id', param_type='File')
60+
an_output = cwlgen.CommandOutputParameter('an_out_id', param_type='File')
6161
self.cwl.outputs.append(an_output)
6262
self.cwl.export(tmp_file)
6363
try:
@@ -69,7 +69,7 @@ def test_full_export(self):
6969
class TestParameter(unittest.TestCase):
7070

7171
def setUp(self):
72-
self.param = pycwl.Parameter('an_id', param_type='File', label='a_label',\
72+
self.param = cwlgen.Parameter('an_id', param_type='File', label='a_label',\
7373
doc='a_doc', param_format='a_format',\
7474
streamable=True, secondary_files='sec_files')
7575

@@ -95,11 +95,11 @@ def test_get_dict(self):
9595
class TestCommandInputParameter(unittest.TestCase):
9696

9797
def setUp(self):
98-
self.frst_inp = pycwl.CommandInputParameter('frst_id', param_type='File',\
98+
self.frst_inp = cwlgen.CommandInputParameter('frst_id', param_type='File',\
9999
label='a_label', \
100100
default='def_value')
101-
binding = pycwl.CommandLineBinding(position=2, prefix='--prefix')
102-
self.scnd_inp = pycwl.CommandInputParameter('scnd_id', param_type='File',\
101+
binding = cwlgen.CommandLineBinding(position=2, prefix='--prefix')
102+
self.scnd_inp = cwlgen.CommandInputParameter('scnd_id', param_type='File',\
103103
input_binding=binding)
104104

105105
def test_init(self):
@@ -130,7 +130,7 @@ def test_get_dict(self):
130130
class TestCommandOutputParameter(unittest.TestCase):
131131

132132
def setUp(self):
133-
self.outp = pycwl.CommandOutputParameter('an_out_id', param_type='File')
133+
self.outp = cwlgen.CommandOutputParameter('an_out_id', param_type='File')
134134

135135
def test_init(self):
136136
self.assertEqual(self.outp.id, 'an_out_id')
@@ -144,7 +144,7 @@ def test_get_dict(self):
144144
class TestCommandLineBinding(unittest.TestCase):
145145

146146
def setUp(self):
147-
self.line_binding = pycwl.CommandLineBinding(load_contents=True, position=1, \
147+
self.line_binding = cwlgen.CommandLineBinding(load_contents=True, position=1, \
148148
prefix='--prefix', separate=True, \
149149
item_separator='-', shell_quote=True,\
150150
value_from='text.txt')
@@ -171,7 +171,7 @@ def test_get_dict(self):
171171
class TestCommandOutputBinding(unittest.TestCase):
172172

173173
def setUp(self):
174-
self.out_binding = pycwl.CommandOutputBinding(glob='file.txt', load_contents=True,\
174+
self.out_binding = cwlgen.CommandOutputBinding(glob='file.txt', load_contents=True,\
175175
output_eval='eval')
176176

177177
def test_init(self):
@@ -189,7 +189,7 @@ def test_get_dict(self):
189189
class TestRequirement(unittest.TestCase):
190190

191191
def setUp(self):
192-
self.requirement = pycwl.Requirement('a_class')
192+
self.requirement = cwlgen.Requirement('a_class')
193193

194194
def test_init(self):
195195
self.assertEqual(self.requirement.req_class, 'a_class')
@@ -198,7 +198,7 @@ def test_init(self):
198198
class TestInlineJavascriptReq(unittest.TestCase):
199199

200200
def setUp(self):
201-
self.js_req = pycwl.InlineJavascriptReq(expression_lib='expression')
201+
self.js_req = cwlgen.InlineJavascriptReq(expression_lib='expression')
202202

203203
def test_init(self):
204204
self.assertEqual(self.js_req.req_class, 'InlineJavascriptRequirement')
@@ -207,7 +207,7 @@ def test_init(self):
207207
class TestDockerRequirement(unittest.TestCase):
208208

209209
def setUp(self):
210-
self.dock_req = pycwl.DockerRequirement(docker_pull='pull', docker_load='load',\
210+
self.dock_req = cwlgen.DockerRequirement(docker_pull='pull', docker_load='load',\
211211
docker_file='file', docker_import='import',\
212212
docker_image_id='id', docker_output_dir='dir')
213213

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