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22df84e Updated setup.py for GenBank
chapmanb authored Jan 20, 2001
1 """Distutils based setup script for Biopython.
2
3 This uses Distutils (http://python.org/sigs/distutils-sig/) the standard
4 python mechanism for installing packages. For the easiest installation
5 just type the command:
6
7 python setup.py install
8
9 For more in-depth instructions, see the installation section of the
10 biopython manual, linked to from:
11
e4e4dc4 @peterjc Updating the documentation URL
peterjc authored Sep 28, 2008
12 http://biopython.org/wiki/Documentation
22df84e Updated setup.py for GenBank
chapmanb authored Jan 20, 2001
13
14 Or for more details about the options available from distutils, look at
15 the 'Installing Python Modules' distutils documentation, available from:
16
17 http://python.org/sigs/distutils-sig/doc/
18
0277345 @peterjc Clarify the mailing list bit
peterjc authored Sep 5, 2008
19 Or, if all else fails, feel free to write to the sign up to the Biopython
e4e4dc4 @peterjc Updating the documentation URL
peterjc authored Sep 28, 2008
20 mailing list and ask for help. See:
21
22 http://biopython.org/wiki/Mailing_lists
fdcb82e added code so that it now checks for dependencies before biopython is
jchang authored Feb 19, 2003
23 """
f726249 merged Andrew's Seq package with the tree
jchang authored Apr 30, 2000
24 import sys
96a6095 Upgrade setup.py for SubsMat
chapmanb authored Nov 15, 2000
25 import os
7db13b0 Updated to check for dependencies and print out warnings and to insta…
chapmanb authored Feb 3, 2001
26
fdcb82e added code so that it now checks for dependencies before biopython is
jchang authored Feb 19, 2003
27 # Make sure I have the right Python version.
c2c11a9 Biopython now works with Python >= 2.3
idoerg authored Feb 16, 2005
28 if sys.version_info[:2] < (2, 3):
29 print "Biopython requires Python 2.3 or better. Python %d.%d detected" % \
fdcb82e added code so that it now checks for dependencies before biopython is
jchang authored Feb 19, 2003
30 sys.version_info[:2]
31 sys.exit(-1)
32
33 from distutils.core import setup
34 from distutils.core import Command
35 from distutils.command.install import install
b9fe0cc the EUtils dtd's were not being installed correctly, when the
jchang authored Nov 7, 2003
36 from distutils.command.install_data import install_data
fdcb82e added code so that it now checks for dependencies before biopython is
jchang authored Feb 19, 2003
37 from distutils.command.build_py import build_py
a8ae40f now installs Martel and doesn't complain about it
jchang authored Sep 13, 2003
38 from distutils.command.build_ext import build_ext
fdcb82e added code so that it now checks for dependencies before biopython is
jchang authored Feb 19, 2003
39 from distutils.extension import Extension
a573247 Even more kludgy fix for c++ compiling with setup.py -- this time it …
chapmanb authored May 4, 2004
40 from distutils import sysconfig
fdcb82e added code so that it now checks for dependencies before biopython is
jchang authored Feb 19, 2003
41
42 def get_yes_or_no(question, default):
43 if default:
44 option_str = "(Y/n)"
45 default_str = 'y'
46 else:
47 option_str = "(y/N)"
48 default_str = 'n'
49
e4e4dc4 @peterjc Updating the documentation URL
peterjc authored Sep 28, 2008
50 while True:
fdcb82e added code so that it now checks for dependencies before biopython is
jchang authored Feb 19, 2003
51 print "%s %s " % (question, option_str),
52 response = raw_input().lower()
53 if not response:
54 response = default_str
55 if response[0] in ['y', 'n']:
56 break
57 print "Please answer y or n."
58 return response[0] == 'y'
59
a8ae40f now installs Martel and doesn't complain about it
jchang authored Sep 13, 2003
60 _CHECKED = None
61 def check_dependencies_once():
62 # Call check_dependencies, but cache the result for subsequent
63 # calls.
64 global _CHECKED
65 if _CHECKED is None:
66 _CHECKED = check_dependencies()
67 return _CHECKED
68
69 def check_dependencies():
70 """Return whether the installation should continue."""
71 # There should be some way for the user to tell specify not to
72 # check dependencies. For example, it probably should not if
73 # the user specified "-q". However, I'm not sure where
74 # distutils stores that information. Also, install has a
75 # --force option that gets saved in self.user_options. It
76 # means overwrite previous installations. If the user has
77 # forced an installation, should we also ignore dependencies?
1003c5c @peterjc Make mxTextTools optional (like ReportLab and Numeric), so that Biopy…
peterjc authored Nov 19, 2007
78
79 #This is a list of tuples, containing:
80 # - package name, string
81 # - is packaged installed, boolean
82 # - is packaged required, boolean
83 # - package website, string
a8ae40f now installs Martel and doesn't complain about it
jchang authored Sep 13, 2003
84 dependencies = [
2669c4d - Updates to move from Numeric python to NumPy. Python modules have b…
chapmanb authored Sep 11, 2008
85 ("Numerical Python (NumPy)", is_Numpy_installed, 0,
5d1245b @peterjc The NumPy webpage has moved to numpy.scipy.org
peterjc authored Sep 22, 2008
86 "http://numpy.scipy.org/"),
a8ae40f now installs Martel and doesn't complain about it
jchang authored Sep 13, 2003
87 ]
88
89 for name, is_installed_fn, is_required, url in dependencies:
90 if is_installed_fn():
91 continue
92
93 print "*** %s *** is either not installed or out of date." % name
94 if is_required:
95
96 print """
97 This package is required for many Biopython features. Please install
98 it before you install Biopython."""
99 default = 0
100 else:
101 print """
102 This package is optional, which means it is only used in a few
b6580cd Fixed spelling error "is you are unsure" ==> "if you are unsure"
mdehoon authored Oct 17, 2003
103 specialized modules in Biopython. You probably don't need this if you
a8ae40f now installs Martel and doesn't complain about it
jchang authored Sep 13, 2003
104 are unsure. You can ignore this requirement, and install it later if
105 you see ImportErrors."""
106 default = 1
107 print "You can find %s at %s." % (name, url)
108 print
5c9fef2 Modified setup.py to try and fix Martel/mxTextTools issues from bug 1…
chapmanb authored Mar 2, 2004
109 # exit automatically if required packages not installed
593e65e Added Affymetrix package from Harry Zuzan
chapmanb authored May 4, 2004
110 if not(default):
111 sys.exit(-1)
a8ae40f now installs Martel and doesn't complain about it
jchang authored Sep 13, 2003
112
113 if not get_yes_or_no(
114 "Do you want to continue this installation?", default):
115 return 0
5a0a5b6 Patch from K. Arun on the mailing list. Ask the user if KDTree (C++) …
mdehoon authored Jul 28, 2006
116
a8ae40f now installs Martel and doesn't complain about it
jchang authored Sep 13, 2003
117 return 1
118
fdcb82e added code so that it now checks for dependencies before biopython is
jchang authored Feb 19, 2003
119 class install_biopython(install):
7db13b0 Updated to check for dependencies and print out warnings and to insta…
chapmanb authored Feb 3, 2001
120 """Override the standard install to check for dependencies.
121
122 This will just run the normal install, and then print warning messages
123 if packages are missing.
b7761b6 Fixes to imported EUtils to get it working happily with Bio:
chapmanb authored Jun 13, 2003
124
7db13b0 Updated to check for dependencies and print out warnings and to insta…
chapmanb authored Feb 3, 2001
125 """
126 def run(self):
a8ae40f now installs Martel and doesn't complain about it
jchang authored Sep 13, 2003
127 if check_dependencies_once():
fdcb82e added code so that it now checks for dependencies before biopython is
jchang authored Feb 19, 2003
128 # Run the normal install.
129 install.run(self)
7db13b0 Updated to check for dependencies and print out warnings and to insta…
chapmanb authored Feb 3, 2001
130
fdcb82e added code so that it now checks for dependencies before biopython is
jchang authored Feb 19, 2003
131 class build_py_biopython(build_py):
132 def run(self):
a8ae40f now installs Martel and doesn't complain about it
jchang authored Sep 13, 2003
133 if not check_dependencies_once():
134 return
593e65e Added Affymetrix package from Harry Zuzan
chapmanb authored May 4, 2004
135 # Add software that requires Numpy to be installed.
a8ae40f now installs Martel and doesn't complain about it
jchang authored Sep 13, 2003
136 if is_Numpy_installed():
593e65e Added Affymetrix package from Harry Zuzan
chapmanb authored May 4, 2004
137 self.packages.extend(NUMPY_PACKAGES)
fdcb82e added code so that it now checks for dependencies before biopython is
jchang authored Feb 19, 2003
138 build_py.run(self)
fc90717 Whew, final thing to add! Added code for displaying pretty pictures u…
chapmanb authored Dec 14, 2001
139
94b412a See bug #2375. Copy data files to the build directory, so the tests run
mdehoon authored Jun 27, 2008
140 # In addition to installing the data files, we also need to make
141 # sure that they are copied to the build directory. Otherwise,
142 # the unit tests will fail because they cannot find the data files
143 # in the build directory.
144 # This is taken care of automatically in Python 2.4 or higher by
145 # using package_data.
146
147 import glob
148 data_files = self.distribution.data_files
149 for entry in data_files:
150 if type(entry) is not type(""):
151 raise ValueError, "data_files must be strings"
152 # Unix- to platform-convention conversion
153 entry = os.sep.join(entry.split("/"))
154 filenames = glob.glob(entry)
155 for filename in filenames:
156 dst = os.path.join(self.build_lib, filename)
157 dstdir = os.path.split(dst)[0]
158 self.mkpath(dstdir)
159 self.copy_file(filename, dst)
160
161
a8ae40f now installs Martel and doesn't complain about it
jchang authored Sep 13, 2003
162 class build_ext_biopython(build_ext):
163 def run(self):
164 if not check_dependencies_once():
165 return
a573247 Even more kludgy fix for c++ compiling with setup.py -- this time it …
chapmanb authored May 4, 2004
166 # add software that requires NumPy to install
a8ae40f now installs Martel and doesn't complain about it
jchang authored Sep 13, 2003
167 if is_Numpy_installed():
2669c4d - Updates to move from Numeric python to NumPy. Python modules have b…
chapmanb authored Sep 11, 2008
168 import numpy
379fbb7 Switched from the old Numerical Python to the new NumPy. Bio.KDTree i…
mdehoon authored Sep 14, 2008
169 numpy_include_dir = numpy.get_include()
170 self.extensions.append(
2669c4d - Updates to move from Numeric python to NumPy. Python modules have b…
chapmanb authored Sep 11, 2008
171 Extension('Bio.Cluster.cluster',
172 ['Bio/Cluster/clustermodule.c',
173 'Bio/Cluster/cluster.c'],
379fbb7 Switched from the old Numerical Python to the new NumPy. Bio.KDTree i…
mdehoon authored Sep 14, 2008
174 include_dirs=[numpy_include_dir],
175 ))
176 self.extensions.append(
177 Extension('Bio.KDTree._CKDTree',
178 ["Bio/KDTree/KDTree.c",
179 "Bio/KDTree/KDTreemodule.c"],
180 include_dirs=[numpy_include_dir],
2669c4d - Updates to move from Numeric python to NumPy. Python modules have b…
chapmanb authored Sep 11, 2008
181 ))
a8ae40f now installs Martel and doesn't complain about it
jchang authored Sep 13, 2003
182 build_ext.run(self)
183
a151e5c workaround for bug in distutils that prevents one from compiling both…
grouse authored Apr 19, 2004
184
fdcb82e added code so that it now checks for dependencies before biopython is
jchang authored Feb 19, 2003
185 class test_biopython(Command):
b50486d Allow setup.py to be able to run tests with python setup.py test
chapmanb authored Mar 2, 2001
186 """Run all of the tests for the package.
187
188 This is a automatic test run class to make distutils kind of act like
189 perl. With this you can do:
190
191 python setup.py build
192 python setup.py install
193 python setup.py test
fdcb82e added code so that it now checks for dependencies before biopython is
jchang authored Feb 19, 2003
194
b50486d Allow setup.py to be able to run tests with python setup.py test
chapmanb authored Mar 2, 2001
195 """
fdcb82e added code so that it now checks for dependencies before biopython is
jchang authored Feb 19, 2003
196 description = "Automatically run the test suite for Biopython."
844496e @peterjc Removing the now redundant --no-gui argument for the test suite.
peterjc authored Dec 4, 2008
197 user_options = []
1d16b65 The modification to setup.py gives the option of --no-gui for the com…
lasher authored Apr 11, 2007
198
199 def initialize_options(self):
844496e @peterjc Removing the now redundant --no-gui argument for the test suite.
peterjc authored Dec 4, 2008
200 pass
1d16b65 The modification to setup.py gives the option of --no-gui for the com…
lasher authored Apr 11, 2007
201
202 def finalize_options(self):
b50486d Allow setup.py to be able to run tests with python setup.py test
chapmanb authored Mar 2, 2001
203 pass
1d16b65 The modification to setup.py gives the option of --no-gui for the com…
lasher authored Apr 11, 2007
204
b50486d Allow setup.py to be able to run tests with python setup.py test
chapmanb authored Mar 2, 2001
205 def run(self):
206 this_dir = os.getcwd()
207
208 # change to the test dir and run the tests
209 os.chdir("Tests")
b720e3d In Python 2.3.2, the current directory '' is not included in the path.
grouse authored Oct 9, 2003
210 sys.path.insert(0, '')
844496e @peterjc Removing the now redundant --no-gui argument for the test suite.
peterjc authored Dec 4, 2008
211 import run_tests
212 run_tests.main([])
b50486d Allow setup.py to be able to run tests with python setup.py test
chapmanb authored Mar 2, 2001
213
214 # change back to the current directory
215 os.chdir(this_dir)
216
fdcb82e added code so that it now checks for dependencies before biopython is
jchang authored Feb 19, 2003
217 def can_import(module_name):
218 """can_import(module_name) -> module or None"""
219 try:
220 return __import__(module_name)
221 except ImportError:
222 return None
223
224 def is_Numpy_installed():
2669c4d - Updates to move from Numeric python to NumPy. Python modules have b…
chapmanb authored Sep 11, 2008
225 return can_import("numpy")
fdcb82e added code so that it now checks for dependencies before biopython is
jchang authored Feb 19, 2003
226
7db13b0 Updated to check for dependencies and print out warnings and to insta…
chapmanb authored Feb 3, 2001
227 # --- set up the packages we are going to install
228 # standard biopython packages
fdcb82e added code so that it now checks for dependencies before biopython is
jchang authored Feb 19, 2003
229 PACKAGES = [
230 'Bio',
231 'Bio.Align',
1231257 @peterjc Include Bio.AlignIO in installation
peterjc authored May 14, 2008
232 'Bio.AlignIO',
193e993 initial checking of Bartek Wilczynski's AlignAce module
jchang authored Jul 28, 2003
233 'Bio.AlignAce',
fdcb82e added code so that it now checks for dependencies before biopython is
jchang authored Feb 19, 2003
234 'Bio.Alphabet',
235 'Bio.Application',
236 'Bio.Blast',
0cd0e9c Modified Files:
idoerg authored Feb 15, 2005
237 'Bio.CAPS',
76ce5ca Added Compass parsing code contributed by James Casbon.
chapmanb authored May 5, 2004
238 'Bio.Compass',
fdcb82e added code so that it now checks for dependencies before biopython is
jchang authored Feb 19, 2003
239 'Bio.Clustalw',
240 'Bio.Crystal',
241 'Bio.Data',
242 'Bio.Emboss',
243 'Bio.Encodings',
8521e25 Moving Bio/Entrez.py to Bio/Entrez/__init__.py.
mdehoon authored Feb 25, 2008
244 'Bio.Entrez',
fdcb82e added code so that it now checks for dependencies before biopython is
jchang authored Feb 19, 2003
245 'Bio.Enzyme',
b7761b6 Fixes to imported EUtils to get it working happily with Bio:
chapmanb authored Jun 13, 2003
246 'Bio.EUtils',
247 'Bio.EUtils.DTDs',
fdcb82e added code so that it now checks for dependencies before biopython is
jchang authored Feb 19, 2003
248 'Bio.Fasta',
249 'Bio.FSSP',
250 'Bio.GA',
251 'Bio.GA.Crossover',
252 'Bio.GA.Mutation',
253 'Bio.GA.Repair',
254 'Bio.GA.Selection',
255 'Bio.GenBank',
256 'Bio.Geo',
257 'Bio.GFF',
258 'Bio.Graphics',
cace008 @peterjc Initial check in of GenomeDiagram by Leighton Pritchard, converted fo…
peterjc authored Dec 9, 2008
259 'Bio.Graphics.GenomeDiagram',
fdcb82e added code so that it now checks for dependencies before biopython is
jchang authored Feb 19, 2003
260 'Bio.HMM',
261 'Bio.IntelliGenetics',
262 'Bio.InterPro',
263 'Bio.KEGG',
264 'Bio.KEGG.Compound',
265 'Bio.KEGG.Enzyme',
266 'Bio.KEGG.Map',
267 'Bio.Medline',
08d88f3 Add Bio.MEME to the packages to be installed.
mdehoon authored Oct 20, 2005
268 'Bio.MEME',
9deacf3 added Bio.Motif to setup.py
bartek authored Dec 9, 2008
269 'Bio.Motif',
fdcb82e added code so that it now checks for dependencies before biopython is
jchang authored Feb 19, 2003
270 'Bio.MetaTool',
271 'Bio.Mindy',
272 'Bio.NBRF',
273 'Bio.Ndb',
274 'Bio.NeuralNetwork',
275 'Bio.NeuralNetwork.BackPropagation',
276 'Bio.NeuralNetwork.Gene',
c2c11a9 Biopython now works with Python >= 2.3
idoerg authored Feb 16, 2005
277 'Bio.Nexus',
7bcfbce Adding NMR files kindly contributed by Bob Bussell
chapmanb authored Jan 21, 2004
278 'Bio.NMR',
fdcb82e added code so that it now checks for dependencies before biopython is
jchang authored Feb 19, 2003
279 'Bio.Parsers',
280 'Bio.Pathway',
281 'Bio.Pathway.Rep',
282 'Bio.PDB',
983daba Add Bio.PDB.mmCIF (but not MMFIFlex) as a module to make sure that
mdehoon authored Jul 21, 2007
283 'Bio.PDB.mmCIF',
4f07b8a Added Bio.PopGen module by Tiago Antao.
mdehoon authored Aug 11, 2007
284 'Bio.PopGen',
285 'Bio.PopGen.Async',
286 'Bio.PopGen.FDist',
287 'Bio.PopGen.GenePop',
96f01d5 2375: Activating SimCoal on Biopython setup
tiagoantao authored Jan 18, 2008
288 'Bio.PopGen.SimCoal',
fdcb82e added code so that it now checks for dependencies before biopython is
jchang authored Feb 19, 2003
289 'Bio.Prosite',
05f9ba2 Added Restriction enzyme package contributed by Frederic Sohm. This i…
chapmanb authored Aug 13, 2004
290 'Bio.Restriction',
291 'Bio.Restriction._Update',
fdcb82e added code so that it now checks for dependencies before biopython is
jchang authored Feb 19, 2003
292 'Bio.Saf',
293 'Bio.SCOP',
294 'Bio.SeqIO',
295 'Bio.SeqUtils',
2214cae Added Sequencing directory to packages
chapmanb authored Feb 5, 2004
296 'Bio.Sequencing',
7738632 Added Bio.Statistics.
mdehoon authored May 8, 2004
297 'Bio.Statistics',
fdcb82e added code so that it now checks for dependencies before biopython is
jchang authored Feb 19, 2003
298 'Bio.SubsMat',
299 'Bio.SVDSuperimposer',
300 'Bio.SwissProt',
301 'Bio.UniGene',
302 'Bio.writers',
303 'Bio.writers.SeqRecord',
3a5d550 Adding Bio.Wise to the distribution
grouse authored Jan 15, 2004
304 'Bio.Wise',
fdcb82e added code so that it now checks for dependencies before biopython is
jchang authored Feb 19, 2003
305 'Bio.WWW',
d81c27e @peterjc Removed the Martel special case code (it should be safe to assume tha…
peterjc authored Sep 24, 2008
306 #Other top level packages,
307 'BioSQL',
308 'Martel', #Deprecated as of Biopython 1.49
fdcb82e added code so that it now checks for dependencies before biopython is
jchang authored Feb 19, 2003
309 ]
310
593e65e Added Affymetrix package from Harry Zuzan
chapmanb authored May 4, 2004
311 # packages that require Numeric Python
312 NUMPY_PACKAGES = [
313 'Bio.Affy',
314 'Bio.Cluster',
379fbb7 Switched from the old Numerical Python to the new NumPy. Bio.KDTree i…
mdehoon authored Sep 14, 2008
315 'Bio.KDTree',
593e65e Added Affymetrix package from Harry Zuzan
chapmanb authored May 4, 2004
316 ]
317
fdcb82e added code so that it now checks for dependencies before biopython is
jchang authored Feb 19, 2003
318 EXTENSIONS = [
319 Extension('Bio.clistfns',
320 ['Bio/clistfnsmodule.c']
321 ),
322 Extension('Bio.cmathfns',
323 ['Bio/cmathfnsmodule.c',
324 'Bio/csupport.c'],
325 include_dirs=["Bio"]
326 ),
327 Extension('Bio.cstringfns',
328 ['Bio/cstringfnsmodule.c']
329 ),
330 Extension('Bio.cpairwise2',
331 ['Bio/cpairwise2module.c',
332 'Bio/csupport.c'],
333 include_dirs=["Bio"]
334 ),
335 Extension('Bio.trie',
336 ['Bio/triemodule.c',
337 'Bio/trie.c'],
338 include_dirs=["Bio"]
339 ),
340 Extension('Bio.cMarkovModel',
341 ['Bio/cMarkovModelmodule.c',
342 'Bio/csupport.c'],
343 include_dirs=["Bio"]
344 ),
844496e @peterjc Removing the now redundant --no-gui argument for the test suite.
peterjc authored Dec 4, 2008
345 #Commented out due to the build dependency on flex, see Bug 2619
346 # Extension('Bio.PDB.mmCIF.MMCIFlex',
347 # ['Bio/PDB/mmCIF/lex.yy.c',
348 # 'Bio/PDB/mmCIF/MMCIFlexmodule.c'],
349 # include_dirs=["Bio"],
350 # libraries=["fl"]
351 # ),
2800c6c *** empty log message ***
idoerg authored Feb 18, 2005
352 Extension('Bio.Nexus.cnexus',
c2c11a9 Biopython now works with Python >= 2.3
idoerg authored Feb 16, 2005
353 ['Bio/Nexus/cnexus.c']
354 ),
05f9ba2 Added Restriction enzyme package contributed by Frederic Sohm. This i…
chapmanb authored Aug 13, 2004
355 Extension('Bio.Restriction.DNAUtils',
356 ['Bio/Restriction/DNAUtils.c']
357 ),
fdcb82e added code so that it now checks for dependencies before biopython is
jchang authored Feb 19, 2003
358 ]
359
9283de6 fixed installation of Bio/EUtils/DTDs
jchang authored Sep 15, 2003
360 DATA_FILES=[
eb7dfb6 Reverting previous change, as this is still needed for Python 2.3.
mdehoon authored Jun 9, 2008
361 "Bio/Entrez/DTDs/*.dtd",
362 "Bio/EUtils/DTDs/*.dtd",
363 "Bio/PopGen/SimCoal/data/*.par"
9283de6 fixed installation of Bio/EUtils/DTDs
jchang authored Sep 15, 2003
364 ]
365
eb7dfb6 Reverting previous change, as this is still needed for Python 2.3.
mdehoon authored Jun 9, 2008
366 # EUtils contains dtd files that need to be installed in the same
367 # directory as the python modules. Distutils doesn't have a simple
368 # way of handling this, and we need to subclass install_data. This
369 # code is adapted from the mx.TextTools distribution.
370
94b412a See bug #2375. Copy data files to the build directory, so the tests run
mdehoon authored Jun 27, 2008
371 # We can use package_data instead once we require Python 2.4 or higher.
eb7dfb6 Reverting previous change, as this is still needed for Python 2.3.
mdehoon authored Jun 9, 2008
372
373 class install_data_biopython(install_data):
374 def finalize_options(self):
375 if self.install_dir is None:
376 installobj = self.distribution.get_command_obj('install')
377 self.install_dir = installobj.install_platlib
378 install_data.finalize_options(self)
379
380 def run (self):
381 import glob
382 if not self.dry_run:
383 self.mkpath(self.install_dir)
384 data_files = self.get_inputs()
385 for entry in data_files:
386 if type(entry) is not type(""):
387 raise ValueError, "data_files must be strings"
388 # Unix- to platform-convention conversion
389 entry = os.sep.join(entry.split("/"))
390 filenames = glob.glob(entry)
391 for filename in filenames:
392 dst = os.path.join(self.install_dir, filename)
393 dstdir = os.path.split(dst)[0]
394 if not self.dry_run:
395 self.mkpath(dstdir)
396 outfile = self.copy_file(filename, dst)[0]
397 else:
398 outfile = dst
399 self.outfiles.append(outfile)
400
fdcb82e added code so that it now checks for dependencies before biopython is
jchang authored Feb 19, 2003
401 setup(
402 name='biopython',
844496e @peterjc Removing the now redundant --no-gui argument for the test suite.
peterjc authored Dec 4, 2008
403 version='1.49',
fdcb82e added code so that it now checks for dependencies before biopython is
jchang authored Feb 19, 2003
404 author='The Biopython Consortium',
405 author_email='biopython@biopython.org',
406 url='http://www.biopython.org/',
65df9bd Minor changes to setup file to make it compatible with the python pac…
chapmanb authored Sep 28, 2008
407 description='Freely available tools for computational molecular biology.',
408 download_url='http://biopython.org/DIST/',
fdcb82e added code so that it now checks for dependencies before biopython is
jchang authored Feb 19, 2003
409 cmdclass={
410 "install" : install_biopython,
411 "build_py" : build_py_biopython,
a8ae40f now installs Martel and doesn't complain about it
jchang authored Sep 13, 2003
412 "build_ext" : build_ext_biopython,
eb7dfb6 Reverting previous change, as this is still needed for Python 2.3.
mdehoon authored Jun 9, 2008
413 "install_data" : install_data_biopython,
fdcb82e added code so that it now checks for dependencies before biopython is
jchang authored Feb 19, 2003
414 "test" : test_biopython,
415 },
416 packages=PACKAGES,
417 ext_modules=EXTENSIONS,
eb7dfb6 Reverting previous change, as this is still needed for Python 2.3.
mdehoon authored Jun 9, 2008
418 data_files=DATA_FILES,
844496e @peterjc Removing the now redundant --no-gui argument for the test suite.
peterjc authored Dec 4, 2008
419 #install_requires = ['numpy>=1.0'],
65df9bd Minor changes to setup file to make it compatible with the python pac…
chapmanb authored Sep 28, 2008
420 #extras_require = {
421 # 'PDF' : ['reportlab>=2.0']
422 # }
94b412a See bug #2375. Copy data files to the build directory, so the tests run
mdehoon authored Jun 27, 2008
423 # package_data = {'Bio.Entrez': ['DTDs/*.dtd']}
424 ## Use this once we require Python version >= 2.4.
fdcb82e added code so that it now checks for dependencies before biopython is
jchang authored Feb 19, 2003
425 )
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