elephant dir packages are back (NeuralEnsemble#239)

* reverted removed imports of elephant's internal packages; download fim during the setup

* download fim from tools/fim_manager.py

* dummy tools/__init__.py to support py2

* include requirements in MANIFEST back

* fixed spade licence typo

* included waveform_features module; removed tools; don't donwload fim at setup while macking a tarball with 'sdist' command

travis not fixed downloading fim

* skip time consuming test_spade_cpp if not HAVE_FIM

* travis pip install generated tarball

* recursive-include elephant *.py

.gitignore

@@ -15,7 +15,9 @@ nosetests.xml
 .pydevproject
 .settings
 *.tmp*
-.idea
+.idea/
+venv/
+env/
 .pytest_cache/
 
 # Compiled source #

.travis.yml

@@ -73,7 +73,8 @@ install:
 
   - pip -V
   - pip install coverage coveralls nose
-  - pip install .
+  - python setup.py install
+  - python -c "from elephant.spade import HAVE_FIM; assert HAVE_FIM"
   - pip list
   - python --version
 

MANIFEST.in

@@ -1,12 +1,13 @@
+recursive-include elephant *.py
+include requirements*.txt
 include README.rst
 include LICENSE.txt
 include AUTHORS.txt
 include elephant/VERSION
 include elephant/current_source_density_src/README.md
 include elephant/current_source_density_src/test_data.mat
-include elephant/spade_src/LICENCE
+include elephant/spade_src/LICENSE
+recursive-include elephant/spade_src *.so *.pyd
 include elephant/test/spike_extraction_test_data.txt
 recursive-include doc *
-
-# special care for the files, used in setup.py
-include elephant/spade_src/fim_manager.py
+prune doc/_build

elephant/__init__.py

@@ -6,6 +6,33 @@
 :license: Modified BSD, see LICENSE.txt for details.
 """
 
+from . import (statistics,
+               spike_train_generation,
+               spike_train_correlation,
+               unitary_event_analysis,
+               cubic,
+               spectral,
+               kernels,
+               spike_train_dissimilarity,
+               spike_train_surrogates,
+               signal_processing,
+               current_source_density,
+               change_point_detection,
+               phase_analysis,
+               sta,
+               conversion,
+               neo_tools,
+               spade,
+               cell_assembly_detection,
+               waveform_features)
+
+try:
+    from . import pandas_bridge
+    from . import asset
+except ImportError:
+    # requirements-extras are missing
+    pass
+
 
 def _get_version():
     import os

elephant/spade.py

@@ -66,13 +66,9 @@
 import quantities as pq
 import warnings
 from elephant.spade_src import fast_fca
-from elephant.spade_src.fim_manager import download_spade_fim
 
 warnings.simplefilter('once', UserWarning)
 
-# if not downloaded during the install, do it now
-download_spade_fim()
-
 
 try:
     from mpi4py import MPI  # for parallelized routines

elephant/test/test_spade.py

@@ -6,7 +6,6 @@
 """
 from __future__ import division
 
-import os
 import unittest
 
 import neo
@@ -18,8 +17,6 @@
 import elephant.spade as spade
 import elephant.spike_train_generation as stg
 from elephant.spade import HAVE_FIM
-from elephant.spade_src.fim_manager import download_spade_fim, \
-    _get_fim_lib_path
 
 
 class SpadeTestCase(unittest.TestCase):
@@ -110,6 +107,7 @@ def setUp(self):
         self.patt_psr = self.patt3 + [self.patt3[-1][:3]]
 
     # Testing cpp
+    @unittest.skipUnless(HAVE_FIM, "Time consuming with pythonic FIM")
     def test_spade_cpp(self):
         output_cpp = spade.spade(self.cpp, self.binsize, 1,
                                  n_subsets=self.n_subset,
@@ -243,7 +241,7 @@ def test_parameters(self):
         # check the lags
         assert_array_equal([len(lags) < self.max_spikes for lags in
                             lags_msip_max_spikes], [True] * len(
-                                lags_msip_max_spikes))
+            lags_msip_max_spikes))
 
         # test max_occ parameter
         output_msip_max_occ = spade.spade(self.msip, self.binsize, self.winlen,
@@ -371,12 +369,11 @@ def test_spectrum(self):
                                             self.winlen, report='3d#')[0]
         assert_array_equal(spectrum_3d, [
             [len(self.lags3) + 1, self.n_occ3, max(self.lags3), 1]])
-    # test the errors raised
 
     def test_spade_raise_error(self):
         # Test list not using neo.Spiketrain
         self.assertRaises(TypeError, spade.spade, [
-                          [1, 2, 3], [3, 4, 5]], 1 * pq.ms, 4)
+            [1, 2, 3], [3, 4, 5]], 1 * pq.ms, 4)
         # Test neo.Spiketrain with different t_stop
         self.assertRaises(AttributeError, spade.spade, [neo.SpikeTrain(
             [1, 2, 3] * pq.s, t_stop=5 * pq.s), neo.SpikeTrain(
@@ -385,7 +382,7 @@ def test_spade_raise_error(self):
         self.assertRaises(ValueError, spade.spade, [neo.SpikeTrain(
             [1, 2, 3] * pq.s, t_stop=6 * pq.s), neo.SpikeTrain(
             [3, 4, 5] * pq.s, t_stop=6 * pq.s)], 1 * pq.ms, 4, n_surr=1,
-            spectrum='try')
+                          spectrum='try')
         # Test negative minimum number of spikes
         self.assertRaises(AttributeError, spade.spade, [neo.SpikeTrain(
             [1, 2, 3] * pq.s, t_stop=5 * pq.s), neo.SpikeTrain(
@@ -394,14 +391,13 @@ def test_spade_raise_error(self):
         self.assertRaises(AttributeError, spade.pvalue_spectrum, [
             neo.SpikeTrain([1, 2, 3] * pq.s, t_stop=5 * pq.s), neo.SpikeTrain(
                 [3, 4, 5] * pq.s, t_stop=5 * pq.s)], 1 * pq.ms, 4, 3 * pq.ms,
-            n_surr=-3)
+                          n_surr=-3)
         # Test wrong correction parameter
         self.assertRaises(AttributeError, spade.test_signature_significance, (
             (2, 3, 0.2), (2, 4, 0.1)), 0.01, corr='try')
         # Test negative number of subset for stability
         self.assertRaises(AttributeError, spade.approximate_stability, (),
                           np.array([]), n_subsets=-3)
-    # test psr
 
     def test_pattern_set_reduction(self):
         output_msip = spade.spade(self.patt_psr, self.binsize, self.winlen,
@@ -426,13 +422,6 @@ def test_pattern_set_reduction(self):
         # check the occurrences time of the patters
         assert_array_equal(len(occ_msip[0]), self.n_occ3)
 
-    def test_download_spade_fim(self):
-        fim_lib_path = _get_fim_lib_path()
-        if os.path.exists(fim_lib_path):
-            os.unlink(fim_lib_path)
-        download_spade_fim()
-        assert os.path.exists(fim_lib_path)
-
 
 def suite():
     suite = unittest.makeSuite(SpadeTestCase, 'test')

setup.py

@@ -1,14 +1,23 @@
 # -*- coding: utf-8 -*-
 
+import os
+import platform
+import struct
 import sys
 
 from setuptools import setup
 
-from elephant import __version__
-from elephant.spade_src.fim_manager import download_spade_fim
-
 python_version_major = sys.version_info.major
 
+if python_version_major == 2:
+    from urllib import urlretrieve
+else:
+    from urllib.request import urlretrieve
+
+with open(os.path.join(os.path.dirname(__file__),
+                       "elephant", "VERSION")) as version_file:
+    version = version_file.read().strip()
+
 with open("README.rst") as f:
     long_description = f.read()
 with open('requirements.txt') as fp:
@@ -18,11 +27,39 @@
     with open('requirements-{0}.txt'.format(extra)) as fp:
         extras_require[extra] = fp.read()
 
-download_spade_fim()
+
+def download_spade_fim():
+    """
+    Downloads SPADE specific PyFIM binary file.
+    """
+    if platform.system() == "Windows":
+        fim_filename = "fim.pyd"
+    else:
+        # Linux
+        fim_filename = "fim.so"
+    spade_src_dir = os.path.join(os.path.dirname(__file__), "elephant",
+                                 "spade_src")
+    fim_lib_path = os.path.join(spade_src_dir, fim_filename)
+    if os.path.exists(fim_lib_path):
+        return
+
+    arch_bits = struct.calcsize("P") * 8
+    url_fim = "http://www.borgelt.net/bin{arch}/py{py_ver}/{filename}". \
+        format(arch=arch_bits, py_ver=python_version_major,
+               filename=fim_filename)
+    try:
+        urlretrieve(url_fim, filename=fim_lib_path)
+        print("Successfully downloaded fim lib to {}".format(fim_lib_path))
+    except Exception:
+        print("Unable to download {url} module.".format(url=url_fim))
+
+
+if len(sys.argv) > 1 and sys.argv[1].lower() != 'sdist':
+    download_spade_fim()
 
 setup(
     name="elephant",
-    version=__version__,
+    version=version,
     packages=['elephant', 'elephant.test'],
     include_package_data=True,