master: Merged release into master

.bumpversion.cfg

@@ -1,5 +1,5 @@
 [bumpversion]
-current_version = 0.0.2
+current_version = 0.0.3
 commit = True
 tag = True
 

.gitignore

@@ -55,11 +55,12 @@ launch_satellite_engine/bin/launch_satellite_engine.exe
 *.cache
 *.pyc
 
-\.coverage
-
-\.idea/
+.idea/
 
 
 build/
 dist/
 pywavesurfer.egg-info/
+.pytest_cache
+htmlcov/
+.coverage

README.rst

@@ -89,6 +89,9 @@ Version History
 
 0.0.2    Oct 14, 2017    Added a check for WS version.
 
+0.0.3    Aug 23, 2018    Added test for WS 0.97 data files, changed an
+                         exception to a warning, updated dependencies.
+
 
 .. |Updates| image:: https://pyup.io/repos/github/JaneliaSciComp/PyWaveSurfer/shield.svg
    :target: https://pyup.io/repos/github/JaneliaSciComp/PyWaveSurfer/

developer-notes.txt

@@ -1,24 +1,54 @@
-Users: This files contains information for the Wavesurfer
+Users: This files contains information for the PyWaveSurfer
 developer(s).  You can safely ignore it.
 
 
 
 To bump version
 ---------------
 
-1. Run: bumpversion patch (or 'minor' or 'major' following: major.minor.patch)
+0. pip install --user bumpversion
 
-2. Add a paragraph to the README about the new release.
+   This installs the bumpversion command-line tool for the current user.
 
-3. Run: python setup.py sdist
+1. Checkout the release branch, merge develop branch into it.
 
-4. Run: twine upload dist\pywaveserfer{version}
+2. Run: bumpversion patch (or 'minor' or 'major' following:
+   major.minor.patch)
+
+   This modifies the setup.py file in the root of the repo.  It also
+   changes .bumpversion.cfg to reflect the new version.  ***It then
+   does a git commit of these changes, with a comment
+   like "Bump version: 0.0.2 -> 0.0.3".***  (That's why you should be
+   on a release branch before you do this.)
+
+3. Add a paragraph to the README about the new release.
+
+4. Commit to the release branch, then switch over to master, and merge
+   in the release branch.
+
+5. Run: python3 setup.py sdist
+
+   Runs the setup.py script that got updated in the "bumpversion" step
+   above.  This creates/updates the dist folder and the
+   pywavesurfer.egg-info folders, which contain a packaged version of
+   the pywavesurfer module, ready for uploading to PyPI, and some
+   metadata pertaining to it.  
+
+6. Run: twine upload dist\pywaveserfer{version}
+
+   This uploads the module to PyPI.
 
 
 
 To run automated tests
 ----------------------
 
+0. Do
+
+       pip install --user pytest
+       pip install --user pytest-pep8
+       pip install --user pytest-coverage
+
 1. Change directory to pywavesurfer
 
 2. Run: pytest --pep8
@@ -27,7 +57,7 @@ To run automated tests
 
 
 
-pyWavesurfer coding/development conventions
+PyWaveSurfer coding/development conventions
 -----------------------------------------
 
 As much as possible please adhere to PEP8.

pywavesurfer/ws.py

@@ -2,9 +2,10 @@
 import math
 import numpy as np
 import h5py
+import warnings
 
 # the latest version pywavesurfer was tested against
-_latest_version = 0.953
+_latest_version = 0.97
 
 # from pywavesurfer.ws import * will only import loadDataFile
 __all__ = ['loadDataFile']
@@ -37,8 +38,8 @@ def loadDataFile(filename, format_string='double'):
         version_string = header["VersionString"]  # this is a scalar numpy array with a weird datatype
         version = float(version_string.tostring().decode('utf-8'))
         if version > _latest_version:
-            raise RuntimeWarning('You are reading a WaveSurfer file version this module was not tested with: '
-                                 'file version %f, latest version tested: %f' % (version, _latest_version))
+            warnings.warn('You are reading a WaveSurfer file version this module was not tested with: '
+                          'file version %f, latest version tested: %f' % (version, _latest_version), RuntimeWarning)
     else:
         # If no VersionsString field, the file is from an old old version
         version = 0

requirements-dev.txt

@@ -1,7 +1,7 @@
 bumpversion==0.5.3
-h5py==2.7.1
-numpy==1.13.3
-pytest==3.2.3
+h5py==2.8.0
+numpy==1.15.1
+pytest==3.7.2
 pytest-pep8==1.0.6
 pytest-cov==2.5.1
-coveralls==1.2.0
+coveralls==1.3.0

requirements.txt

@@ -1,2 +1,2 @@
-h5py == 2.7.1
-numpy == 1.13.3
+h5py==2.8.0
+numpy==1.15.1

setup.py

@@ -16,13 +16,13 @@
 setup(
     name='pywavesurfer',
     packages=['pywavesurfer'],
-    version='0.0.2',
+    version='0.0.3',
     description="Python package for reading WaveSurfer data files",
     long_description=long_description,
     author='Adam L. Taylor, Boaz Mohar',
     author_email='taylora@janelia.hhmi.org, boazmohar@gmail.com',
     url='https://github.com/JaneliaSciComp/PyWaveSurfer',
-    download_url='https://github.com/JaneliaSciComp/PyWaveSurfer/archive/v0.0.2.tar.gz',
+    download_url='https://github.com/JaneliaSciComp/PyWaveSurfer/archive/v0.0.3.tar.gz',
     classifiers=['Development Status :: 3 - Alpha',
                  'Programming Language :: Python :: 2',
                  'Programming Language :: Python :: 2.7',

tests/test_ws.py

@@ -165,13 +165,36 @@ def test_loading_0p933_file():
     assert np.allclose(x.mean(axis=1), np.array([2.49962616]))
 
 
+def test_loading_0p97_file():
+    this_file_path = os.path.realpath(__file__)
+    this_dir_name = os.path.dirname(this_file_path)
+    file_name = os.path.join(this_dir_name, 'ws_0p97_data_0001.h5')
+    dataAsDict = ws.loadDataFile(file_name)
+    acq_sampling_rate = float(dataAsDict['header']['AcquisitionSampleRate'])
+    assert acq_sampling_rate == 20e3
+    n_a_i_channels = dataAsDict['header']['AIChannelScales'].size
+    assert n_a_i_channels == 1
+    n_active_a_i_channels = int(dataAsDict['header']['IsAIChannelActive'].sum())
+    assert n_active_a_i_channels == 1
+    stim_sampling_rate = dataAsDict['header']['StimulationSampleRate']
+    assert stim_sampling_rate == 20e3
+    x = dataAsDict['sweep_0001']['analogScans']
+    assert x.dtype == 'float64'
+    assert np.absolute(np.max(x[0]) - 5) < 0.01
+    assert np.absolute(np.min(x[0]) - 0) < 0.01
+    assert np.allclose(x.mean(axis=1), np.array([2.50221981]))
+
+
 def test_version_higher_then_latest():
     this_file_path = os.path.realpath(__file__)
     this_dir_name = os.path.dirname(this_file_path)
     file_name = os.path.join(this_dir_name, 'ws_v100_data.h5')
-    with pytest.raises(RuntimeWarning) as ex:
+    with pytest.warns(RuntimeWarning) as record:
         _ = ws.loadDataFile(file_name)
-    assert 'You are reading a WaveSurfer file version this module was not' in str(ex.value)
+    # check that only one warning was raised
+    assert len(record) == 1
+    # check that the message matches
+    assert 'You are reading a WaveSurfer file version this module was not' in record[0].message.args[0]
 
 
 def test_identity_function_on_vector():