Merge pull request #58 from SmokinCaterpillar/python38

updated pypet to work with python 3.8 and pandas 1.0

.travis.yml

@@ -15,13 +15,13 @@ addons:
 
 matrix:
   include:
-    - python: 3.5
+    - python: 3.7
       env: COVERAGE=OFF GIT_TEST=OFF EXAMPLES=OFF TEST_SUITE=SINGLECORE SCOOP=OFF
-    - python: 3.6
+    - python: 3.8
       env: COVERAGE=OFF GIT_TEST=OFF EXAMPLES=OFF TEST_SUITE=MULTIPROC SCOOP=OFF
-    - python: 3.5
-      env: COVERAGE=ON GIT_TEST=ON EXAMPLES=OFF TEST_SUITE=OFF SCOOP=OFF
     - python: 3.6
+      env: COVERAGE=ON GIT_TEST=ON EXAMPLES=OFF TEST_SUITE=OFF SCOOP=OFF
+    - python: 3.8
       env: COVERAGE=OFF GIT_TEST=ON EXAMPLES=ON TEST_SUITE=OFF SCOOP=ON
 
 
@@ -75,4 +75,5 @@ branches:
     - master
     - brian2
     - py3only
+    - python38
 

CHANGES.txt

@@ -1,3 +1,10 @@
+pypet 0.5.0
+
+* Fix to work with pandas 1.0
+* Fix to work with brian2 2.3
+* Fix to work with Python 3.7 and 3.8
+* Removal `expectedrows` and `filters` option for HDF5Storage.put as this is no longer supported by pandas
+
 pypet 0.4.3
 
 *   DEPR: Removed pandas Panel and Panel4D (see also https://github.com/pandas-dev/pandas/pull/13776)

LICENSE

@@ -1,4 +1,4 @@
-Copyright (c) 2013-2018, Robert Meyer
+Copyright (c) 2013-2020, Robert Meyer
 All rights reserved.
 
 Redistribution and use in source and binary forms, with or without modification,

README.md

@@ -21,15 +21,15 @@ analyses becomes a piece of cake!
 
 Python 3.5 or 3.6 and
 
-* tables >=  3.1.1
+* tables >=  3.5.0
 
-* pandas >= 0.20.0
+* pandas >= 1.0.0
 
-* numpy >= 1.12.0
+* numpy >= 1.16.0
 
-* scipy >= 0.17.0
+* scipy >= 1.3.0
 
-* HDF5 >= 1.8.9
+* HDF5 >= 1.10.0
 
 
 There are also some optional packages that you can but do not have to install.
@@ -40,15 +40,15 @@ If you want to combine *pypet* with SCOOP you need
 
 For git integration you additionally need
 
-* GitPython >= 0.3.1
+* GitPython >= 3.1.3
 
 To utilize the cap feature for multiprocessing you need
 
-* psutil >= 2.0.0
+* psutil >= 5.7.0
 
 To utilize the continuing of crashed trajectories you need
 
-* dill >= 0.2.1
+* dill >= 0.3.1
 
 Automatic Sumatra records are supported for
 

appveyor.yml

@@ -10,49 +10,49 @@ environment:
 
     matrix:
         - PYTHON: "C:\\Python35_64"
-          PYTHON_VERSION: "3.5"
+          PYTHON_VERSION: "3.8"
           PYTHON_ARCH: "64"
           MULTIPROC: "OFF"
           SINGLECORE: "1"
           EXAMPLES: "ON"
 
         - PYTHON: "C:\\Python35_32"
-          PYTHON_VERSION: "3.5"
+          PYTHON_VERSION: "3.8"
           PYTHON_ARCH: "32"
           MULTIPROC: "1"
           SINGLECORE: "OFF"
           EXAMPLES: "OFF"
 
         - PYTHON: "C:\\Python35_64"
-          PYTHON_VERSION: "3.5"
+          PYTHON_VERSION: "3.8"
           PYTHON_ARCH: "64"
           MULTIPROC: "3"
           SINGLECORE: "OFF"
           EXAMPLES: "OFF"
 
         - PYTHON: "C:\\Python35_32"
-          PYTHON_VERSION: "3.5"
+          PYTHON_VERSION: "3.8"
           PYTHON_ARCH: "32"
           MULTIPROC: "2"
           SINGLECORE: "OFF"
           EXAMPLES: "OFF"
 
         - PYTHON: "C:\\Python35_64"
-          PYTHON_VERSION: "3.5"
+          PYTHON_VERSION: "3.8"
           PYTHON_ARCH: "64"
           MULTIPROC: "4"
           SINGLECORE: "OFF"
           EXAMPLES: "OFF"
 
         - PYTHON: "C:\\Python35_64"
-          PYTHON_VERSION: "3.5"
+          PYTHON_VERSION: "3.8"
           PYTHON_ARCH: "64"
           MULTIPROC: "OFF"
           SINGLECORE: "2"
           EXAMPLES: "ON"
 
         - PYTHON: "C:\\Python35_32"
-          PYTHON_VERSION: "3.5"
+          PYTHON_VERSION: "3.8"
           PYTHON_ARCH: "32"
           MULTIPROC: "OFF"
           SINGLECORE: "3"
@@ -83,6 +83,7 @@ branches:
     - develop
     - brian2
     - py3only
+    - python38
 
 
 test_script:

ciscripts/appveyor/install.ps1

@@ -7,7 +7,7 @@ $MINICONDA_URL = "http://repo.continuum.io/miniconda/"
 
 function DownloadMiniconda ($python_version, $platform_suffix) {
     $webclient = New-Object System.Net.WebClient
-    if ($python_version -match "3.5") {
+    if ($python_version -match "3.8") {
         $filename = "Miniconda3-latest-Windows-" + $platform_suffix + ".exe"
     } else {
         $filename = "Miniconda-latest-Windows-" + $platform_suffix + ".exe"

doc/source/conf.py

@@ -46,16 +46,16 @@
 
 # General information about the project.
 project = u'pypet'
-copyright = u'2013, Robert Meyer'
+copyright = u'2020, Robert Meyer'
 
 # The version info for the project you're documenting, acts as replacement for
 # |version| and |release|, also used in various other places throughout the
 # built documents.
 #
 # The short X.Y version.
-version = '0.4'
+version = '0.5'
 # The full version, including alpha/beta/rc tags.
-release = '0.4.2'
+release = '0.5.0'
 
 # The language for content autogenerated by Sphinx. Refer to documentation
 # for a list of supported languages.

doc/source/manual/introduction.rst

@@ -90,17 +90,17 @@ Getting Started
 Requirements
 ------------
 
-3.4, 3.5, or 3.6 [#pythonversion]_, and
+3.6, 3.7, or 3.8 [#pythonversion]_, and
 
-* numpy_ >= 1.13.0
+* numpy_ >= 1.16.0
 
 * scipy_ >= 1.0.0
 
-* tables_ >= 3.1.1
+* tables_ >= 3.5.0
 
-* pandas_ >= 0.23.0
+* pandas_ >= 1.0.0
 
-* HDF5_ >= 1.8.9
+* HDF5_ >= 1.10.0
 
 Python 2.6 and 2.7 are no longer supported. Still if you
 need *pypet* for these versions check out the legacy `0.3.0`_ package.
@@ -115,15 +115,15 @@ If you want to combine *pypet* with the `SCOOP framework`_ you need
 
 For git integration you additionally need
 
-* GitPython_ >= 0.3.1
+* GitPython_ >= 3.1.3
 
 To utilize the cap feature for :ref:`more-on-multiprocessing` you need
 
-* psutil_ >= 2.0.0
+* psutil_ >= 5.7.0
 
 To utilize the continuing of crashed trajectories you need
 
-* dill_ >= 0.2.1
+* dill_ >= 0.3.1
 
 Automatic sumatra records are supported for
 
@@ -133,7 +133,7 @@ Automatic sumatra records are supported for
 
 .. [#pythonversion]
 
-    *pypet* might also work under Python 3.0-3.2 but has not been tested.
+    *pypet* might also work under Python 3.0-3.5 but has not been tested.
 
 
 -------

pypet/_version.py

@@ -1 +1 @@
-__version__ = '0.4.4dev'
+__version__ = '0.5.0dev'

pypet/brian2/parameter.py

@@ -44,7 +44,7 @@ def unit_from_expression(expr):
         return unit_from_expression(expr)
     elif expr.__class__ is ast.Name:
         return ALLUNITS[expr.id]
-    elif expr.__class__ is ast.Num:
+    elif expr.__class__ is ast.Num or expr.__class__ is ast.Constant:
         return expr.n
     elif expr.__class__ is ast.UnaryOp:
         op = expr.op.__class__.__name__

pypet/storageservice.py

@@ -4182,8 +4182,8 @@ def _prm_write_pandas_data(self, key, data, group, fullname, flag, **kwargs):
         """
         try:
             if 'filters' not in kwargs:
-                filters = self._all_get_filters(kwargs)
-                kwargs['filters'] = filters
+                self._logger.debug(
+                    'filters are no longer supported by pandas')
             if 'format' not in kwargs:
                 kwargs['format'] = self.pandas_format
             if 'encoding' not in kwargs:
@@ -4198,8 +4198,9 @@ def _prm_write_pandas_data(self, key, data, group, fullname, flag, **kwargs):
             else:
                 self._logger.debug('Appending to pandas data `%s` in `%s`' % (key, fullname))
 
-            if data is not None and (kwargs['format'] == 'f' or kwargs['format'] == 'fixed'):
-                kwargs['expectedrows'] = data.shape[0]
+            if 'expectedrows' in kwargs:
+                self._logger.debug('expectedrows no longer supported by pandas, will '
+                                   'ignore the option')
 
             name = group._v_pathname + '/' + key
             self._hdf5store.put(name, data, **kwargs)

pypet/utils/comparisons.py

@@ -184,7 +184,7 @@ def nested_equal(a, b):
             new_frame = a == b
             new_frame = new_frame | (pd.isnull(a) & pd.isnull(b))
             if isinstance(new_frame, pd.DataFrame):
-                return np.all(new_frame.as_matrix())
+                return np.all(new_frame.values)
         except (ValueError, TypeError):
             # The Value Error can happen if the data frame is of dtype=object and contains
             # numpy arrays. Numpy array comparisons do not evaluate to a single truth value

pypet/utils/helpful_classes.py

@@ -62,7 +62,12 @@ def __next__(self):
 
     def __iter__(self):
         while True:
-            yield self.next()
+            try:
+                yield self.next()
+            except StopIteration:
+                # new behavior since PEP479
+                # one should return to stop iteration
+                return
 
 
 class ChainMap(object):