Merge branch 'master' into issue799

Author: apdavison

.circleci/config.yml

@@ -7,11 +7,11 @@ workflows:
   version: 2
   test:
     jobs:
-      - test-3.7
+      - test-3.8
 jobs:
-  test-3.7:
+  test-3.8:
     docker:
-      - image: circleci/python:3.7.7
+      - image: circleci/python:3.8.5
 
     environment:
       - NEO_TEST_FILE_DIR: "/home/circleci/repo/files_for_testing_neo"

.circleci/requirements_testing.txt

@@ -1,4 +1,4 @@
-scipy>=0.12.0
+scipy>=1.0.0
 h5py
 igor
 klusta

.travis.yml

@@ -4,26 +4,26 @@ sudo: false
 
 matrix:
   include:
-    - python: "3.5"
-      env: NUMPY_VERSION="1.11.3"
-    - python: "3.5"
-      env: NUMPY_VERSION="1.18.3"
     - python: "3.6"
-      env: NUMPY_VERSION="1.12.1"
+      env: NUMPY_VERSION="1.14.6"
     - python: "3.6"
       env: NUMPY_VERSION="1.18.3"
     - python: "3.7"
-      env: NUMPY_VERSION="1.14.5"
+      env: NUMPY_VERSION="1.14.6"
     - python: "3.7"
+      env: NUMPY_VERSION="1.19.2"
+    - python: "3.8"
+      env: NUMPY_VERSION="1.14.6"
+    - python: "3.8"
       env: NUMPY_VERSION="1.15.4"
-    - python: "3.7"
+    - python: "3.8"
       env: NUMPY_VERSION="1.16.6"
-    - python: "3.7"
+    - python: "3.8"
       env: NUMPY_VERSION="1.17.5"
-    - python: "3.7"
-      env: NUMPY_VERSION="1.18.3"
     - python: "3.8"
-      env: NUMPY_VERSION="1.18.3"
+      env: NUMPY_VERSION="1.18.5"
+    - python: "3.8"
+      env: NUMPY_VERSION="1.19.2"
 
 # command to install dependencies
 before_install:

doc/source/core.rst

@@ -117,13 +117,14 @@ These relationships are bi-directional, i.e. a child object can access its paren
 Here is an example showing these relationships in use::
 
     from neo.io import AxonIO
-    import urllib
+    import urllib.request
     url = "https://web.gin.g-node.org/NeuralEnsemble/ephy_testing_data/raw/master/axon/File_axon_3.abf"
     filename = './test.abf'
-    urllib.urlretrieve(url, filename)
+    urllib.request.urlretrieve(url, filename)
 
     r = AxonIO(filename=filename)
-    bl = r.read() # read the entire file > a Block
+    blocks = r.read() # read the entire file > a list of Blocks
+    bl = blocks[0]
     print(bl)
     print(bl.segments) # child access
     for seg in bl.segments:

doc/source/install.rst

@@ -5,48 +5,52 @@ Installation
 Neo is a pure Python package, so it should be easy to get it running on any
 system.
 
+Installing from the Python Package Index
+========================================
+
 Dependencies
-============
+------------
 
-    * Python_ >= 3.5
-    * numpy_ >= 1.11.0
+    * Python_ >= 3.6
+    * numpy_ >= 1.13.0
     * quantities_ >= 0.12.1
 
-For Debian/Ubuntu, you can install these using::
-
-    $ apt-get install python-numpy python-pip
-    $ pip install quantities
+You can install the latest published version of Neo and its dependencies using::
 
-You may need to run these as root. For other operating systems, you can
-download installers from the links above, or use a scientific Python distribution
-such as Anaconda_.
+    $ pip install neo
 
 Certain IO modules have additional dependencies. If these are not satisfied,
 Neo will still install but the IO module that uses them will fail on loading:
 
-   * scipy >= 0.12.0 for NeoMatlabIO
+   * scipy >= 1.0.0 for NeoMatlabIO
    * h5py >= 2.5 for Hdf5IO, KwikIO
    * klusta for KwikIO
    * igor >= 0.2 for IgorIO
    * nixio >= 1.5 for NixIO
    * stfio for StimfitIO
    * pillow for TiffIO
 
+These dependencies can be installed by specifying a comma seperated list on the
+``pip install`` command::
 
-Installing from the Python Package Index
-========================================
+    $ pip install neo[hdf5io,tiffio]
 
-.. warning:: alpha and beta releases cannot be installed from PyPI.
+Or when installing a specific version of neo::
 
-If you have pip_ installed::
+    $ pip install neo[hdf5io,tiffio]==0.8.0
 
-    $ pip install neo
+These additional dependencies for IO modules are available::
+
+  * hdf5io
+  * igorproio
+  * kwikio
+  * neomatlabio
+  * nixio
+  * stimfitio
+  * tiffio
 
-This will automatically download and install the latest release (again
-you may need to have administrator privileges on the machine you are installing
-on).
 
-To download and install manually, download:
+To download and install the package manually, download:
 
     |neo_github_url|
 
@@ -60,14 +64,6 @@ Then:
     $ python setup.py install
 
 
-
-or::
-
-    $ python3 setup.py install
-
-depending on which version of Python you are using.
-
-
 Installing from source
 ======================
 

neo/core/analogsignal.py

@@ -443,8 +443,8 @@ def _pp(line):
             with pp.group(indent=1):
                 pp.text(line)
 
-        for line in ["sampling rate: {}".format(self.sampling_rate),
-                     "time: {} to {}".format(self.t_start, self.t_stop)]:
+        for line in ["sampling rate: {!s}".format(self.sampling_rate),
+                     "time: {!s} to {!s}".format(self.t_start, self.t_stop)]:
             _pp(line)
 
     def time_index(self, t):

neo/core/dataobject.py

@@ -331,12 +331,6 @@ def _get_arr_ann_length(self):
             length = 1
         return length
 
-    def duplicate_with_new_array(self, signal, units=None):
-        warnings.warn("Use of the `duplicate_with_new_array function is deprecated. "
-                      "Please use `duplicate_with_new_data` instead.",
-                      DeprecationWarning)
-        return self.duplicate_with_new_data(signal, units=units)
-
     def __deepcopy__(self, memo):
         """
             Create a deep copy of the data object.

neo/core/imagesequence.py

@@ -205,8 +205,8 @@ def _pp(line):
                 pp.text(line)
 
         for line in [
-            "sampling rate: {}".format(self.sampling_rate),
-            "spatial_scale: {}".format(self.spatial_scale),
+            "sampling rate: {!s}".format(self.sampling_rate),
+            "spatial_scale: {!s}".format(self.spatial_scale),
         ]:
             _pp(line)
 

neo/core/spiketrain.py

@@ -599,6 +599,13 @@ def time_slice(self, t_start, t_stop):
             _t_start = -np.inf
         if t_stop is None:
             _t_stop = np.inf
+
+        if _t_start > self.t_stop or _t_stop < self.t_start:
+            # the alternative to raising an exception would be to return
+            # a zero-duration spike train set at self.t_stop or self.t_start
+            raise ValueError("A time slice completely outside the "
+                             "boundaries of the spike train is not defined.")
+
         indices = (self >= _t_start) & (self <= _t_stop)
 
         # Time slicing should create a deep copy of the object

neo/io/asciiimageio.py

@@ -56,11 +56,6 @@ def __init__(self, file_name=None, nb_frame=None, nb_row=None, nb_column=None, u
         self.sampling_rate = sampling_rate
         self.spatial_scale = spatial_scale
 
-    def read(self, lazy=False, **kwargs):
-        if lazy:
-            raise ValueError('This IO module does not support lazy loading')
-        return [self.read_block(lazy=lazy, **kwargs)]
-
     def read_block(self, lazy=False, **kwargs):
 
         file = open(self.filename, 'r')