Merge branch 'NeuralEnsemble:master' into fix/tdt_streams

Author: JuliaSprenger

.github/workflows/caches_cron_job.yml

@@ -60,8 +60,7 @@ jobs:
           git config --global user.email "neo_ci@fake_mail.com"
           git config --global user.name "neo CI"
           python -m pip install -U pip  # Official recommended way
-          pip install --upgrade -e .
-          pip install .[test]
+          pip install --upgrade -e .[test]
 
   create-data-cache-if-missing:
     name: Caching data env

.github/workflows/io-test.yml

@@ -78,7 +78,7 @@ jobs:
         # restore-key hits should result in `cache-hit` == 'false'
         if: steps.cache-conda-env.outputs.cache-hit != 'true'
         run: |
-          conda env update neo-test-env --file environment_testing.yml
+          conda env update --name neo-test-env --file environment_testing.yml --prune
 
       - name: Configure git
         run: |

.gitignore

@@ -66,3 +66,11 @@ neo/test/io/neurosharemergeio.py
 files_for_testing_neo
 /venv
 /neo/test/resources
+doc/examples
+doc/*.abf
+doc/*.png
+doc/*.plx
+doc/*.nev
+doc/*.ns5
+doc/*.nix
+doc/*.nwb

README.rst

@@ -45,7 +45,7 @@ More information
 ----------------
 
 - Home page: http://neuralensemble.org/neo
-- Mailing list: https://groups.google.com/forum/?fromgroups#!forum/neuralensemble
+- Mailing list: http://neuralensemble.org/community
 - Documentation: http://neo.readthedocs.io/
 - Bug reports: https://github.com/NeuralEnsemble/python-neo/issues
 
@@ -74,7 +74,7 @@ No. 785907 (Human Brain Project SGA2) and No. 945539 (Human Brain Project SGA3).
 .. _NiBabel: http://nipy.sourceforge.net/nibabel/
 .. _PyNN: http://neuralensemble.org/PyNN
 .. _quantities: http://pypi.python.org/pypi/quantities
-.. _`NeuralEnsemble mailing list`: http://groups.google.com/group/neuralensemble
+.. _`NeuralEnsemble mailing list`: http://neuralensemble.org/community
 .. _`issue tracker`: https://github.c
 .. _tridesclous: https://github.com/tridesclous/tridesclous
 .. _ephyviewer: https://github.com/NeuralEnsemble/ephyviewer

doc/Makefile

@@ -29,6 +29,7 @@ help:
 
 clean:
 	-rm -rf $(BUILDDIR)/*
+	-rm -rf source/examples
 
 html:
 	$(SPHINXBUILD) -b html $(ALLSPHINXOPTS) $(BUILDDIR)/html

doc/example_data.txt

@@ -0,0 +1,13 @@
+{
+    "filename": "example_data.txt",
+    "delimiter": " ",
+    "timecolumn": null,
+    "units": "mV",
+    "time_units": "ms",
+    "sampling_rate": {
+        "value": 1.0,
+        "units": "kHz"
+    },
+    "method": "genfromtxt",
+    "signal_group_mode": "all-in-one"
+}

doc/example_data_about.json

@@ -15,5 +15,4 @@ A set of examples in :file:`neo/examples/` illustrates the use of Neo classes.
 
 .. literalinclude:: ../../examples/read_files_neo_rawio.py
 
-.. literalinclude:: ../../examples/simple_plot_with_matplotlib.py
-
+.. literalinclude:: ../../examples/plot_with_matplotlib.py