Merge pull request NeuralEnsemble#1179 from JuliaSprenger/new_docs_enh

Further documentation improvements
ocefpaf · Apr 3, 2023 · e42e84d · e42e84d
2 parents f434435 + aa2fbcf
commit e42e84d
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Showing 13 changed files with 50 additions and 141 deletions.
diff --git a/.gitignore b/.gitignore
@@ -66,4 +66,11 @@ neo/test/io/neurosharemergeio.py
 files_for_testing_neo
 /venv
 /neo/test/resources
-doc/source/examples
+doc/examples
+doc/*.abf
+doc/*.png
+doc/*.plx
+doc/*.nev
+doc/*.ns5
+doc/*.nix
+doc/*.nwb
diff --git a/doc/source/bug_reports.rst b/doc/source/bug_reports.rst
@@ -3,7 +3,7 @@ Reporting bugs, requesting new features
 =======================================
 
 If you find a bug, unclear documentation, or would like to add a new feature to Neo,
-please go to https://github.com/NeuralEnsemble/PyNN/issues/.
+please go to https://github.com/NeuralEnsemble/python-neo/issues/.
 
 
 Searching the issue tracker

diff --git a/doc/source/conf.py b/doc/source/conf.py
@@ -111,15 +111,16 @@
 # The theme to use for HTML and HTML Help pages.  Major themes that come with
 # Sphinx are currently 'default' and 'sphinxdoc'.
 # html_theme = 'default'
-html_theme = 'sphinxdoc'
+# html_theme = 'sphinxdoc'
 # html_theme = 'haiku'
 # html_theme = 'scrolls'
 # html_theme = 'agogo'
+html_theme = 'alabaster'
 
 # Theme options are theme-specific and customize the look and feel of a theme
 # further.  For a list of options available for each theme, see the
 # documentation.
-# html_theme_options = {}
+html_theme_options = {'logo': 'neologo_transparent.png'}
 
 # Add any paths that contain custom themes here, relative to this directory.
 # html_theme_path = []
@@ -133,13 +134,13 @@
 
 # The name of an image file (relative to this directory) to place at the top
 # of the sidebar.
-html_logo = 'images/neologo_light.png'
+# html_logo = 'images/neologo_transparent.png'
 
 
 # The name of an image file (within the static path) to use as favicon of the
 # docs.  This file should be a Windows icon file (.ico) being 16x16 or 32x32
 # pixels large.
-html_favicon = None
+html_favicon = 'images/neologo_favicon.png'
 
 
 # Add any paths that contain custom static files (such as style sheets) here,

diff --git a/doc/source/images/neologo_favicon.png b/doc/source/images/neologo_favicon.png
diff --git a/doc/source/images/neologo_transparent.png b/doc/source/images/neologo_transparent.png
diff --git a/doc/source/share_data.rst b/doc/source/share_data.rst
@@ -106,7 +106,7 @@ To quickly take a look at the data, let's plot it:
     In [16]: plt.savefig("open_format_example_cc_step.png")
 
 
-.. image:: open_format_example_cc_step.png
+.. image:: ../open_format_example_cc_step.png
 
 
 Now we've read the data into Neo, we're ready to write them to an open format.

diff --git a/examples/igorio.ipynb b/examples/igorio.ipynb
diff --git a/examples/igorio.py b/examples/igorio.py
@@ -0,0 +1,31 @@
+"""
+IgorProIO Demo
+===========================
+
+"""
+
+import os
+from urllib.request import urlretrieve
+import zipfile
+import matplotlib.pyplot as plt
+from neo.io import get_io
+
+
+# Downloaded from Human Brain Project Collaboratory
+# Digital Reconstruction of Neocortical Microcircuitry (nmc-portal)
+# http://microcircuits.epfl.ch/#/animal/8ecde7d1-b2d2-11e4-b949-6003088da632
+datafile_url = "https://microcircuits.epfl.ch/data/released_data/B95.zip"
+filename_zip = "B95.zip"
+filename = 'grouped_ephys/B95/B95_Ch0_IDRest_107.ibw'
+urlretrieve(datafile_url, filename_zip)
+
+zip_ref = zipfile.ZipFile(filename_zip)  # create zipfile object
+zip_ref.extract(path='.', member=filename)  # extract file to dir
+zip_ref.close()
+
+
+reader = get_io(filename)
+signal = reader.read_analogsignal()
+plt.plot(signal.times, signal)
+plt.xlabel(signal.sampling_period.dimensionality)
+plt.ylabel(signal.dimensionality)
diff --git a/examples/nmc-portal/grouped_ephys/B95/B95_Ch0_IDRest_107.ibw b/examples/nmc-portal/grouped_ephys/B95/B95_Ch0_IDRest_107.ibw
diff --git a/examples/nmc-portal/grouped_ephys/B95/B95_Ch0_IDRest_107.pxp b/examples/nmc-portal/grouped_ephys/B95/B95_Ch0_IDRest_107.pxp
diff --git a/examples/plot_with_matplotlib.py b/examples/plot_with_matplotlib.py
@@ -13,7 +13,7 @@
 import neo
 
 distantfile = 'https://web.gin.g-node.org/NeuralEnsemble/ephy_testing_data/raw/master/plexon/File_plexon_3.plx'
-localfile = './File_plexon_3.plx'
+localfile = 'File_plexon_3.plx'
 
 urllib.request.urlretrieve(distantfile, localfile)
 

diff --git a/examples/read_files_neo_io.py b/examples/read_files_neo_io.py
@@ -12,7 +12,7 @@
 
 # Plexon files
 distantfile = url_repo + 'plexon/File_plexon_3.plx'
-localfile = './File_plexon_3.plx'
+localfile = 'File_plexon_3.plx'
 urllib.request.urlretrieve(distantfile, localfile)
 
 # create a reader

diff --git a/examples/read_files_neo_rawio.py b/examples/read_files_neo_rawio.py
@@ -12,7 +12,7 @@
 
 # Get Plexon files
 distantfile = url_repo + 'plexon/File_plexon_3.plx'
-localfile = './File_plexon_3.plx'
+localfile = 'File_plexon_3.plx'
 urllib.request.urlretrieve(distantfile, localfile)
 
 # create a reader
@@ -56,7 +56,7 @@
 
 # Read event timestamps and times (take another file)
 distantfile = url_repo + 'plexon/File_plexon_2.plx'
-localfile = './File_plexon_2.plx'
+localfile = 'File_plexon_2.plx'
 urllib.request.urlretrieve(distantfile, localfile)
 
 # Count events per channel