Merge pull request #65 from baccuslab/dev

Release 0.4
baccuslab · Dec 12, 2015 · 47836b2 · 47836b2
2 parents 5c7239f + e576d29
commit 47836b2
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diff --git a/.gitignore b/.gitignore
@@ -8,6 +8,7 @@
 *.so
 *.pyc
 build/
+_build/
 dist/
 
 # Packages #

diff --git a/Makefile b/Makefile
@@ -0,0 +1,19 @@
+all:
+	pip install -r requirements.txt
+	python setup.py install
+
+develop:
+	pip install -r requirements-dev.txt
+	python setup.py develop
+
+test:
+	py.test -v --cov=pyret --cov-report=html tests
+
+clean:
+	rm -rf htmlcov/
+	rm -rf pyret.egg-info
+	rm -f pyret/*.pyc
+	rm -rf pyret/__pycache__
+
+upload:
+	python setup.py sdist bdist_wininst upload
diff --git a/README.md b/README.md
@@ -3,8 +3,7 @@
 ### A Python package for analyzing retinal data
 Benjamin Naecker, Niru Maheswaranthan, Pablo Jadzinsky
 
-![receptive field](https://cloud.githubusercontent.com/assets/904854/5329965/f91ee8e2-7d81-11e4-873f-d4253165bce9.png)
-![spikes](https://cloud.githubusercontent.com/assets/904854/5329966/f91f8090-7d81-11e4-92ea-746a659ea285.png)
+<img src="https://cloud.githubusercontent.com/assets/904854/5329965/f91ee8e2-7d81-11e4-873f-d4253165bce9.png" height="256">
 
 Brief description
 -----------------
@@ -15,15 +14,15 @@ analyses, and visualization tools.
 
 Documentation
 -------------
-For more info and documentation, see the [pyret website](http://baccuslab.github.io/pyret/)
+For more info and documentation, see the [pyret documentation](http://pyret.readthedocs.org/en/latest/)
 
 Demo
 ----
-For a demo of how to do analysis using `pyret`, check out the html file and corresponding ipython notebook in the `demo/` folder.
+(coming soon) For a demo of how to do analysis using `pyret`, check out the html file and corresponding ipython notebook in the `demo/` folder.
 
 Contributing
 ------------
-Pull requests are welcome! We follow the [NumPy/SciPy documentation standards](https://github.com/numpy/numpy/blob/master/doc/HOWTO_DOCUMENT.rst.txt#docstring-standard), and [Sphinx](http://sphinx-doc.org/index.html) for generating documentation.
+Pull requests are welcome! We follow the [Numpy/Scipy documentation standards](https://github.com/numpy/numpy/blob/master/doc/HOWTO_DOCUMENT.rst.txt#docstring-standard), and [Sphinx](http://sphinx-doc.org/index.html) for generating documentation.
 
 Testing
 -------

diff --git a/doc/releases/v0.3.rst b/doc/releases/v0.3.rst
diff --git a/doc/Makefile → docs/Makefile b/doc/Makefile → docs/Makefile
@@ -5,7 +5,7 @@
 SPHINXOPTS    =
 SPHINXBUILD   = sphinx-build
 PAPER         =
-BUILDDIR      = ../../pyret-docs
+BUILDDIR      = _build
 
 # User-friendly check for sphinx-build
 ifeq ($(shell which $(SPHINXBUILD) >/dev/null 2>&1; echo $$?), 1)

diff --git a/doc/api.rst → docs/api.rst b/doc/api.rst → docs/api.rst
@@ -7,39 +7,47 @@ API Reference
 filtertools
 -----------
 
-.. automodule:: filtertools
+.. automodule:: pyret.filtertools
     :members:
     :undoc-members:
     :show-inheritance:
 
 nonlinearities
 --------------
 
-.. automodule:: nonlinearities
+.. automodule:: pyret.nonlinearities
     :members:
     :undoc-members:
     :show-inheritance:
 
 spiketools
 ----------
 
-.. automodule:: spiketools
+.. automodule:: pyret.spiketools
     :members:
     :undoc-members:
     :show-inheritance:
 
 stimulustools
 -------------
 
-.. automodule:: stimulustools
+.. automodule:: pyret.stimulustools
     :members:
     :undoc-members:
     :show-inheritance:
 
 visualizations
 --------------
 
-.. automodule:: visualizations
+.. automodule:: pyret.visualizations
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+containers
+----------
+
+.. automodule:: pyret.containers
     :members:
     :undoc-members:
     :show-inheritance:
diff --git a/doc/changelog.rst → docs/changelog.rst b/doc/changelog.rst → docs/changelog.rst
@@ -3,5 +3,6 @@ Changelog
 
 A list of new features, improvements, and bug-fixes in each release.
 
+.. include:: releases/v0.4.rst
 .. include:: releases/v0.3.rst
 .. include:: releases/v0.2.rst
diff --git a/doc/conf.py → docs/conf.py b/doc/conf.py → docs/conf.py
@@ -12,11 +12,19 @@
 # All configuration values have a default; values that are commented out
 # serve to show the default.
 
+# hack to deal with imports that have C extensions
 import sys
 import os
-sys.path.append('..')
-
+from unittest import mock
 import sphinx_rtd_theme
+MOCK_MODULES = ['scipy', 'matplotlib', 'matplotlib.pyplot', 'scipy.optimize',
+                'scipy.linalg.blas', 'scipy.signal', 'scipy.fftpack', 'skimage',
+                'skimage.restoration', 'skimage.measure', 'skimage.filters',
+                'matplotlib.patches']
+for mod_name in MOCK_MODULES:
+    sys.modules[mod_name] = mock.Mock()
+
+import pyret
 
 # If extensions (or modules to document with autodoc) are in another directory,
 # add these directories to sys.path here. If the directory is relative to the
@@ -33,6 +41,7 @@
 # ones.
 extensions = [
     'sphinx.ext.autodoc',
+    'sphinx.ext.autosummary',
     'sphinx.ext.intersphinx',
     'sphinx.ext.todo',
     'sphinx.ext.coverage',
@@ -62,9 +71,9 @@
 # built documents.
 #
 # The short X.Y version.
-version = '0.2.0'
+version = '0.4'
 # The full version, including alpha/beta/rc tags.
-release = '0.2.0'
+release = '0.4.0'
 
 # The language for content autogenerated by Sphinx. Refer to documentation
 # for a list of supported languages.

diff --git a/doc/index.rst → docs/index.rst b/doc/index.rst → docs/index.rst
@@ -24,4 +24,4 @@ standards to adhere to.
     api
     changelog
 
-:ref:`genindex` of all functions.
+:ref:`genindex` of all functions.
diff --git a/doc/install.rst → docs/install.rst b/doc/install.rst → docs/install.rst
@@ -26,10 +26,8 @@ Pyret requires the following dependencies:
 
 - ``matplotlib``
 
-- ``seaborn``
-
 Development
 -----------
 
 To contribute to ``pyret``, you'll need to also install ``sphinx`` and ``numpydoc`` for documentation and
-``nose`` for testing. We adhere to the `NumPy/SciPy documentation standards <https://github.com/numpy/numpy/blob/master/doc/HOWTO_DOCUMENT.rst.txt#docstring-standard>`_.
+``pytest`` for testing. We adhere to the `NumPy/SciPy documentation standards <https://github.com/numpy/numpy/blob/master/doc/HOWTO_DOCUMENT.rst.txt#docstring-standard>`_.
diff --git a/doc/quickstart.rst → docs/quickstart.rst b/doc/quickstart.rst → docs/quickstart.rst
@@ -4,12 +4,10 @@ Quickstart
 
 Overview
 --------
-
 Coming soon
 
 Demo
 ----
-
 Coming soon
 
 Bugs

diff --git a/doc/releases/v0.2.rst → docs/releases/v0.2.rst b/doc/releases/v0.2.rst → docs/releases/v0.2.rst
@@ -1,6 +1,6 @@
-====================
-v0.2 (February 2015)
-====================
+======================
+v0.2 (February 1 2015)
+======================
 
 This is a major release with a number of API changes, enhancements, and bug fixes.
 

diff --git a/docs/releases/v0.3.rst b/docs/releases/v0.3.rst
@@ -0,0 +1,10 @@
+===================
+v0.3 (June 25 2015)
+===================
+
+API changes
+-----------
+- Changed the `filtertools` module's `getste`, `getsta`, and `getstc` to use
+  generators. The `getste` function now returns a generator that yields samples
+  from the spike-triggered ensemble, while `getsta` and `getstc` consume that
+  generator in order to compute their results.
diff --git a/docs/releases/v0.4.rst b/docs/releases/v0.4.rst
@@ -0,0 +1,26 @@
+==================
+v0.4 (In Progress)
+==================
+
+New features
+------------
+- Adds a `containers` module  that contains two classes, and `Experiment` and a
+  `Filter` class, for managing stimuli and spikes (`Experiment`) and spike-triggered averages (`Filter`).
+- New and improved ellipse and contour fitting code (`filtertools.rfsize`,
+  `filtertools.get_ellipse`, `visualizations.ellipse`)
+- New function `filtertools.resample` which is a thin wrapper around `scipy.signal.resample`
+
+API changes
+-----------
+- Flipped the expected dimensions of stimuli and filters to have the temporal dimension first. E.g. functions now expect (time, space, space) or (time, space) instead of (space, space, time) or (space, time).
+- Changes the default value of the argument in `rolling_window` to `time_axis=0`, to be consistent with the rest of pyret (after the flipped dimensions switch)
+- Removes the `prinangles` function (does not really belong in the `filtertools` module, or even in pyret at all)
+- Updated `pyret.plotsta` function
+- Reworked `filtertools.getste` to be a generator, and modified `getsta` and `getstc` to consume that generator.
+
+Issues closed
+-------------
+- `#62 bug in filtertools.decompose <https://github.com/baccuslab/pyret/issues/62>`_.
+- `#63 better ellipse fitting tools <https://github.com/baccuslab/pyret/issues/63>`_.
+- `#60 custom classes for filter <https://github.com/baccuslab/pyret/issues/60>`_.
+- `#53 simplifying filtertools <https://github.com/baccuslab/pyret/issues/53>`_.