standardize references to DABEST

josesho · Oct 8, 2019 · Sep 27, 2019 · Sep 27, 2019 · Sep 27, 2019 · Sep 29, 2019
commit ddf0cd2f3b5999fc8a27228fdb8198f9da1a7445
diff --git a/docs/source/about.rst b/docs/source/about.rst
@@ -7,14 +7,14 @@ About
 
 Authors
 --------
-`dabest` is written in Python by `Joses W. Ho <https://twitter.com/jacuzzijo>`_, with design and input from `Adam Claridge-Chang <https://twitter.com/adamcchang>`_ and other lab members.
+DABEST is written in Python by `Joses W. Ho <https://twitter.com/jacuzzijo>`_, with design and input from `Adam Claridge-Chang <https://twitter.com/adamcchang>`_ and other lab members.
 
 To find out more about the authors’ research, please visit the `Claridge-Chang lab webpage <http://www.claridgechang.net/>`_.
 
 Contributors
 ------------
 
-- Mason Malone (`@MasonM <https://github.com/MasonM>`_) with `PR #30 <https://github.com/ACCLAB/DABEST-python/pull/30>`_:  Fix plot error when effect size is 0
+- Mason Malone (`@MasonM <https://github.com/MasonM>`_) with `PR #30 <https://github.com/ACCLAB/DABEST-python/pull/30>`_:  Fix plot error when effect size is 0.
 
 - Matthew Edwards (`@mje-nz <https://github.com/mje-nz>`_) with `PR #71 <https://github.com/ACCLAB/DABEST-python/pull/30>`_: Specify dependencies correctly in ``setup.py``. 
 
@@ -29,7 +29,7 @@ This documentation uses `Spectral <https://spectral.prototypo.io/>`_ for the bod
 License
 -------
 
-The `dabest` package in Python is licenced under the `BSD 3-clause Clear License <https://choosealicense.com/licenses/bsd-3-clause-clear/>`_.
+The DABEST package in Python is licenced under the `BSD 3-clause Clear License <https://choosealicense.com/licenses/bsd-3-clause-clear/>`_.
 
 Copyright (c) 2016-2019, Joses W. Ho
 All rights reserved.

diff --git a/docs/source/getting-started.rst b/docs/source/getting-started.rst
@@ -8,7 +8,7 @@ Getting Started
 Requirements
 ------------
 
-Python 3.7 is strongly recommended. ``dabest`` has also been tested with Python 3.5 and 3.6.
+Python 3.7 is strongly recommended. DABEST has also been tested with Python 3.5 and 3.6.
 
 In addition, the following packages are also required:
 
@@ -47,7 +47,7 @@ Then, navigate to the cloned repo in the command line and run
 Testing
 -------
 
-To test ``dabest``, you will need to install `pytest <https://docs.pytest.org/en/latest/>`_.
+To test DABEST, you will need to install `pytest <https://docs.pytest.org/en/latest/>`_.
 
 Run ``pytest`` in the root directory of the source distribution. This runs the test suite in ``dabest/tests`` folder. The test suite will ensure that the bootstrapping functions and the plotting functions perform as expected.
 

diff --git a/docs/source/release-notes.rst b/docs/source/release-notes.rst
@@ -69,7 +69,7 @@ Now, every analysis session begins with ``dabest.load()``.
 
     my_data = dabest.load(my_dataframe, idx=("Control", "Test"))
 
-This creates a ``dabest`` object with effect sizes as instances.
+This creates a :py:class:`Dabest` object with effect sizes as instances.
 
 .. code-block:: python
     :linenos:
@@ -123,14 +123,14 @@ v0.1.6
 
 Several keywords have been added to allow more fine-grained control over a selection of plot elements.
 
-* `swarm_dotsize`
-* `difference_dotsize`
-* `ci_linewidth`
-* `summary_linewidth`
+* ``swarm_dotsize``
+* ``difference_dotsize``
+* ``ci_linewidth``
+* ``summary_linewidth``
 
-The new keyword `context` allows you to set the plotting context as defined by seaborn's `plotting_context() <https://seaborn.pydata.org/generated/seaborn.plotting_context.html>`_ .
+The new keyword ``context`` allows you to set the plotting context as defined by seaborn's `plotting_context() <https://seaborn.pydata.org/generated/seaborn.plotting_context.html>`_ .
 
-Now, if `paired=True`, you will need to supply an `id_col`, which is a column in the DataFrame which specifies which sample the datapoint belongs to. See the :doc:`tutorial` for more details.
+Now, if ``paired=True``, you will need to supply an ``id_col``, which is a column in the DataFrame which specifies which sample the datapoint belongs to. See the :doc:`tutorial` for more details.
 
 
 v0.1.5
@@ -149,7 +149,7 @@ Update dependencies to
 
 Aesthetic changes
 
-* add `tick_length` and `tick_pad` arguments to allow tweaking of the axes tick lengths, and padding of the tick labels, respectively.
+* add ``tick_length`` and ``tick_pad`` arguments to allow tweaking of the axes tick lengths, and padding of the tick labels, respectively.
 
 
 v0.1.3
@@ -160,7 +160,7 @@ Update dependencies to
 
 Bugfixes
 
-* fix bug that did not label `swarm_label` if raw data was in tidy form
+* fix bug that did not label ``swarm_label`` if raw data was in tidy form
 * fix bug that did not dropnans for unpaired diff
 
 

diff --git a/docs/source/tutorial.rst b/docs/source/tutorial.rst
@@ -25,7 +25,7 @@ Load Libraries
 Create dataset for demo
 -----------------------
 
-Here, we create a dataset to illustrate how ``dabest`` functions. In
+Here, we create a dataset to illustrate how DABEST functions. In
 this dataset, each column corresponds to a group of observations.
 
 .. code-block:: python3
@@ -207,7 +207,7 @@ list.
 
     two_groups_unpaired = dabest.load(df, idx=("Control 1", "Test 1"), resamples=5000)
 
-Calling this ``Dabest`` object gives you a gentle greeting, as well as
+Calling this :py:class:`Dabest`; object gives you a gentle greeting, as well as
 the comparisons that can be computed.
 
 .. code-block:: python3
@@ -304,7 +304,7 @@ produced.
 Effect sizes
 ------------
 
-``dabest`` now features a range of effect sizes: - the mean difference
+DABEST now features a range of effect sizes: - the mean difference
 (``mean_diff``) - the median difference (``median_diff``) - `Cohen's
 *d* <https://en.wikipedia.org/wiki/Effect_size#Cohen's_d>`__
 (``cohens_d``) - `Hedges'
@@ -313,7 +313,7 @@ Effect sizes
 delta <https://en.wikipedia.org/wiki/Effect_size#Effect_size_for_ordinal_data>`__
 (``cliffs_delta``)
 
-Each of these are attributes of the ``Dabest`` object.
+Each of these are attributes of the :py:class:`Dabest` object.
 
 .. code-block:: python3
   :linenos:
@@ -719,7 +719,7 @@ Both Gardner-Altman and Cumming plots support this.
 .. image:: _images/tutorial_34_0.png
 
 
-The ``dabest`` package also implements a range of estimation plot
+The DABEST package also implements a range of estimation plot
 designs aimed at depicting common experimental designs.
 
 The **multi-two-group estimation plot** tiles two or more Cumming plots
@@ -857,7 +857,7 @@ to ``idx`` has more than two data columns.
 .. image:: _images/tutorial_43_0.png
 
 
-``dabest`` thus empowers you to robustly perform and elegantly present
+DABEST thus empowers you to robustly perform and elegantly present
 complex visualizations and statistics.
 
 .. code-block:: python3
@@ -952,7 +952,7 @@ complex visualizations and statistics.
 Using long (aka 'melted') data frames
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 
-``dabest`` can also work with 'melted' or 'long' data. This term is
+DABEST can also work with 'melted' or 'long' data. This term is
 so used because each row will now correspond to a single datapoint, with
 one column carrying the value and other columns carrying 'metadata'
 describing that datapoint.
@@ -1240,7 +1240,7 @@ better outcome), you can simply invert the tuple passed to
 You can add minor ticks and also change the tick frequency by accessing
 the axes directly.
 
-Each estimation plot produced by ``dabest`` has 2 axes. The first one
+The estimation plot produced by ``dabest.plot()`` has 2 axes. The first one
 contains the rawdata swarmplot; the second one contains the bootstrap
 effect size differences.
 
@@ -1343,7 +1343,7 @@ Applying style sheets
 
 *Implemented in v0.2.0*.
 
-``dabest`` can now apply `matplotlib style
+DABEST can now apply `matplotlib style
 sheets <https://matplotlib.org/tutorials/introductory/customizing.html>`__
 to estimation plots. You can refer to this
 `gallery <https://matplotlib.org/3.0.3/gallery/style_sheets/style_sheets_reference.html>`__