Merge pull request #209 from fedarko/master

Various style/formatting/... fixes; add Bootstrap CSS

CHANGELOG.md

@@ -1,5 +1,54 @@
 # Qurro changelog
 
+## Qurro 0.4.0
+### Features added
+- Started using Bootstrap (v4.3.1) for styling the Qurro visualization
+  interface. Although the functionality available in Qurro is still the same,
+  this interface has received a significant makeover. The bulk of these
+  cosmetic interface changes are not documented here.
+- Added light "grid lines" to the Qurro visualization interface. These clearly
+  split up the interface into four distinct sections (rank plot, sample plot,
+  selected features, selecting features), making it clearer how the interface
+  is structured.
+### Backward-incompatible changes
+### Bug fixes
+- Fixed some problems in how the plots were aligned/positioned in the interface.
+  Now, both plots should "float" toward the middle of the screen, as intended.
+  Also removed some unused whitespace around these plots (the grid lines helped
+  here).
+### Performance enhancements
+### Miscellaneous
+- Adjusted some of the default titles in Qurro's plots to make things clearer
+  and simpler:
+    - Rank plot title: `Feature Ranks` --> `Features`
+    - Rank plot x-axis title: `Sorted Features` --> `Feature Rankings`
+    - Sample plot title: `Log-Ratios of Abundances in Samples` --> `Samples`
+    - Sample plot y-axis title: `log(Numerator / Denominator)` --> `Current Log-Ratio`
+- Renamed the text-searching options in the search type menu (again). This change
+  reflects these options' case insensitivity as of the previous version (v0.3.0).
+    - `contains the exact text` --> `contains the text`
+    - `contains the exact separated text fragment(s)` --> `contains the separated text fragment(s)`
+- The text boxes describing the currently-selected numerator / denominator
+  features are now "read-only" (you can't edit them while using Qurro). This
+  should remove any vulnerability to accidental edits of these text boxes.
+- Cleaned up various parts of Qurro's documentation to specify that
+  feature rankings are what you get from sorting differentials/feature
+  loadings, not just the literal differentials/feature loadings.
+- Reworded the text in the info box in the "Selecting Features" section of
+  the Qurro interface ("To construct a log-ratio...")
+- Modified the "testing dependencies" section of the README to correctly
+  specify the minimum version of QIIME 2 needed.
+- Various improvements to the moving pictures tutorial.
+- Modifed Qurro's python package description to say "**differentially** ranked
+  features" instead of just "ranked features."
+- Darkened the color of the "divider" between the numerator and denominator
+  features text boxes, in order to distinguish it from the grid lines.
+- Removed dependency on [Reset CSS](https://meyerweb.com/eric/tools/css/reset/).
+- Temporarily pinned the required version of Altair at `3.1.0`, to ensure
+  consistency between the Vega-Lite specifications generated and the Vega\*
+  versions used by Qurro.
+- Various minor updates to Qurro's documentation.
+
 ## Qurro 0.3.0 (August 3, 2019)
 ### Features added
 - Now, Songbird no longer needs to be installed in order for the `qiime qurro

README.md

@@ -17,7 +17,8 @@ Qurro visualizes the output from a tool like
 [DEICODE](https://github.com/biocore/DEICODE). It displays a plot of
 __feature rankings__ (either the differentials produced by a tool like
 Songbird, or the loadings in a compositional biplot produced by a tool
-like DEICODE) alongside a plot showing the __log ratios__ of
+like DEICODE -- when sorted numerically, either of these input types provide
+rankings) alongside a plot showing the __log-ratios__ of
 selected features' abundances within samples.
 
 Qurro can be used standalone (as a Python 3 script that generates a
@@ -44,9 +45,9 @@ interactive demos using real datasets.
 <img width="100%" src="https://raw.githubusercontent.com/biocore/qurro/master/screenshots/redsea_data.png" alt="Screenshot showing a Qurro visualization of ranked features (which in this dataset correspond to KEGG orthologs) and a scatterplot plot of the log ratio of certain features' abundances in samples." />
 
 This visualization (which uses data from
-[this study](https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5315489/), with ranks
-generated by [Songbird](https://github.com/biocore/songbird/)) can be viewed
-online [here](https://biocore.github.io/qurro/demos/red_sea/index.html).
+[this study](https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5315489/), with
+differentials generated by [Songbird](https://github.com/biocore/songbird/))
+can be viewed online [here](https://biocore.github.io/qurro/demos/red_sea/index.html).
 
 ## Installation and Usage
 
@@ -124,10 +125,7 @@ licenses (each of which includes a respective copyright notice).
 - [Vega-Lite](https://vega.github.io/vega-lite/)
 - [Vega-Embed](https://github.com/vega/vega-embed)
 - [RequireJS](https://requirejs.org/)
-- [reset](https://meyerweb.com/eric/tools/css/reset/)
-  - Note that `reset` is released under the public domain, so it doesn't have a
-    "license." In any case, thank you to [Eric Meyer](https://meyerweb.com/eric/)
-    for providing this resource!
+- [Bootstrap](https://getbootstrap.com/docs/4.3/getting-started/introduction/)
 
 The following software projects are required for Qurro's python code
 to function, although they are not distributed with Qurro (and are
@@ -146,8 +144,9 @@ For python testing/style checking, Qurro uses
 [pytest-cov](https://github.com/pytest-dev/pytest-cov),
 [flake8](http://flake8.pycqa.org/en/latest/), and
 [black](https://github.com/ambv/black). You'll also need to have QIIME 2
-installed to run most of the python tests (the exact QIIME 2 version shouldn't
-matter too much).
+installed to run most of the python tests (your QIIME 2 version should be at
+least 2019.7, due to the `FeatureData[Differential]` type being merged into
+q2-types starting with this release).
 
 For JavaScript testing/style checking, Qurro uses
 [Mocha](https://mochajs.org/), [Chai](https://www.chaijs.com/),

dependency_licenses/bootstrap.license

@@ -0,0 +1,22 @@
+The MIT License (MIT)
+
+Copyright (c) 2011-2019 Twitter, Inc.
+Copyright (c) 2011-2019 The Bootstrap Authors
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in
+all copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
+THE SOFTWARE.