Merge pull request #286 from fedarko/master

Add tooltips, add export-selected-features button, update MP tutorial, some dependency finagling, minor JS test refactoring

CHANGELOG.md

@@ -1,5 +1,42 @@
 # Qurro changelog
 
+## Qurro 0.6.0 (TBD)
+### Features added
+- Added **tooltips** throughout the Qurro interface explaining what certain
+  controls do. Just hover your mouse over one of the "?" icons to view the
+  tooltips! ([#225](https://github.com/biocore/qurro/issues/225),
+  [#123](https://github.com/biocore/qurro/issues/123))
+  - Although this is a pretty common user-interface thing, our particular use
+    of this was inspired by [Bandage](https://rrwick.github.io/Bandage/)'s
+    similar tooltips.
+- Added two **comprehensive tutorials** explaining how to use Qurro with
+  certain types of data: ([#267](https://github.com/biocore/qurro/issues/267))
+  - [With transcriptomics data](https://nbviewer.jupyter.org/github/biocore/qurro/blob/master/example_notebooks/ALDEx2_TCGA_LUSC/transcriptomic_example.ipynb), courtesy of [@gibsramen](http://github.com/gibsramen/)
+  - [With arbitrary compositional data](https://nbviewer.jupyter.org/github/biocore/qurro/blob/master/example_notebooks/color_compositions/color_example.ipynb), courtesy of [@cameronmartino](http://github.com/cameronmartino/)
+- Updated the [**moving pictures tutorial**](https://nbviewer.jupyter.org/github/biocore/qurro/blob/master/example_notebooks/moving_pictures/moving_pictures.ipynb), after a long drought since the last update!
+  - The newest version of the tutorial has more details, more useful examples,
+    demonstrates using the latest version of Qurro, and has been converted from
+    a markdown document to a Jupyter Notebook. Try running it yourself!
+- Added a `Export currently selected features` button that does what it says on the
+  tin: it lets you export a TSV file listing the features currently selected in
+  a log-ratio. ([#87](https://github.com/biocore/qurro/issues/87))
+### Backward-incompatible changes
+- Qurro now (explicitly) requires that a Python version of at least 3.5.3 is
+  installed. (This is an increase from the previous 3.5 minimum.)
+  ([#74](https://github.com/biocore/qurro/issues/74))
+- As a temporary measure, the version of Pandas required to install Qurro from
+  PyPI has been pinned to below version 1.
+  ([#258](https://github.com/biocore/qurro/issues/258))
+  - This isn't really "backwards incompatible" since trying to run Qurro with
+    Pandas 1.0.0 installed would break.
+### Bug fixes
+### Performance enhancements
+### Miscellaneous
+- Various minor documentation updates.
+  - Updated Qurro's installation instructions: now you need to install `cython`
+    first, alongside NumPy. This addresses a problem some folks started to have
+    when installing Qurro into relatively "fresh" environments.
+
 ## Qurro 0.5.0 (December 17, 2019)
 ### Features added
 - Added **Qarcoal**, a new command for Qurro's QIIME 2 plugin that computes

README.md

@@ -78,17 +78,12 @@ can be viewed online [here](https://biocore.github.io/qurro/demos/red_sea/index.
 
 You can install Qurro using [pip](https://pip.pypa.io/en/stable/):
 
-```
+```bash
+pip install cython "numpy >= 1.12.0"
 pip install qurro
 ```
 
-Note that we recommend using the latest version of pip, to update:
-
-```
-pip install -U pip
-```
-
-A python version of at least 3.5 is required to use Qurro.
+A python version of at least 3.5.3 is required to use Qurro.
 
 ### Temporary Caveat
 
@@ -109,17 +104,17 @@ for context.
 ## Tutorials
 
 ### In-depth
-These tutorials are good places to start, depending on what sort of data and
+These tutorials are all good places to start, depending on what sort of data and
 feature rankings you have.
 
 - [Color Composition tutorial](https://nbviewer.jupyter.org/github/biocore/qurro/blob/master/example_notebooks/color_compositions/color_example.ipynb)
   - **Data Summary:** Color composition data from abstract paintings
   - Feature rankings: Feature loadings in a compositional biplot
   - Qurro used through QIIME 2 or standalone?: Standalone
 
-- ["Moving Pictures" tutorial](https://github.com/biocore/qurro/blob/master/docs/tutorials/moving-pictures/moving-pictures.md)
-  - **Data Summary:** Microbiome 16S rRNA marker gene sequencing data from fecal samples
-  - Feature rankings: feature loadings in a [DEICODE](https://github.com/biocore/DEICODE) biplot
+- ["Moving Pictures" tutorial](https://nbviewer.jupyter.org/github/biocore/qurro/blob/master/example_notebooks/moving_pictures/moving_pictures.ipynb)
+  - **Data Summary:** Microbiome 16S rRNA marker gene sequencing data from four types of body site samples
+  - Feature rankings: Feature loadings in a [DEICODE](https://github.com/biocore/DEICODE) biplot
   - Qurro used through QIIME 2 or standalone?: QIIME 2
 
 - [Transcriptomics tutorial](https://nbviewer.jupyter.org/github/biocore/qurro/blob/master/example_notebooks/ALDEx2_TCGA_LUSC/transcriptomic_example.ipynb)
@@ -165,6 +160,9 @@ licenses (each of which includes a respective copyright notice).
 - [DataTables](https://datatables.net/)
 - [RequireJS](https://requirejs.org/)
 - [Bootstrap](https://getbootstrap.com/docs/4.3/getting-started/introduction/)
+- [Bootstrap Icons](https://icons.getbootstrap.com/)
+  - We make use of the "Question fill" icon's SVG, as well as some example code
+    for embedding this or other icons in CSS.
 - [Popper.js](https://popper.js.org/) (included within the Bootstrap JS "bundle" file)
 
 The following software projects are required for Qurro's python code
@@ -216,9 +214,10 @@ The test data located in `qurro/tests/input/sleep_apnea/`
 are from [this Qiita study](https://qiita.ucsd.edu/study/description/10422),
 which is associated with Tripathi et al.'s 2018 study on sleep apnea [4].
 
-The test data located in `qurro/tests/input/moving_pictures/`
+The test data located in `qurro/tests/input/moving_pictures/` (and in
+`example_notebooks/moving_pictures/data/`)
 are from [the QIIME 2 moving pictures tutorial](https://docs.qiime2.org/2019.1/tutorials/moving-pictures/).
-The `ordination.qza` file in this folder was computed based on the
+The `ordination` files in these folders were computed based on the
 [DEICODE moving pictures tutorial](https://library.qiime2.org/plugins/deicode/19/).
 These data (sans the DEICODE ordination) are associated with Caporaso et al. 2011 [5].