Fixes to some small open issues

README.md

@@ -1,5 +1,5 @@
 # Empress
- [![Build Status](https://travis-ci.org/biocore/empress.svg?branch=master)](https://travis-ci.org/biocore/empress)
+[![Build Status](https://travis-ci.org/biocore/empress.svg?branch=master)](https://travis-ci.org/biocore/empress)
 
 <!---Empress Logo--->
 
@@ -18,7 +18,10 @@ conda activate qiime2-2020.6
 
 You can replace `qiime2-2020.6` above with whichever version of QIIME 2 you have currently installed. 
 
-Now we are ready to install Empress. Run the following commands:
+Now we are ready to install Empress. Run the following commands to do so. (Note
+that Emperor will be _re-installed_ when the second command is run; the reason
+we uninstall it first is so that we can ensure the most up-to-date version of
+it is available.)
 
 ```
 pip uninstall --yes emperor
@@ -328,6 +331,43 @@ This is a good example of when your data can tell you something about your metad
 
 ## Additional Considerations
 
+### Providing multiple metadata files
+
+QIIME 2 allows you to specify multiple metadata files at once by just
+repeating `--m-feature-metadata-file` (or `--m-sample-metadata-file`). For
+example, we may want to visualize feature importances on a tree
+in addition to taxonomic annotations:
+
+```bash
+qiime empress community-plot \
+ --i-tree rooted-tree.qza \
+ --i-feature-table table.qza \
+ --m-sample-metadata-file sample_metadata.tsv \
+ --m-feature-metadata-file taxonomy.qza \
+ --m-feature-metadata-file feature_importance.qza \
+ --o-visualization empress-tree.qzv
+```
+
+However, what QIIME 2 will do internally ([as of writing](https://forum.qiime2.org/t/support-other-metadata-merging-strategies/15907))
+is filter the metadata to
+_just_ the entries contained in _all_ of the input metadata files. So, in the
+example above, if the `feature_importance.qza` file only has entries for a
+couple of features (compared to the `taxonomy.qza` file), then the feature
+metadata Empress receives will be limited to just the features contained in
+both the feature importance and taxonomy metadata files -- which will mean that
+less taxonomy information will be available in the Empress interface!
+
+In the interim, the way to get around this (and to include multiple sources of
+feature or sample metadata in Empress) is to merge metadata yourself before
+creating an Empress visualization. Of course, you'll need to determine what
+value(s) to assign to indicate that a given entry is "missing"; for
+quantitative metadata, `NaN` or an empty value are both reasonable options.
+
+Merging metadata files should be doable in many different programming
+languages or spreadsheet tools; see
+[this GitHub issue](https://github.com/biocore/empress/issues/393) for some
+example Python code that does this.
+
 ### Filtered vs. raw table?
 
 When your ordination was created from a subset of your original dataset (e.g. the feature table was rarefied, or certain low-frequency features or samples were otherwise filtered out), we recommend that you carefully consider *which* feature table you would like to visualize in Empress. You can use either:

empress/support_files/templates/index.html

@@ -15,8 +15,14 @@
  border: none;
  }
 
+ #q2templatesheader {
+ /* border color between header and application matches side panel
+ background color */
+ border-bottom: 1px solid #777;
+ }
+
  #q2templatesheader ~ .row > iframe {
- height: calc(100vh - 85px);
+  height: calc(100vh - 85px);
  }
 </style>
 

setup.py

@@ -37,7 +37,7 @@
 base = ["numpy", "scipy", "pandas", "click",
  "jinja2", "scikit-bio", "biom-format", "iow",
  "emperor @ https://www.github.com/biocore/emperor/archive/master.zip"]
-test = ["pep8", "flake8", "nose"]
+test = ["flake8", "nose"]
 all_deps = base + test
 
 setup(