Merge pull request #181 from fedarko/master

Update links everywhere (code, docs) to point to the biocore URL; a few other small changes; v0.2.1 bump

CHANGELOG.md

@@ -1,23 +1,29 @@
 # Qurro changelog
 
-## Qurro 0.3.0 (in development)
+## Qurro 0.2.1 (in development)
 ### Features added
 ### Backward-incompatible changes
 ### Bug fixes
+- Allowed "exact text" searching (the first search option) using just
+  whitespace.
 ### Performance enhancements
 - Removed some unused data from `qurro/tests/`.
 ### Miscellaneous
+- Updated a bunch of links throughout Qurro's code and documentation to point
+  to its new repository home (https://github.com/biocore/qurro).
+- Renamed the `Regenerate sample plot` button to say `Regenerate plots` (this
+  name makes more sense).
 
 
 ## Qurro 0.2.0 (July 8, 2019)
 ### Features added
 - The color schemes used in the sample plot and rank plot are now customizable!
-  ([#158](https://github.com/fedarko/qurro/issues/158))
+  ([#158](https://github.com/biocore/qurro/issues/158))
 
 - Feature loading names (in Qurro plots produced from DEICODE biplots) are now
   clearer: instead of being labelled `0`, `1`, `2`, etc., the loadings are now
   labelled `Axis 1`, `Axis 2`, `Axis 3`, etc.
-  ([#145](https://github.com/fedarko/qurro/issues/145))
+  ([#145](https://github.com/biocore/qurro/issues/145))
 
 ### Backward-incompatible changes
 ### Bug fixes
@@ -31,14 +37,14 @@
   files. Now, existing files/directories in the specified `-o`/`--output-dir`
   will be overwritten if necessary (previously, individual files would be
   overwritten but directories would cause an error to be thrown).
-  ([#79](https://github.com/fedarko/qurro/issues/79))
+  ([#79](https://github.com/biocore/qurro/issues/79))
 
 - Previously, the use of certain column names in sample metadata, feature
   metadata, or feature rankings would cause either confusing errors or the loss
   of some metadata/ranking fields in a Qurro visualization. Now, these sorts of
   problematic names will just lead to a clear error message when generating a
   Qurro visualization.
-    - See [#55](https://github.com/fedarko/qurro/issues/55) for details about
+    - See [#55](https://github.com/biocore/qurro/issues/55) for details about
       which column names cause problems (at this point, most ordinary inputs
       shouldn't run into any problems). Since problematic names will now lead
       to an error message explaining what's wrong, there shouldn't be any need
@@ -52,17 +58,17 @@
   (previously it used a dense represntation). For inherently sparse datasets
   (like many microbiome datasets), this should result in faster loading times
   in the browser (as well as smaller Qurro visualizations).
-  ([#58](https://github.com/fedarko/qurro/issues/58))
+  ([#58](https://github.com/biocore/qurro/issues/58))
 
 - Significant speedups on how the input data is filtered and matched.
-  ([#172](https://github.com/fedarko/qurro/issues/172))
+  ([#172](https://github.com/biocore/qurro/issues/172))
 
 - Now, empty features are removed from Qurro visualizations (in addition to
   empty samples). Similarly to the sparsity change above, this should make
   Qurro visualizations load faster in the browser, decrease their filesizes,
   and reduce the amount of features on the rank plot (for datasets containing
   empty features). This has affected the Byrd et al. demo.
-  ([#171](https://github.com/fedarko/qurro/issues/171))
+  ([#171](https://github.com/biocore/qurro/issues/171))
 
 - Removed an unused JS file from Qurro's `support_files/`. This change should
   decrease the size of Qurro's generated visualizations by a small amount.
@@ -78,7 +84,7 @@
   with invalid metadata fields were still included). This behavior has been
   changed so that all samples -- regardless of their log ratio or other fields'
   validity -- are included in the .tsv output.
-  ([#176](https://github.com/fedarko/qurro/issues/176))
+  ([#176](https://github.com/biocore/qurro/issues/176))
     - Also, the exported sample data will now include field information about
       the sample plot's current color field in addition to the sample plot's
       current x-axis field.

README.md

@@ -1,12 +1,12 @@
 # Qurro: Quantitative Rank/Ratio Observations
 
 <div align="center">
-<img width="40%" src="https://raw.githubusercontent.com/fedarko/qurro/master/docs/images/logos/qurro_logo.png" alt="Qurro logo" />
+<img width="40%" src="https://raw.githubusercontent.com/biocore/qurro/master/docs/images/logos/qurro_logo.png" alt="Qurro logo" />
 </div>
 
 <div align="center">
-<a href="https://travis-ci.org/fedarko/qurro"><img src="https://travis-ci.org/fedarko/qurro.svg?branch=master" alt="Build Status" /></a>
-<a href="https://codecov.io/gh/fedarko/qurro"><img src="https://codecov.io/gh/fedarko/qurro/branch/master/graph/badge.svg" alt="Code Coverage" /></a>
+<a href="https://travis-ci.org/biocore/qurro"><img src="https://travis-ci.org/biocore/qurro.svg?branch=master" alt="Build Status" /></a>
+<a href="https://codecov.io/gh/biocore/qurro"><img src="https://codecov.io/gh/biocore/qurro/branch/master/graph/badge.svg" alt="Code Coverage" /></a>
 <a href="https://zenodo.org/badge/latestdoi/158270494"><img src="https://zenodo.org/badge/158270494.svg" alt="DOI" /></a>
 <p>(Pronounced "churro.")</p>
 </div>
@@ -34,17 +34,17 @@ occur. If you have any questions, feel free to contact the development team at
 
 ## Demos
 
-See the <a href="https://fedarko.github.io/qurro">Qurro website</a> for a list of
+See the <a href="https://biocore.github.io/qurro">Qurro website</a> for a list of
 interactive demos using real datasets.
 
 ### Screenshot: Visualizing KEGG orthologs in metagenomic data from the Red Sea
 
-<img width="100%" src="https://raw.githubusercontent.com/fedarko/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." />
+<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://fedarko.github.io/qurro/demos/red_sea/index.html).
+online [here](https://biocore.github.io/qurro/demos/red_sea/index.html).
 
 ## Installation and Usage
 
@@ -69,7 +69,7 @@ Certain characters in column names in the the sample metadata, feature metadata,
 | `'`, `"`, or `\ `  | <code>\|</code>  |
 
 This is due to some downstream issues with handling these sorts of characters
-in field names. See [this issue](https://github.com/fedarko/qurro/issues/66)
+in field names. See [this issue](https://github.com/biocore/qurro/issues/66)
 for context.
 
 ### Integration with metabolomics feature metadata
@@ -85,10 +85,10 @@ available in the QIIME 2 plugin version of Qurro.
 
 Examples of using Qurro (both inside and outside of QIIME 2) are
 available in Qurro's example Jupyter notebooks, which are located
-[here](https://github.com/fedarko/qurro/tree/master/example_notebooks):
-- [**`deicode_example.ipynb`**](https://github.com/fedarko/qurro/blob/master/example_notebooks/DEICODE_sleep_apnea/deicode_example.ipynb)
+[here](https://github.com/biocore/qurro/tree/master/example_notebooks):
+- [**`deicode_example.ipynb`**](https://github.com/biocore/qurro/blob/master/example_notebooks/DEICODE_sleep_apnea/deicode_example.ipynb)
   demonstrates using [DEICODE](https://github.com/biocore/DEICODE) and then using Qurro to visualize DEICODE's output.
-- [**`songbird_example.ipynb`**](https://github.com/fedarko/qurro/blob/master/example_notebooks/songbird_red_sea/songbird_example.ipynb)
+- [**`songbird_example.ipynb`**](https://github.com/biocore/qurro/blob/master/example_notebooks/songbird_red_sea/songbird_example.ipynb)
   demonstrates using [songbird](https://github.com/biocore/songbird) and then using Qurro to visualize songbird's output.
 
 ### Interacting with a Qurro visualization

docs/index.html

@@ -21,7 +21,7 @@ <h1>
                 >.
                 <!-- TODO: sync the README with this page -->
                 For information about what Qurro does, see its
-                <a href="https://github.com/fedarko/qurro">GitHub page</a>.
+                <a href="https://github.com/biocore/qurro">GitHub page</a>.
             </p>
         </div>
         <h2>Demos</h2>
@@ -101,7 +101,7 @@ <h2>Tutorials</h2>
         <p class="centeredBlock">
             See
             <a
-                href="https://github.com/fedarko/qurro/tree/master/example_notebooks"
+                href="https://github.com/biocore/qurro/tree/master/example_notebooks"
                 >here</a
             >
             for example Jupyter Notebooks that show how to generate Qurro plots

qurro/__init__.py

@@ -10,5 +10,5 @@
 # The full license is in the file LICENSE.txt, distributed with this software.
 # ----------------------------------------------------------------------------
 
-__version__ = "0.2.0"
+__version__ = "0.2.1"
 name = "qurro"

qurro/_df_utils.py

@@ -385,7 +385,7 @@ def sparsify_count_dict(count_dict):
 def check_column_names(sample_metadata, feature_ranks, feature_metadata=None):
     """Checks that column names in input data will work properly in Qurro.
 
-       See https://github.com/fedarko/qurro/issues/55 for a list of these
+       See https://github.com/biocore/qurro/issues/55 for a list of these
        restrictions.
     """
 

qurro/q2/plugin_setup.py

@@ -30,7 +30,7 @@
 plugin = qiime2.plugin.Plugin(
     name="qurro",
     version=__version__,
-    website="https://github.com/fedarko/qurro",
+    website="https://github.com/biocore/qurro",
     # citations=[citations['martino-unpublished']],
     short_description=("Plugin for visualizing feature ranks and log ratios."),
     description=(

qurro/support_files/index.html

@@ -330,7 +330,7 @@ <h4 class="centeredHeader">Denominator</h4>
                 <a id="downloadHelper" class="invisible"></a>
                 <div class="centeredBlock marginOnTop">
                     <button id="multiFeatureButton">
-                        Regenerate sample plot
+                        Regenerate plots
                     </button>
                     <button id="exportDataButton">
                         Export sample data

qurro/support_files/js/feature_computation.js

@@ -161,7 +161,7 @@ define(function() {
             throw new Error("featureMetadataField not found in data");
         } else if (searchType !== "text" && searchType !== "rank") {
             throw new Error('searchType must be either "text" or "rank"');
-        } else if (inputText.trim().length === 0) {
+        } else if (inputText.length === 0) {
             return [];
         }
 

qurro/tests/web_tests/tests/test_filter_features.js

@@ -154,7 +154,7 @@ define(["feature_computation", "mocha", "chai", "testing_utilities"], function(
                 );
             });
 
-            it("Doesn't find anything if inputText is empty or contains only whitespace", function() {
+            it("Doesn't find anything if inputText is empty, but can do just-text-searching using whitespace", function() {
                 chai.assert.isEmpty(
                     feature_computation.filterFeatures(
                         rpJSON1,
@@ -187,6 +187,17 @@ define(["feature_computation", "mocha", "chai", "testing_utilities"], function(
                         "text"
                     )
                 );
+                chai.assert.sameMembers(
+                    testing_utilities.getFeatureIDsFromObjectArray(
+                        feature_computation.filterFeatures(
+                            rpJSON1,
+                            " ",
+                            "Feature ID",
+                            "text"
+                        )
+                    ),
+                    inputFeatures
+                );
             });
             it("Ignores actual null values", function() {
                 // Feature 6's Taxonomy value is "null", while Feature 7's

setup.py

@@ -60,7 +60,7 @@
     author_email="[email protected]",
     maintainer="Qurro development team",
     maintainer_email="[email protected]",
-    url="https://github.com/fedarko/qurro",
+    url="https://github.com/biocore/qurro",
     packages=find_packages(),
     # Needed in order to ensure that support_files/*, etc. are installed (in
     # turn, these files are specified in MANIFEST.in).