diff --git a/CHANGELOG.md b/CHANGELOG.md index ae3fbb00..fd579ab2 100644 --- a/CHANGELOG.md +++ b/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. diff --git a/README.md b/README.md index 95b7dbf0..8861c333 100644 --- a/README.md +++ b/README.md @@ -1,12 +1,12 @@ # Qurro: Quantitative Rank/Ratio Observations
-Qurro logo +Qurro logo
-Build Status -Code Coverage +Build Status +Code Coverage DOI

(Pronounced "churro.")

@@ -34,17 +34,17 @@ occur. If you have any questions, feel free to contact the development team at ## Demos -See the Qurro website for a list of +See the Qurro website for a list of interactive demos using real datasets. ### Screenshot: Visualizing KEGG orthologs in metagenomic data from the Red Sea -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. +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 `\ ` | \| | 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 diff --git a/docs/index.html b/docs/index.html index 2cf8dc62..d09bf330 100644 --- a/docs/index.html +++ b/docs/index.html @@ -21,7 +21,7 @@

>. For information about what Qurro does, see its - GitHub page. + GitHub page.

Demos

@@ -101,7 +101,7 @@

Tutorials

See here for example Jupyter Notebooks that show how to generate Qurro plots diff --git a/qurro/__init__.py b/qurro/__init__.py index 79252f76..2b75eee3 100644 --- a/qurro/__init__.py +++ b/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" diff --git a/qurro/_df_utils.py b/qurro/_df_utils.py index 675fc9f7..de949b6a 100644 --- a/qurro/_df_utils.py +++ b/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. """ diff --git a/qurro/q2/plugin_setup.py b/qurro/q2/plugin_setup.py index 4015fb9d..ba117817 100644 --- a/qurro/q2/plugin_setup.py +++ b/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=( diff --git a/qurro/support_files/index.html b/qurro/support_files/index.html index c3d3d27e..5ee9ee04 100644 --- a/qurro/support_files/index.html +++ b/qurro/support_files/index.html @@ -330,7 +330,7 @@

Denominator