CHANGELOG.md

Qurro changelog

Qurro 0.8.0 (October 19, 2022)

Features added

• Added an option to Qurro's visualization interface to exclude metadata columns from the "sample plot data" output TSV (#306, #313).
  • This should make it easier to merge the sample log-ratios exported from Qurro with a sample metadata file -- since now these metadata columns won't be duplicated, which would cause problems. (This problem comes up in Gemelli's tutorials.)

Backward-incompatible changes

• Switched the required pandas version from >= 0.24.0, <1 to >= 1. This makes Qurro now compatible with QIIME 2 versions >= 2020.11!
  • However, this change removes support for older QIIME 2 versions. (It may be possible to get this version of Qurro installed into an older QIIME 2 environment, but we do not explicitly support this.) If you need to use Qurro in older QIIME 2 environments, you can install an older version of Qurro (e.g. pip install "qurro==0.7.1").
  • Notably, Songbird has not yet made the shift to pandas >= 1, so Songbird and Qurro will need to be installed into separate environments; the "Red Sea" example notebook details this process.
• Updated a few other dependency versions to fix various problems (e.g. explicitly requiring SciPy and pinning it to scipy < 1.9.0 to fix this scikit-bio issue, removing Black from the development dependencies for reasons discussed in CONTRIBUTING.md).

Bug fixes

Performance enhancements

Miscellaneous

• Updated various parts of Qurro's code to remove various warnings (for example, about certain things being deprecated).
• Updated Qurro's example notebooks:
  • Updated the "Red Sea" notebook to explain how to use Songbird and Qurro in different conda environments.
  • Updated the "ALDEx2" notebook to explain how we recommend installing ALDEx2 nowadays.
• Updated the documentation to refer to the published version of the Mackerel data's paper (Minich et al. 2020).
• Fixed various broken links in the documentation (#318, #320).
• Ported Qurro's continuous integration from Travis CI to GitHub Actions (#316).
• Improved Qurro's continuous integration in multiple ways:
  • Test on multiple QIIME 2 versions.
  • Test the standalone Qurro functionality on multiple Python versions.
  • Test the standalone Qurro functionality in a non-QIIME-2 environment (similar to EMPress' "standalone" CI).
• Updated the development documentation (CONTRIBUTING.md) regarding the minimum QIIME 2 version, dependency version issues, etc.

Qurro 0.7.1 (May 22, 2020)

Features added

Backward-incompatible changes

Bug fixes

Performance enhancements

Miscellaneous

• Small documentation updates, including updating the color composition tutorial about the minimum python version needed (#295).
• Added citation information to Qurro's QIIME 2 plugin -- you can now run qiime qurro --citations, and citation information for Qurro-generated QZVs is now shown with other citation information at places like view.qiime2.org.

Qurro 0.7.0 (May 4, 2020)

Features added

• Added the ability to easily search using multiple text queries at once: this is done using the contains text separated by | (pipe) searching option. You can pass in, e.g. abc | def | ghi to select any features where the selected field contains at least one of abc, def, or ghi. (#224)
  • This works more intuitively than the separated text fragment(s) option, and should be useful for a few cases that that option can't handle (e.g. polyphyletic taxa, as discussed in issue 224).
• Added a Draw borders on scatterplot points? checkbox, which is useful for making light-colored points in the sample plot easier to see on the white background. (#240)
• Added the ability to enter in negative numbers in autoselection to flip the selection (selecting the numerator from the lowest-ranked features and the denominator from the highest-ranked features). (#264)
• Added the Classic QIIME Colors categorical color scheme used in some other visualization tools, including Emperor and Empress, to the sample plot's categorical color scheme options. (#300)
  • (tableau10 is still the default categorical color scheme in Qurro, though.)
• Added a "selection" tutorial describing the various ways of selecting features in Qurro in detail. (#123)
  • (This was previously the appendix in the moving pictures tutorial, but now it's been split off and expanded into its own thing.)

Backward-incompatible changes

• For the time being, we are only supporting Qurro for Python versions of at least 3.6 and less than 3.8. The code hasn't really changed, but this seems like it'll be the simplest option for maintenance in the short term.

Bug fixes

• Previously, the autoselection number field had an implicit "step size" of 1. I don't think this should have prevented users from entering in floating-point numbers here, but some people's browsers may have complained on seeing a floating-point number. This problem should be resolved now. (See here for details about this.)

Performance enhancements

Miscellaneous

• Qurro is now installable on conda through the conda-forge channel! (#153)
• Various minor documentation updates, including adding citation info for Qurro's recently-published paper to the README. (#169)

Qurro 0.6.0 (March 10, 2020)

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, #123)
  • Although this is a pretty common user-interface thing, our particular use of this was inspired by Bandage's similar tooltips.
• Added two comprehensive tutorials explaining how to use Qurro with certain types of data: (#267)
  • With transcriptomics data, courtesy of @gibsramen
  • With arbitrary compositional data, courtesy of @cameronmartino
• Updated the moving pictures tutorial, 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)

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)
• As a temporary measure, the version of Pandas required to install Qurro from PyPI has been pinned to below version 1. (#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 log-ratios from the command line by searching through features' taxonomies. This can be useful in a variety of situations -- for example, if you don't care about feature ranking information and just want to look at log-ratios, or if your BIOM table contains super large numbers that would cause JavaScript to start malfunctioning (see the "bug fixes" section below).

  • Thanks to @gibsramen for adding this in to Qurro!

• Added autoselection, a new method for selecting multiple features in a log-ratio. This method just picks features from the top and bottom of the currently-selected ranking, using a specified equal amount of features from each side (either in percentages of features or in numbers of features). (#189)

  • This feature should be useful when quickly assessing how much a given ranking field "separates" samples along certain metadata categories. It's a great starting point when looking at a Qurro visualization.

• Instead of showing selected features in text boxes, these features are now displayed in fancy DataTables! (#197, #232)

  • Thanks to @antgonza for adding this in to Qurro!
  • This involved adding some dependencies to Qurro's visualization code: jQuery, DataTables, Bootstrap's JS code, and Popper.js.

• When selecting a log-ratio where feature(s) are present in both the numerator and denominator of the log-ratio, a warning will now be shown explaining the situtation (and recommending that you chose a different log-ratio that doesn't involve this "overlap"). (#249)

  • We will try to make selectively removing features from one side or another of log-ratios easier in the future.

• Added an additional text searching option: is provided, and does not contain the text. This will select features where:

  1. The specified feature field (e.g. Feature ID) is provided, and
  2. The specified feature field does not contain the specified text.

  Note the first clause. If a given field is not provided (e.g. no taxonomy information is provided for Feature A), then that feature won't show up in any results that involve searching on feature taxonomy. This behavior is the same as with other text-/number-searching methods, but we've explicitly specified it here so that it's clear (since you could argue that a non-existent taxonomy entry "does not contain" some text). (#221)

• The sample plot's x- and y-axes are now no longer forced to include zero. So if, say, all of your samples have an x-axis value of at least 20, then they won't be squished on the side of the sample plot any more. (#218)

• All features in the rank plot now have a "Sample Presence Count" field shown in their tooltips. A given feature's "Sample Presence Count" value is equal to the number of samples in the Qurro visualization that contain that feature. This should give some context as to why log-ratios between certain features result in more or less samples being dropped from the sample plot. (#217)

Backward-incompatible changes

• Removed the -gnps/--assume-gnps-feature-metadata argument from the standalone Qurro interface. If you'd like to use GNPS data in Qurro, you'll just need to supply a "normal" feature metadata file where the first column corresponds to each feature's ID. (This should be available through GNPS now.) A benefit of this is that you can use this data in either the standalone or QIIME 2 Qurro interfaces. (#49)
• As a side effect of implementing the Sample Presence Count feature, if any of your feature ranks or feature metadata inputs contain a column named qurro_spc then an error will be raised when trying to generate a Qurro visualization.
• Qurro now requires that a Pandas version of at least 0.24.0 is installed.
• Qurro now (explicitly) requires that a Python version of at least 3.5 is installed. (This was already a requirement, but it should be enforced when installing Qurro now.)

Bug fixes

• If your input feature table or feature rankings data contain numbers outside of the range of [-(2**53 - 1), (2**53 - 1)], Qurro's Python code will now fail with an error explaining the situation. This is because numbers outside of this range cannot be precisely represented in JavaScript (at least by default). (#242)
  • The reason for this is that JavaScript is inherently limited in the sizes of numbers it can represent by default. There are a few ways around this, but I do not have the bandwidth to modify and test Qurro to completely support rare corner cases like this (at least right now).
  • Note that this is only a partial solution to this problem; it's still possible to pass in arbitrarily large numbers within your sample/feature metadata to Qurro, and the behavior in these situations is still currently untested.
  • On the bright side of things :), thanks to the efforts of @gibsramen, Qarcoal is now available, so you should be able to compute log-ratios of essentially arbitrarily large numbers through that interface.
• Fixed a minor bug in qurro._df_utils.biom_table_to_sparse_df() where the specified min_row_ct and min_col_ct were not being used to validate the output DataFrame.
  • The validation method was still being called, just with the default min_row_ct and min_col_ct values directly rather than using the specified parameters.
  • ...Long story short, this bug should not have impacted you unless you've been using qurro._df_utils.biom_table_to_sparse_df () with custom validation settings directly. If you've just been using Qurro as a standalone tool, you should be unaffected.

Performance enhancements

Miscellaneous

• Various aesthetic changes to the Qurro visualization interface (e.g. changing the location/styling of certain buttons).
• Renamed the y-axis of the sample plot to say Current Natural Log-Ratio instead of just Current Log-Ratio. (This makes it clearer that these log-ratios are computed using the natural log, i.e. ln.) This change has also been applied to TSV files exported from the sample plot (Current_Log_Ratio --> Current_Natural_Log_Ratio), as well as to the tooltips of samples in the sample plot.
• Renamed the y-axis of the rank plot to say either Differential: or Feature Loading: instead of Magnitude: . (#223)
• Renamed the label for changing the rank plot ranking from Ranking to either Differential or Feature Loading.
• Renamed the Fit bar widths to the plot's default width? option (again) to Fit bar widths to a constant plot width?. This seems like a clearer way of describing this option...
• For searching by the values of a given feature ranking, the header shown above all of the ranking column names said Feature Rankings. This was slightly misleading, since searching is being done on the magnitudes of each ranking column for each feature (i.e. based on the y-axis values shown in the rank plot). To make things clearer, this header has been changed from Feature Rankings to either Differentials or Feature Loadings.
• Improved the command-line documentation of the sample and feature metadata parameters.
• Added the poster from a recent presentation we did on Qurro to this repository, and linked the poster's PDF from the README.
• Various documentation updates in the README.
• Changed the project structure around slightly to ensure that dependency_licenses/ for libraries distributed with Qurro (Vega, Vega-Lite, Vega-Embed, RequireJS, Bootstrap) are now installed in both "source" and "built" distributions of Qurro (previously, these were only installed in "source" distributions).
• Added nbconvert to Qurro's dev requirements, and added a command to rerun all of the example notebooks in Qurro automatically (make notebooks). This command is also run on Travis-CI now in order to ensure that future updates to Qurro don't crash any of these notebooks.
• Updated the "Mackerel" demo / test data to match the latest output of this analysis. Notable changes include using the reference-hit Deblur BIOM output instead of the all Deblur BIOM output (which is generally recommended for 16S analyses), and using SILVA instead of Greengenes for taxonomic classification.
• Updated the "Moving Pictures," "Sleep Apnea," and "Mackerel" demo descriptions to just say "ASVs" instead of "ASVs / sOTUs" (for clarity's sake).

Qurro 0.4.0 (August 15, 2019)

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. (#111)
• 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.
• 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 supervised-rank-plot action (NOTE: this action has been renamed to qiime qurro differential-plot, see below) to be available. (#154)
  • NOTE: this means that Qurro v0.3.0 will not work with pre-2019.7 versions of QIIME 2. See the "Backward-incompatible changes" section below for details.
• Feature ranking values (i.e. differentials or loadings) are now shown in the tooltips for individual features in the rank plot. (#186)
• Added feature rankings as searchable fields in the "Selecting Features" controls. (#97)
• Feature metadata fields and feature ranking fields are now grouped under Feature Metadata or Feature Ranking headers in the searchable fields dropdowns. (#191)
• Added numeric searching: now you can search through numeric feature metadata or feature rankings using basic comparison operators. (Non-numeric input search text will result in the search not identifying any features, and non-numeric feature metadata values for the specified field will just be ignored in searching.) (#141, #97)
• Added a --version parameter to the standalone (i.e. outside of QIIME 2) Qurro interface. You can now check the currently installed Qurro version by running qurro --version. (There's already a --version parameter for the QIIME 2 Qurro plugin; this can be accessed using qiime qurro --version.)
• Sample metadata fields are now ordered alphabetically (and ignoring case) in the x-axis field and color field dropdowns in the sample plot controls. (#76)
• The fractions of selected features out of the total amount of features in the rank plot are now displayed in the numerator and denominator "headers." (#187)
• Replaced the Bar width dropdown with a slider input that lets you easily adjust the bar width (in addition to a checkbox that controls whether or not the bar widths are fitted to the available width).
  • The range of this slider is 1 pixel per bar to 10 pixels per bar. Note that the maximum bar width (when not using the "Fit bar widths" option) has been increased from 3 pixels to 10 pixels.
  • Renamed the Fit bar widths to display width option to say Fit bar widths to the plot's default width?. This is a more accurate description of what this option does.
• More output messages are now used when running Qurro. In particular, the following events will now trigger output messages:
  • Empty samples and/or features being automatically removed
  • Features in the table that weren't in the feature rankings being automatically removed
  • Samples in the table that weren't in the sample metadata being automatically removed (the opposite situation -- samples in the metadata that weren't in the table -- already would trigger output messages, though).
  • More context regarding the details of feature filtering, if specified via the -x/--extreme-feature-count/--p-extreme-feature-count option. These output messages will show up normally when running Qurro standalone or when using the --verbose option when running Qurro through QIIME 2.
• Added a --p-debug option when running Qurro through QIIME 2. This will cause debug messages to be output when the --verbose flag has also been specified to QIIME 2. (Non-debug output messages -- for example, the print messages described above -- will be output when --verbose has been specified to QIIME 2, but regardless of whether or not --p-debug has been specified.) (#95)

Backward-incompatible changes

• Qurro will now try to load the Differential type from q2-types. (#154)
  • This means that Qurro v0.3.0 will only support versions of QIIME 2 of at least 2019.7.
  • This also means that installing Qurro v0.3.0 into an old QIIME 2 environment will break it.
• Renamed Qurro's QIIME 2 actions (#98):
  • Renamed qiime qurro supervised-rank-plot to qiime qurro differential-plot.
  • Renamed qiime qurro unsupervised-rank-plot to qiime qurro loading-plot.
• Text searches are now case-insensitive! You can now search through features' taxonomies for, say, p__firmicutes, and results for p__Firmicutes will show up. (#30)
• Replaced -v/--verbose in Qurro's standalone script with --debug, in order to be consistent with Qurro's QIIME 2 plugin.

Bug fixes

• A clear error is now raised if the feature rankings or feature metadata include a column named qurro_x. (This column name is used internally by Qurro to sort features in the rank plot.) (#183) Before, input datasets with this column name would have caused either the loss of this column of data or confusing errors.
• Previously, there was a small (either almost or entirely impossible) chance that all of the main data within the rank or sample plot JSON could get overwritten due to a collision in the dataset name. Although this should basically never happen anyway, Qurro's code now checks for this scenario and raises an error accordingly. (#190)
• QIIME 2 comment lines in differentials TSV files are now properly handled when running Qurro outside of QIIME 2.
  • Before this fix, trying to use a differentials file in standalone Qurro that included #q2:types comments would cause Qurro to crash. ...However, I'm pretty sure no differentials files including these sorts of comment lines were in use until the release of QIIME 2 2019.7 a few days ago, so I doubt this has been a big problem for anyone.

Performance enhancements

Miscellaneous

• Added a draft "Moving Pictures" tutorial.
• When replacing certain characters within column names, Qurro no longer replaces ' or " characters with | characters. Instead, ' and " characters are just removed from column names entirely.
• Updated the rank plot's y-axis to say Magnitude: [ranking name] instead of Rank: [ranking name]. (#194)
• Replaced uses of log ratio with log-ratio throughout Qurro's code and documentation.
• On the Qurro website:
  • Added a "Mackerel" demo (based on the output of this analysis), and associated with data from this paper.
  • Replaced "OTUs" for the Moving Pictures and Sleep Apnea demo dataset feature types with "ASVs / sOTUs".
  • Replaced "OTUs" for the Byrd dataset feature type with "Taxa".
  • Cleaned up the Byrd demo's dataset citation (to reflect the fact that the Morton/Marotz et al. 2019 paper is now published).
  • Removed the now-incomplete "tutorials" section, in favor of just linking to Qurro's GitHub page.
• DEICODE ordinations used in demos and test inputs have been rerun with DEICODE version 0.2.3. (#188)
• Cleaned up Qurro's command-line interface options and help text.
• When exporting data in the sample plot, the default filename is now just sample_plot_data.tsv instead of rrv_sample_plot_data.tsv. (The prior default filename dates back to when Qurro was named "rankratioviz.")
• A clear error is now raised if Qurro is trying to parse a GNPS feature metadata file, and the feature rankings include a column named LibraryID. This sort of error should already have come up in prior versions of Qurro, but now it will come up a bit earlier (and use a clearer message indicating what's going on).
• Slightly changed the warning message produced when there are indistinguishable rows in a GNPS feature metadata file (now this message is no longer prefixed with something like WARNING:root:).
• The output message letting the user know about samples in the sample metadata that are not also in the BIOM table has been shortened a bit (now it doesn't start with NOTE: ).
• Changed the error message when no samples are shared between the sample metadata file and BIOM table to be a bit clearer:
  • Before: None of the samples in the sample metadata file are present in the input BIOM table.
  • After: No samples are shared between the sample metadata file and BIOM table.
  • The earlier message wasn't technically wrong, but the new message is more direct (and more indicative of what's going on behind the scenes).
• In the sample plot Vega-Lite JSON generated by Qurro, samples are no longer sorted by their IDs. (This is just an internal change, and shouldn't affect Qurro's behavior at all.)
• Updated the "README.txt" file located in the Byrd et al. test data folder to make it clearer that the differentials used here are equivalent to those used in the Morton/Marotz et al. 2019 analysis (https://github.com/knightlab-analyses/reference-frames).
• Reran Songbird on the Red Sea dataset in consultation with Tensorboard to verify that the model fit was reasonable. I changed some of the hyperparameters around a bit; I added a README.txt file to the Red Sea test data folder detailing this process, and also updated the Songbird Jupyter Notebook accordingly.
• Removed some unused images from the screenshots/ directory of Qurro's code repository.
• Updated the screenshot used in the README.
• Various other small updates to Qurro's code and documentation. (#184)

Qurro 0.2.1 (July 10, 2019)

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)

• 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)

Backward-incompatible changes

Bug fixes

• Ensured that missing feature metadata values, and samples' initial balances (aka log ratios), were set to None instead of NaN when being passed to Altair. (In practice this wasn't causing any problems, since Altair converts NaN values to None values, but Qurro should at least be more internally consistent now.)

• Changed the behavior of how Qurro (when run outside of QIIME 2) writes out 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)

• 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 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 to worry about this.

• Qurro should now throw an error if an input GNPS feature metadata file doesn't have parent mass, RTConsensus, and LibraryID columns.

Performance enhancements

• Now, Qurro's JavaScript code uses a sparse representation of the count data (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)

• Significant speedups on how the input data is filtered and matched. (#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)

• 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.

Miscellaneous

• Changed the search type menus to be a bit more clear about what they're doing under the hood:

  • contains the text --> contains the exact text
  • contains the exact taxonomic rank(s) --> contains the exact separated text fragment(s)

• Previously, the Export currently used data button would only export information about samples with valid current log ratios (however, samples 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)

  • 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.
  • Furthermore, redundant fields are now shown in the exported data -- so if you set the x-axis and color fields for the sample plot to both be Sample ID, you'll see three Sample ID columns in the exported data.
  • Note that invalid log ratios (as well as empty/missing metadata fields, as before) will be shown as null values in the exported sample data.
  • The button's name has also been changed to Export sample data, to make its behavior clearer.

• Added citation instructions and some small documentation fixes to the README

• Fixed a typo in the license (forgot to update this when we renamed the tool to "Qurro" a few weeks ago)

• Cleaned up/updated some of Qurro's basic documentation (in its setup.py, example Jupyter Notebooks, etc.).

• Updated the screenshot used in the README.

• Various improvements to Qurro's code and tests.

Qurro 0.1.0 (June 25, 2019)

• Released the first version of Qurro on PyPI!