Added

Adds ocx.FunctionalProfiles to fetch functional analyses results
Adds SampleCollection.to_classification_df() and SampleCollection.to_functional_df() methods to return classification or functional results as DataFrames
Adds option to omit taxonomic labels from plot mappings

Changed

Ensures singleton FASTQ filenames follow the same format as chunked uploads (Oxford Nanopore)

Fixed

Fixes issue with onecodex login requiring an API key for certain accounts

- Python
Published by audy about 1 year ago

Added

Adds SampleCollection.beta_diversity_stats() to test for significant differences between groups of samples based on their beta diversity distances (global and posthoc pairwise PERMANOVA tests are supported)
Adds categorical data palette to onecodex Altair theme
Adds support for passing both facet_by and secondary_haxis to plot_metadata()
Adds filtering and warning if samples are missing abundances in plot_metadata(), plot_pcoa(), plot_mds(), plot_pca(), alpha_diversity_stats(), and beta_diversity_stats()
Adds docs about Shannon diversity being calculated using log base 2 instead of base e

Changed

Upgrades Altair to 5.4.1 and replaces altair_saver with vl-convert
Upgrades notebook to 6.5.7
Upgrades WeasyPrint to 63.0
Removes node and vega npm dependencies
Removes jupyter-client dependency
Removes selenium dependency
Removes pinned pydyf version

Fixed

Fixes Api() call when Altair is not installed
Fixes scikit-bio and pandas warnings
Improves error message and docstring in SampleCollection.to_df(normalize=False)

Deprecated

Deprecates AlphaDiversityStatsResults.posthoc_df in favor of AlphaDiversityStatsResults.posthoc.adjusted_pvalues

- Python
Published by jairideout over 1 year ago

Added

Adds optional secondary_haxis parameter to plot_metadata(), which can be a field name or tuple of field names, if a second grouping is desired
Adds alpha diversity stats tests, which are run via SampleCollection.alpha_diversity_stats()
Adds support for Python 3.12
BIOM export now includes canonical taxonomic lineage
Adds documentation via GitHub Pages at https://onecodex.github.io/onecodex/
Adds support for concatenating ONT files

Changed

Adds scikit-posthocs dependency
Pins scikit-bio to 0.6.0
Updates minimum required version of scipy to 1.11.0
Updates minimum required version of numpy to 1.21.6
Pins pydyf<0.11.0

Fixed

Fixes a bug associated with updating custom metadata on a sample
Fixes metadata non-unique column name bug
Provides a more useful error message if plot_heatmap is called with any samples without abundances calculated
Fixes abundance chart for groups of samples where all samples lack abundance estimates

Removed

Removes Python 3.8 support

- Python
Published by alenajk almost 2 years ago

Changed

Downgrades notebook version pin to 6.4.10

- Python
Published by jairideout over 2 years ago

Added

Adds coerce_haxis_dates=True parameter to plot_metadata()

Fixed

Fixes date field type coercion in plot_metadata()

- Python
Published by jairideout over 2 years ago

Added

Adds new plotting method plot_functional_heatmap to plot a heatmap with specified annotations and metrics of functional profile data

Changed

Pins urllib3<2
Updates jupyter-client version pin to 8.6.0
Updates notebook version pin to 7.0.6
Updates nbconvert minimum version to 6.4.3
Updates WeasyPrint version pin to 60.1
Removes jinja2 version pin
Replaces imp module usage with importlib in preparation for Python 3.12 support

Fixed

Fixes FutureWarnings generated by pandas, scikit-learn, etc.
make test no longer generates warnings
Fixes notebook exporter commands in README.md

- Python
Published by jairideout over 2 years ago

Added

Adds name option to assets upload command in experimental API mode

Fixed

Fixes heatmap plotting for samples without a specified haxis value
Fixes installation by monkeypatching altair-saver for npm >=9

- Python
Published by alenajk almost 3 years ago

Added

Adds support for Python 3.11
Adds assets upload command in experimental API mode

Changed

Handles heatmap display of samples with no abundances calculated
Excludes samples with no abundances calculated from distance heatmap with abundances metric
Pins altair to 4.2.2
Requires jsonschema version >= 3.0
Improves retry handling
Pins version of altair-saver that includes a fix for npm >= 9

Fixed

Fixes unnecessary global loading of numpy and pandas
Fixes chart concatenation

Removed

Removes support for Python 3.7
Removes opening links in new tab functionality (can be added manually to a returned chart with usermeta)

- Python
Published by alenajk almost 3 years ago

Added

Adds support for testing experimental API
Adds functionality to SampleCollection objects to generate tabular data for FunctionalRuns using the .to_df() method
Adds include_taxa_missing_rank parameter to to_df() method for including taxa that do not have a designated parent at rank (will be grouped into a "No " column) (metrics readcount_w_children and abundance_w_children are supported)
Adds support for readcount_w_children metric to plot_bargraph() when passing include_taxa_missing_rank (only abundance_w_children was supported previously)
Adds increased customization of plot legend; plot_bargraph()'s legend parameter now accepts an altair.Legend instance
Adds group_by support to plot_bargraph
Adds support for linking to NCBI taxonomy browser from plots

Changed

Pins selenium to <4.3.0
Pins scipy<1.9
Default plot legend is bigger (displaying up to 40 items)

Fixed

Fixes metadata fetching to support fields that match neither metadata nor taxa instead of raising an error
Fixes box plot display bug for samples with same value
Fixes pandas SettingWithCopyWarning previously raised by to_df and plot_bargraph
Fixes plot_bargraph display bug for empty samples (total count or abundance of zero)
Fixes None artifact in PDFs

- Python
Published by alenajk over 3 years ago

Added

Adds download_samples() function and onecodex download samples CLI command for downloading batches of samples as FASTA/Q files
Adds support for Python 3.9 and 3.10
Adds support for Apple M1 processors

Changed

Improves SampleCollection._collate_results() runtime by at least 20x
Improves missing value coercion in SampleCollection._collate_results()
Updates some dependency versions to address security vulnerabilities, performance enhancements, expanded environment support, and easier installation
numpy is no longer required to be installed prior to installing the onecodex package
Relaxes filelock dependency version pin
Changes help@onecodex.com to support@onecodex.com in user messaging

Fixed

Fixes PCoA/MDS plot URL bug
Fixes metric parameter behavior in SampleCollection constructor (it is no longer ignored)

Removed

Removes Python 2 support
Removes bash completion
Removes Classifications._append_abundance_rollups() in favor of retrieving abundance_w_children metric from One Codex API

- Python
Published by jairideout over 4 years ago

Added

Adds support for functional analysis profiles as experimental feature
Adds improved error messaging for Sample methods

Changed

Pin jupyter-client to version 6.1.12

Fixed

Fixes issue with credential file lock

Removed

Removes Classifications.abundances method

- Python
Published by alenajk over 4 years ago

Added

Adds support for concatenating sequencing data from multiple lanes
Adds support for faceting metadata plots

Changed

Upgrades minimum sentry-sdk version
Adds explicit legend title on distance heatmaps
Adds support for zero-abundance samples in normalization calculations
Warns when empty boxes are present in faceted boxplots
Supports more paired file naming schemes for automatic interleaving
Improves SampleCollection._collate_results runtime
Adds support for an empty domain in interleave_palette
Improves error message handling for samples in an importing state

Fixed

Fixed a race condition when running multiple instances of the CLI
Fixed issues handling symmetry and NaN's in beta diversity calculations
Fixed beta diversity heatmap layout issues
Fixed PCA/MDS/PCoA colouring issues
Fixed broken taxa bargraph links

- Python
Published by clausmith over 5 years ago

Added

Adds Aitchison distance and supports manhattan as a synonym for cityblock

Changed

Ignores vega-lite warning about boxplots not supporting selection
Displays facet field name and values below x-axis for taxa barplot and heatmap
Filters out NaNs from alpha diversity plots

Fixed

Improves support for networks with a custom CA
Fixes support for responsive plots (width=None and width="container" in plot_metadata)

- Python
Published by jairideout over 5 years ago

Changed

Replaces chao1 with observed_taxa
Changes the experimental assembly download api to support async retry logic
Upgrades from deprecated Raven library to sentry_sdk

- Python
Published by bcamarda almost 6 years ago

Fixed

Fix bug preventing calculation of weighted Unifrac metric due to taxonomy structure assumptions in scikit-bio

- Python
Published by boydgreenfield almost 6 years ago

Fixed

Include fonts for report generation in PyPI distribution

- Python
Published by boydgreenfield almost 6 years ago

Changed

Overhaul styling of Jupyter notebook PDF exports
Add One Codex theme for Altair plots (enabled by default)
Refactor how notebooks.report.references helper works internally
Improve upload command to display sample filenames on cancelation
Bump Altair minimum required library version to 4.1.0

- Python
Published by boydgreenfield almost 6 years ago

onecodex - Fix uploader bug introduced in v0.8.1

Fixed

Fix upload callback retry handling broken in v0.8.1 (c87eb76f0dea544b742c5eacf0a4dfcdcebb87bc)

- Python
Published by boydgreenfield about 6 years ago

Changed

Improved retry handling for confirm callback POSTs during Sample uploads

Fixed

Fix upload and export of PDF reports to One Codex documents portal
Fix example notebook links to follow updated v0.8.0 plotting conventions

- Python
Published by boydgreenfield about 6 years ago

onecodex - Significant plotting method improvements (incl. breaking API changes)

Added

Adds more pythonic support for truthy/falsey values to SampleCollection.filter()
Adds support for passing lists to the various sortx and sorty plotting arguments
Adds a property to SampleCollection to track whether we think the collection is all WGS/metagenomic data
Adds support for specifying weightedunifrac and unweightedunifrac as metrics in the SampleCollection.beta_diversity() method
Adds support for calculating alpha and beta diversities on normalized data. This is important since we'll now be using abundances by default for most datasets
Adds support for specifying chart width and height directly in the plot_* functions
Adds option to plot "Other" bars on bargraphs with normalized read counts and abundances
Adds option to plot "No <level>" bars on bargraphs with abundances
Adds abundance rollups so we can use abundances at all taxonomic ranks
Adds a project column to the metadata DataFrame of a SampleCollection

Changed

Changes default alpha diversity metric from simpson to shannon, since shannon is generally a more appropriate default
rank="auto" now defaults to species if the field="abundances" or the dataset is metagenomic, instead of genus
Switches to using a normalized tree for Weighted Unifrac calculations, which gives us Unifrac values in a [0, 1] range
Defaults to using abundances data for metagenomic datasets instead of readcountwchildren

Deprecated

The field kwarg on the SampleCollection constructor has been renamed to metric. We still support passing either, but show a DeprecationWarning when passing field

Removed

Removes support for just specifying unifrac as a metric

- Python
Published by boydgreenfield about 6 years ago

onecodex - Improve reliability of uploads with multiple threads

Bug fixes

Fixes a bug that could sometimes cause boto3 to raise an exception when used with multiple threads

- Python
Published by boydgreenfield over 6 years ago

onecodex - Handle cancelation error affecting multipart uploads

Bug fixes

Fixes a bug where multipart uploads are not properly canceled if, e.g., exiting with Control-C or due to a connectivity issue. This also prints a nice message vs. a verbose stack trace in these cases.

- Python
Published by boydgreenfield over 6 years ago

onecodex - Much improved uploads, misc. library analysis improvements

Enhancements

Uploads now take advantage of backend interleaving, leading to faster, more efficient uploads (see #312)
Upload code has been significantly simplified, leading to fewer edge cases related to, e.g., connection issues
Enable Bray-Curtis on normalized read counts. Closes #291
Warn if mixing analysis types in SampleCollection

Bug fixes

Add incremented number to duplicate plot labels
Don't include host reads in analyses. Closes #285.

- Python
Published by boydgreenfield almost 7 years ago

onecodex - Minor bugfix release

Fixes issue with Sample.__repr__ method for pre-uploaded samples

- Python
Published by boydgreenfield almost 7 years ago

onecodex - Support for pre-uploads, searching samples across an organization

New features: * Add support for --sample-id and --external-sample-id for matching pre-uploaded samples at upload time * Add support for searching an organization's samples (for organization admins), using ocx.Samples.where(organization=True)

- Python
Published by boydgreenfield almost 7 years ago

onecodex - Upload reliability improvements, plotting tweaks

Enables bash autocompletion of files and directories (e.g., onecodex upload AUTOCOMPLETE_A_FILE_HERE)
Improves upload reliability in several ways
- Better handles KeyboardInterrupt with our atexit cancellation handler (closes #298)
- Uses new request.session objects for uploads, reducing the probability of exhausting the connection pool
- Limits uploads to 8 threads for reliability reasons
Improves documentation, adds numpy documentation linting via pydocstyle
Bumps required version of click (older versions were not fully supported for the progress bar)
Displays "normalized" labels in plots where appropriate (closes #274)

- Python
Published by boydgreenfield almost 7 years ago

onecodex - Fix minor authentication bug

Addresses a rare edge case where the API schema and credentials could be cached and invalid when using the experimental API access flag

- Python
Published by boydgreenfield almost 7 years ago

onecodex - Adds experimental model support, minor fixes

Adds support for experimental flag for access to experimental API features. Note: These features are explicitly not provided with the same stability guarantees as the core One Codex v1 API.
Fixes #289
Fixes #290

- Python
Published by boydgreenfield almost 7 years ago

onecodex - Performance improvements and server-side Vega plot rendering

Enhancements

#255 - When an direct upload to One Codex fails, the backup upload route via an S3 intermediate bucket will be retried up to three times.
#264 - Files over 100 GB will skip realtime validation and be uploaded directly to S3 to avoid situations where validation blocks sending a large file that took a really long time to upload.
#269 - Bump Altair version to 3.1.0 which adds some nice new plotting features.
When exporting HTML/PDF reports in the One Codex notebook service, saving of Vega plots as SVGs or PNGs can be controlled with onecodex.viz.render_settings(). When svg_or_png=False is passed to this function, plots will be rendered server-side using vega-cli.
Importing of large dependencies, like scipy, now happens lazily to drastically reduce library loading time.

Bug fixes

#254 - Use a central onecodex namespaced logger rather than overriding the base logging class. This avoids potential conflicts with user code.

Breaking changes

The subset_reads script has been changed to no longer validate FASTQ files by default. Validation is really slow and most of the files this script sees are perfectly fine. The --no-validate option has been renamed --do-not-validate and is set by default. To enable validation, pass --validate.

- Python
Published by polyatail almost 7 years ago

onecodex - Allow even bigger file uploads

This release enables upload chunk size selection dynamically based on input file size, accounting for interleaving of compressed paired-end files. The maximum (uncompressed) file size is now ~1 terabyte.

- Python
Published by polyatail about 7 years ago

onecodex - Allow large file uploads (250GB), misc. small fixes

Allow uploads up to 250GB
Fix paired end interleaving edge case bug (#266)
Detect long format data frames better to avoid issue where resetindex() moves classificationid into DataFrame.columns (#268)
Allow sorting x and y axis labels in plotters (#253)
Fix issue when creating new Tags (#257)

- Python
Published by boydgreenfield about 7 years ago

onecodex - Bugfixes on uploading and filtering samples, bump Altair/Vega version

Bumps Altair/Vega to latest versions
Fixes #261 where direct-to-S3 uploads are attempted even if files are >5GB. Instead, we skip this and use the S3 intermediate bucket.
Fixes #252 where filtering Samples by metadata that doesn't exist returns all samples instead of no samples

- Python
Published by polyatail about 7 years ago

onecodex - Additional cancelation code for failed uploads due to connectivity issues

- Python
Published by boydgreenfield about 7 years ago

onecodex - Fix logging error affecting certain upload error conditions

Fixes bug affecting logging configuration for upload error messages. This could lead to crashes if errors were logged during uploads (e.g., in retry scenarios)
Improves proxy upload flow to handle more upload buffering edge cases

- Python
Published by boydgreenfield about 7 years ago

onecodex - Minor bug fix for older versions of Pandas and Python 2.7

In v0.5.0, we introduced functionality to correctly coerce certain numpy and pandas types into JSON objects. Unfortunately, this could break on installs of the CLI that did not use pip install onecodex[all] as they could have older versions of Pandas without this API. This release fixes that bug.

- Python
Published by boydgreenfield about 7 years ago

onecodex - Client upload improvements (includes breaking changes, see notes)

Changes in v0.5.0 include: - Simplified and improved upload code to better handle a range of file sizes and upload speeds through our validating proxy service - Changes to the upload API for the Python client library for Samples and Documents resources. - A workaround for a bug in Pandas where Series objects do not always coerce their items to Python object types when calling .to_dict. Closes #232

Note, this release contains the following BREAKING CHANGES for library code: - ocx.Samples.upload and ocx.Documents.upload now return objects upon completion and raise an UploadException upon failure vs. only logging an error. Client code should now try/except for an UploadException to gracefully handle these errors. - ocx.Samples.upload now only takes a single file or a tuple of files. It should no longer receive a list of files or tuples as before. A loop can be used to upload multiple files. See the README for examples with and without threading.

- Python
Published by boydgreenfield about 7 years ago

onecodex - Fix upload progress bar bug, handle setting a Pandas Series to Metadata.custom

Allow setting metadata.custom to be a Pandas Series object (handling JSON serialization properly). Closes #232.
Fix a bug where if the number of threads is not specified to ocx.Samples.upload or ocx.Documents.upload the progress bar could throw an error. Closes #240.

- Python
Published by boydgreenfield over 7 years ago

onecodex - Fixes check for CLI version updates

Fixes a bug affecting versions 0.4.0, 0.4.1, 0.4.2, and 0.4.3 in which the user would not always be prompted to update their CLI if a later version was available

- Python
Published by boydgreenfield over 7 years ago

onecodex - Send metadata along with fallback uploads

Bug fixes

This release fixes a single bug where the project, metadata, and tags were not sent to the API in the fallback case where a file is uploaded direct to S3 rather than via proxy (#231).

- Python
Published by polyatail over 7 years ago

onecodex - Fix bug in check_version

Bug fixes

This release fixes a single bug which may have prevented the proper checking for new versions of the client library. One user reported an error when logging in via the ~/.onecodex saved credentials with a schema flagged by the CLI as stale and in need of update.

- Python
Published by polyatail over 7 years ago

onecodex - Updates to plotters and SampleCollection

Enhancements

Faceted plots (grouped by metadata) are supported in plot_bargraph (#215)
Shannon diversity is supported in plot_metadata (#220)
Plotting methods now have a label= kwarg which supports changing the x-axis labels using a lambda function (#221)
Add new filter method on SampleCollection, filter= kwarg on Samples.where, and made instantiation of new SampleCollections more user-friendly (#226)

Bug fixes

Uploading files via Samples.upload was broken if no threads= kwarg was supplied. This has been fixed and now defaults to threads=4 (#224)
Cleaned up check_version code that was a bit old and which was almost made obsolete by changes to our API (#223)
Remove x-axis labels from bargraphs by default
Fixed bug where slices of SampleCollection would not pass on any kwargs used to instantiate the original class

Breaking changes

None

- Python
Published by polyatail over 7 years ago

onecodex - Overhaul of notebook API, uploading, read filtering, and reports

Enhancements

Major changes to manipulation of classifications results and plotting via new SampleCollection API and subclassed pandas ClassificationsDataFrame (#177)
Improved structuring and testing of viz methods of (#136, #151, #171)
Removal of FASTX validation code--all uploads are validated on the server-side by fastx-proxy (
Faster and improved handling of sample uploading (#42, #189, #194, #195, #196)
Much faster filtering of reads by taxon IDs (#79, #163)
API schemas loaded in one shot speeds up CLI loading by seconds (#156)
Command line autocomplete now available if supported by user's system (#155)
Authentication for CLI now possible via environment variables (#154)
Tags can now be searched for on Samples.where (#168)
A new report-generated API has been added for generating PDF reports in jupyter notebooks (#180, #181, #184, #206, #211, #212, #213)
A new stacked bar plot is available in SampleCollection.plot_bargraph() (#198)
Document files >5GB can now be uploaded (and downloaded) from the CLI via onecodex documents (#187, #209)

Bug fixes

Fixed bug where telemetry was sometimes reported incorrectly or vaguely (#153)
Added missing comma from setup.py (#173)
Fixed but where leading zeros on model object IDs were being stripped (#200)

Breaking changes

The filter_reads script has been renamed to subset_reads. It is currently aliased to avoid breaking user code, but is now deprecated and will be removed in a future release.
Plotting classifications results via onecodex.viz is no longer supported. Instead, users must use methods on SampleCollection objects which are returned by Samples.where queries.

- Python
Published by polyatail over 7 years ago

onecodex - Fix uploader edge cases with subset of invalid FASTQs

Bug fixes

Passing --coerce-ascii will warn rename files to ASCII, for downstream compatibility (#140)
Check for data leftover in buffer, catches invalid FASTQ (#161)

- Python
Published by polyatail over 7 years ago

onecodex - Add support for interactive plots with altair

Enhancements

Add support for interactive PCA, heatmap, metadata, and other plots (#146, #133, #132, #131)
Add ability to output "long" format results table (#139)
Significant refactoring and clean up of plotting and plot helper method code

Bug fixes

Fix issue where Classification results were not properly cached (#143)
Fix caching of Api schema, use cached schema by default (reduces initialization time) (#142)

Breaking changes

The API should be stable from v0.2.* to v0.3.0 but we are now using altair instead of matplotlib for plotting. This will break extensions to plots using matplotlib features or syntax, so we're calling this a minor version bump.

- Python
Published by boydgreenfield over 7 years ago

onecodex - Bug fixes, script improvements, and better environment compatibility

Enhancements

Made library compatible with environments with simplejson installed (#111)
Better warnings for bad samples (#125), login requirements (#117), file IO (#113)
Additional filtering options and features for onecodex scripts filter_reads (#114, #83)

Bug fixes

Properly return a ResourceList for several key API objects, allowing updating of, e.g., samples' tags more directly (#40, #129)

- Python
Published by boydgreenfield over 7 years ago

onecodex - Adds support for uploading samples into a project

Major functionality

Adds support for specifying project at upload time by UUID, project name, or project short name

Bug fixes

Fixes issue where paired filenames get improperly formatted
Fixes issue where timezone data wasn't passed to the server on upload
Adds notice to upload help text that metadata and tags specified at upload time are applied to all samples

- Python
Published by clausmith almost 8 years ago

onecodex - Add support for setting metadata and tags at upload time

Major functionality: - Support setting metadata for samples at upload time - Support settings tags for samples at upload time

Minor enhancements and fixes: - Allow login with API key for users with two-factor authentication (2FA), i.e., onecodex --api-key $YOUR_API_KEY login - Fix bug when uploading uncompressed files with the --do-not-validate flag, in which .gz was being erroneously appended to the filename - Properly warn users if they've hit usage limits when trying to upload samples - Standardize return of sample IDs to command line users after upload - Fix client library bug where unsaved model IDs are not properly handled

- Python
Published by boydgreenfield about 8 years ago

onecodex - Minor bug fixes

Fix issues with telemetry metadata
Fix issues with FASTQ files ending with blank lines

- Python
Published by boydgreenfield about 8 years ago

onecodex - New scripts functionality, bug fixes

Changes include: - Improvements to BIOM 1.0 exporter within Python library (#75) - Addition of new onecodex scripts commands, with a filter_reads script for filtering reads based on taxonomic classification results (#71) - Warn if simplejson is installed (#66) - Allow users to manually specify forward and reverse reads (#63)

- Python
Published by boydgreenfield over 8 years ago

onecodex - Misc. bug fixes and enhancements

Specifically: - Fix a situation where a credentials warning could happen even if credentials were found (e2922ea26ab4e999a0eddb4fd9da78d57b25fe10) - Update for pandas >= 0.20, < 0.21 (8d7d3a04debd01de6792526e8dae37ada543ec48) - Move to POST for initializing multipart uploads (API for GET is deprecated and will be removed soon) (e2bcdb38db019814a61caaeb6403dc501f676d86)

- Python
Published by boydgreenfield over 8 years ago

onecodex - Bug fix: Raven install in setup.py

In v0.2.7, we inadvertently required raven for the CLI, but did not specify it in the default install packages. Consequently, pip install onecodex would not work without raven, though pip install onecodex[all] did work properly. This release fixes that bug and adds regression testing around our different environments / extras_require setup.py options.

- Python
Published by boydgreenfield almost 9 years ago

onecodex - Stability, monitoring, and bug fixes

Add support (default on) for telemetry data to be sent to One Codex during a crash of the CLI only. Can be disabled with the --no-telemetry flag.
Fix bug that would crash CLI when trying to fetch an invalid sample or analysis ID (3479a4e6d8de518a4356547a37780089de71dda4)
Fix bug related to corrupt ~/.onecodex credentials files when switching from anonymous to authenticated use of the CLI (8b4a376e4934b5d7f37058f1cdd13d56279acea2)

- Python
Published by boydgreenfield almost 9 years ago

onecodex - Improved plotting, analysis data helper functions, data fetching

Fixes and improvements include: - Update default page size from 20 to 200 items – greatly reducing the number of requests - Remove pandas MultiIndexing from internal DataFrame generated in onecodex.helpers and used by onecodex.viz functions. Multi-indexing requires sorting and is generally hard to work with. Columns returned by collate_classification_results are now simply string Tax IDs. - Allow passing **kwargs from onecodex.viz.plot_* functions to Seaborn/Matplotlib. - Change default plot theme to darkgrid. Override with style= keyword. - Ignore SciPy cluster warnings in sns.clustermap - Fix bug with CLI uploading for paired end gzipped data (previous regression). - Fix issue with CLI failing to run properly if matplotlib existed but was not installed properly (i.e., it could be imported but its import raised an exception). - Set threads to 1 by default in onecodex.lib.upload functions if None is passed in.

- Python
Published by boydgreenfield almost 9 years ago

onecodex - Minor fix

Minor fixes and improvements: - Bump to latest version of potion-client (2.5.1) - Fix bug affecting .where() queries for models that have a public property and not a public route (no models have both)

- Python
Published by boydgreenfield almost 9 years ago

onecodex - Add plotting convenience functions and initial skbio integration

Adds basic convenience plotting functions, including plot_distance, plot_heatmap, plot_metadata, and plot_pca. These are available on One Codex Api instances, e.g., ocx.viz.plot_heatmap(*args, **kwargs).
Adds onecodex.helper that includes unstable helper functions for coercing samples and analyses into classifications, collating multiple classification results, etc.
Add onecodex.distance module with support for several common alpha and beta diversity statistics. Additional statistics are available by calling out to skbio directly.

- Python
Published by boydgreenfield almost 9 years ago