Bug fix release and removal of py27

A summary of the changes in 2.1.8 is below. Thanks in particular to @wwydmanski, @KasperSkytte, @gwarmstrong, @cdiener, @pieterprovoost and @raissameyer for their contributions on this release.

This is a re-release of 2.1.8, which when first pushed out contained a build issue related to latent .c files.

Important:

• Python 2.7 and 3.5 support has been dropped.
• Python 3.8 support has been added into Travis CI.
• A change to the defaults for Table.nonzero_counts was performed such that the default now is to count the number of nonzero features. See issue #685
• We now require a SciPy >= 1.3.1. See issue #816

New Features:

• The detailed report is no longer part of the table validator. See issue #378.
• load_table now accepts open file handles. See issue #481.
• biom export-metadata has been added to export metadata as TSV. See issue #820.
• Table.to_tsv has been modified to allow for direct_io. See issue #836.

Bug fixes:

• Table.to_dataframe(dense=False) does now correctly produce sparse data frames (and not accidentally dense ones as before). See issue #808.
• Order of error evaluations was unstable in Python versions without implicit OrderedDict. See issue #813. Thanks @gwarmstrong for identifying this bug.
• Table._extract_data_from_tsv would fail if taxonomy was provided, and if the first row had the empty string for taxonomy. See issue #827. Thanks @KasperSkytte for identifying this bug.

2.1.7: Bug fixes, performance improvements and new features

A summary of the release is below. Thank you to @stevendbrown, @gregcaporaso, @ElDeveloper, @rec3141, and @nreeve17 for the commits!

Important:

• Python 3.4 support has been dropped. We now only support Python 2.7, 3.5, 3.6 and 3.7.
• We will be dropping Python 2.7 support on the next release.
• Pandas >= 0.20.0 is now the minimum required version.
• pytest is now used instead of nose.

New Features:

• Massive performance boost to Table.collapse with the default collapse function. The difference was 10s of milliseconds vs. minutes stemming from prior use of operator.add. See issue #761.
• Table.align_to for aligning one table to another. This is useful in multi-omic analyses where multiple preparations have been performed on the sample physical samples. This is essentially a helper method around Table.sort_order. See issue #747.
• Added additional sanity checks when calling Table.to_hdf5, see PR #769.
• Table.subsample() can optionally perform subsampling with replacement. See issue #774.
• Table.to_dataframe() now supports a dense argument to return pd.DataFrame. See issue #762.
• Parsing methods for BIOM-Format 1.0.0 tables now preserve dict ordering. See issue #781.

Bug fixes:

• Table.subsample(by_id=True, axis='observation') did not subsample over the 'observations'. Because of the nature of the bug, an empty table was returned, so the scope of the issue is such that it should not have produced misleading results but instead triggered empty table errors, with the exception of the pathological case of the ID namespaces between features and samples not being disjoint. See PR #759 for more information.
• Tables of shape (0, n) or (n, 0) were raising exceptions when being written out. See issue #619.
• Tables loaded with a list of empty dicts will have their metadata attributes set to None. See issue #594.

2.1.6: Bug fixes, and API expansion

This release added several new features and is backward compatible with version 2.1.5.

A subset of the new features include:

• Table.rankdata for ranking abundances over either axis
• Table.concat for concatenating tables rapidly when one axis is disjoint (i.e., merging tables with common observations but unique samples).
• Table.to_dataframe to convert the contained data into a Pandas DataFrame
• biom table-ids to dump out the IDs from a given axis

For full details, see the project's ChangeLog.md file.

2.1.5: added Python 2/3 compatibility

This release added several new features and is backward compatible with version 2.1.4.

New features include:

• Python 2/Python 3 compatibility;
• the new biom head command, which allows for viewing the first few rows and columns of biom file in tab-separated text format;
• the new biom from-uc command, which allows for creation of biom files directly from vsearch/uclust/usearch .uc files.

For full details, see the project's ChangeLog.md file.