HDF5 integration

[ElDeveloper]

In reference to #1583, we are making great progress, thanks everyone! There are still a few things that need to get resolved, if everyone grabs one or two items of the following lists, this will be done faster.

Unit tests

The following is from the Jenkins build:

• [x] qiime/tests/test_beta_metrics.py (@eldeveloper has a PR open)
• [x] qiime/tests/test_core_microbiome.py (Depends on https://github.com/biocore/biom-format/pull/472 )
• [x] qiime/tests/test_format.py (@antgonza has a PR open)
• [x] qiime/tests/test_map_reads_to_reference.py (@antgonza has PR open)
• [x] qiime/tests/test_parallel/test_map_reads_to_reference.py (@ElDeveloper has a PR open)
• [x] qiime/tests/test_parallel/test_multiple_rarefactions.py (@adamrp has a PR open)
• [x] qiime/tests/test_sort.py (@ElDeveloper's changes in this BIOM PR should fix this problem https://github.com/biocore/biom-format/pull/474)
• [x] qiime/tests/test_workflow/test_core_diversity_analyses.py
• [x] qiime/tests/test_workflow/test_downstream.py (@adamrp has a PR open)
• [x] qiime/tests/test_workflow/test_upstream.py (@ElDeveloper has a PR open)

  Script usage tests

The list of scripts is the following (note that a lot if not all of these failures will be resolved once all the library code is functioning correctly):

• [x] compute_core_microbiome.py (depends on https://github.com/biocore/biom-format/pull/472)
• [x] core_diversity_analyses.py
• [x] filter_fasta.py (@eldeveloper has a PR open)
• [x] make_otu_heatmap.py (@teravest has a PR open)
• [x] map_reads_to_reference.py (@antgonza has PR open)
• [x] summarize_taxa.py (@adamrp, @teravest and @antgonza have been working on this)
• [x] summarize_taxa_through_plots.py (@adamrp has a PR open - this workflow depends on summarize_taxa.py)
• [x] parallel_map_reads_to_reference.py (@ElDeveloper has a PR open)

  Misc.

• [x] Add note to change log.

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Please let us know via a comment in this issue if you are going to be working in any of these items.

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New issues should be added to the HDF5 integration milestone.

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cc @squirrelo, @josenavas, @wasade, @antgonza, @adamrp, @teravest.

[ElDeveloper]

core_microbiome should be fixed with the current PR that @Jorge-C has in biom.