Issues

• to_dataframe behaves differently with Pandas 3.0

  biocore/biom-format#1001 · Filter by author mataton opened on Feb 24, 2026

• int32 for indices/indptr

  biocore/biom-format#999 · Filter by author jianshu93 opened on Nov 26, 2025
  1

• Invalid certificate

  biocore/biom-format#998 · Filter by author bernt-matthias opened on Oct 27, 2025
  1

• Reduce import time

  biocore/biom-format#984 · Filter by author wasade opened on Nov 5, 2024

• Support assertAlmostEqual()

  biocore/biom-format#983 · Filter by author AmandaBirmingham opened on Oct 4, 2024

• Throw error if trying to create a biom table containing NaNs

  biocore/biom-format#982 · Filter by author AmandaBirmingham opened on Oct 4, 2024

• MAINT: centralize dataframe schemas

  biocore/biom-format#981 · Filter by author wasade opened on Oct 1, 2024

• API: support COO and pivot formats in dataframe conversions

  biocore/biom-format#980 · Filter by author wasade opened on Oct 1, 2024

• API: Table.read and Table.write

  biocore/biom-format#979 · Filter by author wasade opened on Oct 1, 2024

• API: to/from polars

  biocore/biom-format#978 · Filter by author wasade opened on Oct 1, 2024

• From dataframe

  biocore/biom-format#972 · Filter by author mortonjt opened on Jun 14, 2024

• Adding table metadata

  biocore/biom-format#971 · Filter by author Midnighter opened on May 11, 2024
  3

• TypeError: the JSON object must be str, bytes or bytearray, not File

  biocore/biom-format#965 · Filter by author thomasstjerne opened on May 3, 2024
  9

• add-metadata help messages need clarity

  biocore/biom-format#946 · Filter by author wasade opened on Jan 24, 2024

• Required attribute table type not checked consistently

  biocore/biom-format#903 · Filter by author peterjc opened on Mar 9, 2023
  6

• it would be nice to easily remove blanks

  biocore/biom-format#870 · Filter by author wasade opened on Mar 9, 2022
  2

• Use six's assertRaisesRegex compatibility layer

  biocore/biom-format#794 · Filter by author ElDeveloper opened on Sep 11, 2018

• Add examples of using BIOM executable to the website

  biocore/biom-format#735 · Filter by author colinbrislawn opened on Feb 21, 2017
  4

• Add script usage tests

  biocore/biom-format#656 · Filter by author ebolyen opened on Oct 19, 2015 · 2.1.6

• to_hdf5 cannot handle None's in metadata

  bug
  biocore/biom-format#609 · Filter by author wasade opened on Mar 7, 2015 · BIOM 2.2
  8

• Make the pypi page pretty

  biocore/biom-format#431 · Filter by author wasade opened on May 18, 2014 · 2.1.6
  5

• add script to export sample/observation metadata from a biom file to a sample/observation mapping file

  enhancement
  biocore/biom-format#138 · Filter by author gregcaporaso opened on May 16, 2013
  2

• add description to biom table types

  biocore/biom-format#115 · Filter by author RNAer opened on Feb 15, 2013
  6