14 Pull requests merged by 4 people

• ENH: add new_type arguments for top-level function, fixes #1923

  #1928 merged Jun 27, 2024

• ENH: add reversed field to SeqsData

  #1926 merged Jun 27, 2024

• ENH: SequenceCollection serialisation

  #1922 merged Jun 26, 2024

• TST: Port SeqView tests and #1915

  #1919 merged Jun 25, 2024

• DEV: delete matplotlib as a dependency

  #1920 merged Jun 25, 2024

• refactor seqs.get_translation and add method to rename seqs in a collection

  #1912 merged Jun 25, 2024

• ENH: implement serialisation methods on new_alphabet classes

  #1916 merged Jun 25, 2024

• Bump psutil from 5.9.8 to 6.0.0

  #1914 merged Jun 24, 2024

• TST: port seqview slicing test

  #1913 merged Jun 24, 2024

• Merged changes from develop

  #1911 merged Jun 24, 2024

• MAINT: now support numpy 2.0

  #1910 merged Jun 24, 2024

• TST: xfailing sequence tests

  #1907 merged Jun 24, 2024

• MAINT: type hinting

  #1908 merged Jun 24, 2024

• Amendments to improve genetic code translate

  #1909 merged Jun 24, 2024

3 Pull requests opened by 3 people

• TST: port seqview tests

  #1927 opened Jun 27, 2024

• ENH: deserialisation of `SequenceCollection` and `SeqsData`, fixes #1924

  #1929 opened Jun 27, 2024

• DEV: raise not implemented error on top level stringified type hint

  #1931 opened Jun 28, 2024

6 Issues closed by 2 people

• ENH: `new_type` arguments for top-level function

  #1923 closed Jun 27, 2024

• Thinking of the documentation of apps

  #1378 closed Jun 25, 2024

• Create new branch with sequence collections backend prototypes

  #1860 closed Jun 25, 2024

• begin new_alignment.SequenceCollection

  #1867 closed Jun 25, 2024

• `MolType.make_seq()` incompatible with `SeqDataView`

  #1872 closed Jun 24, 2024

• Define a SeqViewABC

  #1901 closed Jun 24, 2024

7 Issues opened by 3 people

• The upper/lower bounds cannot be successfully imposed on a model app

  #1930 opened Jun 27, 2024

• Cannot get tree with lengths as ENS for a rate heterogeneous model

  #1925 opened Jun 26, 2024

• ENH: deserialise function for SequenceCollection

  #1924 opened Jun 26, 2024

• Sequence and SeqView classes should not be used to replace characters

  #1921 opened Jun 25, 2024

• modify all tests to using new style sequence collections

  #1918 opened Jun 25, 2024

• can we remove tinydb dependency?

  #1917 opened Jun 25, 2024

• new_sequence.Sequence.__str__ method should complement the sequence

  #1915 opened Jun 24, 2024

10 Unresolved conversations

Sometimes conversations happen on old items that aren’t yet closed. Here is a list of all the Issues and Pull Requests with unresolved conversations.

• some app.typing union types not working when importing annotations from future

  #1897 commented on Jun 27, 2024 • 6 new comments

• BUG: updating a db with the same db causes the code to hang

  #1906 commented on Jun 24, 2024 • 1 new comment

• ENH: Prep for plugin infrastructure

  #1748 commented on Jun 25, 2024 • 1 new comment

• Refactor of sequence collections and alignments

  #1861 commented on Jun 25, 2024 • 0 new comments

• Enh: Add bibliography to define_app

  #1792 commented on Jun 25, 2024 • 0 new comments

• Generalise tree infrastructure to handle multifurcating rooted trees

  #1645 commented on Jun 25, 2024 • 0 new comments

• ENH: write a db wrapper class for handling annotations etc...

  #1749 commented on Jun 25, 2024 • 0 new comments

• DOC tutorial on feature handling

  #1513 commented on Jun 25, 2024 • 0 new comments

• Github action for opening issues re: documentation

  #1332 commented on Jun 25, 2024 • 0 new comments

• cookbook for apps

  #1636 commented on Jun 25, 2024 • 0 new comments