Skip to content

Commit

Permalink
deps: unpin biopython, pin bcbio-gff to 0.7*
Browse files Browse the repository at this point in the history
Biopython was fixed to <=1.80 in #1152
because bcbio-gff <=0.6.9 requires deprecated Biopython functionality that was removed in 1.81

A fix to bcbio-gff was released as 0.7.0, see chapmanb/bcbb#137 chapmanb/bcbb#136
So now we can pin bcbio-gff to >=0.7.0 and remove the pin
of Biopython

Note added in #1170 can hence be removed
  • Loading branch information
corneliusroemer authored Mar 13, 2023
1 parent 3cf9671 commit 928fdcf
Showing 1 changed file with 2 additions and 6 deletions.
8 changes: 2 additions & 6 deletions setup.py
Original file line number Diff line number Diff line change
Expand Up @@ -51,12 +51,8 @@
package_data = {'augur': ['data/*']},
python_requires = '>={}'.format('.'.join(str(n) for n in py_min_version)),
install_requires = [
"bcbio-gff >=0.6.0, ==0.6.*",
# TODO: Remove biopython <=1.80 pin when 1.81/higher is supported by a
# new version of bcbio-gff¹ and that is also pinned, or when bcbio-gff
# is no longer a dependency.
# ¹ https://github.com/chapmanb/bcbb/issues/136
"biopython >=1.67, !=1.77, !=1.78, <=1.80",
"bcbio-gff >=0.7.0, ==0.7.*",
"biopython >=1.67, !=1.77, !=1.78",
"cvxopt >=1.1.9, ==1.*",
"isodate ==0.6.*",
"jsonschema >=3.0.0, ==3.*",
Expand Down

0 comments on commit 928fdcf

Please sign in to comment.