Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

deps: unpin biopython, pin bcbio-gff to 0.7* #1178

Merged
merged 2 commits into from
Mar 16, 2023
Merged

deps: unpin biopython, pin bcbio-gff to 0.7* #1178

Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
2 commits
Select commit Hold shift + click to select a range
7204276
deps: unpin biopython, pin bcbio-gff to 0.7*
corneliusroemer Mar 13, 2023
bbd53e5
chore: add note to CHANGES.md for PR #1178
corneliusroemer Mar 14, 2023
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
6 changes: 6 additions & 0 deletions CHANGES.md
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -2,6 +2,12 @@

## __NEXT__

### Features

* Constrain `bcbio-gff` to >=0.7.0 and allow `Biopython` >=1.81 again. We had to introduce the `Biopython` constraint in v21.0.1 (see [#1152][]) due to `bcbio-gff` <0.7.0 relying on the removed `Biopython` feature `UnknownSeq`. [#1178][] (@corneliusroemer)

[#1152]: https://github.com/nextstrain/augur/pull/1152
[#1178]: https://github.com/nextstrain/augur/pull/1178

## 21.1.0 (14 March 2023)

Expand Down
8 changes: 2 additions & 6 deletions setup.py
View file
Open in desktop
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