Re: Biopython 1.88 released - includes security fix for NEXUS parsing

PyPI is now updated with Python 3.15 wheels for Biopython 1.88, thanks
to the timely recent Numpy release:

❯ md5sum biopython-1.88-cp315-*.whl
b8cce1981171f8f4a581424683e3b510
biopython-1.88-cp315-cp315-macosx_11_0_arm64.whl
34ffb0073535a09f7ba9d14444879bbb
biopython-1.88-cp315-cp315-manylinux2014_aarch64.manylinux_2_17_aarch64.manylinux_2_28_aarch64.whl
345154cbe4817c3d4626039fde755799
biopython-1.88-cp315-cp315-manylinux2014_x86_64.manylinux_2_17_x86_64.manylinux_2_28_x86_64.whl
cf885f3b2409731fb94917f1386b88a9  biopython-1.88-cp315-cp315-win_amd64.whl
d529f0e9b8155a737db1857eb2146c44  biopython-1.88-cp315-cp315-win32.whl
1b6faa39d05e97f9e4435404787abd6d
biopython-1.88-cp315-cp315t-macosx_11_0_arm64.whl
70784e9395787eb135caa8fb288c7a02
biopython-1.88-cp315-cp315t-manylinux2014_aarch64.manylinux_2_17_aarch64.manylinux_2_28_aarch64.whl
f65cf94ee1d7069b7720837886ca15fa
biopython-1.88-cp315-cp315t-manylinux2014_x86_64.manylinux_2_17_x86_64.manylinux_2_28_x86_64.whl
733277d27dd73ea71f752b4d8a9c572e  biopython-1.88-cp315-cp315t-win_amd64.whl
9fab718a59173c31d2eff0e3743ff208  biopython-1.88-cp315-cp315t-win32.whl

❯ sha256sum biopython-1.88-cp315-*.whl
f238b612f15166c6a3c869f833b5aa6c0dd448dabb1d4b94b132281de3e91cab
biopython-1.88-cp315-cp315-macosx_11_0_arm64.whl
1c5c795fed9469b1115fd00d7681f4953a2d54ec502715720d11fe986678fa1b
biopython-1.88-cp315-cp315-manylinux2014_aarch64.manylinux_2_17_aarch64.manylinux_2_28_aarch64.whl
9e6e675ff0ecd0822735c9da0b7091eb29a757279bc810039890ae1f54f18fdd
biopython-1.88-cp315-cp315-manylinux2014_x86_64.manylinux_2_17_x86_64.manylinux_2_28_x86_64.whl
d4180714488d2ac6418fd42c445d1cda71fdd85ff71ad6748e7a312fa944e138
biopython-1.88-cp315-cp315-win_amd64.whl
277b54f1b804a74df1eb7f0fe8f6d6a1eda15bc78a94802c000f5f0a20ce4fdc
biopython-1.88-cp315-cp315-win32.whl
e800cacbf8e240105338f8eb52e92a00cd0103881d3cdf1798e89130cf878ed8
biopython-1.88-cp315-cp315t-macosx_11_0_arm64.whl
f300ef2db3d3fd33631364fe3f83a64d281d255dd0e8182feb8e3db9e290ce32
biopython-1.88-cp315-cp315t-manylinux2014_aarch64.manylinux_2_17_aarch64.manylinux_2_28_aarch64.whl
0063aea2051a99b2f278dd8bef23d5eca3f50eb922fb72d4a99678484bae043d
biopython-1.88-cp315-cp315t-manylinux2014_x86_64.manylinux_2_17_x86_64.manylinux_2_28_x86_64.whl
abeda1d57624b82476be498259dbc4531a1957bb1d77c80fd986adaa44f1b406
biopython-1.88-cp315-cp315t-win_amd64.whl
d879c732e0dee158cebf09047fa616451fa30f3abcab4105e3ce5cd336571147
biopython-1.88-cp315-cp315t-win32.whl

Peter

On Thu, Aug 6, 2026 at 4:40 PM Peter Cock <[email protected]> wrote:
>
> Dear Biopythoneers,
>
> Biopython 1.88 was released today, files on PyPI (and Conda-Forge) as usual:
>
> https://pypi.org/project/biopython/1.88/
>
> Release notes here:
>
> https://github.com/biopython/biopython/blob/master/NEWS.rst
>
> This release of Biopython supports Python 3.10, 3.11, 3.12, 3.13, 3.14
> and the Python 3.15 release candidate. It has also been tested on
> PyPy3.10 v7.3.19. Python 3.10 is approaching end of life, our support
> for it is now deprecated. Note that there are no pre-compiled wheels
> for Python 3.15 yet (we are waiting on wheels for NumPy).
>
> The primary driver for this release is a security fix to remove the
> use of Python's built-in function eval following a report by email
> from independent security researcher Anand Patil. This demonstrated
> arbitrary code execution via the Bio.Nexus NEXUS parser. We have
> requested a CVE reference number. If you cannot update, please do not
> parse any untrusted NEXUS files!
>
> Additionally, a number of small bugs and typos have been fixed with
> additions to the test suite and type annotations.
>
> Many thanks to the Biopython developers and community for making this
> release possible, especially the following contributors:
>
> * Al Fattah Suyadi (first contribution)
> * Laura Piñero Roig (first contribution)
> * Marcus Campbell (first contribution)
> * Michiel de Hoon
> * Peter Cock
>
> Thank you all,
>
> Peter
>
> --
>
> Checksums for the files uploaded to PyPI:
>
> ❯ md5sum biopython-1.88* cc8b55ddd91957804279bd6384437896
> biopython-1.88-cp310-cp310-macosx_11_0_arm64.whl
> a765b4d33ed723c644a8617786d38282
> biopython-1.88-cp310-cp310-manylinux2014_aarch64.manylinux_2_17_aarch64.manylinux_2_28_aarch64.whl
> e580b4b0ae1ae46bbcebfc0d2c999fa0
> biopython-1.88-cp310-cp310-manylinux2014_x86_64.manylinux_2_17_x86_64.manylinux_2_28_x86_64.whl
> c09bd5509beef70d3b7038e1c3d66723
> biopython-1.88-cp310-cp310-win_amd64.whl
> 6afa8edff36668a5e30cfcb566d0a0f6 biopython-1.88-cp310-cp310-win32.whl
> 6fdfd67a48f43ecfaeeef28913e7ab3e
> biopython-1.88-cp311-cp311-macosx_11_0_arm64.whl
> 353e6721b37099916d3af88f4b8ab961
> biopython-1.88-cp311-cp311-manylinux2014_aarch64.manylinux_2_17_aarch64.manylinux_2_28_aarch64.whl
> 36c7b29c7cf7edb56bcaa3caa16f7922
> biopython-1.88-cp311-cp311-manylinux2014_x86_64.manylinux_2_17_x86_64.manylinux_2_28_x86_64.whl
> a8b82d70a0de70b39f9c64f01150ced9
> biopython-1.88-cp311-cp311-win_amd64.whl
> 6ec8fd6ed00985916562af0d240a732d biopython-1.88-cp311-cp311-win32.whl
> b3c5963a8a29f30978e63171383ea1b2
> biopython-1.88-cp312-cp312-macosx_11_0_arm64.whl
> 8fc21771d34cafa97c06f618915eecb3
> biopython-1.88-cp312-cp312-manylinux2014_aarch64.manylinux_2_17_aarch64.manylinux_2_28_aarch64.whl
> 7282e0ee0dc3a4ffbbb86d74191da2ca
> biopython-1.88-cp312-cp312-manylinux2014_x86_64.manylinux_2_17_x86_64.manylinux_2_28_x86_64.whl
> bf2b6e303360a6f5b920a7fe8ba6b037
> biopython-1.88-cp312-cp312-win_amd64.whl
> 45be116c1b1063bd5b330bcc9e89a2e2 biopython-1.88-cp312-cp312-win32.whl
> 9682fdef0d0d2accbff1f772cc51159c
> biopython-1.88-cp313-cp313-macosx_11_0_arm64.whl
> 5d693a0b6efbe3916b03ac82d9170f5a
> biopython-1.88-cp313-cp313-manylinux2014_aarch64.manylinux_2_17_aarch64.manylinux_2_28_aarch64.whl
> 53adf6d9f5a88d3b80d6b8f92cba1317
> biopython-1.88-cp313-cp313-manylinux2014_x86_64.manylinux_2_17_x86_64.manylinux_2_28_x86_64.whl
> 8eb83a42e8d5e8cc60dfc83a54189bfc
> biopython-1.88-cp313-cp313-win_amd64.whl
> 335433a086f72a93c58b1f29056aa904 biopython-1.88-cp313-cp313-win32.whl
> 07cf43e642bc58e16009f902666cd987
> biopython-1.88-cp314-cp314-macosx_11_0_arm64.whl
> 285bc522148ff7374cc0b49760ba3cdf
> biopython-1.88-cp314-cp314-manylinux2014_aarch64.manylinux_2_17_aarch64.manylinux_2_28_aarch64.whl
> b1259592deb643155f2876dce6238511
> biopython-1.88-cp314-cp314-manylinux2014_x86_64.manylinux_2_17_x86_64.manylinux_2_28_x86_64.whl
> d4e4f8a524c771ed99394f6ccd910869
> biopython-1.88-cp314-cp314-win_amd64.whl
> 3f2559a82876f1cffaaa53673db81063 biopython-1.88-cp314-cp314-win32.whl
> 0cef19cc0cfea819ae81931270c5b16f
> biopython-1.88-cp314-cp314t-macosx_11_0_arm64.whl
> b82d4ec5963992d696907f48fdbd9029
> biopython-1.88-cp314-cp314t-manylinux2014_aarch64.manylinux_2_17_aarch64.manylinux_2_28_aarch64.whl
> 76ee989ed2fbc572e936c1a672e911ae
> biopython-1.88-cp314-cp314t-manylinux2014_x86_64.manylinux_2_17_x86_64.manylinux_2_28_x86_64.whl
> 7355f8b3f99ec4e5d7febde5993a5c23
> biopython-1.88-cp314-cp314t-win_amd64.whl
> 873162b52a61e135bdafacf50332cfe0 biopython-1.88-cp314-cp314t-win32.whl
> 20484f055dd6bc26d567f73365adc27f biopython-1.88.tar.gz
> 4e4433c703c4cc7a643cf5ada3922d1f biopython-1.88.zip
>
> ❯ sha256sum biopython-1.88*
> 9732e2c74b1e3751810b026e568817afb18101039c30c9b16b9193e40ec1efdb
> biopython-1.88-cp310-cp310-macosx_11_0_arm64.whl
> 02a6d8ed4eea1ee9e1c2a9d7690f21a60406bcfee7c71348363e267cce397bee
> biopython-1.88-cp310-cp310-manylinux2014_aarch64.manylinux_2_17_aarch64.manylinux_2_28_aarch64.whl
> b321ee0f652aaecefe065b11d64b527c4d04f7826dfb7cfa31edea5ab1db07c2
> biopython-1.88-cp310-cp310-manylinux2014_x86_64.manylinux_2_17_x86_64.manylinux_2_28_x86_64.whl
> 0e732f44208f1bab7c42bfea94422609249bd897da6b25b5588618436e80a6d2
> biopython-1.88-cp310-cp310-win_amd64.whl
> 99288eb34ce75cb85a10ab3e5d76ffe45f0c03c7f5cc6d144d3777419e44b31e
> biopython-1.88-cp310-cp310-win32.whl
> 793de1a57d9b75546a4041f547b6a848031a71933f66d4c761857b0b0118c46b
> biopython-1.88-cp311-cp311-macosx_11_0_arm64.whl
> 906a7b2d4bc4515f5718f3ae994bd3bcfe8e87d963954008b57e0109e3772a58
> biopython-1.88-cp311-cp311-manylinux2014_aarch64.manylinux_2_17_aarch64.manylinux_2_28_aarch64.whl
> 99e1f7022ab8eee2ae9e9a05b66ad183b9fe4eeb4e561a65ed0fd85eef5f8267
> biopython-1.88-cp311-cp311-manylinux2014_x86_64.manylinux_2_17_x86_64.manylinux_2_28_x86_64.whl
> 5808c5b980e63226426737b6f71b5dd7747e2e3d0074720cc04edf348ab57eab
> biopython-1.88-cp311-cp311-win_amd64.whl
> 024e438d044a0b1d4a0157af4ab2411b83389696aee3cdeb71f5ee74d0a59df2
> biopython-1.88-cp311-cp311-win32.whl
> 43ce1fbed01c0ddb903fa426fa0f836062d973a09df15560ac8e895da24c1350
> biopython-1.88-cp312-cp312-macosx_11_0_arm64.whl
> fe2dccf88e309dc896e7c2cc974a47be7a7b96d59c7f2ffd74ffcc7cfbdebb0c
> biopython-1.88-cp312-cp312-manylinux2014_aarch64.manylinux_2_17_aarch64.manylinux_2_28_aarch64.whl
> 9384c30460832926e765319040d732d1252a713a05af1dd4cc8b19cb1d590439
> biopython-1.88-cp312-cp312-manylinux2014_x86_64.manylinux_2_17_x86_64.manylinux_2_28_x86_64.whl
> dd5131b70287486af1acef2fc40de51c68de2ea740ab772097ac2d10bad9a0b5
> biopython-1.88-cp312-cp312-win_amd64.whl
> 4904abb18a1e039a631e549529c9b8123a166838cafe27f649f83f0183382d61
> biopython-1.88-cp312-cp312-win32.whl
> 465caece761b9ec22e0dc63bb5969517c901587a27104c4f1cee69f414b4df2d
> biopython-1.88-cp313-cp313-macosx_11_0_arm64.whl
> df709eabdce2fc2cc1059fcefbbea245d2b2c41fc2026eda6194b810474e68d6
> biopython-1.88-cp313-cp313-manylinux2014_aarch64.manylinux_2_17_aarch64.manylinux_2_28_aarch64.whl
> 410eaa083fcc308b44c7051e597ae2f39e4068754bdd605cc32aed025aa132d0
> biopython-1.88-cp313-cp313-manylinux2014_x86_64.manylinux_2_17_x86_64.manylinux_2_28_x86_64.whl
> f0aaf49f0c8919fb7a02cdc3db9e7f89165f53417a18d80508e0f167121cb7c1
> biopython-1.88-cp313-cp313-win_amd64.whl
> e3ac69b8abddac75dce301cbe77fc2650cbe0bd62ab2d2662d0f6f378b8c8018
> biopython-1.88-cp313-cp313-win32.whl
> 5508f8f585d101269982d58abb4ab50cbde5d3c50e21b01986c55ac7cc5f34f9
> biopython-1.88-cp314-cp314-macosx_11_0_arm64.whl
> 8ffa3f911a8ded827663bb98ffcd5fcfcaed2c7262bf6d3be5338332c81c7b66
> biopython-1.88-cp314-cp314-manylinux2014_aarch64.manylinux_2_17_aarch64.manylinux_2_28_aarch64.whl
> 99144485e7723842fe6c6bb0c13f323a550fc30817d3e0814126987f9b06855a
> biopython-1.88-cp314-cp314-manylinux2014_x86_64.manylinux_2_17_x86_64.manylinux_2_28_x86_64.whl
> 0b8fea4940c58915e6d4c670f17f4e9c20797e9e26d4300b6efbe960b99d199d
> biopython-1.88-cp314-cp314-win_amd64.whl
> b86c1e86c829b372995d5e0eb80146551972a1bff25da1698b48844b6e6840cd
> biopython-1.88-cp314-cp314-win32.whl
> 393398c8383217f3f51aaa2372960e697b494a3eee97e1c4d5f62ee60ea9287b
> biopython-1.88-cp314-cp314t-macosx_11_0_arm64.whl
> ab5c2211a9d1ad7d4b8afd7f53caa7f20e104a5ddf0b30f7cb899f039379de68
> biopython-1.88-cp314-cp314t-manylinux2014_aarch64.manylinux_2_17_aarch64.manylinux_2_28_aarch64.whl
> adbafdc7769d46cc9e72aba86b7e2da3aa078d2a533b53757ca88ca6ff1d0489
> biopython-1.88-cp314-cp314t-manylinux2014_x86_64.manylinux_2_17_x86_64.manylinux_2_28_x86_64.whl
> f684b0fddbfe3b37de36d1b377c4c10d968226940c307a5a16e360e63063900f
> biopython-1.88-cp314-cp314t-win_amd64.whl
> 1e29b72bb79786f4157b394fbd852d736ffd883a13a177c21d6d15ea1b67d357
> biopython-1.88-cp314-cp314t-win32.whl
> 9aaa31c0bda4d059f7b2ee00bfdb5cbb73ade3057aa4b737a7cc0187091d071a
> biopython-1.88.tar.gz
> 0c0142bb3cd98a51da658200f5c79b1e6e63778638f2bcb62154ead5ef41f861
> biopython-1.88.zip
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