<div dir="ltr"><div>Please resume merging pull requests, still a formal release notice to write</div><div>but otherwise done. Note another new issue came up with the PDF output:</div><div><br></div><div><a href="https://github.com/biopython/biopython/issues/4764">https://github.com/biopython/biopython/issues/4764</a></div><div><br></div><div>Peter</div><div><br></div></div><br><div class="gmail_quote"><div dir="ltr" class="gmail_attr">On Fri, Jun 28, 2024 at 5:20 AM Peter Cock <<a href="mailto:p.j.a.cock@googlemail.com">p.j.a.cock@googlemail.com</a>> wrote:<br></div><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex"><div dir="ltr"><div>Nearly there, the Biopython 1.84 release is on PyPI now.</div><div><br></div><div>One open question, what should I call the new PDF for the archive here:</div><div><a href="https://github.com/biopython/DIST/tree/gh-pages/docs/tutorial" target="_blank">https://github.com/biopython/DIST/tree/gh-pages/docs/tutorial</a></div><div><br></div><div>Historically it was based on Tutorial.pdf and Tutorial.html, but now</div><div>we have Biopython_doc.pdf reflecting the fact this combines the old</div><div>"Tutorial and Cookbook" and the "API Documentation".<br></div><div><br></div><div>md5 checksums:</div><div><br></div><div>$ md5sum biopython-1.84.tar.gz biopython-1.84*.whl<br>92e639d2f3627759f12f0d000131c24d  biopython-1.84.tar.gz<br>2d121260dc6acc5d0abbd5f9f32bc70a  biopython-1.84-cp310-cp310-macosx_10_9_x86_64.whl<br>6819b274d250b5a9d4dea7bdf40bf77b  biopython-1.84-cp310-cp310-macosx_11_0_arm64.whl<br>af78716df05afd11a550d92faf647cf5  biopython-1.84-cp310-cp310-manylinux_2_17_x86_64.manylinux2014_x86_64.whl<br>4e81ecdff61d2fac377af1958bfbcdc5  biopython-1.84-cp310-cp310-win32.whl<br>dd6a434bf1c1c7af66ef890b0d43d398  biopython-1.84-cp310-cp310-win_amd64.whl<br>d471893df22b6198924f48b96c5c86fc  biopython-1.84-cp311-cp311-macosx_10_9_x86_64.whl<br>54fe09ad0c76ed1d522369470456699b  biopython-1.84-cp311-cp311-macosx_11_0_arm64.whl<br>d47b8a1d0c5dc6fc66ba6c86773d02f9  biopython-1.84-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl<br>1b9e7f5024a47bc17d1f122494bc4ec9  biopython-1.84-cp311-cp311-win32.whl<br>45c924f7245b1a136304d0a17b6e64f6  biopython-1.84-cp311-cp311-win_amd64.whl<br>2296549d1a73b86968bf8af049a3ffde  biopython-1.84-cp312-cp312-macosx_10_9_x86_64.whl<br>c2b8d56c26ac5ef11dcf07097dbdf6da  biopython-1.84-cp312-cp312-macosx_11_0_arm64.whl<br>8ce75d3e2935829082c7e6fbe5e6eaab  biopython-1.84-cp312-cp312-manylinux_2_17_x86_64.manylinux2014_x86_64.whl<br>a2fae5789c1d911948c55c63efe5b72c  biopython-1.84-cp312-cp312-win32.whl<br>1a72201772c299dd6a4c4f4e825ea829  biopython-1.84-cp312-cp312-win_amd64.whl<br>1e268eff35f32b7c0c829296a0527a45  biopython-1.84-cp39-cp39-macosx_10_9_x86_64.whl<br>249a1c92cbed3a645cc17878564baacf  biopython-1.84-cp39-cp39-macosx_11_0_arm64.whl<br>a2bdc8f02dd45e6616b5385138d1b8ff  biopython-1.84-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl<br>310b7676c7ad2528a6ee10f97471f9c0  biopython-1.84-cp39-cp39-win32.whl<br>76161614a81816de4d206b45aa02eb87  biopython-1.84-cp39-cp39-win_amd64.whl</div><div><br></div><div>And sha-256 checksums:</div><div><br></div><div>$ sha256sum  biopython-1.84.tar.gz biopython-1.84*.whl<br>60fbe6f996e8a6866a42698c17e552127d99a9aab3259d6249fbaabd0e0cc7b4  biopython-1.84.tar.gz<br>3c8beded38884abae4c74cb6ce54142da670273fd0b2919bd0f84f6e34d3056b  biopython-1.84-cp310-cp310-macosx_10_9_x86_64.whl<br>b51ef31bfb79872a182a85b4113625e1b553c024bb1586c72ac98b479f8d8fe4  biopython-1.84-cp310-cp310-macosx_11_0_arm64.whl<br>2dc2e77490725060330003f73b6b7d5172f8bc160f180de5877a2e899ad999d4  biopython-1.84-cp310-cp310-manylinux_2_17_x86_64.manylinux2014_x86_64.whl<br>4f39b38e7625c33384954130d90f19984e91cb5af64e2fb128603359f86884ad  biopython-1.84-cp310-cp310-win32.whl<br>9e3f7476fd81f31e048965d7be2826f018686e870d96870f440b609002953954  biopython-1.84-cp310-cp310-win_amd64.whl<br>2d4ed30aebd96b4aadeb1f04adce92795c696f5bd56d1fd45517b89059918dd4  biopython-1.84-cp311-cp311-macosx_10_9_x86_64.whl<br>c792508988fc3ccf18eaae2a826c9cd97f1c27fb55bb87bdce6a101fee9f5a0c  biopython-1.84-cp311-cp311-macosx_11_0_arm64.whl<br>894ee7533cca7f5f9769e2595fbe7b0dba5018f39a2170753d101a13e7585ff4  biopython-1.84-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl<br>7f4c746825721ec367c2f2d6a8cda3bc6495a1e084e5b2fbab26e9467706603f  biopython-1.84-cp311-cp311-win32.whl<br>2cb8e839ab472244b6082635ad1df67c94c05df0bd02a023103ed00ea66c4d20  biopython-1.84-cp311-cp311-win_amd64.whl<br>ba58a6d76288333c5f178a426116953fa68204bd0cfc401694087dd4f96d0059  biopython-1.84-cp312-cp312-macosx_10_9_x86_64.whl<br>ee3566f6dc3acf20e238540daf896f0af20cff531521bf41fdf5143f73e209ae  biopython-1.84-cp312-cp312-macosx_11_0_arm64.whl<br>61765b71f84814a1eeb55ab222f43330aa7ad3e55ab91e8b444706149c67a281  biopython-1.84-cp312-cp312-manylinux_2_17_x86_64.manylinux2014_x86_64.whl<br>52b6098f47d6b90fc8a5e8579b81ee50047e9108f0976e69c891ae0c4817e42d  biopython-1.84-cp312-cp312-win32.whl<br>ecff2fcf5da29b600474c0bfcdbbac0f98b25e22fe60a853d0ee798c00f7396c  biopython-1.84-cp312-cp312-win_amd64.whl<br>f4c1c9ad7da9eaf8d8f4515bf931a7f6548a468e7ef29b8429e31aaff2d95f4c  biopython-1.84-cp39-cp39-macosx_10_9_x86_64.whl<br>9fbd4b67d3e71b0d716a1712ab8b4e57981c6549ba17ce5626ffa8976d170da7  biopython-1.84-cp39-cp39-macosx_11_0_arm64.whl<br>7b69d59f9a762c5bb5f77ed03f197dad05ebd702c34d2cae7be98f1f30e04089  biopython-1.84-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl<br>25f4ef193a307e403eb532e8f060b818e2d75f65803a2b0f4e645b0cae131b4e  biopython-1.84-cp39-cp39-win32.whl<br>b64575363bb2344073c949fd69a0bf3ea015b447aa1494e4813376855b479118  biopython-1.84-cp39-cp39-win_amd64.whl</div><div><br></div></div><br><div class="gmail_quote"><div dir="ltr" class="gmail_attr">On Fri, Jun 28, 2024 at 2:46 AM Peter Cock <<a href="mailto:p.j.a.cock@googlemail.com" target="_blank">p.j.a.cock@googlemail.com</a>> wrote:<br></div><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex"><div dir="ltr"><div>I am working on the release now, forgot I didn't have LaTeX on this machine</div><div>which we still need for a PDF version of the Tutorial (this is the first release</div><div>to use Sphinx and RST for the Tutorial, rather than LaTeX directly).</div><div><br></div><div>Please don't update the master branch until the release is done.<br></div><div><br></div><div>Peter<br></div></div><br><div class="gmail_quote"><div dir="ltr" class="gmail_attr">On Wed, Jun 26, 2024 at 11:37 AM Peter Cock <<a href="mailto:p.j.a.cock@googlemail.com" target="_blank">p.j.a.cock@googlemail.com</a>> wrote:<br></div><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex"><div dir="ltr"><div>I've been working on this (as have Michiel, João,  and others), and still hope to do the release very soon.</div><div><br></div><div>Touch wood the numpy 2.0.0 work is done. Right now I'm fixing a minor regression with the new scipy 1.14.0 release, and hoping there are no more surprises!<br></div><div><br></div><div>Peter<br></div></div><br><div class="gmail_quote"><div dir="ltr" class="gmail_attr">On Wed, May 22, 2024 at 9:39 PM Peter Cock <<a href="mailto:p.j.a.cock@googlemail.com" target="_blank">p.j.a.cock@googlemail.com</a>> wrote:<br></div><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex"><div dir="ltr"><div>Hello all,</div><div><br></div><div>I would have liked to tackle the release sooner, but things have been busy at work. However, I will be on leave soon and should be able to tackle the Biopython 1.84 in early June.</div><div><br></div><div>That will be about six months worth of changes, including dropping Python 3.8 support and deprecating Python 3.9 support.<br></div><div><br></div><div>It is worth noting this coincides with the release of NumPy 2.0. We have lots of code using NumPy, including C code, which was a major concern as there are C API breakages with NumPy 2.0. However, rather than the full NumPy C API, we're only using the buffer API designed for interoperability, so I believe that does not affect us. What does affect us are changes to the NumPy scalar repr output, which means a lot of the documentation tests in Biopython 1.63 fail. We have addressed those already, and the tests now pass on a recent NumPy v1 and on the v2 release candidate. i.e. I am not aware of any blocking issues relating to NumPy for our next release.</div><div><br></div><div>Are there any outstanding issues which the community feels need to be addressed prior to our release?</div><div><br></div><div>Thanks,<br></div><br><div>Peter<br></div></div>
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