From b57ae927fb2941cd20741afbb73adb10aa1879d5 Mon Sep 17 00:00:00 2001 From: squenson1 <125811472+squenson1@users.noreply.github.com> Date: Sat, 4 Jan 2025 20:13:36 +0000 Subject: [PATCH 01/29] Update Category_Cookbook.md to compliment: to praise to complement: to add information to --- wiki/Category_Cookbook.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/wiki/Category_Cookbook.md b/wiki/Category_Cookbook.md index 284bca533..50abe8bfc 100644 --- a/wiki/Category_Cookbook.md +++ b/wiki/Category_Cookbook.md @@ -6,7 +6,7 @@ tag: Cookbook --- The entries contained in the Cookbook category are designed to -compliment the general help given in the +complement the general help given in the [Tutorial](http://biopython.org/DIST/docs/tutorial/Tutorial.html) ([PDF](http://biopython.org/DIST/docs/tutorial/Tutorial.pdf)) with specific examples of problems that can be solved with the Biopython From dcc100ae9082b911e9c2efe5d4e5209fc6ac2e1d Mon Sep 17 00:00:00 2001 From: Peter Cock Date: Wed, 15 Jan 2025 15:01:22 +0000 Subject: [PATCH 02/29] No longer putting Tutorial up onder DICT/docs/tutorial We last did this for Biopython 1.83 from LaTeX source. We did not do this for Biopython 1.84 from RST source. --- wiki/Building_a_release.md | 30 ------------------------------ 1 file changed, 30 deletions(-) diff --git a/wiki/Building_a_release.md b/wiki/Building_a_release.md index 12fba5885..8487092be 100644 --- a/wiki/Building_a_release.md +++ b/wiki/Building_a_release.md @@ -160,36 +160,6 @@ Checking the compiled documentation $ git push origin gh-pages ``` -16. Update Tutorial and PDB FAQ on the website manually. - - - Update the Tutorial and PDB FAQ: - - ``` bash - $ cd ~/repositories/DIST/docs/tutorial/ - $ git fetch origin - $ git checkout gh-pages # should only be this one branch - $ git rebase origin/gh-pages # get any changes - $ cp ../../../biopython/Doc/biopdb_faq.pdf . - $ cp ../../../biopython/Doc/Tutorial.html Tutorial-1.80.html - $ cp ../../../biopython/Doc/Tutorial.pdf Tutorial-1.80.pdf - $ rm Tutorial.html Tutorial.pdf - $ ln -s Tutorial-1.80.html Tutorial.html - $ ln -s Tutorial-1.80.pdf Tutorial.pdf - $ git add Tutorial-1.80.html Tutorial-1.80.pdf - $ git commit Tutorial-1.80.html Tutorial-1.80.pdf Tutorial.html Tutorial.pdf biopdb_faq.pdf -m "Tutorial and FAQ for Biopython 1.80" - ``` - - - Push this to GitHub Pages to update the website: - - ``` bash - $ git push origin gh-pages - ``` - - - Check this is live at , - , - , and - - Making wheels ------------- From 87117688df9514a38afdfa143c0b5f06b498bb0f Mon Sep 17 00:00:00 2001 From: Peter Cock Date: Wed, 15 Jan 2025 15:17:34 +0000 Subject: [PATCH 03/29] Biopython 1.85 --- _config.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/_config.yml b/_config.yml index 7ef467326..13d112e4d 100644 --- a/_config.yml +++ b/_config.yml @@ -20,6 +20,6 @@ author: url: https://biopython.org # Custom variables for Hyde theme -version: "1.84" +version: "1.85" github: repo: https://github.com/biopython/biopython From 807f20fdaff596740798a7dae2bc590bcd8990b8 Mon Sep 17 00:00:00 2001 From: Peter Cock Date: Wed, 15 Jan 2025 15:24:49 +0000 Subject: [PATCH 04/29] Biopython 1.85 --- wiki/Download.md | 29 +++++++++++++++++++---------- 1 file changed, 19 insertions(+), 10 deletions(-) diff --git a/wiki/Download.md b/wiki/Download.md index 1755e6843..ce1c79762 100644 --- a/wiki/Download.md +++ b/wiki/Download.md @@ -6,22 +6,22 @@ redirect_from: - /download/ --- -Current Release - 1.84 - 28 June 2024 -======================================== +Current Release - 1.85 - 15 Jan 2025 +==================================== See also [What's new](https://github.com/biopython/biopython/blob/master/NEWS.rst). ### Files -#### Biopython 1.84 +#### Biopython 1.85 -- [biopython-1.84.tar.gz](http://biopython.org/DIST/biopython-1.84.tar.gz) - 25Mb -- Source Tarball -- [biopython-1.84.zip](http://biopython.org/DIST/biopython-1.84.zip) - 27Mb -- Source Zip File -- [Pre-compiled wheel files on PyPI](https://pypi.python.org/pypi/biopython/1.84) -- [Documentation](https://biopython.org/docs/1.84/) +- [biopython-1.85.tar.gz](http://biopython.org/DIST/biopython-1.85.tar.gz) + 19Mb -- Source Tarball +- [biopython-1.85.zip](http://biopython.org/DIST/biopython-1.85.zip) + 21Mb -- Source Zip File +- [Pre-compiled wheel files on PyPI](https://pypi.python.org/pypi/biopython/1.85) +- [Documentation](https://biopython.org/docs/1.85/) ### Installation Instructions @@ -58,7 +58,7 @@ If you need to install under a specific version of Python, try something like this: ``` bash -python3.9 -m pip install biopython +python3.13 -m pip install biopython pypy -m pip install biopython ``` @@ -157,6 +157,15 @@ Recent releases of Biopython require NumPy (and not Numeric). Version 1.76 is the last release to support Python 2.7 and 3.5, all later releases require Python 3: +- [biopython-1.84.tar.gz](http://biopython.org/DIST/biopython-1.84.tar.gz) + 25Mb -- Source Tarball +- [biopython-1.84.zip](http://biopython.org/DIST/biopython-1.84.zip) + 27Mb -- Source Zip File +- [Pre-compiled wheel files on PyPI](https://pypi.python.org/pypi/biopython/1.84) +- [Documentation](https://biopython.org/docs/1.84/) + + + - [biopython-1.83.tar.gz](http://biopython.org/DIST/biopython-1.83.tar.gz) 19Mb -- Source Tarball (10 January 2024) - [biopython-1.83.zip](http://biopython.org/DIST/biopython-1.83.zip) From 7772a1261001b4b9bb0b1e2bf05c1b0bedfc8e6a Mon Sep 17 00:00:00 2001 From: Peter Cock Date: Wed, 15 Jan 2025 15:25:22 +0000 Subject: [PATCH 05/29] Biopython 1.85 --- wiki/Biopython.md | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/wiki/Biopython.md b/wiki/Biopython.md index 652c80d6c..310a99286 100644 --- a/wiki/Biopython.md +++ b/wiki/Biopython.md @@ -42,5 +42,5 @@ the libraries and tools. | | [ Cookbook (working examples)](wiki/Category%3ACookbook "wikilink") | [Google Summer of Code](wiki/Google_Summer_of_Code "wikilink") | | | [ Discuss and ask questions](wiki/Mailing_lists "wikilink") | [Report bugs](https://github.com/biopython/biopython/issues) | -The latest release is [Biopython 1.84](wiki/Download "wikilink"), released on -28 June 2024. +The latest release is [Biopython 1.85](wiki/Download "wikilink"), released on +15 Jan 2025. From 6c57d10d479508fc3bad364c98e1130af7818fcf Mon Sep 17 00:00:00 2001 From: mdehoon Date: Fri, 17 Jan 2025 10:52:02 +0900 Subject: [PATCH 06/29] Update Download.md --- wiki/Download.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/wiki/Download.md b/wiki/Download.md index ce1c79762..14e93a147 100644 --- a/wiki/Download.md +++ b/wiki/Download.md @@ -158,7 +158,7 @@ Version 1.76 is the last release to support Python 2.7 and 3.5, all later releases require Python 3: - [biopython-1.84.tar.gz](http://biopython.org/DIST/biopython-1.84.tar.gz) - 25Mb -- Source Tarball + 25Mb -- Source Tarball (28 June 2024) - [biopython-1.84.zip](http://biopython.org/DIST/biopython-1.84.zip) 27Mb -- Source Zip File - [Pre-compiled wheel files on PyPI](https://pypi.python.org/pypi/biopython/1.84) From baca79d74ee7f940e29f20a86d6b48d8042147dc Mon Sep 17 00:00:00 2001 From: mdehoon Date: Fri, 17 Jan 2025 10:56:59 +0900 Subject: [PATCH 07/29] Update Download.md Show version date for 1.84 From 388393da3f5bc9f484b951d2d91e4ae568adeaa1 Mon Sep 17 00:00:00 2001 From: Peter Cock Date: Wed, 29 Jan 2025 12:11:01 +0000 Subject: [PATCH 08/29] Point at docstring for SeqIO format names --- wiki/SeqIO.md | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/wiki/SeqIO.md b/wiki/SeqIO.md index 4449e2b8a..c20db00e0 100644 --- a/wiki/SeqIO.md +++ b/wiki/SeqIO.md @@ -54,6 +54,10 @@ requirements, I hope this should suffice. File Formats ------------ +The authorative [list of supported +formats](https://biopython.org/docs/latest/api/Bio.SeqIO.html#file-formats) +is in the code's docstrings. The table here may not be fully up to date. + This table lists the file formats that `Bio.SeqIO` can read, write and index, with the Biopython version where this was first supported (or [git](Git "wikilink") to indicate this is supported in our latest in From 851875e310472c77509b7945cad1f367471b3eba Mon Sep 17 00:00:00 2001 From: mdehoon Date: Fri, 7 Feb 2025 09:57:27 +0900 Subject: [PATCH 09/29] Update GitUsage.md so we can copy "pre-commit instlall" without pre-commit getting confused by the comment --- wiki/GitUsage.md | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/wiki/GitUsage.md b/wiki/GitUsage.md index 0ace9c516..b571743fa 100644 --- a/wiki/GitUsage.md +++ b/wiki/GitUsage.md @@ -242,7 +242,8 @@ style-checks. ``` bash pip install pre-commit -pre-commit install # in biopython directory +# in biopython directory: +pre-commit install ``` See the [CONTRIBUTING.rst](https://github.com/biopython/biopython/blob/master/CONTRIBUTING.rst) file for more. From 9c52792669101a26ebe5a47284cffeca9ba77ac6 Mon Sep 17 00:00:00 2001 From: radekaadek Date: Sun, 15 Jun 2025 19:30:37 +0200 Subject: [PATCH 10/29] Fix typo --- wiki/Active_projects.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/wiki/Active_projects.md b/wiki/Active_projects.md index 284b5cf8e..1ef309cea 100644 --- a/wiki/Active_projects.md +++ b/wiki/Active_projects.md @@ -1,5 +1,5 @@ --- -title: List of active project for Biopython. +title: List of active projects for Biopython. permalink: wiki/Active_projects layout: wiki --- From 3fafdd23d5d0ec1e64bd88982be7378d5842443b Mon Sep 17 00:00:00 2001 From: Janghyeon Date: Tue, 24 Jun 2025 02:29:34 +0200 Subject: [PATCH 11/29] Fix typo and incorrect page number (#210) * fix: Fix incorrect page numbers * fix: Correct grammar --- wiki/Documentation.md | 2 +- wiki/SourceCode.md | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/wiki/Documentation.md b/wiki/Documentation.md index 0eceecb08..43cd8afd7 100644 --- a/wiki/Documentation.md +++ b/wiki/Documentation.md @@ -111,7 +111,7 @@ and/or one of the other listed papers: *The `Bio.PDB` module is described here* 4. De Hoon MJ, Imoto S, Nolan J and Miyano S (2004) Open source clustering software. - [*Bioinformatics*, 20, 1454-1453](http://dx.doi.org/10.1093/bioinformatics/bth078) + [*Bioinformatics*, 20, 1453-1454](http://dx.doi.org/10.1093/bioinformatics/bth078) *The `Bio.Cluster` module is described here* diff --git a/wiki/SourceCode.md b/wiki/SourceCode.md index 306df9cbc..38317e44e 100644 --- a/wiki/SourceCode.md +++ b/wiki/SourceCode.md @@ -94,5 +94,5 @@ Most of the other [Open Bioinformatics Foundation](http://open-bio.org) projects migrated from CVS to SVN (Subversion), and later to git hosted at GitHub. -While Biopython did considering moving from CVS to SVN, instead we +While Biopython did consider moving from CVS to SVN, instead we migrated directly from CVS to git in September 2009. From f276bfc5e53c6b9946faf293ee399d83904676ac Mon Sep 17 00:00:00 2001 From: Peter Cock Date: Tue, 28 Oct 2025 15:54:33 +0000 Subject: [PATCH 12/29] Now on v1.86 --- wiki/Biopython.md | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/wiki/Biopython.md b/wiki/Biopython.md index 310a99286..cf5eb2715 100644 --- a/wiki/Biopython.md +++ b/wiki/Biopython.md @@ -42,5 +42,5 @@ the libraries and tools. | | [ Cookbook (working examples)](wiki/Category%3ACookbook "wikilink") | [Google Summer of Code](wiki/Google_Summer_of_Code "wikilink") | | | [ Discuss and ask questions](wiki/Mailing_lists "wikilink") | [Report bugs](https://github.com/biopython/biopython/issues) | -The latest release is [Biopython 1.85](wiki/Download "wikilink"), released on -15 Jan 2025. +The latest release is [Biopython 1.86](wiki/Download "wikilink"), released on +28 Oct 2025. From e10845710d8ff3c62e5a43fcfd533d0514a272c1 Mon Sep 17 00:00:00 2001 From: Peter Cock Date: Tue, 28 Oct 2025 15:54:57 +0000 Subject: [PATCH 13/29] Biopython 1.86 --- _config.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/_config.yml b/_config.yml index 13d112e4d..0774b1a14 100644 --- a/_config.yml +++ b/_config.yml @@ -20,6 +20,6 @@ author: url: https://biopython.org # Custom variables for Hyde theme -version: "1.85" +version: "1.86" github: repo: https://github.com/biopython/biopython From 0f3c2d213f7ec4e856b60eabfb82847c313e5ec0 Mon Sep 17 00:00:00 2001 From: Peter Cock Date: Tue, 28 Oct 2025 15:56:21 +0000 Subject: [PATCH 14/29] Copy 1.85 to old releases --- wiki/Download.md | 9 +++++++++ 1 file changed, 9 insertions(+) diff --git a/wiki/Download.md b/wiki/Download.md index 14e93a147..8e4d9240f 100644 --- a/wiki/Download.md +++ b/wiki/Download.md @@ -157,6 +157,15 @@ Recent releases of Biopython require NumPy (and not Numeric). Version 1.76 is the last release to support Python 2.7 and 3.5, all later releases require Python 3: +- [biopython-1.85.tar.gz](http://biopython.org/DIST/biopython-1.85.tar.gz) + 19Mb -- Source Tarball +- [biopython-1.85.zip](http://biopython.org/DIST/biopython-1.85.zip) + 21Mb -- Source Zip File +- [Pre-compiled wheel files on PyPI](https://pypi.python.org/pypi/biopython/1.85) +- [Documentation](https://biopython.org/docs/1.85/) + + + - [biopython-1.84.tar.gz](http://biopython.org/DIST/biopython-1.84.tar.gz) 25Mb -- Source Tarball (28 June 2024) - [biopython-1.84.zip](http://biopython.org/DIST/biopython-1.84.zip) From 3044ea0f6c8ec5acae60d719e94bc90dba119e36 Mon Sep 17 00:00:00 2001 From: Peter Cock Date: Tue, 28 Oct 2025 20:05:27 +0000 Subject: [PATCH 15/29] Giving up on Sphinx to PDF via LaTeX for releases Failed for Biopython 1.85, and again today on a fresh LaTeX install for Biopython 1.86 --- wiki/Building_a_release.md | 41 +++++++++++++------------------------- 1 file changed, 14 insertions(+), 27 deletions(-) diff --git a/wiki/Building_a_release.md b/wiki/Building_a_release.md index 8487092be..9b170b4b2 100644 --- a/wiki/Building_a_release.md +++ b/wiki/Building_a_release.md @@ -33,8 +33,6 @@ Biopython optional dependencies as possible for local testing): 1. Python 3 2. git 3. [twine](https://github.com/pypa/twine/), installed with ``pip install twine`` -4. LaTeX, including assorted packages like comments and preprint. -5. [hevea](http://hevea.inria.fr/), I am currently using version 2.32 of 2012-07-04 Final commit(s) --------------- @@ -108,22 +106,13 @@ Making and testing the tar-ball drevil:~tmp1/> cd biopython ``` -11. make the documentation PDF in Doc (we have automated an HTML version online; will need ``latexmk`` etc installed): - - ``` bash - drevil:~tmp1/biopython/> pip install -r .circleci/requirements-sphinx.txt - drevil:~tmp1/biopython/> make -C Doc latexpdf - drevil:~tmp1/biopython/> cp Doc/_build/latex/Biopython_doc.pdf Doc/ - drevil:~tmp1/biopython/> make clean -C Doc - ``` - -12. make the source distribution +11. make the source distribution ``` bash drevil:~tmp1/biopython> python setup.py sdist --formats=gztar,zip ``` -13. untar the file somewhere else +12. untar the file somewhere else ``` bash drevil:~tmp1/biopython/> cd .. @@ -131,9 +120,7 @@ Making and testing the tar-ball drevil:~tmp1/> cd biopython-1.78 ``` - Check to make sure it includes the documentation PDF file under Doc - -14. make sure I can build (won't install and use this) and test it (using the tar-ball test files): +13. make sure I can build (won't install and use this) and test it (using the tar-ball test files): ``` bash drevil:~tmp1/biopython-1.78/> python -m pip install . --prefix /tmp/test-install @@ -146,7 +133,7 @@ Making and testing the tar-ball Checking the compiled documentation ----------------------------------- -15. Since Biopython 1.74, Sphinx has handled the API documentation via continuous +14. Since Biopython 1.74, Sphinx has handled the API documentation via continuous integration, but you still have to update the "latest" symlink. ``` bash @@ -163,7 +150,7 @@ Checking the compiled documentation Making wheels ------------- -17. Now we use https://github.com/biopython/biopython-wheels to build wheels, +15. Now we use https://github.com/biopython/biopython-wheels to build wheels, by updating the ``git checkout`` line in ``.github/workflows/cibuildwheel.yml`` to the new release's commit hash (which all being well will get a git tag). @@ -188,18 +175,18 @@ Making wheels $ git push origin master ``` -18. Successful wheels will in an ``artifact.zip`` file available in the footer of the +16. Successful wheels will in an ``artifact.zip`` file available in the footer of the run via [GitHub Actions runs](https://github.com/biopython/biopython-wheels/actions). Download this and unzip to your ``~/repository/biopython/DIST/`` folder. We will upload these to PyPI later using Twine. -19. If you have a Windows machine, remove any prior Biopython installations, +17. If you have a Windows machine, remove any prior Biopython installations, and confirm the Windows wheel file(s) work. Tagging the release, and uploading ---------------------------------- -20. Back in the main repository, tag the release: +18. Back in the main repository, tag the release: ``` bash $ cd .../tmp1/biopython/ @@ -207,7 +194,7 @@ Tagging the release, and uploading $ git push origin master --tags ``` -21. Upload the new release tar-ball and zip to the website via GitHub Pages `DIST` repository. +19. Upload the new release tar-ball and zip to the website via GitHub Pages `DIST` repository. ``` bash $ cp dist/biopython-1.78.* ~/repositories/DIST/ @@ -220,7 +207,7 @@ Tagging the release, and uploading $ git push origin gh-pages ``` -22. Upload to the python package index (except for beta/alpha level releases): +20. Upload to the python package index (except for beta/alpha level releases): ``` bash $ cd ~/repositories/biopython/ @@ -234,7 +221,7 @@ Tagging the release, and uploading - Check this is live at -23. Update the website: +21. Update the website: - If you haven't already, clone the ``biopython.github.io`` repository, (otherwise make sure your copy is up to date): @@ -260,7 +247,7 @@ Tagging the release, and uploading proof-reading/final corrections. - Make sure the download links work. -24. Announcement: +22. Announcement: - post the announcement on the [www.open-bio.org](https://www.open-bio.org) blog (making sure to use the Biopython category which will update the @@ -270,7 +257,7 @@ Tagging the release, and uploading - forward the email to Linux packagers e.g. debian-med@lists.debian.org -25. Conda-Forge should automatically open a pull request to update the +23. Conda-Forge should automatically open a pull request to update the package once it appears on PyPI. Check for a new pull request on [github.com/conda-forge/biopython-feedstock](https://github.com/conda-forge/biopython-feedstock) which once merged will upload the new release to [anaconda.org/conda-forge/biopython](https://anaconda.org/conda-forge/biopython) @@ -278,7 +265,7 @@ Tagging the release, and uploading Post release version bump ------------------------- -26. Bump version numbers again +24. Bump version numbers again - Update `Bio/__init__.py` version - Start entry in `NEWS.rst` for next version From 883eb50706b70fd9d02eeb5040920ab58f858d50 Mon Sep 17 00:00:00 2001 From: Peter Cock Date: Tue, 28 Oct 2025 20:44:46 +0000 Subject: [PATCH 16/29] Biopython 1.86 links --- wiki/Download.md | 14 +++++++------- 1 file changed, 7 insertions(+), 7 deletions(-) diff --git a/wiki/Download.md b/wiki/Download.md index 8e4d9240f..0cdfebcd9 100644 --- a/wiki/Download.md +++ b/wiki/Download.md @@ -6,7 +6,7 @@ redirect_from: - /download/ --- -Current Release - 1.85 - 15 Jan 2025 +Current Release - 1.86 - 28 Oct 2025 ==================================== See also [What's @@ -14,14 +14,14 @@ new](https://github.com/biopython/biopython/blob/master/NEWS.rst). ### Files -#### Biopython 1.85 +#### Biopython 1.86 -- [biopython-1.85.tar.gz](http://biopython.org/DIST/biopython-1.85.tar.gz) - 19Mb -- Source Tarball -- [biopython-1.85.zip](http://biopython.org/DIST/biopython-1.85.zip) +- [biopython-1.86.tar.gz](http://biopython.org/DIST/biopython-1.86.tar.gz) + 20Mb -- Source Tarball +- [biopython-1.86.zip](http://biopython.org/DIST/biopython-1.86.zip) 21Mb -- Source Zip File -- [Pre-compiled wheel files on PyPI](https://pypi.python.org/pypi/biopython/1.85) -- [Documentation](https://biopython.org/docs/1.85/) +- [Pre-compiled wheel files on PyPI](https://pypi.python.org/pypi/biopython/1.86) +- [Documentation](https://biopython.org/docs/1.86/) ### Installation Instructions From a0e5a32689edc7d59bf316100b3b9965121c6710 Mon Sep 17 00:00:00 2001 From: Peter Cock Date: Wed, 29 Oct 2025 09:22:13 +0000 Subject: [PATCH 17/29] No longer have a PDF Tutorial See #213 --- wiki/Logo.md | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/wiki/Logo.md b/wiki/Logo.md index fe33c21e3..f0ea2153e 100644 --- a/wiki/Logo.md +++ b/wiki/Logo.md @@ -22,8 +22,8 @@ double helix around the word Biopython: As of Biopython release 1.50, we've included the logo on the front cover of the [Biopython Tutorial and Cookbook](http://biopython.org/DIST/docs/tutorial/Tutorial.html) -([PDF](http://biopython.org/DIST/docs/tutorial/Tutorial.pdf)), which had -previously been rather plain. +(final [PDF](https://github.com/biopython/DIST/blob/gh-pages/docs/tutorial/Tutorial-1.83.pdf)), +which had previously been rather plain. This design was chosen from panel of entries to an open competition on the mailing lists back in [Summer From f09db8b3d53fe59ec7854ede8ae60e0250f10a83 Mon Sep 17 00:00:00 2001 From: Peter Cock Date: Wed, 29 Oct 2025 09:23:01 +0000 Subject: [PATCH 18/29] Don't currently have a PDF of the tutorial See #213 --- wiki/Seq.md | 3 +-- 1 file changed, 1 insertion(+), 2 deletions(-) diff --git a/wiki/Seq.md b/wiki/Seq.md index f6aeece17..121c30497 100644 --- a/wiki/Seq.md +++ b/wiki/Seq.md @@ -13,8 +13,7 @@ This page describes the Biopython `Seq` object, defined in the `Bio.Seq` module (together with related objects like the `MutableSeq`, plus some general purpose sequence functions). In addition to this wiki page, there is a whole chapter in the -[Tutorial](http://biopython.org/DIST/docs/tutorial/Tutorial.html) -([PDF](http://biopython.org/DIST/docs/tutorial/Tutorial.pdf)) on the +[Tutorial](http://biopython.org/DIST/docs/tutorial/Tutorial.html) on the `Seq` object - plus its [API documentation](http://biopython.org/DIST/docs/api/Bio.Seq.Seq-class.html) (which you can read online, or from within Python with the help From 0c8556d945c962f8c96e7e72f8839844621c58f4 Mon Sep 17 00:00:00 2001 From: Peter Cock Date: Wed, 29 Oct 2025 09:24:03 +0000 Subject: [PATCH 19/29] Don't currently have a PDF of the Tutorial See #213 --- wiki/Biopython.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/wiki/Biopython.md b/wiki/Biopython.md index cf5eb2715..7f9e815c7 100644 --- a/wiki/Biopython.md +++ b/wiki/Biopython.md @@ -37,7 +37,7 @@ the libraries and tools. | [Get Started](wiki/Getting_Started "wikilink") | [ Get help](wiki/Documentation "wikilink") | [ Contribute](wiki/Contributing "wikilink") | |------------------------------------------------------------------------------------------------------------------------------------------------|---------------------------------------------------------------------------------------------------------------------------------|-------------------------------------------------------------------------------------------------------------------------------| -| [ Download Biopython](wiki/Download "wikilink") | [Tutorial & API](https://biopython.org/docs/latest/) ([PDF](https://biopython.org/DIST/docs/tutorial/Tutorial.pdf)) | [ What's being worked on](wiki/Active_projects "wikilink") | +| [ Download Biopython](wiki/Download "wikilink") | [Tutorial & API](https://biopython.org/docs/latest/) | [ What's being worked on](wiki/Active_projects "wikilink") | | [Main README](https://github.com/biopython/biopython/blob/master/README.rst) | [ Documentation on this wiki](wiki/Category%3AWiki_Documentation "wikilink") | [ Developing on Github ](wiki/GitUsage "wikilink") | | | [ Cookbook (working examples)](wiki/Category%3ACookbook "wikilink") | [Google Summer of Code](wiki/Google_Summer_of_Code "wikilink") | | | [ Discuss and ask questions](wiki/Mailing_lists "wikilink") | [Report bugs](https://github.com/biopython/biopython/issues) | From 55120545c806ee16fbb39016b2b91f8600fc8e32 Mon Sep 17 00:00:00 2001 From: Peter Cock Date: Wed, 29 Oct 2025 09:25:44 +0000 Subject: [PATCH 20/29] No more PDF Tutorial See #213 --- wiki/Documentation.md | 10 ++++------ 1 file changed, 4 insertions(+), 6 deletions(-) diff --git a/wiki/Documentation.md b/wiki/Documentation.md index 43cd8afd7..027fb0a75 100644 --- a/wiki/Documentation.md +++ b/wiki/Documentation.md @@ -10,13 +10,11 @@ New to Biopython? Check out the [Getting Started](Getting_Started "wikilink") page, or follow one of the links below. -- The **Biopython Tutorial and Cookbook** contains the bulk of - Biopython documentation. It provides information to get you started +- The [Biopython Tutorial and + Cookbook](https://biopython.org/docs/latest/Tutorial/) contains the bulk + of Biopython's documentation. It provides information to get you started with Biopython, in addition to specific documentation on a number of - modules - - [HTML](https://biopython.org/docs/latest/Tutorial/), - [PDF](http://biopython.org/DIST/docs/tutorial/Tutorial.pdf) + modules. - API documentation for Biopython modules is generated directly from source code comments Sphinx autodoc: From 31fb2529d4225fefb7db6d551c8c803d64bf2ee1 Mon Sep 17 00:00:00 2001 From: Peter Cock Date: Wed, 29 Oct 2025 09:26:55 +0000 Subject: [PATCH 21/29] No more PDF of Tutorial See #213 --- wiki/Contributing.md | 3 +-- 1 file changed, 1 insertion(+), 2 deletions(-) diff --git a/wiki/Contributing.md b/wiki/Contributing.md index 549e74586..fd6f32774 100644 --- a/wiki/Contributing.md +++ b/wiki/Contributing.md @@ -12,8 +12,7 @@ quickly suck up valuable developer time. (We have day jobs too!) This is a short guide to the recommended way to contribute code to Biopython. See also the chapter about contributing in the -[Tutorial](http://biopython.org/DIST/docs/tutorial/Tutorial.html) -([PDF](http://biopython.org/DIST/docs/tutorial/Tutorial.pdf)). +[Tutorial](http://biopython.org/DIST/docs/tutorial/Tutorial.html). If you get as far as making a pull request with changes, you should read [CONTRIBUTING.rst](https://github.com/biopython/biopython/blob/master/CONTRIBUTING.rst) From 86c944e9e05083362e8035b2273082090b1340b8 Mon Sep 17 00:00:00 2001 From: Peter Cock Date: Wed, 29 Oct 2025 09:27:48 +0000 Subject: [PATCH 22/29] No more PDF Tutorial See #213 --- wiki/SearchIO.md | 3 +-- 1 file changed, 1 insertion(+), 2 deletions(-) diff --git a/wiki/SearchIO.md b/wiki/SearchIO.md index 0174ef09b..d24b3054f 100644 --- a/wiki/SearchIO.md +++ b/wiki/SearchIO.md @@ -22,8 +22,7 @@ background. module, with that caveat dropped in Biopython 1.72. There is a full chapter in the -[Tutorial](http://biopython.org/DIST/docs/tutorial/Tutorial.html) -([PDF](http://biopython.org/DIST/docs/tutorial/Tutorial.pdf)). +[Tutorial](http://biopython.org/DIST/docs/tutorial/Tutorial.html). This wiki describes the important bits with some small examples. For a full reference, consult the [API From 6adc4d74f365d7d115de926c559b934468a29c52 Mon Sep 17 00:00:00 2001 From: Peter Cock Date: Wed, 29 Oct 2025 09:28:25 +0000 Subject: [PATCH 23/29] No more PDF Tutorial See #213 --- wiki/Category_Cookbook.md | 5 ++--- 1 file changed, 2 insertions(+), 3 deletions(-) diff --git a/wiki/Category_Cookbook.md b/wiki/Category_Cookbook.md index 50abe8bfc..ded073cbc 100644 --- a/wiki/Category_Cookbook.md +++ b/wiki/Category_Cookbook.md @@ -8,9 +8,8 @@ tag: Cookbook The entries contained in the Cookbook category are designed to complement the general help given in the [Tutorial](http://biopython.org/DIST/docs/tutorial/Tutorial.html) -([PDF](http://biopython.org/DIST/docs/tutorial/Tutorial.pdf)) with -specific examples of problems that can be solved with the Biopython -tools. +with specific examples of problems that can be solved with the +Biopython tools. This collection of examples is a new effort for Biopython, so is currently a little short. If you have suggestions for topics, please From ea8a41472cba9f505d9149b334b3dd3533461e49 Mon Sep 17 00:00:00 2001 From: Peter Cock Date: Wed, 29 Oct 2025 09:28:51 +0000 Subject: [PATCH 24/29] No more PDF Tutorial See #213 --- wiki/PopGen.md | 3 +-- 1 file changed, 1 insertion(+), 2 deletions(-) diff --git a/wiki/PopGen.md b/wiki/PopGen.md index ffeb42895..a26a98d6b 100644 --- a/wiki/PopGen.md +++ b/wiki/PopGen.md @@ -24,8 +24,7 @@ Documentation on how to access Genepop using `Bio.PopGen` can be found Documentation for interacting with **SIMCOAL2** and **fdist2** can be found on the `PopGen` Chapter in the -[Tutorial](http://biopython.org/DIST/docs/tutorial/Tutorial.html) -([PDF](http://biopython.org/DIST/docs/tutorial/Tutorial.pdf)). +[Tutorial](http://biopython.org/DIST/docs/tutorial/Tutorial.html). Other software -------------- From 678e153cd6c03d539c85ece4cba8c33c561499d7 Mon Sep 17 00:00:00 2001 From: Peter Cock Date: Wed, 29 Oct 2025 09:29:21 +0000 Subject: [PATCH 25/29] No more PDF Tutorial See #213 --- wiki/SeqRecord.md | 3 +-- 1 file changed, 1 insertion(+), 2 deletions(-) diff --git a/wiki/SeqRecord.md b/wiki/SeqRecord.md index e07903ca8..8da95d6fc 100644 --- a/wiki/SeqRecord.md +++ b/wiki/SeqRecord.md @@ -18,8 +18,7 @@ system will *only* return `SeqRecord` objects. In addition to the `SeqRecord` object's [API documentation](http://biopython.org/DIST/docs/api/Bio.SeqRecord.SeqRecord-class.html), there is a whole chapter in the -[Tutorial](http://biopython.org/DIST/docs/tutorial/Tutorial.html) -([PDF](http://biopython.org/DIST/docs/tutorial/Tutorial.pdf)), and the +[Tutorial](http://biopython.org/DIST/docs/tutorial/Tutorial.html), and the [`SeqIO` page](SeqIO "wikilink") is also very relevant. Extracting information from a SeqRecord From c9bb32cb4aa3145a1ab92b7e56381d5b7b3c149a Mon Sep 17 00:00:00 2001 From: mdehoon Date: Wed, 29 Oct 2025 18:56:26 +0900 Subject: [PATCH 26/29] Update Download.md Include the release date of the previous Biopython release. --- wiki/Download.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/wiki/Download.md b/wiki/Download.md index 0cdfebcd9..342308cc1 100644 --- a/wiki/Download.md +++ b/wiki/Download.md @@ -158,7 +158,7 @@ Version 1.76 is the last release to support Python 2.7 and 3.5, all later releases require Python 3: - [biopython-1.85.tar.gz](http://biopython.org/DIST/biopython-1.85.tar.gz) - 19Mb -- Source Tarball + 19Mb -- Source Tarball (15 January 2025) - [biopython-1.85.zip](http://biopython.org/DIST/biopython-1.85.zip) 21Mb -- Source Zip File - [Pre-compiled wheel files on PyPI](https://pypi.python.org/pypi/biopython/1.85) From 5ef20edb735c49856bcbc5c63fb19d44810f8ac8 Mon Sep 17 00:00:00 2001 From: mdehoon Date: Wed, 29 Oct 2025 18:57:41 +0900 Subject: [PATCH 27/29] Update Download.md Fix some weird line breaks in URLs --- wiki/Download.md | 6 ++---- 1 file changed, 2 insertions(+), 4 deletions(-) diff --git a/wiki/Download.md b/wiki/Download.md index 342308cc1..e7cd80551 100644 --- a/wiki/Download.md +++ b/wiki/Download.md @@ -188,10 +188,8 @@ all later releases require Python 3: 19Mb -- Source Tarball (22 December 2023) - [biopython-1.82.zip](http://biopython.org/DIST/biopython-1.82.zip) 20Mb -- Source Zip File -- [Pre-compiled wheel files on PyPI](https://pypi.python.org/pypi/biopython/1\ -.82) -- [Tutorial-1.82.pdf](http://biopython.org/DIST/docs/tutorial/Tutorial-1.82.p\ -df) -- Documentation +- [Pre-compiled wheel files on PyPI](https://pypi.python.org/pypi/biopython/1.82) +- [Tutorial-1.82.pdf](http://biopython.org/DIST/docs/tutorial/Tutorial-1.82.pdf) -- Documentation From ec4030f2e528d2d9e46605fe42fdba5c5d7a3e52 Mon Sep 17 00:00:00 2001 From: Peter Cock Date: Wed, 29 Oct 2025 10:52:50 +0000 Subject: [PATCH 28/29] update blog instructions for release process --- wiki/Building_a_release.md | 11 +++++------ 1 file changed, 5 insertions(+), 6 deletions(-) diff --git a/wiki/Building_a_release.md b/wiki/Building_a_release.md index 9b170b4b2..110887877 100644 --- a/wiki/Building_a_release.md +++ b/wiki/Building_a_release.md @@ -12,8 +12,8 @@ Setup required for a new release manager The instructions below require that you have access to a few servers and the code repository. When you start, be sure to have write access to: -1. [OBF WordPress Blog](https://www.open-bio.org) -2. [Biopython on PyPI](https://pypi.python.org/pypi/biopython) +1. [Biopython on PyPI](https://pypi.python.org/pypi/biopython) +2. A fork of for the OBF blog post. 3. These repositories (e.g. via membership of the *Releases* team, or have someone ready to merge pull requests): - [Source code repository](https://github.com/biopython/biopython) @@ -249,10 +249,9 @@ Tagging the release, and uploading 22. Announcement: - - post the announcement on the [www.open-bio.org](https://www.open-bio.org) - blog (making sure to use the Biopython category which will update the - [news page](News "wikilink") via the news feed) - - send an email to biopython-announce@biopython.org + - submit a pull request for the OBF blog (like this [example for + Biopython 1.86](https://github.com/OBF/OBF.github.io/pull/125)) + - send an email to biopython-announce@biopython.org and biopython@biopython.org (see [mailing lists](Mailing_lists "wikilink")) - forward the email to Linux packagers e.g. debian-med@lists.debian.org From a5796ae03d27bbe8e46d8c52a7fedc0085a5a909 Mon Sep 17 00:00:00 2001 From: Peter Cock Date: Wed, 29 Oct 2025 10:56:10 +0000 Subject: [PATCH 29/29] Add missing link --- wiki/Building_a_release.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/wiki/Building_a_release.md b/wiki/Building_a_release.md index 110887877..ecc10f8b3 100644 --- a/wiki/Building_a_release.md +++ b/wiki/Building_a_release.md @@ -13,7 +13,7 @@ The instructions below require that you have access to a few servers and the code repository. When you start, be sure to have write access to: 1. [Biopython on PyPI](https://pypi.python.org/pypi/biopython) -2. A fork of for the OBF blog post. +2. A fork of https://github.com/OBF/OBF.github.io for the OBF blog post. 3. These repositories (e.g. via membership of the *Releases* team, or have someone ready to merge pull requests): - [Source code repository](https://github.com/biopython/biopython)