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Pysam seems to be working at least under MSYS2 shell.
Author
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Benchmark had some errors. |
Couple of fixes to get pysam compiling on Linux
Couple more fixes for Linux
Member
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Please add a Windows build to the job matrix in .github/workflows/ci.yaml so that we can see this build in operation. |
Author
Looks like I have no idea how to get the build job working nor do I have the time to learn to do so at the moment. |
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Currently hacking away at this myself-the issue I'm running into running it under msvc python is that the cython extensions use posix-isms which...is not something you're really allowed to do. Seeing if I can't work around it. edit: its kinda worse than that-the shared model doesn't quite work because you can't link a .a output from gcc using cython/msvc. |
Author
I think pysam needs major patching to work with MSVC and/or clang-cl. There is a MSVC port of htslib and that might be a good starting point. https://github.com/refresh-bio-sandbox/htslib-msvc/tree/develop |
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the other way to go about doing it would be to use something like CMake's GNUToMS and to link it as such-probably easier, honestly. edit: and as luck would have it htslib's makefile already spits out a .lib if you use build-shared |
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Okay, so I was mostly getting around portability issues with simple find-replace and a few mingw headers (mostly strcasecmp/_stricmp and STDIN_FILENO/ _fileno(stdin) alongside some symbol changes (specifically the data variable exports from htslib get mangled) and this worked until I ran into samtools coverage.c. Apparently msvc doesn't support VLAs. Because why would it? Gonna be a more involved port than I'd like. |
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If you can, please share your progress on Github or elsewhere. |
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Oh i will, don't worry.
…________________________________
From: teepean ***@***.***>
Sent: Tuesday, March 18, 2025 2:07 PM
To: pysam-developers/pysam ***@***.***>
Cc: Andrew Robbins ***@***.***>; Comment ***@***.***>
Subject: Re: [pysam-developers/pysam] MinGW version of pysam (PR #1274)
If you can, please share your progress on Github or elsewhere.
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If you can, please share your progress on Github or elsewhere.
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Author
AFAIK clang-cl supports VLAs. |
Member
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Most likely I will only be interested in merging an MSYS2-based approach such as @teepean's. What you're describing for MSVC support is too invasive for a niche platform. |
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the primary issue there is that msys2-based python is...not widely used. the goal if i can get this to work is for it to be minimally invasive, don't worry! |
Member
AIUI MSYS2 produces native executables without unusual dependencies. If this is the case, or if pysam uses delvewheel when building wheels, this is irrelevant. |
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I might be operating on outdated information here but my understanding was that python extensions proper need to link the pythonXY.lib file for MSVC python, which isn't impossible, just a pain. Will keep posted. edit: actually this may be easier than i thought |
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okay, the good news is that i have it building against MSVC python w/ no major modifications. the bad news is... `ModuleNotFoundError: No module named 'pysam.libchtslib' |
Author
With MinGW builds this means that the module cannot find all of it's dependencies. |
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yeah, I checked that. Delvewheel and all. No dice
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https://github.com/theAeon/pysam/tree/pysam-mingw if you want to give it a try |
Author
Any instructions on how to build this one? |
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Author
This produces a build with gcc not MSVC or am I missing something here? |
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linked w/ msvc python |
Author
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In that case the resulting pyds depend on ucrt64 dlls. |
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which i put in the wheel with delvewheel (specifically give it a go, it won't work |
Author
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I built pysam accidentally with clang64 instead of ucrt64 but decided to go with that. Here's the delvewheel version. Basic functionality seems to be working. https://drive.google.com/file/d/1c9vpNIpwWtFVkLdQxFoXs-wcaIKPoodg/view?usp=sharing |
Author
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Here's a test log. https://gist.github.com/teepean/d50974cffa9f0a4f38da99958eaa70ab |
Huh. Wonder why it wasn't working on end. |
Author
You mean why it wasn't working on your end? Did you test the whl I linked earlier? |
On my end-and I was referring to my delvewheel run. I'll give that a try shortly. |
bizarre |
Author
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I am using official Python 3.13.1. I am going to upgrade and see what happens. |
Author
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Works just fine. You could use Procmon to see which one of the DLLs is not found. |
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looks like its trying to load copies of libbz/libcrypto/libcurl under an un-mangled name? |
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It loaded, but only after my pysam.libs folder was made to look like this. Probably safe to write off as something wrong with my install. Probably. |
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oh, its way stupider than that. there was an extra hts-3.dll in pysam/ that wasn't getting deleted by pip uninstall and was messing everything up. disregard. let me fix ci while i'm at it |
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Build tested on MSYS2 ucrt64 environment.
Test results: