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Resolve issue/1386, fix numpy.compat deprecation warning#1387

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swails merged 4 commits into
ParmEd:masterfrom
MattBurn:issue/1386
Jun 18, 2025
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Resolve issue/1386, fix numpy.compat deprecation warning#1387
swails merged 4 commits into
ParmEd:masterfrom
MattBurn:issue/1386

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@MattBurn

@MattBurn MattBurn commented Feb 3, 2025

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numpy.compat has been deprecated in numpy 2 and will be released in future versions. To prevent this from breaking ParmEd, asbytes and asstr have been implemented in place in the parmed/utls/netcdf.py file.

@vedranmiletic

vedranmiletic commented Jun 11, 2025

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I just stumbled upon this same issue as ParmEd in AmberTools broke after NumPy upgrade in Arch Linux. I am glad to report that this patch solves the issue.

Why is the change not passing the CI pipelines?

@MattBurn

MattBurn commented Jun 17, 2025

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Not sure looking into this now

@MattBurn

MattBurn commented Jun 17, 2025 •
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The tests were failing on my local machine due to issues with downloading from the RCSB FTP site. RCSB deprecated the FTP protocol as of 2024-11-01 as discussed here.

I have created a new issue 1408 to discuss the move from FTP to HTTP/S.

I have updated the calls to ftplib and the old RCSB FTP domain to urllib as per the recommendation from the RCSB.

There was also a single test (test/test_parmed_genopen.py::TestGenopen::test_read_ftp_URL) which tests the calls to the FPT site directly. This test is no longer possible so I have tagged it to always skip this test citing the RCSB reference as a reason.

@MattBurn

MattBurn commented Jun 17, 2025

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Hopefully these changes can now be merged.

@MattBurn MattBurn mentioned this pull request Jun 18, 2025
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@MattBurn

MattBurn commented Jun 18, 2025

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Should resolve ParmEd/ParmEd !1406

swails
swails approved these changes Jun 18, 2025
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Thanks!

@swails swails merged commit 9fa8b08 into ParmEd:master Jun 18, 2025
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@j-wags j-wags mentioned this pull request Jun 19, 2025
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@atravitz atravitz mentioned this pull request Oct 10, 2025
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@mikemhenry

mikemhenry commented Oct 10, 2025

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@swails any chance we can get a new release so we can build a conda-forge pacakge with this fix?

timpalpant pushed a commit to timpalpant/ParmEd that referenced this pull request Nov 21, 2025
Cherry-pick ParmEd#1387
dc8a451
timpalpant pushed a commit to timpalpant/ParmEd that referenced this pull request Nov 21, 2025
Cherry-pick ParmEd#1387
7dc8c97
@jan-janssen jan-janssen mentioned this pull request Jan 4, 2026
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@tE3m tE3m mentioned this pull request Feb 3, 2026
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@MattBurn @vedranmiletic @mikemhenry @swails