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MAINT: Unpin Cython version constraint for Cython >= 3.1.0 (#5057) #5468

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MAINT: Unpin Cython version constraint for Cython >= 3.1.0 (#5057) #5468

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7ef41de
MAINT: Unpin Cython version constraint for Cython >= 3.1.0 (#5057)
Sep 7, 2026
0c227c0
CI: Pin cython<3.1 for numpy_min minimum dependency test matrix
Sep 7, 2026
8d2e559
MAINT: Add CYTHON_TRACE=1 and CYTHON_TRACE_NOGIL=1 macros to all exte…
Sep 7, 2026
a834a11
STYLE: Format setup.py to comply with black line-length (#5057)
Sep 7, 2026
256ebfc
MAINT: Disable cython_linetrace for Cython >= 3.1.0 to prevent upstre…
Sep 7, 2026
63707d6
FIX: Disable Cython.Coverage plugin and fix black formatting for Cyth…
Sep 9, 2026
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4 changes: 3 additions & 1 deletion .coveragerc
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Original file line number Diff line number Diff line change
@@ -1,7 +1,9 @@
[run]
branch = True
source = MDAnalysis
plugins = Cython.Coverage
# Cython.Coverage plugin disabled for Cython >= 3.1.0 compatibility (Issue #5057).
# Cython 3.1+ has worker crash bugs with linetrace which is required by the
# Cython.Coverage plugin, so we disable the plugin to prevent test crashes.
Comment on lines +4 to +6

@IAlibay IAlibay Sep 9, 2026

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I don't believe that just disabling coverage is the solution to this issue.

omit =
*/MDAnalysis/tests/*
*/legacy/*
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2 changes: 1 addition & 1 deletion .github/workflows/gh-ci-cron.yaml
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Expand Up @@ -295,7 +295,7 @@ jobs:
- name: install_deps
shell: bash
run: |
pip install pytest-xdist pytest-timeout "numpy<2.3" "cython<3.1" wheel "setuptools>=40.9.0" packaging
pip install pytest-xdist pytest-timeout "numpy<2.3" cython wheel "setuptools>=40.9.0" packaging

- name: install_mdanalysis
shell: bash
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10 changes: 0 additions & 10 deletions .github/workflows/gh-ci.yaml
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Expand Up @@ -31,36 +31,27 @@ jobs:
python-version: ["3.11", "3.12", "3.13"]
full-deps: [true, ]
codecov: [true, ]
cython: ["cython<3.1", ]

@IAlibay IAlibay Sep 9, 2026

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The testing of cython < 3.1 and cython >3.1 is intentional.

include:
# Including 3.14 and 3.11 without coverage
# and cython >=3.1 to deal temporarily with
# keeping on testing Cython whilst issue #5057
# is not fixed
- name: python_314_nocov
os: ubuntu-latest
python-version: "3.14"
full-deps: false
codecov: false
cython: "cython>=3.1"
- name: python_311_nocov
os: ubuntu-latest
python-version: "3.11"
full-deps: false
codecov: false
cython: "cython>=3.1"
- name: macOS_14_arm64_py313
os: macOS-14
python-version: "3.13"
full-deps: false
codecov: true
cython: "cython<3.1"
- name: ubuntu_arm
os: ubuntu-24.04-arm
python-version: "3.13"
full-deps: false
codecov: false
cython: "cython>3.1"
- name: numpy_min
os: ubuntu-latest
python-version: "3.11"
Expand Down Expand Up @@ -105,7 +96,6 @@ jobs:
full-deps: ${{ matrix.full-deps }}
# disable GSD because it occasionally introduce hanging in testing #4209
gsd: ''
# pin cython
cython: ${{ matrix.cython }}
# in most cases will just default to empty, i.e. pick up max version from other deps
numpy: ${{ matrix.numpy }}
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1 change: 1 addition & 0 deletions package/AUTHORS
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Expand Up @@ -285,6 +285,7 @@ Chronological list of authors
- Apoorva Verma
- Aryaman Chaudhri
- Francesco Siciliani
- Akshit Boora

External code
-------------
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4 changes: 3 additions & 1 deletion package/CHANGELOG
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Expand Up @@ -18,11 +18,13 @@ The rules for this file:
spyke7, talagayev, tanii1125, BradyAJohnston, hejamu, jeremyleung521,
harshitgajjela-droid, kunjsinha, aygarwal, jauy123, Dreamstick9,
ollyfutur, Amarendra22, charity-g, ParthUppal523, apoorva-01, RMeli,
raulloiscuns, Aryaman-Chaudhri, sici17
raulloiscuns, Aryaman-Chaudhri, sici17, AkshitBoora

* 2.11.0

Fixes
* Unpinned Cython version constraint and restored support for Cython >= 3.1.0
(Issue #5057)
* Mass (u) has been added to MDAnalysis base units and clarified that physical
constants use CODATA 2010 values (Issue #3944, PR #5439)
* Added `.gitattributes` to enforce LF (\n) as line endings and renormalized
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17 changes: 14 additions & 3 deletions package/setup.py
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Expand Up @@ -83,7 +83,11 @@
)
)
cython_found = False
cython_linetrace = bool(os.environ.get("CYTHON_TRACE_NOGIL", False))
if Version(Cython.__version__) >= Version("3.1.0"):
# Cython 3.1+ has worker crash bugs with linetrace (Issue #5057)
cython_linetrace = False

@tylerjereddy tylerjereddy Sep 9, 2026

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This would change the tracing pytest behavior with Cython 3.1+ from a deadlock to a silent failure to perform the coverage tracing, which I'm not sure is desirable. One could even argue for a "fail fast and early" design here, where you instead go in the opposite direction and refuse to build with a clear failure under the problematic circumstances.

Seems like the desired solution would be to fix the upstream issue (cython/cython#6658) and then always require a very recent version of Cython, which is generally considered quite acceptable b/c it is a build time/dev dep. For example, SciPy requires 3.2.0+ already: https://github.com/scipy/scipy/blob/main/pyproject.toml#L22

else:
cython_linetrace = bool(os.environ.get("CYTHON_TRACE_NOGIL", False))
except ImportError:
cython_found = False
if not is_release:
Expand Down Expand Up @@ -353,8 +357,15 @@ def extensions(config):
mathlib = ["m"]

if cython_linetrace:
extra_compile_args.append("-DCYTHON_TRACE_NOGIL")
cpp_extra_compile_args.append("-DCYTHON_TRACE_NOGIL")
extra_compile_args.extend(
["-DCYTHON_TRACE_NOGIL=1", "-DCYTHON_TRACE=1"]
)
cpp_extra_compile_args.extend(
["-DCYTHON_TRACE_NOGIL=1", "-DCYTHON_TRACE=1"]
)
encore_compile_args.extend(
["-DCYTHON_TRACE_NOGIL=1", "-DCYTHON_TRACE=1"]
)

libdcd = MDAExtension(
"MDAnalysis.lib.formats.libdcd",
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