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guix-mirror/gnu/packages/patches/python-holodeck-cython-3-compat.patch
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Nicolas Graves 4917d8d86d gnu: python-holodeck: Update to 1.6 and bump cython@0. 
* gnu/packages/patches/python-holodeck-cython-3-compat.patch: New file.
* gnu/local.mk : Record patch.
* gnu/packages/astronomy.scm (python-holodeck): Update to 1.6.
[origin]<source>: Record patch.
[native-inputs]: Replace python-cython-0 by python-cython.

Relates-to: guix/guix!9270
Reviewed-by: Cayetano Santos <csantosb@inventati.org>
Change-Id: Id3fb2d4d536988dc0abdc683233dfa81846e5bd3
Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>
2026-06-14 09:42:25 +01:00

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From 6bd910b83c180687a9cd53ba39f84c539f91c7c6 Mon Sep 17 00:00:00 2001
From: David Wright <dcw3.dev@gmail.com>
Date: Fri, 31 Oct 2025 19:18:01 -0700
Subject: [PATCH 1/2] fix: Cython>=3.0 and Python 3.13 compatibility
---
holodeck/cyutils.pxd | 4 ++--
holodeck/cyutils.pyx | 32 ++++++++++++++++----------------
holodeck/sams/sam_cyutils.pyx | 16 ++++++++--------
pyproject.toml | 4 ++--
requirements.txt | 4 ++--
5 files changed, 30 insertions(+), 30 deletions(-)
diff --git a/holodeck/cyutils.pxd b/holodeck/cyutils.pxd
index 9b12bf09..ede11a17 100644
--- a/holodeck/cyutils.pxd
+++ b/holodeck/cyutils.pxd
@@ -1,5 +1,5 @@
"""Header file for cython `cyutils.py`
"""
-cdef double _interp_between_vals(double xnew, double xl, double xr, double yl, double yr)
-cdef double interp_at_index(int idx, double xnew, double[:] xold, double[:] yold)
\ No newline at end of file
+cdef double _interp_between_vals(double xnew, double xl, double xr, double yl, double yr) noexcept
+cdef double interp_at_index(int idx, double xnew, double[:] xold, double[:] yold) noexcept
\ No newline at end of file
diff --git a/holodeck/cyutils.pyx b/holodeck/cyutils.pyx
index fcdb4d3b..599b496b 100644
--- a/holodeck/cyutils.pyx
+++ b/holodeck/cyutils.pyx
@@ -51,7 +51,7 @@ cdef double GW_SRC_CONST = 8.0 * pow(MY_NWTG, 5.0/3.0) * pow(M_PI, 2.0/3.0) / sq
# ==== Utility Functions ====
-cdef double bessel_recursive(int nn, double ne, double jn_m1, double jn_m2):
+cdef double bessel_recursive(int nn, double ne, double jn_m1, double jn_m2) noexcept:
"""Recursive relation for calculating bessel functions
J_n(x) = 2 * [(n-1) / x] * J_n-1(x) - J_n-2(x)
@@ -76,7 +76,7 @@ cdef double bessel_recursive(int nn, double ne, double jn_m1, double jn_m2):
return jn
-cdef double _gw_ecc_func(double eccen):
+cdef double _gw_ecc_func(double eccen) noexcept:
"""Calculate the GW Hardening rate eccentricitiy dependence F(e).
See [Peters1964]_ Eq. 5.6, or [EN2007]_ Eq. 2.3
@@ -99,7 +99,7 @@ cdef double _gw_ecc_func(double eccen):
@cython.boundscheck(False)
@cython.wraparound(False)
-cdef void my_trapz_grid_weight(int index, int size, double[:] grid, double *rv):
+cdef void my_trapz_grid_weight(int index, int size, double[:] grid, double *rv) noexcept:
"""Determine the trapezoid-rule weight and bin-width for the given grid point.
Parameters
@@ -142,7 +142,7 @@ cdef void my_trapz_grid_weight(int index, int size, double[:] grid, double *rv):
return
-cdef double gw_freq_dist_func__scalar_scalar(int nn, double ee):
+cdef double gw_freq_dist_func__scalar_scalar(int nn, double ee) noexcept:
"""Calculate the GW frequency distribution function at the given harmonic and eccentricity, g(n,e).
See [EN2007]_ Eq. 2.4
@@ -198,7 +198,7 @@ cdef double gw_freq_dist_func__scalar_scalar(int nn, double ee):
@cython.wraparound(False)
@cython.nonecheck(False)
@cython.cdivision(True)
-cdef void unravel(int idx, int[] shape, int *ii_out, int *jj_out):
+cdef void unravel(int idx, int[] shape, int *ii_out, int *jj_out) noexcept:
"""Convert from a 1D/flattened index into a 2D pair of (unraveled) indices.
NOTE: row-major / c-style ordering is assumed. This is the numpy default.
@@ -290,7 +290,7 @@ cdef int sort_compare(const void *a, const void *b) noexcept nogil:
return 0
-cdef void argsort(double *values, int size, int **indices):
+cdef void argsort(double *values, int size, int **indices) noexcept:
"""Find the indices that sort the given 1D array of double values.
This is done using an array of `sorter` struct instances which store both index and value.
@@ -323,7 +323,7 @@ cdef void argsort(double *values, int size, int **indices):
@cython.wraparound(False)
@cython.nonecheck(False)
@cython.cdivision(True)
-cdef double _interp_between_vals(double xnew, double xl, double xr, double yl, double yr):
+cdef double _interp_between_vals(double xnew, double xl, double xr, double yl, double yr) noexcept:
cdef double ynew = yl + (yr - yl) * (xnew - xl) / (xr - xl)
return ynew
@@ -332,7 +332,7 @@ cdef double _interp_between_vals(double xnew, double xl, double xr, double yl, d
@cython.wraparound(False)
@cython.nonecheck(False)
@cython.cdivision(True)
-cdef double interp_at_index(int idx, double xnew, double[:] xold, double[:] yold):
+cdef double interp_at_index(int idx, double xnew, double[:] xold, double[:] yold) noexcept:
"""Perform linear interpolation at the given index in a pair of arrays.
Parameters
@@ -852,7 +852,7 @@ cdef double[:, :, :] _sam_calc_gwb_single_eccen_discrete(
def sam_poisson_gwb(dist, hc2, nreals, normal_threshold=1e10):
- return _sam_poisson_gwb(np.array(dist.shape), dist, hc2, nreals, long(normal_threshold))
+ return _sam_poisson_gwb(np.array(dist.shape), dist, hc2, nreals, int(normal_threshold))
@cython.boundscheck(False)
@@ -934,7 +934,7 @@ def ss_bg_hc(number, h2fdf, nreals, normal_threshold=1e10):
@cython.cdivision(True)
cdef void _ss_bg_hc(long[:] shape, double[:,:,:,:] h2fdf, double[:,:,:,:] number,
long nreals, long thresh,
- double[:,:] hc2ss, double[:,:] hc2bg, long[:,:,:] ssidx):
+ double[:,:] hc2ss, double[:,:] hc2bg, long[:,:,:] ssidx) noexcept:
"""
Calculates the characteristic strain from loud single sources and a background of all other sources.
@@ -1069,7 +1069,7 @@ cdef void _ss_bg_hc_and_par(long[:] shape, double[:,:,:,:] h2fdf, double[:,:,:,:
long nreals, long thresh,
double[:] mt, double[:] mr, double[:] rz,
double[:,:] hc2ss, double[:,:] hc2bg, long[:,:,:] ssidx,
- double[:,:,:] bgpar, double[:,:,:] sspar):
+ double[:,:,:] bgpar, double[:,:,:] sspar) noexcept:
"""
Calculates the characteristic strain from loud single sources and a background of all other sources.
@@ -1204,7 +1204,7 @@ def sort_h2fdf(h2fdf):
return
-cdef (int *) _sort_h2fdf(double[:] flat_h2fdf, long size):
+cdef (int *) _sort_h2fdf(double[:] flat_h2fdf, long size) except NULL:
cdef (double *)array = <double *>malloc(size * sizeof(double))
cdef (int *)indices = <int *>malloc(size * sizeof(int))
@@ -1266,7 +1266,7 @@ def loudest_hc_from_sorted(number, h2fdf, nreals, nloudest, msort, qsort, zsort,
cdef void _loudest_hc_from_sorted(long[:] shape, double[:,:,:,:] h2fdf, double[:,:,:,:] number,
long nreals, long nloudest, long thresh,
long[:] msort, long[:] qsort, long[:] zsort,
- double[:,:,:] hc2ss, double[:,:] hc2bg):
+ double[:,:,:] hc2ss, double[:,:] hc2bg) noexcept:
"""
Calculates the characteristic strain from loud single sources and a background of all other sources.
@@ -1410,7 +1410,7 @@ cdef void _loudest_hc_and_par_from_sorted(long[:] shape, double[:,:,:,:] h2fdf,
long nreals, long nloudest, long thresh,
double[:] mt, double[:] mr, double[:] rz,
long[:] msort, long[:] qsort, long[:] zsort,
- double[:,:,:] hc2ss, double[:,:] hc2bg, double[:,:,:] lspar, double[:,:,:] bgpar, long[:,:,:,:] ssidx):
+ double[:,:,:] hc2ss, double[:,:] hc2bg, double[:,:,:] lspar, double[:,:,:] bgpar, long[:,:,:,:] ssidx) noexcept:
"""
Calculates the characteristic strain from loud single sources and a background of all other sources.
@@ -1617,7 +1617,7 @@ cdef void _loudest_hc_and_par_from_sorted_redz(long[:] shape, double[:,:,:,:] h2
double[:] mt, double[:] mr, double[:] rz,
double[:,:,:,:] redz_final, double[:,:,:,:] dcom_final, double[:,:,:,:] sepa, double[:,:,:,:] angs,
long[:] msort, long[:] qsort, long[:] zsort,
- double[:,:,:] hc2ss, double[:,:] hc2bg, double[:,:,:,:] sspar, double[:,:,:] bgpar):
+ double[:,:,:] hc2ss, double[:,:] hc2bg, double[:,:,:,:] sspar, double[:,:,:] bgpar) noexcept:
"""
Calculates the characteristic strain from loud single sources and a background of all other sources.
@@ -2046,7 +2046,7 @@ def Sh_rest(hc_ss, hc_bg, freqs, nexcl):
cdef void _Sh_rest(
double[:,:,:] hc_ss, double[:,:,] hc_bg, double[:] freqs, long nexcl,
long nreals, long nfreqs, long nloudest,
- double[:,:,:] Sh_rest):
+ double[:,:,:] Sh_rest) noexcept:
"""
Calculate the noise from all the single sources except the source in question
and the next N_excl loudest sources.
diff --git a/holodeck/sams/sam_cyutils.pyx b/holodeck/sams/sam_cyutils.pyx
index ed411270..1a36a9ea 100644
--- a/holodeck/sams/sam_cyutils.pyx
+++ b/holodeck/sams/sam_cyutils.pyx
@@ -50,20 +50,20 @@ cpdef double hard_gw(double mtot, double mrat, double sepa):
@cython.cdivision(True)
-cdef double kepler_freq_from_sepa(double mtot, double sepa):
+cdef double kepler_freq_from_sepa(double mtot, double sepa) noexcept:
cdef double freq = KEPLER_CONST_FREQ * sqrt(mtot) / pow(sepa, 1.5)
return freq
@cython.cdivision(True)
-cdef double kepler_sepa_from_freq(double mtot, double freq):
+cdef double kepler_sepa_from_freq(double mtot, double freq) noexcept:
cdef double sepa = KEPLER_CONST_SEPA * pow(mtot, 1.0/3.0) / pow(freq, 2.0/3.0)
return sepa
@cython.boundscheck(False)
@cython.wraparound(False)
-cdef int while_while_increasing(int start, int size, double val, double[:] edges):
+cdef int while_while_increasing(int start, int size, double val, double[:] edges) noexcept:
"""Step through an INCREASING array of `edges`, first forward, then backward, to find edges bounding `val`.
Use this function when `start` is already a close guess, and we just need to update a bit.
@@ -86,7 +86,7 @@ cdef int while_while_increasing(int start, int size, double val, double[:] edges
@cython.boundscheck(False)
@cython.wraparound(False)
-cdef int while_while_decreasing(int start, int size, double val, double[:] edges):
+cdef int while_while_decreasing(int start, int size, double val, double[:] edges) noexcept:
"""Step through a DECREASING array of `edges`, first forward, then backward, to find edges bounding `val`.
Use this function when `start` is already a close guess, and we just need to update a bit.
@@ -175,7 +175,7 @@ cdef void _integrate_differential_number_3dx1d(
double[:, :, :, :] dnum,
# output
double[:, :, :, :] numb
-):
+) noexcept:
"""Integrate the differential number of binaries over each grid bin into total numbers of binaries.
Trapezoid used over first 3 dims (mtot, mrat, redz), and Riemann over 4th (freq).
@@ -238,7 +238,7 @@ cdef void _integrate_differential_number_3dx1d(
@cython.cdivision(True)
-cdef double _hard_func_2pwl(double norm, double xx, double gamma_inner, double gamma_outer):
+cdef double _hard_func_2pwl(double norm, double xx, double gamma_inner, double gamma_outer) noexcept:
cdef double dadt = - norm * pow(1.0 + xx, -gamma_outer+gamma_inner) / pow(xx, gamma_inner-1)
return dadt
@@ -247,7 +247,7 @@ cdef double _hard_func_2pwl(double norm, double xx, double gamma_inner, double g
cdef double _hard_func_2pwl_gw(
double mtot, double mrat, double sepa,
double norm, double rchar, double gamma_inner, double gamma_outer
-):
+) noexcept:
cdef double dadt = _hard_func_2pwl(norm, sepa/rchar, gamma_inner, gamma_outer)
dadt += hard_gw(mtot, mrat, sepa)
return dadt
@@ -327,7 +327,7 @@ cdef void _get_hardening_norm_2pwl(
lifetime_2pwl_params args,
# output
double[:] norm_log10,
-):
+) noexcept:
cdef double XTOL = 1e-3
cdef double RTOL = 1e-5
diff --git a/pyproject.toml b/pyproject.toml
index ce2b0a69..9158a019 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -1,6 +1,6 @@
[build-system]
# cython/numpy/scipy are required to build cython extensions. The build steps are specified in `setup.py`
-requires = ["setuptools >= 40.6.0", "wheel", "Cython<3.0.0", "numpy", "scipy"]
+requires = ["setuptools >= 40.6.0", "wheel", "Cython>=3.0.0", "numpy>=1.26", "scipy"]
build-backend = "setuptools.build_meta"
[tool.mypy]
@@ -40,4 +40,4 @@ select = [
]
[tool.ruff.mccabe]
-max-complexity = 15
\ No newline at end of file
+max-complexity = 15
diff --git a/requirements.txt b/requirements.txt
index 0ab402e5..171d10fc 100644
--- a/requirements.txt
+++ b/requirements.txt
@@ -4,12 +4,12 @@ h5py
ipywidgets # required for tqdm to work (at the moment, looks like a bug)
kalepy
matplotlib
-numpy
+numpy>=1.26
scipy
# pydoe
psutil
tqdm
-cython<3.0.0
+cython>=3.0.0
# schwimmbad # used in the `gps` submodule
# emcee # used in the `gps` submodule
# george # used in the `gps` submodule
From 303a564aa5443ca766463fc5eee0eb5549fd0076 Mon Sep 17 00:00:00 2001
From: David Wright <dcw3.dev@gmail.com>
Date: Wed, 19 Nov 2025 14:19:42 -0800
Subject: [PATCH 2/2] ci: update CI/CD to include Python 3.13
---
.github/workflows/publish_to_pypi.yaml | 4 ++--
.github/workflows/unit-tests-ci.yaml | 2 +-
tox.ini | 1 +
3 files changed, 4 insertions(+), 3 deletions(-)
diff --git a/.github/workflows/publish_to_pypi.yaml b/.github/workflows/publish_to_pypi.yaml
index 04e74904..e1fcc13d 100644
--- a/.github/workflows/publish_to_pypi.yaml
+++ b/.github/workflows/publish_to_pypi.yaml
@@ -21,8 +21,8 @@ jobs:
- name: Build wheels
uses: pypa/cibuildwheel@v2.16.2
env:
- # Skip CPython 3.6, 3.7, 3.8, 3.12, PyPy, 32-bit, and musl
- CIBW_SKIP: "cp36-* cp37-* cp38-* cp312-* pp* *i686 *musllinux*"
+ # Skip CPython 3.6, 3.7, 3.8, 3.12, 3.13, PyPy, 32-bit, and musl
+ CIBW_SKIP: "cp36-* cp37-* cp38-* cp312-* cp313-* pp* *i686 *musllinux*"
- uses: actions/upload-artifact@v3
with:
diff --git a/.github/workflows/unit-tests-ci.yaml b/.github/workflows/unit-tests-ci.yaml
index 79aa4057..39793f49 100644
--- a/.github/workflows/unit-tests-ci.yaml
+++ b/.github/workflows/unit-tests-ci.yaml
@@ -17,7 +17,7 @@ jobs:
strategy:
matrix:
os: [ubuntu-latest, macOS-latest]
- python-version: ['3.9', '3.10', '3.11', '3.12']
+ python-version: ['3.9', '3.10', '3.11', '3.12', '3.13']
# mpi: [ 'mpich', 'openmpi', 'intelmpi']
# mpi: ['openmpi']
diff --git a/tox.ini b/tox.ini
index 741c5327..a1ee38f3 100644
--- a/tox.ini
+++ b/tox.ini
@@ -24,6 +24,7 @@ envlist =
py310
py311
py312
+ py313
[testenv]
allowlist_externals =
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