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Add support for numpy 2 #1114

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merged 5 commits into from
Jan 30, 2025
Merged

Add support for numpy 2 #1114

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5d80a90
Fix fail message for multiple matches
AlanPearl Jan 27, 2025
ed4fcbb
Numpy 1 -> 2
AlanPearl Jan 27, 2025
f8529d6
Require python>=3.11
aphearin Jan 30, 2025
4ae50fe
Drop python 3.10 in ci workflows
aphearin Jan 30, 2025
15ce02d
Update rtd build env to 3.11 [skip ci]
aphearin Jan 30, 2025
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2 changes: 1 addition & 1 deletion halotools/empirical_models/occupation_models/tinker13_components.py
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Original file line number Diff line number Diff line change
Expand Up @@ -237,7 +237,7 @@ def mean_occupation(self, **kwargs):
"you must pass both ``prim_haloprop`` and ``sfr_designation`` keyword arguments"
)
raise HalotoolsError(msg)
if type(sfr_designation[0]) in (str, unicode, np.string_, np.unicode_):
if type(sfr_designation[0]) in (str, unicode, np.bytes_, np.str_):
if sfr_designation[0] not in ["active", "quiescent"]:
msg = (
"The only acceptable values of "
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4 changes: 2 additions & 2 deletions halotools/mock_observables/pair_counters/cpairs/pairwise_distance_3d_engine.pyx
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Expand Up @@ -70,8 +70,8 @@ def pairwise_distance_3d_engine(double_mesh, x1in, y1in, z1in, x2in, y2in, z2in,
cdef cnp.float64_t[:] y2 = np.ascontiguousarray(y2in[double_mesh.mesh2.idx_sorted], dtype=np.float64)
cdef cnp.float64_t[:] z2 = np.ascontiguousarray(z2in[double_mesh.mesh2.idx_sorted], dtype=np.float64)

cdef vector[cnp.int_t] i_ind
cdef vector[cnp.int_t] j_ind
cdef vector[cnp.int64_t] i_ind
cdef vector[cnp.int64_t] j_ind
cdef vector[cnp.float64_t] distances

cdef cnp.int64_t icell1, icell2
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4 changes: 2 additions & 2 deletions halotools/mock_observables/pair_counters/cpairs/pairwise_distance_xy_z_engine.pyx
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Expand Up @@ -78,8 +78,8 @@ def pairwise_distance_xy_z_engine(double_mesh, x1in, y1in, z1in, x2in, y2in, z2i
cdef cnp.float64_t[:] y2 = np.ascontiguousarray(y2in[double_mesh.mesh2.idx_sorted], dtype=np.float64)
cdef cnp.float64_t[:] z2 = np.ascontiguousarray(z2in[double_mesh.mesh2.idx_sorted], dtype=np.float64)

cdef vector[cnp.int_t] i_ind
cdef vector[cnp.int_t] j_ind
cdef vector[cnp.int64_t] i_ind
cdef vector[cnp.int64_t] j_ind
cdef vector[cnp.float64_t] rp_distances
cdef vector[cnp.float64_t] pi_distances

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18 changes: 9 additions & 9 deletions halotools/mock_observables/pair_counters/cpairs/pairwise_distances.pyx
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Expand Up @@ -87,11 +87,11 @@ def pairwise_distance_no_pbc(np.ndarray[np.float64_t, ndim=1] x_icell1,
"""

#c definitions
cdef vector[np.int_t] i_ind
cdef vector[np.int_t] j_ind
cdef vector[np.int64_t] i_ind
cdef vector[np.int64_t] j_ind
cdef vector[np.float64_t] distances
cdef double d
cdef np.int_t i, j, n
cdef np.int64_t i, j, n
cdef int Ni = len(x_icell1)
cdef int Nj = len(x_icell2)

Expand Down Expand Up @@ -195,8 +195,8 @@ def pairwise_distance_pbc(np.ndarray[np.float64_t, ndim=1] x_icell1,
"""

#c definitions
cdef vector[np.int_t] i_ind
cdef vector[np.int_t] j_ind
cdef vector[np.int64_t] i_ind
cdef vector[np.int64_t] j_ind
cdef vector[np.float64_t] distances
cdef double d
cdef int i, j, n
Expand Down Expand Up @@ -307,8 +307,8 @@ def pairwise_xy_z_distance_no_pbc(


#c definitions
cdef vector[np.int_t] i_ind
cdef vector[np.int_t] j_ind
cdef vector[np.int64_t] i_ind
cdef vector[np.int64_t] j_ind
cdef vector[np.float64_t] para_distances
cdef vector[np.float64_t] perp_distances
cdef double d_perp, d_para
Expand Down Expand Up @@ -429,8 +429,8 @@ def pairwise_xy_z_distance_pbc(
"""

#c definitions
cdef vector[np.int_t] i_ind
cdef vector[np.int_t] j_ind
cdef vector[np.int64_t] i_ind
cdef vector[np.int64_t] j_ind
cdef vector[np.float64_t] para_distances
cdef vector[np.float64_t] perp_distances
cdef double d_perp, d_para
Expand Down
14 changes: 7 additions & 7 deletions halotools/mock_observables/pair_counters/marked_cpairs/conditional_pairwise_distances.pyx
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Expand Up @@ -30,7 +30,7 @@ def conditional_pairwise_distance_no_pbc(np.ndarray[np.float64_t, ndim=1] x_icel
np.float64_t max_r,
np.ndarray[np.float64_t, ndim=2] w_icell1,
np.ndarray[np.float64_t, ndim=2] w_icell2,
np.int_t cond_func_id):
np.int64_t cond_func_id):

"""
Calculate the conditional limited pairwise distance matrix, :math:`d_{ij}`.
Expand Down Expand Up @@ -101,11 +101,11 @@ def conditional_pairwise_distance_no_pbc(np.ndarray[np.float64_t, ndim=1] x_icel
"""

#c definitions
cdef vector[np.int_t] i_ind
cdef vector[np.int_t] j_ind
cdef vector[np.int64_t] i_ind
cdef vector[np.int64_t] j_ind
cdef vector[np.float64_t] distances
cdef double d
cdef np.int_t i, j, n
cdef np.int64_t i, j, n
cdef int Ni = len(x_icell1)
cdef int Nj = len(x_icell2)

Expand Down Expand Up @@ -149,7 +149,7 @@ def conditional_pairwise_xy_z_distance_no_pbc(np.ndarray[np.float64_t, ndim=1] x
np.float64_t max_rp, np.float64_t max_pi,
np.ndarray[np.float64_t, ndim=2] w_icell1,
np.ndarray[np.float64_t, ndim=2] w_icell2,
np.int_t cond_func_id):
np.int64_t cond_func_id):
"""
Calculate the conditional limited pairwise distance matrices, :math:`d_{{\perp}ij}` and :math:`d_{{\parallel}ij}`.

Expand Down Expand Up @@ -228,8 +228,8 @@ def conditional_pairwise_xy_z_distance_no_pbc(np.ndarray[np.float64_t, ndim=1] x


#c definitions
cdef vector[np.int_t] i_ind
cdef vector[np.int_t] j_ind
cdef vector[np.int64_t] i_ind
cdef vector[np.int64_t] j_ind
cdef vector[np.float64_t] para_distances
cdef vector[np.float64_t] perp_distances
cdef double d_perp, d_para
Expand Down
8 changes: 4 additions & 4 deletions halotools/sim_manager/cached_halo_catalog.py
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Expand Up @@ -395,11 +395,11 @@ def _retrieve_matching_ptcl_cache_log_entry(self):
else:
msg += "redshift = ``" + str(self.redshift) + "``\n"

msg += ("\nThere is no matching catalog in cache "
"within dz_tol = "+str(self._dz_tol)+" of these inputs.\n"
)

if len(matching_entries) == 0:
msg += (
"\nThere is no matching catalog in cache "
"within dz_tol = " + str(self._dz_tol) + " of these inputs.\n"
)
suggestion_preamble = ("\nThe following entries in the cache log "
"most closely match your inputs:\n\n")
alt_list1 = list(gen1) # discard the redshift requirement
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16 changes: 8 additions & 8 deletions halotools/sim_manager/rockstar_hlist_reader.py
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Expand Up @@ -708,22 +708,22 @@ def _write_metadata(self):

# Now add the metadata
f = h5py.File(self.output_fname, 'a')
f.attrs.create('simname', np.string_(self.simname))
f.attrs.create('halo_finder', np.string_(self.halo_finder))
redshift_string = np.string_(get_redshift_string(self.redshift))
f.attrs.create('simname', np.bytes_(self.simname))
f.attrs.create('halo_finder', np.bytes_(self.halo_finder))
redshift_string = np.bytes_(get_redshift_string(self.redshift))
f.attrs.create('redshift', redshift_string)
f.attrs.create('version_name', np.string_(self.version_name))
f.attrs.create('fname', np.string_(self.output_fname))
f.attrs.create('version_name', np.bytes_(self.version_name))
f.attrs.create('fname', np.bytes_(self.output_fname))

f.attrs.create('Lbox', self.Lbox)
f.attrs.create('particle_mass', self.particle_mass)
f.attrs.create('orig_ascii_fname', np.string_(self.input_fname))
f.attrs.create('orig_ascii_fname', np.bytes_(self.input_fname))

time_right_now = np.string_(datetime.datetime.now().strftime('%Y-%m-%d %H:%M:%S'))
time_right_now = np.bytes_(datetime.datetime.now().strftime('%Y-%m-%d %H:%M:%S'))
f.attrs.create('time_of_catalog_production', time_right_now)

if self.processing_notes is not None:
f.attrs.create('processing_notes', np.string_(self.processing_notes))
f.attrs.create('processing_notes', np.bytes_(self.processing_notes))

# Store all the choices for row cuts as metadata
for haloprop_key, cut_value in self.row_cut_min_dict.items():
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16 changes: 8 additions & 8 deletions halotools/sim_manager/user_supplied_halo_catalog.py
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Expand Up @@ -415,24 +415,24 @@ def add_halocat_to_cache(self,

redshift_string = get_redshift_string(self.redshift)

f.attrs.create('simname', np.string_(simname))
f.attrs.create('halo_finder', np.string_(halo_finder))
f.attrs.create('version_name', np.string_(version_name))
f.attrs.create('redshift', np.string_(redshift_string))
f.attrs.create('fname', np.string_(fname))
f.attrs.create('simname', np.bytes_(simname))
f.attrs.create('halo_finder', np.bytes_(halo_finder))
f.attrs.create('version_name', np.bytes_(version_name))
f.attrs.create('redshift', np.bytes_(redshift_string))
f.attrs.create('fname', np.bytes_(fname))

f.attrs.create('Lbox', self.Lbox)
f.attrs.create('particle_mass', self.particle_mass)

time_right_now = datetime.datetime.now().strftime(
'%Y-%m-%d %H:%M:%S')

f.attrs.create('time_catalog_was_originally_cached', np.string_(time_right_now))
f.attrs.create('time_catalog_was_originally_cached', np.bytes_(time_right_now))

f.attrs.create('processing_notes', np.string_(processing_notes))
f.attrs.create('processing_notes', np.bytes_(processing_notes))

for key, value in additional_metadata.items():
f.attrs.create(key, np.string_(value))
f.attrs.create(key, np.bytes_(value))

f.close()
############################################################
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12 changes: 6 additions & 6 deletions halotools/sim_manager/user_supplied_ptcl_catalog.py
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Expand Up @@ -300,19 +300,19 @@ def add_ptclcat_to_cache(self, fname, simname, version_name,

redshift_string = get_redshift_string(self.redshift)

f.attrs.create('simname', np.string_(simname))
f.attrs.create('version_name', np.string_(version_name))
f.attrs.create('redshift', np.string_(redshift_string))
f.attrs.create('fname', np.string_(fname))
f.attrs.create('simname', np.bytes_(simname))
f.attrs.create('version_name', np.bytes_(version_name))
f.attrs.create('redshift', np.bytes_(redshift_string))
f.attrs.create('fname', np.bytes_(fname))

f.attrs.create('Lbox', self.Lbox)
f.attrs.create('particle_mass', self.particle_mass)

time_right_now = datetime.datetime.now().strftime(
'%Y-%m-%d %H:%M:%S')
f.attrs.create('time_catalog_was_originally_cached', np.string_(time_right_now))
f.attrs.create('time_catalog_was_originally_cached', np.bytes_(time_right_now))

f.attrs.create('processing_notes', np.string_(processing_notes))
f.attrs.create('processing_notes', np.bytes_(processing_notes))

f.close()

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4 changes: 2 additions & 2 deletions pyproject.toml
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Expand Up @@ -51,8 +51,8 @@ markers = ["slow", "installation_test"]
requires = ["setuptools>=42.0.0",
"setuptools_scm",
"wheel",
"oldest-supported-numpy",
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@bsipocz this PR led by @AlanPearl establishes compatibility between halotools and numpy 2.0. However, I'm not sure about this particular line of code because I never really understood what using oldest-supported-numpy did. But this PR fails unless this line is changed to numpy>=2.0.

On a possibly related note, I'm also not sure whether any additional changes need to be made in order to properly use extension-helpers in the right way.

"cython==3.0.2",
"numpy>=2.0",
"cython>=3.0.2",
"extension-helpers==1.*"]
build-backend = 'setuptools.build_meta'

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2 changes: 1 addition & 1 deletion requirements.txt
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@@ -1,5 +1,5 @@
astropy
numpy<2
numpy
scipy
requests
beautifulsoup4
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