From 84c363fe1a04a458510cd774e8d3fcc57ced16fa Mon Sep 17 00:00:00 2001
From: Jared Lumpe <jared@jaredlumpe.com>
Date: Sat, 3 Aug 2024 23:22:29 -0700
Subject: [PATCH] Remove Cython dependency on Numpy

---
 pyproject.toml                 |  3 ---
 setup.py                       |  3 ---
 src/gambit/_cython/kmers.pxd   |  8 +++----
 src/gambit/_cython/kmers.pyx   | 14 ++++++-------
 src/gambit/_cython/metric.pxd  |  1 +
 src/gambit/_cython/metric.pyx  | 17 +++++----------
 src/gambit/_cython/threads.pyx | 38 +++++++++++++++++++++++++---------
 src/gambit/_cython/types.pxd   | 31 +++++++++++++--------------
 src/gambit/metric.py           | 11 +++++++---
 src/gambit/sigs/__init__.py    |  2 +-
 src/gambit/sigs/base.py        |  7 ++++++-
 src/gambit/sigs/hdf5.py        |  3 +--
 tests/test_metric.py           |  4 ++--
 13 files changed, 79 insertions(+), 63 deletions(-)

diff --git a/pyproject.toml b/pyproject.toml
index a040ee9..b685eb4 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -3,8 +3,5 @@ requires = [
     "setuptools",
     "wheel",
     "Cython >= 3.0",
-    # If the Numpy version is different at runtime than build time, the build version should be
-    # lower as the ABI is forward- but not backwards-compatible.
-    "oldest-supported-numpy",
 ]
 build-backend = "setuptools.build_meta"
diff --git a/setup.py b/setup.py
index 01bbbad..de06f94 100644
--- a/setup.py
+++ b/setup.py
@@ -3,15 +3,12 @@
 from setuptools import setup
 from distutils.extension import Extension
 from Cython.Build import cythonize
-import numpy
 
 
 # Cython extensions
-np_include = numpy.get_include()
 extensions = [Extension(
 	'gambit._cython.*',
 	['src/gambit/_cython/*.pyx'],
-	include_dirs=[np_include],
 	extra_compile_args=['-fopenmp', '-Wno-sign-compare'],
 	extra_link_args=['-fopenmp'],
 )]
diff --git a/src/gambit/_cython/kmers.pxd b/src/gambit/_cython/kmers.pxd
index 87dcfab..c3f57be 100644
--- a/src/gambit/_cython/kmers.pxd
+++ b/src/gambit/_cython/kmers.pxd
@@ -1,9 +1,9 @@
-cimport numpy as np
+from libc.stdint cimport uint64_t, intptr_t
 
 ctypedef unsigned char CHAR
 
 
-cdef np.uint64_t c_kmer_to_index(const CHAR[:], bint*) nogil
-cdef np.uint64_t c_kmer_to_index_rc(const CHAR[:], bint*) nogil
-cdef void c_index_to_kmer(np.uint64_t, CHAR[:]) nogil
+cdef uint64_t c_kmer_to_index(const CHAR[:], bint*) nogil
+cdef uint64_t c_kmer_to_index_rc(const CHAR[:], bint*) nogil
+cdef void c_index_to_kmer(uint64_t, CHAR[:]) nogil
 cdef void c_revcomp(const CHAR[:], CHAR[:]) nogil
diff --git a/src/gambit/_cython/kmers.pyx b/src/gambit/_cython/kmers.pyx
index 3dacc70..022853d 100644
--- a/src/gambit/_cython/kmers.pyx
+++ b/src/gambit/_cython/kmers.pyx
@@ -14,7 +14,7 @@ def kmer_to_index(const CHAR[:] kmer):
 	Convert k-mer byte string to its integer index.
 	"""
 	cdef:
-		np.uint64_t idx
+		uint64_t idx
 		bint exc = False
 
 	if kmer.shape[0] > 32:
@@ -28,9 +28,9 @@ def kmer_to_index(const CHAR[:] kmer):
 	return idx
 
 
-cdef np.uint64_t c_kmer_to_index(const CHAR[:] kmer, bint *exc) nogil:
+cdef uint64_t c_kmer_to_index(const CHAR[:] kmer, bint *exc) nogil:
 	cdef:
-		np.uint64_t idx = 0
+		uint64_t idx = 0
 		int i, k = kmer.shape[0]
 		CHAR nuc
 
@@ -61,7 +61,7 @@ def kmer_to_index_rc(const CHAR[:] kmer):
 	Get the integer index of the reverse complement of a k-mer byte string.
 	"""
 	cdef:
-		np.uint64_t idx
+		uint64_t idx
 		bint exc = False
 
 	if kmer.shape[0] > 32:
@@ -75,9 +75,9 @@ def kmer_to_index_rc(const CHAR[:] kmer):
 	return idx
 
 
-cdef np.uint64_t c_kmer_to_index_rc(const CHAR[:] kmer, bint *exc) nogil:
+cdef uint64_t c_kmer_to_index_rc(const CHAR[:] kmer, bint *exc) nogil:
 	cdef:
-		np.uint64_t idx = 0
+		uint64_t idx = 0
 		int i, k = kmer.shape[0]
 		CHAR nuc
 
@@ -112,7 +112,7 @@ def index_to_kmer(index, int k):
 	return bytes(buf)
 
 
-cdef void c_index_to_kmer(np.uint64_t index, CHAR[:] out) nogil:
+cdef void c_index_to_kmer(uint64_t index, CHAR[:] out) nogil:
 	"""Convert k-mer index to sequence."""
 	cdef:
 		int k = out.shape[0]
diff --git a/src/gambit/_cython/metric.pxd b/src/gambit/_cython/metric.pxd
index 62d3f8e..125ec64 100644
--- a/src/gambit/_cython/metric.pxd
+++ b/src/gambit/_cython/metric.pxd
@@ -1,3 +1,4 @@
+from libc.stdint cimport intptr_t
 from .types cimport SCORE_T, BOUNDS_T, COORDS_T, COORDS_T_2
 
 cdef SCORE_T c_jaccarddist(COORDS_T[:] coords1, COORDS_T_2[:] coords2) nogil
diff --git a/src/gambit/_cython/metric.pyx b/src/gambit/_cython/metric.pyx
index caebced..45f9074 100644
--- a/src/gambit/_cython/metric.pyx
+++ b/src/gambit/_cython/metric.pyx
@@ -1,15 +1,8 @@
 """Cython functions for calculating k-mer distance metrics"""
 
-cimport numpy as np
-import numpy as np
 from cython.parallel import prange, parallel
 
 
-# Numpy dtypes equivalent to SCORE_T and BOUNDS_T
-SCORE_DTYPE = np.dtype(np.float32)
-BOUNDS_DTYPE = np.dtype(np.intp)
-
-
 def jaccard(COORDS_T[:] coords1, COORDS_T_2[:] coords2):
 	"""Compute the Jaccard index between two k-mer sets in sparse coordinate format.
 
@@ -76,15 +69,15 @@ cdef SCORE_T c_jaccarddist(COORDS_T[:] coords1, COORDS_T_2[:] coords2) nogil:
 
 	cdef:
 		# Lengths of the two arrays
-		np.intp_t N = coords1.shape[0]
-		np.intp_t M = coords2.shape[0]
+		intptr_t N = coords1.shape[0]
+		intptr_t M = coords2.shape[0]
 
 		# Index and value of items in each array as we are iterating
-		np.intp_t i = 0, j = 0
+		intptr_t i = 0, j = 0
 		COORDS_T a
 		COORDS_T_2 b
 
-		np.intp_t u = 0  # Size of union
+		intptr_t u = 0  # Size of union
 
 	# Iterate through both arrays simultaneously, advance index for the array
 	# with the smaller value. Advance both if they are equal. Increment the
@@ -136,7 +129,7 @@ def _jaccarddist_parallel(COORDS_T[:] query, COORDS_T_2[:] ref_coords, BOUNDS_T[
 	out : numpy.ndarray
 		Pre-allocated array to write distances to.
 	"""
-	cdef np.intp_t N = ref_bounds.shape[0] - 1
+	cdef intptr_t N = ref_bounds.shape[0] - 1
 	cdef BOUNDS_T begin, end
 	cdef int i
 
diff --git a/src/gambit/_cython/threads.pyx b/src/gambit/_cython/threads.pyx
index dd3c49d..d663efa 100644
--- a/src/gambit/_cython/threads.pyx
+++ b/src/gambit/_cython/threads.pyx
@@ -1,9 +1,10 @@
 """OpenMP stuff."""
 
 from cython import parallel
+import array
 
-import numpy as np
-cimport numpy as np
+cimport cython
+from cpython cimport array
 cimport openmp
 
 
@@ -25,18 +26,35 @@ def omp_get_max_threads():
 	return openmp.omp_get_max_threads()
 
 
-def get_thread_ids(int num_threads):
-	"""Run a multithreaded loop and get the thread ID running in each iteration."""
+@cython.boundscheck(True)
+def get_thread_ids(int n):
+	"""Run a multithreaded loop and get the thread ID running in each iteration.
+
+	Used to check that Cython code parallelization is working correctly. Result should contain
+	integers from 0 to ``num_threads``, repeated up to length ``n``.
+
+	Parameters
+	----------
+	n: int
+		Size of loop. Make this at least as large as the expected number of threads.
+
+	Returns
+	-------
+	array.array
+		Array of size ``n`` containing the thread ID running in each loop iteration.
+	"""
 
 	cdef:
-		np.ndarray[np.intp_t, ndim=1] thread_ids
-		np.intp_t thread_id = -1
+		array.array thread_ids_arr = array.array('i')
+		int[:] thread_ids
 		int i
 
-	thread_ids = np.full(num_threads, -1, dtype=np.intp)
+	for i in range(n):
+		thread_ids_arr.append(-1)
+
+	thread_ids = thread_ids_arr
 
-	for i in parallel.prange(num_threads, nogil=True, schedule='static', chunksize=1):
-		thread_id = parallel.threadid()
-		thread_ids[i] = thread_id
+	for i in parallel.prange(n, nogil=True, schedule='static', chunksize=1):
+		thread_ids[i] = parallel.threadid()
 
 	return thread_ids
diff --git a/src/gambit/_cython/types.pxd b/src/gambit/_cython/types.pxd
index 56992bb..43e9ad7 100644
--- a/src/gambit/_cython/types.pxd
+++ b/src/gambit/_cython/types.pxd
@@ -1,28 +1,29 @@
 """Shared typedefs."""
 
-cimport numpy as np
+from libc.stdint cimport int16_t, uint16_t, int32_t, uint32_t, int64_t, uint64_t, intptr_t
 
 
 # Type for similarity scores
-ctypedef np.float32_t SCORE_T
+ctypedef float SCORE_T
 
 # Type for bounds on c_jaccard_coords_col
-ctypedef np.intp_t BOUNDS_T
+# This should be equal to Numpy's intp dtype
+ctypedef intptr_t BOUNDS_T
 
 # Fused type for storing k-mer coordinates/indices
 ctypedef fused COORDS_T:
-	np.int16_t
-	np.uint16_t
-	np.int32_t
-	np.uint32_t
-	np.int64_t
-	np.uint64_t
+	int16_t
+	uint16_t
+	int32_t
+	uint32_t
+	int64_t
+	uint64_t
 
 # Copy of COORDS_T, used when two arguments have types in this set but may be different than each other.
 ctypedef fused COORDS_T_2:
-	np.int16_t
-	np.uint16_t
-	np.int32_t
-	np.uint32_t
-	np.int64_t
-	np.uint64_t
+	int16_t
+	uint16_t
+	int32_t
+	uint32_t
+	int64_t
+	uint64_t
diff --git a/src/gambit/metric.py b/src/gambit/metric.py
index 2b0f292..b7027c3 100644
--- a/src/gambit/metric.py
+++ b/src/gambit/metric.py
@@ -5,13 +5,18 @@
 
 import numpy as np
 
-from gambit._cython.metric import BOUNDS_DTYPE, SCORE_DTYPE, jaccard, jaccarddist, \
-	_jaccarddist_parallel
-from gambit.sigs.base import KmerSignature, SignatureArray, AbstractSignatureArray, SignatureList
+from gambit._cython.metric import jaccard, jaccarddist, _jaccarddist_parallel
+from gambit.sigs.base import KmerSignature, SignatureArray, AbstractSignatureArray, SignatureList, \
+	BOUNDS_DTYPE
 from gambit.util.misc import chunk_slices
 from gambit.util.progress import get_progress
 
 
+#: Numpy dtype for output of Cython Jaccard distance calculation code
+# Equivalent to SCORE_T in types.pxd
+SCORE_DTYPE = np.dtype(np.float32)
+
+
 def jaccard_generic(set1: Iterable, set2: Iterable) -> float:
 	"""Get the Jaccard index of of two arbitrary sets.
 
diff --git a/src/gambit/sigs/__init__.py b/src/gambit/sigs/__init__.py
index 017470b..fd43484 100644
--- a/src/gambit/sigs/__init__.py
+++ b/src/gambit/sigs/__init__.py
@@ -1,4 +1,4 @@
 """Calculate and store collections of k-mer signatures."""
 
 from .base import KmerSignature, SignatureArray, SignatureList, sigarray_eq, SignaturesMeta,\
-	AnnotatedSignatures, dump_signatures, load_signatures
+	AnnotatedSignatures, dump_signatures, load_signatures, BOUNDS_DTYPE
diff --git a/src/gambit/sigs/base.py b/src/gambit/sigs/base.py
index 5ca383c..0712edf 100644
--- a/src/gambit/sigs/base.py
+++ b/src/gambit/sigs/base.py
@@ -5,7 +5,6 @@
 from attr import attrs, attrib
 
 from gambit.kmers import KmerSpec
-from gambit._cython.metric import BOUNDS_DTYPE
 from gambit.util.indexing import AdvancedIndexingMixin
 from gambit.util.io import FilePath
 
@@ -15,6 +14,12 @@
 # TODO - use nptyping package to specify dimensions and data type?
 
 
+#: Preferred Numpy dtype for :attr:`.ConcatenatedSignatureArray.bounds`. Can be used in parallelized
+#: Cython metric calculation code without conversion.
+# Equivalent to BOUNDS_T in types.pxd
+BOUNDS_DTYPE = np.dtype(np.intp)
+
+
 def sigarray_eq(a1: Sequence[KmerSignature], a2: Sequence[KmerSignature]) -> bool:
 	"""Check two sequences of sparse k-mer signatures for equality.
 
diff --git a/src/gambit/sigs/hdf5.py b/src/gambit/sigs/hdf5.py
index c095f40..b52f9da 100644
--- a/src/gambit/sigs/hdf5.py
+++ b/src/gambit/sigs/hdf5.py
@@ -7,9 +7,8 @@
 import h5py as h5
 
 from .base import SignatureArray, ConcatenatedSignatureArray, AbstractSignatureArray, SignaturesMeta,\
-	ReferenceSignatures, SignaturesFileError
+	ReferenceSignatures, SignaturesFileError, BOUNDS_DTYPE
 from gambit.kmers import KmerSpec
-from gambit._cython.metric import BOUNDS_DTYPE
 from gambit.util.io import FilePath
 
 
diff --git a/tests/test_metric.py b/tests/test_metric.py
index 25b775d..1b16e1b 100644
--- a/tests/test_metric.py
+++ b/tests/test_metric.py
@@ -6,9 +6,9 @@
 import numpy as np
 
 from gambit.metric import jaccard, jaccarddist, jaccard_bits, jaccard_generic, jaccarddist_array, \
-	jaccarddist_matrix, jaccarddist_pairwise, num_pairs, SCORE_DTYPE, BOUNDS_DTYPE
+	jaccarddist_matrix, jaccarddist_pairwise, num_pairs, SCORE_DTYPE
 from gambit.sigs.calc import sparse_to_dense
-from gambit.sigs import SignatureArray, SignatureList, dump_signatures, load_signatures
+from gambit.sigs import SignatureArray, SignatureList, dump_signatures, load_signatures, BOUNDS_DTYPE
 from gambit.kmers import KmerSpec
 from gambit.util.progress import check_progress
 from .common import make_signatures