initial import

README.md

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+# GLMath
+

ext_src/_cosmomath.pyx

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+#cython: language_level=3
+import numpy as np
+cimport numpy as np
+
+np.import_array()
+np.import_ufunc()
+
+cdef extern from "sys/types.h":
+   ctypedef np.int64_t int64_t
+
+cdef extern from "numpy/npy_common.h":
+   ctypedef npy_intp
+
+cdef extern from "special_math.hpp" namespace "CosmoTool":
+   T log_modified_bessel_first_kind[T](T v, T z) except + nogil
+
+cdef extern from "numpy_adaptors.hpp" namespace "CosmoTool":
+   void parallel_ufunc_dd_d[T,IT](char **args, IT* dimensions, IT* steps, void *func)
+
+
+cdef np.PyUFuncGenericFunction loop_func[1]
+cdef char input_output_types[3]
+cdef void *elementwise_funcs[1]
+
+loop_func[0] = <np.PyUFuncGenericFunction>parallel_ufunc_dd_d[double,npy_intp]
+
+input_output_types[0] = np.NPY_DOUBLE
+input_output_types[1] = np.NPY_DOUBLE
+input_output_types[2] = np.NPY_DOUBLE
+
+elementwise_funcs[0] = <void*>log_modified_bessel_first_kind[double]
+
+log_modified_I = np.PyUFunc_FromFuncAndData(
+    loop_func,
+    elementwise_funcs,
+    input_output_types,
+    1, # number of supported input types
+    2, # number of input args
+    1, # number of output args
+    0, # `identity` element, never mind this
+    "log_modified_bessel_first_kind", # function name
+    "log_modified_bessel_first_kind(v: Float, z: Float) -> Float", # docstring
+    0 # unused
+    )
+

ext_src/numpy_adaptors.hpp

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+#ifndef __COSMOTOOL_NUMPY_ADAPTOR_HPP
+#define __COSMOTOOL_NUMPY_ADAPTOR_HPP
+
+namespace CosmoTool {
+
+  template<typename T, typename IT>
+  void parallel_ufunc_dd_d(char **args, IT* dimensions, IT* steps, void *func) {
+    IT i;
+    IT n = dimensions[0];
+    char *in = args[0], *in2 = args[1], *out = args[2];
+    IT in_step = steps[0], in2_step = steps[1], out_step = steps[2];
+
+    double tmp;
+    typedef double (*F_t)(double,double);
+
+    F_t f = (F_t)func;
+
+#pragma omp parallel for schedule(static)
+    for (i = 0; i < n; i++) {
+        T *out_t = (T *)(out + i * out_step);
+        T *in_t = (T *)(in + i * in_step);
+        T *in2_t = (T *)(in2 + i * in2_step);
+        *out_t = f(*in_t, *in2_t);
+    }
+  }
+
+
+}
+
+#endif

ext_src/special_math.hpp

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+// Original code derived from Boost and is distributed here
+// under the Boost license (licenses/boost-license.txt)
+//    Copyright (c) 2006 Xiaogang Zhang
+//    Copyright (c) 2007, 2017 John Maddock
+// Secondary code copyright by its author and is distributed here
+// under the BSD-3 license (LICENSE.md). Derived from
+// stan/math/prim/fun/log_modified_bessel_first_kind.hpp
+
+#ifndef __COSMOTOOL_SPECIAL_MATH_HPP
+#define __COSMOTOOL_SPECIAL_MATH_HPP
+
+#include "algo.hpp"
+#include <boost/math/constants/constants.hpp>
+#include <boost/math/tools/rational.hpp>
+#include <cmath>
+#include <limits>
+
+// Taken and adapted from
+// https://github.com/stan-dev/math/blob/develop/stan/math/prim/fun/log_modified_bessel_first_kind.hpp
+
+namespace CosmoTool {
+
+template <typename T> T log1p_exp(T x) {
+  if (x > T(0)) {
+    return x + std::log1p(std::exp(-x));
+  }
+  return std::log1p(std::exp(x));
+}
+
+template <typename T> T multiply_log(T a, T b) {
+  if (a == 0 && b == 0)
+    return 0;
+  return a * std::log(b);
+}
+
+template <typename T> T inf() { return std::numeric_limits<T>::infinity(); }
+
+template <typename T> T log_sum_exp(T const a, T const b) {
+  if (a == -inf<T>()) {
+    return b;
+  }
+  if (a == inf<T>() && b == inf<T>()) {
+    return inf<T>();
+  }
+  if (a > b) {
+    return a + log1p_exp(b - a);
+  }
+  return b + log1p_exp(a - b);
+}
+
+/* Log of the modified Bessel function of the first kind,
+ * which is better known as the Bessel I function. See
+ * modified_bessel_first_kind.hpp for the function definition.
+ * The derivatives are known to be incorrect for v = 0 because a
+ * simple constant 0 is returned.
+ *
+ * @tparam T common type for calculation
+ * @param v Order, can be a non-integer but must be at least -1
+ * @param z Real non-negative number
+ * @throws std::domain_error if either v or z is NaN, z is
+ * negative, or v is less than -1
+ * @return log of Bessel I function
+ */
+template <typename T> T log_modified_bessel_first_kind(T const v, T const z) {
+  using boost::math::tools::evaluate_polynomial;
+  using std::log;
+  using std::pow;
+  using std::sqrt;
+  static const double LOG_TWO = std::log(2.0);
+  static const double EPSILON = std::numeric_limits<double>::epsilon();
+  static const double TWO_PI = 2.0 * boost::math::constants::pi<double>();
+
+  if (z == 0) {
+    if (v == 0) {
+      return 0.0;
+    }
+    if (v > 0) {
+      return -std::numeric_limits<T>::infinity();
+    }
+    return std::numeric_limits<T>::infinity();
+  }
+  if (std::isinf(z)) {
+    return z;
+  }
+  if (v == 0) {
+    // Modified Bessel function of the first kind of order zero
+    // we use the approximating forms derived in:
+    // "Rational Approximations for the Modified Bessel Function of the
+    // First Kind -- I0(x) for Computations with Double Precision"
+    // by Pavel Holoborodko, see
+    // http://www.advanpix.com/2015/11/11/rational-approximations-for-the-modified-bessel-function-of-the-first-kind-i0-computations-double-precision
+    // The actual coefficients used are [Boost's] own, and extend
+    // Pavel's work to precisions other than double.
+
+    if (z < 7.75) {
+      // Bessel I0 over[10 ^ -16, 7.75]
+      // Max error in interpolated form : 3.042e-18
+      // Max Error found at double precision = Poly : 5.106609e-16
+      //                                       Cheb : 5.239199e-16
+      static const double P[] = {
+          1.00000000000000000e+00, 2.49999999999999909e-01,
+          2.77777777777782257e-02, 1.73611111111023792e-03,
+          6.94444444453352521e-05, 1.92901234513219920e-06,
+          3.93675991102510739e-08, 6.15118672704439289e-10,
+          7.59407002058973446e-12, 7.59389793369836367e-14,
+          6.27767773636292611e-16, 4.34709704153272287e-18,
+          2.63417742690109154e-20, 1.13943037744822825e-22,
+          9.07926920085624812e-25};
+      return log1p_exp(multiply_log(2.0, z) - log(4.0) +
+                       log(evaluate_polynomial(P, 0.25 * square(z))));
+    }
+    if (z < 500) {
+      // Max error in interpolated form : 1.685e-16
+      // Max Error found at double precision = Poly : 2.575063e-16
+      //                                       Cheb : 2.247615e+00
+      static const double P[] = {
+          3.98942280401425088e-01,  4.98677850604961985e-02,
+          2.80506233928312623e-02,  2.92211225166047873e-02,
+          4.44207299493659561e-02,  1.30970574605856719e-01,
+          -3.35052280231727022e+00, 2.33025711583514727e+02,
+          -1.13366350697172355e+04, 4.24057674317867331e+05,
+          -1.23157028595698731e+07, 2.80231938155267516e+08,
+          -5.01883999713777929e+09, 7.08029243015109113e+10,
+          -7.84261082124811106e+11, 6.76825737854096565e+12,
+          -4.49034849696138065e+13, 2.24155239966958995e+14,
+          -8.13426467865659318e+14, 2.02391097391687777e+15,
+          -3.08675715295370878e+15, 2.17587543863819074e+15};
+      return z + log(evaluate_polynomial(P, 1 / z)) - multiply_log(0.5, z);
+    }
+    // Max error in interpolated form : 2.437e-18
+    // Max Error found at double precision = Poly : 1.216719e-16
+    static const double P[] = {3.98942280401432905e-01, 4.98677850491434560e-02,
+                               2.80506308916506102e-02, 2.92179096853915176e-02,
+                               4.53371208762579442e-02};
+    return z + log(evaluate_polynomial(P, 1 / z)) - multiply_log(0.5, z);
+  }
+  if (v == 1) { // WARNING: will not autodiff for v = 1 correctly
+    // modified from Boost's bessel_i1_imp in the double precision case
+    // see credits above in the v == 0 case
+    if (z < 7.75) {
+      // Bessel I0 over[10 ^ -16, 7.75]
+      // Max error in interpolated form: 5.639e-17
+      // Max Error found at double precision = Poly: 1.795559e-16
+
+      static const double P[] = {
+          8.333333333333333803e-02, 6.944444444444341983e-03,
+          3.472222222225921045e-04, 1.157407407354987232e-05,
+          2.755731926254790268e-07, 4.920949692800671435e-09,
+          6.834657311305621830e-11, 7.593969849687574339e-13,
+          6.904822652741917551e-15, 5.220157095351373194e-17,
+          3.410720494727771276e-19, 1.625212890947171108e-21,
+          1.332898928162290861e-23};
+      T a = square(z) * 0.25;
+      T Q[3] = {1, 0.5, evaluate_polynomial(P, a)};
+      return log(z) + log(evaluate_polynomial(Q, a)) - LOG_TWO;
+    }
+    if (z < 500) {
+      // Max error in interpolated form: 1.796e-16
+      // Max Error found at double precision = Poly: 2.898731e-16
+
+      static const double P[] = {
+          3.989422804014406054e-01,  -1.496033551613111533e-01,
+          -4.675104253598537322e-02, -4.090895951581637791e-02,
+          -5.719036414430205390e-02, -1.528189554374492735e-01,
+          3.458284470977172076e+00,  -2.426181371595021021e+02,
+          1.178785865993440669e+04,  -4.404655582443487334e+05,
+          1.277677779341446497e+07,  -2.903390398236656519e+08,
+          5.192386898222206474e+09,  -7.313784438967834057e+10,
+          8.087824484994859552e+11,  -6.967602516005787001e+12,
+          4.614040809616582764e+13,  -2.298849639457172489e+14,
+          8.325554073334618015e+14,  -2.067285045778906105e+15,
+          3.146401654361325073e+15,  -2.213318202179221945e+15};
+      return z + log(evaluate_polynomial(P, 1 / z)) - multiply_log(0.5, z);
+    }
+    // Max error in interpolated form: 1.320e-19
+    // Max Error found at double precision = Poly: 7.065357e-17
+    static const double P[] = {
+        3.989422804014314820e-01, -1.496033551467584157e-01,
+        -4.675105322571775911e-02, -4.090421597376992892e-02,
+        -5.843630344778927582e-02};
+    return z + log(evaluate_polynomial(P, 1 / z)) - multiply_log(0.5, z);
+  }
+  if (z > 100) {
+    // Boost does something like this in asymptotic_bessel_i_large_x
+    T lim = pow((square(v) + 2.5) / (2 * z), 3) / 24;
+    if (lim < (EPSILON * 10)) {
+      T s = 1;
+      T mu = 4 * square(v);
+      T ex = 8 * z;
+      T num = mu - 1;
+      T denom = ex;
+      s -= num / denom;
+      num *= mu - 9;
+      denom *= ex * 2;
+      s += num / denom;
+      num *= mu - 25;
+      denom *= ex * 3;
+      s -= num / denom;
+      s = z - log(sqrt(z * TWO_PI)) + log(s);
+      return s;
+    }
+  }
+
+  T log_half_z = log(0.5 * z);
+  T lgam = (v > -1) ? lgamma(v + 1.0) : 0;
+  T lcons = (2.0 + v) * log_half_z;
+  T out;
+  if (v > -1) {
+    out = log_sum_exp(v * log_half_z - lgam, lcons - lgamma(v + 2));
+    lgam += log1p(v);
+  } else {
+    out = lcons;
+  }
+
+  double m = 2;
+  double lfac = 0;
+  T old_out;
+  do {
+    lfac += log(m);
+    lgam += log(v + m);
+    lcons += 2 * log_half_z;
+    old_out = out;
+    out = log_sum_exp(out, lcons - lfac - lgam); // underflows eventually
+    m++;
+  } while (out > old_out || out < old_out);
+  return out;
+}
+
+} // namespace CosmoTool
+
+#endif

new_release.sh

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+semantic-release version --tag --changelog --vcs-release 

pyproject.toml

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+[project]
+version = "1.0.0"
+requires-python = ">= 3.8"
+name = "pysphereproj"
+dependencies = [
+  "numpy"
+]
+authors = [
+  { name = "Guilhem Lavaux", email = "guilhem.lavaux@iap.fr" }
+]
+readme = "README.md"
+classifiers = [
+  "Intended Audience :: Developers",
+  "License :: OSI Approved :: MIT License",
+  "Programming Language :: Python :: 3"
+]
+
+[project.urls]
+Homepage = "https://git.aquila-consortium.org/guilhem_lavaux/pysphereproj"
+Issues = "https://git.aquila-consortium.org/guilhem_lavaux/pysphereproj/issues"
+
+[build-system]
+requires = ["setuptools >= 61.0", "numpy", "wheel", "Cython", "python-semantic-release"]
+build-backend = "setuptools.build_meta"
+
+[tool.semantic_release]
+assets = []
+version_toml = [
+  "pyproject.toml:project.version",
+]
+version_variables = [
+  "src/sphereproj/__init__.py:__version__"
+]
+build_command_env = []
+commit_message = "{version}\n\nAutomatically generated by python-semantic-release"
+commit_parser = "angular"
+logging_use_named_masks = false
+major_on_zero = true
+allow_zero_version = true
+tag_format = "v{version}"
+
+[tool.semantic_release.branches.main]
+match = "(main|master)"
+prerelease_token = "rc"
+prerelease = false
+
+[tool.semantic_release.default_templates]
+template_dir = "templates"
+changelog_file = "CHANGELOG.md"
+exclude_commit_patterns = []
+
+[tool.semantic_release.changelog.environment]
+block_start_string = "{%"
+block_end_string = "%}"
+variable_start_string = "{{"
+variable_end_string = "}}"
+comment_start_string = "{#"
+comment_end_string = "#}"
+trim_blocks = false
+lstrip_blocks = false
+newline_sequence = "\n"
+keep_trailing_newline = false
+extensions = []
+autoescape = true
+
+[tool.semantic_release.commit_author]
+env = "GIT_COMMIT_AUTHOR"
+default = "semantic-release <semantic-release>"
+
+[tool.semantic_release.commit_parser_options]
+allowed_tags = ["build", "chore", "ci", "docs", "feat", "fix", "perf", "style", "refactor", "test"]
+minor_tags = ["feat"]
+patch_tags = ["fix", "perf"]
+default_bump_level = 0
+
+[tool.semantic_release.remote]
+name = "origin"
+type = "gitea"
+ignore_token_for_push = false
+insecure = false
+domain = "git.aquila-consortium.org"
+
+[tool.semantic_release.publish]
+dist_glob_patterns = ["dist/*"]
+upload_to_vcs_release = true
+
+

setup.py

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+from setuptools import setup, Extension
+from Cython.Build import cythonize
+import numpy
+
+extensions = [
+    Extension(
+        "glmath._cosmomath",
+        sources=[
+            "ext_src/_cosmomath.pyx"
+        ],
+        include_dirs=["ext_src", numpy.get_include()],
+        language="c++"
+    )
+]
+
+
+setup(ext_modules=cythonize(extensions))