Python 3.11 compatible versions of numba JIT-compiled functions (#20)

* update mean_angle for jit-compilation in 3.11

* add haversine dist test

* haversine dist is weird

* update test class names

* update changelog for 0.2.15

* update pyproject file

* add 3.11 to CI workflow

* use 3.8.1 as minimal Py version in CI

* drop 3.8 support !

* bump to 0.3.0 since dropped Python 3.8

* update lock

.github/workflows/python-package.yml

@@ -16,7 +16,7 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        python-version: ["3.8", "3.9", "3.10"]
+        python-version: ["3.9", "3.10", "3.11"]
 
     steps:
     - uses: actions/checkout@main

CHANGELOG.md

@@ -1,5 +1,9 @@
 # Changelog
 
+## v0.3.0 (2023-06-29)
+- Python 3.11 compatible versions of numba JIT-compiled functions
+- drop Python 3.8 support
+
 ## v0.2.14 (2023-04-17)
 - avgbinmap / mean_day_frac: bugfix corner case mean day fraction is almost zero but < 0
 - avgbinmap / add scipy based version of mean angle function

pyfuppes/avgbinmap.py

@@ -4,6 +4,7 @@
 from cmath import phase, rect
 from copy import deepcopy
 from math import degrees, radians
+from math import cos, sin, atan2, pi
 
 import numpy as np
 import pandas as pd
@@ -47,23 +48,29 @@ def mean_angle(deg):
 
 
 @njit
-def mean_angle_numba(deg):
+def mean_angle_numba(angles):
     """
-    Numba-compatible version of mean_angle().
+    mean_angle(), numba-JIT compiled.
 
     - input must be numpy array of type float!
+
+    C version: https://rosettacode.org/wiki/Averages/Mean_angle
     """
-    deg = deg[np.isfinite(deg)]
-    if len(deg) == 0:
+    angles = angles[np.isfinite(angles)]
+    if len(angles) == 0:
         return np.nan
-    elif len(deg) == 1:
-        return deg[0]
+    elif len(angles) == 1:
+        return angles[0]
+
+    size = len(angles)
+    y_part = 0.0
+    x_part = 0.0
 
-    result = 0
-    for d in deg:
-        result += rect(1, radians(d))
+    for i in range(size):
+        x_part += cos(angles[i] * pi / 180)
+        y_part += sin(angles[i] * pi / 180)
 
-    return degrees(phase(result / len(deg)))
+    return atan2(y_part / size, x_part / size) * 180 / pi
 
 
 ###############################################################################
@@ -194,7 +201,7 @@ def bin_t_10s(t, force_t_range=True, drop_empty=True):
 
 @njit
 def get_npnanmean(v):
-    """Njit'ed nan-mean."""
+    """nan-mean, numba-JIT compiled."""
     return np.nanmean(v)
 
 
@@ -579,7 +586,7 @@ def calc_shift(
     _tol: float = 1e-9,
 ) -> np.ndarray:
     """
-    Calculate shift values that, when added to arr, put the values of arr on a regular grid.
+    Calculate shift-values that, when added to arr, put the values of arr on a regular grid. Code gets numba-JIT compiled.
 
     Parameters
     ----------

pyfuppes/geo.py

@@ -1,8 +1,8 @@
 # -*- coding: utf-8 -*-
 """Geospatial helpers, such as Haversine distance or solar zenith angle."""
 
-import math
 from datetime import datetime
+from math import cos, sin, acos, asin, radians, sqrt, degrees, floor
 
 from geopy import distance
 from numba import njit
@@ -13,25 +13,23 @@
 
 @njit
 def haversine_dist(lat, lon):
-    """Calculate Haversine distance along lat/lon coordinates."""
+    """Calculate Haversine distance along lat/lon coordinates in km. Code gets numba-JIT compiled."""
     assert lat.shape[0] == lon.shape[0], "lat/lon must be of same length."
-    R = 6373  # approximate radius of earth in km
+    R = 6372.8  # approximate radius of earth in km
     dist = 0
 
-    lat1 = math.radians(lat[0])
-    lon1 = math.radians(lon[0])
+    lat1, lon1 = lat[0], lon[0]
     for j in range(1, lat.shape[0]):
-        lat0, lat1 = lat1, math.radians(lat[j])
-        lon0, lon1 = lon1, math.radians(lon[j])
+        lat0, lat1 = lat1, lat[j]
+        lon0, lon1 = lon1, lon[j]
 
-        dlon = lon1 - lon0
-        dlat = lat1 - lat0
+        dLat = radians(lat1 - lat0)
+        dLon = radians(lon1 - lon0)
+        lat0 = radians(lat0)
+        lat1 = radians(lat1)
 
-        a = (
-            math.sin(dlat / 2) ** 2
-            + math.cos(lat0) * math.cos(lat1) * math.sin(dlon / 2) ** 2
-        )
-        c = 2 * math.atan2(math.sqrt(a), math.sqrt(1 - a))
+        a = sin(dLat / 2) ** 2 + cos(lat0) * cos(lat1) * sin(dLon / 2) ** 2
+        c = 2 * asin(sqrt(a))
 
         dist += R * c
 
@@ -79,13 +77,13 @@ def sza(UTC=datetime.utcnow(), latitude=52.37, longitude=9.72):
 
     # define trigonometry with degrees
     def cos2(x):
-        return math.cos(math.radians(x))
+        return cos(radians(x))
 
     def sin2(x):
-        return math.sin(math.radians(x))
+        return sin(radians(x))
 
     def acos2(x):
-        return math.degrees(math.acos(x))
+        return degrees(acos(x))
 
     # parameter
     day_of_year = UTC.timetuple().tm_yday
@@ -132,7 +130,7 @@ def get_EoT(date_ts):
     use for: calculation of local solar time
     """
     B = (360 / 365) * (date_ts.timetuple().tm_yday - 81)
-    return 9.87 * math.sin(2 * B) - 7.53 * math.cos(B) - 1.5 * math.sin(B)
+    return 9.87 * sin(2 * B) - 7.53 * cos(B) - 1.5 * sin(B)
 
 
 ###############################################################################
@@ -155,5 +153,5 @@ def get_LSTdayFrac(longitude, tz_offset, EoT, days_delta, time_delta):
     t_corr = (4 * (longitude - LSTM) + EoT) / 60 / 24  # [d]
     LST_frac = (time_delta + tz_offset / 24 - days_delta) + t_corr
     if LST_frac > 1:
-        LST_frac -= math.floor(LST_frac)
+        LST_frac -= floor(LST_frac)
     return LST_frac

pyproject.toml

@@ -1,13 +1,13 @@
 [tool.poetry]
 name = "pyfuppes"
-version = "0.2.14"
+version = "0.3.0"
 description = "A collection of tools in Python"
 authors = ["Florian Obersteiner <f.obersteiner@kit.edu>"]
 license = "MIT"
 readme = "README.md"
 
 [tool.poetry.dependencies]
-python = ">= 3.8.1, < 3.11" # indirect; numba ...
+python = ">= 3.9, < 3.12"
 geopy = ">= 2.0"
 matplotlib = ">= 3.0"
 pandas = ">= 1.0"
@@ -18,9 +18,8 @@ scipy = ">= 1.1"
 netcdf4 = ">= 1.6"
 xarray = ">= 2022, >=2023"
 tomli = ">= 2.0.1"
-numba = "^0.56.4"                # no python 3.11 support as of 2023-02-10
-numpy = "<1.24, >=1.18"          # required by numba 0.56.4
-llvmlite = "<0.40, >=0.39.0dev0" # required by numba 0.56.4
+numba = ">= 0.56.4"
+numpy = ">= 1.18"
 
 [tool.poetry.dev-dependencies]
 pytest = ">=7.0"

tests/test_avgbin.py

@@ -7,7 +7,7 @@
 from pyfuppes import avgbinmap
 
 
-class TestTimeconv(unittest.TestCase):
+class TestAvgbinmap(unittest.TestCase):
     @classmethod
     def setUpClass(cls):
         # to run before all tests

tests/test_filters.py

@@ -7,7 +7,7 @@
 from pyfuppes import filters
 
 
-class TestTimeconv(unittest.TestCase):
+class TestFilters(unittest.TestCase):
     @classmethod
     def setUpClass(cls):
         # to run before all tests

tests/test_geo.py

@@ -0,0 +1,40 @@
+# -*- coding: utf-8 -*-
+
+import unittest
+
+import numpy as np
+
+from pyfuppes import geo
+
+
+class TestGeo(unittest.TestCase):
+    @classmethod
+    def setUpClass(cls):
+        # to run before all tests
+        print("\ntesting pyfuppes.avgbin...")
+
+    @classmethod
+    def tearDownClass(cls):
+        # to run after all tests
+        pass
+
+    def setUp(self):
+        # to run before each test
+        pass
+
+    def tearDown(self):
+        # to run after each test
+        pass
+
+    def test_haversine_dist(self):
+        dist = 2887
+        tol_decimalplaces = 0
+        self.assertAlmostEqual(
+            geo.haversine_dist(np.array((36.12, 33.94)), np.array((-86.67, -118.40))),
+            dist,
+            tol_decimalplaces,
+        )
+
+
+if __name__ == "__main__":
+    unittest.main()

tests/test_interpolate.py

@@ -8,7 +8,7 @@
 from pyfuppes import interpolate
 
 
-class TestCfg(unittest.TestCase):
+class TestInterpolate(unittest.TestCase):
     @classmethod
     def setUpClass(cls):
         pass

tests/test_timecorr.py

@@ -17,7 +17,7 @@ def _make_df(dt_list):
     )
 
 
-class TestTimeconv(unittest.TestCase):
+class TestTimecorr(unittest.TestCase):
     @classmethod
     def setUpClass(cls):
         # to run before all tests

tests/test_v25.py

@@ -15,7 +15,7 @@
 src, dst = wd / "test_input", wd / "test_output"
 
 
-class TestTimeconv(unittest.TestCase):
+class TestV25tools(unittest.TestCase):
     @classmethod
     def setUpClass(cls):
         # to run before all tests