Merge pull request #152 from aburrell/rcv2.1.0

Version 2.1.0 for develop

.github/workflows/docs.yml

@@ -31,7 +31,7 @@ jobs:
       run: |
         pip install build
         python -m build .
-        pip install -r docs/requirements.txt
+        pip install .[doc]
 
     - name: Check documentation build
       run: sphinx-build -E -b html docs dist/docs

.github/workflows/main.yml

@@ -24,12 +24,16 @@ jobs:
           # Support different GA Mac environmnets
           - python-version: "3.9"
             os: "macos-13"
+            numpy_ver: "latest"
           - python-version: "3.10"
             os: "macos-13"
+            numpy_ver: "latest"
           - python-version: "3.11"
             os: "macos-latest"
+            numpy_ver: "latest"
           - python-version: "3.12"
             os: "macos-latest"
+            numpy_ver: "latest"
           # NEP29 compliance settings
           - python-version: "3.10"
             numpy_ver: "1.25"

.zenodo.json

@@ -1,37 +1,37 @@
 {
   "license": {
   "id": "MIT"
-  }, 
+  },
   "notes": "When referencing this package, please cite both the package DOI and the Apex Coordinates journal article: Emmert, J. T., A. D. Richmond, and D. P. Drob (2010), A computationally compact representation of Magnetic-Apex and Quasi-Dipole coordinates with smooth base vectors, J. Geophys. Res., 115(A8), A08322, doi:10.1029/2010JA015326.",
   "references": [
     "Emmert, J. T., A. D. Richmond, and D. P. Drob (2010), A computationally compact representation of Magnetic-Apex and Quasi-Dipole coordinates with smooth base vectors, J. Geophys. Res., 115(A8), A08322, doi:10.1029/2010JA015326.",
     "Richmond, A. D. (1995), Ionospheric Electrodynamics Using Magnetic Apex Coordinates, Journal of geomagnetism and geoelectricity, 47(2), 191–212, doi:10.5636/jgg.47.191."
-  ], 
+  ],
   "keywords": [
     "Magnetic Apex Coordinates",
     "Quasi Dipole Coordinates",
-    "MLT", 
-    "Magnetic Local Time", 
-    "Conversion", 
-    "Coordinate Conversion", 
-    "Converting", 
-    "Ionosphere", 
-    "Magnetic Field", 
-    "Space Physics", 
+    "MLT",
+    "Magnetic Local Time",
+    "Conversion",
+    "Coordinate Conversion",
+    "Converting",
+    "Ionosphere",
+    "Magnetic Field",
+    "Space Physics",
     "Heliophysics"
-  ], 
+  ],
   "creators": [
     {
-      "orcid": "0000-0002-8043-0953", 
+      "orcid": "0000-0002-8043-0953",
       "name": "van der Meeren, Christer"
     },
     {
       "orcid": "0000-0001-5028-4943",
       "name": "Laundal, Karl M."
     },
     {
-      "orcid": "0000-0001-8875-9326", 
-      "affiliation": "Naval Research Laboratory", 
+      "orcid": "0000-0001-8875-9326",
+      "affiliation": "Naval Research Laboratory",
       "name": "Burrell, Angeline G."
     },
     {
@@ -55,6 +55,11 @@
       "orcid": "0000-0001-9741-4063",
       "affiliation": "GFZ German Research Centre for Geosciences",
       "name": "Michaelis, Ingo"
+    },
+    {
+      "orcid": "0000-0001-8321-6074",
+      "affiliation": "Goddard Space Flight Center",
+      "name": "Klenzing, Jeff"
     }
   ]
 }

AUTHORS.rst

@@ -12,10 +12,14 @@ This python wrapper is made by:
 * Ashton Reimer
 * Achim Morschhauser
 * Ingo Michaelis
+* Jeff Klenzing
 
 Fortran code by Emmert et al. [2010] [1]_. Quasi-dipole and modified
 apex coordinates are defined by Richmond [1995] [2]_. The code uses
-IGRF-12 with coefficients valid through 2020 [Thébault et al., 2015] [3]_.
+IGRF-14 with coefficients valid through 2030. A special issue on IGRF-14 is
+currently accepting
+`submissions <https://www.springeropen.com/collections/IGRF14>`_.  A reference
+for IGRF-12 is [Thébault et al., 2015] [3]_.
 
 .. [1] Emmert, J. T., A. D. Richmond, and D. P. Drob (2010),
        A computationally compact representation of Magnetic-Apex

CHANGELOG.rst

@@ -2,13 +2,18 @@
 Changelog
 =========
 
-2.1.0 (2024-12-XX)
+2.1.0 (2025-01-07)
 ------------------
 * Adapted codebase to read IRGF coefficients from a file (updated to IGRF-14)
-* Updated docs to reflect missing command-line executable
 * Updated package to be compliant and installable with numpy 2.0+
 * Added tests for Python 3.12 and NEP29
 * Fixed link to logo in the README
+* Updated pyproject.toml to include most metadata instead of setup.cfg
+* Added a citation section to the docs
+* Fixed the command-line executable
+* Updated code to address deprecation warnings around np.float64 use
+* Updated code to remove use of datetime `utcnow`
+* Updated meson build requirements to include ninja for Windows builds instead of python-dev-tools
 
 2.0.2 (2024-11-12)
 ------------------

MANIFEST.in

@@ -2,7 +2,7 @@ graft docs
 graft fortranapex
 graft .github
 
-recursive-include apexpy *.txt meson.build
+recursive-include apexpy *.txt apexsh.dat meson.build
 
 include *.rst
 include *.md

README.rst

@@ -143,5 +143,5 @@ Badges
 .. |doi| image:: https://www.zenodo.org/badge/doi/10.5281/zenodo.4585641.svg
    :target: https://doi.org/10.5281/zenodo.1214206
 
-.. |logo| image:: https://github.com/aburrell/apexpy/blob/main/docs/apexpy.png
+.. |logo| image:: https://github.com/aburrell/apexpy/blob/main/docs/apexpy.png?raw=true
    :alt: ApexPy logo: yellow magnetic field lines surrounding the Earth's surface, which is blue

apexpy/__init__.py

@@ -1,3 +1,5 @@
+"""Conversion functions between geodetic and apex magnetic coordinates."""
+from importlib import metadata
 from sys import stderr
 
 # Below try..catch required for autodoc to work on readthedocs
@@ -12,5 +14,9 @@
 from apexpy import helpers  # noqa F401
 
 # Define the global variables
-__version__ = "2.0.1"
+try:
+    __version__ = metadata.version('apexpy')
+except metadata.PackageNotFoundError:
+    # Windows installation is not finding the version automatically
+    __version__ = "2.1.0"
 __all__ = ['Apex', 'fortranapex', 'helpers', 'ApexHeightError']

apexpy/__main__.py

@@ -63,8 +63,12 @@ def main():
     lats, lons = apex_obj.convert(arg_array[:, 0], arg_array[:, 1], args.source,
                                   args.dest, args.height, datetime=in_time)
 
-    # Save the output to a file
-    np.savetxt(args.file_out, np.column_stack((lats, lons)), fmt='%.8f')
+    # Save the output to a file.  Use the name for non-stdout inputs
+    if args.file_out.name.lower().find('stdout') >= 0:
+        fout_name = args.file_out
+    else:
+        fout_name = args.file_out.name
+    np.savetxt(fout_name, np.column_stack((lats, lons)), fmt='%.8f')
 
     return
 

apexpy/apex.py

@@ -101,8 +101,7 @@ def __init__(self, date=None, refh=0, datafile=None, fortranlib=None):
         # If datafile is not specified, use the package default, otherwise
         # check that the provided file exists
         if datafile is None:
-            datafile = str(resources.path(__package__,
-                                          'apexsh.dat').__enter__())
+            datafile = os.path.join(resources.files(__package__), 'apexsh.dat')
         else:
             if not os.path.isfile(datafile):
                 raise IOError('Data file does not exist: {}'.format(datafile))
@@ -120,8 +119,8 @@ def __init__(self, date=None, refh=0, datafile=None, fortranlib=None):
         self.fortranlib = fortranlib
 
         # Set the IGRF coefficient text file name
-        self.igrf_fn = str(resources.path(__package__,
-                                          'igrf14coeffs.txt').__enter__())
+        self.igrf_fn = os.path.join(resources.files(__package__),
+                                    'igrf14coeffs.txt')
 
         # Update the Fortran epoch using the year defined above
         self.set_epoch(self.year)
@@ -565,7 +564,10 @@ def geo2apex(self, glat, glon, height):
                 alat[alat == -9999] = np.nan
 
         # If array is returned, dtype is object, so convert to float
-        return np.float64(alat), np.float64(alon)
+        alat = helpers.set_array_float(alat)
+        alon = helpers.set_array_float(alon)
+
+        return alat, alon
 
     def apex2geo(self, alat, alon, height, precision=1e-10):
         """Converts modified apex to geodetic coordinates.
@@ -634,7 +636,10 @@ def geo2qd(self, glat, glon, height):
         qlat, qlon = self._geo2qd(glat, glon, height)
 
         # If array is returned, dtype is object, so convert to float
-        return np.float64(qlat), np.float64(qlon)
+        qlat = helpers.set_array_float(qlat)
+        qlon = helpers.set_array_float(qlon)
+
+        return qlat, qlon
 
     def qd2geo(self, qlat, qlon, height, precision=1e-10):
         """Converts quasi-dipole to geodetic coordinates.
@@ -674,7 +679,11 @@ def qd2geo(self, qlat, qlon, height, precision=1e-10):
         glat, glon, error = self._qd2geo(qlat, qlon, height, precision)
 
         # If array is returned, dtype is object, so convert to float
-        return np.float64(glat), np.float64(glon), np.float64(error)
+        glat = helpers.set_array_float(glat)
+        glon = helpers.set_array_float(glon)
+        error = helpers.set_array_float(error)
+
+        return glat, glon, error
 
     def apex2qd(self, alat, alon, height):
         """Converts modified apex to quasi-dipole coordinates.
@@ -706,7 +715,10 @@ def apex2qd(self, alat, alon, height):
         qlat, qlon = self._apex2qd(alat, alon, height)
 
         # If array is returned, the dtype is object, so convert to float
-        return np.float64(qlat), np.float64(qlon)
+        qlat = helpers.set_array_float(qlat)
+        qlon = helpers.set_array_float(qlon)
+
+        return qlat, qlon
 
     def qd2apex(self, qlat, qlon, height):
         """Converts quasi-dipole to modified apex coordinates.
@@ -737,7 +749,10 @@ def qd2apex(self, qlat, qlon, height):
         alat, alon = self._qd2apex(qlat, qlon, height)
 
         # If array is returned, the dtype is object, so convert to float
-        return np.float64(alat), np.float64(alon)
+        alat = helpers.set_array_float(alat)
+        alon = helpers.set_array_float(alon)
+
+        return alat, alon
 
     def mlon2mlt(self, mlon, dtime, ssheight=318550):
         """Computes the magnetic local time at the specified magnetic longitude
@@ -777,8 +792,11 @@ def mlon2mlt(self, mlon, dtime, ssheight=318550):
         _, ssalon = self.geo2apex(ssglat, ssglon, ssheight)
 
         # Calculate the magnetic local time (0-24 h range) from apex longitude.
-        # np.float64 will ensure lists are converted to arrays
-        mlt = (180 + np.float64(mlon) - ssalon) / 15 % 24
+        # Ensure lists are converted to arrays
+        mlt = (180 + np.asarray(mlon) - ssalon) / 15 % 24
+
+        if mlt.shape == ():
+            mlt = np.float64(mlt)
 
         return mlt
 
@@ -818,8 +836,11 @@ def mlt2mlon(self, mlt, dtime, ssheight=318550):
         _, ssalon = self.geo2apex(ssglat, ssglon, ssheight)
 
         # Calculate the magnetic longitude (0-360 h range) from MLT.
-        # np.float64 will ensure lists are converted to arrays
-        mlon = (15 * np.float64(mlt) - 180 + ssalon + 360) % 360
+        # Ensure lists are converted to arrays
+        mlon = (15 * np.asarray(mlt) - 180 + ssalon + 360) % 360
+
+        if mlon.shape == ():
+            mlon = np.float64(mlon)
 
         return mlon
 
@@ -1130,10 +1151,10 @@ def basevectors_apex(self, lat, lon, height, coords='geo', precision=1e-10):
         k_unit = np.array([0, 0, 1], dtype=np.float64).reshape((3, 1))
 
         # Calculate the remaining quasi-dipole base vectors
-        g1 = ((self.RE + np.float64(height))
+        g1 = ((self.RE + np.asarray(height))
               / (self.RE + self.refh)) ** (3 / 2) * d1 / F_scalar
         g2 = -1.0 / (2.0 * F_scalar * np.tan(np.radians(qlat))) * (
-            k_unit + ((self.RE + np.float64(height))
+            k_unit + ((self.RE + np.asarray(height))
                       / (self.RE + self.refh)) * d2 / cos_mag_inc)
         g3 = k_unit * F_scalar
         f3 = np.cross(g1.T, g2.T).T
@@ -1154,7 +1175,7 @@ def basevectors_apex(self, lat, lon, height, coords='geo', precision=1e-10):
         return out
 
     def get_apex(self, lat, height=None):
-        """ Calculate apex height
+        """Calculate the apex height along a field line.
 
         Parameters
         ----------
@@ -1264,7 +1285,9 @@ def get_babs(self, glat, glon, height):
         babs = self._get_babs(glat, glon, height)
 
         # If array is returned, the dtype is object, so convert to float
-        return np.float64(babs)
+        babs = helpers.set_array_float(babs)
+
+        return babs
 
     def bvectors_apex(self, lat, lon, height, coords='geo', precision=1e-10):
         """Returns the magnetic field vectors in apex coordinates.

apexpy/helpers.py

@@ -1,12 +1,35 @@
 # -*- coding: utf-8 -*-
-
 """This module contains helper functions used by :class:`~apexpy.Apex`."""
 
 import datetime as dt
 import numpy as np
 import time
 
 
+def set_array_float(in_val):
+    """Set array data type to float.
+
+    Parameters
+    ----------
+    in_val : any
+        Input value, only modified if it is a np.ndarray
+
+    Returns
+    -------
+    out_val : any
+        Output value, if `in_val` was an array, `out_val` will be an array of
+        type `np.float64`.
+
+    """
+
+    if isinstance(in_val, np.ndarray):
+        out_val = in_val.astype(np.float64)
+    else:
+        out_val = in_val
+
+    return out_val
+
+
 def checklat(lat, name='lat'):
     """Makes sure the latitude is inside [-90, 90], clipping close values
     (tolerance 1e-4).

apexpy/tests/test_fortranapex.py

@@ -14,6 +14,7 @@
 
 from numpy.testing import assert_allclose
 from importlib import resources
+import os
 import pytest
 
 import apexpy
@@ -25,7 +26,7 @@ class TestFortranApex(object):
 
     def setup_method(self):
         """Initialize each test."""
-        datafile = str(resources.path(apexpy, 'apexsh.dat').__enter__())
+        datafile = os.path.join(resources.files(apexpy), 'apexsh.dat')
         fa.loadapxsh(datafile, 2000)
 
         # Set the inputs