Merge pull request #91 from pysat/rc_0_3_2

Release Candidate 0.3.2

.github/workflows/main.yml

@@ -12,7 +12,7 @@ jobs:
       fail-fast: false
       matrix:
         python-version: ["3.8", "3.9", "3.10"]
-        os: [ubuntu-latest]
+        os: ["ubuntu-latest", "windows-latest"]
         numpy_ver: ["latest"]
 
     name: Python ${{ matrix.python-version }} on ${{ matrix.os }} with numpy ${{ matrix.numpy_ver }}
@@ -32,6 +32,9 @@ jobs:
     - name: Install dependencies
       run: |
         pip install -r requirements.txt
+        pip install aacgmv2 --no-binary==aacgmv2
+        pip install apexpy --no-binary==apexpy
+        pip install OMMBV --no-binary==OMMBV
 
     - name: Set up pysat
       run: |

.zenodo.json

@@ -17,11 +17,16 @@
       },
       {
         "affiliation": "The University of Texas at Dallas",
-        "name": "Depew, Matthew"
+        "name": "Depew, Matthew",
+        "orcid": "0000-0001-9069-4998"
       },
       {
         "name": "Spence, Carey",
         "orcid": "0000-0001-8340-5625"
+      },
+      {
+        "name": "Bhaneja, Preeti",
+        "orcid": "0000-0003-4900-2747"
       }
     ]
 }

CHANGELOG.md

@@ -2,6 +2,22 @@
 All notable changes to this project will be documented in this file.
 This project adheres to [Semantic Versioning](https://semver.org/).
 
+## [0.3.2] - 2022-XX-XX
+* Make fortran dependencies optional installs
+  * aacgmv2
+  * apexpy
+  * OMMBV
+* Access logger directly from pysat
+* Use pysat deprecation tests
+* Incorporate Windows tests into Github Actions
+* Bug Fix
+  * Ensure default num_samples consistent for one day regardless of cadence
+* Maintenance
+  * Update instrument test standards
+  * Added `utils.package_check`, a standard decorator to bypass functions using
+    packages that are optional installs if the package is not installed
+  * Use local vector functions rather than import from OMMBV
+
 ## [0.3.1] - 2022-05-18
 * Include license in package manifest
 

README.md

@@ -16,8 +16,7 @@ pysatMissions allows users to run build simulated satellites for Two-Line Elemen
 Main Features
 -------------
 - Simulate satellite orbits from TLEs and add data from empirical models
-- Import magnetic coordinates through apexpy and aacgmv2
-- Import geomagnetic basis vectors through OMMBV
+- Import magnetic coordinates through apexpy and aacgmv2 (optional install)
 
 Documentation
 ---------------------
@@ -32,12 +31,11 @@ pysatMissions uses common Python modules, as well as modules developed by
 and for the Space Physics community.  This module officially supports
 Python 3.8+.  
 
-| Common modules | Community modules |
-| -------------- | ----------------- |
-| numpy          | aacgmv2           |
-| pandas         | apexpy            |
-| pyEphem        | OMMBV>=1.0        |
-| sgp4>=2.7      | pysat>=3.0        |
+| Common modules | Community modules | Optional modules |
+| -------------- | ----------------- | ---------------- |
+| numpy          | pysat>=3.0.4      | aacgmv2          |
+| pandas         | pyEphem           | apexpy           |
+|                | sgp4>=2.7         | OMMBV            |
 
 
 One way to install is through pip.  Just type
@@ -63,17 +61,19 @@ python setup.py install
 
 Note: pre-1.0.0 version
 -----------------------
-pysatMissions is currently in an initial development phase and requires pysat 3.0.0.  
+pysatMissions is currently in an initial development phase and requires pysat
+3.0.4.  
 
 # Using with pysat
 
-The instrument modules are portable and designed to be run like any pysat instrument.
+The instrument modules are portable and designed to be run like any pysat
+instrument.
 
 ```
 import pysat
-from pysatMissions.instruments import missions_ephem
+from pysatMissions.instruments import missions_sgp4
 
-simInst = pysat.Instrument(inst_module=missions_ephem)
+sim_inst = pysat.Instrument(inst_module=missions_sgp4)
 ```
 Another way to use the instruments in an external repository is to register the instruments.  This only needs to be done the first time you load an instrument.  Afterward, pysat will identify them using the `platform` and `name` keywords.
 
@@ -82,5 +82,20 @@ import pysat
 import pysatMissions
 
 pysat.utils.registry.register_by_module(pysatMissions.instruments)
-simInst = pysat.Instrument('missions', 'ephem')
+sim_inst = pysat.Instrument('missions', 'sgp4')
 ```
+
+# Optional modules
+
+Magnetic vector coordinates through apexpy and aacgmv2 are set up as optional
+installs. Both packages require fortran to install properly, and may require
+additional configuration.  Both can be installed from pip, but may require the
+`--no-binary` option depending on your system.
+
+The instrument `missions_ephem` has been deprecated since pyEphem is no longer
+maintained. This will be removed in v0.4.0.  Note that OMMBV is required for
+this instrument to function correctly, but is not required for the core
+pysatMissions package.  This has also been made optional to improve installation.  
+Please use the `missions_sgp4` instrument for future needs.
+
+The orbital trajectories can be calculated without any of the optional modules.

docs/installation.rst

@@ -15,16 +15,15 @@ Prerequisites
 
 pysatMissions uses common Python modules, as well as modules developed by
 and for the Space Physics community.  This module officially supports
-Python 3.7+ and pysat 3.0.0+.
-
- ================ ==================
- Common  modules   Community modules
- ================ ==================
-  numpy            aacgmv2
-  pandas           apexpy
-  pyEphem          OMMBV>=1.0
-  sgp4>=2.7        pysat>=3.0
- ================ ==================
+Python 3.8+ and pysat 3.0.4+.
+
+ ================ =================== ==================
+ Common  modules   Community modules   Optional Modules
+ ================ =================== ==================
+  numpy            pysat>=3.0.4        aacgmv2
+  pandas           pyEphem             apexpy
+                   sgp4>=2.7           OMMBV>=1.0
+ ================ =================== ==================
 
 
  Installation Options

docs/introduction.rst

@@ -10,7 +10,6 @@ Main Features
 -------------
 - Simulate satellite orbits from TLEs and add data from empirical models
 - Import magnetic coordinates through apexpy and aacgmv2
-- Import geomagnetic basis vectors through OMMBV
 
 This document covers installation, a tutorial on pysatMissions including
 demonstration code, and an API reference.

pysatMissions/__init__.py

@@ -8,20 +8,16 @@
 -------------
 - Simulate satellite orbits from TLEs and add data from empirical models
 - Import magnetic coordinates through apexpy and aacgmv2
-- Import geomagnetic basis vectors through OMMBV
 
 """
 
-import logging
 import os
 
-try:
-    from pysatMissions import instruments
-    from pysatMissions import methods
-except ImportError as errstr:
-    logging.exception('problem importing pysatMissions: ' + str(errstr))
+from pysatMissions import instruments
+from pysatMissions import methods
+from pysatMissions import utils
 
-__all__ = ['instruments', 'methods']
+__all__ = ['instruments', 'methods', 'utils']
 
 # set version
 here = os.path.abspath(os.path.dirname(__file__))

pysatMissions/instruments/missions_ephem.py

@@ -30,7 +30,6 @@
 import warnings
 
 import ephem
-import OMMBV
 import pandas as pds
 import pysat
 
@@ -39,8 +38,6 @@
 from pysatMissions.methods import magcoord as mm_magcoord
 from pysatMissions.methods import spacecraft as mm_sc
 
-logger = pysat.logger
-
 # -------------------------------
 # Required Instrument attributes
 platform = 'missions'
@@ -67,7 +64,7 @@ def init(self):
         'The project uses the pyephem library available at',
         'https://github.com/brandon-rhodes/pyephem'))
     self.references = 'Please contact the pyephem project for references'
-    logger.info(self.acknowledgements)
+    pysat.logger.info(self.acknowledgements)
 
     warnings.warn(' '.join(("`missions_ephem` has been deprecated and will be",
                             "removed in pysatMissions 0.4.0+.",
@@ -84,8 +81,8 @@ def preprocess(self):
 
     """
 
-    mm_magcoord.add_quasi_dipole_coordinates(self)
     mm_magcoord.add_aacgm_coordinates(self)
+    mm_magcoord.add_quasi_dipole_coordinates(self)
     mm_sc.calculate_ecef_velocity(self)
     mm_sc.add_ram_pointing_sc_attitude_vectors(self)
 
@@ -201,13 +198,23 @@ def load(fnames, tag=None, inst_id=None, obs_long=0., obs_lat=0., obs_alt=0.,
         # Elevation of satellite in m, converted to km
         lp['alt'] = sat.elevation / 1000.0
 
-        # Get ECEF position of satellite
-        lp['x'], lp['y'], lp['z'] = OMMBV.trans.geodetic_to_ecef(lp['glat'],
-                                                                 lp['glong'],
-                                                                 lp['alt'])
         output_params.append(lp)
 
     output = pds.DataFrame(output_params, index=index)
+
+    # Get ECEF position of satellite
+    try:
+        output['x'], output['y'], output['z'] = \
+            OMMBV.trans.geodetic_to_ecef(output['glat'], output['glong'],
+                                         output['alt'])
+    except NameError:
+        # Triggered if OMMBV not installed
+        warnings.warn("OMMBV not installed. ECEF coords not generated.",
+                      stacklevel=2)
+        output['x'] = output['glat'] * np.nan
+        output['y'] = output['glat'] * np.nan
+        output['z'] = output['glat'] * np.nan
+
     # Modify input object to include calculated parameters
     # Put data into DataFrame
     data = pds.DataFrame({'glong': output['glong'],

pysatMissions/instruments/missions_sgp4.py

@@ -28,8 +28,6 @@
 from geospacepy import terrestrial_spherical as conv_sph
 from sgp4 import api as sapi
 
-logger = pysat.logger
-
 # -------------------------------
 # Required Instrument attributes
 platform = 'missions'
@@ -59,7 +57,7 @@ def init(self):
         '"Revisiting Spacetrack Report #3," presented at the AIAA/AAS',
         'Astrodynamics Specialist Conference, Keystone, CO, 2006',
         'August 21–24.'))
-    logger.info(self.acknowledgements)
+    pysat.logger.info(self.acknowledgements)
 
     if 'epoch' not in self.kwargs['load'].keys():
         self.kwargs['load']['epoch'] = self.files.files.index[0]
@@ -180,7 +178,9 @@ def load(fnames, tag=None, inst_id=None, tle1=None, tle2=None,
         line2 = tle2
 
     if (num_samples is None) or one_orbit:
-        num_samples = 86400
+        # Calculate one day of samples for default
+        num_samples = len(pds.date_range('2018/1/1', '2018/1/2',
+                                         freq=cadence)) - 1
 
     # Extract list of times from filenames and inst_id
     times, index, dates = ps_meth.generate_times(fnames, num_samples,

pysatMissions/methods/magcoord.py

@@ -1,20 +1,29 @@
 """Routines for projecting aacgmv2 and apexpy model values onto pysat instruments.
 """
 
-import aacgmv2
 import pysat
+from pysatMissions.utils import package_check
 
+# Warn user if aacgmv2 is not configured.  Use of aacgmv2 functions elsewhere in
+# code will produce additional warnings.
+try:
+    import aacgmv2
+except ImportError as ierr:
+    pysat.logger.warning(" ".join(["aacgmv2 module could not be imported.",
+                                   "aacgmv2 interface won't work.",
+                                   "Failed with error:", str(ierr)]))
+
+# Warn user if apexpy is not configured.  Use of apexpy functions elsewhere in
+# code will produce additional warnings.
 try:
-    # Warn user if apexpy is not configured.  Bypass needed to function on
-    # readthedocs.  Use of apexpy functions elsewhere in code will produce
-    # errors.
     import apexpy
 except ImportError as ierr:
     pysat.logger.warning(" ".join(["apexpy module could not be imported.",
                                    "apexpy interface won't work.",
                                    "Failed with error:", str(ierr)]))
 
 
+@package_check('aacgmv2')
 def add_aacgm_coordinates(inst, glat_label='glat', glong_label='glong',
                           alt_label='alt'):
     """Add AACGM coordinates to instrument object using AACGMV2 package.
@@ -75,6 +84,7 @@ def add_aacgm_coordinates(inst, glat_label='glat', glong_label='glong',
     return
 
 
+@package_check('apexpy')
 def add_quasi_dipole_coordinates(inst, glat_label='glat', glong_label='glong',
                                  alt_label='alt'):
     """Add quasi-dipole coordinates to instrument object using Apexpy package.