Merge pull request #37 from pysat/bug/remove_pyglow

BUG/TST: remove pyglow

.travis.yml

@@ -3,15 +3,19 @@ language: python
 dist: xenial
 jobs:
   include:
-    - name: Minimum NEP 029 versions
-      python: 3.6
-      env: NUMPY_VER=1.15
-    # Versions with latest numpy
-    - python: 3.6
-    - python: 3.7
-    - python: 3.8
+    - name: '3.6 w/ numpy 1.16 (NEP 029)'
+      python: '3.6'
+      env: NUMPY_VER=1.16
+      script: pytest --cov=pysatMissions/
+    - name: '3.7 with flake8'
+      python: '3.7'
+      script: pytest --flake8 --cov=pysatMissions/
+    - name: '3.8'
+      python: '3.8'
+      script: pytest --cov=pysatMissions/
 
 services: xvfb
+cache: pip
 addons:
   apt:
     packages:
@@ -30,7 +34,7 @@ install:
   # Useful for debugging any issues with conda
   - conda info -a
   # Create conda test environment
-  - conda create -q -n test-environment python=$TRAVIS_PYTHON_VERSION numpy scipy pandas xarray matplotlib requests beautifulsoup4 lxml netCDF4 h5py nose pytest-cov pytest-ordering coveralls future
+  - conda create -q -n test-environment python=$TRAVIS_PYTHON_VERSION numpy scipy pandas xarray netCDF4 h5py pytest-cov pytest-ordering coveralls portalocker
   - conda activate test-environment
   # Check for custom numpy version install
   - if [ -z ${NUMPY_VER} ]; then
@@ -45,7 +49,6 @@ install:
   - pip install pyEphem
   - pip install sgp4
   - pip install pytest-flake8
-  - pip install pysatCDF >/dev/null
 
   # Prepare modified pysat install
   - cd ..
@@ -58,15 +61,7 @@ install:
   # install pysat
   - git checkout develop-3
   - python setup.py install >/dev/null
-
-  # install pyglow, space science models
-  - cd ..
-  - echo 'cloning pyglow'
-  - git clone https://github.com/timduly4/pyglow.git >/dev/null
-  - echo 'installing pyglow'
-  - cd ./pyglow
-  - make -C src/pyglow/models source >/dev/null
-  - python setup.py install >/dev/null
+  - export PYTHONPATH=$PYTHONPATH:$(pwd)
 
   # Install pysatMagVect after pysat
   - pip install pysatMagVect >/dev/null
@@ -75,12 +70,5 @@ install:
   - cd ../pysatMissions
   - python setup.py install
 
-before_script:
-  # set up display screen
-  - export DISPLAY=:99.0
-
-script:
-  - pytest -vs --cov=pysatMissions/
-
 after_success:
-  - coveralls
+  - coveralls --rcfile=setup.cfg

CHANGELOG.md

@@ -2,8 +2,10 @@
 All notable changes to this project will be documented in this file.
 This project adheres to [Semantic Versioning](http://semver.org/).
 
-## [0.3.0] - 2020-09-30
+## [0.3.0] - 2020-12-03
 - Update sat_id to inst_id for pysat 3.0 compatibility
+- migrate pyglow interface to pysatIncubator
+- Style updates for consistency with pysat 3.0
 
 ## [0.2.1] - 2020-07-29
 - Use conda to manage Travis CI environment

README.md

@@ -7,7 +7,7 @@
 [![Documentation Status](https://readthedocs.org/projects/pysatMissions/badge/?version=latest)](http://pysatMissions.readthedocs.io/en/latest/?badge=latest)
 [![DOI](https://zenodo.org/badge/209358908.svg)](https://zenodo.org/badge/latestdoi/209358908)
 
-[![Build Status](https://travis-ci.org/pysat/pysatMissions.svg?branch=main)](https://travis-ci.org/pysat/pysatMissions)
+[![Build Status](https://travis-ci.com/pysat/pysatMissions.svg?branch=main)](https://travis-ci.com/pysat/pysatMissions)
 [![Coverage Status](https://coveralls.io/repos/github/pysat/pysatMissions/badge.svg?branch=main)](https://coveralls.io/github/pysat/pysatMissions?branch=main)
 [![Maintainability](https://api.codeclimate.com/v1/badges/83011911691b9d2076e9/maintainability)](https://codeclimate.com/github/pysat/pysatMissions/maintainability)
 
@@ -59,10 +59,6 @@ python setup.py install
 ```
 It should be noted that this is a working branch and is subject to change.
 
-A note on empirical models
---------------------------
-pysatMissions allows users to interact with a number of upper atmospheric empirical models through the [pyglow](https://github.com/timduly4/pyglow) package.  However, pyglow currently requires manual install through git.  While pysatMissions can be installed and used without pyglow, it should be installed by the user to access the pyglow methods.  Please follow the install instructions at https://github.com/timduly4/pyglow.
-
 # Using with pysat
 
 The instrument modules are portable and designed to be run like any pysat instrument.
@@ -73,16 +69,3 @@ from pysatMissions.instruments import pysat_ephem
 
 simInst = pysat.Instrument(inst_module=pysat_ephem)
 ```
-
-The methods that run empirical models can also be exported to any pysat instrument. For instance, to add thermal plasma predictions from the IRI model to the C/NOFS IVM instrument, one can invoke
-
-```
-import pysat
-from pysatMissions.methods import empirical
-
-ivm = pysat.Instrument(platform='cnofs', name='ivm')
-ivm.custom.attach(empirical.add_iri_thermal_plasma, 'modify',
-               glat_label='glat',
-               glong_label='glon', alt_label='altitude')
-```
-Once the custom function is added, the model will automatically be run when the dataset is loaded.

docs/installation.rst

@@ -6,7 +6,7 @@ Installation
 
 ----
 
-Python and associated packages for science are freely available. Convenient science python package setups are available from https://www.python.org/ and `Anaconda <https://www.anaconda.com/distribution/>`_. Anaconda also includes a developer environment. Core science packages such as numpy, scipy, matplotlib, pandas and many others may also be installed directly via pip or your favorite package manager.
+Python and associated packages for science are freely available. Convenient science python package setups are available from https://www.python.org/ and `Anaconda <https://www.anaconda.com/distribution/>`_. Anaconda also includes a developer environment. Core science packages such as numpy, scipy, pandas and many others may also be installed directly via pip or your favorite package manager.
 
 For educational users, developer environments from `Jet Brains <https://www.jetbrains.com/student/>`_ are available for free.
 

docs/introduction.rst

@@ -7,7 +7,6 @@ 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 ionosphere and thermosphere model values through pyglow
 - Import magnetic coordinates through apexpy and aacgmv2
 - Import geomagnetic basis vectors through pysatMagVect
 

docs/references.rst

@@ -50,4 +50,4 @@ Naval Research Laboratory Mass Spectrometer Incoherent Scatter radar Exobase (NR
 
 ----
 
-`pysatMagVect <https://github.com/rstoneback/OMMBV>`_ calculates Orthogonal Multipole Magnetic Basis Vectors for the earth's magnetic field.  pysatMagVect is being renamed OMMBV.
+`pysatMagVect <https://github.com/rstoneback/pysatMagVect>`_ calculates Orthogonal Multipole Magnetic Basis Vectors for the earth's magnetic field.

pysatMissions/__init__.py

@@ -6,11 +6,10 @@
 try:
     from pysatMissions import instruments
     from pysatMissions import methods
-    from pysatMissions import plot
 except ImportError as errstr:
     logging.exception('problem importing pysatMissions: ' + str(errstr))
 
-__all__ = ['instruments', 'methods', 'plot']
+__all__ = ['instruments', 'methods']
 
 # set version
 here = os.path.abspath(os.path.dirname(__file__))

pysatMissions/instruments/_core.py

@@ -38,7 +38,7 @@ def _get_times(fnames, inst_id):
     # create timing at 1 Hz (defaults to 1 day)
     # Allow numeric string to set number of time steps
     num = 86399 if inst_id == '' else int(inst_id)
-    times = pds.date_range(start=date, end=date+pds.DateOffset(seconds=num),
+    times = pds.date_range(start=date, end=(date + pds.DateOffset(seconds=num)),
                            freq='1S')
 
     return times

pysatMissions/instruments/pysat_ephem.py

@@ -7,20 +7,17 @@
 
 """
 
-from __future__ import print_function
-from __future__ import absolute_import
 import datetime as dt
 import functools
 import numpy as np
 
 import ephem
+import pysatMagVect
 import pandas as pds
 import pysat
-import pysatMagVect
 
 from pysatMissions.instruments import _core as mcore
 from pysatMissions.methods import magcoord as mm_magcoord
-from pysatMissions.methods import empirical as mm_emp
 from pysatMissions.methods import spacecraft as mm_sc
 
 # pysat required parameters
@@ -50,25 +47,6 @@ def init(self):
     self.custom.attach(mm_magcoord.add_aacgm_coordinates)
     self.custom.attach(mm_sc.calculate_ecef_velocity)
     self.custom.attach(mm_sc.add_ram_pointing_sc_attitude_vectors)
-    # project simulated vectors onto s/c basis
-    # IGRF
-    self.custom.attach(mm_emp.add_igrf)
-    # create metadata to be added along with vector projection
-    in_meta = {'desc': 'IGRF geomagnetic field expressed in the s/c basis.',
-               'units': 'nT'}
-    # project IGRF
-    self.custom.attach(mm_sc.project_ecef_vector_onto_sc,
-                       args=['B_ecef_x', 'B_ecef_y', 'B_ecef_z', 'B_sc_x',
-                             'B_sc_y', 'B_sc_z'],
-                       kwargs={'meta': [in_meta.copy(), in_meta.copy(),
-                                        in_meta.copy()]})
-    # Thermal Ion Parameters
-    self.custom.attach(mm_emp.add_iri_thermal_plasma)
-    # Thermal Neutral parameters
-    self.custom.attach(mm_emp.add_msis)
-    self.custom.attach(mm_emp.add_hwm_winds_and_ecef_vectors)
-    # project total wind vector
-    self.custom.attach(mm_emp.project_hwm_onto_sc)
 
 
 def load(fnames, tag=None, inst_id=None, obs_long=0., obs_lat=0., obs_alt=0.,
@@ -160,7 +138,7 @@ def load(fnames, tag=None, inst_id=None, obs_long=0., obs_lat=0., obs_alt=0.,
         # sublongitude point
         lp['glong'] = np.degrees(sat.sublong)
         # elevation of sat in m, stored as km
-        lp['alt'] = sat.elevation/1000.
+        lp['alt'] = sat.elevation / 1000.
         # get ECEF position of satellite
         lp['x'], lp['y'], lp['z'] = pysatMagVect.geodetic_to_ecef(lp['glat'],
                                                                   lp['glong'],
@@ -186,6 +164,13 @@ def load(fnames, tag=None, inst_id=None, obs_long=0., obs_lat=0., obs_alt=0.,
     return data, meta.copy()
 
 
+def clean(self):
+    """Cleaning function
+    """
+
+    pass
+
+
 list_files = functools.partial(mcore._list_files)
 download = functools.partial(mcore._download)
 
@@ -215,8 +200,8 @@ def load(fnames, tag=None, inst_id=None, obs_long=0., obs_lat=0., obs_alt=0.,
 meta['obs_sat_az_angle'] = {'units': 'degrees',
                             'desc': 'Azimuth of satellite from ground station'}
 meta['obs_sat_el_angle'] = {'units': 'degrees',
-                            'desc': 'Elevation of satellite from ground ' +
-                            'station'}
+                            'desc': ' '.join(('Elevation of satellite from',
+                                              'ground station'))}
 meta['obs_sat_slant_range'] = {'units': 'km',
-                               'desc': 'Distance of satellite from ground ' +
-                               'station'}
+                               'desc': ' '.join(('Distance of satellite from',
+                                                 'ground station'))}

pysatMissions/instruments/pysat_sgp4.py

@@ -5,8 +5,6 @@
 
 """
 
-from __future__ import print_function
-from __future__ import absolute_import
 import datetime as dt
 import functools
 import pandas as pds
@@ -133,6 +131,13 @@ def load(fnames, tag=None, inst_id=None, obs_long=0., obs_lat=0., obs_alt=0.,
     return data, meta.copy()
 
 
+def clean(self):
+    """Cleaning function
+    """
+
+    pass
+
+
 list_files = functools.partial(mcore._list_files)
 download = functools.partial(mcore._download)
 
@@ -146,18 +151,18 @@ def load(fnames, tag=None, inst_id=None, obs_long=0., obs_lat=0., obs_alt=0.,
                  'long_name': 'Time index in milliseconds'}
 meta['position_eci_x'] = {'units': 'km',
                           'long_name': 'ECI x-position',
-                          'desc': 'Earth Centered Inertial x-position of ' +
-                          'satellite.',
+                          'desc': ' '.join(('Earth Centered Inertial',
+                                            'x-position of satellite.')),
                           'label': 'ECI-X'}
 meta['position_eci_y'] = {'units': 'km',
                           'long_name': 'ECI y-position',
-                          'desc': 'Earth Centered Inertial y-position of ' +
-                          'satellite.',
+                          'desc': ' '.join(('Earth Centered Inertial',
+                                            'y-position of satellite.')),
                           'label': 'ECI-Y'}
 meta['position_eci_z'] = {'units': 'km',
                           'long_name': 'ECI z-position',
-                          'desc': 'Earth Centered Inertial z-position of ' +
-                          'satellite.',
+                          'desc': ' '.join(('Earth Centered Inertial',
+                                            'z-position of satellite.')),
                           'label': 'ECI-Z'}
 meta['velocity_eci_x'] = {'units': 'km/s',
                           'desc': 'Satellite velocity along ECI-x',

pysatMissions/methods/__init__.py

@@ -3,8 +3,7 @@
 the methods to interface with numerous empirical model packages
 """
 
-from pysatMissions.methods import empirical
 from pysatMissions.methods import magcoord
 from pysatMissions.methods import spacecraft
 
-__all__ = ['empirical', 'magcoord', 'spacecraft']
+__all__ = ['magcoord', 'spacecraft']