Merge pull request #33 from pysat/develop

v0.2.1
pysat · Jul 29, 2020 · e307266 · e307266
2 parents b53cf6d + f72486e
commit e307266
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diff --git a/.coveragerc b/.coveragerc
@@ -1,5 +1,3 @@
 [run]
 
 [report]
-omit =
-  */tests/*
diff --git a/.github/pull_request_template.md b/.github/pull_request_template.md
@@ -32,7 +32,7 @@ your test configuration
 
 # Checklist:
 
-- [ ] Make sure you are merging into the ``develop`` (not ``master``) branch
+- [ ] Make sure you are merging into the ``develop`` (not ``main``) branch
 - [ ] My code follows the style guidelines of this project
 - [ ] I have performed a self-review of my own code
 - [ ] I have commented my code, particularly in hard-to-understand areas

diff --git a/.travis.yml b/.travis.yml
@@ -17,16 +17,35 @@ addons:
     packages:
     - gfortran
 
-before_install:
+install:
+  - sudo apt-get update
+  # We do this conditionally because it saves us some downloading if the
+  # version is the same.
+  - wget https://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh -O miniconda.sh
+  - bash miniconda.sh -b -p $HOME/miniconda
+  - source "$HOME/miniconda/etc/profile.d/conda.sh"
+  - hash -r
+  - conda config --set always_yes True --set changeps1 False
+  - conda update -q conda
+  # 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 activate test-environment
+  # Check for custom numpy version install
   - if [ -z ${NUMPY_VER} ]; then
       echo 'Using latest numpy';
     else
-      pip install -q numpy==$NUMPY_VER;
+      conda install numpy==$NUMPY_VER;
     fi
-  - pip install pytest-cov
-  - pip install coveralls
-  - pip install future
+  # Dependencies not available through conda, install through pip
   - pip install apexpy
+  - pip install aacgmv2
+  - pip install madrigalWeb
+  - pip install pyEphem
+  - pip install sgp4
+  - pip install pytest-flake8
+  - pip install pysatCDF >/dev/null
 
   # Prepare modified pysat install
   - cd ..
@@ -48,9 +67,12 @@ before_install:
   - cd ./pyglow
   - make -C src/pyglow/models source >/dev/null
   - python setup.py install >/dev/null
-  - cd ../pysatMissions
 
-install:
+  # Install pysatMagVect after pysat
+  - pip install pysatMagVect >/dev/null
+
+  # install pysatMissions
+  - cd ../pysatMissions
   - python setup.py install
 
 before_script:

diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -2,6 +2,13 @@
 All notable changes to this project will be documented in this file.
 This project adheres to [Semantic Versioning](http://semver.org/).
 
+## [0.2.1] - 2020-07-29
+- Use conda to manage Travis CI environment
+- Updated style to be compliant with pandas 2.0 and pysat 3.0
+  - Import datetime from datetime
+  - import DataFrame and Series from pandas rather than pysat
+- Rename default branch as `main`
+
 ## [0.2.0] - 2020-03-07
 - Renamed as pysatMissions
 - Added method files to access aacgmv2, apexpy, pyglow for any pysat instrument

diff --git a/README.md b/README.md
@@ -7,8 +7,8 @@
 [![Documentation Status](https://readthedocs.org/projects/pysatmissions/badge/?version=latest)](https://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=master)](https://travis-ci.org/pysat/pysatMissions)
-[![Coverage Status](https://coveralls.io/repos/github/pysat/pysatMissions/badge.svg?branch=master)](https://coveralls.io/github/pysat/pysatMissions?branch=master)
+[![Build Status](https://travis-ci.org/pysat/pysatMissions.svg?branch=main)](https://travis-ci.org/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)
 
 pysatMissions allows users to run build simulated satellites for Two-Line Elements (TLE) and add empirical data.  It includes the pysat_ephem and pysat_sgp4 instrument modules which can be imported into pysat.

diff --git a/docs/conf.py b/docs/conf.py
@@ -61,7 +61,7 @@
 # source_suffix = ['.rst', '.md']
 source_suffix = '.rst'
 
-# The master toctree document.
+# The main toctree document (using required variable name).
 master_doc = 'index'
 
 # The language for content autogenerated by Sphinx. Refer to documentation

diff --git a/docs/index.rst b/docs/index.rst
@@ -1,4 +1,4 @@
-.. pysatMissions documentation master file
+.. pysatMissions documentation main file
 
 Welcome to pysatMissions's documentation!
 =========================================

diff --git a/docs/tutorial.rst b/docs/tutorial.rst
@@ -35,6 +35,9 @@ A number of methods are included to invoke several python wrappers for empirical
   from pysatMissions.methods import empirical
 
   ivm = pysat.Instrument(platform='cnofs', name='ivm')
-  ivm.custom.attach(empirical.add_iri_thermal_plasma, 'modify', 'end', glat_label='glat', glong_label='glon', alt_label='altitude')
+  ivm.custom.attach(empirical.add_iri_thermal_plasma,
+                    kwargs={'glat_label': 'glat',
+                            'glong_label': 'glon',
+                            'alt_label': 'altitude'})
 
 Note that in this case, the latitude, longitude, and altitude variable names of the instrument must be specified since they are not identical to the default names in the function.
diff --git a/pysatMissions/instruments/_core.py b/pysatMissions/instruments/_core.py
@@ -2,21 +2,21 @@
 Handles the default pysat functions for simulated instruments
 """
 
+import datetime as dt
 import os
 import pandas as pds
-import pysat
 
 
 def _list_files(tag=None, sat_id=None, data_path=None, format_str=None):
     """Produce a fake list of files spanning a year"""
 
-    index = pds.date_range(pysat.datetime(2017, 12, 1),
-                           pysat.datetime(2018, 12, 1))
+    index = pds.date_range(dt.datetime(2017, 12, 1),
+                           dt.datetime(2018, 12, 1))
     # file list is effectively just the date in string format - '%D' works
     # only in Mac. '%x' workins in both Windows and Mac
     names = [data_path + date.strftime('%Y-%m-%d') + '.nofile'
              for date in index]
-    return pysat.Series(names, index=index)
+    return pds.Series(names, index=index)
 
 
 def _download(date_array, tag, sat_id, data_path=None):
@@ -33,7 +33,7 @@ def _get_times(fnames, sat_id):
     yr = int(parts[0])
     month = int(parts[1])
     day = int(parts[2][0:2])
-    date = pysat.datetime(yr, month, day)
+    date = dt.datetime(yr, month, day)
 
     # create timing at 1 Hz (defaults to 1 day)
     # Allow numeric string to set number of time steps

diff --git a/pysatMissions/instruments/pysat_ephem.py b/pysatMissions/instruments/pysat_ephem.py
@@ -9,6 +9,7 @@
 
 from __future__ import print_function
 from __future__ import absolute_import
+import datetime as dt
 import functools
 import numpy as np
 
@@ -29,7 +30,7 @@
 tags = {'': 'Satellite simulation data set'}
 # dictionary of satellite IDs, list of corresponding tags
 sat_ids = {'': ['']}
-_test_dates = {'': {'': pysat.datetime(2018, 1, 1)}}
+_test_dates = {'': {'': dt.datetime(2018, 1, 1)}}
 
 
 def init(self):
@@ -45,29 +46,29 @@ def init(self):
 
     """
 
-    # TODO: Update to custom.attach with release of pysat 3.0.0
-    self.custom.attach(mm_magcoord.add_quasi_dipole_coordinates, 'modify')
-    self.custom.attach(mm_magcoord.add_aacgm_coordinates, 'modify')
-    self.custom.attach(mm_sc.calculate_ecef_velocity, 'modify')
-    self.custom.attach(mm_sc.add_ram_pointing_sc_attitude_vectors, 'modify')
+    self.custom.attach(mm_magcoord.add_quasi_dipole_coordinates)
+    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, 'modify')
+    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, 'modify', 'end',
-                       'B_ecef_x', 'B_ecef_y', 'B_ecef_z', 'B_sc_x', 'B_sc_y',
-                       'B_sc_z', meta=[in_meta.copy(), in_meta.copy(),
-                                       in_meta.copy()])
+    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, 'modify')
+    self.custom.attach(mm_emp.add_iri_thermal_plasma)
     # Thermal Neutral parameters
-    self.custom.attach(mm_emp.add_msis, 'modify')
-    self.custom.attach(mm_emp.add_hwm_winds_and_ecef_vectors, 'modify')
+    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, 'modify')
+    self.custom.attach(mm_emp.project_hwm_onto_sc)
 
 
 def load(fnames, tag=None, sat_id=None, obs_long=0., obs_lat=0., obs_alt=0.,
@@ -169,17 +170,17 @@ def load(fnames, tag=None, sat_id=None, obs_long=0., obs_lat=0., obs_alt=0.,
     output = pds.DataFrame(output_params, index=times)
     # modify input object to include calculated parameters
     # put data into DataFrame
-    data = pysat.DataFrame({'glong': output['glong'],
-                            'glat': output['glat'],
-                            'alt': output['alt'],
-                            'position_ecef_x': output['x'],
-                            'position_ecef_y': output['y'],
-                            'position_ecef_z': output['z'],
-                            'obs_sat_az_angle': output['obs_sat_az_angle'],
-                            'obs_sat_el_angle': output['obs_sat_el_angle'],
-                            'obs_sat_slant_range':
-                            output['obs_sat_slant_range']},
-                           index=times)
+    data = pds.DataFrame({'glong': output['glong'],
+                          'glat': output['glat'],
+                          'alt': output['alt'],
+                          'position_ecef_x': output['x'],
+                          'position_ecef_y': output['y'],
+                          'position_ecef_z': output['z'],
+                          'obs_sat_az_angle': output['obs_sat_az_angle'],
+                          'obs_sat_el_angle': output['obs_sat_el_angle'],
+                          'obs_sat_slant_range':
+                          output['obs_sat_slant_range']},
+                         index=times)
     data.index.name = 'Epoch'
 
     return data, meta.copy()

diff --git a/pysatMissions/instruments/pysat_sgp4.py b/pysatMissions/instruments/pysat_sgp4.py
@@ -7,7 +7,9 @@
 
 from __future__ import print_function
 from __future__ import absolute_import
+import datetime as dt
 import functools
+import pandas as pds
 
 import pysat
 
@@ -20,7 +22,7 @@
 tags = {'': 'Satellite simulation data set'}
 # dictionary of satellite IDs, list of corresponding tags
 sat_ids = {'': ['']}
-_test_dates = {'': {'': pysat.datetime(2018, 1, 1)}}
+_test_dates = {'': {'': dt.datetime(2018, 1, 1)}}
 
 
 def init(self):
@@ -117,13 +119,13 @@ def load(fnames, tag=None, sat_id=None, obs_long=0., obs_lat=0., obs_alt=0.,
         velocity.extend(vel)
 
     # put data into DataFrame
-    data = pysat.DataFrame({'position_eci_x': position[::3],
-                            'position_eci_y': position[1::3],
-                            'position_eci_z': position[2::3],
-                            'velocity_eci_x': velocity[::3],
-                            'velocity_eci_y': velocity[1::3],
-                            'velocity_eci_z': velocity[2::3]},
-                           index=times)
+    data = pds.DataFrame({'position_eci_x': position[::3],
+                          'position_eci_y': position[1::3],
+                          'position_eci_z': position[2::3],
+                          'velocity_eci_x': velocity[::3],
+                          'velocity_eci_y': velocity[1::3],
+                          'velocity_eci_z': velocity[2::3]},
+                         index=times)
     data.index.name = 'Epoch'
 
     # TODO: add call for GEI/ECEF translation here

diff --git a/pysatMissions/methods/empirical.py b/pysatMissions/methods/empirical.py
@@ -58,8 +58,8 @@ def add_iri_thermal_plasma(inst, glat_label='glat', glong_label='glong',
     Example
     -------
         # function added velow modifies the inst object upon every inst.load
-        call inst.custom.attach(add_iri_thermal_plasma, 'modify',
-        glat_label='custom_label')
+        call inst.custom.attach(add_iri_thermal_plasma,
+        kwargs={'glat_label': 'custom_label'})
 
     """
 
@@ -70,7 +70,8 @@ def add_iri_thermal_plasma(inst, glat_label='glat', glong_label='glong',
             # Point class is instantiated. Its parameters are a function of
             # time and spatial location
             pt = Point(time, lat, lon, alt)
-            pt.run_iri()
+            # IRI-2016 currently experiencing bugs in pyglow
+            pt.run_iri(version=2012)
             iri = {}
             # After the model is run, its members like Ti, ni[O+], etc. can be
             # accessed
@@ -142,7 +143,7 @@ def add_igrf(inst, glat_label='glat', glong_label='glong', alt_label='alt'):
     Example
     -------
         # function added velow modifies the inst object upon every inst.load
-        call inst.custom.attach(add_igrf, 'modify', glat_label='custom_label')
+        call inst.custom.attach(add_igrf, kwargs={'glat_label': 'custom_label'})
 
     """
 
@@ -236,7 +237,7 @@ def add_msis(inst, glat_label='glat', glong_label='glong', alt_label='alt'):
     Example
     -------
         # function added velow modifies the inst object upon every inst.load
-        call inst.custom.attach(add_msis, 'modify', glat_label='custom_label')
+        call inst.custom.attach(add_msis, kwargs={'glat_label': 'custom_label'})
 
     """
 
@@ -334,8 +335,8 @@ def add_hwm_winds_and_ecef_vectors(inst, glat_label='glat',
     Example
     -------
         # function added velow modifies the inst object upon every inst.load
-        call inst.custom.attach(add_hwm_winds_and_ecef_vectors, 'modify',
-        glat_label='custom_label')
+        call inst.custom.attach(add_hwm_winds_and_ecef_vectors,
+        kwargs={'glat_label': 'custom_label'})
 
     """
 
@@ -441,7 +442,7 @@ def project_hwm_onto_sc(inst):
     Example
     -------
         # function added velow modifies the inst object upon every inst.load
-        call inst.custom.attach(project_hwm_onto_sc, 'modify')
+        call inst.custom.attach(project_hwm_onto_sc)
 
     """
 

diff --git a/pysatMissions/methods/magcoord.py b/pysatMissions/methods/magcoord.py
@@ -38,8 +38,8 @@ def add_aacgm_coordinates(inst, glat_label='glat', glong_label='glong',
     Example
     -------
         # function added velow modifies the inst object upon every inst.load
-        call inst.custom.attach(add_quasi_dipole_coordinates, 'modify',
-        glat_label='custom_label')
+        call inst.custom.attach(add_quasi_dipole_coordinates,
+        kwargs={'glat_label': 'custom_label'})
 
     """
 
@@ -101,8 +101,8 @@ def add_quasi_dipole_coordinates(inst, glat_label='glat', glong_label='glong',
     Example
     -------
         # function added velow modifies the inst object upon every inst.load
-        call inst.custom.attach(add_quasi_dipole_coordinates, 'modify',
-        glat_label='custom_label')
+        call inst.custom.attach(add_quasi_dipole_coordinates,
+        kwargs={'glat_label': 'custom_label'})
 
     """
 

diff --git a/pysatMissions/tests/test_instruments.py b/pysatMissions/tests/test_instruments.py
@@ -5,6 +5,7 @@
 To be replaced once pysat testing techniques are finalized
 """
 
+import datetime as dt
 import numpy as np
 import pysat
 
@@ -27,7 +28,7 @@ def test_basic_instrument_load(self):
         # Check if instrument is instrument
         assert isinstance(self.testInst, pysat._instrument.Instrument)
 
-        self.testInst.load(date=pysat.datetime(2018, 1, 1))
+        self.testInst.load(date=dt.datetime(2018, 1, 1))
         # Check for completeness of first set of targets
         for target in self.targets1:
             # Check if data is added