pep8 /typehint, matlab template

unify api -- auto or manual geomag indices

make CI cover more by default

add azure

add octave CI

fix indices for test

.appveyor.yml

@@ -1,8 +1,8 @@
 image:
 - Visual Studio 2017
-- ubuntu1804
+#- ubuntu1804  # bad xarray appveyor
 
-stack: python 3.7
+stack: python 3
 
 environment:
   MINGW_DIR: C:\mingw-w64\x86_64-7.2.0-posix-seh-rt_v5-rev1\mingw64\bin

.travis.yml

@@ -22,7 +22,7 @@ matrix:
     python: 3.7
     install:
     - python setup.py install
-    - pip install $(basename $TRAVIS_REPO_SLUG)[tests,full]
+    - pip install $(basename $TRAVIS_REPO_SLUG)[tests]
     script:
     - cd $HOME
     - python -m pytest $TRAVIS_BUILD_DIR/tests -r a -v
@@ -33,6 +33,7 @@ matrix:
     script:
     - flake8
     - mypy .
+    - pytest -r a -v
     after_success:
     - pytest --cov
     - coveralls

MSISE00.py

@@ -16,18 +16,19 @@
 try:
     from matplotlib.pyplot import show
     import msise00.plots as msplots
-    import seaborn as sns
-    sns.set_style('ticks')
 except ImportError as e:
     print(e)
     msplots = None  # type: ignore
+try:
+    import seaborn as sns
+    sns.set_style('ticks')
+except ImportError:
+    pass
 
 
 def main():
     p = ArgumentParser(description='calls MSISE-00 from Python, save to NetCDF4 and/or plot')
-    p.add_argument('-t', '--time',
-                   help='time: (single time or START STOP (1 hour time step) or list of times)',
-                   nargs='+', required=True)
+    p.add_argument('-t', '--time', help='time or times', nargs='+', required=True)
     p.add_argument('-a', '--altkm', help='altitude (km). scalar, or (start,stop,step) or list of alts.',
                    type=float, nargs='+', required=True)
     p.add_argument('-c', '--latlon', help='geodetic latitude/longitude (deg)',

README.md

@@ -1,5 +1,6 @@
 [![Zenodo DOI](https://zenodo.org/badge/32971905.svg)](https://zenodo.org/badge/latestdoi/32971905)
 
+[![Build Status](https://dev.azure.com/mhirsch0512/MSISE00/_apis/build/status/space-physics.msise00?branchName=master)](https://dev.azure.com/mhirsch0512/MSISE00/_build/latest?definitionId=5&branchName=master)
 [![Build Status](https://travis-ci.com/space-physics/msise00.svg?branch=master)](https://travis-ci.com/space-physics/msise00)
 [![Coverage Status](https://coveralls.io/repos/github/space-physics/msise00/badge.svg?branch=master)](https://coveralls.io/github/space-physics/msise00?branch=master)
 [![Build status](https://ci.appveyor.com/api/projects/status/oje6aax4lx4tcryt?svg=true)](https://ci.appveyor.com/project/scivision/msise00)
@@ -115,13 +116,6 @@ Matlab and GNU Octave users can seamlessly access Python modules, as demonstrate
    runtests('tests')
    ```
 
-### Time Utiliies
-
-Time utilities of general interest include:
-
-* `msise00.todatetime`
-* `msise00.todt64`
-
 ## Fortran source
 
 The MSISE00 Fortran source code may also be used directly.

azure-pipelines.yaml

@@ -0,0 +1,65 @@
+jobs:
+
+- job: Ubuntu
+  pool:
+    vmImage: ubuntu-latest
+
+  steps:
+  - task: UsePythonVersion@0
+    inputs:
+      versionSpec: '3.6'
+      addToPath: true
+  - script: sudo apt install -yq --no-install-recommends gfortran
+    displayName: 'Install Prereqs'
+  - script: pip install -e .[tests]
+    displayName: 'Build Python'
+  - script: pytest -r a -v
+    displayName: 'PyTest'
+
+- job: MacOS
+  pool:
+    vmImage: macOS-10.14
+
+  steps:
+  - task: UsePythonVersion@0
+    inputs:
+      versionSpec: '3.6'
+      addToPath: true
+  - script: brew install gcc
+    displayName: 'Install Prereqs'
+  - script: pip install -e .[tests]
+    displayName: 'Build Python'
+  - script: pytest -r a -v
+    displayName: 'PyTest'
+
+- job: MacOS
+  pool:
+    vmImage: macOS-10.14
+
+  steps:
+  - task: UsePythonVersion@0
+    inputs:
+      versionSpec: '3.6'
+      addToPath: true
+  - script: brew install gcc octave
+    displayName: 'Install Prereqs'
+  - script: pip install -e .[tests]
+    displayName: 'Build Python'
+  - script: pytest -r a -v
+    displayName: 'PyTest'
+
+- job: WindowsMinGW
+  pool:
+    vmImage: windows-2019
+
+  steps:
+  - task: UsePythonVersion@0
+    inputs:
+      versionSpec: '3.6'
+      addToPath: true
+  - script: cinst -y mingw
+    displayName: 'Install Prereqs'
+  - script: pip install -e .[tests]
+    displayName: 'Build Python'
+  - script: pytest -r a -v
+    displayName: 'PyTest'

matlab/build.m

@@ -0,0 +1,65 @@
+function build(build_sys, srcdir, builddir)
+% build with 'meson' or 'cmake'
+
+validateattributes(build_sys, {'char'}, {'vector'})
+
+if nargin < 3
+cwd = fileparts(mfilename('fullpath'));
+srcdir =   [cwd, filesep,'..', filesep, 'src'];
+builddir = [cwd, filesep,'..',filesep,'build'];
+end
+
+assert(exist(srcdir,'dir')==7, ['source directory ',srcdir,' does not exist'])
+assert(exist(builddir,'dir')==7, ['build directory ',builddir,' does not exist'])
+
+switch build_sys
+  case 'meson', build_meson(srcdir, builddir)
+  case 'cmake', build_cmake(srcdir, builddir)
+  otherwise error('Specifiy "meson" or "cmake" to build this project.')
+end
+
+end
+
+
+function build_cmake(srcdir, builddir)
+%% build using CMake
+
+validateattributes(srcdir,{'char'},{'vector'})
+validateattributes(builddir,{'char'},{'vector'})
+
+runcmd('cmake --version')
+
+if ispc
+  wopts = '-G "MinGW Makefiles" -DCMAKE_SH="CMAKE_SH-NOTFOUND"';
+else
+  wopts = '';
+end
+
+ccmd = ['cmake ', wopts, ' -S ', srcdir, ' -B ', builddir];
+
+runcmd(ccmd)
+
+runcmd(['cmake --build ',builddir, ' --parallel'])
+
+end
+
+
+function build_meson(srcdir, builddir)
+%% build using Meson + Ninja
+
+validateattributes(srcdir,{'char'},{'vector'})
+validateattributes(builddir,{'char'},{'vector'})
+
+disp('Meson: ')
+runcmd('meson --version')
+
+disp('Ninja: ')
+runcmd('ninja --version')
+
+if ~exist([builddir,filesep,'build.ninja'], 'file')
+  runcmd(['meson setup ',builddir,' ',srcdir])
+end
+
+runcmd(['ninja -C ',builddir])
+
+end

matlab/runcmd.m

@@ -5,5 +5,4 @@ function runcmd(cmd)
 [status, ret] = system(cmd);
 if status~=0, error(ret), end
 disp(ret)
-
 end

msise00/base.py

@@ -9,7 +9,7 @@
 import xarray
 import numpy as np
 import subprocess
-from typing import Union, List
+import typing
 from pathlib import Path
 import io
 import shutil
@@ -31,30 +31,31 @@
 first = True
 
 
-def run(time: datetime, altkm: float,
-        glat: Union[float, np.ndarray], glon: Union[float, np.ndarray], *,
-        f107a: float = None, f107: float = None, Ap: int = None) -> xarray.Dataset:
+def run(time: datetime,
+        altkm: float,
+        glat: typing.Union[float, np.ndarray],
+        glon: typing.Union[float, np.ndarray],
+        indices: typing.Dict[str, typing.Any] = {}) -> xarray.Dataset:
     """
     loops the rungtd1d function below. Figure it's easier to troubleshoot in Python than Fortran.
     """
     glat = np.atleast_2d(glat)
     glon = np.atleast_2d(glon)  # has to be here
 # %% altitude 1-D
     if glat.size == 1 and glon.size == 1 and isinstance(time, (str, date, datetime, np.datetime64)):
-        atmos = rungtd1d(time, altkm, glat.squeeze()[()], glon.squeeze()[()],
-                         f107a=f107a, f107=f107, Ap=Ap)
+        atmos = rungtd1d(time, altkm, glat.squeeze()[()], glon.squeeze()[()], indices)
 # %% lat/lon grid at 1 altitude
     else:
-        atmos = loopalt_gtd(time, glat, glon, altkm,
-                            f107a=f107a, f107=f107, Ap=Ap)
+        atmos = loopalt_gtd(time, glat, glon, altkm, indices)
 
     return atmos
 
 
 def loopalt_gtd(time: datetime,
-                glat: Union[float, np.ndarray], glon: Union[float, np.ndarray],
-                altkm: Union[float, List[float], np.ndarray], *,
-                f107a: float = None, f107: float = None, Ap: int = None) -> xarray.Dataset:
+                glat: typing.Union[float, np.ndarray],
+                glon: typing.Union[float, np.ndarray],
+                altkm: typing.Union[float, typing.Sequence[float], np.ndarray],
+                indices: typing.Dict[str, typing.Any] = {}) -> xarray.Dataset:
     """
     loop over location and time
 
@@ -78,8 +79,7 @@ def loopalt_gtd(time: datetime,
             for j in range(glat.shape[1]):
                 # atmos = xarray.concat((atmos, rungtd1d(t, altkm, glat[i,j], glon[i,j])),
                 #                      data_vars='minimal',coords='minimal',dim='lon')
-                atm = rungtd1d(t, altkm, glat[i, j], glon[i, j],
-                               f107a=f107a, f107=f107, Ap=Ap)
+                atm = rungtd1d(t, altkm, glat[i, j], glon[i, j], indices)
                 atmos = xarray.merge((atmos, atm))
 
     atmos.attrs = atm.attrs
@@ -89,25 +89,24 @@ def loopalt_gtd(time: datetime,
 
 def rungtd1d(time: datetime,
              altkm: np.ndarray,
-             glat: float, glon: float, *,
-             f107a: float = None, f107: float = None, Ap: int = None) -> xarray.Dataset:
+             glat: float,
+             glon: float,
+             indices: typing.Dict[str, typing.Any] = {}) -> xarray.Dataset:
     """
     This is the "atomic" function looped by other functions
     """
     time = todatetime(time)
     # %% get solar parameters for date
-    if f107a and f107a and Ap:
-        pass
-    else:
-        f107Ap = gi.getApF107(time, smoothdays=81)
-        f107a = f107Ap['f107s'].item()
-        f107 = f107Ap['f107'].item()
-        Ap = f107Ap['Ap'].item()
+    if not indices:
+        indices = gi.getApF107(time, smoothdays=81).squeeze()
 # %% dimensions
     altkm = np.atleast_1d(altkm)
-    assert altkm.ndim == 1
-    assert isinstance(glon, (int, float))
-    assert isinstance(glat, (int, float))
+    if altkm.ndim != 1:
+        raise ValueError('altitude read incorrectly')
+    if not isinstance(glon, (int, float, np.int32, np.int64)):
+        raise TypeError('single longitude only')
+    if not isinstance(glat, (int, float, np.int32, np.int64)):
+        raise TypeError('single latitude only')
 
 # %%
     iyd = time.strftime('%y%j')
@@ -119,7 +118,10 @@ def rungtd1d(time: datetime,
         cmd = [EXE,
                iyd, str(time.hour), str(time.minute), str(time.second),
                str(glat), str(glon),
-               str(f107a), str(f107), str(Ap), str(a)]
+               str(indices['f107s']),
+               str(indices['f107']),
+               str(indices['Ap']),
+               str(a)]
 
         ret = subprocess.check_output(cmd,
                                       universal_newlines=True,
@@ -134,7 +136,9 @@ def rungtd1d(time: datetime,
 
     atmos = xarray.Dataset(dsf,
                            coords={'time': [time], 'alt_km': altkm, 'lat': [glat], 'lon': [glon], },
-                           attrs={'Ap': Ap, 'f107': f107, 'f107a': f107a,
-                                  'species': species})
+                           attrs={'species': species,
+                                  'f107s': indices['f107s'],
+                                  'f107': indices['f107'],
+                                  'Ap': indices['Ap']})
 
     return atmos