black_format

Author: scivision

.github/workflows/ci.yml

@@ -13,36 +13,39 @@ jobs:
   linux:
     runs-on: ubuntu-latest
     steps:
-    - uses: actions/checkout@v1
-    - uses: actions/setup-python@v1
+    - uses: actions/checkout@v2
+    - uses: actions/setup-python@v2
       with:
         python-version: '3.x'
-    - run: sudo apt install -yq --no-install-recommends gfortran ninja-build
+
+    - run: sudo apt install -yq --no-install-recommends ninja-build
     - run: pip install -e .[tests,lint]
+
     - run: flake8
-    - run: mypy .
-    - run: pytest -r a -v
+    - run: mypy
+    - run: pytest
 
   macos:
     runs-on: macos-latest
     steps:
-    - uses: actions/checkout@v1
-    - uses: actions/setup-python@v1
+    - uses: actions/checkout@v2
+    - uses: actions/setup-python@v2
       with:
         python-version: '3.x'
-    - run: brew install gcc ninja
+
+    - run: brew install ninja
     - run: pip install -e .[tests]
-    - run: pytest -r a -v
+    - run: pytest
 
   windows:
     runs-on: windows-latest
     steps:
-    - uses: actions/checkout@v1
-    - uses: actions/setup-python@v1
+    - uses: actions/checkout@v2
+    - uses: actions/setup-python@v2
       with:
         python-version: '3.x'
-    - run: cinst -y ninja
+
     - run: echo "[build]`ncompiler=mingw32" | Out-File -Encoding ASCII ~/pydistutils.cfg
       shell: powershell
     - run: pip install -e .[tests]
-    - run: pytest -r a -v
+    - run: pytest

mypy.ini renamed to .mypy.ini

@@ -1,10 +1,8 @@
 [mypy]
+files = iri90/
+
 ignore_missing_imports = True
-strict_optional = False
 allow_redefinition = True
 show_error_context = False
 show_column_numbers = True
 warn_unreachable = False
-
-[mypy-xarray]
-follow_imports = skip

AltitudeProfile.py

@@ -9,23 +9,35 @@
 
 def main():
     p = ArgumentParser()
-    p.add_argument('--alt', help='START STOP STEP altitude [km]', type=float, nargs=3, default=(85, 500, 1.))
-    p.add_argument('-t', '--time', help='date and time of simulation', default='2012-07-21T12:35')
-    p.add_argument('-c', '--latlon', help='geodetic coordinates of simulation', default=(65, -147.5), type=float)
-    p.add_argument('--f107', type=float, default=200.)
-    p.add_argument('--f107a', type=float, default=200.)
-    p.add_argument('--ap', type=int, default=4)
+    p.add_argument(
+        "--alt",
+        help="START STOP STEP altitude [km]",
+        type=float,
+        nargs=3,
+        default=(85, 500, 1.0),
+    )
+    p.add_argument("-t", "--time", help="date and time of simulation", default="2012-07-21T12:35")
+    p.add_argument(
+        "-c",
+        "--latlon",
+        help="geodetic coordinates of simulation",
+        default=(65, -147.5),
+        type=float,
+    )
+    p.add_argument("--f107", type=float, default=200.0)
+    p.add_argument("--f107a", type=float, default=200.0)
+    p.add_argument("--ap", type=int, default=4)
     p = p.parse_args()
-# %% user parameters
+    # %% user parameters
     altkm = np.arange(p.alt[0], p.alt[1], p.alt[2])
     dtime = parse(p.time)
-# %% run IRI90 across altitude
+    # %% run IRI90 across altitude
     iono = iri90.runiri(dtime, altkm, p.latlon, p.f107, p.f107a, ap=p.ap)
-# %% altitude profile plot
+    # %% altitude profile plot
     print(iono)
     ipt.plotalt(iono)
     show()
 
 
-if __name__ == '__main__':
+if __name__ == "__main__":
     main()

TimeProfile.py

@@ -9,28 +9,44 @@
 
 
 def main():
-    p = ArgumentParser(description='IRI90 time profile plot')
-    p.add_argument('-t', '--trange', help='START STOP STEP (hours) time [UTC]', nargs=3,
-                   default=('2012-08-21', '2012-08-22', 0.25))
-    p.add_argument('--alt', help='START STOP STEP altitude [km]', type=float, nargs=3, default=(120, 180, 20))
-    p.add_argument('-c', '--latlon', help='geodetic coordinates of simulation',
-                   type=float, default=(65, -148))
-    p.add_argument('--f107', type=float, default=200.)
-    p.add_argument('--f107a', type=float, default=200.)
-    p.add_argument('--ap', type=int, default=4)
-    p.add_argument('--species', help='species to plot', nargs='+', default=('ne'))
+    p = ArgumentParser(description="IRI90 time profile plot")
+    p.add_argument(
+        "-t",
+        "--trange",
+        help="START STOP STEP (hours) time [UTC]",
+        nargs=3,
+        default=("2012-08-21", "2012-08-22", 0.25),
+    )
+    p.add_argument(
+        "--alt",
+        help="START STOP STEP altitude [km]",
+        type=float,
+        nargs=3,
+        default=(120, 180, 20),
+    )
+    p.add_argument(
+        "-c",
+        "--latlon",
+        help="geodetic coordinates of simulation",
+        type=float,
+        default=(65, -148),
+    )
+    p.add_argument("--f107", type=float, default=200.0)
+    p.add_argument("--f107a", type=float, default=200.0)
+    p.add_argument("--ap", type=int, default=4)
+    p.add_argument("--species", help="species to plot", nargs="+", default=("ne"))
     p = p.parse_args()
-# %% user parameters
+    # %% user parameters
     tlim = (parse(p.trange[0]), parse(p.trange[1]))
     dt = timedelta(hours=p.trange[2])  # timedelta reduces to seconds, etc for sub-hour step size
 
     altkm = np.arange(*p.alt)
-# %% run IRI90 across time
+    # %% run IRI90 across time
     iono = iri90.timeprofile(tlim, dt, altkm, p.latlon, p.f107, p.f107a, ap=p.ap)
-# %% plots
+    # %% plots
     ipt.plottime(iono, p.species)
     show()
 
 
-if __name__ == '__main__':
+if __name__ == "__main__":
     main()

iri90/__init__.py

@@ -6,12 +6,13 @@
 import numpy as np
 import xarray
 from typing import Sequence
+
 #
 import iri90fort
 
 rdir = Path(__file__).parent
-Ts = ['Tn', 'Ti', 'Te']
-simout = ['ne', 'Tn', 'Ti', 'Te', 'nO+', 'nH+', 'nHe+', 'nO2+', 'nNO+']
+Ts = ["Tn", "Ti", "Te"]
+simout = ["ne", "Tn", "Ti", "Te", "nO+", "nH+", "nHe+", "nO2+", "nNO+"]
 
 
 def datetimerange(start: datetime, end: datetime, step: timedelta) -> list:
@@ -20,72 +21,93 @@ def datetimerange(start: datetime, end: datetime, step: timedelta) -> list:
     assert isinstance(end, datetime)
     assert isinstance(step, timedelta)
 
-    return [start + i*step for i in range((end-start) // step)]
-
+    return [start + i * step for i in range((end - start) // step)]
 
-def runiri(time: datetime, altkm: float, glatlon: tuple, f107: float, f107a: float, ap: int) -> xarray.DataArray:
 
+def runiri(
+    time: datetime, altkm: np.ndarray, glatlon: tuple, f107: float, f107a: float, ap: int
+) -> xarray.DataArray:
     def _collect_output() -> xarray.DataArray:
-        """ collect IRI90 output into xarray.DataArray with metadata"""
-        iono = xarray.DataArray(outf[:9, :].T,
-                                coords={'alt_km': altkm, 'sim': simout},
-                                dims=['alt_km', 'sim'],
-                                attrs={'f107': f107, 'f107a': f107a, 'ap': ap, 'glatlon': glatlon, 'time': time})
-
-    #    i=(iono['Ti']<iono['Tn']).values
-    #    iono.ix[i,'Ti'] = iono.ix[i,'Tn']
-
-    #    i=(iono['Te']<iono['Tn']).values
-    #    iono.ix[i,'Te'] = iono.ix[i,'Tn']
-
-# %%   iri90 outputs percentage of Ne
-        iono.loc[:, ['nO+', 'nH+', 'nHe+', 'nO2+', 'nNO+']] *= iono.loc[:, 'ne']/100.
-# %% These two parameters only output if JF(6)=False, otherwise bogus values
+        """collect IRI90 output into xarray.DataArray with metadata"""
+        iono = xarray.DataArray(
+            outf[:9, :].T,
+            coords={"alt_km": altkm, "sim": simout},
+            dims=["alt_km", "sim"],
+            attrs={
+                "f107": f107,
+                "f107a": f107a,
+                "ap": ap,
+                "glatlon": glatlon,
+                "time": time,
+            },
+        )
+
+        #    i=(iono['Ti']<iono['Tn']).values
+        #    iono.ix[i,'Ti'] = iono.ix[i,'Tn']
+
+        #    i=(iono['Te']<iono['Tn']).values
+        #    iono.ix[i,'Te'] = iono.ix[i,'Tn']
+
+        # %%   iri90 outputs percentage of Ne
+        iono.loc[:, ["nO+", "nH+", "nHe+", "nO2+", "nNO+"]] *= iono.loc[:, "ne"] / 100.0
+        # %% These two parameters only output if JF(6)=False, otherwise bogus values
         # iono['nClusterIons'] = iono['ne'] * outf[9,:]/100.
         # iono['nN+'] = iono['ne'] * outf[10,:]/100.
-# %% negative indicates undefined
+        # %% negative indicates undefined
         for c in iono.sim:
-            iono.loc[iono.loc[:, c] <= 0., c] = np.nan
+            iono.loc[iono.loc[:, c] <= 0.0, c] = np.nan
 
         return iono
 
     glat, glon = glatlon
     jmag = 0  # coordinates are: 0:geographic 1: magnetic
 
-    JF = np.array((1, 1, 1, 1, 0, 1,
-                   1, 1, 1, 1, 1, 1), bool)  # Solomon 1993 version of IRI
+    JF = np.array((1, 1, 1, 1, 0, 1, 1, 1, 1, 1, 1, 1), bool)  # Solomon 1993 version of IRI
     # JF = (1,1,1) + (0,0,0) +(1,)*14 + (0,1,0,1,1,1,1,0,0,0,1,1,0,1,0,1,1,1) #for 2013 version of IRI
 
-    monthday = time.month*100 + time.day  # yep, that's how the IRI code wants it, NOT as character.
+    monthday = (
+        time.month * 100 + time.day
+    )  # yep, that's how the IRI code wants it, NOT as character.
     # + 25 hours for UTC time
-    hourfrac = (time.hour+25) + time.minute/60 + time.second/3600
-    datadir = str(rdir/'data')+'/'
-# %% call IRI
-    outf, oarr = iri90fort.iri90(JF, jmag,
-                                 glat, glon % 360.,
-                                 -f107,
-                                 monthday,  # integer
-                                 hourfrac,
-                                 altkm,
-                                 datadir)
+    hourfrac = (time.hour + 25) + time.minute / 60 + time.second / 3600
+    datadir = str(rdir / "data") + "/"
+    # %% call IRI
+    outf, oarr = iri90fort.iri90(
+        JF,
+        jmag,
+        glat,
+        glon % 360.0,
+        -f107,
+        monthday,  # integer
+        hourfrac,
+        altkm,
+        datadir,
+    )
 
     iono = _collect_output()
 
     return iono
 
 
-def timeprofile(tlim: Sequence[datetime], dt: timedelta,
-                altkm: np.ndarray, glatlon: tuple,
-                f107: float, f107a: float, ap: int) -> xarray.DataArray:
+def timeprofile(
+    tlim: Sequence[datetime],
+    dt: timedelta,
+    altkm: np.ndarray,
+    glatlon: tuple,
+    f107: float,
+    f107a: float,
+    ap: int,
+) -> xarray.DataArray:
     """compute IRI90 at a single altiude, over time range"""
 
     T = datetimerange(tlim[0], tlim[1], dt)
 
-    iono = xarray.DataArray(np.empty((len(T), altkm.size, 9)),
-                            coords={'time': T, 'alt_km': altkm, 'sim': simout},
-                            dims=['time', 'alt_km', 'sim'],
-                            attrs={'f107': f107, 'f107a': f107a, 'ap': ap, 'glatlon': glatlon}
-                            )
+    iono = xarray.DataArray(
+        np.empty((len(T), altkm.size, 9)),
+        coords={"time": T, "alt_km": altkm, "sim": simout},
+        dims=["time", "alt_km", "sim"],
+        attrs={"f107": f107, "f107a": f107a, "ap": ap, "glatlon": glatlon},
+    )
 
     for t in T:
         iono.loc[t, ...] = runiri(t, altkm, glatlon, f107, f107a, ap)