Squashed commit of the following:

commit 30fcb0362d06ceedf46abeee729b9398d5d186b4
Author: Michael Hirsch, Ph.D <[email protected]>
Date:   Mon Aug 13 18:50:14 2018 -0400

    allow user to specify wavelength step (short, long, step)

commit 4f0b26421207acaa2d09fcd61d357a765a124532
Author: Michael Hirsch, Ph.D <[email protected]>
Date:   Mon Aug 13 18:07:30 2018 -0400

    cleanup

commit c45c10e76206efade9c0e03543a73aa06601e113
Author: Michael Hirsch, Ph.D <[email protected]>
Date:   Mon Aug 13 18:03:57 2018 -0400

    modularize

Author: scivision

.travis.yml

@@ -28,7 +28,7 @@ script:
 
 after_success:
 - if [[ $TRAVIS_PYTHON_VERSION == 3.6* ]]; then
-  pytest --cov;
+  pytest --cov --cov-config=setup.cfg;
   coveralls;
   fi
 

CMakeLists.txt

@@ -22,17 +22,17 @@ endif()
 
 
 # --- assert lib
-add_library(assert assert.f90)
+add_library(assert src/assert.f90)
 target_compile_options(assert PRIVATE ${FFLAGS})
 
 set(okcomp GNU Intel)
 if(CMAKE_Fortran_COMPILER_ID IN_LIST okcomp)
- target_sources(assert PRIVATE error2008.f90)
+ target_sources(assert PRIVATE src/error2008.f90)
 else()  # non-Fortran 2008 compilers
-  target_sources(assert PRIVATE error2003.f90)
+  target_sources(assert PRIVATE src/error2003.f90)
 endif()
 # ---
-add_executable(testlowtran reference/lowtran_driver.f90 lowtran7.f)
+add_executable(testlowtran reference/lowtran_driver.f90 src/lowtran7.f)
 target_link_libraries(testlowtran PRIVATE assert)
 target_compile_options(testlowtran PRIVATE ${FFLAGS})
 

HorizontalTransmittance.py

@@ -15,13 +15,17 @@ def main():
     p.add_argument('-z', '--obsalt', help='altitude of bother observers on horizontal path [km]', type=float, default=0.3)
     p.add_argument('-r', '--range_km', help='range between observers on horizontal path [km]', type=float, default=1.0)
     p.add_argument('-a', '--zenang', help='zenith angle [deg]  can be single value or list of values', type=float, default=0.)
-    p.add_argument('-w', '--wavelen', help='wavelength range nm (start,stop)', type=float, nargs=2, default=(200, 30000))
+    p.add_argument('-s', '--short', help='shortest wavelength nm ', type=float, default=200)
+    p.add_argument('-l', '--long', help='longest wavelength nm ', type=float, default=30000)
+    p.add_argument('-step', help='wavelength step size cm^-1', type=float, default=20)
     P = p.parse_args()
 
     c1 = {'zmdl': P.obsalt,
           'h1': P.obsalt,
           'range_km': P.range_km,
-          'wlnmlim': P.wavelen,
+          'wlshort': P.short,
+          'wllong': P.long,
+          'wlstep': P.step,
           }
 
     TR = lowtran.horiztrans(c1).squeeze()

README.md

@@ -9,13 +9,11 @@
 
 # Lowtran in Python
 
-LOWTRAN7 atmospheric absorption extinction model. Updated by Michael
-Hirsch to be platform independent and easily accessible from Python.
+LOWTRAN7 atmospheric absorption extinction model. 
+Updated by Michael Hirsch to be platform independent and easily accessible from Python.
 
-The main LOWTRAN program has been made accessible from Python by using
-direct memory transfers instead of the cumbersome and error-prone
-process of writing/reading text files. xarray.Dataset high-performance
-N-D array data is passed out, with all appropriate metadata.
+The main LOWTRAN program has been made accessible from Python by using direct memory transfers instead of the cumbersome and error-prone process of writing/reading text files.
+`xarray.Dataset` high-performance, simple N-D array data is passed out, with appropriate metadata.
 
 
 ## Gallery
@@ -26,7 +24,9 @@ See below for how to make these examples.
 
 ## Install
 
-1. You need a Fortran compiler. If you don't have one, here is how to install Gfortran:
+1. A Fortran compiler such as `gfortran` is needed. 
+   We use `f2py` (part of `numpy`) to seamlessly use the Fortran Lowtran library from Python.
+   If you don't have one, here is how to install Gfortran:
 
    * Linux: `apt install gfortran`
    * Mac: `brew install gcc`
@@ -78,21 +78,25 @@ Right now a lot of configuration features aren't implemented, please request tho
 ### Fortran (optional)
 
 This is not necessary for normal users:
+```sh
+cd bin
+cmake ..
+cmake --build .
+ctest -V
+```
 
-    cd bin
-    cmake ..
-    make
-    make test
-
-should generate [this text output](https://gist.github.com/drhirsch/89ef2060d8f15b0a60914d13a61e33ab).
+should generate 
+[this text output](https://gist.github.com/drhirsch/89ef2060d8f15b0a60914d13a61e33ab).
 
 ### Windows f2py
 
 (this is handled automatically by `setup.py`, noted here for debugging)
 
-Yes, even though you're [using a 64-bit compiler](https://scivision.co/f2py-running-fortran-code-in-python-on-windows/):
-
-    f2py --compiler=mingw32 -m lowtran7 -c lowtran7.f
+Yes, even though you're 
+[using a 64-bit compiler](https://scivision.co/f2py-running-fortran-code-in-python-on-windows/):
+```sh
+f2py --compiler=mingw32 -m lowtran7 -c lowtran7.f
+```
 
 Tested on Windows with
 [MinGW](https://sourceforge.net/projects/mingw-w64/).

ScatterRadiance.py

@@ -15,7 +15,7 @@
 from matplotlib.pyplot import show
 try:
     import seaborn as sns
-    sns.set_context('talk', font_scale=1.5)
+    sns.set_context('talk')
 except ImportError:
     pass
 from argparse import ArgumentParser
@@ -27,7 +27,9 @@ def main():
     p = ArgumentParser(description='Lowtran 7 interface')
     p.add_argument('-z', '--obsalt', help='altitude of observer [km]', type=float, default=0.)
     p.add_argument('-a', '--zenang', help='Observer zenith angle [deg] ', nargs='+', type=float, default=[0., 60, 80])
-    p.add_argument('-w', '--wavelen', help='wavelength range nm (start,stop)', type=float, nargs=2, default=(300, 1000))
+    p.add_argument('-s', '--short', help='shortest wavelength nm ', type=float, default=400)
+    p.add_argument('-l', '--long', help='longest wavelength nm ', type=float, default=700)
+    p.add_argument('-step', help='wavelength step size cm^-1', type=float, default=20)
     p.add_argument('-o', '--outfn', help='NetCDF4 file to write')
     p.add_argument('--model', help='0-6, see Card1 "model" reference. 5=subarctic winter', type=int, default=5)
 
@@ -36,7 +38,9 @@ def main():
     c1 = {'model': P.model,
           'h1': P.obsalt,  # of observer
           'angle': P.zenang,  # of observer
-          'wlnmlim': P.wavelen,
+          'wlshort': P.short,
+          'wllong': P.long,
+          'wlstep': P.step,
           }
 # %%
     TR = lowtran.scatter(c1)

SolarIrradiance.py

@@ -14,14 +14,18 @@ def main():
     p = ArgumentParser(description='Lowtran 7 interface')
     p.add_argument('-z', '--obsalt', help='altitude of observer [km]', type=float, default=0.)
     p.add_argument('-a', '--zenang', help='zenith angle [deg]  of sun or moon', nargs='+', type=float, default=[0, 60, 80])
-    p.add_argument('-w', '--wavelen', help='wavelength range nm (start,stop)', type=float, nargs=2, default=(200, 25000))
+    p.add_argument('-s', '--short', help='shortest wavelength nm ', type=float, default=200)
+    p.add_argument('-l', '--long', help='longest wavelength nm ', type=float, default=30000)
+    p.add_argument('-step', help='wavelength step size cm^-1', type=float, default=20)
     p.add_argument('--model', help='0-6, see Card1 "model" reference. 5=subarctic winter', type=int, default=5)
     P = p.parse_args()
 
     c1 = {'model': P.model,
           'h1': P.obsalt,
           'angle': P.zenang,  # zenith angle of sun or moon
-          'wlnmlim': P.wavelen,
+          'wlshort': P.short,
+          'wllong': P.long,
+          'wlstep': P.step,
           }
 
     irr = lowtran.irradiance(c1)

ThermalRadiance.py

@@ -23,7 +23,9 @@ def main():
     p = ArgumentParser(description='Lowtran 7 interface')
     p.add_argument('-z', '--obsalt', help='altitude of observer [km]', type=float, default=0.)
     p.add_argument('-a', '--zenang', help='Observer zenith angle [deg] ', nargs='+', type=float, default=[0., 60, 80])
-    p.add_argument('-w', '--wavelen', help='wavelength range nm (start,stop)', type=float, nargs=2, default=(200, 30000))
+    p.add_argument('-s', '--short', help='shortest wavelength nm ', type=float, default=200)
+    p.add_argument('-l', '--long', help='longest wavelength nm ', type=float, default=30000)
+    p.add_argument('-step', help='wavelength step size cm^-1', type=float, default=20)
     p.add_argument('-o', '--outfn', help='HDF5 file to write')
     p.add_argument('--model', help='0-6, see Card1 "model" reference. 5=subarctic winter', type=int, default=5)
 
@@ -32,7 +34,9 @@ def main():
     c1 = {'model': P.model,
           'h1': P.obsalt,  # of observer
           'angle': P.zenang,  # of observer
-          'wlnmlim': P.wavelen,
+          'wlshort': P.short,
+          'wllong': P.long,
+          'wlstep': P.step,
           }
 
     TR = lowtran.radiance(c1)

TransmittanceGround2Space.py

@@ -9,14 +9,18 @@ def main():
     p = ArgumentParser(description='Lowtran 7 interface')
     p.add_argument('-z', '--obsalt', help='altitude of observer [km]', type=float, default=0.)
     p.add_argument('-a', '--zenang', help='observer zenith angle [deg]', type=float, nargs='+', default=[0, 60, 80])
-    p.add_argument('-w', '--wavelen', help='wavelength range nm (start,stop)', type=float, nargs=2, default=(200, 30000))
+    p.add_argument('-s', '--short', help='shortest wavelength nm ', type=float, default=200)
+    p.add_argument('-l', '--long', help='longest wavelength cm^-1 ', type=float, default=30000)
+    p.add_argument('-step', help='wavelength step size cm^-1', type=float, default=20)
     p.add_argument('--model', help='0-6, see Card1 "model" reference. 5=subarctic winter', type=int, default=5)
     P = p.parse_args()
 
     c1 = {'model': P.model,
           'h1': P.obsalt,
           'angle': P.zenang,
-          'wlnmlim': P.wavelen,
+          'wlshort': P.short,
+          'wllong': P.long,
+          'wlstep': P.step,
           }
 
     TR = lowtran.transmittance(c1)

UserDataHorizontalRadiance.py

@@ -14,15 +14,19 @@ def main():
     p.add_argument(
         'ptfn', help='csv file with time,relative humidity [%],ambient temperature [K], total pressure (millibar)', nargs='?')
     p.add_argument('-z', '--obsalt', help='altitude of observer [km]', type=float, default=0.05)
-    p.add_argument('-w', '--wavelen', help='wavelength range nm (start,stop)', type=float, nargs=2, default=(200, 30000))
+    p.add_argument('-s', '--short', help='shortest wavelength nm ', type=float, default=200)
+    p.add_argument('-l', '--long', help='longest wavelength nm ', type=float, default=30000)
+    p.add_argument('-step', help='wavelength step size cm^-1', type=float, default=20)
     p.add_argument('-o', '--outfn', help='HDF5 file to write')
     P = p.parse_args()
 
 # %% low-level Lowtran configuration for this scenario, don't change
     c1 = {'range_km': P.obsalt,
           'zmdl': P.obsalt,
           'h1': P.obsalt,
-          'wlnmlim': P.wavelen,
+          'wlshort': P.short,
+          'wllong': P.long,
+          'wlstep': P.step,
           }
 
     TR = lowtran.horizrad(P.ptfn, P.outfn, c1)

UserHorizontalTransmittance.py

@@ -18,13 +18,17 @@ def main():
     p.add_argument('-z', '--obsalt', help='altitude of bother observers on horizontal path [km]', type=float, default=0.3)
     p.add_argument('-r', '--range_km', help='range between observers on horizontal path [km]', type=float, default=1.0)
     p.add_argument('-a', '--zenang', help='zenith angle [deg]  can be single value or list of values', type=float, default=0.)
-    p.add_argument('-w', '--wavelen', help='wavelength range nm (start,stop)', type=float, nargs=2, default=(200, 30000))
+    p.add_argument('-s', '--short', help='shortest wavelength nm ', type=float, default=200)
+    p.add_argument('-l', '--long', help='longest wavelength nm ', type=float, default=30000)
+    p.add_argument('-step', help='wavelength step size cm^-1', type=float, default=20)
     P = p.parse_args()
 
     c1 = {'zmdl': P.obsalt,
           'h1': P.obsalt,
           'range_km': P.range_km,
-          'wlnmlim': P.wavelen,
+          'wlshort': P.short,
+          'wllong': P.long,
+          'wlstep': P.step,
           }
 
     atmos = {'p': 949., 't': 283.8, 'wmol': [93.96, 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0.]}