metadata and Matlab CI

cleanup

cmake/meson template

meson

.appveyor.yml

@@ -8,7 +8,7 @@ environment:
   MINGW_DIR: C:\mingw-w64\x86_64-7.2.0-posix-seh-rt_v5-rev1\mingw64\bin
   PY_DIR: C:\Python37-x64
 
-clone_depth: 3
+clone_depth: 25
 
 build: off
 

.coveragerc

@@ -0,0 +1,20 @@
+[run]
+cover_pylib = false
+omit =
+  /home/travis/virtualenv/*
+  */site-packages/*
+  */bin/*
+
+[report]
+exclude_lines =
+  pragma: no cover
+  def __repr__
+  except RuntimeError
+  except NotImplementedError
+  except ImportError
+  except FileNotFoundError
+  except CalledProcessError
+  logging.warning
+  logging.error
+  logging.critical
+  if __name__ == .__main__.:

.flake8

@@ -0,0 +1,3 @@
+[flake8]
+max-line-length = 132
+exclude = .git,__pycache__,.eggs/,doc/,docs/,build/,dist/,archive/

.travis.yml

@@ -3,7 +3,7 @@ group: travis_latest
 dist: xenial
 
 git:
-  depth: 3
+  depth: 25
   quiet: true
 
 python:
@@ -20,21 +20,21 @@ matrix:
   - os: linux
     python: 3.7
     install: pip install -e .[tests,cov]
-    script: 
+    script:
     - flake8
-    - mypy . --ignore-missing-imports
+    - mypy .
     after_success:
-    - pytest --cov --cov-config=setup.cfg
+    - pytest --cov
     - coveralls
   - os: osx
-    language: sh
-    before_install: brew install gcc
+    language: minimal
+    before_install: brew install gcc > /dev/null
     install: pip3 install -e .[tests]
-  - os: windows
-    language: sh
-    before_install:
-    - choco install python3
-    - export PATH="/c/Python37:/c/Python37/Scripts:$PATH"
+#  - os: windows
+#    language: minimal
+#    before_install:
+#    - choco install python3
+#    - export PATH="/c/Python37:/c/Python37/Scripts:$PATH"
 
 
 install: pip install -e .[tests]

CMakeLists.txt

@@ -1,16 +1,13 @@
 cmake_minimum_required(VERSION 3.7)
+if(NOT CMAKE_BUILD_TYPE)
+  set(CMAKE_BUILD_TYPE Release CACHE STRING "Debug or Release")
+endif()
 project(lowtran Fortran)
 enable_testing()
 
 include(cmake/compilers.cmake)
 
 add_executable(testlowtran src/lowtran_driver.f90 src/lowtran7.f src/assert.f90)
-if(f2008)
- target_sources(testlowtran PRIVATE src/error2008.f90)
-else()  
-  target_sources(testlowtran PRIVATE src/error2003.f90)
-endif()
-target_link_libraries(testlowtran PRIVATE ${FLIBS})
 target_compile_options(testlowtran PRIVATE ${FFLAGS})
 
 add_test(NAME FortranObs2space COMMAND testlowtran obs2space)

README.md

@@ -8,8 +8,8 @@
 
 # Lowtran in Python
 
-LOWTRAN7 atmospheric absorption extinction model. 
-Updated by Michael Hirsch to be platform independent and easily accessible from Python ≥ 3.6 and 
+LOWTRAN7 atmospheric absorption extinction model.
+Updated by Michael Hirsch to be platform independent and easily accessible from Python ≥ 3.6 and
 [Matlab](#matlab).
 
 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.
@@ -39,40 +39,41 @@ We use `f2py` (part of `numpy`) to seamlessly use Fortran libraries from Python
 
 ## Examples
 
-In these examples, you can write to HDF5 with the `-o` option. 
+In these examples, you can write to HDF5 with the `-o` option.
 
 We present examples of:
 
-* ground-to-space transmittance: 
+* ground-to-space transmittance:
   [TransmittanceGround2Space.py](./TransmittanceGround2Space.py)
 
   ![Lowtran Transmission](./doc/txgnd2space.png)
-* sun-to-observer scattered radiance (why the sky is blue): 
+* sun-to-observer scattered radiance (why the sky is blue):
   [ScatterRadiance.py](./ScatterRadiance.py)
 
   ![Lowtran Scatter Radiance](./gfx/whyskyisblue.png)
-* sun-to-observer irradiance: 
+* sun-to-observer irradiance:
   [SolarIrradiance.py](./SolarIrradiance.py)
 
   ![Lowtran Solar Irradiance](./gfx/irradiance.png)
-* observer-to-observer solar single-scattering solar radiance (up-going) with custom Pressure, Temperature and partial pressure for 12 species:    
+* observer-to-observer solar single-scattering solar radiance (up-going) with custom Pressure, Temperature and partial pressure for 12 species:
   [UserDataHorizontalRadiance.py](./UserDataHorizontalRadiance.py)
   ![Lowtran Solar Irradiance](./gfx/thermalradiance.png)
-* observer-to-observer transmittance with custom Pressure, Temperature and partial pressure for 12 species:  
+* observer-to-observer transmittance with custom Pressure, Temperature and partial pressure for 12 species:
   [UserDataHorizontalTransmittance.py](./UserDataHorizontalTransmittance.py)
 * observer-to-observer transmittance:
   [HorizontalTransmittance.py](./HorizontalTransmittance.py)
 
   ![Lowtran Horizontal Path transmittance](./gfx/horizcompare.png)
 
 ### Matlab
-Matlab users can seamlessly access Python modules, as demonstrated in 
-[RunLowtran.m](./matlab/RunLowtran.m) and 
+
+Matlab users can seamlessly access Python modules, as demonstrated in
+[RunLowtran.m](./matlab/RunLowtran.m) and
 [lowtran_transmission.m](./matlab/lowtran_transmission.m).
 
 Here's what's you'll need:
 
-1. [Setup Python ↔ Matlab interface](https://www.scivision.co/matlab-python-user-module-import/).
+1. [Setup Python ↔ Matlab interface](https://www.scivision.dev/matlab-python-user-module-import/).
 2. Install Lowtran in Python as at the top of this Readme.
 3. From Matlab, verify everything is working by from the `lowtran/` directory:
    ```matlab
@@ -82,7 +83,7 @@ Here's what's you'll need:
 
 ## Notes
 
-LOWTRAN7 
+LOWTRAN7
 [User manual](http://www.dtic.mil/dtic/tr/fulltext/u2/a206773.pdf)
 Refer to this to understand what parameters are set to default.
 Currently I don't have any aerosols enabled for example, though it's straightforward to add them into the code.
@@ -106,6 +107,6 @@ cmake --build .
 ctest -V
 ```
 
-should generate 
+should generate
 [this text output](https://gist.github.com/drhirsch/89ef2060d8f15b0a60914d13a61e33ab).
 

cmake/compilers.cmake

@@ -1,8 +1,3 @@
-if(CMAKE_BUILD_TYPE STREQUAL Debug)
-  add_compile_options(-g -O0)
-else()
-  add_compile_options(-O3)
-endif()
 
 if(CMAKE_Fortran_COMPILER_ID STREQUAL GNU)
   list(APPEND FFLAGS -mtune=native)
@@ -14,14 +9,5 @@ elseif(CMAKE_Fortran_COMPILER_ID STREQUAL Intel)
 elseif(CMAKE_Fortran_COMPILER_ID STREQUAL PGI)
 
 elseif(CMAKE_Fortran_COMPILER_ID STREQUAL Flang)
-  list(APPEND FFLAGS -Mallocatable=03)
-  list(APPEND FLIBS -static-flang-libs)
-endif()
-
-# ---
-
-include(CheckFortranSourceCompiles)
-
-check_fortran_source_compiles("program es; error stop; end" f2008
-                              SRC_EXT f90)
 
+endif()

meson.build

@@ -0,0 +1,6 @@
+project('lowtran', 'fortran', default_options : ['default_library=static'])
+
+lowtran_exe = executable('testlowtran', 'src/lowtran_driver.f90', 'src/lowtran7.f', 'src/assert.f90')
+
+test('Obs2space', lowtran_exe, args: 'obs2space')
+test('SolarRadiance', lowtran_exe, args: 'solarrad')

mypy.ini

@@ -0,0 +1,6 @@
+[mypy]
+ignore_missing_imports = True
+strict_optional = False
+allow_redefinition = True
+show_error_context = False
+show_column_numbers = True

setup.cfg

@@ -4,7 +4,7 @@ version = 2.4.0
 author = Michael Hirsch, Ph.D.
 author_email = scivision@users.noreply.github.com
 description = Model of Earth atmosphere absorption and transmission vs. wavelength and location.
-url = https://github.com/scivision/lowtran
+url = https://github.com/space-physics/lowtran
 keywords =
   mesosphere
   stratosphere
@@ -17,8 +17,10 @@ classifiers =
   Programming Language :: Fortran
   Programming Language :: Python :: 3.6
   Programming Language :: Python :: 3.7
+  Programming Language :: Python :: 3.8
   Topic :: Scientific/Engineering :: Atmospheric Science
-license_file = LICENSE
+license_files =
+  LICENSE.txt
 long_description = file: README.md
 long_description_content_type = text/markdown
 
@@ -28,8 +30,16 @@ setup_requires =
   setuptools >= 38.6
   pip >= 10
   twine >= 1.11
-include_package_data = True
 packages = find:
+scripts =
+  HorizontalTransmittance.py
+  ThermalRadiance.py
+  UserHorizontalTransmittance.py
+  ScatterRadiance.py
+  TransmittanceGround2Space.py
+  Wavelength2LowtranWavenumber.py
+  SolarIrradiance.py
+  UserDataHorizontalRadiance.py
 install_requires =
   python-dateutil
   numpy
@@ -57,29 +67,3 @@ console_scripts =
   UserDataHorizontalRadiance = UserDataHorizontalRadiance:main
   UserHorizontalTransmittance = UserHorizontalTransmittance:main
   Wavelength2LowtranWavenumber = Wavelength2LowtranWavenumber:main
-
-[flake8]
-max-line-length = 132
-exclude = .git,__pycache__,.eggs/,doc/,docs/,build/,dist/,archive/
-
-[coverage:run]
-cover_pylib = false
-omit =
-  /home/travis/virtualenv/*
-  */site-packages/*
-  */bin/*
-
-[coverage:report]
-exclude_lines =
-  pragma: no cover
-  def __repr__
-  except RuntimeError
-  except NotImplementedError
-  except ImportError
-  except FileNotFoundError
-  except CalledProcessError
-  logging.warning
-  logging.error
-  logging.critical
-  if __name__ == .__main__.:
-

src/assert.f90

@@ -4,14 +4,13 @@ module assert
   use, intrinsic:: iso_c_binding, only: sp=>c_float, dp=>c_double
   use, intrinsic:: iso_fortran_env, only: stderr=>error_unit
   use, intrinsic:: ieee_arithmetic
-  use error
   implicit none
-  
+
   private
 
   integer,parameter :: wp = sp
-  
-  public :: wp,isclose, assert_isclose, errorstop
+
+  public :: wp,isclose, assert_isclose
 
 contains
 
@@ -42,11 +41,11 @@ elemental logical function isclose(actual, desired, rtol, atol, equal_nan)
   if (present(rtol)) r = rtol
   if (present(atol)) a = atol
   if (present(equal_nan)) n = equal_nan
-  
+
   !print*,r,a,n,actual,desired
 
 !--- sanity check
-  if ((r < 0._wp).or.(a < 0._wp)) call errorstop
+  if ((r < 0._wp).or.(a < 0._wp)) error stop "impossible tolerance"
 !--- simplest case -- too unlikely, especially for arrays?
   !isclose = (actual == desired)
   !if (isclose) return
@@ -79,10 +78,10 @@ impure elemental subroutine assert_isclose(actual, desired, rtol, atol, equal_na
   real(wp), intent(in), optional :: rtol, atol
   logical, intent(in), optional :: equal_nan
   character(*), intent(in), optional :: err_msg
-  
+
   if (.not.isclose(actual,desired,rtol,atol,equal_nan)) then
     write(stderr,*) merge(err_msg,'',present(err_msg)),': actual',actual,'desired',desired
-    call errorstop
+    error stop "values not within specified tolerances"
   endif
 
 end subroutine assert_isclose

tests/test_lowtran.m

@@ -1,11 +1,5 @@
 %% environment
 assert(~verLessThan('matlab', '9.5'), 'Matlab >= R2018b required')
-v = ver('matlab');
-mv = v.Version;
-pv = pyversion;
-switch(mv)
-  case '9.5', assert(pv=="3.6", 'Matlab <-> Python version mismatch')
-end
 
 %% simple
 cwd = fileparts(mfilename('fullpath'));

tests/test_matlab.py

@@ -2,17 +2,16 @@
 from pathlib import Path
 import subprocess
 import pytest
+import shutil
 
 R = Path(__file__).parent
+MATLAB = shutil.which('matlab')
 
 
+@pytest.mark.skipif(not MATLAB, reason='Matlab not found')
 def test_matlab_api():
-    try:
-        subprocess.check_call(['matlab', '-nojvm', '-r',
-                               'r=runtests(); exit(any([r.Failed]))'],
-                              cwd=R, timeout=60)
-    except FileNotFoundError as e:
-        pytest.skip(f'Matlab not available  {e}')
+    subprocess.check_call(['matlab', '-batch', 'r=runtests(); exit(any([r.Failed]))'],
+                          cwd=R, timeout=60)
 
 
 if __name__ == '__main__':