Merge pull request #39 from wtbarnes/master

Reorganize tests to use pytest

.gitignore

@@ -100,6 +100,7 @@ nosetests.xml
 coverage.xml
 *,cover
 .hypothesis/
+.pytest_cache/
 
 # Translations
 *.mo
@@ -144,3 +145,5 @@ ENV/
 
 # Rope project settings
 .ropeproject
+
+

.travis.yml

@@ -9,7 +9,8 @@ jobs:
   include:
   - stage: test
     script:
-    - scons --test
+    - scons
+    - pytest tests
     compiler: gcc
     env: COMPILER=g++-4.8
     addons:
@@ -62,6 +63,6 @@ env:
   - PYTHON_VERSION=3.6
   - NUMPY_VERSION='stable'
   - ASTROPY_VERSION='stable'
-  - CONDA_DEPENDENCIES='matplotlib scons seaborn jinja2 lxml'
-  - PIP_DEPENDENCIES='git+git://github.com/wtbarnes/cldoc.git@py3fix mkdocs mkdocs-material beautifulsoup4'
+  - CONDA_DEPENDENCIES='matplotlib scons seaborn jinja2 lxml pytest'
+  - PIP_DEPENDENCIES='git+git://github.com/wtbarnes/cldoc.git@py3fix mkdocs mkdocs-material beautifulsoup4 hissw'
   - secure: 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

SConstruct

@@ -61,13 +61,4 @@ for sd in subdirs:
 if not os.path.exists('bin'):
     os.makedirs('bin')
 
-print('Compiling ebtel++')
 env.Program('bin/ebtel++.run', allobjs)
-
-if GetOption('test'):
-    print('Running tests...')
-    try:
-        python_path = os.path.join(os.environ['CONDA_PREFIX'], 'bin', 'python')
-    except KeyError:
-        python_path = 'python'
-    env.Command('dummy', None, '{} test/run_tests.py'.format(python_path))

docs/mkdocs/configuration.md

@@ -15,7 +15,7 @@ An ebtel++ run is configured by a single XML configuration file. The table below
 | **calculate_dem** | `bool` | if True, do the TR and coronal DEM calculation; increases compute time significantly |
 | **save_terms** | `bool` | if True, save heat flux, $c_1$ parameter, and radiative loss to a separate file `<output_filename>.terms` |
 | **use_adaptive_solver** | `bool` | if True, use adaptive timestep; significantly smaller compute times. In both cases, a Runge-Kutta Cash-Karp integration method is used (see section 16.2 of [Press et al. (1992)][press_num_recipes])  |
-| **o.utput_filename** | `string` | path to output file |
+| **output_filename** | `string` | path to output file |
 | **adaptive_solver_error** | `float` | Allowed truncation error in adaptive timestep routine |
 | **adaptive_solver_safety** | `float` | Refinement factor, between 0 and 1, used if timestep becomes too large and solution contains NaNs. Especially important for short, infrequently heated loops. Also controls decreases in timestep due to thermal conduction timestep. Suggested value is 0.5 |
 | **c1_cond0** | `float` | Nominal value of $c_1$ during the conduction phase; see Appendix A of [Barnes et al. (2016)][barnes_2016] |

docs/xml_to_md.py

@@ -119,7 +119,7 @@ def func_info(node, value):
         return [f'`{a.find("type").attrs["name"]}` {a.attrs["name"]}' for a in args]
     elif value == 'args':
         args = node.findAll('argument')
-        return [{'name': a.attrs['name'], 'description': '' if a.find('doc') is None 
+        return [{'name': a.attrs['name'], 'description': '' if a.find('doc') is None
                  else a.find('doc').text} for a in args]
     elif value == 'return':
         return node.find('return').find('type').attrs['name']
@@ -134,7 +134,7 @@ def parse_class(filename):
     class_doc = soup.find('html').find('body').find('class')
     # Top level info
     name = class_doc.attrs['name']
-    desc = class_doc.find('doc', recursive=False).text.replace('\n',' ')
+    desc = class_doc.find('doc', recursive=False).text.replace('\n', ' ')
     # Parse Sections
     fields = class_doc.find_all('field', recursive=False)
     variables = class_doc.find_all('variable', recursive=False)
@@ -154,12 +154,13 @@ def parse_struct(filename):
         soup = BeautifulSoup(f, 'lxml')
     struct_doc = soup.find('html').find('body').find('struct')
     name = struct_doc.attrs['name']
-    desc = struct_doc.find('brief', recursive=False).text.replace('\n',' ')
+    desc = struct_doc.find('brief', recursive=False).text.replace('\n', ' ')
     fields = struct_doc.find_all('field', recursive=False)
     env = Environment(loader=DictLoader({'struct': struct_template}))
     env.filters.update({'field_info': field_info})
     return env.get_template('struct').render(name=name, desc=desc, fields=fields,)
 
+
 def parse_typedef(filename):
     with open(filename, 'r') as f:
         soup = BeautifulSoup(f, 'lxml')
@@ -179,7 +180,7 @@ def parse_typedef(filename):
     with open(os.path.join(args.xml_dir, 'index.xml'), 'r') as f:
         index = BeautifulSoup(f, 'lxml').find('html').find('body').find('index')
     entries = [(c.name, c.attrs['name']) for c in index if c.name is not None]
-    entries = {k: [e[1] for e in entries if e[0]==k] for k in set([e[0] for e in entries])}
+    entries = {k: [e[1] for e in entries if e[0] == k] for k in set([e[0] for e in entries])}
     # Setup environment
     env = Environment(loader=DictLoader({'api': api_template}))
     # Parse classes

source/loop.cpp

@@ -150,16 +150,8 @@ state_type Loop::CalculateInitialConditions(void)
   }
 
   // Set current state in order pressure_e, pressure_i, density
-  // Force same if single-fluid enforced
   pi_initial = parameters.boltzmann_correction*BOLTZMANN_CONSTANT*density*temperature;
-  if(parameters.force_single_fluid)
-  {
-    pe_initial = pi_initial;
-  }
-  else
-  {
-    pe_initial = BOLTZMANN_CONSTANT*density*temperature; 
-  }
+  pe_initial = BOLTZMANN_CONSTANT*density*temperature; 
   state = {{ pe_initial, pi_initial, density, temperature, temperature }};
 
   return state;
@@ -386,8 +378,8 @@ double Loop::CalculateScaleHeight(double temperature_e,double temperature_i)
 void Loop::CalculateAbundanceCorrection(double helium_to_hydrogen_ratio)
 {
   double z_avg = (1.0 + 2.0*helium_to_hydrogen_ratio)/(1.0 + helium_to_hydrogen_ratio);
-  parameters.boltzmann_correction = (1.0 + 1.0/z_avg)/2.0;
-  parameters.ion_mass_correction = (1.0 + 4.0*helium_to_hydrogen_ratio)/(2.0 + 3.0*helium_to_hydrogen_ratio)*2.0*parameters.boltzmann_correction;
+  parameters.boltzmann_correction = 1.0/z_avg;
+  parameters.ion_mass_correction = (1.0 + 4.0*helium_to_hydrogen_ratio)/(2.0 + 3.0*helium_to_hydrogen_ratio)*(1.0 + z_avg)/z_avg;
 }
 
 double Loop::CalculateVelocity(double temperature_e, double temperature_i, double pressure_e)

tests/conftest.py

@@ -0,0 +1,12 @@
+import pytest
+
+
+def pytest_addoption(parser):
+    parser.addoption(
+        "--ebtel_idl_path", action="store", default=None, help="Path to EBTEL IDL code"
+    )
+
+
+@pytest.fixture
+def ebtel_idl_path(request):
+    return request.config.getoption("--ebtel_idl_path")