added pbbt, prospector, tests/

pbbt-input.yaml

@@ -0,0 +1,17 @@
+#
+# Copyright (c) 2015, Prometheus Research, LLC
+#
+
+title: RIOS.CONVERTER
+tests:
+  # check Python source syntax and style
+  - sh: flake8 ./src/
+
+  - sh: pip install --quiet coverage nose
+    ignore: true
+
+  - rmdir: ./tests/sandbox
+  - mkdir: ./tests/sandbox
+
+  - sh: nosetests --quiet
+    ignore: true

pbbt-output.yaml

@@ -0,0 +1,20 @@
+#
+# This file contains expected test output data generated by PBBT.
+#
+---
+suite: rios.converter
+tests:
+- sh: flake8 ./src/
+  stdout: ''
+- sh: pip install --quiet coverage nose
+  stdout: ''
+- sh: nosetests --quiet
+  stdout: |
+    Coverage.py warning: Module rios.converter was never imported.
+    Name    Stmts   Miss  Cover   Missing
+    -------------------------------------
+    nose.plugins.cover: WARNING: Failed to generate HTML report: No data to report.
+    ----------------------------------------------------------------------
+    Ran 0 tests in 0.005s
+
+    OK

setup.cfg

@@ -1,20 +1,36 @@
-# coverage.py configuration
-[run]
-source = rios.converter
-branch = True
-data_file = ./build/coverage/coverage.dat
-parallel = True
-[report]
-exclude_lines =
-        raise NotImplementedError
-        return "REQUIRED"
+# setuptools configuration
+[bdist_wheel]
+universal=1
+
+# Prospector configuration
+[prospector]
+output_format = grouped
+profile = .prospector.yaml
+messages_only = true
+autodetect = false
+
+# Nose configuration
+[nosy]
+base_path = ./
+glob_patterns = *.py *.json
+[nosetests]
+with-coverage=1
+cover-package=rios.converter
+cover-erase=1
+cover-branches=1
+cover-html=1
+cover-html-dir=build/coverage
+nocapture=1
 
 # PBBT configuration
-#[pbbt]
-#input = test/input.yaml
-#output = test/output.yaml
+[pbbt]
+input = pbbt-input.yaml
+output = pbbt-output.yaml
+max_errors = 1
 
 # Sphinx configuration
 [build_sphinx]
 build_dir = build/doc
 
+[flake8]
+ignore = E123,E126,E127,E202,E241,E402,W503

setup.py

@@ -22,8 +22,22 @@
         'rex.web >=3.5, <4',
         'rios.conversion >=0.2, <1',
     ],
+    extras_require={
+        'dev': [
+            'pbbt>=0.1.4,<1',
+            'coverage>=3.7,<4',
+            'nose>=1.3,<2',
+            'nosy>=1.1,<2',
+            'prospector[with_pyroma]>=0.10,<0.11',
+            'twine>=1.5,<2',
+            'wheel>=0.24,<0.25',
+            'Sphinx>=1.3,<2',
+            'sphinx-autobuild>=0.5,<0.6',
+            'tox>=2,<3',
+            'flake8>=2.5.0,<3',
+        ],
+    },
+    test_suite='nose.collector',
     rex_init='rios.converter',
     rex_static='static',
 )
-
-

src/rios/__init__.py

@@ -4,5 +4,3 @@
 
 
 __import__('pkg_resources').declare_namespace(__name__)
-
-

src/rios/converter.py

@@ -4,7 +4,6 @@
 from rex.core import get_settings
 from rex.core import AnyVal
 from rex.core import StrVal
-from rex.core import PIntVal
 from rex.core import Setting
 from rex.web import Command
 from rex.web import HandleError
@@ -72,8 +71,9 @@ class ConvertToRios(Command):
         'redcap': RedcapToRios,
         }
 
-
-    def render(self, req,
+    def render(
+            self,
+            req,
             system,
             format,
             instrument_title,
@@ -102,7 +102,7 @@ def render(self, req,
             if not instrument_id:
                 errors.append('Instrument ID is required.')
             if not instrument_title:
-                errors.append('Instrument Title is required.') 
+                errors.append('Instrument Title is required.')
             args.extend([
                 '--id', instrument_id,
                 '--title', instrument_title, ])
@@ -119,7 +119,7 @@ def render(self, req,
             return Response(json={
                     "status": 400,
                     "errors": errors
-                    })        
+                    })
         with open(error_filename, 'wb') as stderr:
             sys.stdin = infile.file
             # I can't explain why I am
@@ -150,7 +150,7 @@ def render(self, req,
             name = outname + '.zip'
             shutil.rmtree(temp_dir)
             return Response(
-                    content_type='application/zip', 
+                    content_type='application/zip',
                     content_disposition='attachment; filename="%s"' % name,
                     body=body)
         else:
@@ -187,15 +187,17 @@ def load_file(self, file_field):
             fo.write(file_field.file.read())
         return filename
 
-    def render(self, req,
+    def render(
+            self,
+            req,
             system,
             format,
             localization,
             instrument_file,
             form_file,
             calculationset_file,
             outname):
-    
+
         self.settings = get_settings()
         tempfile.tempdir = self.settings.temp_dir
         self.temp_dir = tempfile.mkdtemp()
@@ -208,23 +210,23 @@ def render(self, req,
         args = [
                 '--verbose',
                 '--format', format,
-                '--outfile', outfile, 
+                '--outfile', outfile,
                 ]
         if hasattr(instrument_file, 'filename'):
             args.extend([
-                    '--instrument', 
-                    '%s' % self.load_file(instrument_file)])                
+                    '--instrument',
+                    '%s' % self.load_file(instrument_file)])
         else:
             errors.append('An input instrument file is required.')
         if hasattr(form_file, 'filename'):
             args.extend([
-                    '--form', 
+                    '--form',
                     '%s' % self.load_file(form_file)])
         else:
             errors.append('An input form file is required.')
         if hasattr(calculationset_file, 'filename'):
             args.extend([
-                    '--calculationset', 
+                    '--calculationset',
                     '%s' % self.load_file(calculationset_file)])
         if localization:
             args.extend(['--localization', localization])
@@ -233,7 +235,7 @@ def render(self, req,
             return Response(json={
                     "status": 400,
                     "errors": errors
-                    })        
+                    })
         error_filename = outfile + '.stderr'
         with open(error_filename, 'wb') as stderr:
             # I can't eplain why I am
@@ -261,7 +263,7 @@ def render(self, req,
             name = outname + '.zip'
             shutil.rmtree(self.temp_dir)
             return Response(
-                    content_type='application/zip', 
+                    content_type='application/zip',
                     content_disposition='attachment; filename="%s"' % name,
                     body=body)
         else:
@@ -281,8 +283,8 @@ class HandleNotFound(HandleError):
 
     def __call__(self, req):
         return render_to_response(
-                self.template, 
-                req, 
+                self.template,
+                req,
                 status=self.code,
                 path=req.path)
 

src/rios/settings.py

@@ -1,4 +1,6 @@
 from rex.core import Setting
+from rex.core import StrVal
+
 
 class TempDirSetting(Setting):
     """Directory with temporary data."""