Merge branch 'pip' into dev

.travis.yml

@@ -22,7 +22,7 @@ install:
   - conda update -q conda
   # Useful for debugging any issues with conda
   - conda info -a
-  - pip install . --process-dependency-links
+  - pip install .
   - pip install coveralls
 ######################################################
 script: 

requirements.txt

@@ -0,0 +1,11 @@
+cypy>=0.2
+quantities==0.12.1
+pandas>=0.18
+ipython
+matplotlib
+bs4
+lxml
+nbconvert
+ipykernel
+nbformat
+gitpython

sciunit/utils.py

@@ -10,6 +10,7 @@
 import pkgutil
 import importlib
 import json
+import re
 from io import TextIOWrapper,StringIO
 from datetime import datetime
 
@@ -153,7 +154,7 @@ def convert_notebook(self, name):
         file_path = self.get_path("%s.ipynb"%name)
         code = exporter.from_filename(file_path)[0]
         self.write_code(name, code)
-        self.clean_code(name, ['get_ipython'])
+        self.clean_code(name, [])#'get_ipython'])
 
     def convert_and_execute_notebook(self, name):
         """Converts a notebook into a python file and then runs it."""
@@ -179,7 +180,7 @@ def write_code(self, name, code):
             f.write(code)
 
     def clean_code(self, name, forbidden):
-        """Remove lines containing items in forbidden from the code.
+        """Remove lines containing items in 'forbidden' from the code.
         Helpful for executing converted notebooks that still retain IPython
         magic commands.
         """
@@ -188,11 +189,29 @@ def clean_code(self, name, forbidden):
         code = code.split('\n')
         new_code = []
         for line in code:
-            if not [bad for bad in forbidden if bad in line]:
+            if [bad for bad in forbidden if bad in line]:
+                pass
+            else:
+                allowed = ['time','timeit'] # Magics where we want to keep the command
+                line = self.strip_line_magic(line,allowed)
                 new_code.append(line)
         new_code = '\n'.join(new_code)
         self.write_code(name, new_code)
 
+    def strip_line_magic(self,line,magics_allowed):
+        matches = re.findall("run_line_magic\(([^]]+)", line)
+        if matches and matches[0]: # This line contains the pattern
+            match = matches[0]
+            if match[-1] == ')':
+                match = match[:-1] # Just because the re way is hard
+            magic_kind,stripped = eval(match)
+            if magic_kind not in magics_allowed:
+                stripped = "" # If the part after the magic won't work, just get rid of it
+        else:
+            printd("No line magic pattern match in '%s'" % line)
+            stripped = line
+        return stripped
+
     def do_notebook(self, name):
         """Runs a notebook file after optionally
         converting it to a python file."""
@@ -227,20 +246,31 @@ def write(self, s):
             super(MockDevice,self).write(s)
 
 
-def import_all_modules(package,verbose=False):
+def import_all_modules(package, skip=None, verbose=False, prefix="", depth=0):
     """Recursively imports all subpackages, modules, and submodules of a
     given package.
     'package' should be an imported package, not a string.
+    'skip' is a list of modules or subpackages not to import.
     """
 
-    for _, modname, ispkg in pkgutil.walk_packages(path=package.__path__,
-                                                   onerror=lambda x: None):
+    skip = [] if skip is None else skip
+
+    for ff, modname, ispkg in pkgutil.walk_packages(path=package.__path__,
+                                                prefix=prefix,
+                                                onerror=lambda x: None):
+        if ff.path not in package.__path__[0]: # Solves weird bug
+            continue
         if verbose:
-            print(modname,ispkg)
+            print('\t'*depth,modname)
+        if modname in skip:
+            if verbose:
+                print('\t'*depth,'*Skipping*')
+            continue
+        module = '%s.%s' % (package.__name__,modname)
+        subpackage = importlib.import_module(module)
         if ispkg:
-            module = '%s.%s' % (package.__name__,modname)
-            subpackage = importlib.import_module(module)
-            import_all_modules(subpackage,verbose=verbose)
+            import_all_modules(subpackage, skip=skip, 
+                               verbose=verbose,depth=depth+1)
 
 
 def import_module_from_path(module_path, name=None):

setup.py

@@ -1,6 +1,10 @@
 """Setup file for SciUnit"""
 
 import sys
+import os
+
+from pip.req import parse_requirements
+from pip.download import PipSession
 
 try:
     from setuptools import setup
@@ -12,6 +16,13 @@
     ipython = "ipython>=5.1,<6.0"
 else:
     ipython = "ipython>=5.1"    
+
+def read_requirements():
+    '''parses requirements from requirements.txt'''
+    reqs_path = os.path.join('.', 'requirements.txt')
+    install_reqs = parse_requirements(reqs_path, session=PipSession())
+    reqs = [str(ir.req) for ir in install_reqs]
+    return reqs
 
 setup(
     name='sciunit',
@@ -26,19 +37,7 @@
     description='A test-driven framework for formally validating scientific models against data.',
     long_description="",  
     test_suite="sciunit.unit_test.core_tests",    
-    install_requires=['cypy>=0.2',
-                      'quantities==0.12.1',
-                      #'quantities==999',
-                      'pandas>=0.18',
-                      ipython,
-                      'matplotlib',
-                      'bs4',
-                      'lxml',
-                      'nbconvert',
-                      'ipykernel',
-                      'nbformat',
-                      'gitpython'],
-    #dependency_links = ['git+https://github.com/python-quantities/python-quantities.git@master#egg=quantities-999'],
+    install_requires=read_requirements(),
     entry_points={
         'console_scripts': [
             'sciunit = sciunit.__main__:main'