Add more module testing and upgrade to pytest

.coveragerc

@@ -0,0 +1,2 @@
+[run]
+source=OrthoEvol

.travis.yml

@@ -10,7 +10,9 @@ notifications:
 install:
   - "pip install --upgrade pip setuptools wheel"
   - "pip install --only-binary=numpy,scipy numpy scipy"
-  - "pip install matplotlib ipython jupyter sympy nose"
+  - "pip install matplotlib ipython jupyter sympy pytest"
   - "pip install -r requirements.txt"
-# command to run nosetests
-script: nosetests tests/ --verbosity=3
+  - "pip install ."
+# command to run unittests via pytest
+script:
+  - pytest tests/

OrthoEvol/Cookies/cookie_jar.py

@@ -127,7 +127,7 @@ def _check_ingredients(self, cookie, path, no_input, extra_context):
             self.cookielog.info('%s was created. ✔' % str(path))
 
     def bake_the_repo(self, cookie_jar=None):
-        self.cookielog.warn('Creating directories from the Repository Cookie template.')
+        self.cookielog.warning('Creating directories from the Repository Cookie template.')
         """
             This function creates a new repository.  If a repository name
             is given to the class, then it is given a name.  If not, cookiecutter
@@ -163,7 +163,7 @@ def bake_the_user(self, cookie_jar=None):
         :param cookie_jar:  (Default value = None)
         """
 
-        self.cookielog.warn('Creating directories from the User Cookie template.')
+        self.cookielog.warning('Creating directories from the User Cookie template.')
         if cookie_jar:
             self.cookie_jar = cookie_jar
 
@@ -181,7 +181,7 @@ def bake_the_project(self, cookie_jar=None):
         :return: A new project inside the user's project directory.
         """
 
-        self.cookielog.warn('Creating directories from the Project Cookie template.')
+        self.cookielog.warning('Creating directories from the Project Cookie template.')
         if cookie_jar:
             self.cookie_jar = cookie_jar
         # Add the project
@@ -198,7 +198,7 @@ def bake_the_project(self, cookie_jar=None):
             if self.exists(str(self.cookie_jar / Path(self.project))):
                 self.cookielog.info('Project exists. ✔')
             else:
-                self.cookielog.warn('A project linked to a user/repository is being created.')
+                self.cookielog.warning('A project linked to a user/repository is being created.')
                 cookiecutter(str(self.Recipes.project_cookie), extra_context=e_c, no_input=no_input,
                              output_dir=str(self.cookie_jar))
                 # Logging
@@ -212,7 +212,7 @@ def bake_the_project(self, cookie_jar=None):
             if self.exists(str(self.cookie_jar / Path(self.project))):
                 self.cookielog.info('Project exists. ✔')
             else:
-                self.cookielog.warn('A basic standalone project is being created.')
+                self.cookielog.warning('A basic standalone project is being created.')
                 cookiecutter(str(self.Recipes.basic_project_cookie), extra_context=e_c, no_input=no_input,
                              output_dir=str(self.cookie_jar))
                 self.cookielog.info(
@@ -271,7 +271,7 @@ def bake_the_website(self, host, port, website_path, cookie_jar=None):
         :param cookie_jar:  (Default value = None)
         """
 
-        self.cookielog.warn('Creating directories from the Website Cookie template.')
+        self.cookielog.warning('Creating directories from the Website Cookie template.')
         if cookie_jar:
             self.cookie_jar = cookie_jar
         # TODO-ROB:  Add heavy logging here
@@ -290,8 +290,8 @@ def bake_the_website(self, host, port, website_path, cookie_jar=None):
         run_script(script_path=str(script_path), cwd=str(website_path))
         self.cookielog.info(
             'Directories have been created for the Flask Web Server, %s. ✔' % self.website)
-        self.cookielog.warn('The %s Flask Server should now be running on http://%s:%s' %
-                            (self.website, host, port))
+        self.cookielog.warning('The %s Flask Server should now be running on http://%s:%s' %
+                               (self.website, host, port))
 
     def bake_the_research(self, research_type, research, cookie_jar=None):
         """Create a directory for a new research project.
@@ -301,7 +301,7 @@ def bake_the_research(self, research_type, research, cookie_jar=None):
         :param cookie_jar:  (Default value = None)
         """
 
-        self.cookielog.warn('Creating directories from the Research Cookie template.')
+        self.cookielog.warning('Creating directories from the Research Cookie template.')
         if cookie_jar:
             self.cookie_jar = cookie_jar
 
@@ -320,7 +320,7 @@ def bake_the_app(self, app, cookie_jar=None):
         :param cookie_jar:  (Default value = None)
         """
 
-        self.cookielog.warn('Creating directories from the App Cookie template.')
+        self.cookielog.warning('Creating directories from the App Cookie template.')
         if cookie_jar:
             self.cookie_jar = cookie_jar
         e_c = {"app_name": app}

OrthoEvol/Orthologs/Blast/blast.py

@@ -40,7 +40,7 @@ def __init__(self, project, method, acc_file, copy_from_package,
         :param kwargs:"""
 
         super().__init__(project=project, method=method, acc_file=acc_file,
-                         copy_from_package=copy_from_package, 
+                         copy_from_package=copy_from_package,
                          ref_species=ref_species, template=template,
                          save_data=save_data, verbose=verbose, **kwargs)
 
@@ -246,7 +246,7 @@ def configure(self, query_accessions, query_organism, auto_start=False):
 
         self.blastn_log.debug('Blast configuration has begun.')
         self.blastn_log.debug('Configuring the accession file.')
-        
+
         if self.ref_species:
             query_organism = self.ref_species
 
@@ -468,7 +468,7 @@ class OrthoBlastN(BaseBlastN):
 
     def __init__(self, project="orthology-gpcr", project_path=os.getcwd(),
                  method=1, template=None, save_data=True, acc_file="gpcr.csv",
-                 copy_from_package=True, **kwargs):
+                 copy_from_package=True, auto_start=False, **kwargs):
         """This class inherits from the BaseBlastN class.
 
         This class utilizes it's parent classes to search a standalone
@@ -494,6 +494,7 @@ def __init__(self, project="orthology-gpcr", project_path=os.getcwd(),
         self.proj_mana = None
         self.acc_file = acc_file
         self.copy_from_package = copy_from_package
+        self.auto_start = auto_start
 
         # Initialize class
         super().__init__(project=project, method=method, template=template,
@@ -503,11 +504,14 @@ def __init__(self, project="orthology-gpcr", project_path=os.getcwd(),
                          taxon_file=self.taxon_file,
                          post_blast=self.__post_blast,
                          project_path=self.project_path,
-                         proj_mana=self.proj_mana, **kwargs)
+                         proj_mana=self.proj_mana,
+                         auto_start=self.auto_start,
+                         **kwargs)
 
     def run(self):
         """Run the blast using a default configuration."""
-        self.configure(self.blast_human, self.ref_species, auto_start=True)
+        self.configure(self.blast_human, self.ref_species,
+                       auto_start=self.auto_start)
 
 
 class BlastFailure(BaseException):