Prepare release

CHANGES.txt

@@ -1,3 +1,7 @@
+3.1.24
+  Update documentation
+  Fix tests
+  Remove dependency on python3-future
 3.1.23:
   Use pytest instead of nose
 3.1.21:

README.md

@@ -110,7 +110,7 @@ From source:
 
 After dependencies installation, go in BioMAJ source directory:
 
-    python setup.py install
+    pip install .
 
 From packages:
 

setup.py

@@ -36,7 +36,7 @@ def run(self):
     'url': 'http://biomaj.genouest.org',
     'download_url': 'http://biomaj.genouest.org',
     'author_email': '[email protected]',
-    'version': '3.1.23',
+    'version': '3.1.24',
      'classifiers': [
         # How mature is this project? Common values are
         #   3 - Alpha

tests/biomaj_tests.py

@@ -77,7 +77,7 @@ def clean(self):
   def __copy_test_bank_properties(self):
     if self.bank_properties is not None:
       return
-    self.bank_properties = ['alu', 'local', 'testhttp','directhttp',
+    self.bank_properties = ['pdbaa', 'local', 'testhttp','directhttp',
                             'alu_list_error']
     curdir = os.path.dirname(os.path.realpath(__file__))
     for b in self.bank_properties:
@@ -146,10 +146,10 @@ def setup_method(self, m):
     BiomajConfig.load_config(self.utils.global_properties, allow_user_config=False)
 
     # Delete all banks
-    b = Bank('alu')
+    b = Bank('pdbaa')
     b.banks.remove({})
 
-    self.config = BiomajConfig('alu')
+    self.config = BiomajConfig('pdbaa')
     data_dir = self.config.get('data.dir')
     lock_file = os.path.join(data_dir,'alu.lock')
     if os.path.exists(lock_file):
@@ -166,13 +166,13 @@ def test_new_bank(self):
     """
     Checks bank init
     """
-    b = Bank('alu')
+    b = Bank('pdbaa')
 
   def test_new_session(self):
     """
     Checks an empty session is created
     """
-    b = Bank('alu')
+    b = Bank('pdbaa')
     b.load_session(UpdateWorkflow.FLOW)
     for key in b.session._session['status'].keys():
       assert not(b.session.get_status(key))
@@ -181,14 +181,14 @@ def test_session_reload_notover(self):
     """
     Checks a session is used if present
     """
-    b = Bank('alu')
+    b = Bank('pdbaa')
     for i in range(1, 5):
-      s = Session('alu', self.config, UpdateWorkflow.FLOW)
+      s = Session('pdbaa', self.config, UpdateWorkflow.FLOW)
       s._session['status'][Workflow.FLOW_INIT] = True
       b.session = s
       b.save_session()
 
-    b = Bank('alu')
+    b = Bank('pdbaa')
     b.load_session(UpdateWorkflow.FLOW)
     assert (b.session.get_status(Workflow.FLOW_INIT))
 
@@ -198,7 +198,7 @@ def test_clean_old_sessions(self):
     """
     b = Bank('local')
     for i in range(1,5):
-      s = Session('alu', self.config, UpdateWorkflow.FLOW)
+      s = Session('pdbaa', self.config, UpdateWorkflow.FLOW)
       s._session['status'][Workflow.FLOW_INIT] = True
       b.session = s
       b.save_session()
@@ -211,20 +211,20 @@ def test_session_reload_over(self):
     """
     Checks a session if is not over
     """
-    b = Bank('alu')
+    b = Bank('pdbaa')
     for i in range(1,5):
-      s = Session('alu', self.config, UpdateWorkflow.FLOW)
+      s = Session('pdbaa', self.config, UpdateWorkflow.FLOW)
       s._session['status'][Workflow.FLOW_INIT] = True
       s._session['status'][Workflow.FLOW_OVER] = True
       b.session = s
       b.save_session()
 
-    b = Bank('alu')
+    b = Bank('pdbaa')
     b.load_session(UpdateWorkflow.FLOW)
     assert not (b.session.get_status(Workflow.FLOW_INIT))
 
   def test_bank_list(self):
-    b1 = Bank('alu')
+    b1 = Bank('pdbaa')
     b2 = Bank('local')
     banks = Bank.list()
     assert (len(banks) == 2)
@@ -237,7 +237,7 @@ def test_get_release(self):
     """
     Get release
     """
-    b = Bank('alu')
+    b = Bank('pdbaa')
     b.load_session(UpdateWorkflow.FLOW)
     res = b.update()
     assert (b.session.get('update'))
@@ -249,9 +249,9 @@ def test_get_release(self):
   reason='network tests disabled'
   )
   def test_remove_session(self):
-    b = Bank('alu')
+    b = Bank('pdbaa')
     for i in range(1,5):
-      s = Session('alu', self.config, UpdateWorkflow.FLOW)
+      s = Session('pdbaa', self.config, UpdateWorkflow.FLOW)
       s._session['status'][Workflow.FLOW_INIT] = True
       b.session = s
       b.save_session()

tests/alu.properties → tests/pdbaa.properties

@@ -3,11 +3,11 @@
 ### Initialization ###
 
 db.fullname="alu.n : alu repeat element. alu.a : translation of alu.n repeats"
-db.name=alu
+db.name=pdbaa
 db.type=nucleic_protein
 
-offline.dir.name=offline/ncbi/blast/alu_tmp
-dir.version=ncbi/blast/alu
+offline.dir.name=offline/ncbi/blast/pdbaa_tmp
+dir.version=ncbi/blast/pdbaa
 
 frequency.update=0
 
@@ -24,12 +24,12 @@ release.file=
 release.regexp=
 release.file.compressed=
 
-remote.files=^alu.*\.gz$
+remote.files=^pdbaa.*\.gz$
 
 #Uncomment if you don't want to extract the data files.
 #no.extract=true
 
-local.files=^alu\.(a|n).*
+local.files=^pdbaa\.*$
 
 ## Post Process  ##  The files should be located in the projectfiles/process directory