rm some comments + fix PEP8

docker/Dockerfile

@@ -25,8 +25,6 @@ RUN cd /home/imp/tmp \
     && cd trimmomatic-0.32 \
     && ant \
     && cp dist/jar/trimmomatic-0.32.jar /home/imp/lib/. \
-    #&& mkdir -p /usr/db/trimmomatic \
-    #&& cp adapters/* /usr/db/trimmomatic/. \
     && cd .. && rm -rf *rimmomatic*
 
 ## idba ud
@@ -157,14 +155,6 @@ RUN cd /home/imp/lib \
     && cd Platypus_0.8.1 \
     && bash buildPlatypus.sh
 
-## Megahit
-#RUN cd /home/imp/lib \
-#    && git clone https://git-r3lab.uni.lu/R3/megahit.git \
-#    && cd megahit \
-#    && git checkout v0.2.1 \
-#    && make \
-#    && mv megahit* /usr/bin/. \
-#    && mv sdbg_builder_cpu /usr/bin/.
 
 RUN cd /home/imp/lib \
     && rm -rf megahit \
@@ -189,13 +179,6 @@ RUN cd /home/imp/lib \
     && cd quast-release_3.1 \
     && ln -s $PWD/metaquast.py /usr/bin/metaquast
 
-######################
-# ship pipeline code #
-######################
-# (commented for now)
-#RUN cd /home/imp \
-#    && git clone https://git-r3lab.uni.lu/shaman.narayanasamy/IMP.git
-
 ######################
 # set up environment #
 ######################

lib/path.py

@@ -74,6 +74,7 @@ text_type = str
 getcwdu = os.getcwd
 u = lambda x: x
 
+
 def surrogate_escape(error):
     """
     Simulate the Python 3 ``surrogateescape`` handler, but for Python 2 only.
@@ -92,6 +93,7 @@ if PY2:
     u = lambda x: codecs.unicode_escape_decode(x)[0]
     codecs.register_error('surrogateescape', surrogate_escape)
 
+
 @contextlib.contextmanager
 def io_error_compat():
     try:
@@ -1346,7 +1348,7 @@ class Path(text_type):
     # http://www.zopatista.com/python/2013/11/26/inplace-file-rewriting/
     @contextlib.contextmanager
     def in_place(self, mode='r', buffering=-1, encoding=None, errors=None,
-            newline=None, backup_extension=None):
+                 newline=None, backup_extension=None):
         """
         A context in which a file may be re-written in-place with new content.
 
@@ -1384,21 +1386,21 @@ class Path(text_type):
             pass
         os.rename(self, backup_fn)
         readable = io.open(backup_fn, mode, buffering=buffering,
-            encoding=encoding, errors=errors, newline=newline)
+                           encoding=encoding, errors=errors, newline=newline)
         try:
             perm = os.fstat(readable.fileno()).st_mode
         except OSError:
             writable = open(self, 'w' + mode.replace('r', ''),
-                buffering=buffering, encoding=encoding, errors=errors,
-                newline=newline)
+                            buffering=buffering, encoding=encoding, errors=errors,
+                            newline=newline)
         else:
             os_mode = os.O_CREAT | os.O_WRONLY | os.O_TRUNC
             if hasattr(os, 'O_BINARY'):
                 os_mode |= os.O_BINARY
             fd = os.open(self, os_mode, perm)
             writable = io.open(fd, "w" + mode.replace('r', ''),
-                buffering=buffering, encoding=encoding, errors=errors,
-                newline=newline)
+                               buffering=buffering, encoding=encoding, errors=errors,
+                               newline=newline)
             try:
                 if hasattr(os, 'chmod'):
                     os.chmod(self, perm)