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Removed the Martel special case code (it should be safe to assume tha…

…t Martel has not been distributed separately from Biopython from some years now)
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commit d81c27ec4b4806e5a061833f69c530b9c021c40f 1 parent 1283e42
@peterjc peterjc authored
Showing with 3 additions and 60 deletions.
  1. +3 −60 setup.py
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63 setup.py
@@ -80,10 +80,6 @@ def check_dependencies():
# - is packaged required, boolean
# - package website, string
dependencies = [
- #mxTextTools is only used by Martel and other deprecated code.
- #We therefore won't worry about if it is installed or not.
- #("mxTextTools", is_mxTextTools_installed, 0,
- # "http://www.egenix.com/files/python/eGenix-mx-Extensions.html"),
("Numerical Python (NumPy)", is_Numpy_installed, 0,
"http://numpy.scipy.org/"),
]
@@ -134,10 +130,6 @@ class build_py_biopython(build_py):
def run(self):
if not check_dependencies_once():
return
- # Check to see if Martel is installed. If not, then install
- # it automatically.
- if not is_Martel_installed():
- self.packages.append("Martel")
# Add software that requires Numpy to be installed.
if is_Numpy_installed():
self.packages.extend(NUMPY_PACKAGES)
@@ -235,54 +227,6 @@ def can_import(module_name):
return None
raise AssertionError, "how did I get here?"
-def is_Martel_installed():
- old_path = sys.path[:]
-
- # First, check the version of the Martel that's bundled with
- # Biopython.
- sys.path.insert(0, '') # Make sure I'm importing the current one.
- m = can_import("Martel")
- sys.path = old_path
- if m:
- bundled_martel_version = m.__version__
- del sys.modules["Martel"] # Unload the bundled version of Martel.
- else:
- #We won't be able to import the bundled version of Martel if an
- #external dependency like mxTextTools is missing.
- #In this case, we can't compare versions to any pre-installed Martel
- #(even if that could be imported).
- bundled_martel_version = None
-
- # Now try and import a Martel that's not bundled with Biopython.
- # To do that, I need to delete all the references to the current
- # path from sys.path.
- i = 0
- while i < len(sys.path):
- if sys.path[i] in ['', '.', os.getcwd()]:
- del sys.path[i]
- else:
- i += 1
- m = can_import("Martel")
- sys.path = old_path
- if m:
- old_martel_version = m.__version__
- else:
- #Either there is no pre-installed copy of Martel, or if there is
- #it cannot be imported (e.g. missing a dependency like mxTextTools).
- old_martel_version = None
-
- installed = 0
- # If the bundled one is the older, then ignore it
- if old_martel_version and bundled_martel_version and \
- bundled_martel_version < old_martel_version:
- installed = 1
- return installed
-
-def is_mxTextTools_installed():
- if can_import("TextTools"):
- return 1
- return can_import("mx.TextTools")
-
def is_Numpy_installed():
return can_import("numpy")
@@ -369,6 +313,9 @@ def is_Numpy_installed():
'Bio.writers.SeqRecord',
'Bio.Wise',
'Bio.WWW',
+ #Other top level packages,
+ 'BioSQL',
+ 'Martel', #Deprecated as of Biopython 1.49
]
# packages that require Numeric Python
@@ -465,10 +412,6 @@ def run (self):
outfile = dst
self.outfiles.append(outfile)
-
-# Install BioSQL.
-PACKAGES.append("BioSQL")
-
setup(
name='biopython',
version='1.48',
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