Source: jellyfish Severity: wishlist Dear Maintainer,
after a discussion with Andreas Tille [1], I'm wondering if it would be possible to rename the python module of the python bindings from "jellyfish" to "dna_jellyfish", in order to avoid conflicts with an existing PyPI [2] package, which is also in the process of being packaged into Debian [3]. A short background on the nature of this change (more details can be found following he linked discussions, and I'd be happy to provide more specific pointers if needed), according to my understanding: * both packages define a "jellyfish" module. * a consensus in regards to the package names and the module names has been seeked with moderate results (the most likely being that the current DNA-jellyfish bindings should retain the "python-jellyfish" Debian package name, but the actual Python module should be renamed). * the upstream DNA-jellyfish author has already expressed his willingness to rename the Python module [4] as it is still not too widespread, although unfortunately it seems that there has not been too much movement in this regard in the upstream repository yet. I'm attaching two patches that would therefore solve this issue on the Debian end, hoping we can eventually tackle the issue at the upstream level. As for the new name, the patch uses "dna_jellyfish" since it was the first alternative suggested by upstream - I'd be happy to switch to another name if preferred. Both patches are the output of plain "git diff" against the patched Debian sources: rename-python-module-to-dna_jellyfish.patch: * setup.py: invokes swig using the "-module" argument [5] * setup.py: renames the Extension and the package name, and updates the older check to reference the new filename. * test_*.py: replaces the references to the "jellyfish" module with "dna_jellyfish". update-debian-rules-dh_clean.patch: * debian/rules: updates override_dh_clean to remove the swig generated .py file. I still need to do another round to ensure no further changes are needed: in particular, I still have to confirm that the python tests are actually executed (debuild output): --- make check-TESTS ... SKIP: tests/swig_python.sh ... running install_egg_info Writing /tmp/buildd/jellyfish-2.2.5/debian/python3-jellyfish/usr/lib/python3.5/dist-packages/dna_jellyfish-0.0.1.egg-in fo I: pybuild base:184: cd /tmp/buildd/jellyfish-2.2.5/.pybuild/pythonX.Y_3.5/build; python3.5 -m unittest discover -v ---------------------------------------------------------------------- Ran 0 tests in 0.000s OK ... --- The same "SKIP: tests/swig_python.sh" and "Ran 0 tests ..." lines also seem to be present on the current 2.2.5-1 debuild log, so it might not be an issue after all and a result of me not having gone through all the details about the testing yet. [1] https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=806716#79 [2] https://pypi.python.org/pypi/jellyfish [3] https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=806716 [4] https://lists.debian.org/debian-python/2015/12/msg00107.html [5] http://www.swig.org/Doc3.0/SWIGDocumentation.html#SWIG_nn2 -- Diego M. Rodriguez 36B3 42A9 9F2F 2CFB F79B FF9B B6C4 B901 06BC E232
diff --git a/swig/python/setup.py b/swig/python/setup.py
index b980b87..1edd509 100644
--- a/swig/python/setup.py
+++ b/swig/python/setup.py
@@ -12,13 +12,13 @@ from distutils.core import setup, Extension
swig_time = os.path.getmtime('../jellyfish.i')
older = True
try:
- older = os.path.getmtime('jellyfish_wrap.cxx') < swig_time or os.path.getmtime('jellyfish.py') < swig_time
+ older = os.path.getmtime('jellyfish_wrap.cxx') < swig_time or os.path.getmtime('dna_jellyfish.py') < swig_time
except FileNotFoundError:
older = True
if older:
- print("Running swig: swig -c++ -python -o jellyfish_wrap.cxx ../jellyfish.i")
- os.system("swig -c++ -python -o jellyfish_wrap.cxx ../jellyfish.i")
+ print("Running swig: swig -c++ -python -module dna_jellyfish -o jellyfish_wrap.cxx ../jellyfish.i")
+ os.system("swig -c++ -python -module dna_jellyfish -o jellyfish_wrap.cxx ../jellyfish.i")
jf_include = [re.sub(r'-I', '', x) for x in os.popen("pkg-config --cflags-only-I jellyfish-2.0").read().rstrip().split()]
jf_cflags = os.popen("pkg-config --cflags-only-other jellyfish-2.0").read().rstrip().split()
@@ -28,7 +28,7 @@ jf_libdir = [re.sub(r'-L', '', x) for x in os.popen("pkg-config --libs-only-L j
jf_ldflags = os.popen("pkg-config --libs-only-other jellyfish-2.0").read().rstrip().split()
-jellyfish_module = Extension('_jellyfish',
+jellyfish_module = Extension('_dna_jellyfish',
sources = ['jellyfish_wrap.cxx'],
include_dirs = jf_include,
libraries = jf_libs,
@@ -36,9 +36,9 @@ jellyfish_module = Extension('_jellyfish',
extra_compile_args = ["-std=c++0x"] + jf_cflags,
extra_link_args = jf_ldflags,
language = "c++")
-setup(name = 'jellyfish',
+setup(name = 'dna_jellyfish',
version = '0.0.1',
author = 'Guillaume Marcais',
description = 'Access to jellyfish k-mer counting',
ext_modules = [jellyfish_module],
- py_modules = ["jellyfish"])
+ py_modules = ["dna_jellyfish"])
diff --git a/swig/python/test_hash_counter.py b/swig/python/test_hash_counter.py
index 8632d6d..1b1d710 100644
--- a/swig/python/test_hash_counter.py
+++ b/swig/python/test_hash_counter.py
@@ -1,20 +1,20 @@
import unittest
import sys
import random
-import jellyfish
+import dna_jellyfish
class TestHashCounter(unittest.TestCase):
def setUp(self):
- jellyfish.MerDNA.k(100)
- self.hash = jellyfish.HashCounter(1024, 5)
+ dna_jellyfish.MerDNA.k(100)
+ self.hash = dna_jellyfish.HashCounter(1024, 5)
def test_info(self):
- self.assertEqual(100, jellyfish.MerDNA.k())
+ self.assertEqual(100, dna_jellyfish.MerDNA.k())
self.assertEqual(1024, self.hash.size())
self.assertEqual(5, self.hash.val_len())
def test_add(self):
- mer = jellyfish.MerDNA()
+ mer = dna_jellyfish.MerDNA()
good = True
for i in range(1000):
mer.randomize()
diff --git a/swig/python/test_mer_file.py b/swig/python/test_mer_file.py
index 1a1cc6c..54b6faa 100644
--- a/swig/python/test_mer_file.py
+++ b/swig/python/test_mer_file.py
@@ -1,4 +1,4 @@
-import jellyfish
+import dna_jellyfish
import unittest
import sys
import os
@@ -6,7 +6,7 @@ from collections import Counter
class TestMerFile(unittest.TestCase):
def setUp(self):
- self.mf = jellyfish.ReadMerFile(os.path.join(data, "swig_python.jf"))
+ self.mf = dna_jellyfish.ReadMerFile(os.path.join(data, "swig_python.jf"))
def test_histo(self):
histo = Counter()
@@ -46,7 +46,7 @@ class TestMerFile(unittest.TestCase):
def test_query(self):
good = True
- qf = jellyfish.QueryMerFile(os.path.join(data, "swig_python.jf"))
+ qf = dna_jellyfish.QueryMerFile(os.path.join(data, "swig_python.jf"))
for mer, count in self.mf:
good = good and count == qf[mer]
if not good: break
diff --git a/swig/python/test_string_mers.py b/swig/python/test_string_mers.py
index bf7d6b1..226f4b8 100644
--- a/swig/python/test_string_mers.py
+++ b/swig/python/test_string_mers.py
@@ -1,21 +1,21 @@
import unittest
import sys
import random
-import jellyfish
+import dna_jellyfish
class TestStringMers(unittest.TestCase):
def setUp(self):
bases = "ACGTacgt"
self.str = ''.join(random.choice(bases) for _ in range(1000))
self.k = random.randint(10, 110)
- jellyfish.MerDNA.k(self.k)
+ dna_jellyfish.MerDNA.k(self.k)
def test_all_mers(self):
count = 0
good = True
- mers = jellyfish.string_mers(self.str)
+ mers = dna_jellyfish.string_mers(self.str)
for m in mers:
- m2 = jellyfish.MerDNA(self.str[count:count+self.k])
+ m2 = dna_jellyfish.MerDNA(self.str[count:count+self.k])
good = good and m == m2
count += 1
self.assertTrue(good)
@@ -23,9 +23,9 @@ class TestStringMers(unittest.TestCase):
def test_canonical_mers(self):
good = True
- mers = jellyfish.string_canonicals(self.str)
+ mers = dna_jellyfish.string_canonicals(self.str)
for count, m in enumerate(mers):
- m2 = jellyfish.MerDNA(self.str[count:count+self.k])
+ m2 = dna_jellyfish.MerDNA(self.str[count:count+self.k])
rm2 = m2.get_reverse_complement()
good = good and (m == m2 or m == rm2)
good = good and (not (m > m2)) and (not (m > rm2))
diff --git a/debian/rules b/debian/rules index 790ad39..5d9557e 100755 --- a/debian/rules +++ b/debian/rules @@ -55,7 +55,7 @@ override_dh_clean: rmdir debian/tmp_save_tests ; \ fi rm -f tests/compat.sh - rm -f swig/python/jellyfish* + rm -f swig/python/jellyfish* swig/python/dna_jellyfish.py override_dh_auto_build: mkdir -p debian/tmp_save_tests
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