change to rst for PyPI

MANIFEST.in

@@ -0,0 +1,11 @@
+include *.h
+include Makefile
+include ksw2_dispatch.c
+include getopt.c
+include main.c
+include README.md
+include python/minimap2.c
+include python/cminimap2.h
+include python/cminimap2.pxd
+include python/minimap2.pyx
+include python/README.md

python/README.rst

@@ -1,43 +1,55 @@
-## Minimap2 Python Binding
+=======================
+Minimap2 Python Binding
+=======================
 
-[Minimap2][minimap2] is a fast and accurate pairwise aligner for genomic and
+`Minimap2 <https://github.com/lh3/minimap2>` is a fast and accurate pairwise
-transcribed nucleotide sequences. This module wraps minimap2 and provides a
+aligner for genomic and transcribed nucleotide sequences. This module wraps
-convenient interface to calling minimap2 in Python.
+minimap2 and provides a convenient interface to calling minimap2 in Python.
 
-### Installation
+Installation
+------------
 
 The minimap2 model can be installed directly with:
-```sh
-git clone https://github.com/lh3/minimap2
-cd minimap2
-python setup.py install
-```
-or with [pip][pip]:
-```sh
-pip install --user minimap2
-```
 
-### Usage
+.. code:: shell
+
+	git clone https://github.com/lh3/minimap2
+	cd minimap2
+	python setup.py install
+
+or with pip:
+
+.. code:: shell
+
+	pip install --user minimap2
+
+Usage
+-----
 
 The following Python program shows the key functionality of this module:
-```python
+
-import minimap2 as mm
+.. code:: python
-a = mm.Aligner("test/MT-human.fa")
+
-if not a: raise Exception("ERROR: failed to load/build index")
+	import minimap2 as mm
-for hit in a.map("GGTTAAATACAGACCAAGAGCCTTCAAAGCCCTCAGTAAGTTGCAATACTTAATTTCTGT"):
+	a = mm.Aligner("test/MT-human.fa")
-	print("{}\t{}\t{}\t{}".format(hit.ctg, hit.r_st, hit.r_en, hit.cigar_str))
+	if not a: raise Exception("ERROR: failed to load/build index")
-```
+	for hit in a.map("GGTTAAATACAGACCAAGAGCCTTCAAAGCCCTCAGTAAGTTGCAATACTTAATTTCTGT"):
+		print("{}\t{}\t{}\t{}".format(hit.ctg, hit.r_st, hit.r_en, hit.cigar_str))
+
 It builds an index from the specified sequence file (or loads an index if a
 pre-built index is supplied), aligns a sequence against it, traverses each hit
 and prints them out.
 
-### APIs
+APIs
+----
 
-#### Class minimap2.Aligner
+Class minimap2.Aligner
+~~~~~~~~~~~~~~~~~~~~~~
+
+.. code:: python
+
+	Aligner(fn_idx_in, preset=None, ...)
 
-```python
-Aligner(fn_idx_in, preset=None, ...)
-```
 Arguments:
 
 * `fn_idx_in`: index or sequence file name. Minimap2 automatically tests the
@@ -67,13 +79,15 @@ Arguments:
 
 * `fn_idx_out`: name of file to which the index is written
 
-```python
+.. code:: python
-map(query_seq)
+
-```
+	map(query_seq)
+
 This methods maps `query_seq` against the index. It *yields* a generator,
 generating a series of `Alignment` objects.
 
-#### Class minimap2.Alignment
+Class minimap2.Alignment
+~~~~~~~~~~~~~~~~~~~~~~~~
 
 This class has the following properties:
 
@@ -105,11 +119,7 @@ This class has the following properties:
   give the length and the operator of each CIGAR operation.
 
 An Alignment object can be converted to a string in the following format:
-```
-q_st  q_en  strand  ctg  ctg_len  r_st  r_en  blen-NM  blen  mapq  cg:Z:cigar_str
-```
 
+::
 
-
+	q_st  q_en  strand  ctg  ctg_len  r_st  r_en  blen-NM  blen  mapq  cg:Z:cigar_str
-[minimap2]: https://github.com/lh3/minimap2
-[pip]: https://pypi.python.org/pypi/pip

setup.py

@@ -4,9 +4,17 @@ except ImportError:
 	from distutils.core import setup
 	from distutils.extension import Extension
 
-from Cython.Build import cythonize
+cmdclass = {}
-import sys
 
+try:
+	from Cython.Build import build_ext
+except ImportError: # without Cython
+	module_src = 'python/minimap2.c'
+else: # with Cython
+	module_src = 'python/minimap2.pyx'
+	cmdclass['build_ext'] = build_ext
+
+import sys
 sys.path.append('python')
 
 setup(
@@ -16,12 +24,16 @@ setup(
 	description = 'Minimap2 python binding',
 	author = 'Heng Li',
 	author_email = 'lh3@me.com',
+	license = 'MIT',
 	keywords = ['bioinformatics', 'sequence-alignment'],
-    ext_modules = cythonize([Extension('minimap2',
+    ext_modules = [Extension('minimap2',
-		['python/minimap2.pyx', 'align.c', 'bseq.c', 'chain.c', 'format.c', 'hit.c', 'index.c', 'kalloc.c',
+		sources = [module_src, 'align.c', 'bseq.c', 'chain.c', 'format.c', 'hit.c', 'index.c',
-		 'ksw2_extd2_sse.c', 'ksw2_exts2_sse.c', 'ksw2_extz2_sse.c', 'ksw2_ll_sse.c', 'kthread.c', 'map.c',
+				   'ksw2_extd2_sse.c', 'ksw2_exts2_sse.c', 'ksw2_extz2_sse.c', 'ksw2_ll_sse.c',
-		 'misc.c', 'sdust.c', 'sketch.c'],
+				   'kalloc.c', 'kthread.c', 'map.c', 'misc.c', 'sdust.c', 'sketch.c'],
+		depends = ['minimap.h', 'bseq.h', 'kalloc.h', 'kdq.h', 'khash.h', 'kseq.h', 'ksort.h',
+				   'ksw2.h', 'kthread.h', 'kvec.h', 'mmpriv.h', 'sdust.h',
+				   'python/cminimap2.h', 'python/cminimap2.pxd'],
 		extra_compile_args = ['-msse4'], # WARNING: ancient x86_64 CPUs don't have SSE4
 		include_dirs = ['.'],
-		libraries = ['z', 'm', 'pthread'])])
+		libraries = ['z', 'm', 'pthread'])],
-)
+	cmdclass = cmdclass)