[med-svn] [python-pysam] 06/10: Remove patches applied upstream
Afif Elghraoui
afif-guest at moszumanska.debian.org
Thu Nov 12 09:09:14 UTC 2015
This is an automated email from the git hooks/post-receive script.
afif-guest pushed a commit to branch master
in repository python-pysam.
commit 7eb70489937dd567ee926534729a87e0497a5096
Author: Afif Elghraoui <afif at ghraoui.name>
Date: Wed Nov 11 23:20:10 2015 -0800
Remove patches applied upstream
---
debian/patches/correct-spelling-errors.patch | 115 ---------------------
debian/patches/cython23.patch | 39 -------
debian/patches/improve-python3-compatibility.patch | 27 -----
debian/patches/sam_mpileup.patch | 28 -----
debian/patches/series | 4 -
5 files changed, 213 deletions(-)
diff --git a/debian/patches/correct-spelling-errors.patch b/debian/patches/correct-spelling-errors.patch
deleted file mode 100644
index 0b9c5cb..0000000
--- a/debian/patches/correct-spelling-errors.patch
+++ /dev/null
@@ -1,115 +0,0 @@
-Description: Fix spelling errors in source distribution
-Author: Afif Elghraoui <afif at ghraoui.name>
-Bug: https://github.com/pysam-developers/pysam/pull/122
-Last-Update: 2015-06-09
----
-This patch header follows DEP-3: http://dep.debian.net/deps/dep3/
---- python-pysam.orig/pysam/calignmentfile.pyx
-+++ python-pysam/pysam/calignmentfile.pyx
-@@ -1442,7 +1442,7 @@
- .. note::
-
- It is usually not necessary to create an object of this class
-- explicitely. It is returned as a result of call to a
-+ explicitly. It is returned as a result of call to a
- :meth:`AlignmentFile.fetch`.
-
- '''
-@@ -1491,7 +1491,7 @@
- .. note::
-
- It is usually not necessary to create an object of this class
-- explicitely. It is returned as a result of call to a
-+ explicitly. It is returned as a result of call to a
- :meth:`AlignmentFile.fetch`.
-
- """
-@@ -1645,7 +1645,7 @@
-
- .. note::
- It is usually not necessary to create an object of this class
-- explicitely. It is returned as a result of call to a
-+ explicitly. It is returned as a result of call to a
- :meth:`AlignmentFile.fetch`.
-
- """
-@@ -1715,7 +1715,7 @@
-
- .. note::
- It is usually not necessary to create an object of this class
-- explicitely. It is returned as a result of call to a :meth:`AlignmentFile.fetch`.
-+ explicitly. It is returned as a result of call to a :meth:`AlignmentFile.fetch`.
- """
-
- def __init__(self, AlignmentFile samfile, positions, int multiple_iterators=True):
-@@ -3311,7 +3311,7 @@
- section.
-
- *value_type* describes the type of *value* that is to entered
-- into the alignment record.. It can be set explicitely to one
-+ into the alignment record.. It can be set explicitly to one
- of the valid one-letter type codes. If unset, an appropriate
- type will be chosen automatically.
-
-@@ -3421,7 +3421,7 @@
- bytesize, nvalues, values = convertBinaryTagToList(v + 1)
- return values
- else:
-- raise ValueError("unknown auxilliary type '%s'" % auxtype)
-+ raise ValueError("unknown auxiliary type '%s'" % auxtype)
-
- def get_tags(self, with_value_type=False):
- """the fields in the optional aligment section.
-@@ -3504,7 +3504,7 @@
- a list of (tag, value) tuples.
-
- The :term:`value type` of the values is determined from the
-- python type. Optionally, a type may be given explicitely as
-+ python type. Optionally, a type may be given explicitly as
- a third value in the tuple, For example:
-
- x.set_tags([(NM, 2, "i"), (RG, "GJP00TM04", "Z")]
---- python-pysam.orig/pysam/ctabix.pyx
-+++ python-pysam/pysam/ctabix.pyx
-@@ -199,7 +199,7 @@
- +-----------+-----------+------------------------------------------+
-
- Only the first three fields are required. Additional
-- fields are optional, but if one is defined, all the preceeding
-+ fields are optional, but if one is defined, all the preceding
- need to be defined as well.
-
- '''
---- python-pysam.orig/save/pysam_test2.6.py
-+++ python-pysam/save/pysam_test2.6.py
-@@ -355,7 +355,7 @@
-
- If *use_template* is set, the header is copied from infile using the
- template mechanism, otherwise target names and lengths are passed
-- explicitely.
-+ explicitly.
-
- '''
-
---- python-pysam.orig/tests/AlignmentFile_test.py
-+++ python-pysam/tests/AlignmentFile_test.py
-@@ -370,7 +370,7 @@
-
- If *use_template* is set, the header is copied from infile
- using the template mechanism, otherwise target names and
-- lengths are passed explicitely.
-+ lengths are passed explicitly.
-
- The *checkf* is used to determine if the files are
- equal.
---- python-pysam.orig/tests/SamFile_test.py
-+++ python-pysam/tests/SamFile_test.py
-@@ -355,7 +355,7 @@
-
- If *use_template* is set, the header is copied from infile
- using the template mechanism, otherwise target names and
-- lengths are passed explicitely.
-+ lengths are passed explicitly.
-
- '''
-
diff --git a/debian/patches/cython23.patch b/debian/patches/cython23.patch
deleted file mode 100644
index 27afe0f..0000000
--- a/debian/patches/cython23.patch
+++ /dev/null
@@ -1,39 +0,0 @@
-From 6efb22b1a3ee4bc57a691f163b456b417da56db3 Mon Sep 17 00:00:00 2001
-From: Andreas Heger <andreas.heger at gmail.com>
-Date: Thu, 3 Sep 2015 21:25:28 +0100
-Subject: [PATCH] change ctypedef enum to typedef enum for cython 0.23
-Bug: https://github.com/pysam-developers/pysam/issues/164
----
- pysam/chtslib.pxd | 6 +++---
- 1 file changed, 3 insertions(+), 3 deletions(-)
-
-diff --git a/pysam/chtslib.pxd b/pysam/chtslib.pxd
-index 2f8c941..299e84a 100644
---- a/pysam/chtslib.pxd
-+++ b/pysam/chtslib.pxd
-@@ -363,7 +363,7 @@ cdef extern from "htslib/hts.h" nogil:
- hFILE *hfile
- void *voidp
-
-- ctypedef enum htsFormatCategory:
-+ cdef enum htsFormatCategory:
- unknown_category
- sequence_data # Sequence data -- SAM, BAM, CRAM, etc
- variant_data # Variant calling data -- VCF, BCF, etc
-@@ -371,14 +371,14 @@ cdef extern from "htslib/hts.h" nogil:
- region_list # Coordinate intervals or regions -- BED, etc
- category_maximum
-
-- ctypedef enum htsExactFormat:
-+ cdef enum htsExactFormat:
- unknown_format
- binary_format
- text_format
- sam, bam, bai, cram, crai, vcf, bcf, csi, gzi, tbi, bed
- format_maximum
-
-- ctypedef enum htsCompression:
-+ cdef enum htsCompression:
- no_compression, gzip, bgzf, custom
- compression_maximum
-
diff --git a/debian/patches/improve-python3-compatibility.patch b/debian/patches/improve-python3-compatibility.patch
deleted file mode 100644
index 20e8905..0000000
--- a/debian/patches/improve-python3-compatibility.patch
+++ /dev/null
@@ -1,27 +0,0 @@
-Description: Improve python3 compatibility for tests
-Author: Afif Elghraoui <afif at ghraoui.name>
-Forwarded: no
-Applied-Upstream: commit:244a416863aa13c1e9d5abfb3900e70e5d23adb1
-Last-Update: 2015-07-11
----
---- python-pysam.orig/tests/TestUtils.py
-+++ python-pysam/tests/TestUtils.py
-@@ -1,3 +1,5 @@
-+from __future__ import absolute_import
-+from __future__ import print_function
- import sys
- import os
- import pysam
-@@ -68,9 +70,9 @@
- l1 = sorted(l1[:-1].split("\t"))
- l2 = sorted(l2[:-1].split("\t"))
- if l1 != l2:
-- print "mismatch in line %i" % n
-- print l1
-- print l2
-+ print("mismatch in line %i" % n)
-+ print(l1)
-+ print(l2)
- return False
- else:
- return False
diff --git a/debian/patches/sam_mpileup.patch b/debian/patches/sam_mpileup.patch
deleted file mode 100644
index 5239970..0000000
--- a/debian/patches/sam_mpileup.patch
+++ /dev/null
@@ -1,28 +0,0 @@
-Author: Andreas Tille <tille at debian.org>
-Last-Update: 2015-07-24
-Forwarded: https://github.com/pysam-developers/pysam/pull/149
-Description: Update depricated command in test suite
- [Andreas]
- samtools pileup -cf ex1.fa ex1.bam | gzip > ex1.pileup.gz
- [main] The `pileup' command has been removed. Please use `mpileup' instead.
- [Afif]
- --Simply replacing pileup with mpileup introduced a new error:
- samtools mpileup -cf ex1.fa ex1.bam | gzip > ex1.pileup.gz
- mpileup: invalid option -- 'c'
- Invalid option: '?'
- --See:
- samtools man page, under mpileup: "In the pileup format (without -u or -g),"
- http://www.htslib.org/doc/samtools.html
- https://www.biostars.org/p/42094/
- The solution is to remove the "-c" flag
---- python-pysam.orig/tests/pysam_data/Makefile
-+++ python-pysam/tests/pysam_data/Makefile
-@@ -48,7 +48,7 @@
- samtools index $<
-
- ex1.pileup.gz:ex1.bam ex1.fa
-- samtools pileup -cf ex1.fa ex1.bam | gzip > ex1.pileup.gz
-+ samtools mpileup -f ex1.fa ex1.bam | gzip > ex1.pileup.gz
-
- ex2_truncated.bam: ex2.bam
- head -c 124000 ex2.bam > ex2_truncated.bam
diff --git a/debian/patches/series b/debian/patches/series
index 01d5a2d..639025c 100644
--- a/debian/patches/series
+++ b/debian/patches/series
@@ -1,8 +1,4 @@
change-htslib-statement-to-link-to-debian
adding-include-hts-dirs
-correct-spelling-errors.patch
ignore-htslib-dir.patch
-improve-python3-compatibility.patch
-sam_mpileup.patch
strip_online_tests.patch
-cython23.patch
--
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