From: Afif Elghraoui Date: Thu, 12 Nov 2015 07:20:10 +0000 (-0800) Subject: Remove patches applied upstream X-Git-Tag: archive/raspbian/0.22.0+ds-1+rpi1~1^2^2~266 X-Git-Url: https://dgit.raspbian.org/?a=commitdiff_plain;h=7eb70489937dd567ee926534729a87e0497a5096;p=python-pysam.git Remove patches applied upstream --- 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 -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 -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 -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 -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