From 8f33bb5aa61938689804e722b429bcb8a06058b1 Mon Sep 17 00:00:00 2001 From: Justin Lecher Date: Thu, 22 Jan 2015 16:32:54 +0000 Subject: [PATCH] sci-chemistry/ccpn: Drop obsolete patches Package-Manager: portage-2.2.15/cvs/Linux x86_64 Manifest-Sign-Key: 0xB9D4F231BD1558AB! --- sci-chemistry/ccpn/ChangeLog | 8 +- sci-chemistry/ccpn/Manifest | 36 ++++----- .../ccpn/files/2.1.3_1-dynamics.patch | 13 ---- .../ccpn/files/2.1.3_1-impl-dec.patch | 72 ----------------- .../ccpn/files/2.1.3_1-parallel.patch | 25 ------ sci-chemistry/ccpn/files/2.2.1-parallel.patch | 38 --------- sci-chemistry/ccpn/files/2.2.2-parallel.patch | 38 --------- .../ccpn/files/ccpn-2.4.0_p140425-lxml.patch | 78 ------------------- 8 files changed, 22 insertions(+), 286 deletions(-) delete mode 100644 sci-chemistry/ccpn/files/2.1.3_1-dynamics.patch delete mode 100644 sci-chemistry/ccpn/files/2.1.3_1-impl-dec.patch delete mode 100644 sci-chemistry/ccpn/files/2.1.3_1-parallel.patch delete mode 100644 sci-chemistry/ccpn/files/2.2.1-parallel.patch delete mode 100644 sci-chemistry/ccpn/files/2.2.2-parallel.patch delete mode 100644 sci-chemistry/ccpn/files/ccpn-2.4.0_p140425-lxml.patch diff --git a/sci-chemistry/ccpn/ChangeLog b/sci-chemistry/ccpn/ChangeLog index 09b889bc8cd0..5cc5cdb302ef 100644 --- a/sci-chemistry/ccpn/ChangeLog +++ b/sci-chemistry/ccpn/ChangeLog @@ -1,6 +1,12 @@ # ChangeLog for sci-chemistry/ccpn # Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 -# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/ccpn/ChangeLog,v 1.157 2015/01/22 16:25:49 jlec Exp $ +# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/ccpn/ChangeLog,v 1.158 2015/01/22 16:32:53 jlec Exp $ + + 22 Jan 2015; Justin Lecher -files/2.1.3_1-dynamics.patch, + -files/2.1.3_1-impl-dec.patch, -files/2.1.3_1-parallel.patch, + -files/2.2.1-parallel.patch, -files/2.2.2-parallel.patch, + -files/ccpn-2.4.0_p140425-lxml.patch: + Drop obsolete patches *ccpn-2.4.1_p150122 (22 Jan 2015) diff --git a/sci-chemistry/ccpn/Manifest b/sci-chemistry/ccpn/Manifest index c53286f3ca1d..bc5079e044e2 100644 --- a/sci-chemistry/ccpn/Manifest +++ b/sci-chemistry/ccpn/Manifest @@ -1,14 +1,8 @@ -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA512 -AUX 2.1.3_1-dynamics.patch 825 SHA256 53577b6f9621a707b1b5d676d57ed16f3963f3172598d944b823133908226edb SHA512 56d89056a2916cf7c5a90084b151a46a39a456ad84c1d9d4042bfa1bd236b576e3f3232a2e34c0adbeff77a4f954d73b1565e0df701a29a0eca1e0a654728e74 WHIRLPOOL 084bdee6ca240491db0a718e23529887c3b4341217a036be4f87e3172cdb01db364ff4adc6a63d66aa146c605e05891d2d1c879cf0576084c5662e016314b74e -AUX 2.1.3_1-impl-dec.patch 2818 SHA256 f175a1b4a9cc4f1636bf36928883d37a266af830234aa3d7676f4fe4f7f1ddd8 SHA512 11d54abe5578424c601f97e28f7af613284b789ad977c6b1f4e737116828ad0eee3183f65ba20e609065d602028a3cc59ebd6fe232d0c06133b0dcaea5f3dbea WHIRLPOOL 597d03fab86dcd61991a256a06644df0edb3edbbcbc6b916b8b3dd6808f5809a473383facabd46bf1ac343a9d75f9c49cac36c1a1a8cc60974f66b43237634fe -AUX 2.1.3_1-parallel.patch 577 SHA256 7e650ef2fa1ff0626349affdf1bc9578fe1da3b8cee7dd9125d33a2164978b69 SHA512 c8a94fd6622dfdd90dc2f40ce2aea3440a1cb2c56e4143339675995e8cf29dfb73e4e501117db1e1f6c6cbcb62d49dd52a4c239680c2c4db6145f9bbbb2486af WHIRLPOOL f943d5bcef2ae2cdf969b15e03a50c5cb3cd640c6e7400657c78b2120aa0bf7847c93bc652dfc0510bee11b9c2d1a8cff9e8deb8946bf07be6055a6259458943 -AUX 2.2.1-parallel.patch 850 SHA256 318bbf3ae5b04e8cbe0e8e93a7e81a7e793fffa9a0d754464367092d6b79f04d SHA512 332815d3eec610eb2537c3bd803941bff06aa64dddbe730a53657be6139a4ef294995c0a1c962abddef7f45c756fdce4c21616cfee3222dd4005228021745da7 WHIRLPOOL fc97aa74630c0be0372b8c863fc985238cd16849c0f69cb60e483a88cfbe04faea1448ca656a83ed56c2599a45d36869dd293163e4faf240e75c1ffcfe54e204 -AUX 2.2.2-parallel.patch 850 SHA256 318bbf3ae5b04e8cbe0e8e93a7e81a7e793fffa9a0d754464367092d6b79f04d SHA512 332815d3eec610eb2537c3bd803941bff06aa64dddbe730a53657be6139a4ef294995c0a1c962abddef7f45c756fdce4c21616cfee3222dd4005228021745da7 WHIRLPOOL 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depositionFileImporter 322 SHA256 ba96561ccef577126df3454b0ef2207e6fe32ecb178e98bc0e106423553e0f33 SHA512 f45f155da7d92fdfc99c69afa9dff687ff68dd6717dd16561555ed08fc695ba07e3ddda08011d3ec031bbcf06eb14fcc2bf8e5dce05591193871afe120ee90b5 WHIRLPOOL 1a42c6e536fedab84a005001e046a3f98b9b2dad304ca1de2bfd615f4f4cd90d1cca22eaeb239913bbfc06ce2aaca10cfc00ed6864147127a980b2cbbc539882 @@ -24,24 +18,24 @@ DIST ccpn-update-2.4.1-150122.patch.xz 9032 SHA256 68c186762beb4600617f2dd71c14b EBUILD ccpn-2.4.1.ebuild 4685 SHA256 6e4c496453063dee64e64975a5732f6bbbc820bb97dc460691187ad15dc3e935 SHA512 a862d7ea10818bf2f219411019db151255a1e09f8e72c7a37eacbe7220b8640958be43079e995828f055ae62e93d002540de5be8f0cff231bb5ec62dbb0e8a8e WHIRLPOOL 6ed8127f87305e1406aed474089a478423dc0ae6b3c81191d650de680d22aea2112c62ac63c02a76bf219bcad49451477682e3ad187999764bcb02fb105e1e58 EBUILD ccpn-2.4.1_p150108.ebuild 4692 SHA256 cd8f2a9327714d07a88b714353299e078b6177444d746510e55dc7cb4c4b6e91 SHA512 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a/ccpnmr2.1/python/ccpnmr/c/linkSharedObjs b/ccpnmr2.1/python/ccpnmr/c/linkSharedObjs -index 8f56168..4490407 100755 ---- a/ccpnmr2.1/python/ccpnmr/c/linkSharedObjs -+++ b/ccpnmr2.1/python/ccpnmr/c/linkSharedObjs -@@ -5,7 +5,7 @@ ln -s ../../../c/ccpnmr/analysis/ContourFile.so ContourFile.so - ln -s ../../../c/ccpnmr/analysis/ContourLevels.so ContourLevels.so - ln -s ../../../c/ccpnmr/analysis/ContourStyle.so ContourStyle.so - ln -s ../../../c/ccpnmr/analysis/PeakCluster.so PeakCluster.so --ln -s ../../../c/ccpnmr/analysis/PeakClusterList.so PeakClusterList.so -+#ln -s ../../../c/ccpnmr/analysis/PeakClusterList.so PeakClusterList.so - ln -s ../../../c/ccpnmr/analysis/PeakList.so PeakList.so - ln -s ../../../c/ccpnmr/analysis/SliceFile.so SliceFile.so - ln -s ../../../c/ccpnmr/analysis/WinPeakList.so WinPeakList.so diff --git a/sci-chemistry/ccpn/files/2.1.3_1-impl-dec.patch b/sci-chemistry/ccpn/files/2.1.3_1-impl-dec.patch deleted file mode 100644 index a89503208956..000000000000 --- a/sci-chemistry/ccpn/files/2.1.3_1-impl-dec.patch +++ /dev/null @@ -1,72 +0,0 @@ -diff --git a/ccpnmr2.1/c/ccpnmr/analysis/py_slice_file.c b/ccpnmr2.1/c/ccpnmr/analysis/py_slice_file.c -index 451b32a..2f37c34 100644 ---- a/ccpnmr2.1/c/ccpnmr/analysis/py_slice_file.c -+++ b/ccpnmr2.1/c/ccpnmr/analysis/py_slice_file.c -@@ -46,6 +46,7 @@ Development of a Software Pipeline. Proteins 59, 687 - 696. - ===========================REFERENCE END=============================== - */ - #include "py_slice_file.h" -+#include "utility.h" - - #include "py_block_file.h" - #include "py_draw_handler.h" -diff --git a/ccpnmr2.1/c/memops/global/gl_handler.c b/ccpnmr2.1/c/memops/global/gl_handler.c -index 48a6a34..278134f 100644 ---- a/ccpnmr2.1/c/memops/global/gl_handler.c -+++ b/ccpnmr2.1/c/memops/global/gl_handler.c -@@ -46,6 +46,7 @@ Development of a Software Pipeline. Proteins 59, 687 - 696. - ===========================REFERENCE END=============================== - */ - #include "gl_handler.h" -+#include "utility.h" - - #ifndef IGNORE_GL - -diff --git a/ccpnmr2.1/c/memops/global/py_block_file.c b/ccpnmr2.1/c/memops/global/py_block_file.c -index 0d3f863..2f2b0f4 100644 ---- a/ccpnmr2.1/c/memops/global/py_block_file.c -+++ b/ccpnmr2.1/c/memops/global/py_block_file.c -@@ -49,6 +49,7 @@ Development of a Software Pipeline. Proteins 59, 687 - 696. - - #include "py_mem_cache.h" - #include "python_util.h" -+#include "utility.h" - - static PyObject *ErrorObject; /* locally-raised exception */ - -diff --git a/ccpnmr2.1/c/memops/global/py_draw_handler.c b/ccpnmr2.1/c/memops/global/py_draw_handler.c -index 0d354d1..1d0ec59 100644 ---- a/ccpnmr2.1/c/memops/global/py_draw_handler.c -+++ b/ccpnmr2.1/c/memops/global/py_draw_handler.c -@@ -46,6 +46,7 @@ Development of a Software Pipeline. Proteins 59, 687 - 696. - ===========================REFERENCE END=============================== - */ - #include "py_draw_handler.h" -+#include "utility.h" - - #ifndef IGNORE_GL - #include "py_gl_handler.h" -diff --git a/ccpnmr2.1/c/memops/global/py_shape_file.c b/ccpnmr2.1/c/memops/global/py_shape_file.c -index 32673f5..0e62683 100644 ---- a/ccpnmr2.1/c/memops/global/py_shape_file.c -+++ b/ccpnmr2.1/c/memops/global/py_shape_file.c -@@ -46,6 +46,7 @@ Development of a Software Pipeline. Proteins 59, 687 - 696. - ===========================REFERENCE END=============================== - */ - #include "py_shape_file.h" -+#include "utility.h" - - #include "py_mem_cache.h" - #include "python_util.h" -diff --git a/ccpnmr2.1/c/memops/global/py_store_file.c b/ccpnmr2.1/c/memops/global/py_store_file.c -index 6a66a8c..8fa5973 100644 ---- a/ccpnmr2.1/c/memops/global/py_store_file.c -+++ b/ccpnmr2.1/c/memops/global/py_store_file.c -@@ -46,6 +46,7 @@ Development of a Software Pipeline. Proteins 59, 687 - 696. - ===========================REFERENCE END=============================== - */ - #include "py_store_file.h" -+#include "utility.h" - - #include "python_util.h" - diff --git a/sci-chemistry/ccpn/files/2.1.3_1-parallel.patch b/sci-chemistry/ccpn/files/2.1.3_1-parallel.patch deleted file mode 100644 index b1dd4d2f264f..000000000000 --- a/sci-chemistry/ccpn/files/2.1.3_1-parallel.patch +++ /dev/null @@ -1,25 +0,0 @@ -diff --git a/ccpnmr2.1/c/Makefile b/ccpnmr2.1/c/Makefile -index 9fa8500..7a1a186 100644 ---- a/ccpnmr2.1/c/Makefile -+++ b/ccpnmr2.1/c/Makefile -@@ -7,16 +7,16 @@ compile: global structure analysis clouds dynamics - global: - cd memops/global && $(MAKE) - --structure: -+structure: global - cd ccp/structure && $(MAKE) - --analysis: -+analysis: global - cd ccpnmr/analysis && $(MAKE) - --clouds: -+clouds: global - cd ccpnmr/clouds && $(MAKE) - --dynamics: -+dynamics: global - cd ccpnmr/dynamics && $(MAKE) - - clean: global_clean structure_clean analysis_clean clouds_clean dynamics_clean diff --git a/sci-chemistry/ccpn/files/2.2.1-parallel.patch b/sci-chemistry/ccpn/files/2.2.1-parallel.patch deleted file mode 100644 index 9223ea8828c2..000000000000 --- a/sci-chemistry/ccpn/files/2.2.1-parallel.patch +++ /dev/null @@ -1,38 +0,0 @@ -diff --git a/ccpnmr2.2/c/Makefile b/ccpnmr2.2/c/Makefile -index 01fb25a..8e8e1fe 100644 ---- a/ccpnmr2.2/c/Makefile -+++ b/ccpnmr2.2/c/Makefile -@@ -5,22 +5,22 @@ all: compile - compile: global structure analysis clouds dynamics bayes - - global: -- cd memops/global && $(MAKE) -+ $(MAKE) -C memops/global - --structure: -- cd ccp/structure && $(MAKE) -+structure: global -+ $(MAKE) -C ccp/structure - --analysis: -- cd ccpnmr/analysis && $(MAKE) -+analysis: global -+ $(MAKE) -C ccpnmr/analysis - --clouds: -- cd ccpnmr/clouds && $(MAKE) -+clouds: global -+ $(MAKE) -C ccpnmr/clouds - --dynamics: -- cd ccpnmr/dynamics && $(MAKE) -+dynamics: global -+ $(MAKE) -C ccpnmr/dynamics - --bayes: -- cd other/cambridge/bayes && $(MAKE) -+bayes: global -+ $(MAKE) -C other/cambridge/bayes - - clean: global_clean structure_clean analysis_clean clouds_clean dynamics_clean bayes_clean - diff --git a/sci-chemistry/ccpn/files/2.2.2-parallel.patch b/sci-chemistry/ccpn/files/2.2.2-parallel.patch deleted file mode 100644 index 9223ea8828c2..000000000000 --- a/sci-chemistry/ccpn/files/2.2.2-parallel.patch +++ /dev/null @@ -1,38 +0,0 @@ -diff --git a/ccpnmr2.2/c/Makefile b/ccpnmr2.2/c/Makefile -index 01fb25a..8e8e1fe 100644 ---- a/ccpnmr2.2/c/Makefile -+++ b/ccpnmr2.2/c/Makefile -@@ -5,22 +5,22 @@ all: compile - compile: global structure analysis clouds dynamics bayes - - global: -- cd memops/global && $(MAKE) -+ $(MAKE) -C memops/global - --structure: -- cd ccp/structure && $(MAKE) -+structure: global -+ $(MAKE) -C ccp/structure - --analysis: -- cd ccpnmr/analysis && $(MAKE) -+analysis: global -+ $(MAKE) -C ccpnmr/analysis - --clouds: -- cd ccpnmr/clouds && $(MAKE) -+clouds: global -+ $(MAKE) -C ccpnmr/clouds - --dynamics: -- cd ccpnmr/dynamics && $(MAKE) -+dynamics: global -+ $(MAKE) -C ccpnmr/dynamics - --bayes: -- cd other/cambridge/bayes && $(MAKE) -+bayes: global -+ $(MAKE) -C other/cambridge/bayes - - clean: global_clean structure_clean analysis_clean clouds_clean dynamics_clean bayes_clean - diff --git a/sci-chemistry/ccpn/files/ccpn-2.4.0_p140425-lxml.patch b/sci-chemistry/ccpn/files/ccpn-2.4.0_p140425-lxml.patch deleted file mode 100644 index a476e98dfc8b..000000000000 --- a/sci-chemistry/ccpn/files/ccpn-2.4.0_p140425-lxml.patch +++ /dev/null @@ -1,78 +0,0 @@ - ccpnmr2.4/python/ccpnmr/format/general/Conversion.py | 2 +- - ccpnmr2.4/python/memops/metamodel/XmlModelIo.py | 3 +++ - ccpnmr2.4/python/memops/universal/ElementTree.py | 16 +++++++++++----- - ccpnmr2.4/python/pdbe/xml/Util.py | 5 +---- - 4 files changed, 16 insertions(+), 10 deletions(-) - -diff --git a/ccpnmr2.4/python/ccpnmr/format/general/Conversion.py b/ccpnmr2.4/python/ccpnmr/format/general/Conversion.py -index 4e9a13c..66f72d3 100644 ---- a/ccpnmr2.4/python/ccpnmr/format/general/Conversion.py -+++ b/ccpnmr2.4/python/ccpnmr/format/general/Conversion.py -@@ -1969,7 +1969,7 @@ class FormatConversion(object): - - def runFromXml(self,xmlFileName,allowedFormats=None): - -- import xml.etree.ElementTree as ET -+ from memops.universal.ElementTree import ElementTree as ET - - root = ET.ElementTree(file=xmlFileName) - -diff --git a/ccpnmr2.4/python/memops/metamodel/XmlModelIo.py b/ccpnmr2.4/python/memops/metamodel/XmlModelIo.py -index e09a873..05a77a1 100644 ---- a/ccpnmr2.4/python/memops/metamodel/XmlModelIo.py -+++ b/ccpnmr2.4/python/memops/metamodel/XmlModelIo.py -@@ -329,6 +329,9 @@ class XmlModelRead(TextWriter_py_2_1.TextWriter_py_2_1): - # handle contained elements - for elem in modelElem: - tag = elem.tag -+ # lxml also provides comments in addition to normal content -+ if tag is ElementTree.Comment: -+ continue - if classNameMapping.get(tag) is None: - # Element content - handle directly - -diff --git a/ccpnmr2.4/python/memops/universal/ElementTree.py b/ccpnmr2.4/python/memops/universal/ElementTree.py -index 2452217..c53afde 100644 ---- a/ccpnmr2.4/python/memops/universal/ElementTree.py -+++ b/ccpnmr2.4/python/memops/universal/ElementTree.py -@@ -3,14 +3,20 @@ dependent on Python version - """ - - try: -- import xml.etree.cElementTree as ElementTree # in python >=2.5 -+ from lxml import etree as ElementTree - except ImportError: - try: -- from xml.etree import ElementTree # in python >=2.5 -+ import xml.etree.cElementTree as ElementTree # in python >=2.5 - except ImportError: -- from elementtree import ElementTree # effbot's pure Python module -+ try: -+ from xml.etree import ElementTree # in python >=2.5 -+ except ImportError: -+ from elementtree import ElementTree # effbot's pure Python module - - try: -- from xml.etree import ElementInclude # in python >=2.5 -+ from lxml import ElementInclude - except ImportError: -- from elementtree import ElementInclude # effbot's pure Python module -+ try: -+ from xml.etree import ElementInclude # in python >=2.5 -+ except ImportError: -+ from elementtree import ElementInclude # effbot's pure Python module -diff --git a/ccpnmr2.4/python/pdbe/xml/Util.py b/ccpnmr2.4/python/pdbe/xml/Util.py -index eb36031..bc82b01 100644 ---- a/ccpnmr2.4/python/pdbe/xml/Util.py -+++ b/ccpnmr2.4/python/pdbe/xml/Util.py -@@ -1,9 +1,6 @@ - import sys, codecs - --from xml.etree.ElementTree import ElementTree --#from xml.etree import ElementTree # Use this on flynn --#import xml.etree.ElementTree as ET --#import elementtree.ElementTree as ET -+from memops.universal.ElementTree import ElementTree - - # - # Generic class to loop through elements/values of an XML ElementTree -- 2.26.2