Andreas Tille pushed to branch master at Debian Med / pbalign
Commits: d7bd68f1 by Andreas Tille at 2020-02-27T15:26:48+01:00 Try to get rid of pbh5tools - - - - - 86f2ff10 by Andreas Tille at 2020-02-27T15:29:51+01:00 Mention issues with pbcore and pbcommand -> seems not to be maintaineable any more thus asking for removal - - - - - 5 changed files: - debian/changelog - debian/control - debian/patches/2to3.patch - + debian/patches/no_pbh5tools.patch - debian/patches/series Changes: ===================================== debian/changelog ===================================== @@ -9,9 +9,49 @@ pbalign (0.3.2-2) UNRELEASED; urgency=medium * Remove trailing whitespace in debian/rules * Trim trailing whitespace. * Set upstream metadata fields: Repository, Repository-Browse. - TODO: python3-pbh5tools not yet available - pbh5tools is waiting for - https://github.com/PacificBiosciences/pbh5tools/issues/37 + * Drop pbh5tools from Recommends since its not available any more + +Not supported by latest pbcore and pbcommand any more: + +pylint --errors-only pbalign +************* Module pbalign.pbalignrunner +pbalign/pbalignrunner.py:50:0: E0611: No name 'pbparser_runner' in module 'pbcommand.cli' (no-name-in-module) +************* Module pbalign.options +pbalign/options.py:40:0: E0611: No name 'get_pbparser' in module 'pbcommand.models' (no-name-in-module) +************* Module pbalign.alignservice.gmap +pbalign/alignservice/gmap.py:40:0: E0611: No name 'Process' in module 'pbcore.util' (no-name-in-module) +pbalign/alignservice/gmap.py:40:0: E0401: Unable to import 'pbcore.util.Process' (import-error) +************* Module pbalign.alignservice.bowtie +pbalign/alignservice/bowtie.py:39:0: E0611: No name 'Process' in module 'pbcore.util' (no-name-in-module) +pbalign/alignservice/bowtie.py:39:0: E0401: Unable to import 'pbcore.util.Process' (import-error) +************* Module pbalign.alignservice.fastabasedalign +pbalign/alignservice/fastabasedalign.py:40:0: E0611: No name 'Process' in module 'pbcore.util' (no-name-in-module) +pbalign/alignservice/fastabasedalign.py:40:0: E0401: Unable to import 'pbcore.util.Process' (import-error) +************* Module pbalign.tasks.align_minorvariants +pbalign/tasks/align_minorvariants.py:9:0: E0611: No name 'get_pbparser' in module 'pbcommand.models' (no-name-in-module) +pbalign/tasks/align_minorvariants.py:10:0: E0611: No name 'pbparser_runner' in module 'pbcommand.cli' (no-name-in-module) +************* Module pbalign.utils.RgnH5IO +pbalign/utils/RgnH5IO.py:13:0: E0611: No name 'BasH5IO' in module 'pbcore.io' (no-name-in-module) +pbalign/utils/RgnH5IO.py:13:0: E0401: Unable to import 'pbcore.io.BasH5IO' (import-error) +pbalign/utils/RgnH5IO.py:56:0: E1126: Sequence index is not an int, slice, or instance with __index__ (invalid-sequence-index) +************* Module pbalign.utils.fileutil +pbalign/utils/fileutil.py:42:0: E0611: No name 'Process' in module 'pbcore.util' (no-name-in-module) +pbalign/utils/fileutil.py:42:0: E0401: Unable to import 'pbcore.util.Process' (import-error) +************* Module pbalign.utils.progutil +pbalign/utils/progutil.py:37:0: E0611: No name 'Process' in module 'pbcore.util' (no-name-in-module) +pbalign/utils/progutil.py:37:0: E0401: Unable to import 'pbcore.util.Process' (import-error) +************* Module pbalign.tools.createChemistryHeader +pbalign/tools/createChemistryHeader.py:14:0: E0611: No name 'BasH5IO' in module 'pbcore.io' (no-name-in-module) +************* Module pbalign.tools.loadChemistry +pbalign/tools/loadChemistry.py:71:14: E0602: Undefined variable 'BasH5Reader' (undefined-variable) +************* Module pbalign.tools.mask_aligned_reads +pbalign/tools/mask_aligned_reads.py:12:0: E0611: No name 'CmpH5Reader' in module 'pbcore.io' (no-name-in-module) +pbalign/tools/mask_aligned_reads.py:12:0: E0611: No name 'EmptyCmpH5Error' in module 'pbcore.io' (no-name-in-module) +pbalign/tools/mask_aligned_reads.py:124:13: E1123: Unexpected keyword argument 'version' in constructor call (unexpected-keyword-arg) +make: *** [Makefile:19: pylint] Fehler 2 + + +Issue tracker for https://github.com/PacificBiosciences/pbalign/ is disabled - so no idea how to ask for updates -- Andreas Tille <[email protected]> Fri, 13 Dec 2019 10:59:33 +0100 ===================================== debian/control ===================================== @@ -24,8 +24,7 @@ Depends: ${misc:Depends}, python3-pbalign (= ${source:Version}), python3-pkg-resources, blasr -Recommends: python3-pbh5tools, - hdf5-tools +Recommends: hdf5-tools Suggests: bowtie2, gmap, pbalign-doc @@ -42,8 +41,7 @@ Architecture: all Depends: ${misc:Depends}, ${python3:Depends}, blasr -Recommends: python3-pbh5tools, - hdf5-tools +Recommends: hdf5-tools Suggests: bowtie2, gmap, pbalign-doc ===================================== debian/patches/2to3.patch ===================================== @@ -5,7 +5,7 @@ Last-Update: Fri, 13 Dec 2019 10:59:33 +0100 --- a/Makefile +++ b/Makefile -@@ -3,25 +3,25 @@ SHELL = /bin/bash -e +@@ -3,17 +3,17 @@ SHELL = /bin/bash -e all: build install build: @@ -27,9 +27,8 @@ Last-Update: Fri, 13 Dec 2019 10:59:33 +0100 + python3 setup.py develop pylint: -- pylint --errors-only pbalign -+ pylint3 --errors-only pbalign - + pylint --errors-only pbalign +@@ -21,7 +21,7 @@ pylint: test: pylint # Unit tests #find tests/unit -name "*.py" | xargs nosetests ===================================== debian/patches/no_pbh5tools.patch ===================================== @@ -0,0 +1,15 @@ +Description: Drop pbh5tools from Recommends since its not available any more +Author: Andreas Tille <[email protected]> +Last-Update: Thu, 27 Feb 2020 15:10:44 +0100 + +--- a/tests/cram_h5/ccs.t ++++ b/tests/cram_h5/ccs.t +@@ -39,8 +39,6 @@ Set up + + $ rm -f $BAS_CMPOUT + $ pbalign $Q $T $BAS_CMPOUT --useccs=useccsdenovo 2>/dev/null +- $ /mnt/secondary/Smrtanalysis/smrtcmds/bin/smrtwrap cmph5tools.py sort $BAS_CMPOUT --deep --inPlace +- $ /mnt/secondary/Smrtanalysis/smrtcmds/bin/smrtwrap cmph5tools.py sort $CCS_CMPOUT --deep --inPlace + + $ h5diff $CCS_CMPOUT $BAS_CMPOUT /AlnGroup /AlnGroup + $ h5diff $CCS_CMPOUT $BAS_CMPOUT /AlnInfo /AlnInfo ===================================== debian/patches/series ===================================== @@ -1,2 +1,3 @@ find_definitions_from_pbcore.patch 2to3.patch +no_pbh5tools.patch View it on GitLab: https://salsa.debian.org/med-team/pbalign/-/compare/c5c507785a8d3c7a0d2bc16492b4f74dd7bdd645...86f2ff100e4700f0f52cde0817e7cf4ab22cc25b -- View it on GitLab: https://salsa.debian.org/med-team/pbalign/-/compare/c5c507785a8d3c7a0d2bc16492b4f74dd7bdd645...86f2ff100e4700f0f52cde0817e7cf4ab22cc25b You're receiving this email because of your account on salsa.debian.org.
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