[med-svn] [Git][med-team/pbalign][master] 2 commits: Try to get rid of pbh5tools
Andreas Tille
gitlab at salsa.debian.org
Thu Feb 27 14:30:46 GMT 2020
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 <tille at debian.org> 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 <tille at debian.org>
+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
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