[med-svn] [Git][med-team/tombo][master] 12 commits: Use execute_after hooks instead of overriding targets
Ananthu C V (@weepingclown)
gitlab at salsa.debian.org
Wed Nov 27 20:34:50 GMT 2024
Ananthu C V pushed to branch master at Debian Med / tombo
Commits:
b8a67483 by Ananthu C V at 2024-11-27T23:26:00+05:30
Use execute_after hooks instead of overriding targets
- - - - -
8f6b8a6e by Ananthu C V at 2024-11-27T23:42:54+05:30
Remove built doc files from debian source tree after they are installed
- - - - -
d51c536c by Ananthu C V at 2024-11-27T23:45:31+05:30
Make sure to clean built files before next build (Closes: #1049071)
- - - - -
126f30cb by Ananthu C V at 2024-11-28T00:43:59+05:30
Add patch to use importlib instead of deprecated pkg_resources (Closes: #1083801)
- - - - -
7562a4ad by Ananthu C V at 2024-11-28T00:57:53+05:30
Correct patch header metadata
- - - - -
a85384ad by Ananthu C V at 2024-11-28T01:12:43+05:30
Add patch to drop distutils usage
- - - - -
31f64c1b by Ananthu C V at 2024-11-28T01:13:55+05:30
Apply wrap-and-sort
- - - - -
a5746160 by Ananthu C V at 2024-11-28T01:23:26+05:30
Fix installed file permissions
- - - - -
644a316d by Ananthu C V at 2024-11-28T01:26:58+05:30
Add patch to remove badges from built docs
- - - - -
38dfaeab by Ananthu C V at 2024-11-28T01:43:16+05:30
Add patch to fix invalid escape sequence syntax warnings (Closes: #1087117)
- - - - -
88ffd4fe by Ananthu C V at 2024-11-28T01:43:27+05:30
Bump Standards-Version to 4.7.0 (no changes needed)
- - - - -
9302d1ff by Ananthu C V at 2024-11-28T01:43:28+05:30
Upload to unstable
- - - - -
13 changed files:
- debian/changelog
- debian/control
- debian/patches/2to3.patch
- + debian/patches/fix-invalid-escape-sequences.patch
- debian/patches/mathjax.patch
- debian/patches/no_future.patch
- debian/patches/no_install_depends_cython.patch
- + debian/patches/remove-badges-in-doc.patch
- + debian/patches/remove-distutils-usage.patch
- + debian/patches/remove-pkg-resources-usage.patch
- debian/patches/series
- debian/rules
- debian/tombo.install
Changes:
=====================================
debian/changelog
=====================================
@@ -1,3 +1,22 @@
+tombo (1.5.1-7) unstable; urgency=medium
+
+ * Team upload
+ * Use execute_after hooks instead of overriding targets
+ * Remove built doc files from debian source tree after they are installed
+ * Make sure to clean built files before next build (Closes: #1049071)
+ * Add patch to use importlib instead of deprecated pkg_resources
+ (Closes: #1083801)
+ * Correct patch header metadata
+ * Add patch to drop distutils usage
+ * Apply wrap-and-sort
+ * Fix installed file permissions
+ * Add patch to remove badges from built docs
+ * Add patch to fix invalid escape sequence syntax warnings
+ (Closes: #1087117)
+ * Bump Standards-Version to 4.7.0 (no changes needed)
+
+ -- Ananthu C V <weepingclown at disroot.org> Thu, 28 Nov 2024 01:40:55 +0530
+
tombo (1.5.1-6) unstable; urgency=medium
* No runtime dependency from cython
=====================================
debian/control
=====================================
@@ -3,23 +3,23 @@ Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.
Uploaders: Andreas Tille <tille at debian.org>
Section: science
Priority: optional
-Build-Depends: debhelper-compat (= 13),
+Build-Depends: cython3,
+ debhelper-compat (= 13),
dh-python,
- python3-all-dev,
- python3-setuptools,
- cython3,
- sphinx-doc,
- python3-sphinx,
- python3-sphinx-rtd-theme,
- python3-sphinx-argparse,
libjs-mathjax,
+ python3-all-dev,
python3-h5py <!nocheck>,
python3-mappy <!nocheck>,
+ python3-nose2 <!nocheck>,
python3-numpy <!nocheck>,
python3-scipy <!nocheck>,
+ python3-setuptools,
+ python3-sphinx,
+ python3-sphinx-argparse,
+ python3-sphinx-rtd-theme,
python3-tqdm <!nocheck>,
- python3-nose2 <!nocheck>
-Standards-Version: 4.6.2
+ sphinx-doc
+Standards-Version: 4.7.0
Vcs-Browser: https://salsa.debian.org/med-team/tombo
Vcs-Git: https://salsa.debian.org/med-team/tombo.git
Homepage: https://github.com/nanoporetech/tombo
@@ -27,16 +27,16 @@ Rules-Requires-Root: no
Package: tombo
Architecture: any
-Depends: ${shlibs:Depends},
- ${misc:Depends},
- ${python3:Depends},
- python3-h5py,
+Depends: python3-h5py,
python3-mappy,
python3-numpy,
+ python3-packaging,
python3-scipy,
- python3-tqdm
-Recommends: python3-pyfaidx,
- python3-rpy2
+ python3-tqdm,
+ ${misc:Depends},
+ ${python3:Depends},
+ ${shlibs:Depends}
+Recommends: python3-pyfaidx, python3-rpy2
Description: identification of modified nucleotides from raw nanopore sequencing data
Tombo is a suite of tools primarily for the identification of modified
nucleotides from nanopore sequencing data. Tombo also provides tools for
@@ -45,9 +45,7 @@ Description: identification of modified nucleotides from raw nanopore sequencing
Package: tombo-doc
Architecture: all
Section: doc
-Depends: ${sphinxdoc:Depends},
- ${misc:Depends},
- libjs-mathjax
+Depends: libjs-mathjax, ${misc:Depends}, ${sphinxdoc:Depends}
Multi-Arch: foreign
Description: identification of modified nucleotides from raw nanopore sequencing data (doc)
Tombo is a suite of tools primarily for the identification of modified
=====================================
debian/patches/2to3.patch
=====================================
@@ -1,5 +1,5 @@
Author: Andreas Tille <tille at debian.org>
-Last-Update: Mon, 15 Jun 2020 11:13:59 +0200
+Last-Update: 2020-06-15
Description: 2to3 patch
--- a/scripts/dump_per_read_statistics.py
=====================================
debian/patches/fix-invalid-escape-sequences.patch
=====================================
@@ -0,0 +1,24 @@
+Description: use raw strings to fix invalid escape sequences
+Author: Ananthu C V <weepingclown at debian.org>
+Last-Update: 2024-11-28
+--- a/tombo/_preprocess.py
++++ b/tombo/_preprocess.py
+@@ -155,3 +155,3 @@
+ if (re.match('@', fastq_rec[0]) is None or
+- re.match('\+', fastq_rec[2]) is None):
++ re.match(r'\+', fastq_rec[2]) is None):
+ # TODO maybe send this as a warning code to avoid poorly
+--- a/tombo/_event_resquiggle.py
++++ b/tombo/_event_resquiggle.py
+@@ -67,3 +67,3 @@
+ 'cigar', 'rNext', 'pNext', 'tLen', 'seq', 'qual')
+-CIGAR_PAT = re.compile('(\d+)([MIDNSHP=X])')
++CIGAR_PAT = re.compile(r'(\d+)([MIDNSHP=X])')
+ GAP_PAT = re.compile('-+')
+--- a/tombo/_plot_commands.py
++++ b/tombo/_plot_commands.py
+@@ -2252,3 +2252,3 @@
+ 'R and rpy2 are installed from the same channel with ' +
+- '`conda list | grep "r-base\|rpy2"` (last columns should match).')
++ r'`conda list | grep "r-base\|rpy2"` (last columns should match).')
+
=====================================
debian/patches/mathjax.patch
=====================================
@@ -1,5 +1,5 @@
Author: Andreas Tille <tille at debian.org>
-Last-Update: Mon, 15 Jun 2020 11:13:59 +0200
+Last-Update: 2020-06-15
Description: Use Debian packaged MathJax
--- a/docs/conf.py
=====================================
debian/patches/no_future.patch
=====================================
@@ -1,5 +1,5 @@
Author: Andreas Tille <tille at debian.org>
-Last-Update: Mon, 15 Jun 2020 11:13:59 +0200
+Last-Update: 2020-06-15
Description: Do not require future since we are using Python3 anyway
--- a/setup.py
=====================================
debian/patches/no_install_depends_cython.patch
=====================================
@@ -1,7 +1,7 @@
Description: No runtime dependency from cython
Bug-Debian: https://bugs.debian.org/1058010
Author: Andreas Tille <tille at debian.org>
-Last-Update: Mon, 11 Dec 2023 10:10:25 +0100
+Last-Update: 2023-12-11
--- a/setup.py
+++ b/setup.py
=====================================
debian/patches/remove-badges-in-doc.patch
=====================================
@@ -0,0 +1,17 @@
+Description: Remove badges using third party links from built docs
+Author: Ananthu C V <weepingclown at debian.org>
+Forwarded: not-needed
+Last-Update: 2024-11-28
+--- a/docs/index.rst
++++ b/docs/index.rst
+@@ -12,10 +12,2 @@
+
+-|bioconda_badge| |pypi_badge|
+-
+-.. |bioconda_badge| image:: https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg?style=flat-square
+- :target: http://bioconda.github.io/recipes/ont-tombo/README.html
+-
+-.. |pypi_badge| image:: https://badge.fury.io/py/ont-tombo.svg
+- :target: https://badge.fury.io/py/ont-tombo
+-
+ Basic tombo installation (python 2.7 and 3.4+ support)
=====================================
debian/patches/remove-distutils-usage.patch
=====================================
@@ -0,0 +1,35 @@
+Description: replace deprecated distutils usage with packaging
+Author: Ananthu C V <weepingclown at debian.org>
+Last-Update: 2024-11-28
+--- a/tombo/_event_resquiggle.py
++++ b/tombo/_event_resquiggle.py
+@@ -24,3 +24,3 @@
+ from tempfile import NamedTemporaryFile
+-from distutils.version import LooseVersion
++from packaging.version import parse
+ from collections import defaultdict, namedtuple, Counter
+@@ -882,3 +882,3 @@
+ # get albacore version, or if not specified set to 0.0
+- albacore_version = LooseVersion(fast5_data[
++ albacore_version = parse(fast5_data[
+ '/Analyses/' + basecall_group].attrs.get('version')
+@@ -909,3 +909,3 @@
+
+- if albacore_version >= LooseVersion("2.0"):
++ if albacore_version >= parse("2.0"):
+ read_start_rel_to_raw = called_dat['start'][0].astype(np.int64)
+@@ -930,3 +930,3 @@
+ # https://community.nanoporetech.com/posts/albacore-zero-length-even
+- if albacore_version < LooseVersion("1.0"):
++ if albacore_version < parse("1.0"):
+ last_event = called_dat[-1]
+@@ -942,3 +942,3 @@
+ fix_read_start = False
+- elif albacore_version < LooseVersion("2.0"):
++ elif albacore_version < parse("2.0"):
+ # compute event starts from length slot as start slot is less
+@@ -964,3 +964,3 @@
+ # but raw was intorduced into rna basecalling one minor release later
+- if rna and albacore_version < LooseVersion("2.1"):
++ if rna and albacore_version < parse("2.1"):
+ kmer_dom_pos = 2
=====================================
debian/patches/remove-pkg-resources-usage.patch
=====================================
@@ -0,0 +1,146 @@
+Description: replace deprecated pkg_resources usage with importlib
+Author: Ananthu C V <weepingclown at debian.org>
+Bug-Debian: https://bugs.debian.org/1083801
+Last-Update: 2024-11-28
+--- a/tombo/_plot_commands.py
++++ b/tombo/_plot_commands.py
+@@ -20,3 +20,3 @@
+ from itertools import repeat, groupby
+-from pkg_resources import resource_string
++from importlib.resources import files
+
+@@ -169,3 +169,3 @@
+ 'Comparison':r.StrVector(mod_names_for_r)})
+- r.r(resource_string(__name__, 'R_scripts/plotROC.R').decode())
++ r.r(files(__name__).joinpath('R_scripts/plotROC.R').read_bytes().decode())
+ r.r('pdf("' + pdf_fn + '", height=4, width=6)')
+@@ -237,3 +237,3 @@
+ 'Comparison':r.StrVector(mod_names_for_r)})
+- r.r(resource_string(__name__, 'R_scripts/plotROC.R').decode())
++ r.r(files(__name__).joinpath('R_scripts/plotROC.R').read_bytes().decode())
+ r.r('pdf("' + pdf_fn + '", height=4, width=6)')
+@@ -342,3 +342,3 @@
+ if VERBOSE: th.status_message('Plotting.')
+- r.r(resource_string(__name__, 'R_scripts/plotROCPerRead.R').decode())
++ r.r(files(__name__).joinpath('R_scripts/plotROCPerRead.R').read_bytes().decode())
+ r.r('pdf("' + pdf_fn + '", height=4, width=6)')
+@@ -437,3 +437,3 @@
+ 'Comparison':r.StrVector(mod_names_for_r)})
+- r.r(resource_string(__name__, 'R_scripts/plotROCPerRead.R').decode())
++ r.r(files(__name__).joinpath('R_scripts/plotROCPerRead.R').read_bytes().decode())
+ r.r('pdf("' + pdf_fn + '", height=4, width=6)')
+@@ -548,3 +548,3 @@
+ if VERBOSE: th.status_message('Plotting.')
+- r.r(resource_string(__name__, 'R_scripts/plotKmerDist.R').decode())
++ r.r(files(__name__).joinpath('R_scripts/plotKmerDist.R').read_bytes().decode())
+ if not dont_plot: r.r('pdf("' + pdf_fn + '", height=7, width=10)')
+@@ -629,3 +629,3 @@
+ if VERBOSE: th.status_message('Plotting.')
+- r.r(resource_string(__name__, 'R_scripts/plotSingleRead.R').decode())
++ r.r(files(__name__).joinpath('R_scripts/plotSingleRead.R').read_bytes().decode())
+ r.r('png("' + png_fn + '", width=3000, height=1400)')
+@@ -1141,3 +1141,3 @@
+ if VERBOSE: th.status_message('Plotting.')
+- r.r(resource_string(__name__, 'R_scripts/plotReadCorr.R').decode())
++ r.r(files(__name__).joinpath('R_scripts/plotReadCorr.R').read_bytes().decode())
+ r.r('pdf("' + pdf_fn + '", height=7, width=11)')
+@@ -1240,3 +1240,3 @@
+ if VERBOSE: th.status_message('Plotting.')
+- r.r(resource_string(__name__, 'R_scripts/plotMultiReadCorr.R').decode())
++ r.r(files(__name__).joinpath('R_scripts/plotMultiReadCorr.R').read_bytes().decode())
+ r.r('pdf("' + pdf_fn + '", height=5, width=11)')
+@@ -1353,3 +1353,3 @@
+ if VERBOSE: th.status_message('Plotting.')
+- r.r(resource_string(__name__, 'R_scripts/plotSingleRun.R').decode())
++ r.r(files(__name__).joinpath('R_scripts/plotSingleRun.R').read_bytes().decode())
+ r.r('pdf("' + pdf_fn + '", height=5, width=11)')
+@@ -1411,3 +1411,3 @@
+ if VERBOSE: th.status_message('Plotting.')
+- r.r(resource_string(__name__, 'R_scripts/plotGroupComp.R').decode())
++ r.r(files(__name__).joinpath('R_scripts/plotGroupComp.R').read_bytes().decode())
+ r.r('pdf("' + pdf_fn + '", height=5, width=11)')
+@@ -1579,3 +1579,3 @@
+ if VERBOSE: th.status_message('Plotting.')
+- r.r(resource_string(__name__, 'R_scripts/plotMotifStats.R').decode())
++ r.r(files(__name__).joinpath('R_scripts/plotMotifStats.R').read_bytes().decode())
+ r.r('pdf("' + pdf_fn + '", height=5, width=8)')
+@@ -1613,3 +1613,3 @@
+ if VERBOSE: th.status_message('Plotting.')
+- r.r(resource_string(__name__, 'R_scripts/plotModelComp.R').decode())
++ r.r(files(__name__).joinpath('R_scripts/plotModelComp.R').read_bytes().decode())
+ r.r('pdf("' + pdf_fn + '", height=5, width=11)')
+@@ -1645,3 +1645,3 @@
+ if VERBOSE: th.status_message('Plotting.')
+- r.r(resource_string(__name__, 'R_scripts/plotPerReadStats.R').decode())
++ r.r(files(__name__).joinpath('R_scripts/plotPerReadStats.R').read_bytes().decode())
+ r.r('pdf("' + pdf_fn + '", height=5, width=11)')
+@@ -2219,3 +2219,3 @@
+ if VERBOSE: th.status_message('Plotting (and saving data).')
+- r.r(resource_string(__name__, 'R_scripts/plotSigMDS.R').decode())
++ r.r(files(__name__).joinpath('R_scripts/plotSigMDS.R').read_bytes().decode())
+ r.r('pdf("' + pdf_fn + '", height=7, width=7)')
+--- a/tombo/resquiggle.py
++++ b/tombo/resquiggle.py
+@@ -37,3 +37,3 @@
+ from collections import defaultdict
+-from pkg_resources import resource_string
++from importlib.resources import files
+
+@@ -199,3 +199,3 @@
+
+- r.r(resource_string(__name__, 'R_scripts/debugDP.R').decode())
++ r.r(files(__name__).joinpath('R_scripts/debugDP.R').read_bytes().decode())
+ r.globalenv[str('plotDP')](dpDat, tbDat)
+@@ -247,3 +247,3 @@
+
+- r.r(resource_string(__name__, 'R_scripts/debugRawDP.R').decode())
++ r.r(files(__name__).joinpath('R_scripts/debugRawDP.R').read_bytes().decode())
+ r.globalenv[str('plotRawDP')](zDat, fwdDat, tbDat, sigDat)
+@@ -302,3 +302,3 @@
+
+- r.r(resource_string(__name__, 'R_scripts/debugFit.R').decode())
++ r.r(files(__name__).joinpath('R_scripts/debugFit.R').read_bytes().decode())
+ r.globalenv[str('plotFit')](fitDat, bandwidth)
+--- a/tombo/tombo_stats.py
++++ b/tombo/tombo_stats.py
+@@ -10,3 +10,3 @@
+ import random
+-import pkg_resources
++
+
+@@ -31,2 +31,3 @@
+ from itertools import repeat, product, count, combinations
++from importlib.resources import files
+
+@@ -723,4 +724,3 @@
+ # get full filename path with setuptools
+- self.ref_fn = th.resolve_path(pkg_resources.resource_filename(
+- 'tombo', 'tombo_models/' + std_ref_fn))
++ self.ref_fn = th.resolve_path(files('tombo')/'tombo_models'/std_ref_fn)
+
+@@ -740,4 +740,3 @@
+ # get full filename path with setuptools
+- self.ref_fn = th.resolve_path(pkg_resources.resource_filename(
+- 'tombo', 'tombo_models/' + std_ref_fn))
++ self.ref_fn = th.resolve_path(files('tombo')/'tombo_models'/std_ref_fn)
+
+@@ -797,5 +796,3 @@
+ self.seq_samp_type = seq_samp_type
+- self.ref_fn = th.resolve_path(pkg_resources.resource_filename(
+- 'tombo', 'tombo_models/' + STANDARD_MODELS[
+- seq_samp_type.name]))
++ self.ref_fn = th.resolve_path(files('tombo')/'tombo_models'/STANDARD_MODELS[seq_samp_type.name])
+ elif reads_index is not None:
+@@ -1171,4 +1168,3 @@
+ # get full filename path with setuptools
+- alt_model_fn = pkg_resources.resource_filename(
+- 'tombo', 'tombo_models/' + alt_model_fn)
++ alt_model_fn = (files('tombo')/'tombo_models'/alt_model_fn).as_posix()
+ if alt_model_fn is None or not os.path.isfile(alt_model_fn):
+--- a/setup.py
++++ b/setup.py
+@@ -59,3 +59,3 @@
+ install_requires = ['h5py', 'numpy', 'scipy',
+- 'setuptools >= 18.0', 'mappy >= 2.10', 'tqdm'],
++ 'mappy >= 2.10', 'tqdm'],
+ extras_require={'full':extras_require},
=====================================
debian/patches/series
=====================================
@@ -3,3 +3,7 @@ no_future.patch
mathjax.patch
cython3-fix.patch
no_install_depends_cython.patch
+remove-pkg-resources-usage.patch
+remove-distutils-usage.patch
+remove-badges-in-doc.patch
+fix-invalid-escape-sequences.patch
=====================================
debian/rules
=====================================
@@ -8,14 +8,19 @@ export DEB_BUILD_MAINT_OPTIONS=hardening=+all
%:
dh $@ --with python3,sphinxdoc --buildsystem=pybuild
-override_dh_fixperms:
- dh_fixperms
- find debian -name "*.model" -exec chmod -x \{\} \;
+execute_after_dh_auto_clean:
+ rm -f tombo/_c_dynamic_programming.cpp tombo/_c_helper.cpp
-override_dh_auto_build:
- dh_auto_build
+execute_after_dh_fixperms:
+ find debian -name "*.model" -exec chmod -x {} \;
+ find debian -name "shell_tests.sh" -type f -executable -exec chmod -x {} \+
+
+execute_after_dh_auto_build:
sphinx-build -N -bhtml docs docs/build
-override_dh_python3:
- dh_python3
+execute_after_dh_install:
+ rm -f docs/tombo.rst
+ rm -rf docs/build
+
+execute_after_dh_python3:
dh_numpy3
=====================================
debian/tombo.install
=====================================
@@ -1,2 +1,2 @@
-usr
scripts usr/share/tombo
+usr
View it on GitLab: https://salsa.debian.org/med-team/tombo/-/compare/11edc8439b8aa58af7a1b844da52646810d87e44...9302d1ff43a3855d1acb355fc05d893cf78436a5
--
View it on GitLab: https://salsa.debian.org/med-team/tombo/-/compare/11edc8439b8aa58af7a1b844da52646810d87e44...9302d1ff43a3855d1acb355fc05d893cf78436a5
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