[med-svn] [Git][med-team/tombo][master] 6 commits: Fix section

[Andreas Tille]

Andreas Tille pushed to branch master at Debian Med / tombo


Commits:
3072e5ad by Andreas Tille at 2020-06-24T14:32:20+02:00
Fix section

- - - - -
0c9ddc3c by Andreas Tille at 2020-06-24T14:33:17+02:00
Fix typo

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99931f70 by Andreas Tille at 2020-06-24T14:34:35+02:00
libjs-mathjax

- - - - -
d0206479 by Andreas Tille at 2020-06-24T14:41:08+02:00
2to3 patch

- - - - -
18c4bd63 by Andreas Tille at 2020-06-24T15:08:16+02:00
Use Debian packaged MathJax

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28f3c4e6 by Andreas Tille at 2020-06-24T16:00:35+02:00
Upload to new

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7 changed files:

- debian/changelog
- debian/control
- + debian/patches/2to3.patch
- + debian/patches/mathjax.patch
- debian/patches/series
- debian/rules
- debian/tombo-doc.doc-base


Changes:

=====================================
debian/changelog
=====================================
@@ -1,4 +1,4 @@
-tombo (1.5.1-1) UNRELEASED; urgency=medium
+tombo (1.5.1-1) unstable; urgency=medium
 
   * Initial release (Closes: #963596)
 


=====================================
debian/control
=====================================
@@ -12,6 +12,7 @@ Build-Depends: debhelper-compat (= 13),
                python3-sphinx,
                python3-sphinx-rtd-theme,
                python3-sphinx-argparse,
+               libjs-mathjax,
                python3-h5py <!nocheck>,
                python3-mappy <!nocheck>,
                python3-numpy <!nocheck>,
@@ -45,6 +46,7 @@ Architecture: all
 Section: doc
 Depends: ${sphinxdoc:Depends},
          ${misc:Depends},
+         libjs-mathjax
 Description: identification of modified nucleotides from raw nanopore sequencing data (doc)
  Tombo is a suite of tools primarily for the identification of modified
  nucleotides from nanopore sequencing data. Tombo also provides tools for


=====================================
debian/patches/2to3.patch
=====================================
@@ -0,0 +1,23 @@
+Author: Andreas Tille <tille at debian.org>
+Last-Update: Mon, 15 Jun 2020 11:13:59 +0200
+Description: 2to3 patch
+
+--- a/scripts/dump_per_read_statistics.py
++++ b/scripts/dump_per_read_statistics.py
+@@ -1,4 +1,4 @@
+-#! /usr/bin/env python
++#! /usr/bin/env python3
+ """Dump per-read statistics
+ 
+ This script takes a per-read statistics file and dumps its contents out into a tab-separated values file. The columns in the file are 'chrm', 'pos', 'strand', 'read_id' and 'stat'.
+@@ -19,8 +19,8 @@ def extract_per_read_stats(input_file, o
+     with open(output_file, 'w') as out_fp:
+         out_fp.write('{}\t{}\t{}\t{}\t{}\n'.format(
+             'chrm', 'pos', 'strand', 'read_id', 'stat'))
+-        for (chrm, strand), cs_blocks in pr_stats.blocks_index.items():
+-            for start, block_name in cs_blocks.items():
++        for (chrm, strand), cs_blocks in list(pr_stats.blocks_index.items()):
++            for start, block_name in list(cs_blocks.items()):
+                 for pos, stat, read_id in pr_stats.get_region_per_read_stats(
+                         intervalData(chrm, start, start + pr_stats.region_size,
+                                     strand)):


=====================================
debian/patches/mathjax.patch
=====================================
@@ -0,0 +1,15 @@
+Author: Andreas Tille <tille at debian.org>
+Last-Update: Mon, 15 Jun 2020 11:13:59 +0200
+Description: Use Debian packaged MathJax
+
+--- a/docs/conf.py
++++ b/docs/conf.py
+@@ -26,7 +26,7 @@ sys.path.insert(0, os.path.abspath('../t
+ extensions = ['sphinx.ext.autodoc', 'sphinx.ext.viewcode',
+               'sphinx.ext.intersphinx', 'sphinx.ext.mathjax', 'sphinxarg.ext',
+               'sphinx.ext.napoleon',]
+-mathjax_path = "https://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML"
++mathjax_path = "file:///usr/share/javascript/mathjax/MathJax.js?config=TeX-AMS-MML_HTMLorMML"
+ 
+ # don't include class inheritence in docs: https://stackoverflow.com/questions/46279030/how-can-i-prevent-sphinx-from-listing-object-as-a-base-class
+ from sphinx.ext.autodoc import ClassDocumenter, _


=====================================
debian/patches/series
=====================================
@@ -1 +1,3 @@
 no_future.patch
+2to3.patch
+mathjax.patch


=====================================
debian/rules
=====================================
@@ -8,7 +8,7 @@ export DEB_BUILD_MAINT_OPTIONS=hardening=+all
 %:
 	dh $@ --with python3,sphinxdoc --buildsystem=pybuild
 
-overide_dh_fixperms:
+override_dh_fixperms:
 	dh_fixperms
 	find debian -name "*.model" -exec chmod -x \{\} \;
 


=====================================
debian/tombo-doc.doc-base
=====================================
@@ -5,7 +5,7 @@ Abstract: identification of modified nucleotides from raw nanopore sequencing da
  Tombo is a suite of tools primarily for the identification of modified
  nucleotides from nanopore sequencing data. Tombo also provides tools for
  the analysis and visualization of raw nanopore signal.
-Section: Science/{Biology,Medicine} # see /usr/share/doc/doc-base/doc-base.txt.gz "2.3.3. The `section' field"
+Section: Science/Biology
 
 Format: html
 Index: /usr/share/doc/tombo/html/index.html



View it on GitLab: https://salsa.debian.org/med-team/tombo/-/compare/e894e3514544dee2259f55ea84db3bd9c46f7f3a...28f3c4e69376bbbb5f30468a4f68440d2d8b7d43

-- 
View it on GitLab: https://salsa.debian.org/med-team/tombo/-/compare/e894e3514544dee2259f55ea84db3bd9c46f7f3a...28f3c4e69376bbbb5f30468a4f68440d2d8b7d43
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