[med-svn] [Git][med-team/python-ruffus][master] Adapt to sphinx 4.x API
Andreas Tille (@tille)
gitlab at salsa.debian.org
Fri Oct 1 10:24:43 BST 2021
Andreas Tille pushed to branch master at Debian Med / python-ruffus
Commits:
88aa6572 by Andreas Tille at 2021-10-01T10:01:34+02:00
Adapt to sphinx 4.x API
- - - - -
6 changed files:
- debian/changelog
- − debian/patches/fix_test.patch
- debian/patches/series
- + debian/patches/sphinx4.patch
- debian/patches/use_libjs-mathjax.patch
- − debian/patches/use_png_instead_of_jpg.patch
Changes:
=====================================
debian/changelog
=====================================
@@ -2,6 +2,7 @@ python-ruffus (2.8.4-3) UNRELEASED; urgency=medium
* Fix watchfile to detect new versions on github
* Standards-Version: 4.6.0 (routine-update)
+ * Adapt to sphinx 4.x API
-- Andreas Tille <tille at debian.org> Thu, 30 Sep 2021 14:18:35 +0200
=====================================
debian/patches/fix_test.patch deleted
=====================================
@@ -1,20 +0,0 @@
-Author: Andreas Tille <tille at debian.org>
-Last-Update: Wed, 11 Jul 2018 11:21:00 +0200
-Description: For some strange reason without this patch the test ends up in
- .
- ImportError: No module named ruffus
-
---- a/ruffus/test/test_pool_manager.py
-+++ b/ruffus/test/test_pool_manager.py
-@@ -1,3 +1,11 @@
-+#!/usr/bin/env python
-+import os
-+import sys
-+
-+## add grandparent to search path for testing
-+grandparent_dir = os.path.abspath(os.path.join(os.path.dirname(__file__), "..", ".."))
-+sys.path.insert(0, grandparent_dir)
-+
- import contextlib
- import random
- import unittest
=====================================
debian/patches/series
=====================================
@@ -1,3 +1,4 @@
use_libjs-mathjax.patch
#use_png_instead_of_jpg.patch
#fix_test.patch
+sphinx4.patch
=====================================
debian/patches/sphinx4.patch
=====================================
@@ -0,0 +1,15 @@
+Author: Andreas Tille <tille at debian.org>
+Last-Update: Thu, 30 Sep 2021 14:18:35 +0200
+Description: Adapt to sphinx 4.x API
+
+--- a/doc/conf.py
++++ b/doc/conf.py
+@@ -21,7 +21,7 @@ import ruffus, ruffus.task, ruffus.ruffu
+ def setup(app):
+ #app.add_javascript("custom.js")
+ if not on_rtd:
+- app.add_stylesheet("ruffus.css")
++ app.add_css_file("ruffus.css")
+
+
+ # If extensions (or modules to document with autodoc) are in another directory,
=====================================
debian/patches/use_libjs-mathjax.patch
=====================================
@@ -4,7 +4,7 @@ Description: Use Debian packaged mathjax
--- a/doc/conf.py
+++ b/doc/conf.py
-@@ -38,6 +38,8 @@ def setup(app):
+@@ -39,6 +39,8 @@ def setup(app):
extensions = ['sphinx.ext.autodoc', 'sphinx.ext.doctest', 'sphinx.ext.intersphinx', 'sphinx.ext.todo',
'sphinx.ext.coverage', 'sphinx.ext.mathjax', 'sphinx.ext.ifconfig', 'sphinx.ext.viewcode']
=====================================
debian/patches/use_png_instead_of_jpg.patch deleted
=====================================
@@ -1,56 +0,0 @@
-Author: Andreas Tille <tille at debian.org>
-Last-Update: Mon, 25 Jul 2016 13:19:50 +0200
-Description: Create PNG instead of JPG to work around bug #827806
- Thanks to Christian Seiler for the hint
-
---- a/doc/pipeline_functions.rst
-+++ b/doc/pipeline_functions.rst
-@@ -460,7 +460,7 @@ Ruffus Functions
- **Example**:
- ::
-
-- pipeline_printout_graph("flowchart.jpg", "jpg", [task1, task16],
-+ pipeline_printout_graph("flowchart.png", "png", [task1, task16],
- forcedtorun_tasks = [task2],
- no_key_legend = True)
-
---- a/ruffus/task.py
-+++ b/ruffus/task.py
-@@ -4051,7 +4051,7 @@ def pipeline_printout_graph(stream,
-
- :param stream: where to print to
- :type stream: file-like object with ``write()`` function
-- :param output_format: ["dot", "jpg", "svg", "ps", "png"]. All but the
-+ :param output_format: ["dot", "svg", "ps", "png"]. All but the
- first depends on the
- `dot <http://www.graphviz.org>`_ program.
- :param target_tasks: targets task functions which will be run if they are
---- a/ruffus/test/test_pipeline_printout_graph.py
-+++ b/ruffus/test/test_pipeline_printout_graph.py
-@@ -114,7 +114,7 @@ class Test_ruffus(unittest.TestCase):
- os.makedirs(tempdir)
-
- #
-- # check graphviz exists for turning dot files into jpg, svg etc
-+ # check graphviz exists for turning dot files into png, svg etc
- #
- try:
- process = Popen("echo what | dot", stdout=PIPE,
-@@ -136,7 +136,7 @@ class Test_ruffus(unittest.TestCase):
- print(" Run pipeline normally...")
- if self.graph_viz_present:
- pipeline_printout_graph(tempdir + "flowchart.dot", pipeline="main")
-- pipeline_printout_graph(tempdir + "flowchart.jpg",
-+ pipeline_printout_graph(tempdir + "flowchart.png",
- target_tasks=[subdivide_start],
- forcedtorun_tasks=[split_start],
- no_key_legend=True)
-@@ -172,7 +172,7 @@ class Test_ruffus(unittest.TestCase):
- ), tempdir + '{basename[0]}_*.subdivided', tempdir + '{basename[0]}')
- if self.graph_viz_present:
- test_pipeline.printout_graph(tempdir + "flowchart.dot")
-- test_pipeline.printout_graph(tempdir + "flowchart.jpg",
-+ test_pipeline.printout_graph(tempdir + "flowchart.png",
- target_tasks=[subdivide_start],
- forcedtorun_tasks=[split_start],
- no_key_legend=True)
View it on GitLab: https://salsa.debian.org/med-team/python-ruffus/-/commit/88aa6572dafb0e39f1f6dc4fa26d55eb857dd758
--
View it on GitLab: https://salsa.debian.org/med-team/python-ruffus/-/commit/88aa6572dafb0e39f1f6dc4fa26d55eb857dd758
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