[med-svn] [Git][med-team/q2-fragment-insertion][master] 8 commits: Bump versioned Depends
Andreas Tille (@tille)
gitlab at salsa.debian.org
Tue Jan 17 11:22:38 GMT 2023
Andreas Tille pushed to branch master at Debian Med / q2-fragment-insertion
Commits:
4a585305 by Andreas Tille at 2023-01-17T11:37:32+01:00
Bump versioned Depends
- - - - -
f2ecbb3b by Andreas Tille at 2023-01-17T11:38:47+01:00
routine-update: New upstream version
- - - - -
b6081b01 by Andreas Tille at 2023-01-17T11:38:48+01:00
New upstream version 2022.11.1
- - - - -
3915f271 by Andreas Tille at 2023-01-17T11:38:48+01:00
Update upstream source from tag 'upstream/2022.11.1'
Update to upstream version '2022.11.1'
with Debian dir 44fb61d47e822169231a6ce4053306944beb1fee
- - - - -
2b7124e0 by Andreas Tille at 2023-01-17T11:38:49+01:00
routine-update: Standards-Version: 4.6.2
- - - - -
fc1d119b by Andreas Tille at 2023-01-17T12:16:35+01:00
Skip autopkgtest requiring sepp which needs pplacer which is not available in testing since mcl lost OCaml support
- - - - -
5b66362a by Andreas Tille at 2023-01-17T12:17:40+01:00
DEP3
- - - - -
8ee853b6 by Andreas Tille at 2023-01-17T12:22:21+01:00
Upload to experimental
- - - - -
9 changed files:
- + .github/workflows/add-to-project-ci.yml
- debian/changelog
- debian/control
- debian/patches/python2to3.patch
- + debian/patches/sepp_not_in_testing.patch
- debian/patches/series
- debian/tests/control
- q2_fragment_insertion/_insertion.py
- q2_fragment_insertion/_version.py
Changes:
=====================================
.github/workflows/add-to-project-ci.yml
=====================================
@@ -0,0 +1,21 @@
+name: Add new issues and PRs to triage project board
+
+on:
+ issues:
+ types:
+ - opened
+ pull_request_target:
+ types:
+ - opened
+
+jobs:
+ add-to-project:
+ name: Add issue to project
+ runs-on: ubuntu-latest
+ steps:
+ - uses: actions/add-to-project at v0.3.0
+ with:
+ project-url: https://github.com/orgs/qiime2/projects/36
+ github-token: ${{ secrets.ADD_TO_PROJECT_PAT }}
+ labeled: skip-triage
+ label-operator: NOT
=====================================
debian/changelog
=====================================
@@ -1,3 +1,15 @@
+q2-fragment-insertion (2022.11.1-1) experimental; urgency=medium
+
+ * Team upload.
+ * New upstream version
+ * Bump versioned Depends
+ * Standards-Version: 4.6.2 (routine-update)
+ * Skip autopkgtest requiring sepp which needs pplacer which is not
+ available in testing since mcl lost OCaml support
+ * DEP3
+
+ -- Andreas Tille <tille at debian.org> Tue, 17 Jan 2023 11:36:48 +0100
+
q2-fragment-insertion (2022.8.0-2) unstable; urgency=medium
* Team upload.
=====================================
debian/control
=====================================
@@ -7,13 +7,13 @@ Build-Depends: debhelper-compat (= 13),
dh-python,
python3,
python3-setuptools,
- qiime (>= 2022.8.0),
+ qiime (>= 2022.11.1),
python3-pytest <!nocheck>,
python3-pytest-cov <!nocheck>,
python3-biom-format <!nocheck>,
python3-skbio <!nocheck>,
sepp <!nocheck>
-Standards-Version: 4.6.1
+Standards-Version: 4.6.2
Vcs-Browser: https://salsa.debian.org/med-team/q2-fragment-insertion
Vcs-Git: https://salsa.debian.org/med-team/q2-fragment-insertion.git
Homepage: https://qiime2.org/
@@ -24,10 +24,10 @@ Architecture: any
Depends: ${shlibs:Depends},
${misc:Depends},
${python3:Depends},
- qiime (>= 2022.8.0),
python3-biom-format,
python3-skbio,
- q2-types
+ qiime (>= 2022.11.1),
+ q2-types (>= 2022.11.1)
Recommends: sepp,
python3-ijson,
default-jdk
=====================================
debian/patches/python2to3.patch
=====================================
@@ -1,3 +1,7 @@
+Author: Steffen Möller
+Last-Update: 2020-12-13 00:36:37 +0100
+Description: use Python3
+
Index: q2-fragment-insertion/Makefile
===================================================================
--- q2-fragment-insertion.orig/Makefile
=====================================
debian/patches/sepp_not_in_testing.patch
=====================================
@@ -0,0 +1,18 @@
+Description: Skip autopkgtest requiring sepp which needs pplacer which is not
+ available in testing since mcl lost OCaml support
+Author: Andreas Tille <tille at debian.org>
+Last-Update: Tue, 17 Jan 2023 11:36:48 +0100
+
+--- a/q2_fragment_insertion/tests/test_insertion.py
++++ b/q2_fragment_insertion/tests/test_insertion.py
+@@ -19,8 +19,9 @@ from qiime2.sdk import Artifact
+ from qiime2.plugin.testing import TestPluginBase
+
+ from q2_types.feature_data import DNAIterator
++import pytest
+
+-
++ at pytest.mark.skip("sepp is not in testing any more since pplacer is lost due to ocaml bindings missing in latest mcl")
+ class TestSepp(TestPluginBase):
+ package = 'q2_fragment_insertion.tests'
+
=====================================
debian/patches/series
=====================================
@@ -1 +1,2 @@
python2to3.patch
+sepp_not_in_testing.patch
=====================================
debian/tests/control
=====================================
@@ -1,3 +1,4 @@
Tests: run-unit-test
-Depends: @, python3-pytest-cov, sepp (>= 4.3.10+dfsg-4)
+Depends: @, python3-pytest-cov
+ # sepp (>= 4.3.10+dfsg-4)
Restrictions: allow-stderr
=====================================
q2_fragment_insertion/_insertion.py
=====================================
@@ -27,7 +27,7 @@ from q2_fragment_insertion._format import PlacementsFormat, SeppReferenceDirFmt
# which is not necessarily true for SEPP produced insertion trees. We add zero
# branch length information for branches without an explicit length.
def _add_missing_branch_length(tree_fp):
- tree = skbio.TreeNode.read(tree_fp)
+ tree = skbio.TreeNode.read(tree_fp, format="newick")
for node in tree.preorder():
if node.length is None:
node.length = 0
=====================================
q2_fragment_insertion/_version.py
=====================================
@@ -23,9 +23,9 @@ def get_keywords():
# setup.py/versioneer.py will grep for the variable names, so they must
# each be defined on a line of their own. _version.py will just call
# get_keywords().
- git_refnames = " (tag: 2022.8.0)"
- git_full = "4843c553a36b7088183e541bb7172dc5c4155164"
- git_date = "2022-08-23 17:28:26 +0000"
+ git_refnames = " (HEAD -> master, tag: 2022.11.1)"
+ git_full = "ce513ef02c8bdbbae872968080c6fa0af3111c3c"
+ git_date = "2022-12-21 22:17:44 +0000"
keywords = {"refnames": git_refnames, "full": git_full, "date": git_date}
return keywords
View it on GitLab: https://salsa.debian.org/med-team/q2-fragment-insertion/-/compare/7196f5df89b1b360b547cd432748560d74f898ca...8ee853b617035c8a23f61c67a71672d0311c6cb8
--
View it on GitLab: https://salsa.debian.org/med-team/q2-fragment-insertion/-/compare/7196f5df89b1b360b547cd432748560d74f898ca...8ee853b617035c8a23f61c67a71672d0311c6cb8
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