[med-svn] [Git][med-team/q2-dada2][master] 7 commits: Generate debian/control automatically to refresh version number
Andreas Tille (@tille)
gitlab at salsa.debian.org
Tue Jan 30 14:49:22 GMT 2024
Andreas Tille pushed to branch master at Debian Med / q2-dada2
Commits:
c090c3a8 by Andreas Tille at 2024-01-30T15:30:56+01:00
Generate debian/control automatically to refresh version number
- - - - -
1958c4d1 by Andreas Tille at 2024-01-30T15:31:14+01:00
New upstream version 2023.9.0
- - - - -
1a12aca6 by Andreas Tille at 2024-01-30T15:31:14+01:00
routine-update: New upstream version
- - - - -
f9d91b42 by Andreas Tille at 2024-01-30T15:31:17+01:00
Update upstream source from tag 'upstream/2023.9.0'
Update to upstream version '2023.9.0'
with Debian dir f42799d9549b2cf721db993f41bca3cf9937da1a
- - - - -
eb13566e by Andreas Tille at 2024-01-30T15:31:20+01:00
routine-update: Build-Depends: s/dh-python/dh-sequence-python3/
- - - - -
da8a3930 by Andreas Tille at 2024-01-30T15:31:40+01:00
routine-update: Regenerate debian/control from debian/control.in
- - - - -
62256948 by Andreas Tille at 2024-01-30T15:40:05+01:00
routine-update: Ready to upload to unstable
- - - - -
21 changed files:
- + .github/workflows/ci-dev.yaml
- − .github/workflows/ci.yml
- + .github/workflows/join-release.yaml
- + .github/workflows/tag-release.yaml
- LICENSE
- ci/recipe/meta.yaml
- debian/changelog
- debian/control
- + debian/control.in
- debian/rules
- q2_dada2/__init__.py
- q2_dada2/_denoise.py
- q2_dada2/_examples.py
- q2_dada2/_stats.py
- q2_dada2/_transformer.py
- q2_dada2/_version.py
- q2_dada2/plugin_setup.py
- q2_dada2/tests/__init__.py
- q2_dada2/tests/test_denoise.py
- q2_dada2/tests/test_stats.py
- setup.py
Changes:
=====================================
.github/workflows/ci-dev.yaml
=====================================
@@ -0,0 +1,12 @@
+# Example of workflow trigger for calling workflow (the client).
+name: ci-dev
+on:
+ pull_request:
+ branches: ["dev"]
+ push:
+ branches: ["dev"]
+jobs:
+ ci:
+ uses: qiime2/distributions/.github/workflows/lib-ci-dev.yaml at dev
+ with:
+ distro: core
\ No newline at end of file
=====================================
.github/workflows/ci.yml deleted
=====================================
@@ -1,55 +0,0 @@
-# This file is automatically generated by busywork.qiime2.org and
-# template-repos - any manual edits made to this file will be erased when
-# busywork performs maintenance updates.
-
-name: ci
-
-on:
- pull_request:
- push:
- branches:
- - master
-
-jobs:
- lint:
- runs-on: ubuntu-latest
- steps:
- - name: checkout source
- uses: actions/checkout at v2
-
- - name: set up python 3.8
- uses: actions/setup-python at v1
- with:
- python-version: 3.8
-
- - name: install dependencies
- run: python -m pip install --upgrade pip
-
- - name: lint
- run: |
- pip install -q https://github.com/qiime2/q2lint/archive/master.zip
- q2lint
- pip install -q flake8
- flake8
-
- build-and-test:
- needs: lint
- strategy:
- matrix:
- os: [ubuntu-latest, macos-latest]
- runs-on: ${{ matrix.os }}
- steps:
- - name: checkout source
- uses: actions/checkout at v2
- with:
- fetch-depth: 0
-
- - name: set up git repo for versioneer
- run: git fetch --depth=1 origin +refs/tags/*:refs/tags/*
-
- - uses: qiime2/action-library-packaging at alpha1
- with:
- package-name: q2-dada2
- build-target: dev
- additional-tests: py.test --pyargs q2_dada2
- library-token: ${{ secrets.LIBRARY_TOKEN }}
=====================================
.github/workflows/join-release.yaml
=====================================
@@ -0,0 +1,6 @@
+name: join-release
+on:
+ workflow_dispatch: {}
+jobs:
+ release:
+ uses: qiime2/distributions/.github/workflows/lib-join-release.yaml at dev
\ No newline at end of file
=====================================
.github/workflows/tag-release.yaml
=====================================
@@ -0,0 +1,7 @@
+name: tag-release
+on:
+ push:
+ branches: ["Release-*"]
+jobs:
+ tag:
+ uses: qiime2/distributions/.github/workflows/lib-tag-release.yaml at dev
\ No newline at end of file
=====================================
LICENSE
=====================================
@@ -1,6 +1,6 @@
BSD 3-Clause License
-Copyright (c) 2016-2022, QIIME 2 development team.
+Copyright (c) 2016-2023, QIIME 2 development team.
All rights reserved.
Redistribution and use in source and binary forms, with or without
=====================================
ci/recipe/meta.yaml
=====================================
@@ -43,6 +43,9 @@ test:
- q2_dada2
- qiime2.plugins.dada2
+ commands:
+ - py.test --pyargs q2_dada2
+
about:
home: https://qiime2.org
license: BSD-3-Clause
=====================================
debian/changelog
=====================================
@@ -1,3 +1,13 @@
+q2-dada2 (2023.9.0-1) unstable; urgency=medium
+
+ * Team upload.
+ * New upstream version
+ * Generate debian/control automatically to refresh version number
+ * Build-Depends: s/dh-python/dh-sequence-python3/ (routine-update)
+ * Regenerate debian/control from debian/control.in (routine-update)
+
+ -- Andreas Tille <tille at debian.org> Tue, 30 Jan 2024 15:31:40 +0100
+
q2-dada2 (2022.11.2-2) unstable; urgency=medium
* Team upload
=====================================
debian/control
=====================================
@@ -1,13 +1,14 @@
+# This file is autogenerated from control.in to update versioned dependencies
Source: q2-dada2
Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
Uploaders: Steffen Moeller <moeller at debian.org>
Section: science
Priority: optional
Build-Depends: debhelper-compat (= 13),
- dh-python,
+ dh-sequence-python3,
python3,
python3-setuptools,
- qiime (>= 2022.11.1),
+ qiime (>= 2023.9),
r-bioc-dada2
Standards-Version: 4.6.2
Vcs-Browser: https://salsa.debian.org/med-team/q2-dada2
@@ -23,8 +24,8 @@ Depends: ${shlibs:Depends},
r-base-core,
r-bioc-dada2 (>= 1.24.0+dfsg-2~),
r-cran-optparse,
- qiime (>= 2022.11.1),
- q2-types (>= 2022.11.1),
+ qiime (>= 2023.9),
+ q2-types (>= 2023.9),
python3-biom-format,
python3-skbio
Description: QIIME 2 plugin to work with adapters in sequence data
=====================================
debian/control.in
=====================================
@@ -0,0 +1,55 @@
+Source: q2-dada2
+Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
+Uploaders: Steffen Moeller <moeller at debian.org>
+Section: science
+Priority: optional
+Build-Depends: debhelper-compat (= 13),
+ dh-sequence-python3,
+ python3,
+ python3-setuptools,
+ qiime (>= @DEB_VERSION_UPSTREAM@),
+ r-bioc-dada2
+Standards-Version: 4.6.2
+Vcs-Browser: https://salsa.debian.org/med-team/q2-dada2
+Vcs-Git: https://salsa.debian.org/med-team/q2-dada2.git
+Homepage: https://qiime2.org/
+Rules-Requires-Root: no
+
+Package: q2-dada2
+Architecture: any
+Depends: ${shlibs:Depends},
+ ${misc:Depends},
+ ${python3:Depends},
+ r-base-core,
+ r-bioc-dada2 (>= 1.24.0+dfsg-2~),
+ r-cran-optparse,
+ qiime (>= @DEB_VERSION_UPSTREAM@),
+ q2-types (>= @DEB_VERSION_UPSTREAM@),
+ python3-biom-format,
+ python3-skbio
+Description: QIIME 2 plugin to work with adapters in sequence data
+ QIIME 2 is a powerful, extensible, and decentralized microbiome analysis
+ package with a focus on data and analysis transparency. QIIME 2 enables
+ researchers to start an analysis with raw DNA sequence data and finish with
+ publication-quality figures and statistical results.
+ Key features:
+ * Integrated and automatic tracking of data provenance
+ * Semantic type system
+ * Plugin system for extending microbiome analysis functionality
+ * Support for multiple types of user interfaces (e.g. API, command line,
+ graphical)
+ .
+ QIIME 2 is a complete redesign and rewrite of the QIIME 1 microbiome analysis
+ pipeline. QIIME 2 will address many of the limitations of QIIME 1, while
+ retaining the features that makes QIIME 1 a powerful and widely-used analysis
+ pipeline.
+ .
+ QIIME 2 currently supports an initial end-to-end microbiome analysis pipeline.
+ New functionality will regularly become available through QIIME 2 plugins. You
+ can view a list of plugins that are currently available on the QIIME 2 plugin
+ availability page. The future plugins page lists plugins that are being
+ developed.
+ .
+ This package wraps the dada2 R package in BioConductor for modeling and
+ correcting Illumina-sequenced amplicon errors. This was shown to improve the
+ sensitivity of diversity analyses.
=====================================
debian/rules
=====================================
@@ -10,8 +10,15 @@ export PYBUILD_BEFORE_TEST=python{version} setup.py develop --install-dir {build
export PYBUILD_AFTER_TEST=rm -v {build_dir}/site.py {build_dir}/.coverage*; \
python{version} setup.py develop --uninstall --install-dir {build_dir}
+include /usr/share/dpkg/default.mk
+VERSION_UPSTREAM=$(shell echo $(DEB_VERSION_UPSTREAM) | sed -e 's/\(20[0-9][0-9]\.[0-9]\+\)\..*/\1/')
+
+debian/control: debian/control.in
+ echo "# This file is autogenerated from control.in to update versioned dependencies" > $@
+ sed -e"s/@DEB_VERSION_UPSTREAM@/$(VERSION_UPSTREAM)/g" $< >> $@
+
%:
- dh $@ --with python3 --buildsystem=pybuild
+ dh $@ --buildsystem=pybuild
# FIXME: similarly to the qiime and q2-types packages, the build time testing fails, as
# the Qiime plugin system is not fully available at this point of the package
=====================================
q2_dada2/__init__.py
=====================================
@@ -1,5 +1,5 @@
# ----------------------------------------------------------------------------
-# Copyright (c) 2016-2022, QIIME 2 development team.
+# Copyright (c) 2016-2023, QIIME 2 development team.
#
# Distributed under the terms of the Modified BSD License.
#
=====================================
q2_dada2/_denoise.py
=====================================
@@ -1,5 +1,5 @@
# ----------------------------------------------------------------------------
-# Copyright (c) 2016-2022, QIIME 2 development team.
+# Copyright (c) 2016-2023, QIIME 2 development team.
#
# Distributed under the terms of the Modified BSD License.
#
=====================================
q2_dada2/_examples.py
=====================================
@@ -1,5 +1,5 @@
# ----------------------------------------------------------------------------
-# Copyright (c) 2016-2022, QIIME 2 development team.
+# Copyright (c) 2016-2023, QIIME 2 development team.
#
# Distributed under the terms of the Modified BSD License.
#
=====================================
q2_dada2/_stats.py
=====================================
@@ -1,5 +1,5 @@
# ----------------------------------------------------------------------------
-# Copyright (c) 2016-2022, QIIME 2 development team.
+# Copyright (c) 2016-2023, QIIME 2 development team.
#
# Distributed under the terms of the Modified BSD License.
#
=====================================
q2_dada2/_transformer.py
=====================================
@@ -1,5 +1,5 @@
# ----------------------------------------------------------------------------
-# Copyright (c) 2016-2022, QIIME 2 development team.
+# Copyright (c) 2016-2023, QIIME 2 development team.
#
# Distributed under the terms of the Modified BSD License.
#
=====================================
q2_dada2/_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 = " (HEAD -> master, tag: 2022.11.2)"
- git_full = "0f6c02100a7d2c7775b026bd7204c7c762e0b942"
- git_date = "2023-01-12 11:23:23 -0700"
+ git_refnames = " (tag: 2023.9.0, Release-2023.9)"
+ git_full = "412629abd1b2bec8ad62fcc71c18aadd3a85ca99"
+ git_date = "2023-10-03 21:51:55 +0000"
keywords = {"refnames": git_refnames, "full": git_full, "date": git_date}
return keywords
=====================================
q2_dada2/plugin_setup.py
=====================================
@@ -1,5 +1,5 @@
# ----------------------------------------------------------------------------
-# Copyright (c) 2016-2022, QIIME 2 development team.
+# Copyright (c) 2016-2023, QIIME 2 development team.
#
# Distributed under the terms of the Modified BSD License.
#
=====================================
q2_dada2/tests/__init__.py
=====================================
@@ -1,5 +1,5 @@
# ----------------------------------------------------------------------------
-# Copyright (c) 2016-2022, QIIME 2 development team.
+# Copyright (c) 2016-2023, QIIME 2 development team.
#
# Distributed under the terms of the Modified BSD License.
#
=====================================
q2_dada2/tests/test_denoise.py
=====================================
@@ -1,5 +1,5 @@
# ----------------------------------------------------------------------------
-# Copyright (c) 2016-2022, QIIME 2 development team.
+# Copyright (c) 2016-2023, QIIME 2 development team.
#
# Distributed under the terms of the Modified BSD License.
#
=====================================
q2_dada2/tests/test_stats.py
=====================================
@@ -1,5 +1,5 @@
# ----------------------------------------------------------------------------
-# Copyright (c) 2016-2022, QIIME 2 development team.
+# Copyright (c) 2016-2023, QIIME 2 development team.
#
# Distributed under the terms of the Modified BSD License.
#
=====================================
setup.py
=====================================
@@ -1,5 +1,5 @@
# ----------------------------------------------------------------------------
-# Copyright (c) 2016-2022, QIIME 2 development team.
+# Copyright (c) 2016-2023, QIIME 2 development team.
#
# Distributed under the terms of the Modified BSD License.
#
View it on GitLab: https://salsa.debian.org/med-team/q2-dada2/-/compare/023bbe86d886c1ed4759729a7fce5feb4b1d8ec8...6225694853ce7db0ccda5f13f012f672d5347025
--
View it on GitLab: https://salsa.debian.org/med-team/q2-dada2/-/compare/023bbe86d886c1ed4759729a7fce5feb4b1d8ec8...6225694853ce7db0ccda5f13f012f672d5347025
You're receiving this email because of your account on salsa.debian.org.
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://alioth-lists.debian.net/pipermail/debian-med-commit/attachments/20240130/12ac2a77/attachment-0001.htm>
More information about the debian-med-commit
mailing list