[med-svn] [Git][med-team/q2-emperor][master] 7 commits: New upstream version 2021.8.0
Steffen Möller (@moeller)
gitlab at salsa.debian.org
Tue Jul 12 12:03:00 BST 2022
Steffen Möller pushed to branch master at Debian Med / q2-emperor
Commits:
e0b52436 by Steffen at 2021-12-04T22:49:21+01:00
New upstream version 2021.8.0
- - - - -
955a525c by Steffen at 2022-07-12T12:56:55+02:00
New upstream version 2021.8.0
- - - - -
1326b996 by Steffen Moeller at 2022-07-12T13:01:14+02:00
Contributed local changes.
- - - - -
f81099f2 by Steffen Moeller at 2022-07-12T13:01:52+02:00
routine-update: New upstream version
- - - - -
40d89c00 by Steffen Moeller at 2022-07-12T13:01:53+02:00
New upstream version 2022.2.0
- - - - -
46a74c15 by Steffen Moeller at 2022-07-12T13:01:54+02:00
Update upstream source from tag 'upstream/2022.2.0'
Update to upstream version '2022.2.0'
with Debian dir 5098d56724ea48ea9c29243c2a22ae337f1640cc
- - - - -
cf83e188 by Steffen Moeller at 2022-07-12T13:02:21+02:00
routine-update: Ready to upload to unstable
- - - - -
17 changed files:
- + .github/workflows/ci.yml
- − .travis.yml
- LICENSE
- README.md
- − ci/recipe/conda_build_config.yaml
- ci/recipe/meta.yaml
- debian/changelog
- debian/control
- debian/copyright
- q2_emperor/__init__.py
- q2_emperor/_plot.py
- q2_emperor/_version.py
- q2_emperor/plugin_setup.py
- q2_emperor/tests/__init__.py
- q2_emperor/tests/test_plot.py
- q2_emperor/tests/test_plugin_setup.py
- setup.py
Changes:
=====================================
.github/workflows/ci.yml
=====================================
@@ -0,0 +1,55 @@
+# 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-emperor
+ build-target: dev
+ additional-tests: py.test --pyargs q2_emperor
+ library-token: ${{ secrets.LIBRARY_TOKEN }}
=====================================
.travis.yml deleted
=====================================
@@ -1,25 +0,0 @@
-dist: trusty
-sudo: false
-language: python
-before_install:
- - export MPLBACKEND='Agg'
- - wget -q https://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh -O miniconda.sh
- - export MINICONDA_PREFIX="$HOME/miniconda"
- - bash miniconda.sh -b -p $MINICONDA_PREFIX
- - export PATH="$MINICONDA_PREFIX/bin:$PATH"
- - conda config --set always_yes yes
- - conda update -q conda
- - conda info -a
-install:
- - wget -q https://raw.githubusercontent.com/qiime2/environment-files/master/latest/staging/qiime2-latest-py36-linux-conda.yml
- - conda env create -q -n test-env --file qiime2-latest-py36-linux-conda.yml
- - source activate test-env
- - conda install -q pytest-cov
- - pip install -q flake8 coveralls
- - pip install -q https://github.com/qiime2/q2lint/archive/master.zip
- - make install
-script:
- - make lint
- - make test-cov
-after_success:
- - coveralls
=====================================
LICENSE
=====================================
@@ -1,6 +1,6 @@
BSD 3-Clause License
-Copyright (c) 2016-2020, QIIME 2 development team.
+Copyright (c) 2016-2022, QIIME 2 development team.
All rights reserved.
Redistribution and use in source and binary forms, with or without
=====================================
README.md
=====================================
@@ -1,6 +1,5 @@
-# QIIME 2 Emperor plugin
+# q2-emperor
-[](https://travis-ci.org/qiime2/q2-emperor)
-[](https://coveralls.io/github/qiime2/q2-emperor?branch=master)
+
-This is a QIIME 2 plugin. For details on QIIME 2, see https://qiime2.org..
+This is a QIIME 2 plugin. For details on QIIME 2, see https://qiime2.org..
\ No newline at end of file
=====================================
ci/recipe/conda_build_config.yaml deleted
=====================================
@@ -1,2 +0,0 @@
-python:
- - 3.6
=====================================
ci/recipe/meta.yaml
=====================================
@@ -1,6 +1,5 @@
{% set data = load_setup_py_data() %}
{% set version = data.get('version') or 'placehold' %}
-{% set release = '.'.join(version.split('.')[:2]) %}
package:
name: q2-emperor
@@ -22,12 +21,18 @@ requirements:
- numpy
- pandas
- scikit-bio
- - emperor 1.0.1
- - qiime2 {{ release }}.*
- - q2templates {{ release }}.*
- - q2-types {{ release }}.*
+ - emperor ==1.0.3
+ - qiime2 {{ qiime2_epoch }}.*
+ - q2templates {{ qiime2_epoch }}.*
+ - q2-types {{ qiime2_epoch }}.*
test:
+ requires:
+ - qiime2 >={{ qiime2 }}
+ - q2templates >={{ q2templates }}
+ - q2-types >={{ q2_types }}
+ - pytest
+
imports:
- q2_emperor
- qiime2.plugins.emperor
=====================================
debian/changelog
=====================================
@@ -1,3 +1,9 @@
+q2-emperor (2022.2.0-1) unstable; urgency=medium
+
+ * New upstream version
+
+ -- Steffen Moeller <moeller at debian.org> Tue, 12 Jul 2022 13:01:59 +0200
+
q2-emperor (2020.11.1-2) unstable; urgency=high
* Team upload.
=====================================
debian/control
=====================================
@@ -9,11 +9,11 @@ Build-Depends: debhelper-compat (= 13),
python3-setuptools,
python3-pytest <!nocheck>,
python3-pytest-cov <!nocheck>,
- qiime (>= 2019.10.0) <!nocheck>,
python3-emperor <!nocheck>,
- q2templates,
- q2-types
-Standards-Version: 4.6.0
+ qiime <!nocheck>,
+ q2templates (>= 2022.2.0) <!nocheck>,
+ q2-types (>= 2022.2.0) <!nocheck>
+Standards-Version: 4.6.1
Vcs-Browser: https://salsa.debian.org/med-team/q2-emperor
Vcs-Git: https://salsa.debian.org/med-team/q2-emperor.git
Homepage: https://qiime2.org/
=====================================
debian/copyright
=====================================
@@ -6,9 +6,9 @@ Files: *
Copyright: 2016-2020 QIIME 2 development team
License: BSD-3-clause
-Files: versioneer.py
+Files: versioneer.py q2_emperor/_version.py
Copyright: Brian Warner
-License: CC0
+License: CC0-1.0
From the README.md:
.
To make Versioneer easier to embed, all its code is dedicated to the public
@@ -47,3 +47,144 @@ License: BSD-3-clause
CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+
+License: GPL-2+
+ This program is free software; you can redistribute it and/or modify
+ it under the terms of the GNU General Public License as published by
+ the Free Software Foundation; either version 2 of the License, or
+ (at your option) any later version.
+ .
+ This program is distributed in the hope that it will be useful,
+ but WITHOUT ANY WARRANTY; without even the implied warranty of
+ MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ GNU General Public License for more details.
+ .
+ You should have received a copy of the GNU General Public License along
+ with this program; if not, write to the Free Software Foundation, Inc.,
+ 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
+ .
+ For other licensing arrangements, please contact Daniel J. Schaid.
+ .
+ On a Debian system, the GNU GPL license version 2 is distributed in the
+ file /usr/share/common-licenses/GPL-2.
+
+License: CC0-1.0
+ From https://creativecommons.org/publicdomain/zero/1.0/
+ .
+ CREATIVE COMMONS CORPORATION IS NOT A LAW FIRM AND DOES NOT PROVIDE
+ LEGAL SERVICES. DISTRIBUTION OF THIS DOCUMENT DOES NOT CREATE AN
+ ATTORNEY-CLIENT RELATIONSHIP. CREATIVE COMMONS PROVIDES THIS INFORMATION
+ ON AN "AS-IS" BASIS. CREATIVE COMMONS MAKES NO WARRANTIES REGARDING THE
+ USE OF THIS DOCUMENT OR THE INFORMATION OR WORKS PROVIDED HEREUNDER,
+ AND DISCLAIMS LIABILITY FOR DAMAGES RESULTING FROM THE USE OF THIS
+ DOCUMENT OR THE INFORMATION OR WORKS PROVIDED HEREUNDER.
+ .
+ Statement of Purpose
+ .
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+ Related Rights in the Work or (ii) assert any associated claims and
+ causes of action with respect to the Work, in either case contrary
+ to Affirmer's express Statement of Purpose.
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+ 4. Limitations and Disclaimers.
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=====================================
q2_emperor/__init__.py
=====================================
@@ -1,5 +1,5 @@
# ----------------------------------------------------------------------------
-# Copyright (c) 2016-2020, QIIME 2 development team.
+# Copyright (c) 2016-2022, QIIME 2 development team.
#
# Distributed under the terms of the Modified BSD License.
#
=====================================
q2_emperor/_plot.py
=====================================
@@ -1,5 +1,5 @@
# ----------------------------------------------------------------------------
-# Copyright (c) 2016-2020, QIIME 2 development team.
+# Copyright (c) 2016-2022, QIIME 2 development team.
#
# Distributed under the terms of the Modified BSD License.
#
@@ -12,7 +12,9 @@ import pkg_resources
import qiime2
import skbio
import q2templates
+import math
import numpy as np
+import pandas as pd
from emperor import Emperor
from scipy.spatial.distance import euclidean
@@ -22,7 +24,7 @@ TEMPLATES = pkg_resources.resource_filename('q2_emperor', 'assets')
def generic_plot(output_dir: str, master: skbio.OrdinationResults,
metadata: qiime2.Metadata,
other_pcoa: skbio.OrdinationResults,
- plot_name: str,
+ plot_name: str, info: str = None,
custom_axes: str = None, settings: dict = None,
ignore_missing_samples: bool = False,
feature_metadata: qiime2.Metadata = None):
@@ -46,6 +48,7 @@ def generic_plot(output_dir: str, master: skbio.OrdinationResults,
if other_pcoa:
viz.procrustes_names = ['reference', 'other']
+ viz.info = info
viz.settings = settings
html = viz.make_emperor(standalone=True)
@@ -76,12 +79,30 @@ def plot(output_dir: str, pcoa: skbio.OrdinationResults,
def procrustes_plot(output_dir: str, reference_pcoa: skbio.OrdinationResults,
other_pcoa: skbio.OrdinationResults,
- metadata: qiime2.Metadata, custom_axes: str = None,
+ metadata: qiime2.Metadata, m2_stats: pd.DataFrame = None,
+ custom_axes: str = None,
ignore_missing_samples: bool = False) -> None:
+ info = None
+ if m2_stats is not None:
+ m2 = '%.5f' % m2_stats['true M^2 value'][0]
+ permutations = m2_stats['number of Monte Carlo permutations'][0]
+ p_val = m2_stats['p-value for true M^2 value'][0]
+
+ if permutations < 1:
+ p_val = 'N/A'
+ else:
+ # Because the number of p-val dec places is dynamic, we need to
+ # dynamically build the string template up.
+ dec_places = math.ceil(math.log10(permutations))
+ p_val_tmpl = '%%.%df' % dec_places
+ p_val = p_val_tmpl % m2_stats['p-value for true M^2 value'][0]
+
+ info = 'M² = %s p-value = %s' % (m2, p_val)
+
generic_plot(output_dir, master=reference_pcoa, metadata=metadata,
other_pcoa=other_pcoa, custom_axes=custom_axes,
ignore_missing_samples=ignore_missing_samples,
- plot_name='procrustes_plot')
+ plot_name='procrustes_plot', info=info)
def biplot(output_dir: str, biplot: skbio.OrdinationResults,
=====================================
q2_emperor/_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: 2020.11.1)"
- git_full = "f05cd193415232ce62fd3c6144bc8a2adfe89a44"
- git_date = "2020-12-05 20:44:48 +0000"
+ git_refnames = " (tag: 2022.2.0)"
+ git_full = "0f7ca77ef3334269623ad4f5167a4b664032dff1"
+ git_date = "2022-02-18 18:31:39 +0000"
keywords = {"refnames": git_refnames, "full": git_full, "date": git_date}
return keywords
=====================================
q2_emperor/plugin_setup.py
=====================================
@@ -1,5 +1,5 @@
# ----------------------------------------------------------------------------
-# Copyright (c) 2016-2020, QIIME 2 development team.
+# Copyright (c) 2016-2022, QIIME 2 development team.
#
# Distributed under the terms of the Modified BSD License.
#
@@ -12,7 +12,7 @@ from ._plot import plot, procrustes_plot, biplot
from qiime2.plugin import (Plugin, Metadata, Str, List, Citations, Range, Int,
Bool, Properties)
-from q2_types.ordination import PCoAResults
+from q2_types.ordination import PCoAResults, ProcrustesStatistics
PARAMETERS = {'metadata': Metadata, 'custom_axes': List[Str],
'ignore_missing_samples': Bool}
@@ -72,12 +72,15 @@ plugin.visualizers.register_function(
plugin.visualizers.register_function(
function=procrustes_plot,
- inputs={'reference_pcoa': PCoAResults, 'other_pcoa': PCoAResults},
+ inputs={'reference_pcoa': PCoAResults, 'other_pcoa': PCoAResults,
+ 'm2_stats': ProcrustesStatistics},
parameters=PARAMETERS,
input_descriptions={
'reference_pcoa': 'The reference ordination matrix to be plotted.',
'other_pcoa': 'The "other" ordination matrix to be plotted (the one '
- 'that was fitted to the reference).'
+ 'that was fitted to the reference).',
+ 'm2_stats': 'The M^2 value of the procrustes analysis & its associated'
+ ' p value.'
},
parameter_descriptions=PARAMETERS_DESC,
name='Visualize and Interact with a procrustes plot',
=====================================
q2_emperor/tests/__init__.py
=====================================
@@ -1,5 +1,5 @@
# ----------------------------------------------------------------------------
-# Copyright (c) 2016-2020, QIIME 2 development team.
+# Copyright (c) 2016-2022, QIIME 2 development team.
#
# Distributed under the terms of the Modified BSD License.
#
=====================================
q2_emperor/tests/test_plot.py
=====================================
@@ -1,5 +1,5 @@
# ----------------------------------------------------------------------------
-# Copyright (c) 2016-2020, QIIME 2 development team.
+# Copyright (c) 2016-2022, QIIME 2 development team.
#
# Distributed under the terms of the Modified BSD License.
#
=====================================
q2_emperor/tests/test_plugin_setup.py
=====================================
@@ -1,5 +1,5 @@
# ----------------------------------------------------------------------------
-# Copyright (c) 2016-2020, QIIME 2 development team.
+# Copyright (c) 2016-2022, QIIME 2 development team.
#
# Distributed under the terms of the Modified BSD License.
#
=====================================
setup.py
=====================================
@@ -1,5 +1,5 @@
# ----------------------------------------------------------------------------
-# Copyright (c) 2016-2020, QIIME 2 development team.
+# Copyright (c) 2016-2022, QIIME 2 development team.
#
# Distributed under the terms of the Modified BSD License.
#
View it on GitLab: https://salsa.debian.org/med-team/q2-emperor/-/compare/3b36a5b8d23e81147e12927be087de5d2dddfd74...cf83e188a02b83e2c6526740d593d69d1060aa6d
--
View it on GitLab: https://salsa.debian.org/med-team/q2-emperor/-/compare/3b36a5b8d23e81147e12927be087de5d2dddfd74...cf83e188a02b83e2c6526740d593d69d1060aa6d
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