[med-svn] [Git][med-team/q2-longitudinal][upstream] New upstream version 2021.8.0
Steffen Möller (@moeller)
gitlab at salsa.debian.org
Sat Sep 18 20:26:55 BST 2021
Steffen Möller pushed to branch upstream at Debian Med / q2-longitudinal
Commits:
381914c5 by Steffen at 2021-09-18T21:01:07+02:00
New upstream version 2021.8.0
- - - - -
29 changed files:
- + .github/workflows/ci.yml
- − .travis.yml
- LICENSE
- README.md
- − ci/recipe/conda_build_config.yaml
- ci/recipe/meta.yaml
- q2_longitudinal/__init__.py
- q2_longitudinal/_format.py
- q2_longitudinal/_longitudinal.py
- q2_longitudinal/_transformer.py
- q2_longitudinal/_type.py
- q2_longitudinal/_utilities.py
- q2_longitudinal/_vega_specs/__init__.py
- q2_longitudinal/_vega_specs/volatility/__init__.py
- q2_longitudinal/_vega_specs/volatility/axis.py
- q2_longitudinal/_vega_specs/volatility/const.py
- q2_longitudinal/_vega_specs/volatility/data.py
- q2_longitudinal/_vega_specs/volatility/legend.py
- q2_longitudinal/_vega_specs/volatility/mark.py
- q2_longitudinal/_vega_specs/volatility/render.py
- q2_longitudinal/_vega_specs/volatility/scale.py
- q2_longitudinal/_vega_specs/volatility/signal.py
- q2_longitudinal/plugin_setup.py
- q2_longitudinal/tests/__init__.py
- q2_longitudinal/tests/test_format.py
- q2_longitudinal/tests/test_longitudinal.py
- q2_longitudinal/tests/test_transformer.py
- q2_longitudinal/tests/test_type.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-longitudinal
+ build-target: dev
+ additional-tests: py.test --pyargs q2_longitudinal
+ 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 flake8 coveralls
- - pip install -q https://github.com/qiime2/q2lint/archive/master.zip
- - make install
-script:
- - make lint
- - travis_wait make test-cov
-after_success:
- - coveralls
=====================================
LICENSE
=====================================
@@ -1,6 +1,6 @@
BSD 3-Clause License
-Copyright (c) 2017-2020, QIIME 2 development team.
+Copyright (c) 2017-2021, QIIME 2 development team.
All rights reserved.
Redistribution and use in source and binary forms, with or without
=====================================
README.md
=====================================
@@ -1,28 +1,5 @@
# q2-longitudinal
-[](https://travis-ci.org/qiime2/q2-longitudinal) [](https://coveralls.io/github/qiime2/q2-longitudinal?branch=master)
+
-QIIME 2 plugin for analysis of time series data, involving either paired sample comparisons or longitudinal study designs.
-
-## Installation
-
-Follow the QIIME 2 core distribution installation instructions at https://qiime2.org/ to install q2-longitudinal as part of the QIIME 2 analysis platform.
-
-## Tutorials
-
-This is a QIIME 2 plugin. For details on QIIME 2 and tutorials demonstrating how to use this plugin, see the [QIIME 2 documentation](https://qiime2.org/). Tutorials for this plugin can be found [here](https://docs.qiime2.org/2018.11/tutorials/longitudinal/).
-
-## API documentation
-
-API documentation can be found [here](https://docs.qiime2.org/2018.11/plugins/available/longitudinal/).
-
-## Help
-
-For user support, see the [QIIME 2 Forum](https://forum.qiime2.org). Bug reports and feature requests can also be made [via a new issue](https://github.com/qiime2/q2-sample-classifier/issues/new/choose).
-
-## Contributing
-
-QIIME 2 is an open-source project, and we are very interested in contributions from the community. Please see the [contributing guidelines](https://github.com/qiime2/q2-sample-classifier/blob/master/.github/CONTRIBUTING.md) if you would like to get involved.
-
-## Citing q2-longitudinal
-Bokulich NA, Dillon M, Zhang Y, Rideout JR, Bolyen E, Li H, Albert PS, Caporaso JG. 2018. q2-longitudinal: longitudinal and paired-sample analyses of microbiome data. mSystems 3:e00219-18. https://doi.org/10.1128/mSystems.00219-18
+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-longitudinal
@@ -20,22 +19,28 @@ requirements:
run:
- python {{ python }}
- numpy
- - pandas
+ - pandas {{ pandas }}
- scipy >=1.5
- statsmodels >=0.9.0
- patsy
- - scikit-bio
+ - scikit-bio >=0.5.5
- seaborn
- - qiime2 {{ release }}.*
- - q2-types {{ release }}.*
- - q2-sample-classifier {{ release }}.*
- - q2templates {{ release }}.*
- - q2-sample-classifier {{ release }}.*
- - q2-feature-table {{ release }}.*
- - matplotlib <3.3
- - matplotlib-base <3.3
+ - qiime2 {{ qiime2_epoch }}.*
+ - q2-types {{ qiime2_epoch }}.*
+ - q2-sample-classifier {{ qiime2_epoch }}.*
+ - q2templates {{ qiime2_epoch }}.*
+ - q2-feature-table {{ qiime2_epoch }}.*
+ - matplotlib
test:
+ requires:
+ - qiime2 >={{ qiime2 }}
+ - q2-types >={{ q2_types }}
+ - q2-sample-classifier >={{ q2_sample_classifier }}
+ - q2templates >={{ q2templates }}
+ - q2-feature-table >={{ q2_feature_table }}
+ - pytest
+
imports:
- q2_longitudinal
- qiime2.plugins.longitudinal
=====================================
q2_longitudinal/__init__.py
=====================================
@@ -1,5 +1,5 @@
# ----------------------------------------------------------------------------
-# Copyright (c) 2017-2020, QIIME 2 development team.
+# Copyright (c) 2017-2021, QIIME 2 development team.
#
# Distributed under the terms of the Modified BSD License.
#
=====================================
q2_longitudinal/_format.py
=====================================
@@ -1,5 +1,5 @@
# ----------------------------------------------------------------------------
-# Copyright (c) 2017-2020, QIIME 2 development team.
+# Copyright (c) 2017-2021, QIIME 2 development team.
#
# Distributed under the terms of the Modified BSD License.
#
=====================================
q2_longitudinal/_longitudinal.py
=====================================
@@ -1,5 +1,5 @@
# ----------------------------------------------------------------------------
-# Copyright (c) 2017-2020, QIIME 2 development team.
+# Copyright (c) 2017-2021, QIIME 2 development team.
#
# Distributed under the terms of the Modified BSD License.
#
@@ -495,8 +495,9 @@ def maturity_index(ctx,
table, metadata=metadata, where="{0}='{1}'".format(group_by, control))
md_column = metadata.get_column(state_column)
- X_train, X_test = split(control_table, md_column, test_size, random_state,
- stratify, missing_samples='ignore')
+ X_train, X_test, _, _ = split(control_table, md_column, test_size,
+ random_state, stratify,
+ missing_samples='ignore')
sample_estimator, importance = fit(
X_train, md_column, step, cv, random_state, n_jobs, n_estimators,
=====================================
q2_longitudinal/_transformer.py
=====================================
@@ -1,5 +1,5 @@
# ----------------------------------------------------------------------------
-# Copyright (c) 2017-2020, QIIME 2 development team.
+# Copyright (c) 2017-2021, QIIME 2 development team.
#
# Distributed under the terms of the Modified BSD License.
#
=====================================
q2_longitudinal/_type.py
=====================================
@@ -1,5 +1,5 @@
# ----------------------------------------------------------------------------
-# Copyright (c) 2017-2020, QIIME 2 development team.
+# Copyright (c) 2017-2021, QIIME 2 development team.
#
# Distributed under the terms of the Modified BSD License.
#
=====================================
q2_longitudinal/_utilities.py
=====================================
@@ -1,5 +1,5 @@
# ----------------------------------------------------------------------------
-# Copyright (c) 2017-2020, QIIME 2 development team.
+# Copyright (c) 2017-2021, QIIME 2 development team.
#
# Distributed under the terms of the Modified BSD License.
#
@@ -413,9 +413,10 @@ def _regplot_subplots_from_dataframe(state_column, metric, metadata,
ax = axes[num][0]
sns.set_palette(palette)
for name, group_data in metadata.groupby(group_column):
- sns.regplot(state_column, metric, data=group_data, fit_reg=fit_reg,
- scatter_kws={"marker": ".", "s": 100}, label=name,
- ax=ax, lowess=lowess, ci=ci, truncate=False)
+ sns.regplot(x=state_column, y=metric, data=group_data,
+ fit_reg=fit_reg, scatter_kws={"marker": ".", "s": 100},
+ label=name, ax=ax, lowess=lowess, ci=ci,
+ truncate=False)
ax.legend(bbox_to_anchor=(1.05, 1), loc=2, borderaxespad=0.)
return f
@@ -457,7 +458,7 @@ def _visualize(output_dir, multiple_group_test=False, pairwise_tests=False,
residuals=False,
pairwise_test_name='Pairwise group comparison tests'):
- pd.set_option('display.max_colwidth', -1)
+ pd.set_option('display.max_colwidth', None)
if summary is not False:
summary = q2templates.df_to_html(summary.to_frame())
@@ -500,7 +501,7 @@ def _visualize(output_dir, multiple_group_test=False, pairwise_tests=False,
os.path.join(output_dir, 'residuals.png'), bbox_inches='tight')
residuals.savefig(
os.path.join(output_dir, 'residuals.pdf'), bbox_inches='tight')
- plt.close('all')
+ plt.close('all')
index = os.path.join(TEMPLATES, 'index.html')
q2templates.render(index, output_dir, context={
@@ -521,7 +522,7 @@ def _visualize(output_dir, multiple_group_test=False, pairwise_tests=False,
def _visualize_anova(output_dir, pairwise_tests=False, model_results=False,
residuals=False, pairwise_test_name='Pairwise t-tests'):
- pd.set_option('display.max_colwidth', -1)
+ pd.set_option('display.max_colwidth', None)
if pairwise_tests is not False:
pairwise_tests.to_csv(os.path.join(output_dir, 'pairwise_tests.tsv'),
=====================================
q2_longitudinal/_vega_specs/__init__.py
=====================================
@@ -1,5 +1,5 @@
# ----------------------------------------------------------------------------
-# Copyright (c) 2017-2020, QIIME 2 development team.
+# Copyright (c) 2017-2021, QIIME 2 development team.
#
# Distributed under the terms of the Modified BSD License.
#
=====================================
q2_longitudinal/_vega_specs/volatility/__init__.py
=====================================
@@ -1,5 +1,5 @@
# ----------------------------------------------------------------------------
-# Copyright (c) 2017-2020, QIIME 2 development team.
+# Copyright (c) 2017-2021, QIIME 2 development team.
#
# Distributed under the terms of the Modified BSD License.
#
=====================================
q2_longitudinal/_vega_specs/volatility/axis.py
=====================================
@@ -1,5 +1,5 @@
# ----------------------------------------------------------------------------
-# Copyright (c) 2017-2020, QIIME 2 development team.
+# Copyright (c) 2017-2021, QIIME 2 development team.
#
# Distributed under the terms of the Modified BSD License.
#
=====================================
q2_longitudinal/_vega_specs/volatility/const.py
=====================================
@@ -1,5 +1,5 @@
# ----------------------------------------------------------------------------
-# Copyright (c) 2017-2020, QIIME 2 development team.
+# Copyright (c) 2017-2021, QIIME 2 development team.
#
# Distributed under the terms of the Modified BSD License.
#
=====================================
q2_longitudinal/_vega_specs/volatility/data.py
=====================================
@@ -1,5 +1,5 @@
# ----------------------------------------------------------------------------
-# Copyright (c) 2017-2020, QIIME 2 development team.
+# Copyright (c) 2017-2021, QIIME 2 development team.
#
# Distributed under the terms of the Modified BSD License.
#
@@ -19,7 +19,7 @@ from .const import (
def render_data_ctrl(control_chart_data, state):
return [
{'name': DAT_INDIVIDUAL,
- 'values': control_chart_data.to_dict('record'),
+ 'values': control_chart_data.to_dict('records'),
'transform': [
{'type': 'formula', 'as': FLD_GROUP_BY,
'expr': 'datum[%s]' % SIG_GROUP},
@@ -73,7 +73,7 @@ def render_data_ctrl(control_chart_data, state):
def render_data_stats(stats_chart_data):
return [
{'name': DAT_STATS,
- 'values': stats_chart_data.to_dict('record'),
+ 'values': stats_chart_data.to_dict('records'),
'format': {'parse': {'importance': 'number'}}
},
# This gets used to set the initial values for the x-axis extent
=====================================
q2_longitudinal/_vega_specs/volatility/legend.py
=====================================
@@ -1,5 +1,5 @@
# ----------------------------------------------------------------------------
-# Copyright (c) 2017-2020, QIIME 2 development team.
+# Copyright (c) 2017-2021, QIIME 2 development team.
#
# Distributed under the terms of the Modified BSD License.
#
=====================================
q2_longitudinal/_vega_specs/volatility/mark.py
=====================================
@@ -1,5 +1,5 @@
# ----------------------------------------------------------------------------
-# Copyright (c) 2017-2020, QIIME 2 development team.
+# Copyright (c) 2017-2021, QIIME 2 development team.
#
# Distributed under the terms of the Modified BSD License.
#
=====================================
q2_longitudinal/_vega_specs/volatility/render.py
=====================================
@@ -1,5 +1,5 @@
# ----------------------------------------------------------------------------
-# Copyright (c) 2017-2020, QIIME 2 development team.
+# Copyright (c) 2017-2021, QIIME 2 development team.
#
# Distributed under the terms of the Modified BSD License.
#
=====================================
q2_longitudinal/_vega_specs/volatility/scale.py
=====================================
@@ -1,5 +1,5 @@
# ----------------------------------------------------------------------------
-# Copyright (c) 2017-2020, QIIME 2 development team.
+# Copyright (c) 2017-2021, QIIME 2 development team.
#
# Distributed under the terms of the Modified BSD License.
#
=====================================
q2_longitudinal/_vega_specs/volatility/signal.py
=====================================
@@ -1,5 +1,5 @@
# ----------------------------------------------------------------------------
-# Copyright (c) 2017-2020, QIIME 2 development team.
+# Copyright (c) 2017-2021, QIIME 2 development team.
#
# Distributed under the terms of the Modified BSD License.
#
=====================================
q2_longitudinal/plugin_setup.py
=====================================
@@ -1,5 +1,5 @@
# ----------------------------------------------------------------------------
-# Copyright (c) 2017-2020, QIIME 2 development team.
+# Copyright (c) 2017-2021, QIIME 2 development team.
#
# Distributed under the terms of the Modified BSD License.
#
=====================================
q2_longitudinal/tests/__init__.py
=====================================
@@ -1,5 +1,5 @@
# ----------------------------------------------------------------------------
-# Copyright (c) 2017-2020, QIIME 2 development team.
+# Copyright (c) 2017-2021, QIIME 2 development team.
#
# Distributed under the terms of the Modified BSD License.
#
=====================================
q2_longitudinal/tests/test_format.py
=====================================
@@ -1,5 +1,5 @@
# ----------------------------------------------------------------------------
-# Copyright (c) 2017-2020, QIIME 2 development team.
+# Copyright (c) 2017-2021, QIIME 2 development team.
#
# Distributed under the terms of the Modified BSD License.
#
=====================================
q2_longitudinal/tests/test_longitudinal.py
=====================================
@@ -1,5 +1,5 @@
# ----------------------------------------------------------------------------
-# Copyright (c) 2017-2020, QIIME 2 development team.
+# Copyright (c) 2017-2021, QIIME 2 development team.
#
# Distributed under the terms of the Modified BSD License.
#
@@ -14,7 +14,7 @@ import tempfile
import numpy as np
import pandas as pd
-import pandas.util.testing as pdt
+import pandas.testing as pdt
import skbio
import qiime2
from qiime2.plugin.testing import TestPluginBase
=====================================
q2_longitudinal/tests/test_transformer.py
=====================================
@@ -1,5 +1,5 @@
# ----------------------------------------------------------------------------
-# Copyright (c) 2017-2020, QIIME 2 development team.
+# Copyright (c) 2017-2021, QIIME 2 development team.
#
# Distributed under the terms of the Modified BSD License.
#
@@ -9,7 +9,7 @@
import unittest
import pandas as pd
-import pandas.util.testing as pdt
+import pandas.testing as pdt
import qiime2
from qiime2.plugin.testing import TestPluginBase
=====================================
q2_longitudinal/tests/test_type.py
=====================================
@@ -1,5 +1,5 @@
# ----------------------------------------------------------------------------
-# Copyright (c) 2017-2020, QIIME 2 development team.
+# Copyright (c) 2017-2021, QIIME 2 development team.
#
# Distributed under the terms of the Modified BSD License.
#
=====================================
setup.py
=====================================
@@ -1,5 +1,5 @@
# ----------------------------------------------------------------------------
-# Copyright (c) 2017-2020, QIIME 2 development team.
+# Copyright (c) 2017-2021, QIIME 2 development team.
#
# Distributed under the terms of the Modified BSD License.
#
View it on GitLab: https://salsa.debian.org/med-team/q2-longitudinal/-/commit/381914c59efb7cb09b98b3f842b8a0d32bbf4bd2
--
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