[med-svn] [Git][med-team/q2-taxa][master] 6 commits: New upstream version 2021.8.0+dfsg
Andreas Tille (@tille)
gitlab at salsa.debian.org
Wed Sep 29 13:46:30 BST 2021
Andreas Tille pushed to branch master at Debian Med / q2-taxa
Commits:
e8554fbd by Andreas Tille at 2021-09-29T14:15:31+02:00
New upstream version 2021.8.0+dfsg
- - - - -
ca130aec by Andreas Tille at 2021-09-29T14:15:31+02:00
routine-update: New upstream version
- - - - -
3fcb499f by Andreas Tille at 2021-09-29T14:15:31+02:00
Update upstream source from tag 'upstream/2021.8.0+dfsg'
Update to upstream version '2021.8.0+dfsg'
with Debian dir a48523944e829ac2d406e106c8ee3b41fc8f844f
- - - - -
80dca528 by Andreas Tille at 2021-09-29T14:15:32+02:00
routine-update: Standards-Version: 4.6.0
- - - - -
150c7f1c by Andreas Tille at 2021-09-29T14:21:05+02:00
Versioned (Build-)Depends from qiime and its modules (>= 2021.8.0-1)
- - - - -
83cddb66 by Andreas Tille at 2021-09-29T14:45:53+02:00
Fix Versions and upload to unstable
- - - - -
21 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
- q2_taxa/__init__.py
- q2_taxa/_method.py
- q2_taxa/_util.py
- q2_taxa/_version.py
- q2_taxa/_visualizer.py
- q2_taxa/assets/barplot/index.html
- q2_taxa/assets/barplot/src/render.js
- q2_taxa/plugin_setup.py
- q2_taxa/tests/__init__.py
- q2_taxa/tests/test_methods.py
- q2_taxa/tests/test_plugin_setup.py
- q2_taxa/tests/test_visualizer.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-taxa
+ build-target: dev
+ additional-tests: py.test --pyargs q2_taxa
+ 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) 2016-2021, QIIME 2 development team.
All rights reserved.
Redistribution and use in source and binary forms, with or without
=====================================
README.md
=====================================
@@ -1,6 +1,5 @@
# q2-taxa
-[](https://travis-ci.org/qiime2/q2-taxa)
-[](https://coveralls.io/github/qiime2/q2-taxa?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-taxa
@@ -21,11 +20,17 @@ requirements:
run:
- python {{ python }}
- pandas
- - qiime2 {{ release }}.*
- - q2templates {{ release }}.*
- - q2-types {{ release }}.*
+ - qiime2 {{ qiime2_epoch }}.*
+ - q2templates {{ qiime2_epoch }}.*
+ - q2-types {{ qiime2_epoch }}.*
test:
+ requires:
+ - qiime2 >={{ qiime2 }}
+ - q2templates >={{ q2templates }}
+ - q2-types >={{ q2_types }}
+ - pytest
+
imports:
- q2_taxa
- qiime2.plugins.taxa
=====================================
debian/changelog
=====================================
@@ -1,4 +1,6 @@
-q2-taxa (2020.11.1+dfsg-3) UNRELEASED; urgency=medium
+q2-taxa (2021.8.0+dfsg-1) unstable; urgency=medium
+
+ * Team upload.
[ Steffen Moeller ]
* Fixed d/u/watch - now finds new version to download
@@ -6,7 +8,11 @@ q2-taxa (2020.11.1+dfsg-3) UNRELEASED; urgency=medium
[ Nilesh Patra ]
* d/salsa-ci.yml: Disable build on i386 due to missing python3-skbio
- -- Steffen Moeller <moeller at debian.org> Mon, 26 Jul 2021 00:43:56 +0530
+ [ Andreas Tille ]
+ * Standards-Version: 4.6.0 (routine-update)
+ * Versioned (Build-)Depends from qiime and its modules (>= 2021.8.0)
+
+ -- Andreas Tille <tille at debian.org> Wed, 29 Sep 2021 14:21:11 +0200
q2-taxa (2020.11.1+dfsg-2) unstable; urgency=medium
=====================================
debian/control
=====================================
@@ -11,9 +11,9 @@ Build-Depends: debhelper-compat (= 13),
python3-pytest-cov,
python3-pandas,
nodejs,
- qiime (>= 2020.11.0),
- q2templates,
- q2-types,
+ qiime (>= 2021.8.0),
+ q2templates (>= 2021.8.0),
+ q2-types (>= 2021.8.0),
node-webpack,
node-uglifyjs-webpack-plugin,
node-babel-loader,
@@ -21,7 +21,7 @@ Build-Depends: debhelper-compat (= 13),
node-natural-sort,
node-thenby,
node-d3
-Standards-Version: 4.5.1
+Standards-Version: 4.6.0
Vcs-Browser: https://salsa.debian.org/med-team/q2-taxa
Vcs-Git: https://salsa.debian.org/med-team/q2-taxa.git
Homepage: https://qiime2.org/
@@ -33,9 +33,9 @@ Depends: ${shlibs:Depends},
${misc:Depends},
${python3:Depends},
python3-pandas,
- qiime,
- q2templates,
- q2-types,
+ qiime (>= 2021.8.0),
+ q2templates (>= 2021.8.0),
+ q2-types (>= 2021.8.0),
node-d3-scale-chromatic,
node-natural-sort,
node-thenby
=====================================
q2_taxa/__init__.py
=====================================
@@ -1,5 +1,5 @@
# ----------------------------------------------------------------------------
-# Copyright (c) 2016-2020, QIIME 2 development team.
+# Copyright (c) 2016-2021, QIIME 2 development team.
#
# Distributed under the terms of the Modified BSD License.
#
=====================================
q2_taxa/_method.py
=====================================
@@ -1,5 +1,5 @@
# ----------------------------------------------------------------------------
-# Copyright (c) 2016-2020, QIIME 2 development team.
+# Copyright (c) 2016-2021, QIIME 2 development team.
#
# Distributed under the terms of the Modified BSD License.
#
@@ -7,13 +7,14 @@
# ----------------------------------------------------------------------------
import pandas as pd
+import biom
import qiime2
from ._util import _collapse_table, _get_max_level
-def collapse(table: pd.DataFrame, taxonomy: pd.Series,
- level: int) -> pd.DataFrame:
+def collapse(table: biom.Table, taxonomy: pd.Series,
+ level: int) -> biom.Table:
if level < 1:
raise ValueError('Requested level of %d is too low. Must be greater '
'than or equal to 1.' % level)
=====================================
q2_taxa/_util.py
=====================================
@@ -1,5 +1,5 @@
# ----------------------------------------------------------------------------
-# Copyright (c) 2016-2020, QIIME 2 development team.
+# Copyright (c) 2016-2021, QIIME 2 development team.
#
# Distributed under the terms of the Modified BSD License.
#
@@ -12,7 +12,7 @@ def _get_max_level(taxonomy):
def _collapse_table(table, taxonomy, level, max_observed_level):
- table_ids = set(table.columns)
+ table_ids = set(table.ids(axis='observation'))
taxonomy_ids = set(taxonomy.index)
missing_ids = table_ids.difference(taxonomy_ids)
if len(missing_ids) > 0:
@@ -21,15 +21,15 @@ def _collapse_table(table, taxonomy, level, max_observed_level):
table = table.copy()
- def _collapse(tax):
+ def _collapse(id_, md):
+ tax = taxonomy.loc[id_]
tax = [x.strip() for x in tax.split(';')]
if len(tax) < max_observed_level:
padding = ['__'] * (max_observed_level - len(tax))
tax.extend(padding)
return ';'.join(tax[:level])
- table.columns = taxonomy.apply(_collapse)[table.columns]
- return table.groupby(table.columns, axis=1).agg(sum)
+ return table.collapse(_collapse, axis='observation', norm=False)
def _extract_to_level(taxonomy, table):
@@ -40,6 +40,7 @@ def _extract_to_level(taxonomy, table):
# Collapse table at specified level
for level in range(1, max_obs_lvl + 1):
collapsed_table = _collapse_table(table, taxonomy, level, max_obs_lvl)
- collapsed_tables.append(collapsed_table)
+ as_df = collapsed_table.transpose().to_dataframe(dense=True)
+ collapsed_tables.append(as_df)
return collapsed_tables
=====================================
q2_taxa/_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 = "1499d2d7a5f0bd958e19f8b2fffb6205e8fe50ad"
- git_date = "2020-12-05 20:44:48 +0000"
+ git_refnames = " (tag: 2021.8.0)"
+ git_full = "b148b8ec248a63b43e8986ea74fe727dde0c07bb"
+ git_date = "2021-09-09 18:35:31 +0000"
keywords = {"refnames": git_refnames, "full": git_full, "date": git_date}
return keywords
=====================================
q2_taxa/_visualizer.py
=====================================
@@ -1,5 +1,5 @@
# ----------------------------------------------------------------------------
-# Copyright (c) 2016-2020, QIIME 2 development team.
+# Copyright (c) 2016-2021, QIIME 2 development team.
#
# Distributed under the terms of the Modified BSD License.
#
@@ -11,6 +11,7 @@ import os.path
import pkg_resources
import shutil
+import biom
import pandas as pd
import q2templates
@@ -22,13 +23,19 @@ from ._util import _extract_to_level
TEMPLATES = pkg_resources.resource_filename('q2_taxa', 'assets')
-def barplot(output_dir: str, table: pd.DataFrame, taxonomy: pd.Series,
- metadata: Metadata) -> None:
- ids_not_in_metadata = set(table.index) - set(metadata.ids)
+def barplot(output_dir: str, table: biom.Table, taxonomy: pd.Series,
+ metadata: Metadata = None) -> None:
+
+ if metadata is None:
+ metadata = Metadata(
+ pd.DataFrame({'id': table.ids(axis='sample')}).set_index('id'))
+
+ ids_not_in_metadata = set(table.ids(axis='sample')) - set(metadata.ids)
if ids_not_in_metadata:
raise ValueError('Sample IDs found in the table are missing in the '
f'metadata: {ids_not_in_metadata!r}.')
+ num_metadata_cols = metadata.column_count
metadata = metadata.to_dataframe()
jsonp_files, csv_files = [], []
collapsed_tables = _extract_to_level(taxonomy, table)
@@ -62,7 +69,9 @@ def barplot(output_dir: str, table: pd.DataFrame, taxonomy: pd.Series,
# Now that the tables have been collapsed, write out the index template
index = os.path.join(TEMPLATES, 'barplot', 'index.html')
- q2templates.render(index, output_dir, context={'jsonp_files': jsonp_files})
+ q2templates.render(index, output_dir,
+ context={'jsonp_files': jsonp_files,
+ 'num_metadata_cols': num_metadata_cols})
# Copy assets for rendering figure
shutil.copytree(os.path.join(TEMPLATES, 'barplot', 'dist'),
=====================================
q2_taxa/assets/barplot/index.html
=====================================
@@ -45,4 +45,5 @@
<script src='{{ level }}?callback=load_data'></script>
{% endfor %}
<script src='dist/bundle.js'></script>
+ <p>Number of sample metadata columns provided: {{ num_metadata_cols }}</p>
{% endblock %}
=====================================
q2_taxa/assets/barplot/src/render.js
=====================================
@@ -34,7 +34,10 @@ export default function render(svg, colorScheme, xOrdering, dataMeta, barWidth)
const range = [];
const domain = [];
for (let i = 0; i < keys.length; i += 1) {
- range.push(scheme.scheme[i % scheme.scheme.length]);
+ // Assign colors from the "end" of the color scheme, which causes the
+ // color scheme to consistently give the topmost value in the barplot the
+ // same color (https://github.com/qiime2/q2-taxa/issues/111)
+ range.push(scheme.scheme[(keys.length - 1 - i) % scheme.scheme.length]);
domain.push(i);
}
z = scaleOrdinal(range).domain(domain);
=====================================
q2_taxa/plugin_setup.py
=====================================
@@ -1,5 +1,5 @@
# ----------------------------------------------------------------------------
-# Copyright (c) 2016-2020, QIIME 2 development team.
+# Copyright (c) 2016-2021, QIIME 2 development team.
#
# Distributed under the terms of the Modified BSD License.
#
=====================================
q2_taxa/tests/__init__.py
=====================================
@@ -1,5 +1,5 @@
# ----------------------------------------------------------------------------
-# Copyright (c) 2016-2020, QIIME 2 development team.
+# Copyright (c) 2016-2021, QIIME 2 development team.
#
# Distributed under the terms of the Modified BSD License.
#
=====================================
q2_taxa/tests/test_methods.py
=====================================
@@ -1,5 +1,5 @@
# ----------------------------------------------------------------------------
-# Copyright (c) 2016-2020, QIIME 2 development team.
+# Copyright (c) 2016-2021, QIIME 2 development team.
#
# Distributed under the terms of the Modified BSD License.
#
@@ -8,8 +8,10 @@
import unittest
+import numpy as np
+import biom
import pandas as pd
-import pandas.util.testing as pdt
+import pandas.testing as pdt
import qiime2
from q2_taxa import collapse, filter_table, filter_seqs
@@ -31,63 +33,70 @@ class CollapseTests(unittest.TestCase):
check_index_type=True,
check_column_type=True,
check_frame_type=True,
- check_less_precise=False,
check_names=True,
by_blocks=False,
check_exact=False)
self.assert_index_equal(left.index, right.index)
def test_collapse(self):
- table = pd.DataFrame([[2.0, 2.0], [1.0, 1.0], [9.0, 8.0], [0.0, 4.0]],
- index=['A', 'B', 'C', 'D'],
- columns=['feat1', 'feat2'])
+ table = biom.Table(np.array([[2.0, 2.0], [1.0, 1.0], [9.0, 8.0],
+ [0.0, 4.0]]),
+ ['A', 'B', 'C', 'D'],
+ ['feat1', 'feat2']).transpose()
taxonomy = pd.Series(['a; b; c', 'a; b; d'],
index=['feat1', 'feat2'])
actual = collapse(table, taxonomy, 1)
- expected = pd.DataFrame([[4.0], [2.0], [17.0], [4.0]],
- index=['A', 'B', 'C', 'D'],
- columns=['a'])
- self.assert_data_frame_almost_equal(actual, expected)
+ actual.del_metadata()
+ expected = biom.Table(np.array([[4.0], [2.0], [17.0], [4.0]]),
+ ['A', 'B', 'C', 'D'],
+ ['a']).transpose()
+ self.assertEqual(actual, expected)
actual = collapse(table, taxonomy, 2)
- expected = pd.DataFrame([[4.0], [2.0], [17.0], [4.0]],
- index=['A', 'B', 'C', 'D'],
- columns=['a;b'])
- self.assert_data_frame_almost_equal(actual, expected)
+ actual.del_metadata()
+ expected = biom.Table(np.array([[4.0], [2.0], [17.0], [4.0]]),
+ ['A', 'B', 'C', 'D'],
+ ['a;b']).transpose()
+ self.assertEqual(actual, expected)
actual = collapse(table, taxonomy, 3)
- expected = pd.DataFrame([[2.0, 2.0], [1.0, 1.0], [9.0, 8.0],
- [0.0, 4.0]],
- index=['A', 'B', 'C', 'D'],
- columns=['a;b;c', 'a;b;d'])
- self.assert_data_frame_almost_equal(actual, expected)
+ actual.del_metadata()
+ expected = biom.Table(np.array([[2.0, 2.0], [1.0, 1.0], [9.0, 8.0],
+ [0.0, 4.0]]),
+ ['A', 'B', 'C', 'D'],
+ ['a;b;c', 'a;b;d']).transpose()
+ self.assertEqual(actual, expected)
def test_collapse_missing_level(self):
- table = pd.DataFrame([[2.0, 2.0], [1.0, 1.0], [9.0, 8.0], [0.0, 4.0]],
- index=['A', 'B', 'C', 'D'],
- columns=['feat1', 'feat2'])
+ table = biom.Table(np.array([[2.0, 2.0], [1.0, 1.0], [9.0, 8.0],
+ [0.0, 4.0]]),
+ ['A', 'B', 'C', 'D'],
+ ['feat1', 'feat2']).transpose()
taxonomy = pd.Series(['a; b', 'a; b; d'],
index=['feat1', 'feat2'])
actual = collapse(table, taxonomy, 1)
- expected = pd.DataFrame([[4.0], [2.0], [17.0], [4.0]],
- index=['A', 'B', 'C', 'D'],
- columns=['a'])
- self.assert_data_frame_almost_equal(actual, expected)
+ actual.del_metadata()
+ expected = biom.Table(np.array([[4.0], [2.0], [17.0], [4.0]]),
+ ['A', 'B', 'C', 'D'],
+ ['a']).transpose()
+ self.assertEqual(actual, expected)
actual = collapse(table, taxonomy, 2)
- expected = pd.DataFrame([[4.0], [2.0], [17.0], [4.0]],
- index=['A', 'B', 'C', 'D'],
- columns=['a;b'])
- self.assert_data_frame_almost_equal(actual, expected)
+ actual.del_metadata()
+ expected = biom.Table(np.array([[4.0], [2.0], [17.0], [4.0]]),
+ ['A', 'B', 'C', 'D'],
+ ['a;b']).transpose()
+ self.assertEqual(actual, expected)
actual = collapse(table, taxonomy, 3)
- expected = pd.DataFrame([[2.0, 2.0], [1.0, 1.0], [9.0, 8.0],
- [0.0, 4.0]],
- index=['A', 'B', 'C', 'D'],
- columns=['a;b;__', 'a;b;d'])
- self.assert_data_frame_almost_equal(actual, expected)
+ actual.del_metadata()
+ expected = biom.Table(np.array([[2.0, 2.0], [1.0, 1.0], [9.0, 8.0],
+ [0.0, 4.0]]),
+ ['A', 'B', 'C', 'D'],
+ ['a;b;__', 'a;b;d']).transpose()
+ self.assertEqual(actual, expected)
def test_collapse_bad_level(self):
table = pd.DataFrame([[2.0, 2.0], [1.0, 1.0], [9.0, 8.0], [0.0, 4.0]],
@@ -102,12 +111,12 @@ class CollapseTests(unittest.TestCase):
collapse(table, taxonomy, 0)
def test_collapse_missing_table_ids_in_taxonomy(self):
- table = pd.DataFrame([[2.0, 2.0],
- [1.0, 1.0],
- [9.0, 8.0],
- [0.0, 4.0]],
- index=['A', 'B', 'C', 'D'],
- columns=['feat1', 'feat2'])
+ table = biom.Table(np.array([[2.0, 2.0],
+ [1.0, 1.0],
+ [9.0, 8.0],
+ [0.0, 4.0]]),
+ ['A', 'B', 'C', 'D'],
+ ['feat1', 'feat2']).transpose()
taxonomy = pd.Series(['a; b; c', 'a; b; d'],
index=['feat1', 'feat3'])
with self.assertRaisesRegex(ValueError, 'missing.*feat2'):
=====================================
q2_taxa/tests/test_plugin_setup.py
=====================================
@@ -1,5 +1,5 @@
# ----------------------------------------------------------------------------
-# Copyright (c) 2016-2020, QIIME 2 development team.
+# Copyright (c) 2016-2021, QIIME 2 development team.
#
# Distributed under the terms of the Modified BSD License.
#
=====================================
q2_taxa/tests/test_visualizer.py
=====================================
@@ -1,5 +1,5 @@
# ----------------------------------------------------------------------------
-# Copyright (c) 2016-2020, QIIME 2 development team.
+# Copyright (c) 2016-2021, QIIME 2 development team.
#
# Distributed under the terms of the Modified BSD License.
#
@@ -10,6 +10,8 @@ import os
import tempfile
import unittest
+import biom
+import numpy as np
import pandas as pd
import qiime2
@@ -19,10 +21,10 @@ from q2_taxa import barplot
class BarplotTests(unittest.TestCase):
def setUp(self):
- self.table = pd.DataFrame([[2.0, 2.0], [1.0, 1.0], [9.0, 8.0],
- [0.0, 4.0]],
- index=['A', 'B', 'C', 'D'],
- columns=['feat1', 'feat2'])
+ self.table = biom.Table(np.array([[2.0, 2.0], [1.0, 1.0], [9.0, 8.0],
+ [0.0, 4.0]]),
+ ['A', 'B', 'C', 'D'],
+ ['feat1', 'feat2']).transpose()
self.taxonomy = pd.Series(['a; b; c', 'a; b; d'],
index=['feat1', 'feat2'])
@@ -39,6 +41,7 @@ class BarplotTests(unittest.TestCase):
open(index_fp).read())
csv_lvl3_fp = os.path.join(output_dir, 'level-3.csv')
self.assertTrue(os.path.exists(csv_lvl3_fp))
+ self.assertTrue('val1' in open(csv_lvl3_fp).read())
def test_barplot_metadata_extra_id(self):
metadata = qiime2.Metadata(
@@ -62,3 +65,14 @@ class BarplotTests(unittest.TestCase):
with tempfile.TemporaryDirectory() as output_dir:
with self.assertRaisesRegex(ValueError, 'missing.*D'):
barplot(output_dir, self.table, self.taxonomy, metadata)
+
+ def test_barplot_no_metadata(self):
+ with tempfile.TemporaryDirectory() as output_dir:
+ barplot(output_dir, self.table, self.taxonomy)
+ index_fp = os.path.join(output_dir, 'index.html')
+ self.assertTrue(os.path.exists(index_fp))
+ self.assertTrue("src='level-1.jsonp?callback=load_data'" in
+ open(index_fp).read())
+ csv_lvl3_fp = os.path.join(output_dir, 'level-3.csv')
+ self.assertTrue(os.path.exists(csv_lvl3_fp))
+ self.assertTrue('val1' not in open(csv_lvl3_fp).read())
=====================================
setup.py
=====================================
@@ -1,5 +1,5 @@
# ----------------------------------------------------------------------------
-# Copyright (c) 2016-2020, QIIME 2 development team.
+# Copyright (c) 2016-2021, QIIME 2 development team.
#
# Distributed under the terms of the Modified BSD License.
#
View it on GitLab: https://salsa.debian.org/med-team/q2-taxa/-/compare/a8e78df1d12563fec666639d4a2dde550244de37...83cddb66837d5ca1621f88d32235e913babb86a6
--
View it on GitLab: https://salsa.debian.org/med-team/q2-taxa/-/compare/a8e78df1d12563fec666639d4a2dde550244de37...83cddb66837d5ca1621f88d32235e913babb86a6
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