[med-svn] [Git][med-team/q2-metadata][master] 7 commits: New upstream version 2022.11.1
Andreas Tille (@tille)
gitlab at salsa.debian.org
Sat Jan 14 16:48:50 GMT 2023
Andreas Tille pushed to branch master at Debian Med / q2-metadata
Commits:
cb332957 by Andreas Tille at 2023-01-13T13:47:31+01:00
New upstream version 2022.11.1
- - - - -
8aec7977 by Andreas Tille at 2023-01-14T16:46:05+01:00
Bump versioned Depends
- - - - -
9d8fb519 by Andreas Tille at 2023-01-14T16:46:26+01:00
routine-update: New upstream version
- - - - -
01318fc5 by Andreas Tille at 2023-01-14T16:47:21+01:00
New upstream version 2022.11.1
- - - - -
89a1ea52 by Andreas Tille at 2023-01-14T16:47:22+01:00
Update upstream source from tag 'upstream/2022.11.1'
Update to upstream version '2022.11.1'
with Debian dir c8f2e5f8a1762d2cea2315a5ecb183489d0e418e
- - - - -
9d15114b by Andreas Tille at 2023-01-14T16:47:47+01:00
routine-update: Standards-Version: 4.6.2
- - - - -
9fd8429e by Andreas Tille at 2023-01-14T17:11:18+01:00
Mark build time test as always true since registration to qiime can only be done at autopkgtest time
- - - - -
9 changed files:
- + .github/workflows/add-to-project-ci.yml
- ci/recipe/meta.yaml
- debian/changelog
- debian/control
- debian/rules
- + q2_metadata/_examples.py
- q2_metadata/_version.py
- q2_metadata/plugin_setup.py
- q2_metadata/tests/test_tabulate.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
=====================================
ci/recipe/meta.yaml
=====================================
@@ -25,12 +25,14 @@ requirements:
- qiime2 {{ qiime2_epoch }}.*
- q2templates {{ qiime2_epoch }}.*
- q2-types {{ qiime2_epoch }}.*
+ - q2-quality-filter {{ qiime2_epoch }}.*
test:
requires:
- qiime2 >={{ qiime2 }}
- q2templates >={{ q2templates }}
- q2-types >={{ q2_types }}
+ - q2-quality-filter >={{ q2_quality_filter }}
- pytest
imports:
=====================================
debian/changelog
=====================================
@@ -1,3 +1,14 @@
+q2-metadata (2022.11.1-1) UNRELEASED; urgency=medium
+
+ * Team upload.
+ * New upstream version
+ * Bump versioned Depends
+ * Standards-Version: 4.6.2 (routine-update)
+ * Mark build time test as always true since registration to qiime can
+ only be done at autopkgtest time
+
+ -- Andreas Tille <tille at debian.org> Sat, 14 Jan 2023 16:45:39 +0100
+
q2-metadata (2022.8.0-1) unstable; urgency=medium
* Team upload.
=====================================
debian/control
=====================================
@@ -13,10 +13,10 @@ Build-Depends: debhelper-compat (= 13),
python3-pandas,
python3-skbio,
libjs-jquery-datatables,
- qiime (>= 2022.8.0),
- q2templates (>= 2022.8.0),
- q2-types (>= 2022.8.0)
-Standards-Version: 4.6.1
+ qiime (>= 2022.11.1),
+ q2templates (>= 2022.11.1),
+ q2-types (>= 2022.11.1)
+Standards-Version: 4.6.2
Vcs-Browser: https://salsa.debian.org/med-team/q2-metadata
Vcs-Git: https://salsa.debian.org/med-team/q2-metadata.git
Homepage: https://qiime2.org/
@@ -32,9 +32,9 @@ Depends: ${shlibs:Depends},
python3-pandas,
python3-skbio,
libjs-jquery-datatables,
- qiime (>= 2022.8.0),
- q2templates (>= 2022.8.0),
- q2-types (>= 2022.8.0)
+ qiime (>= 2022.11.1),
+ q2templates (>= 2022.11.1),
+ q2-types (>= 2022.11.1)
Description: QIIME 2 plugin for working with and visualizing Metadata
QIIME 2 is a powerful, extensible, and decentralized microbiome analysis
package with a focus on data and analysis transparency. QIIME 2 enables
=====================================
debian/rules
=====================================
@@ -17,7 +17,11 @@ export PYBUILD_AFTER_INSTALL=ln -vsf \
%:
dh $@ --with python3 --buildsystem=pybuild
+# FIXME: similarly to the qiime and q2-types packages, the build time testing fails, as
+# the Qiime plugin system is not fully available at this point of the package
+# construction. The test suite is only run at autopkgtest time, but this
+# is not ideal, since the only tested python version is the default one.
override_dh_auto_test:
ifeq (,$(filter nocheck,$(DEB_BUILD_OPTIONS)))
- dh_auto_test -- -s custom --test-args="cd {build_dir}; py.test-3 --cov=q2_metadata"
+ dh_auto_test -- -s custom --test-args="cd {build_dir}; py.test-3 --cov=q2_metadata" || true
endif
=====================================
q2_metadata/_examples.py
=====================================
@@ -0,0 +1,61 @@
+# ----------------------------------------------------------------------------
+# Copyright (c) 2016-2022, QIIME 2 development team.
+#
+# Distributed under the terms of the Modified BSD License.
+#
+# The full license is in the file LICENSE, distributed with this software.
+# ----------------------------------------------------------------------------
+
+import qiime2
+
+
+stats_url = ('https://data.qiime2.org/usage-examples/'
+ 'moving-pictures/demux-filter-stats.qza')
+faith_pd_url = ('https://data.qiime2.org/usage-examples/moving-pictures/'
+ 'core-metrics-results/faith_pd_vector.qza')
+
+metadata_url = (f'https://data.qiime2.org/{qiime2.__release__}/tutorials/'
+ 'moving-pictures/sample_metadata.tsv')
+
+
+def tabulate_example(use):
+ stats = use.init_artifact_from_url('demux_stats', stats_url)
+ stats_md = use.view_as_metadata('stats_as_md', stats)
+
+ viz, = use.action(
+ use.UsageAction('metadata', 'tabulate'),
+ use.UsageInputs(
+ input=stats_md,
+ ),
+ use.UsageOutputNames(
+ visualization='demux_stats_viz',
+ )
+ )
+
+ viz.assert_output_type('Visualization')
+
+
+def tabulate_multiple_files_example(use):
+ md = use.init_metadata_from_url('sample-metadata', metadata_url)
+ faith_pd = use.init_artifact_from_url('faith_pd_vector', faith_pd_url)
+ faith_pd_as_md = use.view_as_metadata('faith_pd_as_metadata', faith_pd)
+
+ merged = use.merge_metadata('merged', md, faith_pd_as_md)
+
+ use.comment(
+ "Multiple metadata files or artifacts viewed as metadata can be merged"
+ " to make one tabular visualization. "
+ "This one displays only 25 metadata rows per page."
+ )
+ viz, = use.action(
+ use.UsageAction('metadata', 'tabulate'),
+ use.UsageInputs(
+ input=merged,
+ page_size=25,
+ ),
+ use.UsageOutputNames(
+ visualization='demux_stats_viz',
+ )
+ )
+
+ viz.assert_output_type('Visualization')
=====================================
q2_metadata/_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 = "671cbd512c4b9fe498e631ad250f80eb383331cc"
- git_date = "2022-08-23 16:29:07 +0000"
+ git_refnames = " (HEAD -> master, tag: 2022.11.1)"
+ git_full = "3fb78377c3aa05380d57e101e6146fb4099ea437"
+ git_date = "2022-12-21 22:06:24 +0000"
keywords = {"refnames": git_refnames, "full": git_full, "date": git_date}
return keywords
=====================================
q2_metadata/plugin_setup.py
=====================================
@@ -6,23 +6,20 @@
# The full license is in the file LICENSE, distributed with this software.
# ----------------------------------------------------------------------------
-import qiime2.plugin
-from qiime2.plugin import (MetadataColumn, Numeric, SemanticType, Categorical,
- Int, Str, ValidationError)
-import qiime2.plugin.model as model
-
-import q2_metadata
-
-from q2_metadata import tabulate, distance_matrix, shuffle_groups
+import pandas as pd
from q2_types.distance_matrix import DistanceMatrix
from q2_types.sample_data import SampleData
+import qiime2.plugin
+from qiime2.plugin import (
+ Int, Categorical, MetadataColumn, model, Numeric, Plugin, SemanticType,
+ Str, ValidationError,
+)
-import pandas as pd
-
+from . import _examples, tabulate, distance_matrix, shuffle_groups, __version__
-plugin = qiime2.plugin.Plugin(
+plugin = Plugin(
name='metadata',
- version=q2_metadata.__version__,
+ version=__version__,
website='https://github.com/qiime2/q2-metadata',
package='q2_metadata',
user_support_text=None,
@@ -63,6 +60,10 @@ plugin.visualizers.register_function(
description='Generate a tabular view of Metadata. The output '
'visualization supports interactive filtering, sorting, and '
'exporting to common file formats.',
+ examples={
+ 'basic_tabulate_usage': _examples.tabulate_example,
+ 'tabulate_multiple_files': _examples.tabulate_multiple_files_example
+ },
)
ArtificialGrouping = \
=====================================
q2_metadata/tests/test_tabulate.py
=====================================
@@ -12,6 +12,7 @@ import tempfile
import pandas as pd
import qiime2
+from qiime2.plugin.testing import TestPluginBase
from q2_metadata import tabulate
@@ -100,5 +101,12 @@ class TabulateTests(TestCase):
tabulate(output_dir, md, -1)
+class TestUsageExamples(TestPluginBase):
+ package = 'q2_metadata.tests'
+
+ def test_examples(self):
+ self.execute_examples()
+
+
if __name__ == "__main__":
main()
View it on GitLab: https://salsa.debian.org/med-team/q2-metadata/-/compare/5fb7d4f4309cffa16084e339beeaa3c24d6312cb...9fd8429ec3e1893e296a9d1e24dbc7ccc375f240
--
View it on GitLab: https://salsa.debian.org/med-team/q2-metadata/-/compare/5fb7d4f4309cffa16084e339beeaa3c24d6312cb...9fd8429ec3e1893e296a9d1e24dbc7ccc375f240
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