Merge branch 'dev' into ancombc2

.copier-answers.yml

@@ -0,0 +1,12 @@
+# Changes here will be overwritten by Copier; NEVER EDIT MANUALLY
+_commit: dfb0404
+_src_path: https://github.com/qiime2/q2-setup-template.git
+module_name: composition
+plugin_name: q2_composition
+plugin_scripts: q2_composition/assets/run_ancombc.R
+project_author_email: jamietmorton@gmail.com
+project_author_name: Jamie Morton
+project_description: Compositional statistics plugin for QIIME2.
+project_name: q2-composition
+project_urls_homepage: https://qiime2.org
+project_urls_repository: https://github.com/qiime2/q2-composition

.gitattributes

@@ -1 +1 @@
-q2_composition/_version.py export-subst
+pyproject.toml export-subst

.github/workflows/ci-dev.yaml

@@ -9,4 +9,5 @@ jobs:
   ci:
     uses: qiime2/distributions/.github/workflows/lib-ci-dev.yaml@dev
     with:
-      distro: amplicon
+      distro: amplicon
+      recipe-path: 'conda-recipe'

.github/workflows/update-copyright-headers.yaml

@@ -0,0 +1,58 @@
+name: Update Copyright Headers
+
+on:
+  # Runs at 00:00 UTC on Jan 4th or via manual trigger
+  schedule:
+    - cron: '0 0 4 1 *'
+  workflow_dispatch:
+    inputs:
+      newYear:
+        description: "Desired year to update to (e.g., 2025). If not provided, will auto-detect."
+        required: false
+
+jobs:
+  update-headers:
+    runs-on: ubuntu-latest
+    steps:
+      - name: Check out repository
+        uses: actions/checkout@v3
+
+      - name: Determine years for update
+        id: determine-years
+        run: |
+          INPUT_YEAR="${{ github.event.inputs.newYear }}"
+
+          if [ -z "$INPUT_YEAR" ]; then
+            CURRENT_YEAR="$(date +'%Y')"
+            echo "No 'newYear' input. Using current year: ${CURRENT_YEAR}"
+          else
+            CURRENT_YEAR="$INPUT_YEAR"
+            echo "Received user input. Updating to: ${CURRENT_YEAR}"
+          fi
+
+          echo "CURRENT_YEAR=$CURRENT_YEAR" >> $GITHUB_ENV
+
+      - name: Bump ending year in QIIME 2 headers
+        run: |
+          source $GITHUB_ENV
+
+          echo "Will update any QIIME 2 header years in [2015..$((CURRENT_YEAR-1))] to $CURRENT_YEAR"
+
+          for OLD_YEAR in $(seq 2015 $((CURRENT_YEAR - 1))); do
+            find . -type f -exec \
+              sed -i -E "s/(Copyright \(c\) [0-9]{4})-${OLD_YEAR}, QIIME 2/\1-${CURRENT_YEAR}, QIIME 2/g" {} +
+          done
+
+      - name: Commit and push changes
+        run: |
+          git config --global user.name "q2d2"
+          git config --global user.email "q2d2.noreply@gmail.com"
+
+          if [ -n "$(git status --porcelain)" ]; then
+            git add .
+            git commit -m "Auto-update copyright year to $CURRENT_YEAR"
+            git push
+          else
+            echo "No changes to commit."
+            exit 0
+          fi

.gitignore

@@ -74,4 +74,5 @@ output.summary.txt
 
 .DS_Store
 
-pyproject.toml
+# Version file from versioningit
+_version.py

LICENSE

@@ -1,6 +1,6 @@
 BSD 3-Clause License
 
-Copyright (c) 2016-2023, QIIME 2 development team.
+Copyright (c) 2016-2025, QIIME 2 development team.
 All rights reserved.
 
 Redistribution and use in source and binary forms, with or without

Makefile

@@ -15,7 +15,7 @@ test-cov: all
 	py.test --cov=q2_composition
 
 install: all
-	$(PYTHON) setup.py install
+	$(PYTHON) -m pip install -v .
 
 dev: all
 	pip install -e .

ci/recipe/meta.yaml → conda-recipe/meta.yaml

@@ -1,21 +1,16 @@
-{% set data = load_setup_py_data() %}
-{% set version = data.get('version') or 'placehold' %}
-
 package:
   name: q2-composition
-  version: {{ version }}
-
+  version: { { PLUGIN_VERSION } }
 source:
-  path: ../..
-
+  path: ..
 build:
   script: make install
-
 requirements:
   host:
     - python {{ python }}
     - setuptools
-
+    - versioningit
+    - wheel
   run:
     - python {{ python }}
     - scikit-bio {{ scikit_bio }}
@@ -33,21 +28,20 @@ requirements:
     - q2-types {{ qiime2_epoch }}.*
     - altair
     - rpy2 {{ rpy2 }}
-
+  build:
+    - setuptools
+    - versioningit
 test:
   requires:
     - qiime2 >={{ qiime2 }}
     - q2templates >={{ q2templates }}
     - q2-types >={{ q2_types }}
     - pytest
-
   imports:
     - q2_composition
     - qiime2.plugins.composition
-
   commands:
     - py.test --pyargs q2_composition
-
 about:
   home: https://qiime2.org
   license: BSD-3-Clause

pyproject.toml

@@ -0,0 +1,53 @@
+[project]
+name = "q2-composition"
+authors = [
+    { name = "Jamie Morton", email = "jamietmorton@gmail.com" }
+]
+description = "Compositional statistics plugin for QIIME2."
+readme = {file = "README.md", content-type = "text/markdown"}
+license = {file = "LICENSE"}
+dynamic = ["version"]
+
+[project.urls]
+Homepage = "https://qiime2.org"
+Repository = "https://github.com/qiime2/q2-composition"
+
+[project.entry-points.'qiime2.plugins']
+"q2-composition" = "q2_composition.plugin_setup:plugin"
+
+[build-system]
+requires = [
+    "setuptools",
+    "versioningit",
+    "wheel"
+]
+build-backend = "setuptools.build_meta"
+
+[tool.versioningit.vcs]
+method = "git-archive"
+describe-subst = "$Format:%(describe)$"
+default-tag = "0.0.1"
+
+[tool.versioningit.next-version]
+method = "minor"
+
+[tool.versioningit.format]
+distance = "{base_version}+{distance}.{vcs}{rev}"
+dirty = "{base_version}+{distance}.{vcs}{rev}.dirty"
+distance-dirty = "{base_version}+{distance}.{vcs}{rev}.dirty"
+
+[tool.versioningit.write]
+file = "q2-composition/_version.py"
+
+[tool.setuptools]
+include-package-data = true
+script-files = [
+    "q2_composition/assets/run_ancombc.R"
+]
+
+[tool.setuptools.packages.find]
+where = ["."]
+include = ["q2_composition*"]
+
+[tool.setuptools.package-data]
+q2_composition = ["**/*"]

q2_composition/__init__.py

@@ -1,12 +1,11 @@
 # ----------------------------------------------------------------------------
-# Copyright (c) 2016-2023, QIIME 2 development team.
+# Copyright (c) 2016-2025, 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.
 # ----------------------------------------------------------------------------
 
-from ._version import get_versions
 
 from ._format import (FrictionlessCSVFileFormat,
                       DataPackageSchemaFileFormat,
@@ -20,8 +19,10 @@
 from ._dataloaf_tabulate import tabulate
 from ._diff_abundance_plots import da_barplot
 
-__version__ = get_versions()['version']
-del get_versions
+try:
+    from ._version import __version__
+except ModuleNotFoundError:
+    __version__ = '0.0.0+notfound'
 
 __all__ = ['FrictionlessCSVFileFormat', 'DataPackageSchemaFileFormat',
            'DataLoafPackageDirFmt', 'DifferentialAbundance', 'add_pseudocount',

q2_composition/_ancom.py

@@ -1,5 +1,5 @@
 # ----------------------------------------------------------------------------
-# Copyright (c) 2016-2023, QIIME 2 development team.
+# Copyright (c) 2016-2025, QIIME 2 development team.
 #
 # Distributed under the terms of the Modified BSD License.
 #

q2_composition/_ancombc.py

@@ -1,5 +1,5 @@
 # ----------------------------------------------------------------------------
-# Copyright (c) 2016-2023, QIIME 2 development team.
+# Copyright (c) 2016-2025, QIIME 2 development team.
 #
 # Distributed under the terms of the Modified BSD License.
 #

q2_composition/_dataloaf_tabulate/__init__.py

@@ -1,5 +1,5 @@
 # ----------------------------------------------------------------------------
-# Copyright (c) 2016-2023, QIIME 2 development team.
+# Copyright (c) 2016-2025, QIIME 2 development team.
 #
 # Distributed under the terms of the Modified BSD License.
 #

q2_composition/_dataloaf_tabulate/_visualizer.py

@@ -1,5 +1,5 @@
 # ----------------------------------------------------------------------------
-# Copyright (c) 2016-2023, QIIME 2 development team.
+# Copyright (c) 2016-2025, QIIME 2 development team.
 #
 # Distributed under the terms of the Modified BSD License.
 #

q2_composition/_diff_abundance_plots.py

@@ -1,5 +1,5 @@
 # ----------------------------------------------------------------------------
-# Copyright (c) 2016-2023, QIIME 2 development team.
+# Copyright (c) 2016-2025, QIIME 2 development team.
 #
 # Distributed under the terms of the Modified BSD License.
 #
@@ -110,6 +110,9 @@ def _plot_differentials(
                              significance_label, error_label,
                              "error-lower", "error-upper"]),
         color=alt.Color('enriched', title="Relative to reference",
+                        scale=alt.Scale(
+                            domain=["enriched", "depleted"],
+                            range=["#4c78a8", "#f58518"]),
                         sort="descending")
     )
 

q2_composition/_examples.py

@@ -1,5 +1,5 @@
 # ----------------------------------------------------------------------------
-# Copyright (c) 2022-2023, QIIME 2 development team.
+# Copyright (c) 2022-2025, QIIME 2 development team.
 #
 # Distributed under the terms of the Modified BSD License.
 #

q2_composition/_format.py

@@ -1,5 +1,5 @@
 # ----------------------------------------------------------------------------
-# Copyright (c) 2022-2023, QIIME 2 development team.
+# Copyright (c) 2022-2025, QIIME 2 development team.
 #
 # Distributed under the terms of the Modified BSD License.
 #

q2_composition/_impute.py

@@ -1,5 +1,5 @@
 # ----------------------------------------------------------------------------
-# Copyright (c) 2016-2023, QIIME 2 development team.
+# Copyright (c) 2016-2025, QIIME 2 development team.
 #
 # Distributed under the terms of the Modified BSD License.
 #

q2_composition/_type.py

@@ -1,5 +1,5 @@
 # ----------------------------------------------------------------------------
-# Copyright (c) 2022-2023, QIIME 2 development team.
+# Copyright (c) 2022-2025, QIIME 2 development team.
 #
 # Distributed under the terms of the Modified BSD License.
 #