Transition from setup.py & friends to pyproject.toml

.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: diversity
+plugin_name: q2_diversity
+plugin_scripts: q2_diversity/_beta/adonis_assets/run_adonis.R
+project_author_email: [email protected]
+project_author_name: Greg Caporaso
+project_description: Core diversity analyses.
+project_name: q2-diversity
+project_urls_homepage: https://qiime2.org
+project_urls_repository: https://github.com/qiime2/q2-diversity

.gitattributes

@@ -1 +1 @@
-q2_diversity/_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'

Makefile

@@ -37,7 +37,7 @@ viz-alpha-group-significance: q2_diversity/_alpha/alpha_group_significance_asset
 viz-alpha-rarefaction: q2_diversity/_alpha/alpha_rarefaction_assets/dist
 
 install: all
-	$(PYTHON) setup.py install
+	$(PYTHON) -m pip install -v .
 
 dev: all
 	pip install -e .

conda-recipe/meta.yaml

@@ -0,0 +1,60 @@
+package:
+  name: q2-diversity
+  version: {{ PLUGIN_VERSION }}
+source:
+  path: ..
+build:
+  script: make install
+requirements:
+  build:
+  - nodejs
+  - setuptools
+  - versioningit
+  host:
+  - python {{ python }}
+  - setuptools
+  - versioningit
+  - wheel
+  run:
+  - python {{ python }}
+  - numpy
+  - scipy {{ scipy }}
+  - pandas {{ pandas }}
+  - statsmodels
+  - seaborn
+  - ipywidgets
+  - scikit-bio {{ scikit_bio }}
+  - scikit-learn {{ scikit_learn }}
+  - psutil
+  - natsort
+  - biom-format {{ biom_format }}
+  - qiime2 {{ qiime2_epoch }}.*
+  - q2templates {{ qiime2_epoch }}.*
+  - q2-types {{ qiime2_epoch }}.*
+  - q2-feature-table {{ qiime2_epoch }}.*
+  - q2-metadata {{ qiime2_epoch }}.*
+  - q2-emperor {{ qiime2_epoch }}.*
+  - q2-diversity-lib {{ qiime2_epoch }}.*
+  - r-base {{ r_base }}
+  - r-vegan >=2.5_3
+  - umap-learn
+  - numba
+test:
+  requires:
+  - qiime2 >={{ qiime2 }}
+  - q2templates >={{ q2templates }}
+  - q2-types >={{ q2_types }}
+  - q2-feature-table >={{ q2_feature_table }}
+  - q2-metadata >={{ q2_metadata }}
+  - q2-emperor >={{ q2_emperor }}
+  - q2-diversity-lib >={{ q2_diversity_lib }}
+  - pytest
+  imports:
+  - q2_diversity
+  - qiime2.plugins.diversity
+  commands:
+  - py.test --pyargs q2_diversity
+about:
+  home: https://qiime2.org
+  license: BSD-3-Clause
+  license_family: BSD

pyproject.toml

@@ -0,0 +1,53 @@
+[project]
+name = "q2-diversity"
+authors = [
+    { name = "Greg Caporaso", email = "[email protected]" }
+]
+description = "Core diversity analyses."
+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-diversity"
+
+[project.entry-points.'qiime2.plugins']
+"q2-diversity" = "q2_diversity.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-diversity/_version.py"
+
+[tool.setuptools]
+include-package-data = true
+script-files = [
+    "q2_diversity/_beta/adonis_assets/run_adonis.R"
+]
+
+[tool.setuptools.packages.find]
+where = ["."]
+include = ["q2_diversity*"]
+
+[tool.setuptools.package-data]
+q2_diversity = ["**/*"]

q2_diversity/__init__.py

@@ -15,10 +15,11 @@
 from ._procrustes import procrustes_analysis, partial_procrustes
 from ._core_metrics import core_metrics_phylogenetic, core_metrics
 from ._filter import filter_distance_matrix, filter_alpha_diversity
-from ._version import get_versions
 
-__version__ = get_versions()['version']
-del get_versions
+try:
+    from ._version import __version__
+except ModuleNotFoundError:
+    __version__ = '0.0.0+notfound'
 
 
 __all__ = ['beta', 'beta_phylogenetic', 'alpha', 'alpha_phylogenetic',