Transition from setup.py & friends to pyproject.toml (#175)

.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: dada2
+plugin_name: q2_dada2
+plugin_scripts: q2_dada2/assets/run_dada.R
+project_author_email: gregcaporaso@gmail.com
+project_author_name: Greg Caporaso and Benjamin Callahan
+project_description: Apply DADA2 to generate denoised sequence variants.
+project_name: q2-dada2
+project_urls_homepage: https://qiime2.org
+project_urls_repository: https://github.com/qiime2/q2-dada2

.gitattributes

@@ -1 +1 @@
-q2_dada2/_version.py export-subst
+pyproject.toml export-subst

.github/workflows/ci-dev.yaml

@@ -10,3 +10,4 @@ jobs:
     uses: qiime2/distributions/.github/workflows/lib-ci-dev.yaml@dev
     with:
       distro: amplicon
+      recipe-path: 'conda-recipe'

.gitignore

@@ -70,3 +70,7 @@ target/
 
 .DS_Store
 .Rhistory
+
+# Version file from versioningit
+_version.py
+

Makefile

@@ -15,7 +15,7 @@ test-cov: all
 	py.test --cov=q2_dada2
 
 install: all
-	$(PYTHON) setup.py install
+	$(PYTHON) -m pip install -v .
 
 dev: all
 	pip install -e .

conda-recipe/meta.yaml

@@ -0,0 +1,39 @@
+package:
+  name: q2-dada2
+  version: {{ PLUGIN_VERSION }}
+source:
+  path: ..
+build:
+  script: make install
+requirements:
+  host:
+  - python {{ python }}
+  - setuptools
+  - versioningit
+  - wheel
+  run:
+  - python {{ python }}
+  - biom-format {{ biom_format }}
+  - bioconductor-dada2
+  - r-base {{ r_base }}
+  - r-optparse >=1.7.1
+  - openjdk
+  - qiime2 {{ qiime2_epoch }}.*
+  - q2-types {{ qiime2_epoch }}.*
+  build:
+  - setuptools
+  - versioningit
+test:
+  requires:
+  - qiime2 >={{ qiime2 }}
+  - q2-types >={{ q2_types }}
+  - pytest
+  imports:
+  - q2_dada2
+  - qiime2.plugins.dada2
+  commands:
+  - py.test --pyargs q2_dada2
+about:
+  home: https://qiime2.org
+  license: BSD-3-Clause
+  license_family: BSD

pyproject.toml

@@ -0,0 +1,53 @@
+[project]
+name = "q2-dada2"
+authors = [
+    { name = "Greg Caporaso and Benjamin Callahan", email = "gregcaporaso@gmail.com" }
+]
+description = "Apply DADA2 to generate denoised sequence variants."
+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-dada2"
+
+[project.entry-points.'qiime2.plugins']
+"q2-dada2" = "q2_dada2.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-dada2/_version.py"
+
+[tool.setuptools]
+include-package-data = true
+script-files = [
+    "q2_dada2/assets/run_dada.R"
+]
+
+[tool.setuptools.packages.find]
+where = ["."]
+include = ["q2_dada2*"]
+
+[tool.setuptools.package-data]
+q2_dada2 = ["**/*"]

q2_dada2/__init__.py

@@ -7,12 +7,13 @@
 # ----------------------------------------------------------------------------
 
 from ._denoise import denoise_single, denoise_paired, denoise_pyro, denoise_ccs
-from ._version import get_versions
 from ._stats import DADA2Stats, DADA2StatsDirFmt, DADA2StatsFormat
 
 
-__version__ = get_versions()['version']
-del get_versions
+try:
+    from ._version import __version__
+except ModuleNotFoundError:
+    __version__ = '0.0.0+notfound'
 
 __all__ = ['denoise_single', 'denoise_paired', 'denoise_pyro', 'denoise_ccs',
            'DADA2Stats', 'DADA2StatsFormat', 'DADA2StatsDirFmt']