Transition from setup.py & friends to pyproject.toml (#101)

.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: phylogeny
+plugin_name: q2_phylogeny
+plugin_scripts: null
+project_author_email: [email protected]
+project_author_name: Greg Caporaso and Michael Robeson
+project_description: Create and work with Phylogenetic trees in QIIME 2.
+project_name: q2-phylogeny
+project_urls_homepage: https://qiime2.org
+project_urls_repository: https://github.com/qiime2/q2-phylogeny

.gitattributes

@@ -1 +1 @@
-q2_phylogeny/_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'

.gitignore

@@ -90,3 +90,7 @@ ENV/
 
 # vi
 .*.swp
+
+# Version file from versioningit
+_version.py
+

Makefile

@@ -15,7 +15,7 @@ test-cov: all
 	py.test --cov=q2_phylogeny
 
 install: all
-	$(PYTHON) setup.py install
+	$(PYTHON) -m pip install -v .
 
 dev: all
 	pip install -e .

conda-recipe/meta.yaml

@@ -0,0 +1,41 @@
+package:
+  name: q2-phylogeny
+  version: {{ PLUGIN_VERSION }}
+source:
+  path: ..
+build:
+  script: make install
+requirements:
+  host:
+  - python {{ python }}
+  - setuptools
+  - versioningit
+  - wheel
+  run:
+  - python {{ python }}
+  - scikit-bio {{ scikit_bio }}
+  - qiime2 {{ qiime2_epoch }}.*
+  - q2-types {{ qiime2_epoch }}.*
+  - q2-alignment {{ qiime2_epoch }}.*
+  - fasttree
+  - raxml
+  - iqtree
+  - h5py
+  build:
+  - setuptools
+  - versioningit
+test:
+  commands:
+  - py.test --pyargs q2_phylogeny
+  requires:
+  - qiime2 >={{ qiime2 }}
+  - q2-types >={{ q2_types }}
+  - q2-alignment >={{ q2_alignment }}
+  - pytest
+  imports:
+  - q2_phylogeny
+  - qiime2.plugins.phylogeny
+about:
+  home: https://qiime2.org
+  license: BSD-3-Clause
+  license_family: BSD

pyproject.toml

@@ -0,0 +1,50 @@
+[project]
+name = "q2-phylogeny"
+authors = [
+    { name = "Greg Caporaso and Michael Robeson", email = "[email protected]" }
+]
+description = "Create and work with Phylogenetic trees in QIIME 2."
+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-phylogeny"
+
+[project.entry-points.'qiime2.plugins']
+"q2-phylogeny" = "q2_phylogeny.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-phylogeny/_version.py"
+
+[tool.setuptools]
+include-package-data = true
+
+[tool.setuptools.packages.find]
+where = ["."]
+include = ["q2_phylogeny*"]
+
+[tool.setuptools.package-data]
+q2_phylogeny = ["**/*"]

q2_phylogeny/__init__.py

@@ -11,13 +11,14 @@
 from ._raxml import raxml, raxml_rapid_bootstrap
 from ._iqtree import iqtree, iqtree_ultrafast_bootstrap
 from ._filter import filter_table, filter_tree
-from ._version import get_versions
 from ._align_to_tree_mafft_fasttree import align_to_tree_mafft_fasttree
 from ._align_to_tree_mafft_iqtree import align_to_tree_mafft_iqtree
 from ._align_to_tree_mafft_raxml import align_to_tree_mafft_raxml
 
-__version__ = get_versions()['version']
-del get_versions
+try:
+    from ._version import __version__
+except ModuleNotFoundError:
+    __version__ = '0.0.0+notfound'
 
 __all__ = ["midpoint_root", "fasttree", "align_to_tree_mafft_fasttree",
            "raxml", "raxml_rapid_bootstrap", "iqtree", "filter_table",