MAINT: transition setup.py to pyproject.toml (#107)

* Transition from setup.py & friends to pyproject.toml

* fix setup.cfg

---------

Co-authored-by: Liz Gehret <[email protected]>

Author: q2d2

.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: assembly
+plugin_name: q2_assembly
+plugin_scripts: null
+project_author_email: [email protected]
+project_author_name: Michal Ziemski
+project_description: QIIME 2 plugin for (meta)genome assembly.
+project_name: q2-assembly
+project_urls_homepage: https://github.com/bokulich-lab/q2-assembly
+project_urls_repository: https://github.com/bokulich-lab/q2-assembly

.gitattributes

@@ -1 +1 @@
-q2_assembly/_version.py export-subst
+pyproject.toml export-subst

.github/workflows/ci-dev.yaml

@@ -10,6 +10,7 @@ jobs:
     uses: qiime2/distributions/.github/workflows/lib-ci-dev.yaml@dev
     with:
       distro: metagenome
+      recipe-path: 'conda-recipe'
       additional-reports-path: ./coverage.xml
       additional-reports-name: coverage
 

.gitignore

@@ -144,3 +144,7 @@ test_megahit.py
 exported_*
 reads/*
 *.qza
+
+# Version file from versioningit
+_version.py
+

MANIFEST.in

@@ -16,7 +16,7 @@ test-cov: all
 	coverage xml
 
 install: all
-	$(PYTHON) setup.py install
+	$(PYTHON) -m pip install -v .
 
 dev: all
 	pip install pre-commit

Makefile

@@ -0,0 +1,47 @@
+package:
+  name: q2-assembly
+  version: {{ PLUGIN_VERSION }}
+source:
+  path: ..
+build:
+  script: make install
+requirements:
+  host:
+  - python {{ python }}
+  - setuptools
+  - versioningit
+  - wheel
+  run:
+  - quast
+  - beautifulsoup4
+  - biopython
+  - bowtie2 {{ bowtie2 }}
+  - gridss
+  - insilicoseq
+  - megahit ==1.2.9
+  - pysam {{ pysam }}
+  - qiime2 {{ qiime2_epoch }}.*
+  - q2-types {{ qiime2_epoch }}.*
+  - q2templates {{ qiime2_epoch }}.*
+  - q2-demux {{ qiime2_epoch }}.*
+  - samtools
+  - shortuuid
+  - spades ==3.15.2
+  build:
+  - setuptools
+  - versioningit
+test:
+  requires:
+  - coverage
+  - pytest
+  - pytest-cov
+  - parameterized
+  imports:
+  - q2_assembly
+  - qiime2.plugins.assembly
+  commands:
+  - pytest --cov q2_assembly --cov-report xml:coverage.xml --pyargs q2_assembly
+about:
+  home: https://github.com/bokulich-lab/q2-assembly
+  license: BSD-3-Clause
+  license_family: BSD

ci/recipe/meta.yaml

@@ -0,0 +1,50 @@
+[project]
+name = "q2-assembly"
+authors = [
+    { name = "Michal Ziemski", email = "[email protected]" }
+]
+description = "QIIME 2 plugin for (meta)genome assembly."
+readme = {file = "README.md", content-type = "text/markdown"}
+license = {file = "LICENSE"}
+dynamic = ["version"]
+
+[project.urls]
+Homepage = "https://github.com/bokulich-lab/q2-assembly"
+Repository = "https://github.com/bokulich-lab/q2-assembly"
+
+[project.entry-points.'qiime2.plugins']
+"q2-assembly" = "q2_assembly.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-assembly/_version.py"
+
+[tool.setuptools]
+include-package-data = true
+
+[tool.setuptools.packages.find]
+where = ["."]
+include = ["q2_assembly*"]
+
+[tool.setuptools.package-data]
+q2_assembly = ["**/*"]

conda-recipe/meta.yaml

@@ -6,15 +6,16 @@
 # The full license is in the file LICENSE, distributed with this software.
 # ----------------------------------------------------------------------------
 
-from ._version import get_versions
 from .bowtie2 import indexing, mapping
 from .helpers import helpers
 from .iss import iss
 from .megahit import megahit
 from .quast import quast
 from .spades import spades
 
-__version__ = get_versions()["version"]
-del get_versions
+try:
+    from ._version import __version__
+except ModuleNotFoundError:
+    __version__ = '0.0.0+notfound'
 
 __all__ = ["indexing", "mapping", "iss", "megahit", "quast", "spades", "helpers"]