setup.py to pyproject.toml migration

.gitignore

@@ -1,7 +1,7 @@
 /*
-taxtastic/data/ver
+taxtastic/taxtastic.egg-info/
 __pycache__
-!setup.py
+!pyproject.toml
 !MANINFEST.in
 !README.rst
 !taxtastic/

CHANGES.rst

@@ -2,6 +2,11 @@
  change log for taxtastic
 ==========================
 
+0.11.2-dev
+==========
+
+* Migrated setup.py to pyproject.toml [GH-172]
+
 0.11.1
 ======
 

Dockerfile

@@ -2,17 +2,18 @@
 FROM python:3.11-slim-bullseye
 
 ARG VERSION
-ENV PIP_ROOT_USER_ACTION=ignore TAXTASTIC_VERSION=${VERSION#v}
+ENV PIP_ROOT_USER_ACTION=ignore
 
-RUN apt-get -y update && apt-get upgrade -y && apt-get install -y unzip wget
+RUN apt-get -y update && apt-get upgrade -y && apt-get install -y git unzip wget
 
 WORKDIR /opt/build
 
 COPY dev/install_pplacer.sh ./
 RUN /opt/build/install_pplacer.sh /usr/local
 
-COPY setup.py MANIFEST.in README.rst ./
+COPY pyproject.toml MANIFEST.in README.rst ./
 COPY taxtastic/ ./taxtastic/
+COPY .git/ ./.git/
 RUN pip3 install --upgrade pip && pip3 install .
 
 WORKDIR /opt/run

pyproject.toml

@@ -0,0 +1,50 @@
+[build-system]
+requires = ["setuptools>=64", "setuptools-scm>=8"]
+build-backend = "setuptools.build_meta"
+
+[project]
+authors = [
+  {email = "[email protected]", name = "Noah Hoffman"}
+]
+classifiers = [
+"Development Status :: 3 - Alpha",
+"Programming Language :: Python :: 3.8",
+"Programming Language :: Python :: 3.9",
+"Programming Language :: Python :: 3.10",
+"Programming Language :: Python :: 3.11",
+"Programming Language :: Python :: 3.12",
+"Topic :: Scientific/Engineering :: Bio-Informatics"
+]
+dependencies = [
+"decorator",
+"DendroPy",
+"fastalite",
+"jinja2",
+"psycopg-binary",
+"psycopg2-binary",
+"PyYAML",
+"sqlalchemy>=2",
+"sqlparse"
+]
+description = "Tools for taxonomic naming and annotation"
+dynamic = ["version"]  # https://setuptools-scm.readthedocs.io/en/latest/
+license = {text = "GPL-3.0-only"}
+maintainers = [
+  {email = "[email protected]", name = "Chris Rosenthal"},
+  {email = "[email protected]", name="Dan Hoogestraat"}
+]
+name = "taxtastic"
+readme = "README.rst"
+requires-python = ">=3.8"
+
+[project.urls]
+repository = "https://github.com/fhcrc/taxtastic"
+
+[project.scripts]
+taxit = "taxtastic.scripts.taxit:main"
+
+[tool.setuptools.packages.find]
+exclude = ["testfiles", "tests"]
+
+[tool.setuptools_scm]
+# can be empty if no extra settings are needed, presence enables setuptools-scm

taxtastic/__init__.py

@@ -1,11 +1,8 @@
-import os
+from importlib.metadata import version, PackageNotFoundError
 
-ver = os.path.join(os.path.dirname(__file__), 'data', 'ver')
-if 'TAXTASTIC_VERSION' in os.environ:
-    __version__ = os.environ['TAXTASTIC_VERSION']
-elif os.path.isfile(ver):
-    with open(ver) as f:
-        __version__ = f.read().strip().replace('-', '+', 1).replace('-', '.')
-        __version__ = __version__.lstrip('v')
-else:
-    __version__ = ''
+# https://setuptools-scm.readthedocs.io/en/latest/usage/#at-runtime
+try:
+    __version__ = version("taxtastic")
+except PackageNotFoundError:
+    # package is not installed
+    pass