Merge branch 'master' into lazy

.github/workflows/python-package-conda.yml

@@ -10,7 +10,7 @@ on:
 
 env:
   latest_python: "3.12"
-  supported_pythons: '["3.7", "3.8", "3.9", "3.10", "3.11", "3.12"]'
+  supported_pythons: '["3.9", "3.10", "3.11", "3.12", "3.13"]'
   miniforge_version: "22.9.0-2"
   miniforge_variant: "Mambaforge"
 
@@ -98,13 +98,13 @@ jobs:
         shell: bash -l {0}
         run: |
           conda install -q --yes -c conda-forge --file ci/conda_requirements.txt
-          pip install . --no-deps
+          pip install -e . --no-deps
           conda list
       - name: Install dependencies (pip)
         if: ${{ !matrix.use_conda }}
         shell: bash -l {0}
         run: |
-          pip install .
+          pip install -e .
           conda list
       - name: Run unit tests
         shell: bash -l {0}

.github/workflows/release.yml

@@ -6,7 +6,7 @@ on:
       - '*'
 
 env:
-  earliest_python: "3.8"
+  earliest_python: "3.9"
   latest_python: "3.12"
   miniforge_version: "23.11.0-0"
   miniforge_variant: "Mambaforge"

ChangeLog.md

@@ -4,6 +4,10 @@ BIOM-Format ChangeLog
 biom-2.1.16-dev
 ---------------
 
+Maintenance:
+
+* Python 3.7 and 3.8 removed from CI as they are [end-of-life](https://devguide.python.org/versions/). Python 3.13 added to CI. See PR[#986](https://github.com/biocore/biom-format/pull/986).
+
 biom 2.1.16
 -----------
 

Makefile

@@ -7,9 +7,9 @@
 # ----------------------------------------------------------------------------
 
 ifeq ($(WITH_DOCTEST), TRUE)
-	TEST_COMMAND = python setup.py test -a --doctest-modules --doctest-glob='*.pyx'
+	TEST_COMMAND = pytest --doctest-modules --doctest-glob='*.pyx'
 else
-	TEST_COMMAND = python setup.py test 
+	TEST_COMMAND = pytest
 endif
 
 .PHONY: doc lint test

aarch64.Dockerfile

@@ -10,6 +10,6 @@ COPY . /work
 WORKDIR /work
 RUN bash -c ". /opt/conda/etc/profile.d/conda.sh && conda activate testing && conda env update -q -f ci/conda_host_env.yml"
 RUN bash -c ". /opt/conda/etc/profile.d/conda.sh && conda activate testing && conda install -q --yes --file ci/aarch64.conda_requirements.txt"
-RUN bash -c ". /opt/conda/etc/profile.d/conda.sh && conda activate testing && pip install . --no-deps"
+RUN bash -c ". /opt/conda/etc/profile.d/conda.sh && conda activate testing && pip install -e . --no-deps"
 RUN bash -c ". /opt/conda/etc/profile.d/conda.sh && conda activate testing && conda list"
 RUN bash -c ". /opt/conda/etc/profile.d/conda.sh && conda activate testing && make test"

setup.py

@@ -12,7 +12,6 @@
 
 from setuptools import setup, find_packages
 from setuptools.extension import Extension
-from setuptools.command.test import test as TestCommand
 import numpy as np
 from Cython.Build import cythonize
 
@@ -37,37 +36,6 @@
 __email__ = "[email protected]"
 
 
-# derived from https://docs.pytest.org/en/3.8.0/goodpractices.html
-class PyTest(TestCommand):
-    user_options = [("pytest-args=", "a", "Arguments to pass to pytest")]
-
-    def initialize_options(self):
-        TestCommand.initialize_options(self)
-        self.pytest_args = ""
-
-    def run_tests(self):
-        try:
-            import numpy
-            try:
-                # NumPy 1.14 changed repr output breaking our doctests,
-                # request the legacy 1.13 style
-                numpy.set_printoptions(legacy="1.13")
-            except TypeError:
-                # Old Numpy, output should be fine as it is :)
-                # TypeError: set_printoptions() got an unexpected
-                # keyword argument 'legacy'
-                pass
-        except ImportError:
-            numpy = None
-
-        import shlex
-
-        # import here, cause outside the eggs aren't loaded
-        import pytest
-        errno = pytest.main(shlex.split(self.pytest_args))
-        sys.exit(errno)
-
-
 long_description = """BIOM: Biological Observation Matrix
 http://www.biom-format.org
 
@@ -152,7 +120,6 @@ def run_tests(self):
                       'anndata': ["anndata"],
                       },
       classifiers=classifiers,
-      cmdclass={"pytest": PyTest},
       entry_points='''
           [console_scripts]
           biom=biom.cli:cli