Drop 3.8 and 3.9, default to 3.10 for most CI tasks

.github/workflows/build_wheel.yml

@@ -42,7 +42,7 @@ jobs:
       - uses: actions/setup-python@v4
         name: Install Python
         with:
-          python-version: '3.9'
+          python-version: '3.10'
 
       - name: Build wheels
         uses: pypa/[email protected]

.github/workflows/build_wheel_all_archs.yml

@@ -42,7 +42,7 @@ jobs:
       - uses: actions/setup-python@v4
         name: Install Python
         with:
-          python-version: '3.9'
+          python-version: '3.10'
 
       # Added due to weird error when building inside docker container
       # for other platforms...

.github/workflows/dev_envs.yml

@@ -45,7 +45,7 @@ jobs:
       uses: conda-incubator/setup-miniconda@3b0f2504dd76ef23b6d31f291f4913fb60ab5ff3
       with:
         auto-update-conda: true
-        python-version: 3.9
+        python-version: "3.10"
         channels: conda-forge,bioconda
         miniforge-variant: Mambaforge
         miniforge-version: latest
@@ -59,6 +59,6 @@ jobs:
       shell: bash -l {0}
       run: mamba install 'tox>=3.27,<4' tox-conda rust git compilers pandoc
 
-    - name: run tests for 3.9
+    - name: run tests for 3.10
       shell: bash -l {0}
-      run: tox -e py39
+      run: tox -e py310

.github/workflows/python.yml

@@ -14,7 +14,7 @@ jobs:
     strategy:
       matrix:
         os: [ubuntu-22.04, macos-latest]
-        py: ["3.11", "3.10", "3.9", "3.8"]
+        py: ["3.12", "3.11", "3.10"]
       fail-fast: false
 
     steps:
@@ -49,14 +49,14 @@ jobs:
         uses: r-lib/actions/setup-pandoc@v2
 
       - name: Set up IPFS
-        if: startsWith(runner.os, 'Linux') && (matrix.py == '3.9')
+        if: startsWith(runner.os, 'Linux') && (matrix.py == '3.10')
         uses: ibnesayeed/setup-ipfs@master
         with:
           ipfs_version: 0.6
           run_daemon: true
 
       - name: Start Redis
-        if: startsWith(runner.os, 'Linux') && (matrix.py == '3.9')
+        if: startsWith(runner.os, 'Linux') && (matrix.py == '3.10')
         uses: supercharge/[email protected]
         with:
           redis-version: 6

README.md

@@ -61,7 +61,7 @@ A quickstart tutorial [is available](https://sourmash.readthedocs.io/en/latest/t
 
 ### Requirements
 
-sourmash runs under Python 3.7 and later.  The base
+sourmash runs under Python 3.10 and later.  The base
 requirements are screed, cffi, numpy, matplotlib, and scipy.  Conda
 (see below) will install everything necessary, and is our recommended
 installation method.

binder/environment.yml

@@ -3,8 +3,8 @@ channels:
   - bioconda
   - defaults
 dependencies:
-  - python>=3.9
-  - sourmash>=4.8.2
+  - python>=3.10
+  - sourmash>=4.8.4
   - screed
   - matplotlib
   - pandas

doc/developer.md

@@ -10,7 +10,7 @@ You can get the latest development branch with:
 ```
 git clone https://github.com/sourmash-bio/sourmash.git
 ```
-sourmash runs under Python 3.8 and later.
+sourmash runs under Python 3.10 and later.
 
 We recommend using `conda` or `Nix` for setting up an environment for developing
 new features, running tests and code quality checks.
@@ -87,7 +87,7 @@ running tests and checks during development.
 `tox -l` lists available tasks.
 
 You can run tests by invoking `make test` in the sourmash directory;
-`tox -e py39` will run the Python tests with Python 3.9,
+`tox -e py310` will run the Python tests with Python 3.10,
 and `cargo test` will run the Rust tests.
 
 ## Adding new changes

doc/requirements.md

@@ -11,7 +11,7 @@ in a second or so on a rather slow 2016 Mac laptop.
 MinHash sketches and signatures are quite small on disk.
 
 sourmash should run with no modification on Linux and Mac OS X,
-under Python 3.8 and later.  Please see [the development repository README][0]
+under Python 3.10 and later.  Please see [the development repository README][0]
 for
 information on source code, tests, and continuous integration.
 

doc/runtime.txt

@@ -1 +1 @@
-3.7
+3.10

doc/support.md

@@ -101,9 +101,9 @@ and our intent is that it will support as-yet unreleased versions of Python 3.x
 (e.g. 3.10) moving forward.
 
 For future versions of sourmash, we plan to follow the
-[Numpy NEP 29](https://numpy.org/neps/nep-0029-deprecation_policy.html)
+[Scientific Python SPEC 0](https://scientific-python.org/specs/spec-0000/)
 proposal for Python version support. For example, this
-would mean that we would drop support for Python 3.8 on April 14,
+means that we dropped support for Python 3.9 on October 10,
 2023.
 
 ### Rust API

flake.nix

@@ -93,9 +93,9 @@
 
             git
             stdenv.cc.cc.lib
+            (python312.withPackages (ps: with ps; [ virtualenv ]))
             (python311.withPackages (ps: with ps; [ virtualenv tox cffi ]))
             (python310.withPackages (ps: with ps; [ virtualenv ]))
-            (python39.withPackages (ps: with ps; [ virtualenv ]))
 
             rust-cbindgen
             maturin

pyproject.toml

@@ -64,8 +64,8 @@ classifiers = [
   "Operating System :: POSIX :: Linux",
   "Operating System :: MacOS :: MacOS X",
   "Programming Language :: Rust",
-  "Programming Language :: Python :: 3.8",
-  "Programming Language :: Python :: 3.9",
+  "Programming Language :: Python :: 3.12",
+  "Programming Language :: Python :: 3.11",
   "Programming Language :: Python :: 3.10",
   "Topic :: Scientific/Engineering :: Bio-Informatics",
 ]
@@ -79,10 +79,9 @@ dependencies = [
   "deprecation>=2.0.6",
   "cachetools>=4,<6",
   "bitstring>=3.1.9,<5",
-  "importlib_metadata>=3.6;python_version<'3.10'"
 ]
 
-requires-python = ">=3.8"
+requires-python = ">=3.10"
 
 [metadata]
 license = { text = "BSD 3-Clause License" }
@@ -164,7 +163,7 @@ line_length = 88
 known_first_party = ["sourmash"]
 
 [tool.cibuildwheel]
-build = "cp39-*"
+build = "cp310-*"
 skip = "*-win32 *-manylinux_i686 *-musllinux_ppc64le *-musllinux_s390x"
 before-all = [
   "curl https://sh.rustup.rs -sSf | sh -s -- -y --default-toolchain=stable",

tests/sourmash_tst_utils.py

@@ -13,14 +13,6 @@
 from importlib import resources
 from importlib.metadata import entry_points
 
-# Remove when we drop support for 3.8
-if sys.version_info < (3, 9):
-    import importlib_resources as resources
-
-# Remove when we drop support for 3.9
-if sys.version_info < (3, 10):
-    from importlib_metadata import entry_points
-
 
 SIG_FILES = [os.path.join('demo', f) for f in (
   "SRR2060939_1.sig", "SRR2060939_2.sig", "SRR2241509_1.sig",

tox.ini

@@ -1,12 +1,11 @@
 [tox]
 env_list =
-  py310,
   py311,
-  py39,
+  py312,
+  py310,
   coverage,
   docs,
   package_description
-  py38,
   fix_lint,
   hypothesis,
   khmer,
@@ -67,7 +66,7 @@ commands = pytest \
            {posargs:.}
 
 [testenv:khmer]
-basepython = python3.8
+basepython = python3.10
 deps =
   khmer
 commands = pytest \
@@ -79,7 +78,7 @@ commands = pytest \
            {posargs:.}
 
 [testenv:khmer_master]
-basepython = python3.8
+basepython = python3.10
 deps =
   -e git+https://github.com/dib-lab/khmer.git\#egg=khmer
 commands = pytest \
@@ -113,7 +112,7 @@ commands = sphinx-build -d "{toxworkdir}/docs_doctree" doc "{toxworkdir}/docs_ou
 
 [testenv:package_description]
 description = check that the long description is valid
-basepython = python3.8
+basepython = python3.10
 deps = twine >= 1.12.1
        # TODO installing readme-renderer[md] should not be necessary
        readme-renderer[md] >= 24.0
@@ -126,7 +125,7 @@ commands = pip wheel -w {envtmpdir}/build --no-deps .
 
 [testenv:mypy]
 description = run mypy checker
-basepython = python3.8
+basepython = python3.10
 pass_env = {[testenv]pass_env}
           # without PROGRAMDATA cloning using git for Windows will fail with an `error setting certificate verify locations` error
           PROGRAMDATA
@@ -135,7 +134,7 @@ commands = mypy src/sourmash
 
 [testenv:fix_lint]
 description = format the code base to adhere to our styles, and complain about what we cannot do automatically
-basepython = python3.8
+basepython = python3.10
 pass_env = {[testenv]pass_env}
           # without PROGRAMDATA cloning using git for Windows will fail with an `error setting certificate verify locations` error
           PROGRAMDATA
@@ -161,7 +160,7 @@ commands = coverage combine
            coverage xml -i -o {toxworkdir}/coverage.xml
            coverage html -i -d {toxworkdir}/htmlcov
            diff-cover --compare-branch {env:DIFF_AGAINST:origin/latest} {toxworkdir}/coverage.xml
-depends = py39, py38, py37, pypy3
+depends = py312, py311, py310, pypy3
 parallel_show_output = True
 
 [testenv:X]
@@ -198,8 +197,7 @@ source = src/sourmash/
 python =
   3.10: py310, docs, package_description, coverage
   3.11: py311, coverage
-  3.9: py39, coverage
-  3.8: py38, coverage
+  3.12: py312, coverage
 
 [flake8]
 max-complexity = 22