Add Python 3.12 support

.github/workflows/ci.yaml

@@ -13,11 +13,11 @@ on:
 
 jobs:
   test:
-    runs-on: ubuntu-20.04
+    runs-on: ubuntu-22.04
     strategy:
       fail-fast: false
       matrix:
-        tox-env: [py38, py39, py310, py311, docs, linters, package]
+        tox-env: [py38, py39, py310, py311, py312, docs, linters, package]
         include:
           - tox-env: py38
             python-version: 3.8
@@ -27,15 +27,17 @@ jobs:
             python-version: "3.10"
           - tox-env: py311
             python-version: "3.11"
+          - tox-env: py312
+            python-version: "3.12"
           - tox-env: linters
-            python-version: 3.8
+            python-version: "3.11"
           - tox-env: package
-            python-version: 3.8
+            python-version: "3.11"
 
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v4
       - name: Set up Python ${{ matrix.python-version }}
-        uses: actions/setup-python@v2
+        uses: actions/setup-python@v5
         with:
           python-version: ${{ matrix.python-version }}
       - name: Install Dependencies
@@ -45,24 +47,24 @@ jobs:
         run: >
           tox -e ${{ matrix.tox-env }}
       - name: Upload coverage to Codecov
-        if: matrix.tox-env == 'py38' || matrix.tox-env == 'py39' || matrix.tox-env == 'py310' || matrix.tox-env == 'py311'
+        if: matrix.tox-env == 'py38' || matrix.tox-env == 'py39' || matrix.tox-env == 'py310' || matrix.tox-env == 'py311' || matrix.tox-env == 'py312'
         uses: codecov/codecov-action@v1
         with:
           file: .coverage
 
   build:
-    runs-on: ubuntu-20.04
+    runs-on: ubuntu-22.04
 
     needs: test
 
     if: "startsWith(github.ref, 'refs/tags')"
 
     steps:
-      - uses: actions/checkout@v1
-      - name: Set up Python 3.8
-        uses: actions/setup-python@v1
+      - uses: actions/checkout@v4
+      - name: Set up Python 3.11
+        uses: actions/setup-python@v5
         with:
-          python-version: 3.8
+          python-version: "3.11"
       - name: Install build
         run: python -m pip install --user build
       - name: Build a binary wheel and a source tarball

docs/CHANGELOG.rst

@@ -15,6 +15,7 @@ Added
 - Optionally show progress bar when uploading files
 - Add ``modified`` as read-only field to the ``AnnotationValue`` resource
 - Add md5 checksum after file is downloaded
+- Add support for Python3.12
 
 Fixed
 -----

docs/conf.py

@@ -48,4 +48,4 @@
 html_theme = 'sphinx_rtd_theme'
 
 # Example configuration for intersphinx: refer to the Python standard library.
-intersphinx_mapping = {'https://docs.python.org/': None}
+intersphinx_mapping = {'python': ('https://docs.python.org/3', None)}

docs/contributing.rst

@@ -30,7 +30,7 @@ change directory::
 
 Prepare Resolwe SDK for Python for development::
 
-    pip install -e .[docs,package,test]
+    pip install -e '.[docs,package,test]'
 
 .. note::
 

pyproject.toml

@@ -14,7 +14,7 @@ authors = [
 dynamic = ["version"]
 readme = "README.rst"
 license = {file = "LICENSE"}
-requires-python = ">=3.8, <3.12"
+requires-python = ">=3.8, <3.13"
 keywords = [
     "bio",
     "bioinformatics",
@@ -38,35 +38,35 @@ classifiers = [
     "Programming Language :: Python :: 3.9",
     "Programming Language :: Python :: 3.10",
     "Programming Language :: Python :: 3.11",
+    "Programming Language :: Python :: 3.12",
 ]
 dependencies = [
-    "aiohttp~=3.8.5",
-    "requests>=2.6.0",
+    "aiohttp~=3.9.3",
+    "requests",
     "urllib3>=2;python_version >= '3.10'",
     "slumber>=0.7.1",
     "wrapt",
-    "pytz>=2018.4",
-    "tzlocal>=1.5.1",
-    "pandas>=1.0.0",
+    "pytz",
+    "tzlocal",
+    "pandas",
     "tqdm",
     "openpyxl",
     "xlrd",
-    "boto3[crt]~=1.24",
-    "boto3-stubs[s3]~=1.24",
-    'importlib-metadata; python_version<"3.8"',
+    "boto3[crt]",
+    "boto3-stubs[s3]",
     "packaging",
 ]
 [project.optional-dependencies]
 docs = [
-    "sphinx~=5.2.3",
-    "sphinx_rtd_theme~=1.0.0",
+    "sphinx",
+    "sphinx_rtd_theme",
     # TODO: Consider using sphinx-pyproject in the future. At the time of this
     # writing the missing feature was disability of sphinx-pyproject to detect
     # dynamic project version
 ]
 package = [
-    "twine~=4.0.1",
-    "check-manifest>=0.48",
+    "twine",
+    "check-manifest",
     "build",
 ]
 test = [
@@ -86,7 +86,7 @@ documentation = "https://resdk.readthedocs.io/en/latest/"
 [tool.setuptools_scm]
 
 [tool.black]
-target-version = ["py38", "py39", "py310", "py311"]
+target-version = ["py38", "py39", "py310", "py311", "py312"]
 
 [tool.pydocstyle]
 add-select = "D404"

tox.ini

@@ -1,5 +1,5 @@
 [tox]
-envlist = py{38,39,310,311},docs,linters,package
+envlist = py{38,39,310,311,312},docs,linters,package
 skip_missing_interpreters = True
 minversion = 3.5.0
 isolated_build = true
@@ -8,12 +8,12 @@ isolated_build = true
 extras =
     docs: docs
     package: package
-    py{38,39,310,311},linters: test
+    py{38,39,310,311,312},linters: test
 # Run all command in environment to see their output even if one of the commands fail.
 ignore_errors = true
 commands =
     # Run tests.
-    py{38,39,310,311}: pytest --verbose --cov=resdk
+    py{38,39,310,311,312}: pytest --verbose --cov=resdk
 
     # Build documentation.
     docs: sphinx-build docs build/sphinx -a -E -W