Update to python 3.12; skip kinfitr tests if not installed

.github/workflows/constraints.txt

@@ -1,5 +1,5 @@
-pip==23.2.1
-nox==2023.4.22
+pip==24.0
+nox==2024.4.15
 nox-poetry==1.0.3
-poetry==1.5.1
-virtualenv==20.24.5
+poetry==1.8.2
+virtualenv==20.25.3

.github/workflows/labeler.yml

@@ -10,7 +10,7 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - name: Check out the repository
-        uses: actions/checkout@v3
+        uses: actions/checkout@v4
 
       - name: Run Labeler
         uses: crazy-max/[email protected]

.github/workflows/release.yml

@@ -12,14 +12,14 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - name: Check out the repository
-        uses: actions/checkout@v3
+        uses: actions/checkout@v4
         with:
           fetch-depth: 2
 
       - name: Set up Python
-        uses: actions/setup-python@v4
+        uses: actions/setup-python@v5
         with:
-          python-version: "3.11"
+          python-version: "3.12"
 
       - name: Upgrade pip
         run: |
@@ -57,21 +57,21 @@ jobs:
 
       - name: Publish package on PyPI
         if: steps.check-version.outputs.tag
-        uses: pypa/[email protected].10
+        uses: pypa/[email protected].14
         with:
           user: __token__
           password: ${{ secrets.PYPI_TOKEN }}
 
       - name: Publish package on TestPyPI
         if: ! steps.check-version.outputs.tag
-        uses: pypa/[email protected].10
+        uses: pypa/[email protected].14
         with:
           user: __token__
           password: ${{ secrets.TEST_PYPI_TOKEN }}
           repository-url: https://test.pypi.org/legacy/
 
       - name: Publish the release notes
-        uses: release-drafter/release-drafter@v5.23.0
+        uses: release-drafter/release-drafter@v6.0.0
         with:
           publish: ${{ steps.check-version.outputs.tag != '' }}
           tag: ${{ steps.check-version.outputs.tag }}

.github/workflows/tests.yml

@@ -12,13 +12,16 @@ jobs:
       fail-fast: false
       matrix:
         include:
-          - { python: "3.11", os: "ubuntu-latest", session: "pre-commit" }
-          - { python: "3.11", os: "ubuntu-latest", session: "safety" }
+          - { python: "3.12", os: "ubuntu-latest", session: "pre-commit" }
+          - { python: "3.12", os: "ubuntu-latest", session: "safety" }
+          - { python: "3.12", os: "ubuntu-latest", session: "mypy" }
+          - { python: "3.12", os: "ubuntu-latest", session: "tests" }
+          - { python: "3.12", os: "ubuntu-latest", session: "typeguard" }
+          - { python: "3.12", os: "ubuntu-latest", session: "xdoctest" }
+          - { python: "3.12", os: "ubuntu-latest", session: "docs-build" }
           - { python: "3.11", os: "ubuntu-latest", session: "mypy" }
           - { python: "3.11", os: "ubuntu-latest", session: "tests" }
-          - { python: "3.11", os: "ubuntu-latest", session: "typeguard" }
           - { python: "3.11", os: "ubuntu-latest", session: "xdoctest" }
-          - { python: "3.11", os: "ubuntu-latest", session: "docs-build" }
 
     env:
       NOXSESSION: ${{ matrix.session }}
@@ -27,7 +30,7 @@ jobs:
 
     steps:
       - name: Check out the repository
-        uses: actions/checkout@v3
+        uses: actions/checkout@v4
 
       - name: Install R
         uses: r-lib/actions/setup-r@v2
@@ -39,7 +42,7 @@ jobs:
             github::mathesong/kinfitr
 
       - name: Set up Python ${{ matrix.python }}
-        uses: actions/setup-python@v4
+        uses: actions/setup-python@v5
         with:
           python-version: ${{ matrix.python }}
 
@@ -84,7 +87,7 @@ jobs:
           print("::set-output name=result::{}".format(result))
 
       - name: Restore pre-commit cache
-        uses: actions/cache@v3
+        uses: actions/cache@v4
         if: matrix.session == 'pre-commit'
         with:
           path: ~/.cache/pre-commit
@@ -98,14 +101,14 @@ jobs:
 
       - name: Upload coverage data
         if: always() && matrix.session == 'tests'
-        uses: "actions/upload-artifact@v3"
+        uses: "actions/upload-artifact@v4"
         with:
           name: coverage-data
           path: ".coverage.*"
 
       - name: Upload documentation
         if: matrix.session == 'docs-build'
-        uses: actions/upload-artifact@v3
+        uses: actions/upload-artifact@v4
         with:
           name: docs
           path: docs/_build
@@ -115,12 +118,12 @@ jobs:
     needs: tests
     steps:
       - name: Check out the repository
-        uses: actions/checkout@v3
+        uses: actions/checkout@v4
 
       - name: Set up Python
-        uses: actions/setup-python@v4
+        uses: actions/setup-python@v5
         with:
-          python-version: "3.11"
+          python-version: "3.12"
 
       - name: Upgrade pip
         run: |
@@ -139,7 +142,7 @@ jobs:
           nox --version
 
       - name: Download coverage data
-        uses: actions/download-artifact@v3
+        uses: actions/download-artifact@v4
         with:
           name: coverage-data
 
@@ -152,4 +155,4 @@ jobs:
           nox --session=coverage -- xml
 
       - name: Upload coverage report
-        uses: codecov/codecov-action@v3
+        uses: codecov/codecov-action@v4

docs/conf.py

@@ -1,4 +1,5 @@
 """Sphinx configuration."""
+
 project = "Dynamic PET"
 author = "Murat Bilgel"
 copyright = "2023, Murat Bilgel"

docs/requirements.txt

@@ -1,4 +1,4 @@
-furo==2023.5.20
-sphinx==7.1.1
+furo>=2023.5.20
+sphinx>=7.1.1
 sphinx-click
 myst_parser==2.0.0

noxfile.py

@@ -1,4 +1,5 @@
 """Nox sessions."""
+
 import os
 import shlex
 import shutil
@@ -23,7 +24,7 @@
 
 
 package = "dynamicpet"
-python_versions = ["3.11"]
+python_versions = ["3.12", "3.11"]
 nox.needs_version = ">= 2021.6.6"
 nox.options.sessions = (
     "pre-commit",