Require Python 3.9 (#200)

... and fix some related tox/flake issues

Author: dweindl

.flake8

@@ -4,11 +4,12 @@ extend-ignore =
     F403
     F405
 exclude =
-    build
-    dist
-    doc
-    env
-    venv
-    example
-    tmp
-    _*
+    build,
+    dist,
+    doc,
+    env,
+    venv,
+    example,
+    tmp,
+    _*,
+    .tox,

.github/workflows/ci_tests.yml

@@ -11,7 +11,7 @@ jobs:
     strategy:
       matrix:
         platform: [windows-latest, macos-latest, ubuntu-latest]
-        python-version: ["3.8", "3.11"]
+        python-version: ["3.9", "3.11"]
     runs-on: ${{ matrix.platform }}
 
     steps:

.github/workflows/deploy.yml

@@ -14,7 +14,7 @@ jobs:
     - name: Set up python
       uses: actions/setup-python@v4
       with:
-        python-version: 3.8
+        python-version: 3.11
     - name: Install dependencies
       run: |
         python -m pip install --upgrade pip

.readthedocs.yaml

@@ -7,9 +7,12 @@ sphinx:
    configuration: doc/conf.py
    fail_on_warning: true
 
+build:
+  os: "ubuntu-22.04"
+  tools:
+    python: "3.9"
 
 python:
-   version: 3.8
    install:
    - method: pip
      path: .

setup.py

@@ -28,9 +28,9 @@ def absolute_links(txt):
     return txt
 
 
-# Python version check. We need >= 3.6 due to e.g. f-strings
-if sys.version_info < (3, 8, 0):
-    sys.exit("PEtab requires at least Python version 3.8")
+# Python version check
+if sys.version_info < (3, 9, 0):
+    sys.exit("PEtab requires at least Python version 3.9")
 
 # read version from file
 __version__ = ""
@@ -67,7 +67,7 @@ def absolute_links(txt):
         "jsonschema",
     ],
     include_package_data=True,
-    python_requires=">=3.8.0",
+    python_requires=">=3.9.0",
     entry_points=ENTRY_POINTS,
     extras_require={
         "tests": [

tox.ini

@@ -1,4 +1,6 @@
 [tox]
+envlist = quality,unit
+isolated_build = True
 
 [testenv]
 
@@ -12,7 +14,7 @@ description =
 [testenv:unit]
 extras = tests,reports,combine,vis
 commands =
-  pytest --cov=petab --cov-report=xml --cov-append \
+  python -m pytest --cov=petab --cov-report=xml --cov-append \
     tests
 description =
   Basic tests