Merge pull request #190 from LUMC/pytest8.0

Add 3.12 python support, drop 3.7 support

.github/workflows/ci.yml

@@ -14,7 +14,7 @@ jobs:
     strategy:
       matrix:
         python-version:
-          - "3.7"
+          - "3.8"
     steps:
       - uses: actions/checkout@v2.3.4
       - name: Set up Python ${{ matrix.python-version }}
@@ -42,11 +42,11 @@ jobs:
     strategy:
       matrix:
         python-version:
-          - "3.7"
           - "3.8"
           - "3.9"
           - "3.10"
           - "3.11"
+          - "3.12"
     steps:
       - uses: actions/checkout@v2.3.4
       - name: Set up Python ${{ matrix.python-version }}
@@ -64,7 +64,7 @@ jobs:
     runs-on: ubuntu-latest
     strategy:
       matrix:
-        python-version: ["3.7"]
+        python-version: ["3.11"]
         test-program: [snakemake, miniwdl]
     steps:
       - uses: actions/checkout@v2.3.4

HISTORY.rst

@@ -2,11 +2,6 @@
 Changelog
 ==========
 
-version 2.0.2
----------------------------
-+ Fixed a bug where pytest 8.1+ would raise a ``PluginValidationError`` because
-  the hook ``pytest_collect_file()`` has finally dropped the deprecated
-  argument ``path`` from its specification.
 
 .. Newest changes should be on top.
 
@@ -15,6 +10,11 @@ version 2.0.2
 
 version 2.1.0-dev
 ---------------------------
++ Python version 3.7 support is dropped because it is deprecated. Python
+  version 3.12 was added.
++ Fixed a bug where pytest 8.1+ would raise a ``PluginValidationError`` because
+  the hook ``pytest_collect_file()`` has finally dropped the deprecated
+  argument ``path`` from its specification.
 + Add extract_md5sum check on uncompressed contents of compressed output files.
   Gzipped files contain a timestamp which makes it hard to directly compare the
   md5sums of gzipped files.

setup.py

@@ -39,18 +39,18 @@
     classifiers=[
         "Programming Language :: Python :: 3 :: Only",
         "Programming Language :: Python :: 3",
-        "Programming Language :: Python :: 3.7",
         "Programming Language :: Python :: 3.8",
         "Programming Language :: Python :: 3.9",
         "Programming Language :: Python :: 3.10",
         "Programming Language :: Python :: 3.11",
+        "Programming Language :: Python :: 3.12",
         "Development Status :: 5 - Production/Stable",
         "License :: OSI Approved :: "
         "GNU Affero General Public License v3 or later (AGPLv3+)",
         "Framework :: Pytest",
     ],
-    # Because we cannot test anymore on Python 3.6.
-    python_requires=">=3.7",
+    # Because we cannot test anymore on Python 3.8.
+    python_requires=">=3.8",
     install_requires=[
         "pytest>=7.0.0",  # To use pathlib Path's in pytest
         "pyyaml",

src/pytest_workflow/plugin.py

@@ -121,7 +121,8 @@ def pytest_collect_file(file_path, parent):
     """Collection hook
     This collects the yaml files that start with "test" and end with
     .yaml or .yml"""
-    if file_path.suffix in [".yml", ".yaml"] and file_path.name.startswith("test"):
+    if (file_path.suffix in [".yml", ".yaml"] and
+            file_path.name.startswith("test")):
         return YamlFile.from_parent(parent, path=file_path)
     return None
 

tests/functional/simple_snakefile_test_cases.yml

@@ -1,26 +1,26 @@
 - name: test-dry-run
-  command: snakemake -n -r -p -s SimpleSnakefile --config N_LINES_TO_READ=1
+  command: snakemake -n -p -s SimpleSnakefile --config N_LINES_TO_READ=1
 - name: test-config-missing
-  command: snakemake -n -r -p -s SimpleSnakefile
+  command: snakemake -n -p -s SimpleSnakefile
   exit_code: 1
-  stdout:
+  stderr:
     contains:
       - "You must set --config N_LINES_TO_READ=<a value>."
 - name: test-config-wrong-type
-  command: snakemake -n -r -p -s SimpleSnakefile --config N_LINES_TO_READ=one
+  command: snakemake -n -p -s SimpleSnakefile --config N_LINES_TO_READ=one
   exit_code: 1
-  stdout:
+  stderr:
     contains:
       - "N_LINES_TO_READ must be an integer."
 - name: test-config-invalid-value
-  command: snakemake -n -r -p -s SimpleSnakefile --config N_LINES_TO_READ=-1
+  command: snakemake -n -p -s SimpleSnakefile --config N_LINES_TO_READ=-1
   exit_code: 1
-  stdout:
+  stderr:
     contains:
       - "N_LINES_TO_READ must at least be 1."
 - name: test-snakemake-run
   command: >-
-    snakemake --cores 1 -r -p -s SimpleSnakefile --config N_LINES_TO_READ=500
+    snakemake --cores 1 -p -s SimpleSnakefile --config N_LINES_TO_READ=500
   files:
     - path: rand/0.txt
     - path: rand/1.txt