Update Config Files

.gitignore

@@ -61,8 +61,7 @@ build/
 develop-eggs/
 dist/
 downloads/
-eggs/
-.eggs/
+.?eggs/
 lib/
 lib64/
 parts/
@@ -177,10 +176,10 @@ celerybeat.pid
 *.sage.py
 
 # Virtual Python environments
-*env*/
-*venv*/
-*ENV*/
-*VENV*/
+.?ENV*/
+.?env*/
+.?VENV*/
+.?venv*/
 
 # Spyder project settings
 .spyderproject

.pre-commit-config.yaml

@@ -10,7 +10,7 @@
 # Now pre-commit will run automatically on every `git commit`.
 # Bypass pre-commit and commit-msg hook with `git commit --no-verify`.
 
-minimum_pre_commit_version: "2.0"
+minimum_pre_commit_version: "3.0"
 
 default_language_version:
   python: "python3"
@@ -107,7 +107,7 @@ repos:
       - id: "check-pre-commit-ci-config"
 
   - repo: "https://github.com/python-jsonschema/check-jsonschema"
-    rev: "0.20.0"
+    rev: "0.21.0"
     hooks:
       # Validate Dependabot Config (v2) against the schema provided by
       # SchemaStore.
@@ -144,7 +144,7 @@ repos:
       - id: "rst-inline-touching-normal"
 
   - repo: "https://github.com/PyCQA/isort"
-    rev: "5.11.4"
+    rev: "5.12.0"
     hooks:
       # Sort import statements with isort
       - id: "isort"
@@ -168,7 +168,7 @@ repos:
     # to XX but somehow the pre-commit hook has version YY when
     # specifying the hook version without the prefix.  See
     # https://github.com/psf/black/issues/2493#issuecomment-1081987650
-    rev: "refs/tags/22.12.0:refs/tags/22.12.0"
+    rev: "refs/tags/23.1.0:refs/tags/23.1.0"
     hooks:
       # Format Python code with black.
       - id: "black"
@@ -181,7 +181,7 @@ repos:
           - "--color"
 
   - repo: "https://github.com/PyCQA/flake8"
-    rev: "5.0.4"
+    rev: "6.0.0"
     hooks:
       # Lint Python code with Flake8.
       - id: "flake8"

.readthedocs.yaml

@@ -6,7 +6,7 @@
 version: 2
 
 build:
-  os: ubuntu-22.04
+  os: "ubuntu-22.04"
   tools:
     python: "3.10"
 

.vscode/settings.json

@@ -82,70 +82,49 @@
         79,
     ],
     "editor.tabSize": 4,
+    "explorer.excludeGitIgnore": true,
     "files.insertFinalNewline": true,
     "files.encoding": "utf8",
-    "files.exclude": {
+    "files.trimFinalNewlines": true,
+    "files.trimTrailingWhitespace": true,
+    "files.watcherExclude": {
+        // Byte-compiled / optimized / DLL files.
         "**/__pycache__/": true,
-        "**/__pypackages__/": true,
-        "**/_sphinx_autosummary*/": true,
-        "**/.cache/": true,
-        "**/.eggs/": true,
-        "**/.ENV*/": true,
-        "**/.env*/": true,
-        "**/.hypothesis/": true,
-        "**/.ipynb_checkpoints": true,
-        "**/.mypy_cache/": true,
-        "**/.pybuilder/": true,
-        "**/.pytest_cache/": true,
-        "**/.Python": true,
-        "**/.VENV*/": true,
-        "**/.venv*/": true,
-        "**/.webassets-cache/": true,
-        "**/*.egg": true,
-        "**/*.egg-info/": true,
         "**/*.py[cod]": true,
         "**/*$py.class": true,
+        // Distribution / packaging
+        "**/.Python": true,
         "**/develop-eggs/": true,
         "**/dist/": true,
-        "**/eggs/": true,
-        "**/.installed.cfg": true,
+        "**/.?eggs/": true,
         "**/lib64/": true,
-        "**/python-wheels/": true,
         "**/sdist/": true,
         "**/wheels/": true,
-    },
-    "files.trimFinalNewlines": true,
-    "files.trimTrailingWhitespace": true,
-    "files.watcherExclude": {
-        "**/__pycache__/": true,
-        "**/__pypackages__/": true,
-        "**/_sphinx_autosummary*/": true,
+        "**/python-wheels/": true,
+        "**/*.egg-info/": true,
+        "**/.installed.cfg": true,
+        "**/*.egg": true,
+        // Unit test / coverage reports.
         "**/.cache/": true,
-        "**/.eggs/": true,
-        "**/.ENV*/": true,
-        "**/.env*/": true,
         "**/.hypothesis/": true,
-        "**/.ipynb_checkpoints": true,
-        "**/.mypy_cache/": true,
-        "**/.pybuilder/": true,
         "**/.pytest_cache/": true,
-        "**/.Python": true,
-        "**/.VENV*/": true,
-        "**/.venv*/": true,
+        // Flask stuff.
         "**/.webassets-cache/": true,
-        "**/*.egg": true,
-        "**/*.egg-info/": true,
-        "**/*.py[cod]": true,
-        "**/*$py.class": true,
-        "**/build/": true,
-        "**/develop-eggs/": true,
-        "**/dist/": true,
-        "**/eggs/": true,
-        "**/.installed.cfg": true,
-        "**/lib64/": true,
-        "**/python-wheels/": true,
-        "**/sdist/": true,
-        "**/wheels/": true,
+        // Sphinx documentation.
+        "**/_sphinx_autosummary*/": true,
+        // PyBuilder.
+        "**/.pybuilder/": true,
+        // Jupyter Notebook.
+        "**/.ipynb_checkpoints": true,
+        // PEP 582.
+        "**/__pypackages__/": true,
+        // Virtual Python environments.
+        "**/.?ENV*/": true,
+        "**/.?env*/": true,
+        "**/.?VENV*/": true,
+        "**/.?venv*/": true,
+        // mypy.
+        "**/.mypy_cache/": true,
     },
     "git.branchProtection": [
         "main",

pyproject.toml

@@ -10,7 +10,7 @@ name = "hpcss"
 version = "0.1.0"
 description = "Slurm scripts to run and analyze MD simulations on HPC clusters"
 readme = "README.rst"
-requires-python = ">=3.8, <3.11"
+requires-python = ">=3.8, <3.12"
 license = {file = "LICENSE.txt"}
 authors = [
     {name = "Andreas Thum", email = "coding.andthum@e.mail.de"},
@@ -69,9 +69,8 @@ discussions = "https://github.com/andthum/hpc_submit_scripts/discussions"
 skips = ["B404", "B603"]
 
 [tool.black]
-required-version = 22
+required-version = 23
 line-length = 79
-target-version = ["py39"]
 
 [tool.isort]
 # profile should go on top so that it does not overwrite other settings.

requirements-dev.txt

@@ -6,8 +6,8 @@
 # `.flake8`!
 
 bandit >=1.0, <2.0
-black >=22.0, <23.0
-flake8 >=5.0, <6.0
+black >=23.0, <24.0
+flake8 >=6.0, <7.0
 flake8-bandit >=4.0, <5.0
 flake8-bugbear >=23.0, <24.0
 flake8-builtins >=2.0, <3.0
@@ -19,7 +19,7 @@ flake8-pytest-style >=1.0, <2.0
 flake8-rst-docstrings >=0.2.6, <1.0
 isort >=5.0, <6.0
 pep8-naming >=0.1, <1.0
-pre-commit >=2.0, <3.0
+pre-commit >=3.0, <4.0
 pytest >=7.0, <8.0
 shellcheck-py >=0.1, <1.0
 shfmt-py >=3.0, <4.0