Pre Commit update w/ docs update

.pre-commit-config.yaml

@@ -1,22 +1,29 @@
 repos:
   - repo: https://github.com/pre-commit/pre-commit-hooks
-    rev: v4.4.0  # this is optional, use `pre-commit autoupdate` to get the latest rev!
+    rev: v5.0.0
     hooks:
-    -   id: check-yaml
-    -   id: end-of-file-fixer
-    -   id: trailing-whitespace
+      - id: check-yaml
+      - id: end-of-file-fixer
+      - id: trailing-whitespace
 
-  - repo: local
+  - repo: https://github.com/astral-sh/ruff-pre-commit
+    rev: v0.9.10
     hooks:
       - id: ruff
-        name: ruff
-        entry: python3 -m ruff check ./src
+        args: [ --fix ]
+
+  - repo: local
+    hooks:
+      - id: pylint
+        name: pylint
+        entry: pylint --disable=all -e W0311 -e C0303 --jobs=0 --indent-string='  ' --recursive=y ./src
         language: system
+        types: [python]
         always_run: true
         pass_filenames: false
       - id: tests
         name: tests
-        entry: pytest tests
+        entry: bash -c "PYTHONPATH=src pytest tests/"
         language: system
-        always_run: false
+        always_run: true
         pass_filenames: false

LICENSE

@@ -1,2 +1,2 @@
 YEAR: 2024
-COPYRIGHT HOLDER:  Ryan Duecker
+COPYRIGHT HOLDER:  Ryan Duecker

docs/Makefile

@@ -17,4 +17,4 @@ help:
 # Catch-all target: route all unknown targets to Sphinx using the new
 # "make mode" option.  $(O) is meant as a shortcut for $(SPHINXOPTS).
 %: Makefile
-	@$(SPHINXBUILD) -M $@ "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)
+	@$(SPHINXBUILD) -M $@ "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)

docs/source/conf.py

@@ -10,7 +10,7 @@
 project = 'PySiMMMulator'
 copyright = '2024, Ryan Duecker'
 author = 'Ryan Duecker'
-release = pysimmmulator.__version__ 
+release = pysimmmulator.__version__
 
 # -- General configuration ---------------------------------------------------
 # https://www.sphinx-doc.org/en/master/usage/configuration.html#general-configuration
@@ -26,4 +26,4 @@
 # https://www.sphinx-doc.org/en/master/usage/configuration.html#options-for-html-output
 
 html_theme = 'sphinx_rtd_theme'
-html_static_path = ['_static']
+html_static_path = ['_static']

docs/source/study.rst

@@ -7,4 +7,3 @@ Studies
 .. automodule:: pysimmmulator.study
     :members:
     :undoc-members:
-

logging.conf

@@ -24,4 +24,4 @@ formatter=pysimmmulatorFormatter
 args=(sys.stdout,)
 
 [formatter_pysimmmulatorFormatter]
-format=%(asctime)s - %(name)s - %(levelname)s - %(message)s
+format=%(asctime)s - %(name)s - %(levelname)s - %(message)s

src/pysimmmulator/simulate.py

@@ -602,4 +602,3 @@ def run(self, config: dict, runs: int, sensitivity_config: dict = None) -> None:
       self.stash_outputs(result=result)
       logger.info(f"{run + 1}/{runs} completed")
     logger.info(f"{runs} runs complete and stored")
-

tests/test_edge_cases.py

@@ -175,4 +175,3 @@ def test_reproducibility():
 
     pd.testing.assert_frame_equal(result1.df, result2.df)
     assert result1.channel_roi == result2.channel_roi
-