update pre-commit hooks and apply linting checks (#242)

.pre-commit-config.yaml

@@ -4,7 +4,7 @@ default_language_version:
   python: python3.10
 repos:
   - repo: https://github.com/pre-commit/pre-commit-hooks
-    rev: v4.5.0
+    rev: v5.0.0
     hooks:
       - id: trailing-whitespace
       - id: end-of-file-fixer
@@ -16,40 +16,40 @@ repos:
     hooks:
       - id: poetry-check
   - repo: https://github.com/tox-dev/pyproject-fmt
-    rev: "2.2.4"
+    rev: "v2.5.0"
     hooks:
       - id: pyproject-fmt
   - repo: https://github.com/codespell-project/codespell
-    rev: v2.2.6
+    rev: v2.3.0
     hooks:
       - id: codespell
         exclude: >
           (?x)^(
-              .*\.lock|.*\.csv
+              .*\.lock|.*\.csv|.*\.cff
           )$
         additional_dependencies:
           - tomli
   - repo: https://github.com/executablebooks/mdformat
-    rev: 0.7.17
+    rev: 0.7.18
     hooks:
       - id: mdformat
         additional_dependencies:
           - mdformat-myst
           - mdformat-gfm
   - repo: https://github.com/adrienverge/yamllint
-    rev: v1.33.0
+    rev: v1.35.1
     hooks:
       - id: yamllint
   - repo: https://github.com/psf/black
-    rev: 23.12.1
+    rev: 24.10.0
     hooks:
       - id: black
   - repo: https://github.com/asottile/blacken-docs
-    rev: 1.16.0
+    rev: 1.19.1
     hooks:
       - id: blacken-docs
   - repo: https://github.com/PyCQA/bandit
-    rev: 1.7.6
+    rev: 1.7.10
     hooks:
       - id: bandit
         args: ["-c", "pyproject.toml"]
@@ -59,19 +59,19 @@ repos:
     hooks:
       - id: isort
   - repo: https://github.com/jendrikseipp/vulture
-    rev: v2.10
+    rev: v2.13
     hooks:
       - id: vulture
   - repo: https://github.com/pre-commit/mirrors-mypy
-    rev: v1.8.0
+    rev: v1.13.0
     hooks:
       - id: mypy
   - repo: https://github.com/citation-file-format/cffconvert
     rev: 5295f87c0e261da61a7b919fc754e3a77edd98a7
     hooks:
       - id: validate-cff
   - repo: https://github.com/PyCQA/pylint
-    rev: v3.0.3
+    rev: v3.3.1
     hooks:
       - id: pylint
         name: pylint

cytotable/sources.py

@@ -163,14 +163,17 @@ def _get_source_filepaths(
         for unique_source in set(source["source_path"].name for source in sources):
             grouped_sources[unique_source.capitalize()] = [
                 # case for files besides sqlite
-                source if source["source_path"].suffix.lower() != ".sqlite"
-                # if we have sqlite entries, update the source_path to the parent
-                # (the parent table database file) as grouped key name will now
-                # encapsulate the table name details.
-                else {
-                    "source_path": source["source_path"].parent,
-                    "table_name": source["table_name"],
-                }
+                (
+                    source
+                    if source["source_path"].suffix.lower() != ".sqlite"
+                    # if we have sqlite entries, update the source_path to the parent
+                    # (the parent table database file) as grouped key name will now
+                    # encapsulate the table name details.
+                    else {
+                        "source_path": source["source_path"].parent,
+                        "table_name": source["table_name"],
+                    }
+                )
                 for source in sources
                 # focus only on entries which include the unique_source name
                 if source["source_path"].name == unique_source

docs/source/code_of_conduct.md

@@ -2,7 +2,7 @@
 
 ## Our Pledge
 
-We as members, contributors, and leaders pledge to make participation in our community a harassment-free experience for everyone, regardless of age, body size, visible or invisible disability, ethnicity, sex characteristics, gender identity and expression, level of experience, education, socio-economic status, nationality, personal appearance, race, religion, or sexual identity and orientation.
+We as members, contributors, and leaders pledge to make participation in our community a harassment-free experience for everyone, regardless of age, body size, visible or invisible disability, ethnicity, sex characteristics, gender identity and expression, level of experience, education, socioeconomic status, nationality, personal appearance, race, religion, or sexual identity and orientation.
 
 We pledge to act and interact in ways that contribute to an open, welcoming, diverse, inclusive, and healthy community.
 

tests/data/in-carta/colas-lab/shrink_colas_lab_data_for_tests.py

@@ -50,7 +50,7 @@
         # as a pyarrow table then output to a new and
         # smaller csv for testing purposes.
 
-        output_filename = (
+        OUTPUT_FILENAME = (
             f"Test 0 Day{idx} Test Test_2024_Jan-0{idx+1}-{idx+12}-12-12_Test.csv"
         )
 
@@ -67,9 +67,11 @@
                 """
             ).arrow(),
             # output the filtered data as a CSV to a new location
-            output_file=f"{TARGET_DATA_DIR}/{output_filename}"
-            # For some files lowercase the first letter of the file
-            # as a simulation of the source data.
-            if idx < 3
-            else f"{TARGET_DATA_DIR}/{output_filename[0].lower() + output_filename[1:]}",
+            output_file=(
+                f"{TARGET_DATA_DIR}/{OUTPUT_FILENAME}"
+                # For some files lowercase the first letter of the file
+                # as a simulation of the source data.
+                if idx < 3
+                else f"{TARGET_DATA_DIR}/{OUTPUT_FILENAME[0].lower() + OUTPUT_FILENAME[1:]}"
+            ),
         )