Minor fixes (#119)

.pre-commit-config.yaml

@@ -2,7 +2,7 @@ exclude: '^docs/conf.py'
 
 repos:
 - repo: https://github.com/pre-commit/pre-commit-hooks
-  rev: v4.4.0
+  rev: v4.6.0
   hooks:
   - id: trailing-whitespace
   - id: check-added-large-files
@@ -40,13 +40,13 @@ repos:
   hooks:
   - id: seed-isort-config
 - repo: https://github.com/pycqa/isort
-  rev: 5.12.0
+  rev: 5.13.2
   hooks:
   - id: isort
     args: ["--profile", "black", "--filter-files"]
 
 - repo: https://github.com/ambv/black
-  rev: 23.7.0
+  rev: 24.8.0
   hooks:
     - id: black
       language_version: python3.10
@@ -59,7 +59,7 @@ repos:
 #     additional_dependencies: [black]
 
 - repo: https://github.com/PyCQA/flake8
-  rev: 6.1.0
+  rev: 7.1.1
   hooks:
   - id: flake8
     args:

setup.cfg

@@ -49,6 +49,7 @@ install_requires =
     frictionless[pandas,visidata]
     lxml
     pandas>=1.5.3
+    numpy<2.0.0
     pathos
     webcolors
     tqdm

src/ms3/bs4_parser.py

@@ -1476,7 +1476,7 @@ def get_raw_labels(self):
             columns={v: k for k, v in cols.items() if v in df.columns}, inplace=True
         )
         if "harmony_layer" in df.columns:
-            df.harmony_layer.fillna(0, inplace=True)
+            df.harmony_layer = df.harmony_layer.fillna(0)
         columns = [c for c in main_cols if c in df.columns]
         additional_cols = {
             c: c[8:]

src/ms3/expand_dcml.py

@@ -624,9 +624,9 @@ def propagate_keys(
             logger.info(
                 "Dataframe needs to have a 'mc' column. Ignoring volta_structure."
             )
-            df[localkey].ffill(inplace=True)
+            df[localkey] = df[localkey].ffill()
     else:
-        df[localkey].ffill(inplace=True)
+        df[localkey] = df[localkey].ffill()
 
     if add_bool:
         gm = f"{globalkey}_is_minor"