Bump codecov/codecov-action from 5 to 6

.github/workflows/pipeline.yml

@@ -10,7 +10,7 @@ jobs:
     runs-on: ubuntu-latest
     strategy:
       matrix:
-        python-version: ["3.8", "3.10", "3.11", "3.12"]
+        python-version: ["3.11", "3.14"]
         pymc-version: ["without", "'pymc>=5.0.0'"]
     steps:
     - uses: actions/checkout@v6
@@ -31,14 +31,14 @@ jobs:
     - name: Test without PyMC
       if: matrix.pymc-version == 'without'
       run: |
-        pytest --cov=./bletl --cov-report xml --cov-report term-missing tests/
+        pytest -v --cov=./bletl --cov-report xml --cov-report term-missing tests/
     - name: Install and test with PyMC
       if: matrix.pymc-version != 'without'
       run: |
         pip install ${{ matrix.pymc-version }}
-        pytest --cov=./bletl --cov-report xml --cov-report term-missing tests/
+        pytest -v --cov=./bletl --cov-report xml --cov-report term-missing tests/
     - name: Upload coverage
-      uses: codecov/codecov-action@v5
+      uses: codecov/codecov-action@v6
       with:
         file: ./coverage.xml
     - name: Test Wheel build, install and import

.pre-commit-config.yaml

@@ -3,23 +3,23 @@
 exclude: docs/|\.(csv|zip|json)$
 repos:
 - repo: https://github.com/pre-commit/pre-commit-hooks
-  rev: v4.2.0
+  rev: v6.0.0
   hooks:
     - id: check-merge-conflict
     - id: check-toml
     - id: check-yaml
     - id: end-of-file-fixer
     - id: trailing-whitespace
 - repo: https://github.com/PyCQA/isort
-  rev: 5.12.0
+  rev: 8.0.1
   hooks:
     - id: isort
       name: isort
 - repo: https://github.com/psf/black
-  rev: 22.3.0
+  rev: 26.3.1
   hooks:
     - id: black
 - repo: https://github.com/pre-commit/mirrors-mypy
-  rev: v1.3.0
+  rev: v1.20.1
   hooks:
   -   id: mypy

.readthedocs.yml

@@ -7,9 +7,9 @@ version: 2
 
 # Set the OS, Python version and other tools you might need
 build:
-  os: ubuntu-22.04
+  os: ubuntu-24.04
   tools:
-    python: "3.11"
+    python: "3.12"
 
 # Build documentation in the docs/ directory with Sphinx
 sphinx:

bletl/__init__.py

@@ -18,6 +18,7 @@
 BioLector files, applying calibration transformations and representing them in a standardized
 format.
 """
+
 import importlib.metadata
 
 from . import utils

bletl/core.py

@@ -1,4 +1,5 @@
 """Specifies the base types for parsing and representing BioLector CSV files."""
+
 import json
 import zipfile
 from collections.abc import Iterable

bletl/features.py

@@ -4,10 +4,10 @@
 import time
 import typing
 
-import fastprogress
 import numpy
 import pandas
 import tsfresh
+from rich.progress import track
 
 from . import splines
 from .types import BLData, FilterTimeSeries
@@ -416,7 +416,7 @@ def from_bldata(
     _log.info("Applying custom extractors to %i wells.", len(wells))
     s_time = time.time()
     df_result = pandas.DataFrame(index=wells)
-    for well in fastprogress.progress_bar(wells):
+    for well in track(wells):
         for mname, method in extraction_methods.items():
             t, y = bldata[mname.split("__")[0]].get_timeseries(well, last_cycle=last_cycles.get(well))
             df_result.loc[well, mname] = method(t, y)

bletl/heuristics.py

@@ -1,6 +1,7 @@
 """
 Signal analysis based on simple, deterministic heuristics.
 """
+
 import logging
 import typing
 
@@ -17,7 +18,7 @@ def find_do_peak(
     threshold_a: float,
     delay_b: float,
     threshold_b: float,
-    initial_delay: float = 1
+    initial_delay: float = 1,
 ) -> typing.Optional[int]:
     """Finds the index of a DO peak in the inputs [x] and [y].
 

bletl/parsing/bl1.py

@@ -1,4 +1,5 @@
 """Parsing functions for the BioLector 1"""
+
 import configparser
 import datetime
 import io

bletl/parsing/blpro.py

@@ -1,4 +1,5 @@
 """Parsing functions for the BioLector Pro"""
+
 import collections
 import datetime
 import io
@@ -562,13 +563,13 @@ def search_for_lot(calibration_file, lot_number):
         return element
 
     element = search_for_lot(calibration_file, lot_number)
-    if not element:
+    if element is None or len(element) == 0:
         if not utils.download_calibration_data():
             return None
         else:
             element = search_for_lot(calibration_file, lot_number)
 
-    if not element:
+    if element is None or len(element) == 0:
         raise InvalidLotNumberError(
             "Latest calibration information was downloaded from m2p-labs, "
             f"but the provided lot number/temperature combination (lot_number={lot_number}, temp={temp}) could not be found. "

bletl/types.py

@@ -1,4 +1,5 @@
 """Specifies the base types for parsing and representing BioLector CSV files."""
+
 import abc
 import enum
 import os

pyproject.toml

@@ -6,30 +6,30 @@ build-backend = "setuptools.build_meta"
 
 [project]
 name = "bletl"
-version = "1.6.2"
+version = "1.7.0"
 description = "Package for parsing and transforming BioLector raw data."
 readme = "README.md"
-requires-python = ">=3.8"
+requires-python = ">=3.11"
 license = {text = "GNU Affero General Public License v3"}
 authors = [
     {name = "Michael Osthege", email = "m.osthege@fz-juelich.de"},
 ]
 classifiers = [
     "Programming Language :: Python",
             "Operating System :: OS Independent",
-            "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",
+            "Programming Language :: Python :: 3.13",
+            "Programming Language :: Python :: 3.14",
             "Intended Audience :: Science/Research",
             "License :: OSI Approved :: GNU Affero General Public License v3",
 ]
 dependencies = [
     "csaps>=0.11",
-    "fastprogress",
     "joblib",
     "numpy",
     "pandas",
+    "rich",
     "scipy",
     "tsfresh",
     "setuptools",

requirements.txt

@@ -1,8 +1,8 @@
 csaps>=0.11
-fastprogress
 joblib
 numpy
 pandas
+rich
 scipy
 tsfresh
 setuptools

tests/test_core.py

@@ -1,4 +1,5 @@
 """Contains unit tests for the `bletl` package"""
+
 import datetime
 import pathlib
 
@@ -285,7 +286,7 @@ def test_get_unified_dataframe(self):
         idx = unified_df.index.get_indexer([5], method="nearest")
         col = unified_df.columns.get_indexer(["A05"])
         values = unified_df.iloc[idx, col].to_numpy()
-        numpy.testing.assert_approx_equal(values, 63.8517, significant=6)
+        numpy.testing.assert_approx_equal(values[0, 0], 63.8517, significant=6)
 
     def test_get_narrow_data(self):
         fp = pathlib.Path(
@@ -672,12 +673,12 @@ def test_issue_38(self):
         assert bldata.module.index.names == ["well", "valve", "cycle"]
         assert bldata.valves.index.names == ["well", "valve", "cycle"]
         # Check some initial and final well volumes against values shown in the BioLection
-        assert bldata.fluidics.loc["C01", "volume"][0] == 800
-        assert bldata.fluidics.loc["C01", "volume"][-1] == 1201.776
-        assert bldata.fluidics.loc["D01", "volume"][-1] == 1204.892
-        assert bldata.fluidics.loc["D02", "volume"][-1] == 954.68
-        assert bldata.fluidics.loc["E06", "volume"][-1] == 913.16
-        assert bldata.fluidics.loc["F01", "volume"][-1] == 1202.719
+        assert bldata.fluidics.loc["C01", "volume"].values[0] == 800
+        assert bldata.fluidics.loc["C01", "volume"].values[-1] == 1201.776
+        assert bldata.fluidics.loc["D01", "volume"].values[-1] == 1204.892
+        assert bldata.fluidics.loc["D02", "volume"].values[-1] == 954.68
+        assert bldata.fluidics.loc["E06", "volume"].values[-1] == 913.16
+        assert bldata.fluidics.loc["F01", "volume"].values[-1] == 1202.719
         pass
 
     def test_fluidics_source(self):