Release/1.5.3

.github/workflows/docs-tests.yml

@@ -1,7 +1,16 @@
 name: Docs test on push and PR
 
 
-on: [push, pull_request, workflow_dispatch]
+on:
+  push:
+    branches:
+      - main
+      - development
+  pull_request:
+    branches:
+      - main
+      - development
+  workflow_dispatch:
 
 
 jobs:
@@ -35,10 +44,12 @@ jobs:
 
       - name: Get pip cache location
         id: pip-cache
+        shell: bash
         run: echo "dir=$(pip cache dir)" >> $GITHUB_OUTPUT
 
       - name: Get date
         id: date
+        shell: bash
         run: >
           python -c
           "import datetime;

.github/workflows/unit-tests.yml

@@ -1,7 +1,16 @@
 name: Unit test on push and PR
 
 
-on: [push, pull_request, workflow_dispatch]
+on:
+  push:
+    branches:
+      - main
+      - development
+  pull_request:
+    branches:
+      - main
+      - development
+  workflow_dispatch:
 
 
 jobs:
@@ -12,10 +21,7 @@ jobs:
       fail-fast: false
       matrix:
         os: [windows-latest, ubuntu-latest, macos-latest]
-        python-version: ['3.7', '3.8', '3.9', '3.10', '3.11']
-        exclude:
-          - os: ubuntu-latest
-            python-version: '3.6'
+        python-version: ['3.8', '3.9', '3.10', '3.11', '3.12']
 
     env:
       OS: ${{ matrix.os }}

README.md

@@ -1,4 +1,4 @@
-![unit tests](https://github.com/midetechnology/endaq-python/actions/workflows/unit-tests.yml/badge.svg) [![codecov](https://codecov.io/gh/MideTechnology/endaq-python/branch/develop/graph/badge.svg)](https://codecov.io/gh/MideTechnology/endaq-python)
+[![PyPI Latest Release](https://img.shields.io/pypi/v/endaq-python.svg)](https://pypi.org/project/endaq-python/) ![example workflow](https://github.com/MideTechnology/endaq-python/actions/workflows/unit-tests.yml/badge.svg)
 
 # `endaq-python`: A comprehensive, user-centric Python API for working with enDAQ data and devices
 

docs/endaq/ide_usage.rst

@@ -43,6 +43,11 @@ Summarizing IDE files: :py:func:`endaq.ide.get_channel_table()`
 Once an IDE file has been loaded, :py:func:`~endaq.ide.get_channel_table()` will
 retrieve basic summary information about its contents.
 
+Some environments, such as `Jupyter Notebook <https://jupyter.org/>`_ or `Colab <https://colab.research.google.com/>`_,
+will automatically render and display the channel table data. From inside the standard Python interactive interpreter,
+use `get_channel_table(doc).data` to display the raw information, or to access the table's contents directly as a
+Pandas `DataFrame`.
+
 .. code:: python3
 
     get_channel_table(doc)

docs/requirements.txt

@@ -1,4 +1,4 @@
-Sphinx==4.2.0
+Sphinx>=5.0.2
 sphinxcontrib-applehelp==1.0.2
 sphinxcontrib-devhelp==1.0.2
 sphinxcontrib-htmlhelp==2.0.0
@@ -9,4 +9,4 @@ sphinxcontrib-serializinghtml==1.1.5
 pydata-sphinx-theme==0.7.1
 sphinx-plotly-directive==0.1.3
 nbsphinx==0.8.8
-ipython==8.1.0
+ipython==8.10

endaq/__init__.py

@@ -5,4 +5,4 @@
 import endaq.batch
 
 
-__version__ = "1.5.2"
+__version__ = "1.5.3"

endaq/batch/analyzer.py

@@ -6,10 +6,7 @@
 import sys
 import warnings
 
-if sys.version_info[:2] >= (3, 8):
-    from functools import cached_property
-else:
-    from backports.cached_property import cached_property
+from functools import cached_property
 
 import numpy as np
 import pandas as pd
@@ -112,8 +109,8 @@ def to_pandas(self, time_mode="datetime"):
                 timedelta=(pd.TimedeltaIndex, "TimedeltaIndex"),
                 datetime=(pd.DatetimeIndex, "DatetimeIndex"),
                 seconds=(
-                    (pd.Float64Index, pd.Int64Index, pd.UInt64Index, pd.RangeIndex),
-                    "{Float64/Int64/UInt64/Range}Index",
+                    (pd.Index, pd.RangeIndex),
+                    "{Numeric/Range}Index",
                 ),
             )
             if not isinstance(self.data.index, expected_index_types[time_mode][0]):

endaq/batch/core.py

@@ -7,6 +7,7 @@
 from functools import partial
 import warnings
 import os
+import sys
 
 import numpy as np
 import pandas as pd
@@ -207,13 +208,13 @@ def _make_peak_windows(ch_data_cache: analyzer.CalcCache, margin_len):
     )
 
     # Format results
-    result = (
-        aligned_peak_data.stack()
-        .stack()
-        .reorder_levels(["axis", "peak time", "peak offset"])
-    )
 
-    return result
+    # Use new implementation of future_stack if Python version >= 3.9
+    levels = ["axis", "peak time", "peak offset"]
+    if sys.version_info < (3, 9):
+        return aligned_peak_data.stack().stack().reorder_levels(levels)
+
+    return aligned_peak_data.stack(future_stack=True).stack().reorder_levels(levels)
 
 
 def _make_vc_curves(ch_data_cache: analyzer.CalcCache):

endaq/calc/integrate.py

@@ -19,7 +19,7 @@ def _integrate(
     dt = utils.sample_spacing(df)
 
     result = df.apply(
-        functools.partial(scipy.integrate.cumtrapz, dx=dt, initial=0),
+        functools.partial(scipy.integrate.cumulative_trapezoid, dx=dt, initial=0),
         axis=0,
         raw=True,
     )

endaq/ide/files.py

@@ -11,7 +11,7 @@
 import typing
 from typing import Union, Tuple
 
-from datetime import datetime
+from datetime import datetime, timezone
 import os
 from pathlib import Path
 import tempfile
@@ -249,7 +249,7 @@
 
             session_start = doc.lastSession.utcStartTime
             if session_start:
-                session_start = datetime.utcfromtimestamp(session_start)
+                session_start = datetime.fromtimestamp(session_start, tz=timezone.utc)
 
             if start:
                 read_kwargs['startTime'] = parse_time(start, session_start)
@@ -303,7 +303,7 @@
 
     session_start = doc.lastSession.utcStartTime
     if session_start:
-        session_start = datetime.utcfromtimestamp(session_start)
+        session_start = datetime.fromtimestamp(session_start, tz=timezone.utc)
 
     if start:
         kwargs['startTime'] = parse_time(start, session_start)

endaq/ide/info.py

@@ -179,7 +179,7 @@ def get_channel_table(dataset: typing.Union[idelib.dataset.Dataset, list],
 
         data = source.getSession(session)
         if data.session.utcStartTime:
-            session_start = datetime.datetime.utcfromtimestamp(data.session.utcStartTime)
+            session_start = datetime.datetime.fromtimestamp(data.session.utcStartTime, tz=datetime.timezone.utc)
         start = parse_time(start, session_start)
         end = parse_time(end, session_start)
 

endaq/plot/dashboards.py

@@ -206,7 +206,7 @@
 
 
         # Loop through each of the sub-channels, and their respective '0-height rectangle mask'
-        for subchannel_name, cur_min_max_equal in min_max_equal[channel_data.columns].iteritems():
+        for subchannel_name, cur_min_max_equal in min_max_equal[channel_data.columns].items():
 
             traces = []
             cur_color = colorway[subplot_num % len(colorway)]
@@ -396,7 +396,7 @@
         else:
             time = channel_data.index
 
-        for c_i, (subchannel_name, subchannel_data) in enumerate(channel_data.iteritems()):
+        for c_i, (subchannel_name, subchannel_data) in enumerate(channel_data.items()):
             for metric in rolling_metrics_to_plot:
                 if n == 0:
                     data = subchannel_data.values

requirements.txt

@@ -1,6 +1,6 @@
 backports.cached-property; python_version<'3.8'
 ebmlite>=3.2.0
-idelib>=3.2.3
+idelib>=3.2.8
 jinja2
 numpy>=1.19.5
 pandas>=1.3

setup.py

@@ -24,7 +24,7 @@ def get_version(rel_path):
 INSTALL_REQUIRES = [
     "backports.cached-property; python_version<'3.8'",
     "ebmlite>=3.2.0",
-    "idelib>=3.2.3",
+    "idelib>=3.2.8",
     "jinja2",
     "numpy>=1.19.5",
     "pandas>=1.3",
@@ -68,11 +68,11 @@ def get_version(rel_path):
         classifiers=['Development Status :: 4 - Beta',
                      'License :: OSI Approved :: MIT License',
                      'Natural Language :: English',
-                     'Programming Language :: Python :: 3.7',
                      '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',
                      'Topic :: Scientific/Engineering',
                      ],
         keywords='ebml binary ide mide endaq',