Updating for python 3.13.

.github/workflows/docs-tests.yml

@@ -22,16 +22,16 @@ jobs:
 
     env:
       OS: ubuntu-latest
-      PYTHON-VERSION: "3.9"
+      PYTHON-VERSION: "3.13"
 
     runs-on: ubuntu-latest
 
     steps:
 
       - name: Setup Python
-        uses: actions/setup-python@v4
+        uses: actions/setup-python@v5
         with:
-          python-version: "3.9"
+          python-version: "3.13"
 
       - name: Install Pandoc
         run: sudo apt-get install pandoc
@@ -40,7 +40,7 @@ jobs:
         run: python -m pip install --upgrade pip
 
       - name: Checkout code
-        uses: actions/checkout@v3
+        uses: actions/checkout@v4
 
       - name: Get pip cache location
         id: pip-cache
@@ -57,10 +57,10 @@ jobs:
           print(f'text={now.year}/{now.month}-part{1 + now.day // 8}')" >> $GITHUB_OUTPUT
 
       - name: Load pip cache
-        uses: actions/cache@v3
+        uses: actions/cache@v4
         with:
           path: ${{ steps.pip-cache.outputs.dir }}
-          key: doctests-${{ runner.os }}-Python3.9-${{ steps.date.outputs.text }}-pip-${{ hashFiles('**/setup.py', './.github/workflows/unit-tests.yml') }}
+          key: doctests-${{ runner.os }}-Python3.13-${{ steps.date.outputs.text }}-pip-${{ hashFiles('**/setup.py', './.github/workflows/unit-tests.yml') }}
 
       - name: Install spellcheck library
         run: sudo apt-get install libenchant-2-2

.github/workflows/publish-to-pypi.yml

@@ -14,7 +14,7 @@ jobs:
     - uses: actions/checkout@master
 
     - name: Set up Python 3.9
-      uses: actions/setup-python@v4
+      uses: actions/setup-python@v5
       with:
         python-version: 3.9
 

.github/workflows/unit-tests.yml

@@ -21,7 +21,7 @@ jobs:
       fail-fast: false
       matrix:
         os: [windows-latest, ubuntu-latest, macos-latest]
-        python-version: ['3.8', '3.9', '3.10', '3.11', '3.12']
+        python-version: ['3.9', '3.10', '3.11', '3.12', '3.13']
 
     env:
       OS: ${{ matrix.os }}

.gitignore

@@ -179,6 +179,7 @@ cython_debug/
 .idea/**/usage.statistics.xml
 .idea/**/dictionaries
 .idea/**/shelf
+.vscode/*
 
 # Generated files
 .idea/**/contentModel.xml
@@ -244,3 +245,6 @@ fabric.properties
 
 # Test files
 *_scratch.ipynb
+
+# Backup files
+*.bak

.readthedocs.yaml

@@ -7,9 +7,9 @@ version: 2
 
 # Set the version of Python and other tools you might need
 build:
-  os: ubuntu-20.04
+  os: ubuntu-24.04
   tools:
-    python: "3.8"
+    python: "3.13"
 
 # Build documentation in the docs/ directory with Sphinx
 sphinx:

docs/conf.py

@@ -13,18 +13,35 @@
 # documentation root, use os.path.abspath to make it absolute, like shown here.
 #
 
-import pkg_resources
+import codecs
+import os.path
+import sys
+
+# go up a dir and include that guy =
+p = os.path.abspath(os.path.join(os.path.dirname(__file__), '..'))
+sys.path.insert(0, p)
 
-import endaq
 
 # -- Project information -----------------------------------------------------
 
+def get_version(rel_path):
+    """ Read the version number directly from the source. """
+    with codecs.open(rel_path, 'r') as fp:
+        for line in fp:
+            if line.startswith('__version__'):
+                delim = '"' if '"' in line else "'"
+                return line.split(delim)[1]
+        else:
+            raise RuntimeError("Unable to find version string.")
+
+
 project = 'enDAQ'
 copyright = '2021, Mide Technology Corp.'
 author = ''
 
 # The full version, including alpha/beta/rc tags
-release = pkg_resources.get_distribution("endaq").version
+release = get_version(os.path.abspath(os.path.join(os.path.dirname(__file__), '..', 'endaq', '__init__.py')))
+
 # The short X.Y version
 version = '.'.join(release.split(".")[:2])
 
@@ -44,6 +61,7 @@
     'sphinx.ext.ifconfig',
     'sphinx.ext.githubpages',
     'sphinx_plotly_directive',
+    'sphinxcontrib.spelling',
     'nbsphinx',
 ]
 
@@ -64,7 +82,7 @@
 #
 # This is also used if you do content translation via gettext catalogs.
 # Usually you set "language" from the command line for these cases.
-language = None
+language = 'en'
 
 # List of patterns, relative to source directory, that match files and
 # directories to ignore when looking for source files.
@@ -100,7 +118,9 @@
     "github_url": "https://github.com/MideTechnology/endaq-python",
     "twitter_url": "https://twitter.com/enDAQ_sensors",
     "collapse_navigation": True,
-    "google_analytics_id": "G-E9QXH4H5LP",
+    "analytics": {
+        "google_analytics_id": "G-E9QXH4H5LP",
+    }
 }
 
 # Add any paths that contain custom static files (such as style sheets) here,

docs/endaq/ide_usage.rst

@@ -37,6 +37,68 @@ parameters:
 
     doc3 = get_doc("tests/test.ide", start="5s", end="10s")
 
+Accessing measurement data in a Dataset/IDE file
+------------------------------------------------
+An enDAQ device consists of many different sensors, and enDAQ devices record their measurement data into separate
+Channels that correspond to the sensor taking the measurement. This is done because each Channel samples at a different
+rate, so while Channel 59 (the Control Pad Pressure/Temperature/Humidity sensor) samples at 10 Hz, Channel 8 (the main
+analog accelerometer channel) may sample at 20000 Hz. Channels themselves consist of different subchannels, which may be
+different axes (X, Y, Z) or completely different measurements like temperature and pressure. All subchannels in a
+channel are sampled at approximately the same time.
+
+The Channel data are stored in the ``channels`` property of a Dataset, which is returned from the :py:func:`~endaq.ide.get_doc() function. The easiest way to access this is to convert it to a
+Pandas DataFrame using :py:func:`~endaq.ide.to_pandas(doc)`. Visit `our internal documentation <https://docs.endaq.com/en/latest/webinars/Webinar_Introduction_NumPy_and_Pandas.html#Pandas>`_
+for some quick tips on Pandas, or go `straight to the source <https://pandas.pydata.org/docs/>`_.
+
+.. code:: python3
+
+    import endaq.ide
+    # Read in a doc
+    doc2 = endaq.ide.get_doc("https://drive.google.com/file/d/1t3JqbZGhuZbIK9agH24YZIdVE26-NOF5/view?usp=sharing")
+    # List the available Channels
+    print(f"{doc2.channels=}")
+    # Convert the Control Pad Pressure/Temperature/Humidity Channel (Channel 59) to a Pandas DataFrame
+    control_pad_data = endaq.ide.to_pandas(doc2.channels[59])
+    # Print the subchannel names
+    print(f"{control_pad_data.columns=}")
+    # Print the max and min temperatures seen
+    print(f"Max Temp={control_pad_data['Control Pad Temperature'].max()}, Min Temp={control_pad_data['Control Pad Temperature'].min()}")
+
+The output of the above code is:
+
+.. code-block::
+
+    doc2.channels={32: <Channel 32 '16g DC Acceleration': Acceleration (g)>, 80: <Channel 80 '8g DC Acceleration': Acceleration (g)>, 36: <Channel 36 'Pressure/Temperature': Pressure (Pa), Temperature (°C)>, 70: <Channel 70 'Relative Orientation': Quaternion (q)>, 59: <Channel 59 'Control Pad Pressure/Temperature/Humidity': Pressure (Pa), Temperature (°C)>, 76: <Channel 76 'Light Sensor': Light (Ill), Light (Index)>}
+    control_pad_data.columns=Index(['Control Pad Pressure', 'Control Pad Temperature'], dtype='object')
+    Max Temp=24.899999618530273, Min Temp=24.260000228881836
+
+Note that by default, :py:func:`~endaq.ide.to_pandas(doc)` uses ``datetime`` for the index format, meaning the
+measurements are accessed based on the absolute time they were recorded. Users often prefer to access the data using
+``timedelta``, the amount of time since the recording started. Using this, to get the duration of the Control Pad data
+and the average of the first 5 seconds, we could use:
+
+.. code:: python3
+
+    import endaq.ide
+    import pandas as pd
+    # Read in a doc
+    doc2 = endaq.ide.get_doc("https://drive.google.com/file/d/1t3JqbZGhuZbIK9agH24YZIdVE26-NOF5/view?usp=sharing")
+    # Convert the Control Pad Pressure/Temperature/Humidity Channel (Channel 59) to a Pandas DataFrame
+    control_pad_data = endaq.ide.to_pandas(doc2.channels[59], time_mode='timedelta')
+    # Print the time duration
+    print(f"Duration={control_pad_data.index[-1]-control_pad_data.index[0]}")
+    # Print the mean of the first 5 seconds
+    print(f"{control_pad_data[pd.Timedelta(seconds=0):pd.Timedelta(seconds=5)].mean()}")
+
+The output of the above code is:
+
+.. code-block::
+
+    Duration=0 days 00:00:17.931518
+    Control Pad Pressure       101728.414991
+    Control Pad Temperature        24.607073
+    dtype: float64
+
 Summarizing IDE files: :py:func:`endaq.ide.get_channel_table()`
 ---------------------------------------------------------------
 

docs/requirements.txt

@@ -1,12 +1,13 @@
-Sphinx>=5.0.2
-sphinxcontrib-applehelp==1.0.2
-sphinxcontrib-devhelp==1.0.2
-sphinxcontrib-htmlhelp==2.0.0
+Sphinx>=8.1.3
+sphinxcontrib-applehelp==2.0.0
+sphinxcontrib-devhelp==2.0.0
+sphinxcontrib-htmlhelp==2.1.0
 sphinxcontrib-jsmath==1.0.1
-sphinxcontrib-qthelp==1.0.3
-sphinxcontrib-serializinghtml==1.1.5
+sphinxcontrib-qthelp==2.0.0
+sphinxcontrib-serializinghtml==2.0.0
+sphinxcontrib-spelling==8.0.1
 
-pydata-sphinx-theme==0.7.1
+pydata-sphinx-theme==0.16.1
 sphinx-plotly-directive==0.1.3
-nbsphinx==0.8.8
-ipython==8.10
+nbsphinx==0.9.7
+ipython==9.2.0

docs/spelling_wordlist.txt

@@ -5,14 +5,29 @@ sinusoids
 centric
 
 enDAQ
+Mide
 NumPy
 SciPy
 Pandas
 Plotly
+Matplotlib
+Colab
+Jupyter
+Seaborn
 Tukey
 Chebyshev
 Butterworth
 Fourier
+Heatmaps
+ide
+calc
+endaq
+accel
+str
+psd
+pkl
+kth
+GetDataBuilder
 
 basename
 pathname
@@ -24,6 +39,7 @@ subchannel
 subchannels
 DataFrame
 dataframe
+dataframes
 ndarray
 dropdown
 iterable
@@ -36,10 +52,13 @@ periodogram
 periodograms
 spectrogram
 spectrograms
+spectrums
 resample
 resampled
 resampling
 SNE
 integrations
 quaternion
 quaternions
+Welch
+kurtosis

docs/webinars/Webinar_Intro_Python_Acceleration_CSV_Analysis.ipynb

@@ -14,7 +14,7 @@
     "## Introduction\n",
     "This notebook serves as an introduction to Python for a mechanical engineer looking to plot and analyze some acceleration data in a CSV file. Being a Colab, this tool can freely be used without installing anything.\n",
     "\n",
-    "For more information on making the swith to Python see [enDAQ's blog, Why and How to Get Started in Python for a MATLAB User](https://blog.endaq.com/why-and-how-to-get-started-in-python-for-a-matlab-user).\n",
+    "For more information on making the switch to Python see [enDAQ's blog, Why and How to Get Started in Python for a MATLAB User](https://blog.endaq.com/why-and-how-to-get-started-in-python-for-a-matlab-user).\n",
     "\n",
     "This is part of our webinar series on Python for Mechanical Engineers:\n",
     "\n",
@@ -1493,7 +1493,7 @@
    },
    "source": [
     "### FFT from PSD\n",
-    "Here we can use the output of a PSD and convet it to a typical DFT. This has the benefit of allowing you to explicitely define the frequency bin width."
+    "Here we can use the output of a PSD and convert it to a typical DFT. This has the benefit of allowing you to explicitly define the frequency bin width."
    ]
   },
   {
@@ -1887,4 +1887,4 @@
  },
  "nbformat": 4,
  "nbformat_minor": 4
-}
+}

docs/webinars/Webinar_Introduction_NumPy_and_Pandas.ipynb

@@ -14,7 +14,7 @@
     "\n",
     "1. [Get Started with Python](https://colab.research.google.com/drive/1_pcGtgJleapV9tz5WfuRuqfWryjqhPHy#scrollTo=ikUJITDDIp19)\n",
     "   * Blog: [Get Started with Python: Why and How Mechanical Engineers Should Make the Switch](https://blog.endaq.com/get-started-with-python-why-how-mechanical-engineers-should-make-the-switch)\n",
-    "2. **Introduction to Numpy & Pandas**\n",
+    "2. **Introduction to NumPy & Pandas**\n",
     "   * [Watch Recording of This](https://info.endaq.com/pandas-and-numpy-for-data-analysis-webinar)\n",
     "3. [Introduction to Plotly](https://colab.research.google.com/drive/1pag2pKQQW5amWgRykAH8uMAPqHA2yUfU?usp=sharing)\n",
     "4. [Introduction of the enDAQ Library](https://colab.research.google.com/drive/1WAtQ8JJC_ny0fki7eUABACMA-isZzKB6)\n",
@@ -505,7 +505,7 @@
     "id": "cv0nw1SnLb5x"
    },
    "source": [
-    "Logspace is the equivalent of rasing a base by a linspaced array."
+    "Logspace is the equivalent of raising a base by a linspaced array."
    ]
   },
   {
@@ -7821,7 +7821,7 @@
    "source": [
     "### Installation\n",
     "\n",
-    "The code is live on [GitHub](https://github.com/MideTechnology/endaq-python), [PyPI](https://pypi.org/project/endaq/), and cleaner documentation is in process that will eventually live on a subdomain of endaq.com.\n",
+    "The code is live on [GitHub](https://github.com/MideTechnology/endaq-python), [PyPI](https://pypi.org/project/endaq/), and cleaner documentation lives at [docs.endaq.com](https://docs.endaq.com/en/latest/).\n",
     "\n",
     "It can easily be installed with pip."
    ]

docs/webinars/Webinar_Introduction_Plotly.ipynb

@@ -345,7 +345,7 @@
    },
    "source": [
     "### [ggplot](https://plotnine.readthedocs.io/en/stable/)\n",
-    "Introduces a \"grammer of graphics\" logic to plotting data which allows explicit mapping of data to the visual representation. This is something plotly express excels at."
+    "Introduces a \"grammar of graphics\" logic to plotting data which allows explicit mapping of data to the visual representation. This is something plotly express excels at."
    ]
   },
   {
@@ -1304,7 +1304,7 @@
     "id": "u_pZeZ5An8PG"
    },
    "source": [
-    "Now let's get crazy and customize all the \"common\" settings. But note that there are a LOT of different parameters that can be explicitely defined. Remember, Plotly has very thorough documentation, so check it out!\n",
+    "Now let's get crazy and customize all the \"common\" settings. But note that there are a LOT of different parameters that can be explicitly defined. Remember, Plotly has very thorough documentation, so check it out!\n",
     "* [Figure Layout](https://plotly.com/python/reference/layout/)\n",
     "* [X Axis](https://plotly.com/python/reference/layout/xaxis/)\n",
     "* [Y Axis](https://plotly.com/python/reference/layout/yaxis/)\n",