Update Python version to 3.12 in documentation and code examples

Author: hackdna

.readthedocs.yaml

@@ -7,9 +7,9 @@ version: 2
 
 # Set the version of Python and other tools you might need
 build:
-  os: ubuntu-22.04
+  os: ubuntu-24.04
   tools:
-    python: "3.11"
+    python: "3.12"
 
 # Optionally declare the Python requirements required to build your docs
 python:

README.md

@@ -31,7 +31,7 @@ Output: typically summary files
 
 # Usage
 
-Please note that Forest uses Python 3.11. To install, clone this repository to a local directory and then:
+Please note that Forest is tested again Python 3.11 and 3.12 only. To install, clone this repository to a local directory and then:
 
 ```console
 pip install path/to/forest

docs/source/aws.md

@@ -593,10 +593,10 @@ to that user.
 Assume we are ssh-ed to the EC2 instance.
 
 To create a new environment named `forest_main` with Python version
-`3.11` use
+`3.12` use
 
 ``` sh
-conda create --name forest_main python=3.11
+conda create --name forest_main python=3.12
 ```
 
 To activate an environment named `forest_main` use
@@ -678,12 +678,12 @@ base                  *  /opt/anaconda
 [Forest](https://github.com/onnela-lab/forest) is a Python library for
 analyzing smartphone-based high-throughput digital phenotyping data
 collected with the Beiwe platform. Forest implements methods as a Python
-3.11 package. Forest is integrated into the Beiwe back-end on AWS but can
+3.12 package. Forest is integrated into the Beiwe back-end on AWS but can
 also be run locally.
 
 Assume we are ssh-ed to the EC2 instance. Use the commands below to
 activate Anaconda environment of choice (here, `forest_main` that has
-Python `3.11` installed) and install `git`, `pip`.
+Python `3.12` installed) and install `git`, `pip`.
 
 ``` sh
 conda activate forest_main

docs/source/index.md

@@ -32,7 +32,7 @@ passive-data.md
 
 # Home
 
-Forest is a library for analyzing smartphone-based high-throughput digital phenotyping data collected with the [Beiwe platform](https://www.beiwe.org/). Forest implements methods as a Python 3.11 package. Forest is integrated into the Beiwe back-end on AWS but can also be run locally.
+Forest is a library for analyzing smartphone-based high-throughput digital phenotyping data collected with the [Beiwe platform](https://www.beiwe.org/). Forest implements methods as a Python 3.12 package. Forest is integrated into the Beiwe back-end on AWS but can also be run locally.
 
 **Table of Contents**
 ```{contents}

docs/source/logging.md

@@ -358,4 +358,4 @@ a, b, c = wrapper(x, y, z, 'path/to/log/output/directory')
 
 * [The Python Standard Library's documentation for `logging`](https://docs.python.org/3/library/logging.html)
 * Vinay Sajip's [*Logging HOWTO*](https://docs.python.org/3/howto/logging.html)
-* [`LogRecord` attributes](https://docs.python.org/3.11/library/logging.html#logrecord-attributes)
+* [`LogRecord` attributes](https://docs.python.org/3.12/library/logging.html#logrecord-attributes)

pyproject.toml

@@ -54,6 +54,7 @@ classifiers = [
     "Operating System :: Microsoft :: Windows",
     "Operating System :: POSIX :: Linux",
     "Programming Language :: Python :: 3.11",
+    "Programming Language :: Python :: 3.12",
     "Topic :: Scientific/Engineering :: Information Analysis",
 ]
 

src/forest/poplar/functions/log.py

@@ -15,7 +15,7 @@
 
 # Dictionary of available log record attributes:
 # For details, see:
-# https://docs.python.org/3.11/library/logging.html#logrecord-attributes
+# https://docs.python.org/3.12/library/logging.html#logrecord-attributes
 AVAILABLE_ATTRIBUTES = {
     "asctime,msecs": "%(asctime)s",  # Human-readable time with milliseconds.
     "created": "%(created)f",  # Unix timestamp (seconds since epoch).
@@ -134,7 +134,7 @@ def log_to_csv(
         log_name (str): Name for the log file.
         log_format (str): The format argument for logging.basicConfig.
             For available attributes and formatting instructions, see:
-            https://docs.python.org/3.11/library/logging.html#logrecord-attributes
+            https://docs.python.org/3.12/library/logging.html#logrecord-attributes
         header (list): Header for the csv.
 
     Returns:

tutorials/forest_usage.ipynb

@@ -30,7 +30,7 @@
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "Before we begin, we need to check the current distribution of Python. Note that forest is built using Python 3.11. "
+    "Before we begin, we need to check the current distribution of Python. Note that forest is built using Python 3.12. "
    ]
   },
   {
@@ -74,7 +74,7 @@
    "source": [
     "*The output should display two lines.* \n",
     "\n",
-    "1. The Python version installed: make sure you are not using a version of Python that is earlier than 3.11\n",
+    "1. The Python version installed: make sure you are not using a version of Python that is earlier than 3.12\n",
     "2. The path to where Python is currently installed"
    ]
   },
@@ -709,10 +709,10 @@
      "evalue": "name 'response_data' is not defined",
      "output_type": "error",
      "traceback": [
-      "\u001B[0;31m---------------------------------------------------------------------------\u001B[0m",
-      "\u001B[0;31mNameError\u001B[0m                                 Traceback (most recent call last)",
-      "\u001B[0;32m/var/folders/nl/92kzg8c56mn1872898r7rjr40000gn/T/ipykernel_96458/1316156180.py\u001B[0m in \u001B[0;36m<module>\u001B[0;34m\u001B[0m\n\u001B[1;32m      1\u001B[0m \u001B[0;31m## Make sure the data is sorted according to date\u001B[0m\u001B[0;34m\u001B[0m\u001B[0;34m\u001B[0m\u001B[0m\n\u001B[0;32m----> 2\u001B[0;31m \u001B[0mresponse_data\u001B[0m\u001B[0;34m.\u001B[0m\u001B[0msort_values\u001B[0m\u001B[0;34m(\u001B[0m\u001B[0;34m'Date'\u001B[0m\u001B[0;34m,\u001B[0m \u001B[0minplace\u001B[0m \u001B[0;34m=\u001B[0m \u001B[0;32mTrue\u001B[0m\u001B[0;34m)\u001B[0m\u001B[0;34m\u001B[0m\u001B[0;34m\u001B[0m\u001B[0m\n\u001B[0m\u001B[1;32m      3\u001B[0m \u001B[0mresponse_data\u001B[0m\u001B[0;34m.\u001B[0m\u001B[0mreset_index\u001B[0m\u001B[0;34m(\u001B[0m\u001B[0mdrop\u001B[0m \u001B[0;34m=\u001B[0m \u001B[0;32mTrue\u001B[0m\u001B[0;34m,\u001B[0m \u001B[0minplace\u001B[0m \u001B[0;34m=\u001B[0m \u001B[0;32mTrue\u001B[0m\u001B[0;34m)\u001B[0m\u001B[0;34m\u001B[0m\u001B[0;34m\u001B[0m\u001B[0m\n\u001B[1;32m      4\u001B[0m \u001B[0;34m\u001B[0m\u001B[0m\n\u001B[1;32m      5\u001B[0m \u001B[0;32mdef\u001B[0m \u001B[0mtime_series_plot\u001B[0m\u001B[0;34m(\u001B[0m\u001B[0mvar_to_plot\u001B[0m\u001B[0;34m,\u001B[0m \u001B[0mylab\u001B[0m \u001B[0;34m=\u001B[0m \u001B[0;34m''\u001B[0m\u001B[0;34m,\u001B[0m \u001B[0mxlab\u001B[0m \u001B[0;34m=\u001B[0m \u001B[0;34m'Date'\u001B[0m\u001B[0;34m,\u001B[0m \u001B[0mnum_x_ticks\u001B[0m \u001B[0;34m=\u001B[0m \u001B[0;36m4\u001B[0m\u001B[0;34m)\u001B[0m\u001B[0;34m:\u001B[0m\u001B[0;34m\u001B[0m\u001B[0;34m\u001B[0m\u001B[0m\n",
-      "\u001B[0;31mNameError\u001B[0m: name 'response_data' is not defined"
+      "\u001b[0;31m---------------------------------------------------------------------------\u001b[0m",
+      "\u001b[0;31mNameError\u001b[0m                                 Traceback (most recent call last)",
+      "\u001b[0;32m/var/folders/nl/92kzg8c56mn1872898r7rjr40000gn/T/ipykernel_96458/1316156180.py\u001b[0m in \u001b[0;36m<module>\u001b[0;34m\u001b[0m\n\u001b[1;32m      1\u001b[0m \u001b[0;31m## Make sure the data is sorted according to date\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m----> 2\u001b[0;31m \u001b[0mresponse_data\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0msort_values\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;34m'Date'\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0minplace\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0;32mTrue\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m      3\u001b[0m \u001b[0mresponse_data\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mreset_index\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mdrop\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0;32mTrue\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0minplace\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0;32mTrue\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m      4\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m      5\u001b[0m \u001b[0;32mdef\u001b[0m \u001b[0mtime_series_plot\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mvar_to_plot\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mylab\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0;34m''\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mxlab\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0;34m'Date'\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mnum_x_ticks\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0;36m4\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n",
+      "\u001b[0;31mNameError\u001b[0m: name 'response_data' is not defined"
      ]
     }
    ],