Merge pull request #16 from gjbex/development

Development

Author: gjbex

hands-on/julia.ipynb

@@ -11,16 +11,7 @@
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "Install the `sh` module since this is a bit off the beaten track."
-   ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": null,
-   "metadata": {},
-   "outputs": [],
-   "source": [
-    "!pip install sh"
+    "Install the `sh` module if it is not installed since this is a bit off the beaten track."
    ]
   },
   {
@@ -35,19 +26,23 @@
    "outputs": [],
    "source": [
     "import matplotlib.pyplot as plt\n",
-    "%matplotlib inline\n",
     "import numpy as np\n",
     "from pathlib import Path\n",
     "import psutil\n",
-    "import sh\n",
+    "try:\n",
+    "    import sh\n",
+    "except ModuleNotFoundError:\n",
+    "    print('installing sh using pip')\n",
+    "    !pip install sh\n",
+    "    import sh\n",
     "import time"
    ]
   },
   {
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "Download the source code from GitHub."
+    "Download the source code from GitHub if it is not in the current working directory."
    ]
   },
   {
@@ -56,7 +51,9 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "!wget https://raw.githubusercontent.com/gjbex/PythonSysProg/master/julia_omp.f90"
+    "julia_src = Path.cwd() / 'julia_omp.f90'\n",
+    "if not julia_src.exists():\n",
+    "    sh.wget('https://raw.githubusercontent.com/gjbex/Python-for-systems-programming/refs/heads/master/hands-on/julia_omp.f90')"
    ]
   },
   {
@@ -229,7 +226,7 @@
  ],
  "metadata": {
   "kernelspec": {
-   "display_name": "Python 3",
+   "display_name": "Python 3 (ipykernel)",
    "language": "python",
    "name": "python3"
   },
@@ -243,9 +240,9 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.7.5"
+   "version": "3.11.6"
   }
  },
  "nbformat": 4,
- "nbformat_minor": 2
+ "nbformat_minor": 4
 }

hands-on/shell_interaction.ipynb

@@ -51,6 +51,15 @@
     "sh.ls('-l')"
    ]
   },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "!ls -l"
+   ]
+  },
   {
    "cell_type": "code",
    "execution_count": null,
@@ -611,6 +620,15 @@
     "If you need to add or modify environment variables, it is good practice to do that on a copy of `os.environ`."
    ]
   },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "import os"
+   ]
+  },
   {
    "cell_type": "code",
    "execution_count": null,

source-code/enviroment-variables/README.md

@@ -1,13 +1,17 @@
 # Environment variables
 
-This directory shows some examples of how to use environment variables in a Python
-script.
+This directory shows some examples of how to use environment variables in a
+Python script.
+
 
 ## What is it?
 
-1. `accumulate_data.py`: script that will read all `.txt` files in a directory defined
-  in an environment variable `DATA_DIR`.
+1. `accumulate_data.py`: script that will read all `.txt` files in a directory
+   defined in an environment variable `DATA_DIR`.
 1. `data`: directory that contains two text files with data.
+1. `dotenv`: the `dotenv` package is used to load environment variables from a
+   `.env` file.
+
 
 ## How to use it?
 

source-code/enviroment-variables/dotenv/.gitignore

@@ -0,0 +1,2 @@
+# include .env file to prevent sensitive data from being committed
+.env

source-code/enviroment-variables/dotenv/README.md

@@ -0,0 +1,17 @@
+# dotenv
+
+The `dotenv` package is a simple and efficient way to load environment
+variables from a `.env` file into your application's environment. It is
+commonly used in development and testing environments to manage configuration
+settings without hardcoding them into the source code.  Another important use
+case is to keep sensitive information, such as API keys and database
+credentials, out of version control systems.
+
+
+## What is it?
+
+1. `dot_env`: file to be renamed to `.env` in the directory where the script is
+   run.
+1. `dotenv_demo.py`: demo script that uses `dotenv` to load environment
+   variables from the `.env` file.
+1. `.gitignore`: to ignore the `.env` file in version control.

source-code/enviroment-variables/dotenv/dot_env

@@ -0,0 +1,2 @@
+MY_SECRET="if you see this, expect black helicopters"
+MY_PATH="somewhere/to/go"

source-code/enviroment-variables/dotenv/dotenv_demo.py

@@ -0,0 +1,26 @@
+#!/usr/bin/env python3
+
+from dotenv import load_dotenv
+import os
+
+
+def main():
+    # Check whether the environment variable is already set
+    if 'MY_SECRET' in os.environ:
+        print('MY_SECRET is already set in the environment.')
+    else:
+        # Load environment variables from .env file
+        print('Loading environment variables from .env file...')
+        load_dotenv()
+
+    # Access an environment variable
+    secret_key = os.getenv('MY_SECRET')
+
+    if secret_key:
+        print(f'MY_SECRET: {secret_key}')
+    else:
+        print('MY_SECRET not found in environment variables.')
+
+
+if __name__ == '__main__':
+    main()

source-code/hydra/README.md

@@ -51,6 +51,14 @@ or
 $ ./gen_rand.py  --config-name=file_config.yaml
 ```
 
+Application logging is configured through Hydra in
+`conf/hydra/job_logging/custom.yaml`.  The script still uses Python's
+`logging.getLogger(__name__)`, but formatting and log level are controlled
+from configuration.  For example, to change the root log level:
+```bash
+$ ./gen_rand.py  hydra.job_logging.root.level=DEBUG
+```
+
 To perform multiple runs with different parameter values:
 ```bash
 $ ./gen_rand.py -m distr=uniform,gauss

source-code/hydra/conf/config.yaml

@@ -2,4 +2,5 @@ n: 1
 file: false
 defaults:
   - distr: gauss
+  - override hydra/job_logging: custom
   - _self_

source-code/hydra/conf/hydra/job_logging/custom.yaml

@@ -0,0 +1,14 @@
+version: 1
+formatters:
+  simple:
+    format: '[%(asctime)s][%(name)s][%(levelname)s] %(message)s'
+handlers:
+  console:
+    class: logging.StreamHandler
+    formatter: simple
+    stream: ext://sys.stdout
+root:
+  level: INFO
+  handlers:
+    - console
+disable_existing_loggers: false