Merge branch 'main' into 3-add-pyprojecttoml-and-arrange-files-per-st…

…andards

.github/workflows/ci.yml

@@ -0,0 +1,31 @@
+name: Sample CI
+
+on:
+    push:
+    workflow_dispatch:
+
+jobs:
+    main:
+        runs-on: ubuntu-latest
+
+        steps:
+            - name: Checkout
+              uses: actions/checkout@v4
+
+            - name: Apt dependencies
+              shell: bash
+              run: |
+                sudo apt -y update
+                sudo apt install -y python3-dev
+
+            - name: Python dependencies
+              shell: bash
+              run: |
+                pip3 install numpy \
+                            pytest
+
+            - name: Test
+              shell: bash
+              run: |
+                pytest -v .
+       

README.md

@@ -1,2 +1,61 @@
 # py-template
-Template for a new python project
+This repository serves as a template for new python projects and a way to express best practices
+
+## Best Practices - Coding Practices
+
+### User input
+* Always use [`argparse`](https://docs.python.org/3/library/argparse.html) for command-line arguments
+* Assume the use of [`yaml`](https://python.land/data-processing/python-yaml) for structured input files unless there are compelling reasons for something else
+
+### User output
+* Always use `logger` for status output
+* Carefully choose an output format for standard formats, considering the following in order of priority:
+    * [CSV](https://docs.python.org/3/library/csv.html) with direct support in NumPy, Pandas, etc
+    * [yaml](https://python.land/data-processing/python-yaml)
+    * [json](https://docs.python.org/3/library/json.html)
+    * [HDF5](https://www.h5py.org/)
+    * SQL, for example [SQLite](https://docs.python.org/3/library/sqlite3.html)
+
+### Modularity
+* All runnable scripts [should include a block like](https://stackoverflow.com/questions/419163/what-does-if-name-main-do):
+
+``` python
+if __name__ == "__main__":
+    do_main_task()
+```
+
+### Testing
+* Always use [`pytest`](https://docs.pytest.org/en/8.2.x/) for testing
+* Introduce a simple continuous integration (CI) action ASAP
+
+### Collaboration
+* Generate pull requests (PRs) with as little code change as possible
+* Include tests in all PRs
+* Do not merge your own PR; there should always be at least one review by a
+  non-author, and a non-author should merge
+
+### Packaging and installation
+* Introduce a `pyproject.toml` file ASAP
+
+## Best Practices - Style
+
+### Code formatting
+* Follow PEP8 style guide, ideally with a tools like
+  [`black`](https://pypi.org/project/black/) to help enforce it, especially via
+  a plugin to your editor
+
+### Variable naming
+* Generally, choose nouns for variables and verbs for methods
+* Clear variable and method names can reduce the need for comments
+
+### Comments
+* Include a docstring in every method
+* Rely on clear variable and method names and add comments sparingly where the
+  intent/approach is non-intuitive
+
+### Modularity
+* If you have cut & paste code in two different places, it probably should be a
+  method
+* Even very short methods can be valuable if the method name makes the code more
+  readable
+* Ideally, methods should be no longer than one screen worth of lines

do_task.py

@@ -0,0 +1,111 @@
+import argparse
+import logging
+import yaml
+
+logger = logging.getLogger(__name__)
+
+
+def perform_action(args, input_data):
+    """Perform some action
+
+    Following the principle of separation of concerns, this method only
+    performs the action, but does not have any input or output.
+
+    inputs
+    ------
+    args : argparse object with many possible members based on argparse configuration
+    input_data : dictionary of input data read from YAML file
+
+    outputs
+    --------
+    string that describes the input quantities
+
+    """
+
+    return f"Some results based on args:\n{args}\n and input_data:\n{input_data}\n"
+
+
+def report_results(args, input_data, results):
+    """Report the result of the action
+
+    Following the principle of separation of concerns, this method only
+    performs output and does not do any actions.
+
+    inputs
+    ------
+    args : argparse object with many possible members based on argparse configuration
+    input_data : dictionary of input data read from YAML file
+    results : the results of the action
+
+    outputs
+    --------
+    None
+
+    """
+
+    logger.info(
+        f"Based on the values of args:\n{args}\n and input_data:\n{input_data}\n"
+        + "Here are the results:\n{results}\n"
+    )
+
+
+def task_args():
+    """Setup argparse for this script
+
+    Add an argparse.ArgumentParser with standard entries of:
+    `filename` : required positional argument
+    `verbose` : optional keyword argument
+
+    inputs
+    -------
+    None
+
+    outputs
+    --------
+    argparse object with various members depending on configuration
+    """
+
+    parser = argparse.ArgumentParser(
+        prog="do-task",
+        description="A program to perform a certain task.",
+        epilog="Some text at the bottom of the help message",
+    )
+
+    parser.add_argument("filename", help="A filename to read for input")
+    parser.add_argument(
+        "--verbose", "-v", type=int, default=0, help="Level of verbosity for logging"
+    )
+
+    return parser.parse_args()
+
+
+def read_input(input_filename):
+    """Read input from yaml
+
+    Read input in YAML format from a specified filename.
+
+    inputs
+    -------
+    input_filename : a string with a filename/path accessible from the current location
+    """
+
+    with open(input_filename, "r") as yaml_file:
+        input_data = yaml.safe_load(yaml_file)
+
+    return input_data
+
+
+def do_task():
+    """Main function to perform the actions for this script."""
+    args = task_args()
+
+    logging.basicConfig(level=(logging.WARN - args.verbose))
+
+    input_data = read_input(args.filename)
+
+    results = perform_action(args, input_data)
+    report_results(results)
+
+
+if __name__ == "__main__":
+    do_task()

test_do_task.py

@@ -0,0 +1,13 @@
+import do_task
+
+def test_perform_action():
+    args = 'foo'
+    input_data = 'bar'
+
+    exp = f"Some results based on args:\n{args}\n and input_data:\n{input_data}\n"
+
+    obs = do_task.perform_action(args, input_data)
+
+    assert exp == obs
+
+