diff --git a/README.md b/README.md index 54be6ad..d807d9f 100644 --- a/README.md +++ b/README.md @@ -25,22 +25,18 @@ If you want to adapt this material to your course, this repository has the guides in the `docs/` folder and the rest in the `Deepnote/` folder. ## Development -If you want to contribute to this repository, create a virtual environment, -preferably with Python 3.10 for compatibility with Deepnote, and install the software: -```bash -python3.10 -m venv venv -. venv/bin/activate -pip install --upgrade pip -pip install -r requirements.txt -``` -To preview the documentation that will be in GitHub Pages, enter `mkdocs serve`. +This repository is developed with [poetry](https://python-poetry.org). +After installing `poetry`, enter `poetry install` to create the development environment. + +To preview the documentation that will be in GitHub Pages, enter `poetry run mkdocs serve`. The documentation must be written in strict Markdown: -blank line before a new list; break lines with two spaces; indent with 4 spaces. +blank line before a new list; line breaks are two spaces; indentation is 4 spaces. -To build the documentation in the `docs/` folder, enter `mkdocs build`. -(Don't use `mkdocs gh-deploy` because it also pushes untracked files. For example, -it was going to push all 37k+ venv files, even though `venv` is on `.gitignore`!) +To build the documentation in the `docs/` folder from the `src/docs` files, +enter `poetry run mkdocs build`. +(Don't use `mkdocs gh-deploy` because it pushes untracked and other files, +without giving you a chance to check what will be pushed.) After accepting a commit to folder `Deepnote/`, the owners will upload the updated files to the Deepnote project linked above. diff --git a/mkdocs.yml b/mkdocs.yml index 7fcde9b..3f03647 100644 --- a/mkdocs.yml +++ b/mkdocs.yml @@ -10,9 +10,9 @@ plugins: - mkdocstrings: handlers: python: - paths: [Deepnote] + paths: [src] options: - docstring_style: null + docstring_style: "google" separate_signature: true show_signature_annotations: true show_source: false diff --git a/poetry.lock b/poetry.lock new file mode 100644 index 0000000..bda48c2 --- /dev/null +++ b/poetry.lock @@ -0,0 +1,2653 @@ +# This file is automatically @generated by Poetry 1.7.1 and should not be changed by hand. + +[[package]] +name = "allowed" +version = "1.3.0" +description = "Check if a program only uses a subset of the Python language." +optional = false +python-versions = ">=3.10,<4.0" +files = [ + {file = "allowed-1.3.0-py3-none-any.whl", hash = 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hash = "sha256:72ea0c06399eb286d978fdedb6923a9eb47e1c486ce63e9b4e64fc18303972b5"}, +] + +[[package]] +name = "webencodings" +version = "0.5.1" +description = "Character encoding aliases for legacy web content" +optional = false +python-versions = "*" +files = [ + {file = "webencodings-0.5.1-py2.py3-none-any.whl", hash = "sha256:a0af1213f3c2226497a97e2b3aa01a7e4bee4f403f95be16fc9acd2947514a78"}, + {file = "webencodings-0.5.1.tar.gz", hash = "sha256:b36a1c245f2d304965eb4e0a82848379241dc04b865afcc4aab16748587e1923"}, +] + +[metadata] +lock-version = "2.0" +python-versions = "^3.10" +content-hash = "4ffc3f35f31283294cef41bfc4ef5c0f084986621584b909bab12d3cecde2148" diff --git a/pyproject.toml b/pyproject.toml new file mode 100644 index 0000000..5801509 --- /dev/null +++ b/pyproject.toml @@ -0,0 +1,42 @@ +[tool.poetry] +name = "algoesup" +version = "0.1.0" +description = "Algorithmic essay support library" +authors = [ + "Michel Wermelinger ", + "Michael Snowden" +] +packages = [ + { include = "algoesup", from = "src" }, +] +readme = "src/README.md" +license = "BSD-3-Clause" +repository = "https://github.com/dsa-ou/algoesup" +homepage = "https://dsa-ou.github.io/algoesup/" +keywords = ["education"] +classifiers = [ + "Intended Audience :: Education", + "License :: OSI Approved :: BSD License", + "Programming Language :: Python :: 3.10", + "Topic :: Education", + "Operating System :: OS Independent", + ] + +[tool.poetry.dependencies] +python = "^3.10" +ipython = "^8.13.1" +matplotlib = "^3.4.2" + +[tool.poetry.group.dev.dependencies] +ruff = "^0.1.11" +allowed = "^1.3" +pytype = {version = ">=2023.04.27", markers = "platform_system != 'Windows'"} +mkdocs = "^1.5.3" +mkdocs-material = "^9.5.11" +mkdocstrings = { version = "^0.24.0", extras = ["python"] } +mkdocs-jupyter = "^0.24.6" +mkdocs-open-in-new-tab = "^1.0.3" + +[build-system] +requires = ["poetry-core"] +build-backend = "poetry.core.masonry.api" diff --git a/requirements.txt b/requirements.txt deleted file mode 100644 index 8fcd0c6..0000000 --- a/requirements.txt +++ /dev/null @@ -1,10 +0,0 @@ -jupyter -black[jupyter] -matplotlib==3.8.0 -pytype==2023.12.8 -ruff==0.1.8 -mkdocs -mkdocs-material -mkdocstrings[python] -mkdocs-jupyter -mkdocs-open-in-new-tab diff --git a/src/README.md b/src/README.md new file mode 100644 index 0000000..ca69dec --- /dev/null +++ b/src/README.md @@ -0,0 +1,34 @@ +# Algoesup + +This small library was written to support the writing of +[algorithmic essays](https://dsa-ou.github.io/algoesup), +but can be used independently of that purpose. +The library provides auxiliary functions that make it easier to: + - write unit tests for functions + - measure and plot run-times for best, average and worst case inputs + - use linters within Jupyter Notebook environments. + +Guidance on how to use the library is [here](https://dsa-ou.github.io/algoesup/writing/#code). + +To install in the global Python environment, open a terminal or PowerShell, and enter +```bash +pip install algoesup +``` +To install in a virtual environment, activate it before entering the command above. + +The library supports the [ruff](https://docs.astral.sh/ruff) and +[allowed](https://dsa-ou.github.io/allowed) linters, and the +[pytype](https://google.github.io/pytype) type checker. +You have to install them explicitly if you want to use them from within a notebook: +```bash +pip install ruff allowed pytype +``` +Note that `pytype` is not available for Windows. + +## Licence + +`algoesup` is Copyright © 2023–2024 by The Open University, UK. +The code is licensed under a +[BSD 3-clause licence](https://github.com/dsa-ou/algoesup/blob/main/LICENSE). +The documentation is licensed under a +[Creative Commons Attribution 4.0 International Licence](https://creativecommons.org/licenses/by/4.0/) \ No newline at end of file diff --git a/src/algoesup/__init__.py b/src/algoesup/__init__.py new file mode 100644 index 0000000..f8a3b5d --- /dev/null +++ b/src/algoesup/__init__.py @@ -0,0 +1,2 @@ +from .test import test +from .time import time_cases, time_functions, time_functions_int \ No newline at end of file diff --git a/src/algoesup/magics.py b/src/algoesup/magics.py new file mode 100644 index 0000000..d79d1e5 --- /dev/null +++ b/src/algoesup/magics.py @@ -0,0 +1,247 @@ +"""Linting tools for Jupyter Notebook environments""" + +import json +import os +import re +import subprocess +import tempfile +from typing import Callable + +from IPython.core.inputtransformer2 import TransformerManager +from IPython.core.magic import register_line_magic +from IPython.core.magic_arguments import argument, magic_arguments, parse_argstring +from IPython.display import display_markdown + + +def show_errors(checker: str, output: str, filename: str) -> None: + """Print the errors for the given file in the checker's output.""" + md = [f"**{checker}** found issues:"] + for line in output.split("\n"): + if "syntax" in line.lower() and "error" in line.lower(): + continue # syntax errors already reported when running the cell + if m := re.match(rf".*{filename}[^\d]*(\d+[^:]*:.*)", line): + md.append(f"- {m.group(1)}") + if len(md) > 1: + display_markdown("\n".join(md), raw=True) + + +def show_ruff_json(checker: str, output: str, filename: str) -> None: + """Print the errors in ruff's JSON output for the given file.""" + if errors := json.loads(output): + md = [f"**{checker}** found issues:"] + # the following assumes errors come in line order + for error in errors: + line = error["location"]["row"] + code = error["code"] + url = error["url"] + msg = error["message"] + if error["fix"]: + msg += f". Suggested fix: {error['fix']['message']}" + md.append(f"- {line}: \[[{code}]({url})\] {msg}") + display_markdown("\n".join(md), raw=True) + + +def show_pytype_errors(checker: str, output: str, filename: str) -> None: + """Print the errors in pytype's output for the given file.""" + md = [f"**{checker}** found issues:"] + for error in output.split("\n"): + if "syntax" in error.lower() and "error" in error.lower(): + continue # syntax errors already reported when running the cell + if m := re.match(rf".*{filename}[^\d]*(\d+)[^:]*:(.*)\[(.*)\]", error): + line = m.group(1) + msg = m.group(2) + code = m.group(3) + md.append( + f"- {line}:{msg}\[[{code}](https://google.github.io/pytype/errors.html#{code})\]" + ) + if len(md) > 1: + display_markdown("\n".join(md), raw=True) + + +# register the supported checkers, their commands and the output processor +checkers: dict[str, tuple[str, Callable]] = { + "pytype": ("pytype", show_pytype_errors), + "allowed": ("allowed", show_errors), + "ruff": ("ruff check --output-format json", show_ruff_json), +} +# initially no checker is active +active: set[str] = set() + + +def process_status(name: str, status: str) -> None: + """Process the status of a checker.""" + if status is None: + print(name, "is", "active" if name in active else "inactive") + elif status == "on": + active.add(name) + print(name, "was activated") + elif status == "off": + active.discard(name) + print(name, "was deactivated") + + +@magic_arguments() +@argument( + "status", + choices=["on", "off"], + type=str.lower, + help="Activate or deactivate the linter. If omitted, show the current status.", + nargs="?", + default=None, +) +@register_line_magic +def pytype(line: str) -> None: + """Activate/deactivate the `pytype` linter. + + This ipython magic command controls the activation state of the `pytype` linter within + the ipython environment. It can be toggled on or off, or queried for its + current state. + + Examples: + ``` + %pytype on + pytype was activated + %pytype off + pytype was deactivated + %pytype + pytype is inactive + ``` + """ + args = parse_argstring(pytype, line) + process_status("pytype", args.status) + + +@magic_arguments() +@argument( + "-c", + "--config", + default=None, + help="Use configuration file CONFIG (default: m269.json).", +) +@argument( + "status", + choices=["on", "off"], + type=str.lower, + help="Activate or deactivate the linter. If omitted, show the current status.", + nargs="?", + default=None, +) +@register_line_magic +def allowed(line: str) -> None: + """Activate/deactivate the `pytype` linter. + + This magic command controls the activation state of the `pytype` linter within + the ipython environment. It can be toggled on or off, or queried for its + current state. + + Examples: + ``` + %pytype on + pytype was activated + %pytype off + pytype was deactivated + %pytype + pytype is inactive + ``` + """ + args = parse_argstring(allowed, line) + config = f"-c {args.config}" if args.config else "" + checkers["allowed"] = (f"allowed {config}", show_errors) + process_status("allowed", args.status) + + +@magic_arguments() +@argument( + "status", + choices=["on", "off"], + type=str.lower, + help="Activate or deactivate the linter. If omitted, show the current status.", + nargs="?", + default=None, +) +@register_line_magic +def ruff(line: str) -> None: + """Activate/deactivate the `ruff` linter. + + This ipython magic command controls the activation state of the `ruff` linter within + the interactive environment. It can be toggled on or off, or queried for its + current state. + + Examples: + `%ruff on` + `ruff was activated` + `%ruff off` + `ruff was deactivated` + `%ruff` + `ruff is inactive` + """ + args = parse_argstring(ruff, line) + process_status("ruff", args.status) + + +# TODO: add an option to set the output processor function +@register_line_magic +def checker(line: str) -> None: + """Define or turn on/off a given checker.""" + global checkers, active + + args = line.split() + if len(args) == 0: + print("Active checkers:", *active) + print("Inactive checkers:", *(set(checkers) - active)) + return + + name = args[0] + if len(args) == 1: + if name not in checkers: + print(f"Checker {name} isn't defined.") + else: + status = "active" if name in active else "inactive" + print(f"Checker {name} is {status} and defined as '{checkers[name]}'.") + elif args[1].lower() == "on": + if name not in checkers: + print(f"Error: checker {name} isn't defined.") + else: + active.add(name) + print(f"Checker {name} has been activated.") + elif args[1].lower() == "off": + if name not in checkers: + print(f"Error: checker {name} isn't defined.") + else: + active.discard(name) + print(f"Checker {name} has been deactivated.") + else: + command = " ".join(args[1:]) + status = "redefined" if name in checkers else "defined" + checkers[name] = command + active.add(name) + print(f"Checker {name} has been {status} and activated.") + + +def run_checkers(result) -> None: + """Run all active checkers after a cell is executed.""" + if not active: + return + try: + with tempfile.NamedTemporaryFile(mode="w", suffix=".py", delete=False) as temp: + # transform IPython to pure Python to avoid linters reporting syntax errors + temp.write(TransformerManager().transform_cell(result.info.raw_cell)) + temp_name = temp.name + for checker in active: + command, display = checkers[checker] + command += " " + temp_name + try: + output = subprocess.run( + command, capture_output=True, text=True, check=False, shell=True + ).stdout + display(checker, output, temp_name) + except Exception as e: + print(f"Error on executing {command}:\n{e}") + except Exception as e: + print(f"Error on writing cell to a temporary file:\n{e}") + finally: + os.remove(temp_name) + + +def load_ipython_extension(ipython): + ipython.events.register("post_run_cell", run_checkers) # type: ignore[name-defined] diff --git a/src/algoesup/test.py b/src/algoesup/test.py new file mode 100644 index 0000000..493549a --- /dev/null +++ b/src/algoesup/test.py @@ -0,0 +1,23 @@ +"""Simplified testing for Python functions""" + +from typing import Callable + + +def test(function: Callable, test_table: list) -> None: + """Test the function with the test_table. Report failed tests. + + Args: + function (Callable): The function to be tested. + test_table (list): The list of tests. Each element of test_table is a list or + tuple with: a string (the test case name); one or more values (the inputs to the function); + the expected output value. + """ + print(f"Testing {function.__name__}:") + for test_case in test_table: + name = test_case[0] + inputs = test_case[1:-1] + expected = test_case[-1] + actual = function(*inputs) + if actual != expected: + print(name, "FAILED:", actual, "instead of", expected) + print("Tests finished.") diff --git a/src/algoesup/time.py b/src/algoesup/time.py new file mode 100644 index 0000000..5038831 --- /dev/null +++ b/src/algoesup/time.py @@ -0,0 +1,224 @@ +"""Tools for measuring and plotting run-times""" + +from typing import Callable + +import timeit +import matplotlib.pyplot as plt + + +# Input generators +# ---------------- + + +def int_value(n: int) -> tuple[int]: + """Return the value n.""" + return (n,) + + +# Timing functions +# ----------------- + + +def scale_and_unit(seconds: float) -> tuple[int, str]: + """Given a time in seconds, return the appropriate scale factor and time unit.""" + if seconds < 1e-6: + return 1_000_000_000, "ns" + if seconds < 1e-3: + return 1_000_000, "µs" + if seconds < 1: + return 1_000, "ms" + return 1, "s" + + +def time_it(function: Callable, *args, loops=0, repeat=3) -> float: + """Return the fastest time, in seconds, of running `function` on `*args`. + + By default (zero loops), use enough loops to take >= 0.2 seconds. + """ + assert loops >= 0, "loops must be non-negative" + assert repeat > 0, "repeat must be positive" + + timer = timeit.Timer(lambda: function(*args)) + if loops == 0: + loops, run_time = timer.autorange() + run_times = timer.repeat(repeat - 1, loops) + run_times.append(run_time) + else: + run_times = timer.repeat(repeat, loops) + return min(run_times) / loops + + +def time_cases( + function: Callable, + cases: list[Callable], + start_size: int, + double: int, + text: bool = True, + chart: bool = False, +) -> None: + """Print or plot the run-times of `function` for different input cases. + + `time_cases` prints or plots the run-times of a single function using a list of + different input generators. Inputs are generated based on a starting size and are + doubled a specified number of times. + + Args: + function (Callable): A functions whose run-times will be measured. + cases (list[Callable]): A list of functions to generate inputs of different cases. + E.g best- normal- and worst-case. + start_size (int): The starting size for the inputs. Must be positive. + double (int): The number of times to double the input size. Must be non-negative. + text (bool, optional): If True, print the run-times in text format. + chart (bool, optional): If True plot the run-times using a chart. + + Raises: + AssertionError: If input conditions are not satisfied. + """ + assert start_size > 0, "the start size must be positive" + assert double >= 0, "must double the input size at least zero times" + assert 0 < len(cases) < 7, "there must be 1 to 6 input functions" + assert text or chart, "at least one of text and chart must be enabled" + + sizes = [start_size] # the input sizes used + for _ in range(double): + sizes.append(sizes[-1] * 2) + scale = unit = None # no scale determined yet + if chart: + markers = ["bo-", "ko--", "ro:", "ys-", "cs--", "gs:"] + times: list[list[float]] = [] + for _ in range(len(cases)): + times.append([]) + plt.title(f"Run-times for {function.__name__}") + if text: + print(f"Run-times for {function.__name__}\n") + print("Input size", end=" ") + for case in cases: + print(f"{case.__name__[:15]:>15}", end=" ") + for size in sizes: + if text: + print(f"\n{size:>10}", end=" ") + for index in range(len(cases)): + instance = cases[index](size) + run_time = time_it(function, *instance) + if not scale: + scale, unit = scale_and_unit(run_time) + run_time = run_time * scale + if chart: + times[index].append(run_time) + if text: + print(f"{run_time:>15.1f}", end=" ") + if text: + print(f"{unit}", end="") + if chart: + plt.xlabel("Input size") + plt.ylabel(f"Run-time ({unit})") + for index in range(len(cases)): + plt.plot(sizes, times[index], markers[index], label=cases[index].__name__) + plt.legend() + plt.show() + + +def time_functions( + functions: list[Callable], + inputs: Callable, + start: int, + double: int, + text: bool = True, + chart: bool = False, + value: bool = False, +) -> None: + """Print or plot the run-times of different functions for the same inputs. + + `time_functions` prints or plots the run-times given list of functions and an input + generator. Inputs are generated based on a starting size and are doubled a specified + number of times. + + Args: + functions (list[Callable]): A list of functions whose run-times will be measured. + Must be 1 to 6 functions. + inputs (Callable): A function to generate inputs when given a specific size. + start (int): The starting size for the inputs. Must be positive. + double (int): The number of times to double the input size. Must be non-negative. + text (bool, optional): If True, print the run-times in text format + chart (bool, optional): If True plot the run-times using a chart. + value (bool, optional): If True x-axis is labelled "Input value" otherwise "Input size". + + Raises: + AssertionError: If input conditions are not satisfied. + """ + assert start > 0, "the start size/value can't be negative" + assert double >= 0, "must double the input size/value at least zero times" + assert 0 < len(functions) < 7, "there must be 1 to 6 functions" + assert text or chart, "at least one of text and chart must be enabled" + + x_label = "Input " + ("value" if value else "size") + text_width = len(x_label) + sizes = [start] # the input sizes used + for _ in range(double): + sizes.append(sizes[-1] * 2) + scale = unit = None # no scale determined yet + if chart: + markers = ["bo-", "ko--", "ro:", "ys-", "cs--", "gs:"] + times: list[list[float]] = [] + for _ in range(len(functions)): + times.append([]) + plt.title(f"Inputs generated by {inputs.__name__}") + if text: + print(f"Inputs generated by {inputs.__name__}\n") + print(x_label, end=" ") + for index in range(len(functions)): + print(f"{functions[index].__name__[:15]:>15}", end=" ") + for size in sizes: + if text: + print(f"\n{size:>{text_width}}", end=" ") + instance = inputs(size) + for index in range(len(functions)): + run_time = time_it(functions[index], *instance) + if not scale: + scale, unit = scale_and_unit(run_time) + run_time = run_time * scale + if chart: + times[index].append(run_time) + if text: + print(f"{run_time:>15.1f}", end=" ") + if text: + print(f"{unit}", end="") + if chart: + plt.xlabel(x_label) + plt.ylabel(f"Run-time ({unit})") + for index in range(len(functions)): + plt.plot( + sizes, times[index], markers[index], label=functions[index].__name__ + ) + plt.legend() + plt.show() + + +def time_functions_int( + functions: list[Callable], + generator: Callable = int_value, + start_size: int = 1, + double: int = 10, + text: bool = True, + chart: bool = True, +) -> None: + """Time functions that take a single integer as input. + + `time_functions_int` uses `time_functions` to measure and display the run-times + of a given list of functions that accept a single integer input. The integer inputs + are generated starting from a specified value that defaults to 1, and are doubled + a specified number of times that defaults to 10. + + Args: + functions (list[Callable]): A list of functions whose run-times will be measured. + Each function must accept a single integer argument. Must be 1 to 6 functions. + generator (Callable, optional): A function to generate integer inputs. Defaults to + `int_value`, which should generate an integer based on the input size. + start_size (int, optional): The starting integer value for inputs. Defaults to 1. + Must be positive. + double (int, optional): The number of times to double the input integer value. + Defaults to 10. Must be non-negative. + text (bool, optional): If True, print the run-times in text format. + chart (bool, optional): If True, plot the run-times using a chart. + """ + time_functions(functions, generator, start_size, double, text, chart, True) diff --git a/src/docs/library.md b/src/docs/library.md index fd5b6be..286b43a 100644 --- a/src/docs/library.md +++ b/src/docs/library.md @@ -2,13 +2,11 @@ The `algoesup` library provides support for testing, timing and linting code. -## Testing - -This function can be used with any Python program. +This library requires `ipython` and `matplotlib` -The library requires `matplotlib` and `ipython`. +## Testing -::: algoesup +::: algoesup.test options: heading_level: 3 show_root_toc_entry: false @@ -17,7 +15,7 @@ The library requires `matplotlib` and `ipython`. ## Timing -::: algoesup +::: algoesup.time options: heading_level: 3 show_root_toc_entry: false @@ -30,7 +28,7 @@ The library requires `matplotlib` and `ipython`. These are to lint within a Jupyter notebook, cell by cell. -::: algoesup +::: algoesup.magics options: heading_level: 3 show_root_toc_entry: false