From b50b4a76eb679ec2de11cc02a1bc637e552cd0ee Mon Sep 17 00:00:00 2001 From: fernandocrz Date: Mon, 4 Dec 2023 16:50:56 -0300 Subject: [PATCH] Add support for jupyter notebooks Credits to @pakio and @mateuslatrova for the contributions --- .github/workflows/tests.yml | 7 +- README.rst | 9 + pipreqs/pipreqs.py | 87 +- poetry.lock | 988 ++++++++++++++++++++- pyproject.toml | 2 + tests/_data_notebook/magic_commands.ipynb | 65 ++ tests/_data_notebook/markdown_test.ipynb | 37 + tests/_data_notebook/models.py | 0 tests/_data_notebook/test.ipynb | 102 +++ tests/_invalid_data_notebook/invalid.ipynb | 34 + tests/test_pipreqs.py | 76 +- tox.ini | 2 +- 12 files changed, 1397 insertions(+), 12 deletions(-) create mode 100644 tests/_data_notebook/magic_commands.ipynb create mode 100644 tests/_data_notebook/markdown_test.ipynb create mode 100644 tests/_data_notebook/models.py create mode 100644 tests/_data_notebook/test.ipynb create mode 100644 tests/_invalid_data_notebook/invalid.ipynb diff --git a/.github/workflows/tests.yml b/.github/workflows/tests.yml index 0f39b4d..d98c199 100644 --- a/.github/workflows/tests.yml +++ b/.github/workflows/tests.yml @@ -39,13 +39,14 @@ jobs: - name: Install dependencies run: | python -m pip install --upgrade pip - pip install coverage docopt yarg requests + pip install poetry + poetry install --with dev - name: Calculate coverage - run: coverage run --source=pipreqs -m unittest discover + run: poetry run coverage run --source=pipreqs -m unittest discover - name: Create XML report - run: coverage xml + run: poetry run coverage xml - name: Upload coverage to Codecov uses: codecov/codecov-action@v3 diff --git a/README.rst b/README.rst index 22a3aef..0b5433e 100644 --- a/README.rst +++ b/README.rst @@ -25,6 +25,14 @@ Installation pip install pipreqs +Obs.: if you don't want support for jupyter notebooks, you can install pipreqs without the dependencies that give support to it. +To do so, run: + +.. code-block:: sh + + pip install --no-deps pipreqs + pip install yarg==0.1.9 docopt==0.6.2 + Usage ----- @@ -57,6 +65,7 @@ Usage | e.g. Flask~=1.1.2 | e.g. Flask>=1.1.2 | e.g. Flask + --scan-notebooks Look for imports in jupyter notebook files. Example ------- diff --git a/pipreqs/pipreqs.py b/pipreqs/pipreqs.py index 20ccf70..2162c8b 100644 --- a/pipreqs/pipreqs.py +++ b/pipreqs/pipreqs.py @@ -35,6 +35,7 @@ | e.g. Flask~=1.1.2 | e.g. Flask>=1.1.2 | e.g. Flask + --scan-notebooks Look for imports in jupyter notebook files. """ from contextlib import contextmanager import os @@ -53,6 +54,18 @@ REGEXP = [re.compile(r"^import (.+)$"), re.compile(r"^from ((?!\.+).*?) import (?:.*)$")] +scan_noteboooks = False + + +class NbconvertNotInstalled(ImportError): + default_message = ( + "In order to scan jupyter notebooks, please install the nbconvert and ipython libraries" + ) + + def __init__(self, message=default_message): + super().__init__(message) + + @contextmanager def _open(filename=None, mode="r"): """Open a file or ``sys.stdout`` depending on the provided filename. @@ -89,7 +102,16 @@ def get_all_imports(path, encoding="utf-8", extra_ignore_dirs=None, follow_links raw_imports = set() candidates = [] ignore_errors = False - ignore_dirs = [".hg", ".svn", ".git", ".tox", "__pycache__", "env", "venv"] + ignore_dirs = [ + ".hg", + ".svn", + ".git", + ".tox", + "__pycache__", + "env", + "venv", + ".ipynb_checkpoints", + ] if extra_ignore_dirs: ignore_dirs_parsed = [] @@ -97,18 +119,22 @@ def get_all_imports(path, encoding="utf-8", extra_ignore_dirs=None, follow_links ignore_dirs_parsed.append(os.path.basename(os.path.realpath(e))) ignore_dirs.extend(ignore_dirs_parsed) + extensions = get_file_extensions() + walk = os.walk(path, followlinks=follow_links) for root, dirs, files in walk: dirs[:] = [d for d in dirs if d not in ignore_dirs] candidates.append(os.path.basename(root)) - files = [fn for fn in files if os.path.splitext(fn)[1] == ".py"] + py_files = [file for file in files if file_ext_is_allowed(file, [".py"])] + candidates.extend([os.path.splitext(filename)[0] for filename in py_files]) + + files = [fn for fn in files if file_ext_is_allowed(fn, extensions)] - candidates += [os.path.splitext(fn)[0] for fn in files] for file_name in files: file_name = os.path.join(root, file_name) - with open(file_name, "r", encoding=encoding) as f: - contents = f.read() + contents = read_file_content(file_name, encoding) + try: tree = ast.parse(contents) for node in ast.walk(tree): @@ -145,6 +171,40 @@ def get_all_imports(path, encoding="utf-8", extra_ignore_dirs=None, follow_links return list(packages - data) +def get_file_extensions(): + return [".py", ".ipynb"] if scan_noteboooks else [".py"] + + +def read_file_content(file_name: str, encoding="utf-8"): + if file_ext_is_allowed(file_name, [".py"]): + with open(file_name, "r", encoding=encoding) as f: + contents = f.read() + elif file_ext_is_allowed(file_name, [".ipynb"]) and scan_noteboooks: + contents = ipynb_2_py(file_name, encoding=encoding) + return contents + + +def file_ext_is_allowed(file_name, acceptable): + return os.path.splitext(file_name)[1] in acceptable + + +def ipynb_2_py(file_name, encoding="utf-8"): + """ + + Args: + file_name (str): notebook file path to parse as python script + encoding (str): encoding of file + + Returns: + str: parsed string + + """ + exporter = PythonExporter() + (body, _) = exporter.from_filename(file_name) + + return body.encode(encoding) + + def generate_requirements_file(path, imports, symbol): with _open(path, "w") as out_file: logging.debug( @@ -427,10 +487,27 @@ def dynamic_versioning(scheme, imports): return imports, symbol +def handle_scan_noteboooks(): + if not scan_noteboooks: + logging.info("Not scanning for jupyter notebooks.") + return + + try: + global PythonExporter + from nbconvert import PythonExporter + except ImportError: + raise NbconvertNotInstalled() + + def init(args): + global scan_noteboooks encoding = args.get("--encoding") extra_ignore_dirs = args.get("--ignore") follow_links = not args.get("--no-follow-links") + + scan_noteboooks = args.get("--scan-notebooks", False) + handle_scan_noteboooks() + input_path = args[""] if encoding is None: diff --git a/poetry.lock b/poetry.lock index 5385f69..d3d9f3a 100644 --- a/poetry.lock +++ b/poetry.lock @@ -11,6 +11,53 @@ files = [ {file = "alabaster-0.7.13.tar.gz", hash = "sha256:a27a4a084d5e690e16e01e03ad2b2e552c61a65469419b907243193de1a84ae2"}, ] +[[package]] 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"d731e0ae8c80090092ff87b4fac42ab736692484e4032018471e2d5ab5f1b343" +content-hash = "ed6c41db6778e2e966381d1ea0d7790b6aa2475c694b283e8647ca811a892623" diff --git a/pyproject.toml b/pyproject.toml index 7dd9b6a..53b2ced 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -28,6 +28,8 @@ pipreqs = "pipreqs.pipreqs:main" python = ">=3.8.1,<=3.12" yarg = "0.1.9" docopt = "0.6.2" +nbconvert = "^7.11.0" +ipython = "8.12.3" [tool.poetry.group.dev.dependencies] flake8 = "^6.1.0" diff --git a/tests/_data_notebook/magic_commands.ipynb b/tests/_data_notebook/magic_commands.ipynb new file mode 100644 index 0000000..23dc2d2 --- /dev/null +++ b/tests/_data_notebook/magic_commands.ipynb @@ -0,0 +1,65 @@ +{ + "cells": [ + { + "cell_type": "markdown", + "metadata": {}, + "source": [ + "# Magic test" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "metadata": {}, + "outputs": [], + "source": [ + "%automagic true" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "metadata": {}, + "outputs": [], + "source": [ + "ls -la\n", + "logstate" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "metadata": {}, + "outputs": [], + "source": [ + "ls -la" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "metadata": {}, + "outputs": [], + "source": [ + "%automagic false" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "metadata": {}, + "outputs": [], + "source": [ + "ls -la" + ] + } + ], + "metadata": { + "language_info": { + "name": "python" + }, + "orig_nbformat": 4 + }, + "nbformat": 4, + "nbformat_minor": 2 +} diff --git a/tests/_data_notebook/markdown_test.ipynb b/tests/_data_notebook/markdown_test.ipynb new file mode 100644 index 0000000..54712d3 --- /dev/null +++ b/tests/_data_notebook/markdown_test.ipynb @@ -0,0 +1,37 @@ +{ + "cells": [ + { + "cell_type": "markdown", + "metadata": {}, + "source": [ + "# Markdown test\n", + "import sklearn\n", + "\n", + "```python\n", + "import FastAPI\n", + "```" + ] + } + ], + "metadata": { + "kernelspec": { + "display_name": "Python 3", + "language": "python", + "name": "python3" + }, + "language_info": { + "codemirror_mode": { + "name": "ipython", + "version": 3 + }, + "file_extension": ".py", + "mimetype": "text/x-python", + "name": "python", + "nbconvert_exporter": "python", + "pygments_lexer": "ipython3", + "version": "3.8.1" + } + }, + "nbformat": 4, + "nbformat_minor": 4 +} diff --git a/tests/_data_notebook/models.py b/tests/_data_notebook/models.py new file mode 100644 index 0000000..e69de29 diff --git a/tests/_data_notebook/test.ipynb b/tests/_data_notebook/test.ipynb new file mode 100644 index 0000000..16c07d9 --- /dev/null +++ b/tests/_data_notebook/test.ipynb @@ -0,0 +1,102 @@ +{ + "cells": [ + { + "cell_type": "code", + "execution_count": null, + "metadata": {}, + "outputs": [], + "source": [ + "\"\"\"unused import\"\"\"\n", + "# pylint: disable=undefined-all-variable, import-error, no-absolute-import, too-few-public-methods, missing-docstring\n", + "import xml.etree # [unused-import]\n", + "import xml.sax # [unused-import]\n", + "import os.path as test # [unused-import]\n", + "from sys import argv as test2 # [unused-import]\n", + "from sys import flags # [unused-import]\n", + "# +1:[unused-import,unused-import]\n", + "from collections import deque, OrderedDict, Counter\n", + "# All imports above should be ignored\n", + "import requests # [unused-import]\n", + "\n", + "# setuptools\n", + "import zipimport # command/easy_install.py\n", + "\n", + "# twisted\n", + "from importlib import invalidate_caches # python/test/test_deprecate.py\n", + "\n", + "# astroid\n", + "import zipimport # manager.py\n", + "# IPython\n", + "from importlib.machinery import all_suffixes # core/completerlib.py\n", + "import importlib # html/notebookapp.py\n", + "\n", + "from IPython.utils.importstring import import_item # Many files\n", + "\n", + "# pyflakes\n", + "# test/test_doctests.py\n", + "from pyflakes.test.test_imports import Test as TestImports\n", + "\n", + "# Nose\n", + "from nose.importer import Importer, add_path, remove_path # loader.py\n", + "\n", + "import atexit\n", + "from __future__ import print_function\n", + "from docopt import docopt\n", + "import curses, logging, sqlite3\n", + "import logging\n", + "import os\n", + "import sqlite3\n", + "import time\n", + "import sys\n", + "import signal\n", + "import bs4\n", + "import nonexistendmodule\n", + "import boto as b, peewee as p\n", + "# import django\n", + "import flask.ext.somext # # #\n", + "from sqlalchemy import model" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "metadata": {}, + "outputs": [], + "source": [ + "try:\n", + " import ujson as json\n", + "except ImportError:\n", + " import json\n", + "\n", + "import models\n", + "\n", + "\n", + "def main():\n", + " pass\n", + "\n", + "import after_method_is_valid_even_if_not_pep8" + ] + } + ], + "metadata": { + "kernelspec": { + "display_name": "Python 3", + "language": "python", + "name": "python3" + }, + "language_info": { + "codemirror_mode": { + "name": "ipython", + "version": 3 + }, + "file_extension": ".py", + "mimetype": "text/x-python", + "name": "python", + "nbconvert_exporter": "python", + "pygments_lexer": "ipython3", + "version": "3.8.1" + } + }, + "nbformat": 4, + "nbformat_minor": 4 +} diff --git a/tests/_invalid_data_notebook/invalid.ipynb b/tests/_invalid_data_notebook/invalid.ipynb new file mode 100644 index 0000000..cacff3f --- /dev/null +++ b/tests/_invalid_data_notebook/invalid.ipynb @@ -0,0 +1,34 @@ +{ + "cells": [ + { + "cell_type": "code", + "execution_count": null, + "metadata": {}, + "outputs": [], + "source": [ + "cd ." + ] + } + ], + "metadata": { + "kernelspec": { + "display_name": "Python 3", + "language": "python", + "name": "python3" + }, + "language_info": { + "codemirror_mode": { + "name": "ipython", + "version": 3 + }, + "file_extension": ".py", + "mimetype": "text/x-python", + "name": "python", + "nbconvert_exporter": "python", + "pygments_lexer": "ipython3", + "version": "3.6.4" + } + }, + "nbformat": 4, + "nbformat_minor": 4 +} diff --git a/tests/test_pipreqs.py b/tests/test_pipreqs.py index 38559e5..1418b87 100644 --- a/tests/test_pipreqs.py +++ b/tests/test_pipreqs.py @@ -10,7 +10,7 @@ from io import StringIO import logging -from unittest.mock import patch +from unittest.mock import patch, Mock import unittest import os import requests @@ -48,7 +48,7 @@ def setUpClass(cls): "after_method_is_valid_even_if_not_pep8", ] cls.modules2 = ["beautifulsoup4"] - cls.local = ["docopt", "requests", "nose", "pyflakes"] + cls.local = ["docopt", "requests", "nose", "pyflakes", "ipython"] cls.project = os.path.join(os.path.dirname(__file__), "_data") cls.empty_filepath = os.path.join(cls.project, "empty.txt") cls.imports_filepath = os.path.join(cls.project, "imports.txt") @@ -84,6 +84,12 @@ def setUpClass(cls): cls.alt_requirement_path = os.path.join(cls.project, "requirements2.txt") cls.non_existing_filepath = "xpto" + cls.project_with_notebooks = os.path.join(os.path.dirname(__file__), "_data_notebook") + cls.project_with_invalid_notebooks = os.path.join(os.path.dirname(__file__), "_invalid_data_notebook") + + cls.python_path_same_imports = os.path.join(os.path.dirname(__file__), "_data/test.py") + cls.notebook_path_same_imports = os.path.join(os.path.dirname(__file__), "_data_notebook/test.ipynb") + def test_get_all_imports(self): imports = pipreqs.get_all_imports(self.project) self.assertEqual(len(imports), 15) @@ -519,6 +525,44 @@ def test_output_requirements(self): stdout_content = capturedOutput.getvalue().lower() self.assertTrue(file_content == stdout_content) + def test_import_notebooks(self): + """ + Test the function get_all_imports() using .ipynb file + """ + self.mock_scan_notebooks() + imports = pipreqs.get_all_imports(self.project_with_notebooks) + for item in imports: + self.assertTrue(item.lower() in self.modules, "Import is missing: " + item) + not_desired_imports = ["time", "logging", "curses", "__future__", "django", "models", "FastAPI", "sklearn"] + for not_desired_import in not_desired_imports: + self.assertFalse( + not_desired_import in imports, + f"{not_desired_import} was imported, but it should not have been." + ) + + def test_invalid_notebook(self): + """ + Test that invalid notebook files cannot be imported. + """ + self.mock_scan_notebooks() + self.assertRaises(SyntaxError, pipreqs.get_all_imports, self.project_with_invalid_notebooks) + + def test_ipynb_2_py(self): + """ + Test the function ipynb_2_py() which converts .ipynb file to .py format + """ + python_imports = pipreqs.get_all_imports(self.python_path_same_imports) + notebook_imports = pipreqs.get_all_imports(self.notebook_path_same_imports) + self.assertEqual(python_imports, notebook_imports) + + def test_file_ext_is_allowed(self): + """ + Test the function file_ext_is_allowed() + """ + self.assertTrue(pipreqs.file_ext_is_allowed("main.py", [".py"])) + self.assertTrue(pipreqs.file_ext_is_allowed("main.py", [".py", ".ipynb"])) + self.assertFalse(pipreqs.file_ext_is_allowed("main.py", [".ipynb"])) + def test_parse_requirements(self): """ Test parse_requirements function @@ -561,6 +605,34 @@ def test_parse_requirements_handles_file_not_found(self, exit_mock): self.assertEqual(printed_text, "File xpto was not found. Please, fix it and run again.") + def test_ignore_notebooks(self): + """ + Test if notebooks are ignored when the scan-notebooks parameter is False + """ + notebook_requirement_path = os.path.join(self.project_with_notebooks, "requirements.txt") + + pipreqs.init( + { + "": self.project_with_notebooks, + "--savepath": None, + "--use-local": None, + "--force": True, + "--proxy": None, + "--pypi-server": None, + "--print": False, + "--diff": None, + "--clean": None, + "--mode": None, + "--scan-notebooks": False, + } + ) + assert os.path.exists(notebook_requirement_path) == 1 + assert os.path.getsize(notebook_requirement_path) == 1 # file only has a "\n", meaning it's empty + + def mock_scan_notebooks(self): + pipreqs.scan_noteboooks = Mock(return_value=True) + pipreqs.handle_scan_noteboooks() + def tearDown(self): """ Remove requiremnts.txt files that were written diff --git a/tox.ini b/tox.ini index 2c547c5..5da6ede 100644 --- a/tox.ini +++ b/tox.ini @@ -23,4 +23,4 @@ exclude = tests/_data_duplicated_deps/ tests/_data_ignore/ tests/_invalid_data/ -max-line-length = 120 +max-line-length = 120 \ No newline at end of file