From 29ca2201b16bcd2240dd05c66173dacc2c26460b Mon Sep 17 00:00:00 2001 From: Dave Bunten Date: Wed, 23 Oct 2024 14:59:54 -0600 Subject: [PATCH] Add citability measure (#120) * add functions for reading blobs; measure citation * linting * move blobs to git * add test for the almanack itself * Update src/almanack/metrics/metrics.yml Co-authored-by: Gregory Way * add additional cases for citabillity in readmes Co-Authored-By: Gregory Way --------- Co-authored-by: Gregory Way --- poetry.lock | 199 ++++++++++-------- pyproject.toml | 1 + src/almanack/git.py | 71 ++++++- src/almanack/metrics/data.py | 54 ++++- src/almanack/metrics/metrics.yml | 7 + tests/conftest.py | 53 ++++- tests/data/almanack/repo_setup/create_repo.py | 47 ++--- tests/metrics/test_data.py | 71 ++++++- tests/test_git.py | 48 +++++ 9 files changed, 422 insertions(+), 129 deletions(-) diff --git a/poetry.lock b/poetry.lock index 1c68568e..86fa107e 100644 --- a/poetry.lock +++ b/poetry.lock @@ -409,101 +409,116 @@ pycparser = "*" [[package]] name = "charset-normalizer" -version = "3.3.2" +version = "3.4.0" description = "The Real First Universal Charset Detector. 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"2.0" python-versions = ">=3.9,<=3.12" -content-hash = "7cb5f65c0e0257a8bd64b42242811e92c3bd80034eeb04288cf40ab3980680d5" +content-hash = "6790c7774563a59adcbca6222e6c9b0bd571ca41d5fd8753fddefb8acc3feade" diff --git a/pyproject.toml b/pyproject.toml index 8582b3d6..4742ca51 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -18,6 +18,7 @@ pyyaml = "^6.0.1" pygit2 = "^1.15.1" fire = "^0.6.0" tabulate = "^0.9.0" +charset-normalizer = "^3.4.0" [tool.poetry.group.book.dependencies] jupyter-book = "^1.0.0" diff --git a/src/almanack/git.py b/src/almanack/git.py index 6992cd00..76db560e 100644 --- a/src/almanack/git.py +++ b/src/almanack/git.py @@ -4,9 +4,10 @@ import pathlib import tempfile -from typing import Dict, List +from typing import Dict, List, Optional import pygit2 +from charset_normalizer import from_bytes def clone_repository(repo_url: str) -> pathlib.Path: @@ -144,3 +145,71 @@ def get_most_recent_commits(repo_path: pathlib.Path) -> tuple[str, str]: target_commit = commits[0] # Most recent return str(source_commit.id), str(target_commit.id) + + +""" +Module for handling various tasks with git repo blobs. +""" + + +import pygit2 + + +def detect_encoding(blob_data: bytes) -> str: + """ + Detect the encoding of the given blob data using charset-normalizer. + + Args: + blob_data (bytes): The raw bytes of the blob to analyze. + + Returns: + str: The best detected encoding of the blob data. + + Raises: + ValueError: If no encoding could be detected. + """ + if not blob_data: + raise ValueError("No data provided for encoding detection.") + + result = from_bytes(blob_data) + if result.best(): + # Get the best encoding found + return result.best().encoding + raise ValueError("Encoding could not be detected.") + + +def find_and_read_file(repo: pygit2.Repository, filename: str) -> Optional[str]: + """ + Find and read the content of a file in the repository that matches the filename pattern. + + Args: + repo (str): The path to the repository. + filename (str): The pattern to match against filenames. + + Returns: + Optional[str]: The content of the found file, or None if no matching files are found. + """ + + # Get the tree associated with the latest commit + tree = repo.head.peel().tree + + # find the first occurrence of a matching file + found_file: Optional[pygit2.Blob] = next( + ( + entry + for entry in tree + if entry.type == pygit2.GIT_OBJECT_BLOB + and filename.lower() == entry.name.lower() + ), + None, + ) + + # if we have none, return it early to avoid trying to read nothing + if found_file is None: + return found_file + + # Read the content of the first found blob + blob_data: bytes = found_file.data + + # Decode and return content as a string + return blob_data.decode(detect_encoding(blob_data)) diff --git a/src/almanack/metrics/data.py b/src/almanack/metrics/data.py index d0c6b3fe..01d282c7 100644 --- a/src/almanack/metrics/data.py +++ b/src/almanack/metrics/data.py @@ -11,7 +11,7 @@ import pygit2 import yaml -from ..git import clone_repository, get_commits, get_edited_files +from ..git import clone_repository, find_and_read_file, get_commits, get_edited_files from .entropy.calculate_entropy import ( calculate_aggregate_entropy, calculate_normalized_entropy, @@ -115,6 +115,57 @@ def file_exists_in_repo( return False +def is_citable(repo: pygit2.Repository) -> bool: + """ + Check if the given repository is citable. + + A repository is considered citable if it contains a CITATION.cff or CITATION.bib + file, or if the README.md file contains a citation section indicated by "## Citation" + or "## Citing". + + Args: + repo (pygit2.Repository): The repository to check for citation files. + + Returns: + bool: True if the repository is citable, False otherwise. + """ + + # Check for a CITATION.cff or CITATION.bib file + if file_exists_in_repo( + repo=repo, + expected_file_name="citation", + check_extension=True, + extensions=[".cff", ".bib"], + ): + return True + + # Look for a README.md file and read its content + if ( + file_content := find_and_read_file(repo=repo, filename="readme.md") + ) is not None: + # Check for an H2 heading indicating a citation section + if any( + check_string in file_content + for check_string in [ + # markdown sub-headers + "## Citation", + "## Citing", + "## Cite", + "## How to cite", + # RST sub-headers + "Citation\n--------", + "Citing\n------", + "Cite\n----", + "How to cite\n-----------", + # DOI shield + "[![DOI](https://img.shields.io/badge/DOI", + ] + ): + return True + + return False + + def compute_repo_data(repo_path: str) -> None: """ Computes comprehensive data for a GitHub repository. @@ -183,6 +234,7 @@ def compute_repo_data(repo_path: str) -> None: repo=repo, expected_file_name="license", ), + "is-citable": is_citable(repo=repo), "normalized_total_entropy": normalized_total_entropy, "file_level_entropy": file_entropy, } diff --git a/src/almanack/metrics/metrics.yml b/src/almanack/metrics/metrics.yml index c5bac5b3..f7f85975 100644 --- a/src/almanack/metrics/metrics.yml +++ b/src/almanack/metrics/metrics.yml @@ -52,6 +52,13 @@ metrics: description: >- Boolean value indicating the presence of a LICENSE file in the repository. + - name: "is-citable" + id: "SGA-GL-0005" + result-type: "bool" + result-data-key: "is-citable" + description: >- + Boolean value indicating the presence of a CITATION file + or some other means of indicating how to cite the work. - name: "agg-info-entropy" id: "SGA-VS-0001" result-type: "float" diff --git a/tests/conftest.py b/tests/conftest.py index 526a48c6..5989f2d2 100644 --- a/tests/conftest.py +++ b/tests/conftest.py @@ -7,11 +7,13 @@ import shutil import subprocess +import pygit2 import pytest from tests.data.almanack.repo_setup.create_repo import ( - create_community_health_repository, create_entropy_repositories, + repo_setup, + set_repo_user_config, ) from .utils import check_subproc_run_for_nonzero @@ -110,7 +112,50 @@ def community_health_repository_path(tmp_path_factory): Fixture to call create_community_health_repository, create the repositories, then delete them using the tmp_path_factory fixture to provide a temporary directory for tests. """ - # Create a base temporary directory - base_path = tmp_path_factory.mktemp("almanack_community_health") - yield create_community_health_repository(base_path) + # Create a temporary directory for the session + temp_dir = tmp_path_factory.mktemp("community_health_repo") + + yield repo_setup( + repo_path=pathlib.Path(temp_dir), + files={ + "README.md": "# This is an example readme\n\nWelcome to our repo!", + "CONTRIBUTING.md": "# This is a stub for a CONTRIBUTING.md", + "CODE_OF_CONDUCT.md": "# This is a stub for a CODE_OF_CONDUCT.md", + "LICENSE.txt": "This is an example LICENSE file.", + }, + ) + + +@pytest.fixture +def repo_with_citation_in_readme(tmp_path): + """Create a temporary repository with a specific structure for testing.""" + # Create a new repository in the temporary path + repo = pygit2.init_repository(tmp_path, bare=False) + + # Set user.name and user.email in the config + set_repo_user_config(repo) + + (tmp_path / "README.md").write_text("## Citation") + + index = repo.index + + index.add_all() + index.write() + + author = repo.default_signature + + tree = repo.index.write_tree() + + repo.create_commit( + "refs/heads/main", + author, + author, + "Committing nested files", + tree, + [], + ) + # set the head to the main branch + repo.set_head("refs/heads/main") + + yield repo # Provide the repository to the tests diff --git a/tests/data/almanack/repo_setup/create_repo.py b/tests/data/almanack/repo_setup/create_repo.py index fc449db3..58c335dc 100644 --- a/tests/data/almanack/repo_setup/create_repo.py +++ b/tests/data/almanack/repo_setup/create_repo.py @@ -155,46 +155,45 @@ def create_entropy_repositories(base_path: pathlib.Path) -> None: commit_changes(repo_path, "Commit with added lines of code") -def create_community_health_repository(base_path: pathlib.Path) -> str: +def repo_setup(repo_path: pathlib.Path, files: dict) -> pygit2.Repository: + """ + Set up a temporary repository with specified files. - filenames_and_contents = { - "README.md": "# This is an example readme\n\nWelcome to our repo!", - "CONTRIBUTING.md": "# This is a stub for a CONTRIBUTING.md", - "CODE_OF_CONDUCT.md": "# This is a stub for a CODE_OF_CONDUCT.md", - "LICENSE.txt": "This is an example LICENSE file.", - } + Args: + tmp_path (Path): The temporary directory where the repo will be created. + files (dict): A dictionary where keys are filenames and values are their content. - repo_path = base_path / "community_health" - repo_path.mkdir(parents=True, exist_ok=True) - repo = pygit2.init_repository(path=str(repo_path), bare=False) + Returns: + pygit2.Repository: The initialized repository with files. + """ + # Create a new repository in the temporary path + repo = pygit2.init_repository(repo_path, bare=False) # Set user.name and user.email in the config set_repo_user_config(repo) - for filename, content in filenames_and_contents.items(): - # add content to each file based on the filenames and contents dict - with open((repo_path / filename).resolve(), "w") as f: - f.write(content) + # Create files in the repository + for filename, content in files.items(): + (repo_path / filename).write_text(content) - # add all files to the index - repo.index.add_all() - # write the files to the index - repo.index.write() + # Stage and commit the files + index = repo.index + index.add_all() + index.write() - # create a tree for the index - tree = repo.index.write_tree() - # gather a default signature author author = repo.default_signature + tree = repo.index.write_tree() + repo.create_commit( "refs/heads/main", author, author, - "Committing community health files", + "Initial commit with setup files", tree, [], ) - # set the head to the main branch + # Set the head to the main branch repo.set_head("refs/heads/main") - return str(repo_path) + return repo diff --git a/tests/metrics/test_data.py b/tests/metrics/test_data.py index 5fd3ed80..430a6845 100644 --- a/tests/metrics/test_data.py +++ b/tests/metrics/test_data.py @@ -1,5 +1,5 @@ """ -Testing generate_data functionality +Testing metrics/data functionality """ import pathlib @@ -16,7 +16,9 @@ compute_repo_data, file_exists_in_repo, get_table, + is_citable, ) +from tests.data.almanack.repo_setup.create_repo import repo_setup def test_generate_repo_data(entropy_repository_paths: dict[str, pathlib.Path]) -> None: @@ -133,7 +135,7 @@ def test_metrics_yaml(): ], ) def test_file_exists_in_repo( - community_health_repository_path: str, + community_health_repository_path: pygit2.Repository, expected_file_name: str, check_extension: bool, extensions: List[str], @@ -143,12 +145,8 @@ def test_file_exists_in_repo( Combined test for file_exists_in_repo function using different scenarios. """ - # test a synthetic repo - repo_path = pathlib.Path(community_health_repository_path).resolve() - repo = pygit2.Repository(str(repo_path)) - result = file_exists_in_repo( - repo=repo, + repo=community_health_repository_path, expected_file_name=expected_file_name, check_extension=check_extension, extensions=extensions, @@ -168,3 +166,62 @@ def test_file_exists_in_repo( ) assert result == expected_result + + +@pytest.mark.parametrize( + "files, expected", + [ + # Test with CITATION.cff + ({"CITATION.cff": "CITATION content."}, True), + # Test with CITATION.bib + ({"CITATION.bib": "CITATION content."}, True), + # Test citation sections in markdown format + ( + {"readme.md": "## Citation\nThis is a citation."}, + True, + ), + ( + {"readme.md": "## Citing us\n\nHere's our awesome citation."}, + True, + ), + # RST scenarios + ({"README.md": "Citation\n--------"}, True), + ({"README.md": "Citing\n------"}, True), + ({"README.md": "Cite\n----"}, True), + ({"README.md": "How to cite\n-----------"}, True), + # DOI badge + ( + { + "README.md": ( + "# Awesome project\n\n" + "[![DOI](https://img.shields.io/badge/DOI-10.48550/arXiv.2311.13417-blue)]" + "(https://doi.org/10.48550/arXiv.2311.13417)" + ), + }, + True, + ), + ({"README.md": "## How to cite"}, True), + # Test with README without citation + ( + {"readme.md": "This is a readme."}, + False, + ), + # Test with no citation files + ({"random.txt": "Some random text."}, False), + # test the almanack itseft as a special case + (None, True), + ], +) +def test_is_citable(tmp_path, files, expected): + """ + Test if the repository is citable based on various file configurations. + """ + + if files is not None: + repo = repo_setup(repo_path=tmp_path, files=files) + else: + # test the almanack itself + repo_path = pathlib.Path(".").resolve() + repo = pygit2.Repository(str(repo_path)) + + assert is_citable(repo) == expected diff --git a/tests/test_git.py b/tests/test_git.py index a2a57ca5..654cb7a5 100644 --- a/tests/test_git.py +++ b/tests/test_git.py @@ -6,9 +6,12 @@ from typing import Any import pygit2 +import pytest from almanack.git import ( clone_repository, + detect_encoding, + find_and_read_file, get_commits, get_edited_files, get_loc_changed, @@ -99,3 +102,48 @@ def test_get_most_recent_commits(entropy_repository_paths: dict[str, Any]): # Validate the commit hashes match assert source_commit_hash == str(commits[1].id) assert target_commit_hash == str(commits[0].id) + + +@pytest.mark.parametrize( + "byte_data, expected_encoding, should_raise", + [ + ( + b"\xef\xbb\xbf\xf0\x9f\xa9\xb3", + "utf_8", + False, + ), # Test detection of UTF-8 encoding + (b"", None, True), # Test detection on empty byte sequence + # Add more test cases here if needed + ], +) +def test_detect_encoding(byte_data, expected_encoding, should_raise): + """Test detection of encoding based on various byte inputs.""" + if should_raise: + with pytest.raises(ValueError): + detect_encoding(byte_data) + else: + detected_encoding = detect_encoding(byte_data) + assert detected_encoding == expected_encoding + + +@pytest.mark.parametrize( + "filename, expected_content", + [ + ("README.md", "## Citation"), # Exact match for file1.txt + ("readme", None), # Partial match, should return content of file1.txt + ("nonexistent.txt", None), # Non-existent file + ], +) +def test_find_and_read_file(repo_with_citation_in_readme, filename, expected_content): + """Test finding and reading files in the repository with various filename patterns.""" + + # Call the function under test + result = find_and_read_file(repo_with_citation_in_readme, filename) + + # Assert the result based on the expected content + if expected_content is None: + assert result is None # Expecting None for non-existent files + else: + assert ( + result == expected_content + ) # Expecting the actual content for found files