Merge master into 77-github2prov-prototype-implementation

CHANGELOG.md

@@ -0,0 +1,191 @@
+# Changelog
+
+All notable changes to this project will be documented in this file.
+
+The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/),
+and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html)
+
+## [Unreleased]
+
+
+## [2.1.0] - 2023-04-17
+
+### Added
+- CHANGELOG.md file to document all notable changes to this project.
+- README.md section on how to get started with gitlab2prov.
+- README.md note that gitlab2prov requires a git installation.
+- README.md section on dependencies and their respective licenses. See #91 for more details.
+- pyproject.toml comments documenting the license information of all dependencies. See #91 for more details.
+- Project documentation on how to obtain a GitLab API token.
+
+### Changed
+- Tool will check for a git installation and exit with an error message if none is found. See #93 for more details.
+
+### Fixed
+- Click package is now listed as a dependency in pyproject.toml. Thank you [@daniel-mohr](https://github.com/daniel-mohr) for reporting this oversight.
+
+
+## [2.0.0] - 2022-10-31
+### Added
+- New command line interface composed of multiple subcommands that can be chained together to build any desired gitlab2prov pipeline.
+- New YAML configuration file format to specify gitlab2prov pipelines in textual format and save them for later reruns or simple on-the-fly edits.
+- JSON-Schema file to check the config file for syntactical errors.
+- `bumpversion` support to change the version number with a single command.
+
+### Changed
+- New build system that minimizes the number of necessary metadata files.
+- New CLI replaces the old CLI.
+- New config file format replaces the old config file format.
+- Deprecate setup.py, setup.cfg in favor of pyproject.toml. See #70 for more details.
+
+### Fixed
+- Tool runs on Windows should no longer trigger WinError 5/267. See #67.
+- Special characters such as emojis no longer trigger a UnicodeEncodeError when serializing files. See #66.
+
+
+## [1.1.4] - 2022-07-18
+
+### Added
+- A GitHub workflow to validate the citation file on changes.
+
+### Changed
+- Current version and release date in citation file.
+
+### Fixed
+- Update the start- and endpoint of relations during pseudonymization.  
+- User details and agent IDs are pseudonymized using hashing for flexible pseudonymization and merging of provenance graphs (#62).
+
+
+## [1.1.3] - 2022-07-03
+
+### Fixed
+- FileRevision objects that do not have a previous revision no longer lead to a TypeError when serializing the modification model. (see #64)
+
+## [1.1.2] - 2022-07-01
+
+### Fixed
+- Disable project features no longer lead to a 403 Forbidden. (see #61)
+- Default annotation classifier no longer keys into a dictionary resulting in a KeyError (#63)
+
+## [1.1.1] - 2022-06-27
+
+### Fixed
+- Fix a memory bloating issue by not using mutable objects as function argument default value (see #60)
+- Fix a spelling mistake in `config.formats` to `config.format`
+
+## [1.1] - 2022-06-12
+
+### Added
+- Multi-format support for provenance graph serialization supported by the `multi-format` subcommand. (see #54)
+- `outfile` option to section `OUTPUT` in the config file to specify the output file name.
+
+### Changed
+- README now includes a section about multi-format serialization.
+
+## [1.0] - 2022-06-12
+
+### Added
+- Qualified relations for relationship types `wasGeneratedBy`, `wasInvalidatedBy`, `used`, `wasAssociatedWith` (see #52)
+- Command line flag `--v` enables logging to the console.
+- Command line flag `--profile` enables profiling of a tool run.
+- Test suite.
+- Documentation for config file options in the config file example.
+- Model documentation including descriptions of each node and relationship with their respective properties.
+- `requirements_dev.txt` to install development dependencies.
+
+### Fixed
+- Releases without evidence no longer lead to IndexError. (see #53)
+- Processing parent commits no longer leads to errors. (#37)
+- Missing event classifiers are now handled gracefully. (#38)
+
+### Changed
+- Support comma-seperated lists of URLs for config file option `project_urls`.
+- Rename `aliases` to `double_agents` in the config file and command line interface.
+- Rename `pseudonymize` to `pseudonymous` in the config file and command line interface.
+- Rename the config file sections to match the new CLI subcommands
+- Stop manual file history computation. Each file revision now has exactly one previous revision instead of one or more.
+- Use the modification model for commit statuses: MODIFIED, RENAMED, COPIED, CHANGED.
+- Ignore file revisions with unkown commit status.
+- Change event classification to use the package `regex` that supports branch reset expressions.
+- Change build process to use `pyproject.toml` aswell as `setup.cfg`
+- Change architecture to messagebus in anticipation of future features.
+- Bump minimum required `prov` version to 2.0.0
+
+### Removed
+- Rate limit flag/option `--r`/`rate_limit`. Asynchronicity during retrieval is no longer supported.
+- Quiet flag/option `--q`/`quiet`. Default behavior is to be quiet by default unless the `--v` flag is set.
+
+
+## [0.5] - 2021-06-21
+
+### Added
+- Support for 'tags' and 'releases' to PROV model (see #39)
+- CITATION file in Citation File Format (CFF) (see #49)
+
+### Changed
+- Revisions (changes) of files expressed in PROV model (see #40)
+
+### Fixed
+- API client pagination (see #41)
+- 'wasGeneratedBy' relation for 'tags' corrected (see #51)
+
+### Removed
+- Resource names from attributes (see #47, #48)
+
+## [0.4.1] - 2021-04-23
+### Added
+- Support for wider range of GitLab events.
+- Documentation for all new supported events.
+
+### Fixed
+- Errors when requesting deactivated API endpoints are now handled gracefully.
+
+## [0.4] Pre-release - 2021-04-23
+### Added
+- Support for additional GitLab events.
+
+### Fixed
+- Error handling hotfix for requests to deactivated API endpoints.
+
+## [0.3] - 2020-10-15
+
+### Changed
+- Updated PROV models in /docs to reflect changes in the PROV model.
+- Updated config file example.
+- Update usage section in README.
+
+### Fixed
+- Updated `setup.py` to resolve an issue for python versions below 3.8.
+- Configuration errors are now handled gracefully.
+
+### Removed
+- Dependency on `prov-db-connector`. Neo4j import functionality is no longer part of this package.
+
+## [0.2] - 2020-08-01
+
+### Changed
+- Project status marked for `gitlab2prov` usage in [@cdboer's](https://github.com/cdboer) bachelor thesis.
+
+## [0.1] - 2020-01-22
+
+### Added
+- Revised README to provide a comprehensive overview of the project's objectives and instructions for usage.
+- Initial public version of the gitlab2prov package.
+- Preset queries tailored for use on the property graphs produced by the tool, implemented in Neo4j.
+- `requirements.txt` file specifying the list of dependencies required to run the tool.
+
+[unreleased]: https://github.com/dlr-sc/gitlab2prov/compare/v2.1.0...HEAD
+[2.1.0]: https://github.com/dlr-sc/gitlab2prov/compare/v2.0.0...v2.1.0
+[2.0.0]: https://github.com/dlr-sc/gitlab2prov/compare/v1.1.4...v2.0.0
+[1.1.4]: https://github.com/dlr-sc/gitlab2prov/compare/v1.1.3...v1.1.4
+[1.1.3]: https://github.com/dlr-sc/gitlab2prov/compare/v1.1.2...v1.1.3
+[1.1.2]: https://github.com/dlr-sc/gitlab2prov/compare/v1.1.1...v1.1.2
+[1.1.1]: https://github.com/dlr-sc/gitlab2prov/compare/v1.1...v1.1.1
+[1.1]: https://github.com/dlr-sc/gitlab2prov/compare/v1.0...v1.1
+[1.0]: https://github.com/dlr-sc/gitlab2prov/compare/v0.5...v1.0
+[0.5]: https://github.com/dlr-sc/gitlab2prov/compare/v0.4.1...v0.5
+[0.4.1]: https://github.com/dlr-sc/gitlab2prov/compare/v0.4...v0.4.1
+[0.4]: https://github.com/dlr-sc/gitlab2prov/compare/v0.3...v0.4
+[0.3]: https://github.com/dlr-sc/gitlab2prov/compare/v0.2...v0.3
+[0.2]: https://github.com/dlr-sc/gitlab2prov/compare/v0.1...v0.2
+[0.1]: https://github.com/dlr-sc/gitlab2prov/releases/tag/v0.1

CITATION.cff

@@ -12,8 +12,8 @@ authors:
     given-names: Andreas
     affiliation: "German Aerospace Center (DLR)"
     orcid: "https://orcid.org/0000-0001-5750-5649"
-version: 2.0.0
-date-released: "2022-10-31"
+version: "2.1.0"
+date-released: "2023-04-17"
 license: MIT
 repository-code: "https://github.com/DLR-SC/gitlab2prov"
 references:

gitlab2prov/__init__.py

@@ -3,5 +3,5 @@
 __author__ = "Claas de Boer, Andreas Schreiber"
 __copyright__ = "Copyright 2020, German Aerospace Center (DLR) and individual contributors"
 __license__ = "MIT"
-__version__ = "2.0.0"
+__version__ = "2.1.0"
 __status__ = "Development"

gitlab2prov/entrypoints/cli.py

@@ -5,6 +5,7 @@
 from prov.model import ProvDocument
 
 import click
+import git
 
 from gitlab2prov import __version__
 from gitlab2prov import bootstrap
@@ -14,6 +15,24 @@
 from gitlab2prov.prov import operations
 
 
+def is_git_available():
+    """Check whether git is installed using the GitPython package."""
+    try:
+        git.Git().execute(["git", "--version"])
+        return True
+    except git.exc.GitCommandNotFound:
+        return False
+
+
+def is_git_available():
+    """Check whether git is installed using the GitPython package."""
+    try:
+        git.Git().execute(["git", "--version"])
+        return True
+    except git.exc.GitCommandNotFound:
+        return False
+
+
 def enable_logging(ctx: click.Context, param: str, enable: bool):
     """Callback that optionally enables logging."""
     if enable:
@@ -116,6 +135,8 @@ def gitlab2prov(ctx):
     """
     Extract provenance information from GitLab projects.
     """
+    if not is_git_available():
+        ctx.fail("Could not find git. Please install git.")
     ctx.obj = bootstrap.bootstrap("gitlab")
 
 

pyproject.toml

@@ -1,5 +1,8 @@
 [build-system]
-requires = ["setuptools>=65.0", "wheel"]
+requires = [
+    "setuptools>=65.0", # MIT License
+    "wheel",            # MIT License
+]
 build-backend = "setuptools.build_meta"
 
 [project]
@@ -13,14 +16,14 @@ maintainers = [
     { name = "Andreas Schreiber", email = "andreas.schreiber@dlr.de" },
 ]
 dependencies = [
-    "prov>=2.0.0",
-    "git-python",
-    "python-gitlab",
-    "jsonschema",
-    "ruamel.yaml",
-    "pydot>=1.2.0",
-    "PyGithub",
-    "click",
+    "prov>=2.0.0",   # MIT License
+    "git-python",    # BSD 3-Clause License
+    "python-gitlab", # LGPL-3.0 License
+    "jsonschema",    # MIT License
+    "ruamel.yaml",   # MIt License
+    "pydot>=1.2.0",  # MIT License
+    "PyGithub",      # LGPL-3.0 License
+    "click",         # BSD 3-Clause License
 ]
 keywords = [
     "prov",
@@ -45,7 +48,13 @@ classifiers = [
 dynamic = ["version"]
 
 [project.optional-dependencies]
-dev = ["pytest", "pytest-mock", "black", "isort", "bump2version"]
+dev = [
+    "pytest",       # MIT License
+    "pytest-mock",  # MIT License
+    "black",        # MIT License
+    "isort",        # MIT License
+    "bump-my-version", # MIT License
+]
 
 [project.scripts]
 gitlab2prov = "gitlab2prov.entrypoints.cli:gitlab2prov"
@@ -72,3 +81,25 @@ py_version = 310
 [tool.black]
 line-length = 99
 target-version = ['py310']
+
+[tool.bumpversion]
+current_version = "2.1.0"
+commit = true
+tag = true
+tag_name = "{new_version}"
+message = "Bump version: {current_version} → {new_version}"
+
+[[tool.bumpversion.files]]
+filename = "gitlab2prov/__init__.py"
+search = '__version__ = "{current_version}"'
+replace = '__version__ = "{new_version}"'
+
+[[tool.bumpversion.files]]
+filename = "CITATION.cff"
+search = 'version: "{current_version}"'
+replace = 'version: "{new_version}"'
+
+[[tool.bumpversion.files]]
+filename = "CITATION.cff"
+search = 'date-released: "\d{{4}}-\d{{2}}-\d{{2}}"'
+replace = 'date-released: "{now:%Y-%m-%d}"'