Devel

[JoshuaSBrown]

PR Description

Update Tony branch from devel.

Tasks

• - A description of the PR has been provided, and a diagram included if it is a new feature.
• - Formatter has been run
• - CHANGELOG comment has been added
• - Labels have been assigned to the pr
• - A reviwer has been added
• - A user has been assigned to work on the pr
• - If new feature a unit test has been added

Summary by Sourcery

Refactor code, fix bugs and update dependencies.

Bug Fixes:

• Fix bug in authz library parsing of authz.conf file where Globus paths were incorrectly sanitized when using just '/'.
• Fix bug in libauthz where log_path variable was not being read from the config file.
• Fix unbound variable in Foxx entrypoint file.
• Fix Jupyter notebooks in documentation.

Enhancements:

• Refactor authz Foxx module, split into objects and added unit tests.
• Fix deprecated method usage for Protobuf in Python client library.

Tests:

• Add authz unit testing to the CI.

[sourcery-ai]

Reviewer's Guide by Sourcery

This pull request implements multiple improvements throughout the repository. Major updates include significant modifications to nearly all the Jupyter notebooks (updating content, exercise instructions, formatting and documentation), enhancements to CI/CD and build configurations, library and dependency upgrades (e.g. updating protobuf from 4.21.1 to 5.27.1 and replacing deprecated reflection APIs), and changes in CMake and repository structure. In addition, the CHANGELOG was updated to reflect reordering of changelog entries and new items. Overall, these changes aim to improve developer experience, code consistency and reliability of builds and tests.

No diagrams generated as the changes look simple and do not need a visual representation.

File-Level Changes

Change	Details	Files
Update and standardize Jupyter Notebooks	Updated notebook content across several notebooks (e.g. Basics, Data Records, Data Transfer, Collections, Collaborative Exercise, and verify notebooks) including reformatting markdown, exercise instructions, and code examples. Removed or revised placeholders and added new exercise instructions. Added a new GitHub workflow to lint Jupyter notebooks with nbQA, flake8, and black.	jupyter_notebooks/0_verify.ipynb jupyter_notebooks/1_Basics.ipynb jupyter_notebooks/1_Basics_with_Solutions.ipynb jupyter_notebooks/2_Data_Records.ipynb jupyter_notebooks/2_Data_Records_with_Solutions.ipynb jupyter_notebooks/3_Data_Transfer.ipynb jupyter_notebooks/3_Data_Transfer_with_Solutions.ipynb jupyter_notebooks/4_Collections_Queries.ipynb jupyter_notebooks/5_Collaborative_Exercise.ipynb .github/workflows/jupyternotebook-lint.yml jupyter_notebooks/.flake8
Enhance CI/CD and Build Script configurations	Updated GitLab build scripts (build_repo_image.yml and build_gcs_image.yml) to include additional file paths (e.g. CMakeLists.txt, cmake directory, repository/server, repository/gridftp) in the change detection. Modified GitHub workflow for format-check to adjust Black formatting arguments (adding --line-length 88) and removed redundant max-line-length parameters from flake8. Added new configuration files for code formatting including a pyproject.toml with Black settings and a root .flake8 file.	.gitlab/build/build_repo_image.yml .gitlab/build/build_gcs_image.yml .github/workflows/format-check.yml pyproject.toml .flake8
Upgrade dependencies and update library APIs	Updated the protobuf dependency in requirements.txt from version 4.21.1 to 5.27.1. Replaced deprecated protobuf reflection API usage in python/datafed_pkg/datafed/Connection.py – eliminated calls to google.protobuf.reflection.MakeClass and ParseMessage, and replaced them with calls to a GetMessageClass helper function. Adjusted the makeMessage function to use GetMessageClass for consistency.	python/datafed_pkg/datafed/Connection.py python/datafed_pkg/requirements.txt
Update CMake and repository structure	Modified repository/CMakeLists.txt to include or exclude relevant subdirectories. Added file changes in cmake// and repository/server//* to reflect new build structure. Updated build scripts to detect changes in the CMake related files.	repository/CMakeLists.txt cmake/**/* repository/server/**/* repository/gridftp/**/*
Revise CHANGELOG to reflect recent fixes and improvements	Reordered and modified changelog entries to include a new entry for deprecated method usage and updated dependency versions. Added a new changelog entry for documentation fix in Jupyter notebooks.	CHANGELOG.md

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[sourcery-ai]

Hey @JoshuaSBrown - I've reviewed your changes - here's some feedback:

Overall Comments:

• Consider using a tool like pre-commit to run linters and formatters before committing.

Here's what I looked at during the review

• 🟡 General issues: 3 issues found
• 🟢 Security: all looks good
• 🟢 Testing: all looks good
• 🟢 Complexity: all looks good
• 🟢 Documentation: all looks good

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[sourcery-ai]

issue (bug_risk): Missing closing quote in the context argument may cause a syntax error.

It appears that the context string is not properly closed. Please verify that the intended string (likely 'p/trn001') is correctly delimited.

[JoshuaSBrown]

Please add this to issue #1300

[JoshuaSBrown]

Please add this in an issue and link to #1300

[sourcery-ai]

I have created an issue for your comment: #1308

[sourcery-ai]

issue (typo): Typo: "section" should be "tab"

Under the "References Tab" section, it currently says, "This section lists locations...". It should be "This tab lists locations...".

Suggested change

	- **References Tab**:
	This section lists locations where the schema is referenced within DataFed.
	- **References Tab**:
	- This tab lists locations where the schema is referenced within DataFed.

[JoshuaSBrown]

Please add this to issue #1300

[sourcery-ai]

I have created an issue for your comment: #1303

[sourcery-ai]

issue (typo): Typo: "Jupyternote books" should be "Jupyter notebooks"

Suggested change

	25. [1288] - Bug Jupyternote books in documentation were fixed.
	25. [1288] - Bug Jupyter notebooks in documentation were fixed.

[JoshuaSBrown]

Please add this to issue #1300

[JoshuaSBrown]

Please add this in an issue and link to #1300

[sourcery-ai]

I have created an issue for your comment: #1307