CHANGES.rst

Release Notes

This is the list of Slicer Package Manager changes between each release. For full details, see the commit logs at https://github.com/girder/slicer_package_manager

Next Release

0.9.0

New Features

Server

• Sanitize description field for new or updated extension to ensure only a subset of HTML tags and attributes can be used. See html-sanitizer default settings.

Bug fixes

• Prevent incompatibility pinning version of girder, girder-hashsum-download, girder_client and pytest-girder to be >=3.1.20 and <3.2.

Tests

• Improve PackageMetadataChecksumUpdate tests to check extensions package.

Internal

• Fix documentation build adding .readthedocs.yml
• Switch server plugin Python wheel build-system to pyproject.toml.
• Require Python >= 3.8 for the server and update Girder test Docker to use image girder/girder_test:py38-node14 built from girder/.circleci/Dockerfile.

0.8.0

New Features

Server

• Associate application & extension package item with checksum.

  • After uploading an application or extension package, the item metadata will include sha512 metadata entry.
  • After uploading additional files, the item metadata remains unchanged.
  • After removing the second to last files, the sha512 item metadata is updated to match the checksum of the last file.
  • After removing all the files, the sha512 item metadata is set to an empty string.

Documentation

• Remove obsolete cleanNightly.sh script and update faq.
• Update developer installation instructions to use Girder 3.x commands.

Bug fixes

Python Client

• Fix python client test requirements adding "pytest" and "pytest-girder".
• Attempting to install the python client using Python < 3.7 will now report an error message.

Server

• Update extension & package delete endpoints
  • Explicitly check that user can access the associated application folder.
  • Return a confirmation message.

Internal

• Require Python >= 3.6 for the server. This is consistent with the version associated with the Girder test Docker image girder/girder_test:latest built from girder/.circleci/Dockerfile.
• The required version previously set to "3.7" in version "0.7.0" for both client and server but it was not enforced due to an incorrect setup parameter. It should have been specified as python_requires instead of python_require (as defined in PEP 440).
• Re-factor and simplify code based on the newly introduced pre-commit hooks and ruff checks (codespell, pyupgrade and ruff).
• Add type annotations to python client CLI.

Tests

• Add GitHub Actions workflow to run pre-commit hooks.

  • Add "codespell" pre-commit hook and fix typos.

  • Add pyupgrade pre-commit hook specifying "--py36-plus" and updates codes accordingly.

  • Add ruff pre-commit hook enabling the following checks:

    "A",           # flake8-builtins
    "ARG",         # flake8-unused-arguments
    "B",           # flake8-bugbear
    "BLE",         # flake8-blind-except
    "C4",          # flake8-comprehensions
    "COM",         # flake8-commas
    "D",           # pydocstyle (aka flake8-docstrings)
    "E", "F", "W", # flake8
    "EXE",         # flake8-executable
    "EM",          # flake8-errmsg
    "G",           # flake8-logging-format
    "ICN",         # flake8-import-conventions
    "ISC",         # flake8-implicit-str-concat
    "N",           # pep8-naming
    "PIE",         # flake8-pie
    "PGH",         # pygrep-hooks
    "PL",          # pylint
    "PT",          # flake8-pytest-style
    "Q",           # flake8-quotes
    "RSE",         # flake8-raise
    "RUF",         # Ruff-specific
    "S",           # flake8-bandit
    "SIM",         # flake8-simplify
    "SLF",         # flake8-self
    "YTT",         # flake8-2020
    

0.7.1

Bug fixes

Python Client

• Fix wheel ensuring _vendor.bson package is distributed.

0.7.0

Documentation

• Re-organize and simplify documentation.

Internal

• Require Python >= 3.7 for both python client and server.
• Update development status to Production/Stable.
• Vendorize bson.objectid from PyMongo to support installing the client alongside the server and workaround incompatibilities between standalone bson package and the one provided by PyMongo.

Python Client

• Support publishing python client sdist and wheel named slicer-package-manager-client.

0.6.0

New Features

• Support listing extension with a query parameter specifying the text expected to be found in the extension name or description.

Bug fixes

Server

• Fix creation of extension in private application.
• Ensure user or administrator errors associated with API endpoints are displayed and associated with HTTP error code 400 by raising a :exc:`RestException` instead of a generic :exc:`Exception`.
• Update API endpoint GET /app/{app_id}/extension to always check user credentials.

0.5.0

New Features

• Require version information to be specified when uploading application packages. See :issue:`97`.
• Add application package build_date metadata. User may specify a custom value formatted as a datetime string using the API endpoint or the python client. Default is set to current date and time.

Server

• Automatically update release metadata when packages are moved (or copied) between draft and release folders.
• Add convenience functions :func:`slicer_package_manager.utilities.isApplicationFolder`, :func:`slicer_package_manager.utilities.isReleaseFolder` and :func:`slicer_package_manager.utilities.isDraftReleaseFolder`.
• Add :func:`slicer_package_manager.utilities.getReleaseFolder` and simplify update of downloadStats release metadata to use the new function.

Bug fixes

• Remove partially implemented codebase metadata.
• Remove support for unused packagetype metadata.

Tests

• ExternalData:
  • Fix re-download of files if checksum does not match.
  • Re-factor fixture introducing downloadExternals.

0.4.0

New Features

• Support querying application packages given a release name. See :issue:`96`.

Bug fixes

Server

• Ensure permissions are consistently checked in API endpoints implementation. See :issue:`95`.
• Fix support for unauthenticated use of public API endpoints. See :issue:`95`.

0.3.0

Bug fixes

Server

• Update implementation of GET /app/:app_id/package endpoint to properly handle limit=0 parameter. See :issue:`94`.

Documentation

• Add documentation to :func:`slicer_package_manager.utilities.getOrCreateReleaseFolder`.

0.2.0

Bug fixes

Server

• Update access level of API endpoints. See :issue:`89`.
  • Creating or updating packages now always require credentials.
  • Retrieving list of applications, releases and packages are now public. Note that credentials are still required to retrieve data associated with private applications.

Python Client

• Fix handling of --public, --all and --pre_release flags. See :issue:`85`.
• Update draft list command to support --limit argument. See :issue:`82`.

Documentation

• Add maintainer documentation along with :doc:`/make_a_release` section.
• Improve description of limit in :func:`slicer_package_manager_client.SlicerPackageClient.listExtension` and :func:`slicer_package_manager_client.SlicerPackageClient.listApplicationPackage`. See :issue:`84`.

Tests

• Simplify and refactor python client tests to facilitate maintenance. See :issue:`83` and :issue:`88`.

0.1.0

New Features

• Transition server plugin from Girder 2.x to Girder 3.x. See :issue:`88`.

Initial version

Developed by :user:`Pierre-Assemat` during his internship at Kitware in 2018.

Features

• Girder plugin implementing REST API endpoints.
• CLI slicer_package_manager_client
• Python client class :class:`SlicerPackageClient`.

Documentation

• Administrator, user and developer documentation written in reStructuredText (RST), generated using sphinx and published at https://slicer-package-manager.readthedocs.io

Tests

• Continuous integration (CI) configured to run on CircleCI.
• Girder plugin tests.
• CLI and Python client tests leveraging pytest-vcr.

Provisioning

• Dockerfile and docker-compose files for provisioning a demo server.