Submit-cgap

Latest version: v4.2.0

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4.2.0

=====

* Support for Python 3.12.
* Dropped support for Python 3.7 (minimum is 3.8.1).
* TODO: Note that one of the tests (marked with TODO/2024-07-03) within each of the below test modules never worked
properly. While upgrading to Python 3.12 found that the correct way to do it is to invoke assert_called_with rather
than doing an assert on called_with; the latter merely checks that the called_with returns a non-falsey value which
is not really checking anything; and making this change breaks this test, meaning it never worked right.
- submit_cgap/tests/test_show_upload_info.py
- submit_cgap/tests/test_submit_metadata_bundle.py
- submit_cgap/tests/test_submit_ontology.py

4.1.2

=====

* Fix ``pip install`` command in installation docs

4.1.1

=====

* Various documentation changes, mostly ported back from the ``submitr`` fork:
* Change Submit-CGAP throughout to SubmitCGAP for internal branding consistency.
* Small wording changes for clarity, especially in Overview.
* Fix some ``.rtf`` syntax errors (especially uses of single-backquote where double-backquote required).
* Clearer section names.
* "Installing Prerequisites" (instead of "Basic Setup") for clarity about what content to expect.
* "Using SubmitCGAP" (instead of "Getting Started") again for clarity.
* "Implementation of submit_cgap package" instead of "submit_cgap package" so that the user is less likely
to feel they need to understand this section to use the tool.
* Put information about ``rclone`` at the end, and make it clear that it's an alternative to using this tool
rather than the main documentation of how to use this tool.
* Put subpackage information at the end of package list, not at the beginning.
* Don't show package content ``submit_cgap.tests`` or ``submit_cgap.scripts`` (which would show info from
``__init__.py``, which we don't do). This avoids some useless/confusing section headings.

* Add some additional ``Makefile`` recipes, most importantly ``make preview-locally`` to preview what Sphinx
will do on ReadTheDocs.

* Backport some improvements to GithubActions (GA) workflows that were debugged for ``submitr``.
* Use ``make build`` rather than explicit ``poetry`` initialization (to avoid extra dependency on version).
* Use ``ref=`` instead of ``branches=`` when submitting a doc build job.
* Trigger auto-build of doc on any non-beta checkin.
(For betas, use the new ``make preview-locally`` since
the recipe for building will just build from master and
doesn't parameterize the branch.)

4.1.0

=====

* Support for a check-submission command.
* Very basic support for SMaHT.
* Commands can now take ``--app smaht`` (which will use ``~/.smaht-keys.json``)
* submit-ontology takes ``--consortium`` and ``submission_center`` arguments.
* Some other functionality may still be missing. Send email if you're missing something you need.

4.0.0

=====

* Add command submit-ontology with new SubmissionProtocol.S3 support that allows upload first via S3
when initiating a connection. This is not an incompatible change, but it is a very major feature addition,
so I'm going to bump the major version.

* In ``base.py``:

* New class ``GenericKeyManager`` to manage possibility of either Fourfront or CGAP keys files
(``~/.fourfront-keys.json`` vs ``~/.cgap-keys.json``)

* Appropriate unit test coverage.

* Use poetry 1.3.2 for building. Update other dependencies.

* -------

* Verify ontology file first before processing in submit-ontology.

* Added --verbose and --debug options to submit-xyz and show-upload-info.

* Fixed show-upload-info to work with new --app option etc.

* Updated show-upload-info to show more info on the given ingestion uuid.

3.1.0

=====

`PR 34: Increase submission timeout <https://github.com/dbmi-bgm/SubmitCGAP/pull/34>`_

* Increase submission timeout from 2 to 10 minutes

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