Upgrade syntax using `pyupgrade --py36-plus` .
Manually drop several `six` imports.
Also:
- Remove broken pr_cache in scripts/bootstrap_history.py
- Fix broken prefix removal in lib/galaxy/tool_util/deps/mulled/mulled_build.py
clean_multiline_string was used in multiple places across modules in different packages so I simply refactored it into galaxy.util and added a test case (used in multiple places and has tests a lower bar then some other code in galaxy.util).
The tempfilecache abstraction was only used in one place, so I've refactored it right into that file.
Together these should simplify the package tests for galaxy-data (and hopefully other packages also).
Add quota to data/ (should be refactored to not use trans but is straight forward and the imports are fine for now), and add three new packages.
- auth
- authnz
- app
A lot more needs to be added to app but we need to de-tangle the circular imports between app and web stuff and webapp stuff. It is messier than I thought.
Uses a stripped down, updated variant of like Pulsar/Planemo/ephemeris Makefile stuff. Modified in dozens of ways for tags, version and path differences, etc.. Symbolic links to keep everything in line.
- Update setup.py to reflect Galaxy no longer supports Python 3.4.
- Move PROJECT_DESCRIPTION into a variable imported into setup.py dynamically, reducing the differences in setup.py across packages.
- Fix some project descriptions.
- Fix versions and HISTORY.rst for a release this cycle, didn't get any 19.5.0 packages out.
The included script takes in an object store definition to write to, model store output target (e.g. tar file or directory or bagit file/directory format matching the new history exports added in 7367), and a bunch of files in defined via an upload-2.0-style YAML - and writes the physical files into the object store and writes persisted metadata into the model store. The supplied script describes the input format as do the new unit tests in test_model_discover.py.
Right now datasets for a history and whole libraries (including recursive folders and library datasets) can be described this way. These concepts have been extended to collections in #7058 but only in the context of discovering job outputs and writing them to an export model store current.
This script was created mostly by refactoring stuff out of output_collect.py that is used to create datasets during output discovery (i.e. parsing the same data out of galaxy.json files).
Nicola Soranzo