[WIP] Use `StorageManager` in `execute_DAG`

[dwhswenson]

This is a subset of the work in #234, split off to facilitate review. This PR will merge into #186 (making it easier to see the additions specific to the PR, but meaning that this should be merged before that). It also includes the work in #257 (one of the old tests fails without that).

This PR integrates StorageManager into execute_DAG. Note that this still isn't a complete replacement of the storage system: a follow-up PR will handle serialization of StagingPaths.

TODO:

• [x] Check that we can exactly reproduce the old behavior with the ReproduceOldBehaviorStorageManager; I think some paths aren't quite right.
• [x] Add some tests that the directories are as expected in the ExecutionStorageDemoTest subclasses
• [ ] Revisit when/where dag_label is given (also needed in #186)
• [x] Switch it so the context managers return Context (executor shouldn't need to assemble that)

[pep8speaks]

Hello @dwhswenson! Thanks for updating this PR. We checked the lines you've touched for PEP 8 issues, and found:

• In the file gufe/protocols/protocoldag.py:

Line 384:80: E501 line too long (82 > 79 characters) Line 385:80: E501 line too long (82 > 79 characters) Line 393:80: E501 line too long (80 > 79 characters)

• In the file gufe/tests/storage/test_stagingserialization.py:

Line 68:1: E303 too many blank lines (3)

Comment last updated at 2024-01-22 17:35:11 UTC