When enabling the `warn_unused_ignores = True` option of mypy, this
was making the `test_galaxy_packages` tests fail with:
```
mypy .
Traceback (most recent call last):
File "/tmp/gxpkgtestenvu3fgDr/bin/mypy", line 8, in <module>
sys.exit(console_entry())
File "/tmp/gxpkgtestenvu3fgDr/lib/python3.10/site-packages/mypy/__main__.py", line 15, in console_entry
main()
File "mypy/main.py", line 100, in main
File "mypy/main.py", line 182, in run_build
File "mypy/build.py", line 192, in build
File "mypy/build.py", line 266, in _build
File "mypy/build.py", line 2942, in dispatch
File "mypy/build.py", line 3333, in process_graph
File "mypy/build.py", line 3414, in process_fresh_modules
File "mypy/build.py", line 2110, in fix_cross_refs
File "mypy/fixup.py", line 52, in fixup_module
File "mypy/fixup.py", line 127, in visit_symbol_table
File "mypy/lookup.py", line 49, in lookup_fully_qualified
AssertionError: Cannot find component 'util' for 'galaxy.util'
make: *** [Makefile:96: mypy] Error 1
```
Moreover, installing packages in editable mode was hiding some issues
with how files from other packages were accessed.
It's not used in many places, this shouldn't have much impact on
performance, and I guess it's a fair assumption that something called
json.safe_loads would return a deepcopy. That's complementary to the
previous commit and would also separately fix the issues referenced
there.
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).
Nicola Soranzo