Inputs - JDFTx IO Module (#4189)

* JDFTx IO module - input submodules

* JDFTx IO module - input submodules testing

* Moving "flatten_list" utility function to "generic_tags" submodule and deleting "_input_utils.py" as it contained only one method that was used once in "generic_tags.py"

* privatizing utility method "flatten_list"

* Update from master

* empty file for tmp

* Update from master

* explicit testing of "initial-magnetic-moments"

* Correction for ruff - PLC0206 (Extracting value from dictionary without calling `.items()`) - This does not appear in my local pre-commit (which I believe is running correctly) but started causing the "lint" action to fail starting around 11/22 (along with other failures from unrelated pre-existing parts of pymatgen)

* changing the previous "as_dict" method to be private, making a public "as_dict" method that passes through the __setitem__ method so that the values within the dictionary fed to "as_dict" can be as flexible as the values set explicitly by the user (also made minor updates to __setitem__ to handle setting multiple values for repeatable tags better)

* Partial cleanup of tests

* Partial cleanup of tests

* Partial cleanup of tests

* Cleanup of inputs - homogenized wording in error messages, added value validation methods to AbstractTag for validations that are called multiple times, cleaned up cluttered tests and added comments to make it more clear what is being tested

* pre-commit auto-fixes

* Length units consistency in inputs module

* Changing all "zopen" to just "open" due to an error raised when monty.io tries to raise an "EncondingWarning", changing the dump files dir to be a fixture that creates itself, yields the path, and then removes itself (parts after a "yield" only run once the test using the fixture has finished)

---------

Co-authored-by: Matthew Horton <mkhorton@users.noreply.github.com>
Co-authored-by: Shyue Ping Ong <shyuep@users.noreply.github.com>
Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>

src/pymatgen/io/jdftx/__init__.py

@@ -0,0 +1 @@
+# Empty __init__.py file