Remove automatic recursive to_dict/from_dict again #1632
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This turned out to have negative interactions when writing and reading objects from GenericJob which currently employs a mixture of to_hdf and newer to_dict interfaces. When reading the objects again the recursive strategy can get confused which interface to use. Since it is anyway mostly relevant for the DataContainer, I have extracted this functionality into stand- alone functions that operate on the obj_dicts. Classes that wish to use it and do not confuse the two interfaces can call these functions in their implementations of _to_dict and _from_dict as done by DataContainer now.
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pmrv
added
the
integration
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@jan-janssen I will still update docs, but at least integration tests seem to pass now! |
for more information, see https://pre-commit.ci
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@jan-janssen What's your plan with #1613, should we merge that PR first or this one? |
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@pmrv can you rebase the integration tests to use the changes in this branch so we can validate the pyiron_atomistics tests pass? Then the order how we merge the pull requests does not really matter to me. |
Previously we tried to install the deps of atomistics/contrib on top of the base environment, now we install those dependencies first and then add pyiron_base HEAD without dependencies. The former breaks when there are incompatible versions, the latter can break if base actually needs features or whole modules from its own environment, but we're betting that that's rarer.
Update integration tests and a new one for notebooks
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This turned out to have negative interactions when writing and reading objects from GenericJob which currently employs a mixture of to_hdf and newer to_dict interfaces. When reading the objects again the recursive strategy can get confused which interface to use. Since it is anyway mostly relevant for the DataContainer, I have extracted this functionality into stand- alone functions that operate on the obj_dicts. Classes that wish to use it and do not confuse the two interfaces can call these functions in their implementations of _to_dict and _from_dict as done by DataContainer now.