F gaps in int columns

Summary

For #126 (closed). Adds support for empty values in integer columns and Pandas-specific datatypes. This is needed for https://gitlab.indiscale.com/caosdb/customers/geomar/management/-/issues/269.

Focus

The most important part is to use the dtype argument in Pandas' read_csv function. We also replace the np.issubdtype and isinstance functions in the datatype checks by helper functions that support the relevant Pandas datatypes.

Test Environment

For the actual bug, the new unit test should be sufficient. Also use this branch in the Geomar server-profile and the bis-custom submodule in branch f-nan-in-int and test a sample upload with empty fields in, e.g., the integer-valued AphiaID.

Check List for the Author

Please, prepare your MR for a review. Be sure to write a summary and a focus and create gitlab comments for the reviewer. They should guide the reviewer through the changes, explain your changes and also point out open questions. For further good practices have a look at our review guidelines

• All automated tests pass
• Reference related issues
• Up-to-date CHANGELOG.md (or not necessary)
• Up-to-date JSON schema (or not necessary)
• Appropriate user and developer documentation (or not necessary)
  • How do I use the software? Assume "stupid" users.
  • How do I develop or debug the software? Assume novice developers.
• Annotations in code (Gitlab comments)
  • Intent of new code
  • Problems with old code
  • Why this implementation?

Check List for the Reviewer

• I understand the intent of this MR
• All automated tests pass
• Up-to-date CHANGELOG.md (or not necessary)
• Appropriate user and developer documentation (or not necessary)
• The test environment setup works and the intended behavior is reproducible in the test environment
• In-code documentation and comments are up-to-date.
• Check: Are there specifications? Are they satisfied?

For further good practices have a look at our review guidelines.

assigned to @florian

added 1 commit

• f8e283ae - STY: autopep8'd

Compare with previous version

added 1 commit

• 6e41fd1d - MAINT: Remove debugging output

Compare with previous version

marked the checklist item Reference related issues as completed

marked the checklist item Up-to-date CHANGELOG.md (or not necessary) as completed

marked the checklist item Up-to-date JSON schema (or not necessary) as completed

marked the checklist item Appropriate user and developer documentation (or not necessary) as completed

marked the checklist item Annotations in code (Gitlab comments) as completed

marked the checklist item All automated tests pass as completed

changed the description

added 1 commit

• 7787203e - DOC: Some rewording and typos.

Compare with previous version

resolved all threads

marked the checklist item I understand the intent of this MR as completed

marked the checklist item Up-to-date CHANGELOG.md (or not necessary) as completed

marked the checklist item Appropriate user and developer documentation (or not necessary) as completed

marked the checklist item The test environment setup works and the intended behavior is reproducible in the test as completed

marked the checklist item In-code documentation and comments are up-to-date. as completed

enabled an automatic merge when the pipeline for 7787203e succeeds

canceled the automatic merge

enabled an automatic merge when the pipeline for 7787203e succeeds

mentioned in commit 0a6e5c5d

merged

marked the checklist item All automated tests pass as completed