in addition to the presence check of field basisOfRecord, add a check of the column content to match DWC recommended vocabulary: https://dwc.tdwg.org/terms/#dwc:basisOfRecord

Crediting OGSL and DFO with the initial effort should come with some visual aid, perhaps we should add their logos to the README especially if it's not too big a file for either logo

When a user uses 'names_taxons_ids' in check_scientificname_and_ids and obtain a result from Worms database for a given row that has an Itis LSID, it will return as a no match because the validation will be done comparing a Worms LSID to an Itis LSID even though the Itis LSID value could be valid.

Acknowledgements template:
https://github.com/marbl/MUMmer3/blob/master/ACKNOWLEDGEMENTS

Our fields check is far more robust than the current R offering, we should allow a user to specify whether to get confirmations of well-formed columns and entries in the returned report, and also support which formats to check compliance with: Event Core, Occurrence Core, Event w/ Occurrence Extension.

Tracking the testing infrastructure setup using pytest.

• Standardize on linting rules, setup configuration files in repository
• Notes in docs/README on how to setup and run the tests/linting locally
• Running tests/lints using GH Action on each Push/PR

Some of the functions have HTML and logic together in a single function, where we find those we should identify and split them into logic and display functions. ie:

The aim is to have functions that perform roughly the same tasks as the R package functions in the pyobistools module, with implementations / decorators using those functions and still performing the same tasks they were already doing seamlessly.

First order functions to write/migrate:

• check_fields - functionality in types_analyses_bio/table_format_analysis.py @BeauvillierS
• check_eventids - functionality validations_bio/eventid_fonction.py @BeauvillierS
• check_extension_eventids - functionality in validations_bio/eventid_fonction.py @BeauvillierS
• #32
• check_depth - xylookup API https://github.com/iobis/xylookup @jdpye
• check_outliers_dataset - https://github.com/iobis/obistools/blob/master/R/check_outliers.R
• check_outliers_species - https://github.com/iobis/obistools/blob/master/R/check_outliers.R
• check_eventdate - functionality in validations_bio/eventdate_fonction.py @SoftwareMonk
• match_taxa - functionality in validations_bio/validation_Worms_Itis_fonction.py @kwilcox

Looks like the OBIS / WoRMS checks are replicated across these two files.

taxa.py works against obis's API, but doesn't actually implement anything to do with ITIS, just has an empty placeholder function there.

I think taxa.py tries to name things and put things where a R obistools user might expect them, but that the check_scientificname_and_ids.py implementation is far more advanced and actually functions.

Suggestions on how to move forward? We could migrate the functionality from the check_scientificname_and_ids.py into the naming scheme from taxa.py , rename the check_scientificname_and_ids.py functions in-place, or decide not to be congruous with the R implementation, as we please.

Function check_scientificname_and_ids must handle empty values and ensure values are proper types before attemping operations on them

Integrate the publishing of the documentation to GH Pages via GH Actions

recommended to use https://pypi.org/project/python-dateutil/ for date verification/parsing

pyobis and xylookup aren't registered with any package index, it would benefit us when using them as dependencies to get them registered into places they can be installed automatically.

Add this on the README? https://cioos-siooc.github.io/pyobistools/

The 4 archive types and their required fields are inline in the code right now, and it could be cleaner to separate them into definitional YML and then reimport them in the check functions.

yaml.load() will bring in a dictionary and can be crafted to produce the same structures as are expected by the function presently.

We have text strings in bilingual French/English format right now, we can localize those strings with python i18n perhaps and open the door to translation into more languages.

When querying Worms with a scientific name, the answer might might be longer than 1. Currently, the function returns the first answer. In the updated code, the functions should check the status of the answer it returns to make sure it is accepted.

A check can be made with scientific name 'Monstrilla grandis' to see how the function currently works.

R based doc:
https://github.com/iobis/obistools/blob/master/README.md

Build up a similar resource for the pyobistools version of the same tests.

Running record of the packages that are flagged to me as i run through the check notebooks. So far it's been nbformat and httpx for me.

This will be a bit of an ongoing saga, but there are tests that do not behave as expected with latest Pandas. We need to find and pin a stable but fresh-er version of Pandas that doesn't break the current codebase.

If the Pandas expected behaviour changes, we will change with it at that point.