isa-api

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ImportError: cannot import name 'soft_unicode' from 'markupsafe'

5

FYI: seen at BioHackathon with @proccaserra ``` erwan@computer:~/Code/plant-brapi-to-isa$ sudo docker run -it -v /home/erwan/Code/plant-brapi-to-isa/outputdir:/outputdir brapi2isa -t aHR0cHM6Ly9kb2kub3JnLzEwLjE1NDU0L0lBU1NUTg%3D%3D -e https://urgi.versailles.inra.fr/faidare/brapi/v1/ [sudo] password for erwan: Traceback (most recent call last): File "/brapi_to_isa.py",...

erlefloch

comment_schema.json is different depending on the source

4

The `comment_schema.json` in the repo at: isatools/resources/schemas/isa_model_version_1_0_schemas/core/comment_schema.json Is different from the one at the read the docs: https://isa-specs.readthedocs.io/en/latest/isajson.html#comment-schema-json The `"@id": { "type": "string", "format": "uri" },` property is missing in...

rabuono

Create a Data File Header Definition format referenceable form ISA Assay Tables.

1

- discussed by @muehlhaus and @cpommier - relates to https://github.com/ISA-tools/isa-api/issues/473 - the idea is to allow referencing of a file structure description (data dictionary of the filed header) from an...

proccaserra

discussion with @terazus and @cpommier, @sbeir, @danielarend, @timmo during Biohackathon Paris 2022 and DenBI Hackathon 12/2022 Follow-up with crosstalks with RO-crate (@stian)

proccaserra

Bump certifi from 2021.5.30 to 2022.12.7

2

Bumps [certifi](https://github.com/certifi/python-certifi) from 2021.5.30 to 2022.12.7. Commits 9e9e840 2022.12.07 b81bdb2 2022.09.24 939a28f 2022.09.14 aca828a 2022.06.15.2 de0eae1 Only use importlib.resources's new files() / Traversable API on Python ≥3.11 ... b8eb5e9 2022.06.15.1...

dependabot[bot]

- add a method to isatab.write.py - pd.to_excel(): https://pandas.pydata.org/docs/reference/api/pandas.DataFrame.to_excel.html - one worksheet per isa-tab file. see: https://github.com/nfdi4plants/ARC-specification/blob/main/ARC%20specification.md#appendix-conversion-of-arcs-to-ro-crates requested by @muehlhaus

proccaserra

Following discussions with MARS

proccaserra