Migrate example code and docs

[bobturneruk]

Migrate:

https://github.com/FAIRDataPipeline/pyDataPipeline/tree/dev/data_pipeline_api/ext

to

https://github.com/FAIRDataPipeline/pySimpleModel

Will impact CI on https://github.com/FAIRDataPipeline/FAIR-CLI

[bobturneruk]

cc @RyanJField, @bruvio, @richardreeve

[bobturneruk]

This is where the CI needs to change:

https://github.com/FAIRDataPipeline/FAIR-CLI/blob/d7c28ffa2b152bb4bc99ab27513cf95c39bb2d4d/.github/workflows/implementations.yml#L12

[bruvio]

ok open a PR. have you check if this move impacts other repos? like I presume the api also will need changes

[bobturneruk]

Cheers @bruvio - when I get to the point of making a commit, I'll be ready for a draft PR! 😄

[bobturneruk]

Currently trying to run pySimpleModel following these instructions (which I just wrote):

Installation

1. Create a and activate new python virtual environment.
2. pip install fair-cli.
3. Clone this repository: git clone https://github.com/FAIRDataPipeline/pySimpleModel.git.
4. Change directory cd pySimpleModel.
5. Install this package pip install -e ..

[bobturneruk]

Getting:

ERROR: pip's dependency resolver does not currently take into account all the packages that are installed. This behaviour is the source of the following dependency conflicts.
data-pipeline-api 0.7.5 requires PyYAML<7.0,>=6.0, but you have pyyaml 5.4.1 which is incompatible.

[bobturneruk]

Or I can chose:

pip install pyyaml==6.0

ERROR: pip's dependency resolver does not currently take into account all the packages that are installed. This behaviour is the source of the following dependency conflicts.
fair-cli 0.2.3 requires PyYAML<6.0.0,>=5.4.1, but you have pyyaml 6.0 which is incompatible.

[bruvio]

this error is ok as far as I know and the model is installed.

[bruvio]

https://github.com/FAIRDataPipeline/pyDataPipeline/runs/5677886707?check_suite_focus=true

[bobturneruk]

What am I looking for in the above, please, @bruvio?

[bruvio]

https://github.com/FAIRDataPipeline/pyDataPipeline/runs/5677886707?check_suite_focus=true#step:12:210

it line 210 of the step run test for other OS

[bruvio]

that is a successful pipeline where the error you bumped in occurs, so no worries

[bobturneruk]

Thanks. Would be good if there wasn't an error, I suppose. Might worry someone using the software.

[bruvio]

I guess the error could be solved by updating the dependencies of the simple model to match the ones in the API.