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Warn if no input for sprm-to-anndata #88

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merged 3 commits into from
Apr 15, 2022

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mccalluc
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@mccalluc mccalluc commented Mar 2, 2022

Fix #87. Not familiar with this codebase, so apologies if I'm not doing this right.

@mccalluc mccalluc requested a review from ilan-gold March 2, 2022 15:37
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mccalluc commented Mar 2, 2022

hmm:

ERROR: Cannot install cwltool because these package versions have conflicting dependencies.

The conflict is caused by:
    schema-salad 4.5.20191229160203 depends on rdflib-jsonld<0.5.0 and >=0.3.0
    schema-salad 4.5.20191204060541 depends on rdflib-jsonld<0.5.0 and >=0.3.0
    schema-salad 4.5.20191203162929 depends on rdflib-jsonld<0.5.0 and >=0.3.0
    schema-salad 4.5.20191023134839 depends on rdflib-jsonld<0.5.0 and >=0.3.0
    schema-salad 4.5.20191017101802 depends on rdflib-jsonld<0.5.0 and >=0.3.0
    schema-salad 4.5.20190906201758 depends on rdflib-jsonld<0.5.0 and >=0.3.0
    schema-salad 4.5.20190815125611 depends on rdflib-jsonld<0.5.0 and >=0.3.0
    schema-salad 4.5.20190729164411 depends on rdflib-jsonld<0.5.0 and >=0.3.0
    schema-salad 4.5.20190621200723 depends on rdflib-jsonld<0.5.0 and >=0.3.0

To fix this you could try to:
1. loosen the range of package versions you've specified
2. remove package versions to allow pip attempt to solve the dependency conflict

I'll start a separate branch and try to sort this out, and if that works, merge that into this.

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ilan-gold commented Apr 15, 2022

@mccalluc I switched our cwltool to the HuBMAP fork (since that is presumably what is running in production anyway) and things seem to be working now. At least now, presumably, if things start failing for us, they will start failing for all.

@mccalluc mccalluc merged commit 6d88b87 into master Apr 15, 2022
@mccalluc mccalluc deleted the mccalluc/error-if-no-match-for-glob branch April 15, 2022 13:46
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Error if no matches for glob
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