PathMe

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next, I found incompatibilities running import SqlAlchemy and Pybel how to fix pip3 uninstall purge sqlalchemy python3 -m pip install SQLAlchemy==1.3.0 python3 -m pip install seaborn python3 -m pip uninstall...

flalix

Possibly, pathme (and viewer) cannot be installed with python 3.8 or greater. Perhaps due to 'compath'. I tried in many ways and did not find a solution. Looking at the...

flalix

Hi, Looks like `sqlalchemy==1.3.24` is a required package for the distribution. Please add it to `setup.cfg`. Your current version of the code does not support the most recent version of...

shivashankarv

Hi, I get the following error while running `pathme kegg bel`. This is likely because `module_name` is a required param of the function `bio2bel.utils.get_connection()`. It isn't in more recent versions...

shivashankarv

…andler double-close; minor other linting improvements; [setup.cfg] Add missing dependency;

SamuelMarks

PathMe looks pretty good. Nice work! At a glance it seems to focus on established pathways, so will miss more tenuous links. Related to this would be the opportunity to...

SamuelMarks

Hi, `pathme kegg bel` runs fine ```bash 2021-04-10 01:41:29,852 - INFO - pathme.cli - Initiating HGNC Manager 2021-04-10 01:41:29,939 - INFO - pathme.cli - Initiating ChEBI Manager Exporting KEGG to...

MahShaaban

Update reactome version

1

- [ ] TODO: Fix the SPARQL query to get the names of all pathways and their identifiers GET_ALL_PATHWAYS = """ SELECT DISTINCT ?uri_id ?name WHERE { ?uri_id rdf:type biopax3:Pathway...

ddomingof

Add NCI PID - Pathways

1

http://www.ndexbio.org/#/networkset/8a2d7ee9-1513-11e9-bb6a-0ac135e8bacf

ddomingof

Would be better to go to readthedocs rather than to keep looking up the content hosted by the journal/springer

cthoyt