ncihtan / HTAN-data-curator

HTAN Data Ingest Shiny App
https://sagebio.shinyapps.io/HTAN-data-curator/
Apache License 2.0
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Update DCA from upstream to be level with v23.3.1 #69

Closed adamjtaylor closed 1 year ago

adamjtaylor commented 1 year ago

This PR updates HTANs DCA to fix #68


afwillia commented 1 year ago

RE the merge conflict, keep

          echo Installing pypi version of schematic
          git clone --single-branch --branch main https://github.com/Sage-Bionetworks/schematic.git
          cp schematic_config.yml schematic/config.yml
          pip3 install schematicpy

and discard

          # use 'poetry' to install schematic dev schematic
          # If commit is tagged for release or in main branch, install schematic from pypi
          if [[ $GITHUB_REF_NAME == v*.*.* ]] || [[ $GITHUB_REF_NAME == main ]]; then
            echo Installing pypi version of schematic
            git clone --single-branch --branch main https://github.com/Sage-Bionetworks/schematic.git
            cp schematic_config.yml schematic/config.yml
            cd schematic
            pip3 install schematicpy
          else
            pip3 install poetry
            echo Installing develop branch of schematic from github
            git clone --single-branch --main develop https://github.com/Sage-Bionetworks/schematic.git
            cp schematic_config.yml schematic/config.yml
            cd schematic
            poetry build
            pip3 install dist/schematicpy-*-py3-none-any.whl
          fi

The reason is because schematic installed from github requires python 3.9+ which is incompatible with shinyapps.io.

afwillia commented 1 year ago

@adamjtaylor release 23.3.1 is ready containing exactly the same content as this PR

adamjtaylor commented 1 year ago

@afwillia Would you be able to resolve the conflicts in the PR for me? I can't get it to work through GH Desktop or the CLI. Thank you

afwillia commented 1 year ago

@adamjtaylor Yes, I just did. FYI I created a new branch for the commit which the PR automatically updated to.