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cancerDHC / ccdhmodel

CRDC-H model in LinkML, developed by the Center for Cancer Data Harmonization (CCDH)
https://cancerdhc.github.io/ccdhmodel/
BSD 3-Clause "New" or "Revised" License
16 stars 8 forks source link

make all/test both ok #123 #125

Closed turbomam closed 2 years ago

turbomam commented 2 years ago

after moving mike* out of Pipfile's dev dependencies

I didn't consider any other criteria other than getting those two Makefile steps to work

turbomam commented 2 years ago

Working on this now.

ccdhmodel$ make install

Could not find a version that satisfies the requirement sheet2linkml==1.0.1

pipenv install Creating a virtualenv for this project… Using /usr/bin/python3 (3.8.10) to create virtualenv… ⠋created virtual environment CPython3.8.10.final.0-64 in 125ms creator CPython3Posix(dest=/home/mark/.local/share/virtualenvs/ccdhmodel-xtc7c06K, clear=False, global=False) seeder FromAppData(download=False, pip=latest, setuptools=latest, wheel=latest, pkg_resources=latest, via=copy, app_data_dir=/home/mark/.local/share/virtualenv/seed-app-data/v1.0.1.debian.1) activators BashActivator,CShellActivator,FishActivator,PowerShellActivator,PythonActivator,XonshActivator

Virtualenv location: /home/mark/.local/share/virtualenvs/ccdhmodel-xtc7c06K Pipfile.lock not found, creating… Locking [dev-packages] dependencies… Locking [packages] dependencies… Updated Pipfile.lock (d72d1b)! Installing dependencies from Pipfile.lock (d72d1b)… An error occurred while installing sheet2linkml==1.0.1! Will try again. 🐍 ▉▉▉▉▉▉▉▉▉▉▉▉▉▉▉▉▉▉▉▉▉▉▉▉▉▉▉▉▉▉▉▉ 109/109 — 00:00:39 Installing initially–failed dependencies… ☤ ▉▉▉▉▉▉▉▉▉▉▉▉▉▉▉▉▉▉▉▉▉▉▉▉▉▉▉▉▉▉▉▉ 0/1 — 00:00:00 ERROR: Could not find a version that satisfies the requirement sheet2linkml==1.0.1 (from -r /tmp/pipenv-kqq3qulp-requirements/pipenv-wg6rpzb0-requirement.txt (line 1)) (from versions: 1.0.0) ERROR: No matching distribution found for sheet2linkml==1.0.1 (from -r /tmp/pipenv-kqq3qulp-requirements/pipenv-wg6rpzb0-requirement.txt (line 1))

☤ ▉▉▉▉▉▉▉▉▉▉▉▉▉▉▉▉▉▉▉▉▉▉▉▉▉▉▉▉▉▉▉▉ 0/1 — 00:00:01 make: *** [Makefile:59: install] Error 1

turbomam commented 2 years ago 
$ pipenv shell
(ccdhmodel-xtc7c06K) ccdhmodel$ pip install sheet2linkml

... Installing collected packages: setuptools, sheet2linkml Attempting uninstall: setuptools Found existing installation: setuptools 44.0.0 Uninstalling setuptools-44.0.0: Successfully uninstalled setuptools-44.0.0 Successfully installed setuptools-52.0.0 sheet2linkml-1.0.0

turbomam commented 2 years ago

My latest push is working off of the PyPI sheet2linkml on my LBL MacBook now.

I created a new makefile rule: model/schema/crdch_model.yaml

I'm having trouble with the Linux workstation I've been using for a few weeks now, but that could be due to the slightly different dev environment, or maybe I didn't move over some of the config files. I couldn't get sheet2linkml 1.0.1 to install on my Linux workstation, but 1.0.0 installed.

turbomam commented 2 years ago

works in Ubuntu 20 now with 3.9 requirement in Pipfile

gaurav commented 2 years ago

Might overlap with #128

turbomam commented 2 years ago

I believe the functionality I was trying to add has already been added in one of @sujaypatil96's PRs.