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

missing mkdocs dependency? #123

Open balhoff opened 3 years ago

balhoff commented 3 years ago

Trying to run make I encounter this error:

ccdhmodel jim (main)$ make
rm -rf target/docs
mkdir -p target/docs
pipenv install
Creating a virtualenv for this project...
Pipfile: /Users/jim/Documents/Source/ccdhmodel/Pipfile
Using /usr/local/bin/python3 (3.9.2) to create virtualenv...
⠦ Creating virtual environment...created virtual environment CPython3.9.2.final.0-64 in 1150ms
  creator CPython3Posix(dest=/Users/jim/.local/share/virtualenvs/ccdhmodel-cVGW5Wdt, clear=False, global=False)
  seeder FromAppData(download=False, pip=bundle, setuptools=bundle, wheel=bundle, via=copy, app_data_dir=/Users/jim/Library/Application Support/virtualenv)
    added seed packages: pip==20.2.4, setuptools==50.3.2, wheel==0.35.1
  activators BashActivator,CShellActivator,FishActivator,PowerShellActivator,PythonActivator,XonshActivator

✔ Successfully created virtual environment! 
Virtualenv location: /Users/jim/.local/share/virtualenvs/ccdhmodel-cVGW5Wdt
Installing dependencies from Pipfile.lock (31aef1)...
  🐍   ▉▉▉▉▉▉▉▉▉▉▉▉▉▉▉▉▉▉▉▉▉▉▉▉▉▉▉▉▉▉▉▉ 72/72 — 00:03:57
To activate this project's virtualenv, run pipenv shell.
Alternatively, run a command inside the virtualenv with pipenv run.
PIPENV_IGNORE_INSTALLED=1 pipenv run gen-markdown --log_level WARNING --mergeimports --notypesdir --warnonexist --dir target/docs model/schema/crdch_model.yaml
mkdir -p model/docs
cp -R model/docs/*.md target/docs
# mkdocs.yml moves from the target/docs to the docs directory
PIPENV_IGNORE_INSTALLED=1 pipenv run mkdocs build
Error: the command mkdocs could not be found within PATH or Pipfile's [scripts].
make: *** [docs/index.md] Error 1
jooho-lee-kim commented 3 years ago

It happened to me, too. I did install mkdocs and mkdocs-material, manually.

balhoff commented 3 years ago

I had a chat with @gaurav; he says that the targets that need this tool should depend on the install-dev target. It's not totally clear to me if the distinction between the install and install-dev targets is needed.

turbomam commented 3 years ago

I'm going to make a branch, remove all of the old sheet2linkml dependencies, and move more of the packages out of dev.

turbomam commented 3 years ago

branch issue-123-smaller-Pipfile-dev. Haven't pushed yet.

turbomam commented 3 years ago

make all and make test work. I pushed. I didn't consider any criteria other than getting those Makefile steps to work.