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Contributing to CASE-Utilities-Python

Deploying a new ontology version

  1. After cloning this repository, ensure the CASE submodule is checked out. This can be done with either git submodule init && git submodule update, make .git_submodule_init.done.log, or make check.
  2. Update the CASE submodule pointer to the new tagged release.
  3. The version of CASE is also hard-coded in case_utils/ontology/version_info.py. Edit the variable CURRENT_CASE_VERSION.
  4. A list of built versions of CASE is also hard-coded in case_utils/ontology/version_info.py. Edit the variable built_version_choices_list.
  5. From the top source directory, run make clean. This guarantees a clean state of this repository as well as the ontology submodules.
  6. Still from the top source directory, run make.
  7. Any new .ttl files will be created under case_utils/ontology/. Use git add to add each of them. (The patch-weight of these files could overshadow manual revisions, so it is fine to commit the built files separately from the manual changes being committed. Preferably, commit the built files before manual changes - this prevents later issues with a git bisect that relies on CI passing.)

Here is a sample sequence of shell commands to run the build:

# (Starting from fresh `git clone`.)
make check
pushd dependencies/CASE
  git checkout master
  git pull
popd
git add dependencies/CASE
# (Here, edits should be made to case_utils/ontology/version_info.py)
make
pushd case_utils/ontology
  git add case-0.6.0.ttl  # Assuming CASE 0.6.0 was just released.
  # and/or
  git add uco-0.8.0.ttl   # Assuming UCO 0.8.0 was adopted in CASE 0.6.0.

  git add ontology_and_version_iris.txt
popd
make check
# Assuming `make check` passes:
git commit -m "Build CASE 0.6.0 monolithic .ttl files" case_utils/ontology/case-0.6.0-subclasses.ttl case_utils/ontology/case-0.6.0.ttl case_utils/ontology/ontology_and_version_iris.txt
git commit -m "Update CASE ontology pointer to version 0.6.0" dependencies/CASE case_utils/ontology/version_info.py

This project uses the pre-commit tool for linting The easiest way to install it is with pip:

pip install pre-commit
pre-commit --version

The pre-commit tool hooks into Git's commit machinery to run a set of linters and static analyzers over each change. To install pre-commit into Git's hooks, run:

pre-commit install