[X] The name of the branch is meaningful and well formatted following the standards, using [AD_username (or 5 letters of AD if AD is too long)-[brief_description_of_branch].
[X] I have set up or verified the branch protection rule following the github standards before opening this pull request.
[X] I have added the changes included in this pull request to NEWS under the next release version or unreleased, and updated the date.
[X] I have updated the version number in metadata.yaml and DESCRIPTION.
[X] Both R CMD build and R CMD check run successfully.
These changes are intended to move toward an input format to fit the general use case. The child column is no longer needed, and the cellular prevalence column format was standardised. (Previously, a user could specify any column name - now it must be named CP).
Removes steps from prep.tree, and separates some preparation steps into their own functions (for example, reorder_clones was completely refactored). Expands unit testing for these refactored functions.
Reduced linear end-to-end test cases to one data set, as they were quite repetitive.
[X] I have read the code review guidelines and the code review best practice on GitHub check-list.
[X] The name of the branch is meaningful and well formatted following the standards, using [AD_username (or 5 letters of AD if AD is too long)-[brief_description_of_branch].
[X] I have set up or verified the branch protection rule following the github standards before opening this pull request.
[X] I have added the changes included in this pull request to
NEWSunder the next release version or unreleased, and updated the date.[X] I have updated the version number in
metadata.yamlandDESCRIPTION.[X] Both
R CMD buildandR CMD checkrun successfully.These changes are intended to move toward an input format to fit the general use case. The
childcolumn is no longer needed, and the cellular prevalence column format was standardised. (Previously, a user could specify any column name - now it must be namedCP).Removes steps from
prep.tree, and separates some preparation steps into their own functions (for example,reorder_cloneswas completely refactored). Expands unit testing for these refactored functions.Reduced linear end-to-end test cases to one data set, as they were quite repetitive.