Cptac

This release contains some small bug fixes. We removed duplicate rows from the colon cancer dataset's somatic_mutation dataframe, and renamed a column in the endometrial cancer's derived_molecular dataframe that was causing a column name overlap when joining the derived molecular dataframe to mutations for the JAK1 gene.

This release adds a feature that, in the future, will prevent an old version of the package from loading data versions that were released after that version of the package was released, and it fixes indexing errors in joins with the HNSCC dataset.

This release adds some minor edits so the package can still load the old GBM data freeze (1.0), in addition to the new data freeze (2.0).

This update includes data freeze 2.0 of the glioblastoma (GBM) data, as well as other minor data cleanups in the other datasets, including dropping 28 samples from the CCRCC methylation and CNV tables that had been later excluded from analysis, and dropping 9 duplicate columns in the CCRCC transcriptomics table that were filled with zeros.

- Added Gbm, Hnscc, Brca, and Luad datasets
- Where needed, gave dataframes multi-level column indices to remove duplicates and provide additional identifiers. Edited join functions to handle multi-level indices, and created the reduce_muiltiindex function for simplifying multi-level indices.
- Package checks its own version and warns if it's out of date
- Renamed RenalCcrcc to Ccrcc
- Optimized join functions
- Changed join functions to use full outer joins, and warn you if they fill any missing values with NaNs
- Errors and warnings generated by cptac are now sent to stderr, instead of being printed to stdout
- Renamed the algorithms submodule to utils
- get_mutations renamed to get_somatic_mutation, and get_mutations_binary renamed to get_somatic_mutation_binary

The package dependency requirements are now more specific, to make sure it can run properly.