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Database upgrades

Over time, the database structure of pcvct will evolve to reflect new capabilities, features, and improvements. Not every release will change the database structure, but when one does in a way that could affect your workflow, pcvct will throw a warning. The warning will link to this page and the function will wait for user input to proceed. Changes are listed in reverse chronological order.

to v0.0.15

Introduce XML-based ECM initial conditions. This introduces ic_ecm_variations. Also, introduce Dirichlet initial conditions from file, which introduces the ic_dc_id in the database. For any simulations in the database before upgrading, both of these will be set to -1 (i.e., no initial conditions) except if ic_ecm_id is not -1, in which case ic_ecm_variation_id will be set to 0 (i.e., the default ECM initial conditions which is all the original CSV version can handle).

to v0.0.10

Start tracking the PhysiCell version used in the simulation. This introduces the physicell_versions table which tracks the PhysiCell versions used in simulations. Currently, only supports reading the PhysiCell version, not setting it (e.g., through git commands). Key changes include:

  • Adding the physicell_version_id column to the simulations, monads, and samplings tables.
  • Adding the physicell_versions table.
    • If PhysiCell is a git-tracked repo, this will store the commit hash as well as any tag and repo owner it can find based on the remotes. It will also store the date of the commit.
    • If PhysiCell is not a git-tracked repo, it will read the VERSION.txt file and store that as the commit_hash with -download appended to the version.

to v0.0.3

Introduce XML-based cell initial conditions. This introduces ic_cell_variations. Also, standardized the use of config_variation in place of variation. Key changes include:

  • Renaming the variation_id column in the simulations and monads tables to config_variation_id.
  • Adding the ic_cell_variation_id column to the simulations and monads tables.
  • In data/inputs/configs, renaming all instances of "variation" to "config_variation" in filenames and databases.