refactor: extract all enclone only print code (#415)

* Extract all of the enclone-only part of print_clonotypes into a function and move it into enclone.
* Extract sort_exact_clonotypes as a function.
* Unfold the clonotype filtering/printing loop and clean up.
* Move all the enclone-specific code into enclone proper.
* Inject enclone-specific behavior via a OrbitProcessor trait.
* Rename enclone_print -> enclone_process.
* Delete the code generation part of enclone_vars.

Cargo.toml

@@ -9,7 +9,7 @@ members = [
     "enclone",
     "enclone_args",
     "enclone_core",
-    "enclone_print",
+    "enclone_process",
     "enclone_proto",
     "enclone_ranger",
     "enclone_stuff",

GUIDE

@@ -10,7 +10,7 @@ enclone_exec          just the actual main program
 enclone_help          help menus from the command line
 enclone_main          this includes the enclone main program guts
 enclone_paper         calculations for enclone paper
-enclone_print         prints clonotypes in the sense of creating the "pictures" (much of core logic)
+enclone_process       final filtering and output of clonotypes
 enclone_proto         stuff for communicating with Loupe, and reused for other purposes
 enclone_ranger        entry point for cellranger
 enclone_stuff         things called by enclone_main and enclone_ranger

enclone_core/Cargo.toml

@@ -15,7 +15,7 @@ authors = ["""David Jaffe <[email protected]>,
 edition = "2021"
 license-file = "LICENSE.txt"
 publish = false
-include = ["src/*.rs", "LICENSE.txt", "src/mammalian_fixed_len.table"]
+include = ["src/*.rs", "LICENSE.txt"]
 
 # Please do not edit crate versions within this file.  Instead edit the file master.toml
 # in the root of the enclone repo.

enclone_core/src/lib.rs

@@ -12,11 +12,9 @@ pub mod hcomp;
 pub mod join_one;
 pub mod linear_condition;
 pub mod logging;
-pub mod mammalian_fixed_len;
 pub mod median;
 pub mod opt_d;
 pub mod print_tools;
-pub mod set_speakers;
 pub mod slurp;
 pub mod stringulate;
 pub mod test_def;