delete pretty trace (#391)

Deletes all uses of pretty_trace. Moves lingering necessary features to enclone proper.

Cargo.toml

@@ -24,7 +24,6 @@ members = [
     "kmer_lookup",
     "load_feature_bc",
     "perf_stats",
-    "pretty_trace",
     "stats_utils",
     "stirling_numbers",
     "string_utils",

GUIDE

@@ -18,7 +18,6 @@ enclone_tail          last part of the code
 enclone_tools         miscellaneous binaries
 enclone_vars          variable definitions
 enclone_version       determine current version string
-enclone_visual        experimental GUI client
 
 credits               credits
 fonts                 DejaVuSansMono, in case not otherwise available

enclone/Cargo.toml

@@ -32,17 +32,13 @@ io_utils = { path = "../io_utils" }
 itertools.workspace = true
 perf_stats = { path = "../perf_stats" }
 petgraph = "0.6"
-pretty_trace = { path = "../pretty_trace" }
 qd = { git = "https://github.com/Barandis/qd" }
 rayon = "1"
 stats_utils = { path = "../stats_utils" }
 string_utils = { path = "../string_utils" }
 vdj_ann = { path = "../vdj_ann" }
 vector_utils = { path = "../vector_utils" }
 
-[dev-dependencies]
-assert_cmd = "2"
-
 [target.'cfg(not(windows))'.dependencies]
 pager = "0.16"
 

enclone/src/UNDOC_OPTIONS

@@ -271,9 +271,6 @@ NO_UNCAP_SIM: turn off uncapping simulation
 
 HAPS_DEBUG: turn on debug mode for the HAPS option
 
-PROFILE: turn on profiling, normally used with NOPRINT; paging is turned off because this
-This won't work with paging, however you can pipe to "less -r".
-
 ===================================================================================================
 
 ROW_FILL_VERBOSE: special option for debugging

enclone/src/bin/update_enclone_binary.rs

@@ -5,15 +5,14 @@
 
 use enclone_core::defs::get_config;
 use io_utils::path_exists;
-use pretty_trace::PrettyTrace;
+
 use std::collections::HashMap;
 use std::env;
 
 #[cfg(not(target_os = "windows"))]
 use std::os::unix::fs::PermissionsExt;
 
 fn main() {
-    PrettyTrace::new().on();
     let mut config = HashMap::<String, String>::new();
     let mut config_file = String::new();
     for (key, value) in env::vars() {

enclone_args/src/proc_args.rs

@@ -504,7 +504,6 @@ pub fn proc_args(ctl: &mut EncloneControl, args: &[String]) -> Result<(), String
         ("UTR_CON", &mut ctl.gen_opt.utr_con),
         ("VDUP", &mut ctl.clono_filt_opt.vdup),
         ("VIS_DUMP", &mut ctl.gen_opt.vis_dump),
-        ("VISUAL", &mut ctl.visual_mode),
         ("WEAK", &mut ctl.gen_opt.weak),
         ("WHITEF", &mut ctl.clono_filt_opt_def.whitef),
     ];
@@ -650,7 +649,6 @@ pub fn proc_args(ctl: &mut EncloneControl, args: &[String]) -> Result<(), String
         "COMP",
         "COMPE",
         "COMP2",
-        "CTRLC",
         "DUMP_INTERNAL_IDS",
         "EVIL_EYE",
         "FORCE_EXTERNAL",
@@ -667,7 +665,6 @@ pub fn proc_args(ctl: &mut EncloneControl, args: &[String]) -> Result<(), String
         "PLAIN",
         "PRINT_CPU",
         "PRINT_CPU_INFO",
-        "PROFILE",
         "SVG",
     ];
 
@@ -939,14 +936,6 @@ pub fn proc_args(ctl: &mut EncloneControl, args: &[String]) -> Result<(), String
         }
     }
 
-    // Force visual mode if plot file is gui or if VIS_DUMP was invoked.
-
-    if (ctl.plot_opt.plot_file == "gui" || ctl.plot_opt.plot_file == "gui_stdout")
-        && !ctl.gen_opt.vis_dump
-    {
-        ctl.visual_mode = true;
-    }
-
     // Record time.
 
     ctl.perf_stats(&targs, "in main args loop");

enclone_args/src/proc_args2.rs

@@ -203,7 +203,7 @@ pub fn proc_args_tail(ctl: &mut EncloneControl, args: &[String]) -> Result<(), S
     // Get origin descriptions.  Flaky and particularly flaky when internal origin args are paths,
     // since it will look in outs for the file.
 
-    if ctl.gen_opt.internal_run || ctl.gen_opt.descrip || ctl.visual_mode || ctl.gen_opt.vis_dump {
+    if ctl.gen_opt.internal_run || ctl.gen_opt.descrip || ctl.gen_opt.vis_dump {
         ctl.origin_info.descrips.clear();
         let mut results = vec![(0, "".to_string()); ctl.origin_info.n()];
         for i in 0..ctl.origin_info.n() {

enclone_core/src/defs.rs

@@ -207,7 +207,6 @@ pub struct GeneralOpt {
     pub subset_json: String,
     pub fold_headers: bool,
     pub no_uncap_sim: bool,
-    pub profile: bool,
     pub nopager: bool,
     pub info: Option<String>,
     pub info_fields: Vec<String>,
@@ -513,30 +512,29 @@ pub struct PerfOpt {
 
 #[derive(Default)]
 pub struct EncloneControl {
-    pub visual_mode: bool,                       // running as enclone visual
-    pub perf_opt: PerfOpt,                       // computational performance options
-    pub start_time: Option<Instant>,             // enclone start time
-    pub gen_opt: GeneralOpt,                     // miscellaneous general options
-    pub plot_opt: PlotOpt,                       // plot options
-    pub pretty: bool,                            // use escape characters to enhance view
-    pub nogray: bool,                            // don't gray in per cell lines
-    pub silent: bool,                            // turn off extra logging
-    pub force: bool,                             // make joins even if redundant
-    pub debug_table_printing: bool,              // turn on debugging for table printing
-    pub merge_all_impropers: bool,               // merge all improper exact subclonotypes
-    pub heur: ClonotypeHeuristics,               // algorithmic heuristics
-    pub origin_info: OriginInfo,                 // origin (sample) info
-    pub allele_alg_opt: AlleleAlgOpt,            // algorithmic options for allele finding
-    pub allele_print_opt: AllelePrintOpt,        // print options for allele finding
-    pub join_alg_opt: JoinAlgOpt,                // algorithmic options for join
-    pub join_print_opt: JoinPrintOpt,            // printing options for join operations
+    pub perf_opt: PerfOpt,                // computational performance options
+    pub start_time: Option<Instant>,      // enclone start time
+    pub gen_opt: GeneralOpt,              // miscellaneous general options
+    pub plot_opt: PlotOpt,                // plot options
+    pub pretty: bool,                     // use escape characters to enhance view
+    pub nogray: bool,                     // don't gray in per cell lines
+    pub silent: bool,                     // turn off extra logging
+    pub force: bool,                      // make joins even if redundant
+    pub debug_table_printing: bool,       // turn on debugging for table printing
+    pub merge_all_impropers: bool,        // merge all improper exact subclonotypes
+    pub heur: ClonotypeHeuristics,        // algorithmic heuristics
+    pub origin_info: OriginInfo,          // origin (sample) info
+    pub allele_alg_opt: AlleleAlgOpt,     // algorithmic options for allele finding
+    pub allele_print_opt: AllelePrintOpt, // print options for allele finding
+    pub join_alg_opt: JoinAlgOpt,         // algorithmic options for join
+    pub join_print_opt: JoinPrintOpt,     // printing options for join operations
     pub clono_filt_opt_def: ClonoFiltOptDefault, // default filtering options for clonotypes
-    pub clono_filt_opt: ClonoFiltOpt,            // filtering options for clonotypes
-    pub clono_print_opt: ClonoPrintOpt,          // printing options for clonotypes
-    pub clono_group_opt: ClonoGroupOpt,          // grouping options for clonotypes
-    pub parseable_opt: ParseableOpt,             // parseable output options
-    pub pathlist: Vec<String>,                   // list of input files
-    pub last_modified: Vec<SystemTime>,          // last modified for pathlist
+    pub clono_filt_opt: ClonoFiltOpt,     // filtering options for clonotypes
+    pub clono_print_opt: ClonoPrintOpt,   // printing options for clonotypes
+    pub clono_group_opt: ClonoGroupOpt,   // grouping options for clonotypes
+    pub parseable_opt: ParseableOpt,      // parseable output options
+    pub pathlist: Vec<String>,            // list of input files
+    pub last_modified: Vec<SystemTime>,   // last modified for pathlist
 }
 
 pub static mut WALLCLOCK: f64 = 0.0;

enclone_core/src/lib.rs

@@ -107,7 +107,6 @@ pub fn expand_integer_ranges(x: &str) -> String {
 }
 
 lazy_static! {
-    pub static ref BUG_REPORT_ADDRESS: Mutex<Vec<String>> = Mutex::new(Vec::<String>::new());
     pub static ref REMOTE_HOST: Mutex<Vec<String>> = Mutex::new(Vec::<String>::new());
 }
 

enclone_vars/Cargo.toml

@@ -23,6 +23,6 @@ exclude = ["src/bin/var_test.rs", "src/vars"]
 [dependencies]
 io_utils = { path = "../io_utils" }
 itertools.workspace = true
-pretty_trace = { path = "../pretty_trace" }
+
 string_utils = { path = "../string_utils" }
 vector_utils = { path = "../vector_utils" }

enclone_vars/src/bin/export_code.rs

@@ -6,12 +6,10 @@
 
 use enclone_vars::export_code::export_code;
 use io_utils::{fwrite, open_for_write_new};
-use pretty_trace::PrettyTrace;
 
 use std::io::Write;
 
 fn main() {
-    PrettyTrace::new().on();
     let outs = export_code(0);
     for out in outs {
         let mut f = open_for_write_new![&out.0];

enclone_vars/src/bin/var_sort.rs

@@ -3,11 +3,10 @@
 // Sort and replace the vars file.
 
 use enclone_vars::sort_vars;
-use pretty_trace::PrettyTrace;
+
 use std::io::Write;
 
 fn main() {
-    PrettyTrace::new().on();
     let old = std::fs::read_to_string("enclone_vars/src/vars").unwrap();
     let new = sort_vars(&old);
     if new != old {

enclone_vars/src/bin/var_test.rs

@@ -3,10 +3,8 @@
 // Parse the vars file to test if it's valid.
 
 use enclone_vars::var::parse_variables;
-use pretty_trace::PrettyTrace;
 
 fn main() {
-    PrettyTrace::new().on();
     let old = std::fs::read_to_string("enclone_vars/src/vars").unwrap();
     let _ = parse_variables(&old);
 }

equiv/src/lib.rs

@@ -176,7 +176,6 @@ impl EquivRel {
     // there are 1618950 orbits
     // 1.5 seconds, delta peak mem = 258 Mb
     // disjoint-sets = "0.4.2"
-    // extern crate disjoint_sets;
 
     use disjoint_sets::UnionFind;
     let mut uf = UnionFind::<u32>::new(N as usize);