Delete all custom perf-related code (#394)

Deletes the perf_stats crate, and all of the custom perf-tracking code.

Cargo.toml

@@ -23,7 +23,6 @@ members = [
     "io_utils",
     "kmer_lookup",
     "load_feature_bc",
-    "perf_stats",
     "stats_utils",
     "stirling_numbers",
     "string_utils",

enclone/Cargo.toml

@@ -30,7 +30,6 @@ equiv = { path = "../equiv" }
 graph_simple = { path = "../graph_simple" }
 io_utils = { path = "../io_utils" }
 itertools.workspace = true
-perf_stats = { path = "../perf_stats" }
 petgraph = "0.6"
 qd = { git = "https://github.com/Barandis/qd" }
 rayon = "1"

enclone/src/UNDOC_OPTIONS

@@ -275,8 +275,6 @@ HAPS_DEBUG: turn on debug mode for the HAPS option
 
 ROW_FILL_VERBOSE: special option for debugging
 
-COMPE: COMP, plus enforce no unaccounted time (except up to 0.02 seconds)
-UNACCOUNTED: show unaccounted time at each step
 EVIL_EYE: print logging to facilitate diagnosis of mysterious hanging
 
 TOOLTIP: add tooltip text to honeycomb plots

enclone/src/allele.rs

@@ -595,5 +595,4 @@ pub fn sub_alts(
             }
         }
     }
-    ctl.perf_stats(&t, "substituting alt alleles");
 }

enclone/src/enclone.test.tcr

@@ -5,5 +5,5 @@ set rootdir = `dirname $0`
 enclone \
     TCR=`cat $rootdir/../../enclone_core/src/enclone.testdata.tcr | tail -n +3 | grep -v '#' | \
         tr -d ' ' | head --bytes=-1 | tr '\n' ';' | tr -s ';'` \
-    ANN COMP SHOW_BC MIN_DONORS=2 PLAIN NSILENT PRINT_FAILED_JOINS \
+    ANN SHOW_BC MIN_DONORS=2 PLAIN NSILENT PRINT_FAILED_JOINS \
     PRE=/mnt/assembly/vdj/current15 $*

enclone/src/enclone.test2

@@ -5,5 +5,5 @@ set rootdir = `dirname $0`
 enclone \
     BCR=`cat $rootdir/../../enclone_core/src/testdata.public.bcr.human | grep -v '#' | tr -d ' ' | grep -v '^$' | head --bytes=-1 | \
         tr '\n' ';' | tr -s ';'` \
-    ANN COMP SHOW_BC MIN_DONORS=2 PLAIN NSILENT PRINT_FAILED_JOINS \
+    ANN SHOW_BC MIN_DONORS=2 PLAIN NSILENT PRINT_FAILED_JOINS \
     PRE=/mnt/assembly/vdj/current15 $*

enclone/src/join.rs

@@ -104,7 +104,7 @@ pub fn join_exacts(
     if !ctl.silent {
         println!("comparing {} simple clonotypes", info.len());
     }
-    ctl.perf_stats(&timer1, "join setup");
+
     let timer2 = Instant::now();
 
     let joinf = |r: &mut (
@@ -601,7 +601,6 @@ pub fn join_exacts(
 
     results.par_iter_mut().for_each(joinf);
 
-    ctl.perf_stats(&timer2, "in main part of join");
     for r in &results {
         for &j in &r.5 {
             raw_joins.push((j.0 as i32, j.1 as i32));

enclone/src/join2.rs

@@ -90,6 +90,6 @@ pub fn finish_join(
         let bad_rate = percent_ratio(bads, denom);
         println!("whitelist contamination rate = {bad_rate:.2}%");
     }
-    ctl.perf_stats(&timer3, "in tail of join");
+
     eq
 }

enclone/src/misc1.rs

@@ -10,7 +10,7 @@ use equiv::EquivRel;
 use itertools::Itertools;
 #[cfg(not(target_os = "windows"))]
 use pager::Pager;
-use perf_stats::elapsed;
+
 use std::collections::HashMap;
 use std::time::Instant;
 use string_utils::stringme;
@@ -161,7 +161,7 @@ pub fn lookup_heavy_chain_reuse(
         }
         println!(
             "\nused {:.2} seconds in heavy chain reuse calculation\n",
-            elapsed(&t)
+            t.elapsed().as_secs_f64()
         );
     }
 }

enclone/src/misc2.rs

@@ -321,7 +321,7 @@ pub fn find_exact_subclonotypes(
         groups.push((r, s));
         r = s;
     }
-    ctl.perf_stats(&t, "finding exact subclonotypes one");
+
     let t = Instant::now();
     let mut results = Vec::<(
         usize,
@@ -423,7 +423,7 @@ pub fn find_exact_subclonotypes(
             res.1.push(ExactClonotype { share, clones });
         }
     });
-    ctl.perf_stats(&t, "finding exact subclonotypes two");
+
     let t = Instant::now();
     let mut max_exact = 0;
     for i in 0..results.len() {
@@ -519,7 +519,7 @@ pub fn find_exact_subclonotypes(
         }
         println!();
     }
-    ctl.perf_stats(&t, "finding exact subclonotypes three");
+
     exact_clonotypes
 }
 

enclone_args/src/load_gex.rs

@@ -132,7 +132,6 @@ pub fn get_gex_info(ctl: &mut EncloneControl) -> Result<GexInfo, String> {
                 .collect()
         })
         .collect();
-    ctl.perf_stats(&t, "after load_gex");
 
     // Answer.
 

enclone_args/src/load_gex_core.rs

@@ -554,7 +554,6 @@ pub fn load_gex(
     for (_, r) in &results {
         ctl.pathlist.extend(r.f15.iter().cloned());
     }
-    ctl.perf_stats(&t, "in load_gex main loop");
 
     // Test for error.
 
@@ -631,6 +630,5 @@ pub fn load_gex(
 
     // Done.
 
-    ctl.perf_stats(&t, "in load_gex tail");
     Ok(())
 }

enclone_args/src/proc_args.rs

@@ -500,7 +500,6 @@ pub fn proc_args(ctl: &mut EncloneControl, args: &[String]) -> Result<(), String
             "UMI_RATIO_FILT_MARK",
             &mut ctl.clono_filt_opt_def.umi_ratio_filt_mark,
         ),
-        ("UNACCOUNTED", &mut ctl.perf_opt.unaccounted),
         ("UTR_CON", &mut ctl.gen_opt.utr_con),
         ("VDUP", &mut ctl.clono_filt_opt.vdup),
         ("VIS_DUMP", &mut ctl.gen_opt.vis_dump),
@@ -646,9 +645,6 @@ pub fn proc_args(ctl: &mut EncloneControl, args: &[String]) -> Result<(), String
 
     let set_nothing_simple = [
         "CELLRANGER",
-        "COMP",
-        "COMPE",
-        "COMP2",
         "DUMP_INTERNAL_IDS",
         "EVIL_EYE",
         "FORCE_EXTERNAL",
@@ -938,8 +934,6 @@ pub fn proc_args(ctl: &mut EncloneControl, args: &[String]) -> Result<(), String
 
     // Record time.
 
-    ctl.perf_stats(&targs, "in main args loop");
-
     // Do residual argument processing.
 
     if ctl.gen_opt.internal_run && ctl.gen_opt.config.is_empty() {

enclone_args/src/proc_args2.rs

@@ -259,6 +259,6 @@ pub fn proc_args_tail(ctl: &mut EncloneControl, args: &[String]) -> Result<(), S
             }
         }
     }
-    ctl.perf_stats(&tall, "in proc_args_tail");
+
     Ok(())
 }

enclone_args/src/proc_args3.rs

@@ -507,7 +507,7 @@ pub fn proc_xcr(
              other's structure.\n"
         ));
     }
-    ctl.perf_stats(&t, "in proc_xcr 1");
+
     let t = Instant::now();
     for (id, d) in donor_groups.iter().enumerate() {
         let origin_groups = if ctl.gen_opt.cellranger {
@@ -609,7 +609,6 @@ pub fn proc_xcr(
             }
         }
     }
-    ctl.perf_stats(&t, "in proc_xcr 2");
 
     // Get paths.  This will need to change when cellranger switches to multi.  This code is
     // parallelized because this code can indirectly make many calls to path_exists, and the wall
@@ -641,7 +640,7 @@ pub fn proc_xcr(
             }
         }
     }
-    ctl.perf_stats(&t, "in proc_xcr 3");
+
     let t = Instant::now();
     let spinlock: Arc<AtomicUsize> = Arc::new(AtomicUsize::new(0));
     results.par_iter_mut().for_each(|res| {
@@ -688,7 +687,7 @@ pub fn proc_xcr(
         ctl.origin_info.dataset_path.push(result.0);
         ctl.origin_info.gex_path.push(result.1);
     }
-    ctl.perf_stats(&t, "in proc_xcr 4");
+
     Ok(())
 }
 

enclone_args/src/proc_args_check.rs

@@ -778,12 +778,12 @@ pub fn check_lvars(ctl: &EncloneControl, gex_info: &GexInfo) -> Result<(), Strin
             to_check.push(x.clone());
         }
     }
-    ctl.perf_stats(&t, "checking lvars top");
+
     let t = Instant::now();
     if !to_check.is_empty() {
         check_gene_fb(ctl, gex_info, &to_check, "lead")?;
     }
-    ctl.perf_stats(&t, "checking gene");
+
     Ok(())
 }
 

enclone_args/src/proc_args_post.rs

@@ -488,7 +488,6 @@ pub fn proc_args_post(
                 .to_string(),
         );
     }
-    ctl.perf_stats(&t, "after main args loop 1");
 
     // Process TCR, BCR and META.
 
@@ -515,7 +514,7 @@ pub fn proc_args_post(
             .collect();
         proc_meta_core(&lines, ctl)?;
     }
-    ctl.perf_stats(&t, "in proc_meta");
+
     if !xcrs.is_empty() {
         let arg = &xcrs[xcrs.len() - 1];
         proc_xcr(arg, gex, bc, have_gex, ctl)?;
@@ -669,7 +668,7 @@ pub fn proc_args_post(
             ctl.clono_filt_opt_def.donor = true;
         }
     }
-    ctl.perf_stats(&t, "after main args loop 2");
+
     proc_args_tail(ctl, args)?;
 
     // Sort chains_to_align.

enclone_core/Cargo.toml

@@ -31,7 +31,6 @@ evalexpr = ">=7, <12"
 io_utils = { path = "../io_utils" }
 itertools.workspace = true
 lazy_static = "1"
-perf_stats = { path = "../perf_stats" }
 qd = { git = "https://github.com/Barandis/qd" }
 rayon = "1"
 regex = { version = "1", default-features = false, features = ["std", "perf"] }