Delete simple uses of pretty_trace and some missed visual args.

Remove most all uses of pretty_trace.
Remove more pretty_trace references and extern crate.

Author: macklin-10x

Cargo.lock

@@ -63,18 +63,19 @@ split-debuginfo = "unpacked"
 # improved.
 
 [workspace.dependencies]
-align_tools = { git = "https://github.com/10XGenomics/enclone_ranger", branch = "main" }
-amino = { git = "https://github.com/10XGenomics/enclone_ranger", branch = "main" }
+align_tools = { git = "https://github.com/10XGenomics/enclone_ranger", branch = "macklin/delete_pretty_trace" }
+amino = { git = "https://github.com/10XGenomics/enclone_ranger", branch = "macklin/delete_pretty_trace" }
 anyhow = "1"
-ansi_escape = { git = "https://github.com/10XGenomics/enclone_ranger", branch = "main" }
+ansi_escape = { git = "https://github.com/10XGenomics/enclone_ranger", branch = "macklin/delete_pretty_trace" }
 arboard = "2"
 assert_cmd = "2"
 async-trait = "0.1"
 attohttpc = { version = "0.18", default-features = false, features = ["compress", "tls-rustls"] }
+backtrace = "0.3"
 base64 = "0.13"
-binary_vec_io = { git = "https://github.com/10XGenomics/enclone_ranger", branch = "main" }
+binary_vec_io = { git = "https://github.com/10XGenomics/enclone_ranger", branch = "macklin/delete_pretty_trace" }
 bio = "0.39"
-bio_edit = { git = "https://github.com/10XGenomics/enclone_ranger", branch = "main" }
+bio_edit = { git = "https://github.com/10XGenomics/enclone_ranger", branch = "macklin/delete_pretty_trace" }
 byteorder = "1"
 bytes = "1"
 chrono = { version = "0.4", default-features = false, features = ["std", "clock"] }
@@ -85,41 +86,41 @@ core-graphics = "0.22"
 crc = "2"
 debruijn = "0.3"
 dirs = "4"
-dna = { git = "https://github.com/10XGenomics/enclone_ranger", branch = "main" }
+dna = { git = "https://github.com/10XGenomics/enclone_ranger", branch = "macklin/delete_pretty_trace" }
 edit-distance = "2"
-enclone_args = { git = "https://github.com/10XGenomics/enclone_ranger", branch = "main" }
-enclone_core = { git = "https://github.com/10XGenomics/enclone_ranger", branch = "main" }
+enclone_args = { git = "https://github.com/10XGenomics/enclone_ranger", branch = "macklin/delete_pretty_trace" }
+enclone_core = { git = "https://github.com/10XGenomics/enclone_ranger", branch = "macklin/delete_pretty_trace" }
 enclone_denovo = { path = "../enclone_denovo" }
 enclone_help = { path = "../enclone_help" }
-enclone = { git = "https://github.com/10XGenomics/enclone_ranger", branch = "main" }
-enclone_print = { git = "https://github.com/10XGenomics/enclone_ranger", branch = "main" }
-enclone_proto = { git = "https://github.com/10XGenomics/enclone_ranger", branch = "main" }
-enclone_ranger = { git = "https://github.com/10XGenomics/enclone_ranger", branch = "main" }
+enclone = { git = "https://github.com/10XGenomics/enclone_ranger", branch = "macklin/delete_pretty_trace" }
+enclone_print = { git = "https://github.com/10XGenomics/enclone_ranger", branch = "macklin/delete_pretty_trace" }
+enclone_proto = { git = "https://github.com/10XGenomics/enclone_ranger", branch = "macklin/delete_pretty_trace" }
+enclone_ranger = { git = "https://github.com/10XGenomics/enclone_ranger", branch = "macklin/delete_pretty_trace" }
 enclone_server_proto = { path = "../enclone_server_proto" }
-enclone_stuff = { git = "https://github.com/10XGenomics/enclone_ranger", branch = "main" }
+enclone_stuff = { git = "https://github.com/10XGenomics/enclone_ranger", branch = "macklin/delete_pretty_trace" }
 enclone_tail = { path = "../enclone_tail" }
-enclone_vars = { git = "https://github.com/10XGenomics/enclone_ranger", branch = "main" }
+enclone_vars = { git = "https://github.com/10XGenomics/enclone_ranger", branch = "macklin/delete_pretty_trace" }
 enclone_version = { path = "../enclone_version" }
-equiv = { git = "https://github.com/10XGenomics/enclone_ranger", branch = "main" }
+equiv = { git = "https://github.com/10XGenomics/enclone_ranger", branch = "macklin/delete_pretty_trace" }
 evalexpr = "7"
-expr_tools = { git = "https://github.com/10XGenomics/enclone_ranger", branch = "main" }
-fasta_tools = { git = "https://github.com/10XGenomics/enclone_ranger", branch = "main" }
+expr_tools = { git = "https://github.com/10XGenomics/enclone_ranger", branch = "macklin/delete_pretty_trace" }
+fasta_tools = { git = "https://github.com/10XGenomics/enclone_ranger", branch = "macklin/delete_pretty_trace" }
 file-lock = "2"
 flate2 = "1"
 float-ord = "0.3"
 fontdb = "0.7"
 fs_extra = "1"
 git = "https://github.com/10xGenomics/hdf5-rust.git"
-graph_simple = { git = "https://github.com/10XGenomics/enclone_ranger", branch = "main" }
+graph_simple = { git = "https://github.com/10XGenomics/enclone_ranger", branch = "macklin/delete_pretty_trace" }
 hdf5 = { git = "https://github.com/10XGenomics/hdf5-rust.git", branch = "conda_nov2021", features = ["conda"], default-features = false }
 home = "0.5"
-hyperbase = { git = "https://github.com/10XGenomics/enclone_ranger", branch = "main" }
+hyperbase = { git = "https://github.com/10XGenomics/enclone_ranger", branch = "macklin/delete_pretty_trace" }
 image = { version = "0.23", features = ["jpeg", "png", "jpeg_rayon"], default-features = false }
 include_dir = { version = "0.6", features = ["search"] }
-io_utils = { git = "https://github.com/10XGenomics/enclone_ranger", branch = "main" }
+io_utils = { git = "https://github.com/10XGenomics/enclone_ranger", branch = "macklin/delete_pretty_trace" }
 itertools = "0.10"
 jpeg-decoder = "0.2"
-kmer_lookup = { git = "https://github.com/10XGenomics/enclone_ranger", branch = "main" }
+kmer_lookup = { git = "https://github.com/10XGenomics/enclone_ranger", branch = "macklin/delete_pretty_trace" }
 lazy_static = "1"
 libc = "0.2"
 log = "0.4"
@@ -132,12 +133,12 @@ num-traits = "0.2"
 objc = "0.2"
 pager = "0.16"
 palette = "0.6"
-perf_stats = { git = "https://github.com/10XGenomics/enclone_ranger", branch = "main" }
+perf_stats = { git = "https://github.com/10XGenomics/enclone_ranger", branch = "macklin/delete_pretty_trace" }
 permutation = "0.4"
 petgraph = "0.6"
 plotters = { version = "0.3", default_features = false, features = ["svg_backend", "point_series"] }
 png-decoder = "0.1"
-pretty_trace = { git = "https://github.com/10XGenomics/enclone_ranger", branch = "main", features = ["pprof"]}
+pretty_trace = { git = "https://github.com/10XGenomics/enclone_ranger", branch = "macklin/delete_pretty_trace", features = ["pprof"]}
 procfs = { version = "0.12", default_features = false }
 # prost: enclone will compile without the std and prost-derive features, but other things
 #        (such as enclone_proto) break.
@@ -153,12 +154,12 @@ serde = "1"
 serde_derive = "1"
 serde_json = "1"
 sha2 = "0.10"
-stats_utils = { git = "https://github.com/10XGenomics/enclone_ranger", branch = "main" }
+stats_utils = { git = "https://github.com/10XGenomics/enclone_ranger", branch = "macklin/delete_pretty_trace" }
 statrs = "0.15"
-stirling_numbers = { git = "https://github.com/10XGenomics/enclone_ranger", branch = "main" }
-string_utils = { git = "https://github.com/10XGenomics/enclone_ranger", branch = "main" }
+stirling_numbers = { git = "https://github.com/10XGenomics/enclone_ranger", branch = "macklin/delete_pretty_trace" }
+string_utils = { git = "https://github.com/10XGenomics/enclone_ranger", branch = "macklin/delete_pretty_trace" }
 superslice = "1"
-tables = { git = "https://github.com/10XGenomics/enclone_ranger", branch = "main" }
+tables = { git = "https://github.com/10XGenomics/enclone_ranger", branch = "macklin/delete_pretty_trace" }
 tar = "0.4"
 thiserror = "1"
 tilde-expand = "0.1"
@@ -170,9 +171,9 @@ tonic-build = { version = "0.6", default-features = false, features = ["transpor
 triple_accel = "0.4"
 users = "0.11"
 usvg = { version = "0.19", features = ["text"] }
-vdj_types = { git = "https://github.com/10XGenomics/enclone_ranger", branch = "main" }
-vdj_ann = { git = "https://github.com/10XGenomics/enclone_ranger", branch = "main" }
-vdj_ann_ref = { git = "https://github.com/10XGenomics/enclone_ranger", branch = "main" }
-vector_utils = { git = "https://github.com/10XGenomics/enclone_ranger", branch = "main" }
+vdj_types = { git = "https://github.com/10XGenomics/enclone_ranger", branch = "macklin/delete_pretty_trace" }
+vdj_ann = { git = "https://github.com/10XGenomics/enclone_ranger", branch = "macklin/delete_pretty_trace" }
+vdj_ann_ref = { git = "https://github.com/10XGenomics/enclone_ranger", branch = "macklin/delete_pretty_trace" }
+vector_utils = { git = "https://github.com/10XGenomics/enclone_ranger", branch = "macklin/delete_pretty_trace" }
 whoami = "1"
 yaml-rust = "0.4"

Cargo.toml

@@ -6,11 +6,12 @@ edition = "2021"
 # See more keys and their definitions at https://doc.rust-lang.org/cargo/reference/manifest.html
 
 [dependencies]
+assert_cmd.workspace = true
+backtrace.workspace = true
 chrono.workspace = true
 itertools.workspace = true
-pretty_trace.workspace = true
 string_utils.workspace = true
-enclone_core.workspace = true
+rayon.workspace = true
 
 [build-dependencies]
 chrono.workspace = true

enclone_build/Cargo.toml

@@ -0,0 +1,37 @@
+// Copyright (c) 2021 10X Genomics, Inc. All rights reserved.
+
+// Check that an out-of-range reference within a rayon parallel loop yields a correct traceback.
+
+use enclone_build::set_panic_handler;
+use rayon::prelude::*;
+
+fn main() {
+    set_panic_handler(&[]);
+    let z = vec![0; 100];
+    let mut x = vec![0; 100];
+    x.par_iter_mut().for_each(|r| {
+        let _ = z[100 + *r];
+    });
+}
+
+#[test]
+fn test_traceback1() {
+    use assert_cmd::prelude::*;
+    use std::process::Command;
+    let mut cmd = Command::cargo_bin("traceback1").expect(
+        "\nAttempt to run traceback1 failed.  The most likely explanation for this is that\n\
+        somehow you did not run \"cargo b\".  Please try that now, and be sure you are doing\n\
+        it from the top-level enclone directory.\n",
+    );
+    let cmd = cmd
+        .output()
+        .unwrap_or_else(|_| panic!("{}", "very strange, failed to execute test_traceback1"));
+
+    let err = std::str::from_utf8(&cmd.stderr).unwrap();
+    let source = "panicked at enclone_build/src/bin/traceback1.rs:13";
+    let count = err.matches(source).count();
+    assert_eq!(
+        1, count,
+        "expected to find exactly one instance of traceback source \"{source}\" but found {count}"
+    );
+}

enclone_build/src/bin/traceback1.rs

@@ -1,4 +1,89 @@
-pub mod prepare_for_apocalypse;
+use chrono::{TimeZone, Utc};
+use itertools::Itertools;
+
+use std::env;
+use string_utils::TextUtils;
+
+use backtrace::Backtrace;
+
+use std::{panic, sync::atomic::AtomicBool, sync::atomic::Ordering::SeqCst, thread};
+
+static PANICKING: AtomicBool = AtomicBool::new(false);
+
+/// Set up panic handling.
+/// This function ensures that we always collect a stack trace, regardless of
+/// whether or not an env var was set. It also limits concurrent panics to a
+/// single thread, whichever panics first, to ensure that if more than one thread
+/// panics at once, we don't end up with interleaved stack trace messages.
+pub fn set_panic_handler(args: &[String]) {
+    let now = Utc::now().naive_utc().timestamp();
+    let build_date = version_string().after(":").between(": ", " :").to_string();
+    let build_datetime = format!("{} 00:00:00", build_date);
+    let then = Utc
+        .datetime_from_str(&build_datetime, "%Y-%m-%d %H:%M:%S")
+        .unwrap()
+        .timestamp();
+    let days_since_build = (now - then) / (60 * 60 * 24);
+    let mut elapsed_message = String::new();
+    if days_since_build > 30 {
+        elapsed_message = format!(
+            "Your build is {} days old.  You might want to check \
+            to see if there is a newer build now.\n\n",
+            days_since_build
+        );
+    }
+
+    let trailer = format!(
+        "You have probably encountered an internal \
+            error in enclone.\n\n\
+            Please email us at enclone@10xgenomics.com, including the traceback shown\n\
+            above and also the following version information:\n\
+            {} : {}.\n\n\
+            Your command was:\n\n{}\n\n\
+            {}\
+            🌸 Thank you for reporting this bug and have a nice day! 🌸",
+        env!("CARGO_PKG_VERSION"),
+        version_string(),
+        args.iter().format(" "),
+        elapsed_message,
+    );
+
+    assert_eq!(thread::current().name().unwrap_or("<none>"), "main");
+    let _ = panic::take_hook();
+    panic::set_hook(Box::new(move |info| {
+        // Prevent multiple threads from issuing tracebacks.
+        if PANICKING.load(SeqCst) {
+            return;
+        }
+        PANICKING.store(true, SeqCst);
+
+        // Get backtrace.
+        let backtrace = Backtrace::new();
+
+        let thread = thread::current();
+        let thread = thread.name().unwrap_or("unnamed");
+        match info.location() {
+            Some(location) => eprintln!(
+                "thread '{}' panicked at {}:{}",
+                thread,
+                location.file(),
+                location.line()
+            ),
+            None => eprintln!("thread '{thread}' panicked "),
+        };
+
+        let msg = match info.payload().downcast_ref::<&'static str>() {
+            Some(s) => *s,
+            None => match info.payload().downcast_ref::<String>() {
+                Some(s) => s.as_str(),
+                None => "Box<Any>",
+            },
+        };
+        eprintln!("{msg}\n{backtrace:?}\n{trailer}");
+
+        std::process::exit(101);
+    }));
+}
 
 const VERSION_STRING: &str = env!("VERSION_STRING");
 

enclone_build/src/lib.rs

@@ -23,7 +23,6 @@ fasta_tools.workspace = true
 io_utils.workspace = true
 itertools.workspace = true
 perf_stats.workspace = true
-pretty_trace.workspace = true
 rayon.workspace = true
 string_utils.workspace = true
 superslice.workspace = true