From 9342474f7c5475737011bb46f32539ee2d5bb771 Mon Sep 17 00:00:00 2001 From: Chris Macklin Date: Wed, 6 Mar 2024 17:49:32 -0800 Subject: [PATCH] Delete TOY_COM and everything related to it. --- Cargo.lock | 67 +- enclone_build/Cargo.toml | 8 +- enclone_com/Cargo.toml | 31 - enclone_com/LICENSE.txt | 1 - enclone_com/src/bin/enclone_client.rs | 111 -- enclone_com/src/enclone_server.rs | 129 --- enclone_com/src/lib.rs | 4 - enclone_com/src/typed_com.rs | 99 -- enclone_com/tests/test_com.rs.aside | 97 -- enclone_com/tests/test_output | 1433 ------------------------- enclone_denovo/Cargo.toml | 32 +- enclone_exec/Cargo.toml | 22 +- enclone_help/Cargo.toml | 10 +- enclone_main/Cargo.toml | 34 +- enclone_main/src/setup.rs | 6 +- enclone_main/src/stop.rs | 16 - enclone_paper/Cargo.toml | 20 +- enclone_tail/Cargo.toml | 30 +- enclone_tools/Cargo.toml | 38 +- enclone_version/Cargo.toml | 2 +- enclone_versions/Cargo.toml | 12 +- master.toml | 60 +- 22 files changed, 170 insertions(+), 2092 deletions(-) delete mode 100644 enclone_com/Cargo.toml delete mode 120000 enclone_com/LICENSE.txt delete mode 100644 enclone_com/src/bin/enclone_client.rs delete mode 100644 enclone_com/src/enclone_server.rs delete mode 100644 enclone_com/src/lib.rs delete mode 100644 enclone_com/src/typed_com.rs delete mode 100644 enclone_com/tests/test_com.rs.aside delete mode 100644 enclone_com/tests/test_output diff --git a/Cargo.lock b/Cargo.lock index 50c205b165..2ad9f1aacb 100644 --- a/Cargo.lock +++ b/Cargo.lock @@ -35,7 +35,7 @@ dependencies = [ [[package]] name = "align_tools" version = "0.1.12" -source = "git+https://github.com/10XGenomics/enclone_ranger?branch=main#cdda245c3574d017161932bc2cf554dbb34c3c41" +source = "git+https://github.com/10XGenomics/enclone_ranger?branch=macklin/delete-client-server#12e8f11e04f492ac4da8288bbb79045b4e4bafa5" dependencies = [ "bio_edit", "debruijn", @@ -47,7 +47,7 @@ dependencies = [ [[package]] name = "amino" version = "0.1.7" -source = "git+https://github.com/10XGenomics/enclone_ranger?branch=main#cdda245c3574d017161932bc2cf554dbb34c3c41" +source = "git+https://github.com/10XGenomics/enclone_ranger?branch=macklin/delete-client-server#12e8f11e04f492ac4da8288bbb79045b4e4bafa5" dependencies = [ "debruijn", "string_utils", @@ -56,7 +56,7 @@ dependencies = [ [[package]] name = "ansi_escape" version = "0.1.3" -source = "git+https://github.com/10XGenomics/enclone_ranger?branch=main#cdda245c3574d017161932bc2cf554dbb34c3c41" +source = "git+https://github.com/10XGenomics/enclone_ranger?branch=macklin/delete-client-server#12e8f11e04f492ac4da8288bbb79045b4e4bafa5" dependencies = [ "string_utils", "vector_utils", @@ -163,7 +163,7 @@ checksum = "904dfeac50f3cdaba28fc6f57fdcddb75f49ed61346676a78c4ffe55877802fd" [[package]] name = "binary_vec_io" version = "0.1.12" -source = "git+https://github.com/10XGenomics/enclone_ranger?branch=main#cdda245c3574d017161932bc2cf554dbb34c3c41" +source = "git+https://github.com/10XGenomics/enclone_ranger?branch=macklin/delete-client-server#12e8f11e04f492ac4da8288bbb79045b4e4bafa5" dependencies = [ "itertools", ] @@ -232,7 +232,7 @@ dependencies = [ [[package]] name = "bio_edit" version = "0.1.1" -source = "git+https://github.com/10XGenomics/enclone_ranger?branch=main#cdda245c3574d017161932bc2cf554dbb34c3c41" +source = "git+https://github.com/10XGenomics/enclone_ranger?branch=macklin/delete-client-server#12e8f11e04f492ac4da8288bbb79045b4e4bafa5" dependencies = [ "bio-types", "bit-set", @@ -609,7 +609,7 @@ dependencies = [ [[package]] name = "dna" version = "0.1.3" -source = "git+https://github.com/10XGenomics/enclone_ranger?branch=main#cdda245c3574d017161932bc2cf554dbb34c3c41" +source = "git+https://github.com/10XGenomics/enclone_ranger?branch=macklin/delete-client-server#12e8f11e04f492ac4da8288bbb79045b4e4bafa5" [[package]] name = "edit-distance" @@ -626,7 +626,7 @@ checksum = "e78d4f1cc4ae33bbfc157ed5d5a5ef3bc29227303d595861deb238fcec4e9457" [[package]] name = "enclone" version = "0.5.219" -source = "git+https://github.com/10XGenomics/enclone_ranger?branch=main#cdda245c3574d017161932bc2cf554dbb34c3c41" +source = "git+https://github.com/10XGenomics/enclone_ranger?branch=macklin/delete-client-server#12e8f11e04f492ac4da8288bbb79045b4e4bafa5" dependencies = [ "amino", "ansi_escape", @@ -653,7 +653,7 @@ dependencies = [ [[package]] name = "enclone_args" version = "0.5.219" -source = "git+https://github.com/10XGenomics/enclone_ranger?branch=main#cdda245c3574d017161932bc2cf554dbb34c3c41" +source = "git+https://github.com/10XGenomics/enclone_ranger?branch=macklin/delete-client-server#12e8f11e04f492ac4da8288bbb79045b4e4bafa5" dependencies = [ "debruijn", "enclone_core", @@ -686,7 +686,7 @@ dependencies = [ [[package]] name = "enclone_core" version = "0.5.219" -source = "git+https://github.com/10XGenomics/enclone_ranger?branch=main#cdda245c3574d017161932bc2cf554dbb34c3c41" +source = "git+https://github.com/10XGenomics/enclone_ranger?branch=macklin/delete-client-server#12e8f11e04f492ac4da8288bbb79045b4e4bafa5" dependencies = [ "amino", "ansi_escape", @@ -851,7 +851,7 @@ dependencies = [ [[package]] name = "enclone_print" version = "0.5.219" -source = "git+https://github.com/10XGenomics/enclone_ranger?branch=main#cdda245c3574d017161932bc2cf554dbb34c3c41" +source = "git+https://github.com/10XGenomics/enclone_ranger?branch=macklin/delete-client-server#12e8f11e04f492ac4da8288bbb79045b4e4bafa5" dependencies = [ "amino", "ansi_escape", @@ -883,7 +883,7 @@ dependencies = [ [[package]] name = "enclone_proto" version = "0.5.219" -source = "git+https://github.com/10XGenomics/enclone_ranger?branch=main#cdda245c3574d017161932bc2cf554dbb34c3c41" +source = "git+https://github.com/10XGenomics/enclone_ranger?branch=macklin/delete-client-server#12e8f11e04f492ac4da8288bbb79045b4e4bafa5" dependencies = [ "bio_edit", "byteorder", @@ -896,7 +896,7 @@ dependencies = [ [[package]] name = "enclone_ranger" version = "0.5.219" -source = "git+https://github.com/10XGenomics/enclone_ranger?branch=main#cdda245c3574d017161932bc2cf554dbb34c3c41" +source = "git+https://github.com/10XGenomics/enclone_ranger?branch=macklin/delete-client-server#12e8f11e04f492ac4da8288bbb79045b4e4bafa5" dependencies = [ "enclone", "enclone_args", @@ -912,7 +912,7 @@ dependencies = [ [[package]] name = "enclone_stuff" version = "0.5.219" -source = "git+https://github.com/10XGenomics/enclone_ranger?branch=main#cdda245c3574d017161932bc2cf554dbb34c3c41" +source = "git+https://github.com/10XGenomics/enclone_ranger?branch=macklin/delete-client-server#12e8f11e04f492ac4da8288bbb79045b4e4bafa5" dependencies = [ "amino", "debruijn", @@ -1029,7 +1029,7 @@ dependencies = [ [[package]] name = "enclone_vars" version = "0.5.219" -source = "git+https://github.com/10XGenomics/enclone_ranger?branch=main#cdda245c3574d017161932bc2cf554dbb34c3c41" +source = "git+https://github.com/10XGenomics/enclone_ranger?branch=macklin/delete-client-server#12e8f11e04f492ac4da8288bbb79045b4e4bafa5" dependencies = [ "io_utils", "itertools", @@ -1069,7 +1069,7 @@ dependencies = [ [[package]] name = "equiv" version = "0.1.3" -source = "git+https://github.com/10XGenomics/enclone_ranger?branch=main#cdda245c3574d017161932bc2cf554dbb34c3c41" +source = "git+https://github.com/10XGenomics/enclone_ranger?branch=macklin/delete-client-server#12e8f11e04f492ac4da8288bbb79045b4e4bafa5" [[package]] name = "errno" @@ -1101,7 +1101,7 @@ checksum = "1d4fd7bd9e32c1205549decf6f36772d7b606a579b26afaffa335ae148151a5d" [[package]] name = "exons" version = "0.1.5" -source = "git+https://github.com/10XGenomics/enclone_ranger?branch=main#cdda245c3574d017161932bc2cf554dbb34c3c41" +source = "git+https://github.com/10XGenomics/enclone_ranger?branch=macklin/delete-client-server#12e8f11e04f492ac4da8288bbb79045b4e4bafa5" dependencies = [ "io_utils", "string_utils", @@ -1111,7 +1111,7 @@ dependencies = [ [[package]] name = "expr_tools" version = "0.1.3" -source = "git+https://github.com/10XGenomics/enclone_ranger?branch=main#cdda245c3574d017161932bc2cf554dbb34c3c41" +source = "git+https://github.com/10XGenomics/enclone_ranger?branch=macklin/delete-client-server#12e8f11e04f492ac4da8288bbb79045b4e4bafa5" dependencies = [ "evalexpr", "statrs", @@ -1122,7 +1122,7 @@ dependencies = [ [[package]] name = "fasta_tools" version = "0.1.8" -source = "git+https://github.com/10XGenomics/enclone_ranger?branch=main#cdda245c3574d017161932bc2cf554dbb34c3c41" +source = "git+https://github.com/10XGenomics/enclone_ranger?branch=macklin/delete-client-server#12e8f11e04f492ac4da8288bbb79045b4e4bafa5" dependencies = [ "debruijn", "flate2", @@ -1292,7 +1292,7 @@ checksum = "6fb8d784f27acf97159b40fc4db5ecd8aa23b9ad5ef69cdd136d3bc80665f0c0" [[package]] name = "graph_simple" version = "0.1.5" -source = "git+https://github.com/10XGenomics/enclone_ranger?branch=main#cdda245c3574d017161932bc2cf554dbb34c3c41" +source = "git+https://github.com/10XGenomics/enclone_ranger?branch=macklin/delete-client-server#12e8f11e04f492ac4da8288bbb79045b4e4bafa5" dependencies = [ "petgraph", "vector_utils", @@ -1337,7 +1337,7 @@ name = "hdf5-sys" version = "0.8.1" source = "git+https://github.com/10XGenomics/hdf5-rust.git?branch=conda_nov2021#2d4a40b7ef75de530bc53fd2eb0fe75047e083ad" dependencies = [ - "attohttpc 0.18.0", + "attohttpc 0.19.1", "bzip2", "libc", "libloading", @@ -1408,7 +1408,7 @@ dependencies = [ [[package]] name = "hyperbase" version = "0.1.8" -source = "git+https://github.com/10XGenomics/enclone_ranger?branch=main#cdda245c3574d017161932bc2cf554dbb34c3c41" +source = "git+https://github.com/10XGenomics/enclone_ranger?branch=macklin/delete-client-server#12e8f11e04f492ac4da8288bbb79045b4e4bafa5" dependencies = [ "debruijn", "equiv", @@ -1451,7 +1451,7 @@ dependencies = [ [[package]] name = "io_utils" version = "0.3.2" -source = "git+https://github.com/10XGenomics/enclone_ranger?branch=main#cdda245c3574d017161932bc2cf554dbb34c3c41" +source = "git+https://github.com/10XGenomics/enclone_ranger?branch=macklin/delete-client-server#12e8f11e04f492ac4da8288bbb79045b4e4bafa5" dependencies = [ "bincode", "flate2", @@ -1517,7 +1517,7 @@ dependencies = [ [[package]] name = "kmer_lookup" version = "0.1.5" -source = "git+https://github.com/10XGenomics/enclone_ranger?branch=main#cdda245c3574d017161932bc2cf554dbb34c3c41" +source = "git+https://github.com/10XGenomics/enclone_ranger?branch=macklin/delete-client-server#12e8f11e04f492ac4da8288bbb79045b4e4bafa5" dependencies = [ "debruijn", "rayon", @@ -1732,7 +1732,6 @@ dependencies = [ "bitflags 1.3.2", "cfg-if", "libc", - "memoffset", ] [[package]] @@ -1892,7 +1891,7 @@ checksum = "d4fd5641d01c8f18a23da7b6fe29298ff4b55afcccdf78973b24cf3175fee32e" [[package]] name = "perf_stats" version = "0.1.8" -source = "git+https://github.com/10XGenomics/enclone_ranger?branch=main#cdda245c3574d017161932bc2cf554dbb34c3c41" +source = "git+https://github.com/10XGenomics/enclone_ranger?branch=macklin/delete-client-server#12e8f11e04f492ac4da8288bbb79045b4e4bafa5" dependencies = [ "io_utils", "libc", @@ -2049,13 +2048,13 @@ checksum = "eb9f9e6e233e5c4a35559a617bf40a4ec447db2e84c20b55a6f83167b7e57872" [[package]] name = "pretty_trace" version = "0.5.24" -source = "git+https://github.com/10XGenomics/enclone_ranger?branch=main#cdda245c3574d017161932bc2cf554dbb34c3c41" +source = "git+https://github.com/10XGenomics/enclone_ranger?branch=macklin/delete-client-server#12e8f11e04f492ac4da8288bbb79045b4e4bafa5" dependencies = [ "backtrace", "io_utils", "lazy_static", "libc", - "nix 0.24.2", + "nix 0.27.1", "pprof", "stats_utils", "string_utils", @@ -2536,12 +2535,12 @@ dependencies = [ [[package]] name = "stats_utils" version = "0.1.3" -source = "git+https://github.com/10XGenomics/enclone_ranger?branch=main#cdda245c3574d017161932bc2cf554dbb34c3c41" +source = "git+https://github.com/10XGenomics/enclone_ranger?branch=macklin/delete-client-server#12e8f11e04f492ac4da8288bbb79045b4e4bafa5" [[package]] name = "string_utils" version = "0.1.4" -source = "git+https://github.com/10XGenomics/enclone_ranger?branch=main#cdda245c3574d017161932bc2cf554dbb34c3c41" +source = "git+https://github.com/10XGenomics/enclone_ranger?branch=macklin/delete-client-server#12e8f11e04f492ac4da8288bbb79045b4e4bafa5" dependencies = [ "vector_utils", ] @@ -2617,7 +2616,7 @@ dependencies = [ [[package]] name = "tables" version = "0.1.5" -source = "git+https://github.com/10XGenomics/enclone_ranger?branch=main#cdda245c3574d017161932bc2cf554dbb34c3c41" +source = "git+https://github.com/10XGenomics/enclone_ranger?branch=macklin/delete-client-server#12e8f11e04f492ac4da8288bbb79045b4e4bafa5" dependencies = [ "io_utils", "itertools", @@ -2869,7 +2868,7 @@ checksum = "bc5cf98d8186244414c848017f0e2676b3fcb46807f6668a97dfe67359a3c4b7" [[package]] name = "vdj_ann" version = "0.4.4" -source = "git+https://github.com/10XGenomics/enclone_ranger?branch=main#cdda245c3574d017161932bc2cf554dbb34c3c41" +source = "git+https://github.com/10XGenomics/enclone_ranger?branch=macklin/delete-client-server#12e8f11e04f492ac4da8288bbb79045b4e4bafa5" dependencies = [ "align_tools", "amino", @@ -2891,7 +2890,7 @@ dependencies = [ [[package]] name = "vdj_ann_ref" version = "0.2.1" -source = "git+https://github.com/10XGenomics/enclone_ranger?branch=main#cdda245c3574d017161932bc2cf554dbb34c3c41" +source = "git+https://github.com/10XGenomics/enclone_ranger?branch=macklin/delete-client-server#12e8f11e04f492ac4da8288bbb79045b4e4bafa5" dependencies = [ "debruijn", "exons", @@ -2909,7 +2908,7 @@ dependencies = [ [[package]] name = "vdj_types" version = "0.2.0" -source = "git+https://github.com/10XGenomics/enclone_ranger?branch=main#cdda245c3574d017161932bc2cf554dbb34c3c41" +source = "git+https://github.com/10XGenomics/enclone_ranger?branch=macklin/delete-client-server#12e8f11e04f492ac4da8288bbb79045b4e4bafa5" dependencies = [ "serde", ] @@ -2926,7 +2925,7 @@ dependencies = [ [[package]] name = "vector_utils" version = "0.1.5" -source = "git+https://github.com/10XGenomics/enclone_ranger?branch=main#cdda245c3574d017161932bc2cf554dbb34c3c41" +source = "git+https://github.com/10XGenomics/enclone_ranger?branch=macklin/delete-client-server#12e8f11e04f492ac4da8288bbb79045b4e4bafa5" dependencies = [ "permutation", "superslice", diff --git a/enclone_build/Cargo.toml b/enclone_build/Cargo.toml index 3b49a051a5..44a0c7a9be 100644 --- a/enclone_build/Cargo.toml +++ b/enclone_build/Cargo.toml @@ -8,10 +8,10 @@ edition = "2021" [dependencies] chrono = { version = "0.4", default-features = false, features = ["std", "clock"] } itertools = "0.10" -pretty_trace = { git = "https://github.com/10XGenomics/enclone_ranger", branch = "main", features = ["pprof"]} -string_utils = { git = "https://github.com/10XGenomics/enclone_ranger", branch = "main" } -enclone_core = { git = "https://github.com/10XGenomics/enclone_ranger", branch = "main" } +pretty_trace = { git = "https://github.com/10XGenomics/enclone_ranger", branch = "macklin/delete-client-server", features = ["pprof"]} +string_utils = { git = "https://github.com/10XGenomics/enclone_ranger", branch = "macklin/delete-client-server" } +enclone_core = { git = "https://github.com/10XGenomics/enclone_ranger", branch = "macklin/delete-client-server" } [build-dependencies] chrono = { version = "0.4", default-features = false, features = ["std", "clock"] } -string_utils = { git = "https://github.com/10XGenomics/enclone_ranger", branch = "main" } +string_utils = { git = "https://github.com/10XGenomics/enclone_ranger", branch = "macklin/delete-client-server" } diff --git a/enclone_com/Cargo.toml b/enclone_com/Cargo.toml deleted file mode 100644 index 94755638ca..0000000000 --- a/enclone_com/Cargo.toml +++ /dev/null @@ -1,31 +0,0 @@ -[package] -name = "enclone_com" -version = "0.5.219" -authors = ["""David Jaffe , - Nigel Delaney , - Keri Dockter , - Jessica Hamel , - Lance Hepler , - Shaun Jackman , - Sreenath Krishnan , - Meryl Lewis , - Alvin Liang , - Patrick Marks , - Wyatt McDonnell """] -edition = "2018" -license-file = "LICENSE.txt" -publish = false - -# Please do not edit crate versions within this file. Instead edit the file master.toml -# in the root of the enclone repo. - -[dependencies] -bytes = "1" -enclone_core = { git = "https://github.com/10XGenomics/enclone_ranger", branch = "main" } -io_utils = { git = "https://github.com/10XGenomics/enclone_ranger", branch = "main" } -lazy_static = "1" -pretty_trace = { git = "https://github.com/10XGenomics/enclone_ranger", branch = "main", features = ["pprof"]} -string_utils = { git = "https://github.com/10XGenomics/enclone_ranger", branch = "main" } -tokio = { version = "1", default-features = false, features = ["io-util", "macros", "rt-multi-thread"] } -vdj_ann = { git = "https://github.com/10XGenomics/enclone_ranger", branch = "main" } - diff --git a/enclone_com/LICENSE.txt b/enclone_com/LICENSE.txt deleted file mode 120000 index 4ab43736a8..0000000000 --- a/enclone_com/LICENSE.txt +++ /dev/null @@ -1 +0,0 @@ -../LICENSE.txt \ No newline at end of file diff --git a/enclone_com/src/bin/enclone_client.rs b/enclone_com/src/bin/enclone_client.rs deleted file mode 100644 index bf60c2a43f..0000000000 --- a/enclone_com/src/bin/enclone_client.rs +++ /dev/null @@ -1,111 +0,0 @@ -// Copyright (c) 2021 10X Genomics, Inc. All rights reserved. - -// Toy enclone client. Not useful, except pedagogically. -// -// based on code in the rust tokio crate - -use enclone_com::typed_com::*; -use pretty_trace::*; -use std::error::Error; -use std::io::{self, BufRead, Write}; -use string_utils::*; -use tokio::io::{AsyncReadExt, AsyncWriteExt}; -use tokio::net::TcpListener; - -#[tokio::main] -async fn main() -> Result<(), Box> { - PrettyTrace::new().on(); - println!( - "\nHello, I am the goofball enclone client. Now that you've started me, you need\n\ - to start enclone in a separate window, with the argument TOY_COM and enough other\n\ - arguments to run enclone (e.g. providing a dataset).\n" - ); - - // Initiate communication. - - let addr = "127.0.0.1:8080"; - let listener = TcpListener::bind(&addr).await?; - let (mut socket, _) = listener.accept().await?; - let mut buf = vec![0; 1024]; - - // Loop forever. - - loop { - // Ask for a request from the user. - - print!("clonotype number or PLOT_BY_ISOTYPE or q to quit? "); - std::io::stdout().flush().unwrap(); - let stdin = io::stdin(); - let line = stdin.lock().lines().next().unwrap().unwrap(); - if line == "q" { - println!(""); - std::process::exit(0); - } - if line != "PLOT_BY_ISOTYPE" && !line.parse::().is_ok() { - println!("That doesn't make sense.\n"); - continue; - } - - // Send the request to the server. - - let id = line.as_bytes(); - let msg = pack_object(ENCLONE_SUBCHANNEL, "request", &id); - socket - .write_all(&msg) - .await - .expect("client failed to write data to socket"); - - // Get the response. - - buf.clear(); - loop { - let mut bufbit = vec![0; 1024]; - let n = socket - .read(&mut bufbit) - .await - .expect("client failed to read data from socket"); - buf.append(&mut bufbit[0..n].to_vec()); - if n < 1024 { - break; - } - } - let n = buf.len(); - - // Unpack the response. - - let mut id = 0_u64; - let mut type_name = Vec::::new(); - let mut body = Vec::::new(); - unpack_message(&mut buf[0..n], &mut id, &mut type_name, &mut body); - if !String::from_utf8(body.clone()).is_ok() { - println!("received body but it's not UTF-8"); - std::process::exit(1); - } - - // Check for error. - - if type_name == b"error" { - print!("{}", strme(&body)); - continue; - } - - // Check for the expected response. - - if type_name == b"colored-text" { - println!("\n{}", strme(&body)); - continue; - } - if type_name == b"svg" { - println!("\n{}", strme(&body)); - continue; - } - - // Otherwise it's an internal error. - - println!( - "response from server has type {}, which is unknown", - strme(&type_name) - ); - std::process::exit(1); - } -} diff --git a/enclone_com/src/enclone_server.rs b/enclone_com/src/enclone_server.rs deleted file mode 100644 index 56f484fb7f..0000000000 --- a/enclone_com/src/enclone_server.rs +++ /dev/null @@ -1,129 +0,0 @@ -// Copyright (c) 2021 10X Genomics, Inc. All rights reserved. - -// Toy enclone server. Not useful, except pedagogically. -// -// based on code in the rust tokio crate - -use crate::typed_com::*; -use enclone_core::defs::*; -use enclone_tail::plot::*; -use std::cmp::min; -use std::error::Error; -use string_utils::*; -use tokio::io::AsyncWriteExt; -use tokio::net::TcpStream; -use vdj_ann::refx::RefData; - -pub async fn enclone_server( - ctl: &EncloneControl, - refdata: &RefData, - exacts: &Vec>, - exact_clonotypes: &Vec, - groups: &Vec>, - pics: &Vec, -) -> Result<(), Box> { - // Fixed address for now. - - let addr = "127.0.0.1:8080"; - - // Create socket. - - let stream = TcpStream::connect(addr).await; - if !stream.is_ok() { - println!( - "Connection failed. The most likely explanation is that you did not start \ - enclone_client before\nyou started enclone. However, in case that's not the problem, \ - here is the error message:\n{:?}\n", - stream.err() - ); - std::process::exit(1); - } - let mut stream = stream.unwrap(); - - // Loop forever. - - let mut buf = vec![0; 1024]; - loop { - // Wait for message from client. - - let n; - loop { - stream.readable().await?; - let result = stream.try_read(&mut buf); - if result.is_ok() { - n = result.unwrap(); - break; - } - } - - // Unpack the message. - - let mut id = 0_u64; - let mut type_name = Vec::::new(); - let mut body = Vec::::new(); - unpack_message(&mut buf[0..n], &mut id, &mut type_name, &mut body); - - // Process request. - - if type_name == b"request" { - let bs = strme(&body); - if bs != "PLOT_BY_ISOTYPE" && !bs.parse::().is_ok() { - println!( - "received the request \"{}\", which doesn't make sense", - strme(&body) - ); - continue; - } - let msg; - if bs == "PLOT_BY_ISOTYPE" { - let mut svg = String::new(); - let mut plot_opt = PlotOpt::default(); - plot_opt.plot_by_isotype = true; - plot_opt.plot_file = "stdout".to_string(); - - // Make plot. - - let res = plot_clonotypes( - &ctl, - &plot_opt, - &refdata, - &exacts, - &exact_clonotypes, - &groups, - &mut svg, - ); - if res.is_err() { - eprintln!("{}", res.unwrap_err()); - std::process::exit(1); - } - let svg_bytes = svg.as_bytes().to_vec(); - msg = pack_object(ENCLONE_SUBCHANNEL, "svg", &svg_bytes); - } else { - { - let id = strme(&body).force_usize(); - if id >= pics.len() { - println!("clonotype id is too large"); - continue; - } - - // Send back the clonotype picture. - - let pic_bytes = pics[id].as_bytes().to_vec(); - msg = pack_object(ENCLONE_SUBCHANNEL, "colored-text", &pic_bytes); - } - } - let mut start = 0; - while start < msg.len() { - let stop = min(start + 1024, msg.len()); - let n = stream.write(&msg[start..stop]).await.unwrap(); - start += n; - } - continue; - } - println!( - "client has sent type {}, which is unknown", - strme(&type_name) - ); - std::process::exit(1); - } -} diff --git a/enclone_com/src/lib.rs b/enclone_com/src/lib.rs deleted file mode 100644 index 4531c513a9..0000000000 --- a/enclone_com/src/lib.rs +++ /dev/null @@ -1,4 +0,0 @@ -// Copyright (c) 2021 10x Genomics, Inc. All rights reserved. - -pub mod enclone_server; -pub mod typed_com; diff --git a/enclone_com/src/typed_com.rs b/enclone_com/src/typed_com.rs deleted file mode 100644 index 5a7a59726b..0000000000 --- a/enclone_com/src/typed_com.rs +++ /dev/null @@ -1,99 +0,0 @@ -// Copyright (c) 2021 10X Genomics, Inc. All rights reserved. - -// Generic typed communication. -// -// A generic typed message consists of a type name plus a blob of bytes. The name is tacked -// on with no restrictions, but one could add validity checking for some types. -// -// We include a 64-bit subchannel identifier because it seems like a port could accidentally -// receive a spurious message, and this can be used to drive that possibility to near zero. -// -// In a more sophisticated version, the message could be compressed and/or encrypted. Encryption -// might be desirable because it is not necessarily desirable for all users on a given computer -// to have visibility of port traffic. -// -// Here is the structure of a generic typed message: -// -// NAME TYPE BYTES -// subchannel identifier u64 8 -// type name length in bytes u16 2 -// type name [u8] up to 256 -// body length in bytes u64 8 -// body [u8] up to 2^64 - 1 -// -// Some hypothetical candidates for types: -// -// NAME CONTENT -// json any JSON file -// svg any SVG file -// rust: any rust structure of the given name, packed using serde -// string any UTF-8-encoded string -// colored-text a UTF-8-encoded string representing text with coloring/bolding via ANSI escapes -// html any html file -// request any UTF-8-encoded string that client would sent to server -// error any UTF-8-encoded string representing an error, sent from server to client - -use std::convert::TryInto; -use std::mem::size_of_val; - -type SubChannelIdentifier = u64; - -pub const ENCLONE_SUBCHANNEL: SubChannelIdentifier = 123456789; // temporary - -pub fn pack_object(id: SubChannelIdentifier, type_name: &str, body: &[u8]) -> Vec { - assert!(type_name.as_bytes().len() <= u16::MAX as usize); - let type_name_length = type_name.as_bytes().len() as u16; - let body_length = body.len() as u64; - let len = size_of_val(&id) - + size_of_val(&type_name_length) - + type_name.as_bytes().len() - + size_of_val(&body_length) - + body.len(); - let mut bytes = Vec::::new(); - bytes.reserve_exact(len); - bytes.append(&mut id.to_ne_bytes().to_vec()); - bytes.append(&mut type_name_length.to_ne_bytes().to_vec()); - bytes.append(&mut type_name.as_bytes().to_vec()); - bytes.append(&mut body_length.to_ne_bytes().to_vec()); - bytes.append(&mut body.to_vec()); - assert_eq!(bytes.len(), len); - bytes -} - -pub fn unpack_message(msg: &[u8], id: &mut u64, type_name: &mut Vec, body: &mut Vec) { - if msg.len() == 0 { - println!("Looks like enclone_client exited, bye!\n"); - std::process::exit(0); - } - if msg.len() < 10 { - eprintln!( - "\nReceived a coded message of length {}, and thus appears to be truncated.\n", - msg.len() - ); - std::process::exit(1); - } - *id = u64::from_ne_bytes(msg[0..8].try_into().unwrap()); - let type_name_length = u16::from_ne_bytes(msg[8..10].try_into().unwrap()) as usize; - if msg.len() < 10 + type_name_length + 8 { - eprintln!( - "\nReceived a coded message of length {}, which appears to be truncated.\n", - msg.len() - ); - std::process::exit(1); - } - *type_name = msg[10..10 + type_name_length].to_vec(); - let body_length = u64::from_ne_bytes( - msg[10 + type_name_length..10 + type_name_length + 8] - .try_into() - .unwrap(), - ) as usize; - let body_length = body_length as usize; - if msg.len() != 10 + type_name_length + 8 + body_length { - eprintln!( - "\nReceived a coded message of length {}, which appears to be wrong.\n", - msg.len() - ); - std::process::exit(1); - } - *body = msg[10 + type_name_length + 8..].to_vec(); -} diff --git a/enclone_com/tests/test_com.rs.aside b/enclone_com/tests/test_com.rs.aside deleted file mode 100644 index 563331f35b..0000000000 --- a/enclone_com/tests/test_com.rs.aside +++ /dev/null @@ -1,97 +0,0 @@ -// Copyright (c) 2021 10X Genomics, Inc. All rights reserved. - -// Test enclone server/client interaction. -// -// To test this alone, use "cargo test --test test_com -- --nocapture". -// -// ./test runs this and many other tests. - -use io_utils::*; -use pretty_trace::*; -use std::fs::File; -use std::io::prelude::*; -use std::io::BufWriter; -use std::process::{Command, Stdio}; -use std::thread; -use std::time; -use string_utils::*; - -#[test] -fn test_com() { - PrettyTrace::new().on(); - - // Define server command. - - let args = ["BCR=123085", "TOY_COM"]; - - // Define requests that would be given to enclone_client. - - let requests = ["7", "100", "PLOT_BY_ISOTYPE", "q"]; - - // Define sleep time in milliseconds. - - let pause = 100; - - // Fork client. - - let client_process = match Command::new("enclone_client") - .stdin(Stdio::piped()) - .stdout(Stdio::piped()) - .spawn() - { - Err(why) => panic!("couldn't spawn client: {}", why), - Ok(client_process) => client_process, - }; - - // Wait until client has printed something. - - let mut client_buffer = [0; 50]; - let mut client_stdout = client_process.stdout.unwrap(); - client_stdout.read(&mut client_buffer).unwrap(); - - // Start the server. - - let server_process = match Command::new("enclone") - .args(&args) - .stdout(Stdio::piped()) - .spawn() - { - Err(why) => panic!("couldn't spawn server: {}", why), - Ok(server_process) => server_process, - }; - - // Wait until server has printed something. - - let mut buffer = [0; 50]; - let mut server_stdout = server_process.stdout.unwrap(); - server_stdout.read(&mut buffer).unwrap(); - thread::sleep(time::Duration::from_millis(pause)); - - // Send enclone_client the requests. - - let mut client_input = client_process.stdin.unwrap(); - for x in requests.iter() { - let msg = format!("{}\n", x); - client_input.write_all(msg.as_bytes()).unwrap(); - thread::sleep(time::Duration::from_millis(pause)); - } - - // Read the rest of what client printed. - - let mut rest = String::new(); - client_stdout.read_to_string(&mut rest).unwrap(); - - // Form total message from client. - - let total = format!("{}{}", strme(&client_buffer), rest); - let save_output = false; - if save_output { - let mut f = open_for_write_new!["test_output"]; - fwrite!(f, "{}", total); - } - - // Verify that client output is correct. - - let total_control = include_str!["test_output"]; - assert_eq!(total, total_control); -} diff --git a/enclone_com/tests/test_output b/enclone_com/tests/test_output deleted file mode 100644 index 1524f1801c..0000000000 --- a/enclone_com/tests/test_output +++ /dev/null @@ -1,1433 +0,0 @@ - -Hello, I am the goofball enclone client. Now that you've started me, you need -to start enclone in a separate window, with the argument TOY_COM and enough other -arguments to run enclone (e.g. providing a dataset). - -clonotype number or PLOT_BY_ISOTYPE or q to quit? -CLONOTYPE = 21 CELLS -┌───────────┬──────────────────────────────────────┬───────────────────────────────┐ -│ │ CHAIN 1 │ CHAIN 2 │ -│ │ 203|IGHV5-51 ◆ 53|IGHJ3 │ 327|IGLV1-47 ◆ 313|IGLJ3 │ -│ ├──────────────────────────────────────┼───────────────────────────────┤ -│ │ 1111111111111111 │ 11111111111 │ -│ │ 6777 1111112222222222 │ 467 00011111111 │ -│ │ 5257 4567890123456789 │ 490 78901234567 │ -│ │ ══════CDR3══════ │ ════CDR3═══ │ -│reference │ WGDR ◦◦◦◦◦◦◦◦◦◦◦◦◦◦◦W │ SSN CAAWD◦◦◦◦◦◦ │ -│donor ref │ WGDR ◦◦◦◦◦◦◦◦◦◦◦◦◦◦◦W │ SSN CAAWD◦◦◦◦◦◦ │ -├───────────┼──────────────────────────────────────┼───────────────────────────────┤ -│# n │ x... ................ u const │ ... ........... u const│ -│1 15 │ FAHT CARPKSDYIIDAFDIW 105 IGHG1 │ NRS CAAWDDSLWVF 539 IGLC3│ -│2 1 │ FAHT CARPKSDYIIDAFDIW 8909 IGHA1 │ NRS CAAWDDSLWVF 11086 IGLC3│ -│3 1 │ FAHT CARPKSDYIIDAFDIW 20 IGHG1 │ NRS CAAWDDSLWVF 21 IGLC2│ -│4 1 │ WAHT CARPKSDYIIDAFDIW 15 IGHG1 │ NRS CAAWDDSLWVF 711 IGLC3│ -│5 1 │ FAHT CARPKSDYIIDAFDIW 6 IGHG1 │ NRS CAAWDDSLWVF 5 IGLC1│ -│6 1 │ │ NRS CAAWDDSLWVF 9 IGLC2│ -│7 1 │ │ NRS CAAWDDSLWVF 8 IGLC3│ -└───────────┴──────────────────────────────────────┴───────────────────────────────┘ - -clonotype number or PLOT_BY_ISOTYPE or q to quit? -CLONOTYPE = 2 CELLS -┌───────────┬─────────────────────────────────────────┬──────────────────────────────┐ -│ │ CHAIN 1 │ CHAIN 2 │ -│ │ 124|IGHV3-30 ◆ 51|IGHJ2 │ 233|IGKV1-5 ◆ 215|IGKJ3 │ -│ ├─────────────────────────────────────────┼──────────────────────────────┤ -│ │ 111 111111111111111111 │ 11111111111 │ -│ │ 2678001 111111222222222233 │ 33569 01111111111 │ -│ │ 1894261 456789012345678901 │ 46261 90123456789 │ -│ │ ═══════CDR3═══════ │ ════CDR3═══ │ -│reference │ QVAGNAV ◦◦◦◦◦◦◦◦◦◦◦◦◦◦◦◦LW │ AVSKE CQQ◦◦◦◦◦◦◦◦ │ -│donor ref │ QVAGNAV ◦◦◦◦◦◦◦◦◦◦◦◦◦◦◦◦LW │ AVSKE CQQ◦◦◦◦◦◦◦◦ │ -├───────────┼─────────────────────────────────────────┼──────────────────────────────┤ -│# n │ ....... .................. u const │ ..... ........... u const│ -│1 1 │ QIAASTV CAKERAPTHIPDWYFDLW 17 IGHG1 │ AVNKD CQQYNSYSITF 39 IGKC │ -│2 1 │ │ AVNKD CQQYNSYSITF 8 IGKC │ -└───────────┴─────────────────────────────────────────┴──────────────────────────────┘ - -clonotype number or PLOT_BY_ISOTYPE or q to quit? - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -IGHA1 - -IGHA2 - -IGHD - -IGHE - -IGHG1 - -IGHG2 - -IGHG3 - -IGHG4 - -IGHM - -undetermined - - -clonotype number or PLOT_BY_ISOTYPE or q to quit? diff --git a/enclone_denovo/Cargo.toml b/enclone_denovo/Cargo.toml index 1f99163660..5652c9c33d 100644 --- a/enclone_denovo/Cargo.toml +++ b/enclone_denovo/Cargo.toml @@ -16,29 +16,29 @@ edition = "2018" publish = false [dependencies] -amino = { git = "https://github.com/10XGenomics/enclone_ranger", branch = "main" } -binary_vec_io = { git = "https://github.com/10XGenomics/enclone_ranger", branch = "main" } +amino = { git = "https://github.com/10XGenomics/enclone_ranger", branch = "macklin/delete-client-server" } +binary_vec_io = { git = "https://github.com/10XGenomics/enclone_ranger", branch = "macklin/delete-client-server" } bio = "0.39" debruijn = "0.3" -equiv = { git = "https://github.com/10XGenomics/enclone_ranger", branch = "main" } -fasta_tools = { git = "https://github.com/10XGenomics/enclone_ranger", branch = "main" } -graph_simple = { git = "https://github.com/10XGenomics/enclone_ranger", branch = "main" } -hyperbase = { git = "https://github.com/10XGenomics/enclone_ranger", branch = "main" } -io_utils = { git = "https://github.com/10XGenomics/enclone_ranger", branch = "main" } +equiv = { git = "https://github.com/10XGenomics/enclone_ranger", branch = "macklin/delete-client-server" } +fasta_tools = { git = "https://github.com/10XGenomics/enclone_ranger", branch = "macklin/delete-client-server" } +graph_simple = { git = "https://github.com/10XGenomics/enclone_ranger", branch = "macklin/delete-client-server" } +hyperbase = { git = "https://github.com/10XGenomics/enclone_ranger", branch = "macklin/delete-client-server" } +io_utils = { git = "https://github.com/10XGenomics/enclone_ranger", branch = "macklin/delete-client-server" } itertools = "0.10" -kmer_lookup = { git = "https://github.com/10XGenomics/enclone_ranger", branch = "main" } +kmer_lookup = { git = "https://github.com/10XGenomics/enclone_ranger", branch = "macklin/delete-client-server" } # poa_hmm = { git = "https://github.com/ban-m/partial_order_alignment.git" } -perf_stats = { git = "https://github.com/10XGenomics/enclone_ranger", branch = "main" } +perf_stats = { git = "https://github.com/10XGenomics/enclone_ranger", branch = "macklin/delete-client-server" } permutation = "0.4" petgraph = "0.6" -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-client-server", features = ["pprof"]} rayon = "1" regex = { version = "1", default-features = false, features = ["std", "perf"] } serde_json = "1" -stats_utils = { git = "https://github.com/10XGenomics/enclone_ranger", branch = "main" } -string_utils = { git = "https://github.com/10XGenomics/enclone_ranger", branch = "main" } +stats_utils = { git = "https://github.com/10XGenomics/enclone_ranger", branch = "macklin/delete-client-server" } +string_utils = { git = "https://github.com/10XGenomics/enclone_ranger", branch = "macklin/delete-client-server" } superslice = "1" -tables = { 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" } +tables = { git = "https://github.com/10XGenomics/enclone_ranger", branch = "macklin/delete-client-server" } +vdj_ann = { git = "https://github.com/10XGenomics/enclone_ranger", branch = "macklin/delete-client-server" } +vdj_ann_ref = { git = "https://github.com/10XGenomics/enclone_ranger", branch = "macklin/delete-client-server" } +vector_utils = { git = "https://github.com/10XGenomics/enclone_ranger", branch = "macklin/delete-client-server" } diff --git a/enclone_exec/Cargo.toml b/enclone_exec/Cargo.toml index 12f61afbb7..b4d6c310c8 100644 --- a/enclone_exec/Cargo.toml +++ b/enclone_exec/Cargo.toml @@ -25,36 +25,36 @@ path = "src/bin/enclone.rs" [dependencies] chrono = { version = "0.4", default-features = false, features = ["std", "clock"] } -enclone_core = { git = "https://github.com/10XGenomics/enclone_ranger", branch = "main" } +enclone_core = { git = "https://github.com/10XGenomics/enclone_ranger", branch = "macklin/delete-client-server" } enclone_main = { path = "../enclone_main" } enclone_testlist = { path = "../enclone_testlist" } flate2 = "1" home = "0.5" -io_utils = { git = "https://github.com/10XGenomics/enclone_ranger", branch = "main" } +io_utils = { git = "https://github.com/10XGenomics/enclone_ranger", branch = "macklin/delete-client-server" } itertools = "0.10" nix = { version = "0.27", features = ["signal"] } -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-client-server", features = ["pprof"]} serde_json = "1" -string_utils = { git = "https://github.com/10XGenomics/enclone_ranger", branch = "main" } +string_utils = { git = "https://github.com/10XGenomics/enclone_ranger", branch = "macklin/delete-client-server" } tokio = { version = "1", default-features = false, features = ["io-util", "macros", "rt-multi-thread"] } -vector_utils = { git = "https://github.com/10XGenomics/enclone_ranger", branch = "main" } +vector_utils = { git = "https://github.com/10XGenomics/enclone_ranger", branch = "macklin/delete-client-server" } [dev-dependencies] -ansi_escape = { git = "https://github.com/10XGenomics/enclone_ranger", branch = "main" } +ansi_escape = { git = "https://github.com/10XGenomics/enclone_ranger", branch = "macklin/delete-client-server" } anyhow = "1" attohttpc = { version = "0.18", default-features = false, features = ["compress", "tls-rustls"] } -enclone_vars = { 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_vars = { git = "https://github.com/10XGenomics/enclone_ranger", branch = "macklin/delete-client-server" } +enclone_proto = { git = "https://github.com/10XGenomics/enclone_ranger", branch = "macklin/delete-client-server" } +enclone_ranger = { git = "https://github.com/10XGenomics/enclone_ranger", branch = "macklin/delete-client-server" } enclone_tools = { path = "../enclone_tools" } flate2 = "1" fs_extra = "1" itertools = "0.10" -perf_stats = { git = "https://github.com/10XGenomics/enclone_ranger", branch = "main" } +perf_stats = { git = "https://github.com/10XGenomics/enclone_ranger", branch = "macklin/delete-client-server" } rayon = "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-client-server" } yaml-rust = "0.4" [features] diff --git a/enclone_help/Cargo.toml b/enclone_help/Cargo.toml index 25dea36114..9a1f8ea2fa 100644 --- a/enclone_help/Cargo.toml +++ b/enclone_help/Cargo.toml @@ -20,12 +20,12 @@ publish = false # in the root of the enclone repo. [dependencies] -ansi_escape = { git = "https://github.com/10XGenomics/enclone_ranger", branch = "main" } -enclone_core = { git = "https://github.com/10XGenomics/enclone_ranger", branch = "main" } -io_utils = { git = "https://github.com/10XGenomics/enclone_ranger", branch = "main" } +ansi_escape = { git = "https://github.com/10XGenomics/enclone_ranger", branch = "macklin/delete-client-server" } +enclone_core = { git = "https://github.com/10XGenomics/enclone_ranger", branch = "macklin/delete-client-server" } +io_utils = { git = "https://github.com/10XGenomics/enclone_ranger", branch = "macklin/delete-client-server" } itertools = "0.10" -string_utils = { git = "https://github.com/10XGenomics/enclone_ranger", branch = "main" } -tables = { git = "https://github.com/10XGenomics/enclone_ranger", branch = "main" } +string_utils = { git = "https://github.com/10XGenomics/enclone_ranger", branch = "macklin/delete-client-server" } +tables = { git = "https://github.com/10XGenomics/enclone_ranger", branch = "macklin/delete-client-server" } enclone_build = {path = "../enclone_build"} diff --git a/enclone_main/Cargo.toml b/enclone_main/Cargo.toml index fe34ab4cc2..3561120f62 100644 --- a/enclone_main/Cargo.toml +++ b/enclone_main/Cargo.toml @@ -21,30 +21,30 @@ publish = false [dependencies] dirs = "4" -enclone_core = { git = "https://github.com/10XGenomics/enclone_ranger", branch = "main" } +enclone_core = { git = "https://github.com/10XGenomics/enclone_ranger", branch = "macklin/delete-client-server" } enclone_help = { path = "../enclone_help" } -enclone_print = { git = "https://github.com/10XGenomics/enclone_ranger", branch = "main" } -enclone_proto = { git = "https://github.com/10XGenomics/enclone_ranger", branch = "main" } -enclone_stuff = { git = "https://github.com/10XGenomics/enclone_ranger", branch = "main" } +enclone_print = { git = "https://github.com/10XGenomics/enclone_ranger", branch = "macklin/delete-client-server" } +enclone_proto = { git = "https://github.com/10XGenomics/enclone_ranger", branch = "macklin/delete-client-server" } +enclone_stuff = { git = "https://github.com/10XGenomics/enclone_ranger", branch = "macklin/delete-client-server" } enclone_tail = { path = "../enclone_tail" } enclone_build = { path = "../enclone_build" } -enclone_vars = { git = "https://github.com/10XGenomics/enclone_ranger", branch = "main" } -enclone = { git = "https://github.com/10XGenomics/enclone_ranger", branch = "main" } -enclone_args = { git = "https://github.com/10XGenomics/enclone_ranger", branch = "main" } +enclone_vars = { git = "https://github.com/10XGenomics/enclone_ranger", branch = "macklin/delete-client-server" } +enclone = { git = "https://github.com/10XGenomics/enclone_ranger", branch = "macklin/delete-client-server" } +enclone_args = { git = "https://github.com/10XGenomics/enclone_ranger", branch = "macklin/delete-client-server" } enclone_testlist = { path = "../enclone_testlist" } -expr_tools = { git = "https://github.com/10XGenomics/enclone_ranger", branch = "main" } -io_utils = { git = "https://github.com/10XGenomics/enclone_ranger", branch = "main" } +expr_tools = { git = "https://github.com/10XGenomics/enclone_ranger", branch = "macklin/delete-client-server" } +io_utils = { git = "https://github.com/10XGenomics/enclone_ranger", branch = "macklin/delete-client-server" } itertools = "0.10" -perf_stats = { git = "https://github.com/10XGenomics/enclone_ranger", branch = "main" } -pretty_trace = { git = "https://github.com/10XGenomics/enclone_ranger", branch = "main", features = ["pprof"]} +perf_stats = { git = "https://github.com/10XGenomics/enclone_ranger", branch = "macklin/delete-client-server" } +pretty_trace = { git = "https://github.com/10XGenomics/enclone_ranger", branch = "macklin/delete-client-server", features = ["pprof"]} rayon = "1" serde_json = "1" -stats_utils = { git = "https://github.com/10XGenomics/enclone_ranger", branch = "main" } -string_utils = { git = "https://github.com/10XGenomics/enclone_ranger", branch = "main" } -tables = { 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" } +stats_utils = { git = "https://github.com/10XGenomics/enclone_ranger", branch = "macklin/delete-client-server" } +string_utils = { git = "https://github.com/10XGenomics/enclone_ranger", branch = "macklin/delete-client-server" } +tables = { git = "https://github.com/10XGenomics/enclone_ranger", branch = "macklin/delete-client-server" } +vdj_ann = { git = "https://github.com/10XGenomics/enclone_ranger", branch = "macklin/delete-client-server" } +vdj_ann_ref = { git = "https://github.com/10XGenomics/enclone_ranger", branch = "macklin/delete-client-server" } +vector_utils = { git = "https://github.com/10XGenomics/enclone_ranger", branch = "macklin/delete-client-server" } hdf5 = {git = "https://github.com/10XGenomics/hdf5-rust.git", branch = "conda_nov2021", features = ["conda"], default-features = false } diff --git a/enclone_main/src/setup.rs b/enclone_main/src/setup.rs index 082e7a8e67..379c565402 100644 --- a/enclone_main/src/setup.rs +++ b/enclone_main/src/setup.rs @@ -232,7 +232,7 @@ pub fn setup( ctl.gen_opt.profile = true; } for i in 1..args.len() { - if args[i] == "NOPAGER" || args[i] == "EVIL_EYE" || args[i] == "TOY_COM" { + if args[i] == "NOPAGER" || args[i] == "EVIL_EYE" { nopager = true; ctl.gen_opt.nopager = true; to_delete[i] = true; @@ -298,7 +298,7 @@ pub fn setup( *argsx = args.clone(); if args.len() == 1 || args.contains(&"help".to_string()) { PrettyTrace::new().on(); - if !nopager && !ctl.gen_opt.profile && !ctl.gen_opt.toy_com { + if !nopager && !ctl.gen_opt.profile { using_pager = true; setup_pager(true); } @@ -382,7 +382,7 @@ pub fn setup( prepare_for_apocalypse(args_orig, false, &bug_reports); let mut nopager = false; for i in 1..args_orig.len() { - if args_orig[i] == "NOPAGER" || args_orig[i] == "TOY_COM" { + if args_orig[i] == "NOPAGER" { nopager = true; } } diff --git a/enclone_main/src/stop.rs b/enclone_main/src/stop.rs index 35739e5181..eaa016f2b8 100644 --- a/enclone_main/src/stop.rs +++ b/enclone_main/src/stop.rs @@ -243,22 +243,6 @@ pub fn main_enclone_stop(mut inter: EncloneIntermediates) -> Result::new(); diff --git a/enclone_paper/Cargo.toml b/enclone_paper/Cargo.toml index 3e5ada6adc..ad0e274e74 100644 --- a/enclone_paper/Cargo.toml +++ b/enclone_paper/Cargo.toml @@ -22,22 +22,22 @@ publish = false # To keep compile time down, this file should *not* access the enclone crate. [dependencies] -bio_edit = { git = "https://github.com/10XGenomics/enclone_ranger", branch = "main" } +bio_edit = { git = "https://github.com/10XGenomics/enclone_ranger", branch = "macklin/delete-client-server" } debruijn = "0.3" -enclone_core = { git = "https://github.com/10XGenomics/enclone_ranger", branch = "main" } +enclone_core = { git = "https://github.com/10XGenomics/enclone_ranger", branch = "macklin/delete-client-server" } enclone_tail = { path = "../enclone_tail" } enclone_testlist = { path = "../enclone_testlist" } flate2 = "1" -io_utils = { git = "https://github.com/10XGenomics/enclone_ranger", branch = "main" } +io_utils = { git = "https://github.com/10XGenomics/enclone_ranger", branch = "macklin/delete-client-server" } itertools = "0.10" -perf_stats = { git = "https://github.com/10XGenomics/enclone_ranger", branch = "main" } +perf_stats = { git = "https://github.com/10XGenomics/enclone_ranger", branch = "macklin/delete-client-server" } plotters = { version = "0.3", default_features = false, features = ["svg_backend", "point_series"] } rand_chacha = "0.3" rayon = "1" -pretty_trace = { git = "https://github.com/10XGenomics/enclone_ranger", branch = "main", features = ["pprof"]} -string_utils = { git = "https://github.com/10XGenomics/enclone_ranger", branch = "main" } -tables = { git = "https://github.com/10XGenomics/enclone_ranger", branch = "main" } +pretty_trace = { git = "https://github.com/10XGenomics/enclone_ranger", branch = "macklin/delete-client-server", features = ["pprof"]} +string_utils = { git = "https://github.com/10XGenomics/enclone_ranger", branch = "macklin/delete-client-server" } +tables = { git = "https://github.com/10XGenomics/enclone_ranger", branch = "macklin/delete-client-server" } triple_accel = "0.4" -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_ann = { git = "https://github.com/10XGenomics/enclone_ranger", branch = "macklin/delete-client-server" } +vdj_ann_ref = { git = "https://github.com/10XGenomics/enclone_ranger", branch = "macklin/delete-client-server" } +vector_utils = { git = "https://github.com/10XGenomics/enclone_ranger", branch = "macklin/delete-client-server" } diff --git a/enclone_tail/Cargo.toml b/enclone_tail/Cargo.toml index ccc55e54b1..dbf226965b 100644 --- a/enclone_tail/Cargo.toml +++ b/enclone_tail/Cargo.toml @@ -22,40 +22,40 @@ publish = false # To keep compile time down, this file should *not* access the enclone crate. [dependencies] -align_tools = { git = "https://github.com/10XGenomics/enclone_ranger", branch = "main" } -amino = { git = "https://github.com/10XGenomics/enclone_ranger", branch = "main" } -ansi_escape = { git = "https://github.com/10XGenomics/enclone_ranger", branch = "main" } -bio_edit = { git = "https://github.com/10XGenomics/enclone_ranger", branch = "main" } +align_tools = { git = "https://github.com/10XGenomics/enclone_ranger", branch = "macklin/delete-client-server" } +amino = { git = "https://github.com/10XGenomics/enclone_ranger", branch = "macklin/delete-client-server" } +ansi_escape = { git = "https://github.com/10XGenomics/enclone_ranger", branch = "macklin/delete-client-server" } +bio_edit = { git = "https://github.com/10XGenomics/enclone_ranger", branch = "macklin/delete-client-server" } crc = "2" debruijn = "0.3" -enclone_core = { git = "https://github.com/10XGenomics/enclone_ranger", branch = "main" } -enclone_proto = { git = "https://github.com/10XGenomics/enclone_ranger", branch = "main" } -equiv = { git = "https://github.com/10XGenomics/enclone_ranger", branch = "main" } +enclone_core = { git = "https://github.com/10XGenomics/enclone_ranger", branch = "macklin/delete-client-server" } +enclone_proto = { git = "https://github.com/10XGenomics/enclone_ranger", branch = "macklin/delete-client-server" } +equiv = { git = "https://github.com/10XGenomics/enclone_ranger", branch = "macklin/delete-client-server" } float-ord = "0.3" fontdb = "0.7" -io_utils = { git = "https://github.com/10XGenomics/enclone_ranger", branch = "main" } +io_utils = { git = "https://github.com/10XGenomics/enclone_ranger", branch = "macklin/delete-client-server" } itertools = "0.10" lazy_static = "1" ndarray = "0.15" 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-client-server" } plotters = { version = "0.3", default_features = false, features = ["svg_backend", "point_series"] } -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-client-server", features = ["pprof"]} rayon = "1" resvg = { version = "0.19", default-features = false } serde = "1" serde_derive = "1" serde_json = "1" -stats_utils = { git = "https://github.com/10XGenomics/enclone_ranger", branch = "main" } -string_utils = { git = "https://github.com/10XGenomics/enclone_ranger", branch = "main" } +stats_utils = { git = "https://github.com/10XGenomics/enclone_ranger", branch = "macklin/delete-client-server" } +string_utils = { git = "https://github.com/10XGenomics/enclone_ranger", branch = "macklin/delete-client-server" } superslice = "1" -tables = { git = "https://github.com/10XGenomics/enclone_ranger", branch = "main" } +tables = { git = "https://github.com/10XGenomics/enclone_ranger", branch = "macklin/delete-client-server" } tar = "0.4" tiny-skia = "0.6" triple_accel = "0.4" usvg = { version = "0.19", features = ["text"] } -vdj_ann = { git = "https://github.com/10XGenomics/enclone_ranger", branch = "main" } -vector_utils = { git = "https://github.com/10XGenomics/enclone_ranger", branch = "main" } +vdj_ann = { git = "https://github.com/10XGenomics/enclone_ranger", branch = "macklin/delete-client-server" } +vector_utils = { git = "https://github.com/10XGenomics/enclone_ranger", branch = "macklin/delete-client-server" } enclone_help = { path = "../enclone_help" } enclone_build = { path = "../enclone_build" } # to replace by this after bumping version diff --git a/enclone_tools/Cargo.toml b/enclone_tools/Cargo.toml index d67328ebdc..e24deb0283 100644 --- a/enclone_tools/Cargo.toml +++ b/enclone_tools/Cargo.toml @@ -20,41 +20,41 @@ publish = false # in the root of the enclone repo. [dependencies] -amino = { git = "https://github.com/10XGenomics/enclone_ranger", branch = "main" } -ansi_escape = { git = "https://github.com/10XGenomics/enclone_ranger", branch = "main" } +amino = { git = "https://github.com/10XGenomics/enclone_ranger", branch = "macklin/delete-client-server" } +ansi_escape = { git = "https://github.com/10XGenomics/enclone_ranger", branch = "macklin/delete-client-server" } attohttpc = { version = "0.18", default-features = false, features = ["compress", "tls-rustls"] } -binary_vec_io = { git = "https://github.com/10XGenomics/enclone_ranger", branch = "main" } -bio_edit = { git = "https://github.com/10XGenomics/enclone_ranger", branch = "main" } +binary_vec_io = { git = "https://github.com/10XGenomics/enclone_ranger", branch = "macklin/delete-client-server" } +bio_edit = { git = "https://github.com/10XGenomics/enclone_ranger", branch = "macklin/delete-client-server" } chrono = { version = "0.4", default-features = false, features = ["std", "clock"] } debruijn = "0.3" -dna = { git = "https://github.com/10XGenomics/enclone_ranger", branch = "main" } +dna = { git = "https://github.com/10XGenomics/enclone_ranger", branch = "macklin/delete-client-server" } edit-distance = "2" -enclone = { git = "https://github.com/10XGenomics/enclone_ranger", branch = "main" } -enclone_core = { git = "https://github.com/10XGenomics/enclone_ranger", branch = "main" } +enclone = { git = "https://github.com/10XGenomics/enclone_ranger", branch = "macklin/delete-client-server" } +enclone_core = { git = "https://github.com/10XGenomics/enclone_ranger", branch = "macklin/delete-client-server" } enclone_denovo = { path = "../enclone_denovo" } enclone_testlist = { path = "../enclone_testlist" } -equiv = { git = "https://github.com/10XGenomics/enclone_ranger", branch = "main" } +equiv = { git = "https://github.com/10XGenomics/enclone_ranger", branch = "macklin/delete-client-server" } 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-client-server" } +fasta_tools = { git = "https://github.com/10XGenomics/enclone_ranger", branch = "macklin/delete-client-server" } flate2 = "1" fs_extra = "1" -io_utils = { git = "https://github.com/10XGenomics/enclone_ranger", branch = "main" } +io_utils = { git = "https://github.com/10XGenomics/enclone_ranger", branch = "macklin/delete-client-server" } itertools = "0.10" lz4 = "1" -perf_stats = { git = "https://github.com/10XGenomics/enclone_ranger", branch = "main" } -pretty_trace = { git = "https://github.com/10XGenomics/enclone_ranger", branch = "main", features = ["pprof"]} +perf_stats = { git = "https://github.com/10XGenomics/enclone_ranger", branch = "macklin/delete-client-server" } +pretty_trace = { git = "https://github.com/10XGenomics/enclone_ranger", branch = "macklin/delete-client-server", features = ["pprof"]} rand_chacha = "0.3" rayon = "1" regex = { version = "1", default-features = false, features = ["std", "perf"] } serde_json = "1" statrs = "0.15" -tables = { git = "https://github.com/10XGenomics/enclone_ranger", branch = "main" } -stats_utils = { git = "https://github.com/10XGenomics/enclone_ranger", branch = "main" } -string_utils = { 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" } +tables = { git = "https://github.com/10XGenomics/enclone_ranger", branch = "macklin/delete-client-server" } +stats_utils = { git = "https://github.com/10XGenomics/enclone_ranger", branch = "macklin/delete-client-server" } +string_utils = { git = "https://github.com/10XGenomics/enclone_ranger", branch = "macklin/delete-client-server" } +vdj_ann = { git = "https://github.com/10XGenomics/enclone_ranger", branch = "macklin/delete-client-server" } +vdj_ann_ref = { git = "https://github.com/10XGenomics/enclone_ranger", branch = "macklin/delete-client-server" } +vector_utils = { git = "https://github.com/10XGenomics/enclone_ranger", branch = "macklin/delete-client-server" } [target.'cfg(not(windows))'.dependencies] pager = "0.16" diff --git a/enclone_version/Cargo.toml b/enclone_version/Cargo.toml index f1e1581319..6f114f2fc9 100644 --- a/enclone_version/Cargo.toml +++ b/enclone_version/Cargo.toml @@ -21,4 +21,4 @@ publish = false [dependencies] chrono = { version = "0.4", default-features = false, features = ["std", "clock"] } -string_utils = { git = "https://github.com/10XGenomics/enclone_ranger", branch = "main" } +string_utils = { git = "https://github.com/10XGenomics/enclone_ranger", branch = "macklin/delete-client-server" } diff --git a/enclone_versions/Cargo.toml b/enclone_versions/Cargo.toml index ca6b135aa1..8454c53ead 100644 --- a/enclone_versions/Cargo.toml +++ b/enclone_versions/Cargo.toml @@ -22,23 +22,23 @@ byteorder = "1" bytes = "1" dirs = "4" flate2 = "1" -io_utils = { git = "https://github.com/10XGenomics/enclone_ranger", branch = "main" } +io_utils = { git = "https://github.com/10XGenomics/enclone_ranger", branch = "macklin/delete-client-server" } itertools = "0.10" ndarray = "0.15" permutation = "0.4" petgraph = "0.6" -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-client-server", features = ["pprof"]} prost = { version = "0.9", default_features = false, features = ["std", "prost-derive"] } prost-build = "0.9" rayon = "1" regex = { version = "1", default-features = false, features = ["std", "perf"] } serde = "1" serde_derive = "1" -stats_utils = { git = "https://github.com/10XGenomics/enclone_ranger", branch = "main" } -stirling_numbers = { git = "https://github.com/10XGenomics/enclone_ranger", branch = "main" } -string_utils = { git = "https://github.com/10XGenomics/enclone_ranger", branch = "main" } +stats_utils = { git = "https://github.com/10XGenomics/enclone_ranger", branch = "macklin/delete-client-server" } +stirling_numbers = { git = "https://github.com/10XGenomics/enclone_ranger", branch = "macklin/delete-client-server" } +string_utils = { git = "https://github.com/10XGenomics/enclone_ranger", branch = "macklin/delete-client-server" } tar = "0.4" -vector_utils = { git = "https://github.com/10XGenomics/enclone_ranger", branch = "main" } +vector_utils = { git = "https://github.com/10XGenomics/enclone_ranger", branch = "macklin/delete-client-server" } [target.'cfg(not(windows))'.dependencies] pager = "0.16" diff --git a/master.toml b/master.toml index 99bd8690b6..03f510f6e6 100755 --- a/master.toml +++ b/master.toml @@ -4,18 +4,18 @@ # of the Cargo.toml files in the crates within this repo. Then use sync_to_master (which # is in the enclone crate) to propagate the change. When you run "cargo t", this is enforced. -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-client-server" } +amino = { git = "https://github.com/10XGenomics/enclone_ranger", branch = "macklin/delete-client-server" } 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-client-server" } arboard = "2" assert_cmd = "2" async-trait = "0.1" attohttpc = { version = "0.18", default-features = false, features = ["compress", "tls-rustls"] } 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-client-server" } 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-client-server" } byteorder = "1" bytes = "1" chrono = { version = "0.4", default-features = false, features = ["std", "clock"] } @@ -26,40 +26,40 @@ 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-client-server" } 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-client-server" } +enclone_core = { git = "https://github.com/10XGenomics/enclone_ranger", branch = "macklin/delete-client-server" } 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-client-server" } +enclone_print = { git = "https://github.com/10XGenomics/enclone_ranger", branch = "macklin/delete-client-server" } +enclone_proto = { git = "https://github.com/10XGenomics/enclone_ranger", branch = "macklin/delete-client-server" } +enclone_ranger = { git = "https://github.com/10XGenomics/enclone_ranger", branch = "macklin/delete-client-server" } 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-client-server" } 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-client-server" } 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-client-server" } 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-client-server" } +fasta_tools = { git = "https://github.com/10XGenomics/enclone_ranger", branch = "macklin/delete-client-server" } 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-client-server" } home = "0.5" -hyperbase = { git = "https://github.com/10XGenomics/enclone_ranger", branch = "main" } +hyperbase = { git = "https://github.com/10XGenomics/enclone_ranger", branch = "macklin/delete-client-server" } 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-client-server" } 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-client-server" } lazy_static = "1" libc = "0.2" log = "0.4" @@ -71,12 +71,12 @@ 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-client-server" } 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-client-server", 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. @@ -92,12 +92,12 @@ 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-client-server" } 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-client-server" } +string_utils = { git = "https://github.com/10XGenomics/enclone_ranger", branch = "macklin/delete-client-server" } superslice = "1" -tables = { git = "https://github.com/10XGenomics/enclone_ranger", branch = "main" } +tables = { git = "https://github.com/10XGenomics/enclone_ranger", branch = "macklin/delete-client-server" } tar = "0.4" thiserror = "1" tilde-expand = "0.1" @@ -110,8 +110,8 @@ triple_accel = "0.4" users = "0.11" usvg = { version = "0.19", features = ["text"] } # vdj_ann = "0.4" -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_ann = { git = "https://github.com/10XGenomics/enclone_ranger", branch = "macklin/delete-client-server" } +vdj_ann_ref = { git = "https://github.com/10XGenomics/enclone_ranger", branch = "macklin/delete-client-server" } +vector_utils = { git = "https://github.com/10XGenomics/enclone_ranger", branch = "macklin/delete-client-server" } whoami = "1" yaml-rust = "0.4"