From 6366f919631cd49009b9e21b4f85ea91f2de438b Mon Sep 17 00:00:00 2001 From: Chris Macklin Date: Tue, 2 Apr 2024 00:09:08 -0700 Subject: [PATCH] Rename enclone_print -> enclone_process. --- Cargo.lock | 6 +++--- Cargo.toml | 2 +- GUIDE | 2 +- {enclone_print => enclone_process}/Cargo.toml | 2 +- {enclone_print => enclone_process}/LICENSE.txt | 0 .../src/define_column_info.rs | 0 {enclone_print => enclone_process}/src/define_mat.rs | 0 {enclone_print => enclone_process}/src/delete_weaks.rs | 0 {enclone_print => enclone_process}/src/filter.rs | 0 .../src/get_gex_matrix_entry.rs | 0 {enclone_print => enclone_process}/src/lib.rs | 0 {enclone_print => enclone_process}/src/loupe.rs | 0 .../src/process_clonotypes.rs | 0 enclone_ranger/Cargo.toml | 2 +- enclone_ranger/src/main_enclone.rs | 2 +- enclone_stuff/Cargo.toml | 2 +- enclone_stuff/src/doublets.rs | 2 +- enclone_stuff/src/fcell.rs | 2 +- enclone_stuff/src/some_filters.rs | 4 ++-- enclone_stuff/src/split_orbits.rs | 2 +- enclone_stuff/src/start.rs | 4 ++-- enclone_stuff/src/weak_chains.rs | 2 +- enclone_vars/src/export_code.rs | 4 ++-- 23 files changed, 19 insertions(+), 19 deletions(-) rename {enclone_print => enclone_process}/Cargo.toml (98%) rename {enclone_print => enclone_process}/LICENSE.txt (100%) rename {enclone_print => enclone_process}/src/define_column_info.rs (100%) rename {enclone_print => enclone_process}/src/define_mat.rs (100%) rename {enclone_print => enclone_process}/src/delete_weaks.rs (100%) rename {enclone_print => enclone_process}/src/filter.rs (100%) rename {enclone_print => enclone_process}/src/get_gex_matrix_entry.rs (100%) rename {enclone_print => enclone_process}/src/lib.rs (100%) rename {enclone_print => enclone_process}/src/loupe.rs (100%) rename {enclone_print => enclone_process}/src/process_clonotypes.rs (100%) diff --git a/Cargo.lock b/Cargo.lock index 2e66ddeb9..f27e461f1 100644 --- a/Cargo.lock +++ b/Cargo.lock @@ -469,7 +469,7 @@ dependencies = [ ] [[package]] -name = "enclone_print" +name = "enclone_process" version = "0.5.219" dependencies = [ "amino", @@ -518,7 +518,7 @@ dependencies = [ "enclone", "enclone_args", "enclone_core", - "enclone_print", + "enclone_process", "enclone_stuff", "hdf5", "rayon", @@ -535,7 +535,7 @@ dependencies = [ "enclone", "enclone_args", "enclone_core", - "enclone_print", + "enclone_process", "enclone_proto", "equiv", "evalexpr", diff --git a/Cargo.toml b/Cargo.toml index d7a0adc98..faeb49a24 100644 --- a/Cargo.toml +++ b/Cargo.toml @@ -9,7 +9,7 @@ members = [ "enclone", "enclone_args", "enclone_core", - "enclone_print", + "enclone_process", "enclone_proto", "enclone_ranger", "enclone_stuff", diff --git a/GUIDE b/GUIDE index d603966cb..72942aecd 100644 --- a/GUIDE +++ b/GUIDE @@ -10,7 +10,7 @@ enclone_exec just the actual main program enclone_help help menus from the command line enclone_main this includes the enclone main program guts enclone_paper calculations for enclone paper -enclone_print prints clonotypes in the sense of creating the "pictures" (much of core logic) +enclone_process final filtering and output of clonotypes enclone_proto stuff for communicating with Loupe, and reused for other purposes enclone_ranger entry point for cellranger enclone_stuff things called by enclone_main and enclone_ranger diff --git a/enclone_print/Cargo.toml b/enclone_process/Cargo.toml similarity index 98% rename from enclone_print/Cargo.toml rename to enclone_process/Cargo.toml index 08558ff80..77dbb883c 100644 --- a/enclone_print/Cargo.toml +++ b/enclone_process/Cargo.toml @@ -1,5 +1,5 @@ [package] -name = "enclone_print" +name = "enclone_process" version = "0.5.219" authors = ["""David Jaffe , Nigel Delaney , diff --git a/enclone_print/LICENSE.txt b/enclone_process/LICENSE.txt similarity index 100% rename from enclone_print/LICENSE.txt rename to enclone_process/LICENSE.txt diff --git a/enclone_print/src/define_column_info.rs b/enclone_process/src/define_column_info.rs similarity index 100% rename from enclone_print/src/define_column_info.rs rename to enclone_process/src/define_column_info.rs diff --git a/enclone_print/src/define_mat.rs b/enclone_process/src/define_mat.rs similarity index 100% rename from enclone_print/src/define_mat.rs rename to enclone_process/src/define_mat.rs diff --git a/enclone_print/src/delete_weaks.rs b/enclone_process/src/delete_weaks.rs similarity index 100% rename from enclone_print/src/delete_weaks.rs rename to enclone_process/src/delete_weaks.rs diff --git a/enclone_print/src/filter.rs b/enclone_process/src/filter.rs similarity index 100% rename from enclone_print/src/filter.rs rename to enclone_process/src/filter.rs diff --git a/enclone_print/src/get_gex_matrix_entry.rs b/enclone_process/src/get_gex_matrix_entry.rs similarity index 100% rename from enclone_print/src/get_gex_matrix_entry.rs rename to enclone_process/src/get_gex_matrix_entry.rs diff --git a/enclone_print/src/lib.rs b/enclone_process/src/lib.rs similarity index 100% rename from enclone_print/src/lib.rs rename to enclone_process/src/lib.rs diff --git a/enclone_print/src/loupe.rs b/enclone_process/src/loupe.rs similarity index 100% rename from enclone_print/src/loupe.rs rename to enclone_process/src/loupe.rs diff --git a/enclone_print/src/process_clonotypes.rs b/enclone_process/src/process_clonotypes.rs similarity index 100% rename from enclone_print/src/process_clonotypes.rs rename to enclone_process/src/process_clonotypes.rs diff --git a/enclone_ranger/Cargo.toml b/enclone_ranger/Cargo.toml index 3d9a6a03d..569060864 100644 --- a/enclone_ranger/Cargo.toml +++ b/enclone_ranger/Cargo.toml @@ -21,7 +21,7 @@ publish = false [dependencies] enclone_core = { path = "../enclone_core" } -enclone_print = { path = "../enclone_print" } +enclone_process = { path = "../enclone_process" } enclone_stuff = { path = "../enclone_stuff" } enclone = { path = "../enclone" } enclone_args = { path = "../enclone_args" } diff --git a/enclone_ranger/src/main_enclone.rs b/enclone_ranger/src/main_enclone.rs index 691ab4231..ba45cf423 100644 --- a/enclone_ranger/src/main_enclone.rs +++ b/enclone_ranger/src/main_enclone.rs @@ -10,7 +10,7 @@ use enclone_args::load_gex::get_gex_info; use enclone_args::proc_args::proc_args; use enclone_core::defs::EncloneControl; use enclone_core::enclone_structs::EncloneSetup; -use enclone_print::process_clonotypes::{process_clonotypes, OrbitProcessor}; +use enclone_process::process_clonotypes::{process_clonotypes, OrbitProcessor}; use enclone_stuff::start::main_enclone_start; use std::sync::atomic::Ordering::SeqCst; use std::{ diff --git a/enclone_stuff/Cargo.toml b/enclone_stuff/Cargo.toml index b74f333e4..61a9d3ea6 100644 --- a/enclone_stuff/Cargo.toml +++ b/enclone_stuff/Cargo.toml @@ -23,7 +23,7 @@ publish = false amino = { path = "../amino" } debruijn = "0.3" enclone_core = { path = "../enclone_core" } -enclone_print = { path = "../enclone_print" } +enclone_process = { path = "../enclone_process" } enclone_proto = { path = "../enclone_proto" } enclone = { path = "../enclone" } enclone_args = { path = "../enclone_args" } diff --git a/enclone_stuff/src/doublets.rs b/enclone_stuff/src/doublets.rs index 6b7c71f36..f11c4c10d 100644 --- a/enclone_stuff/src/doublets.rs +++ b/enclone_stuff/src/doublets.rs @@ -9,7 +9,7 @@ use enclone_core::{ defs::{CloneInfo, EncloneControl, ExactClonotype}, enclone_structs::BarcodeFates, }; -use enclone_print::define_mat::{define_mat, setup_define_mat}; +use enclone_process::define_mat::{define_mat, setup_define_mat}; use enclone_proto::types::DonorReferenceItem; use itertools::Itertools; use qd::Double; diff --git a/enclone_stuff/src/fcell.rs b/enclone_stuff/src/fcell.rs index e27b3cd2a..6e52ff9ab 100644 --- a/enclone_stuff/src/fcell.rs +++ b/enclone_stuff/src/fcell.rs @@ -4,7 +4,7 @@ use enclone_core::defs::{CloneInfo, ExactClonotype}; use enclone_core::enclone_structs::EncloneSetup; -use enclone_print::get_gex_matrix_entry::get_gex_matrix_entry; +use enclone_process::get_gex_matrix_entry::get_gex_matrix_entry; use evalexpr::{ContextWithMutableVariables, HashMapContext}; use vector_utils::{bin_position, erase_if}; diff --git a/enclone_stuff/src/some_filters.rs b/enclone_stuff/src/some_filters.rs index 80b0f8d6f..bcd0d48d7 100644 --- a/enclone_stuff/src/some_filters.rs +++ b/enclone_stuff/src/some_filters.rs @@ -7,8 +7,8 @@ use crate::weak_chains::weak_chains; use enclone_core::barcode_fate::BarcodeFate; use enclone_core::defs::{CloneInfo, EncloneControl, ExactClonotype}; use enclone_core::enclone_structs::BarcodeFates; -use enclone_print::define_column_info::define_column_info; -use enclone_print::define_mat::{define_mat, setup_define_mat}; +use enclone_process::define_column_info::define_column_info; +use enclone_process::define_mat::{define_mat, setup_define_mat}; use enclone_proto::types::DonorReferenceItem; use equiv::EquivRel; use qd::Double; diff --git a/enclone_stuff/src/split_orbits.rs b/enclone_stuff/src/split_orbits.rs index 3e83e3901..b0a04f11c 100644 --- a/enclone_stuff/src/split_orbits.rs +++ b/enclone_stuff/src/split_orbits.rs @@ -1,7 +1,7 @@ // Copyright (c) 2021 10x Genomics, Inc. All rights reserved. use enclone_core::defs::{CloneInfo, EncloneControl, ExactClonotype}; -use enclone_print::define_mat::{define_mat, setup_define_mat}; +use enclone_process::define_mat::{define_mat, setup_define_mat}; use enclone_proto::types::DonorReferenceItem; use equiv::EquivRel; use qd::Double; diff --git a/enclone_stuff/src/start.rs b/enclone_stuff/src/start.rs index 4ef7dcf0e..ee715a803 100644 --- a/enclone_stuff/src/start.rs +++ b/enclone_stuff/src/start.rs @@ -23,8 +23,8 @@ use enclone_core::barcode_fate::BarcodeFate; use enclone_core::defs::{AlleleData, CloneInfo}; use enclone_core::enclone_structs::{BarcodeFates, EncloneExacts, EncloneSetup, JoinInfo}; use enclone_core::hcomp::heavy_complexity; -use enclone_print::define_mat::{define_mat, setup_define_mat, Od}; -use enclone_print::loupe::make_donor_refs; +use enclone_process::define_mat::{define_mat, setup_define_mat, Od}; +use enclone_process::loupe::make_donor_refs; use equiv::EquivRel; use io_utils::{fwriteln, open_for_read}; use itertools::Itertools; diff --git a/enclone_stuff/src/weak_chains.rs b/enclone_stuff/src/weak_chains.rs index 0e7a37c84..98ca876f6 100644 --- a/enclone_stuff/src/weak_chains.rs +++ b/enclone_stuff/src/weak_chains.rs @@ -8,7 +8,7 @@ use enclone_core::{ defs::{CloneInfo, EncloneControl, ExactClonotype}, enclone_structs::BarcodeFates, }; -use enclone_print::define_mat::{define_mat, setup_define_mat}; +use enclone_process::define_mat::{define_mat, setup_define_mat}; use enclone_proto::types::DonorReferenceItem; use qd::Double; use rayon::prelude::*; diff --git a/enclone_vars/src/export_code.rs b/enclone_vars/src/export_code.rs index 6e68150b5..4dc17d696 100644 --- a/enclone_vars/src/export_code.rs +++ b/enclone_vars/src/export_code.rs @@ -647,7 +647,7 @@ pub fn export_code(level: usize) -> Vec<(String, String)> { // Build cvar auto file. - let actual_out = "enclone_print/src/proc_cvar_auto.rs".to_string(); + let actual_out = "enclone_process/src/proc_cvar_auto.rs".to_string(); let mut temp_out = "enclone_exec/testx/outputs/proc_cvar_auto.rs".to_string(); let mut vars_loc = "enclone_vars/src/vars".to_string(); if level == 1 { @@ -819,7 +819,7 @@ pub fn export_code(level: usize) -> Vec<(String, String)> { // Build lvar auto file. - let actual_out = "enclone_print/src/proc_lvar_auto.rs".to_string(); + let actual_out = "enclone_process/src/proc_lvar_auto.rs".to_string(); let mut temp_out = "enclone_exec/testx/outputs/proc_lvar_auto.rs".to_string(); let mut vars_loc = "enclone_vars/src/vars".to_string(); if level == 1 {