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remove internal run #422

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merged 2 commits into from
Apr 19, 2024
Merged

remove internal run #422

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94ec2ac
Eliminate internal runs/config.
macklin-10x Apr 18, 2024
0d56af1
Remove attohttpc direct dependency.
macklin-10x Apr 18, 2024
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1 change: 0 additions & 1 deletion Cargo.lock
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4 changes: 0 additions & 4 deletions enclone/src/UNDOC_OPTIONS
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Original file line number Diff line number Diff line change
Expand Up @@ -99,8 +99,6 @@ CURRENT_REF: temp option to force CR 4.0 reference

H5_SLICE: read GEX data slice by slice rather than preloading

FORCE_EXTERNAL: do not test for internal run

STABLE_DOC: print documentation in a way that it won't change when the git version changes

LVARS entries
Expand Down Expand Up @@ -299,8 +297,6 @@ barcode, and fb1_n is the number of UMIs for that feature barcode
SIM_MAT_PLOT=filename,v1,...,vn
generate a plot of the all-vs-all per cell cosine similarity for the variables vi

NO_BUG_REPORTS: don't automatically report bugs

SUBSAMPLE: subsample barcodes at the indicated fraction; at present this is deliberately
randomly seeded and so nonreproducible

Expand Down
43 changes: 0 additions & 43 deletions enclone/src/bin/update_enclone_binary.rs
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11 changes: 1 addition & 10 deletions enclone_args/src/proc_args.rs
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Original file line number Diff line number Diff line change
Expand Up @@ -226,7 +226,7 @@ pub fn proc_args(ctl: &mut EncloneControl, args: &[String]) -> Result<(), String
for i in 1..args.len() {
if args[i].starts_with("BI=") || args[i].starts_with("BIB=") || args[i].starts_with("BIP") {
let bix = format!("{}=", args[i].before("="));
if !ctl.gen_opt.internal_run && !args[i].starts_with("BIP=") {
if !args[i].starts_with("BIP=") {
return Err(format!("\nUnrecognized argument {}.\n", args[i]));
}
let x = args[i].after(&bix).split(',').collect::<Vec<&str>>();
Expand Down Expand Up @@ -429,7 +429,6 @@ pub fn proc_args(ctl: &mut EncloneControl, args: &[String]) -> Result<(), String
("INDELS", &mut ctl.gen_opt.indels),
("INFO_RESOLVE", &mut ctl.gen_opt.info_resolve),
("INKT", &mut ctl.clono_filt_opt.inkt),
("INTERNAL", &mut ctl.gen_opt.internal_run),
("JC1", &mut ctl.gen_opt.jc1),
("JOIN_FULL_DIFF", &mut ctl.join_alg_opt.join_full_diff),
("MAIT", &mut ctl.clono_filt_opt.mait),
Expand Down Expand Up @@ -591,7 +590,6 @@ pub fn proc_args(ctl: &mut EncloneControl, args: &[String]) -> Result<(), String
),
("CLUSTAL_AA", &mut ctl.gen_opt.clustal_aa),
("CLUSTAL_DNA", &mut ctl.gen_opt.clustal_dna),
("CONFIG", &mut ctl.gen_opt.config_file),
("EXT", &mut ctl.gen_opt.ext),
("GROUP_CDR3", &mut ctl.clono_group_opt.cdr3),
("PCHAINS", &mut ctl.parseable_opt.pchains),
Expand Down Expand Up @@ -646,7 +644,6 @@ pub fn proc_args(ctl: &mut EncloneControl, args: &[String]) -> Result<(), String
"CELLRANGER",
"DUMP_INTERNAL_IDS",
"EVIL_EYE",
"FORCE_EXTERNAL",
"LONG_HELP",
"MARKED_B",
"MARK_STATS",
Expand Down Expand Up @@ -674,7 +671,6 @@ pub fn proc_args(ctl: &mut EncloneControl, args: &[String]) -> Result<(), String
"GEX",
"HTML",
"INTERNAL",
"BUG_REPORTS",
"PRE",
"PREPOST",
"SOURCE",
Expand Down Expand Up @@ -935,11 +931,6 @@ pub fn proc_args(ctl: &mut EncloneControl, args: &[String]) -> Result<(), String

// Do residual argument processing.

if ctl.gen_opt.internal_run && ctl.gen_opt.config.is_empty() {
return Err(
"\nYou need to set up your configuration file, please ask for help.\n".to_string(),
);
}
if ctl.gen_opt.gamma_delta && !have_tcrgd || !ctl.gen_opt.gamma_delta && have_tcrgd {
return Err(
"\n. GAMMA_DELTA flag has to be enabled for using TCRGD= and vice versa.\n".to_string(),
Expand Down
2 changes: 1 addition & 1 deletion enclone_args/src/proc_args2.rs
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Expand Up @@ -199,7 +199,7 @@ pub fn proc_args_tail(ctl: &mut EncloneControl, args: &[String]) -> Result<(), S
// Get origin descriptions. Flaky and particularly flaky when internal origin args are paths,
// since it will look in outs for the file.

if ctl.gen_opt.internal_run || ctl.gen_opt.descrip || ctl.gen_opt.vis_dump {
if ctl.gen_opt.descrip || ctl.gen_opt.vis_dump {
ctl.origin_info.descrips.clear();
let mut results = vec![(0, String::new()); ctl.origin_info.n()];
for i in 0..ctl.origin_info.n() {
Expand Down
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