remove internal run (#422)

* Eliminate internal runs/config. * Remove attohttpc direct dependency.
10XGenomics · Apr 19, 2024 · 8b3ca8f · 8b3ca8f
1 parent d8eeecc
commit 8b3ca8f
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Showing 13 changed files with 24 additions and 358 deletions.
diff --git a/Cargo.lock b/Cargo.lock
diff --git a/enclone/src/UNDOC_OPTIONS b/enclone/src/UNDOC_OPTIONS
@@ -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
@@ -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
 

diff --git a/enclone/src/bin/update_enclone_binary.rs b/enclone/src/bin/update_enclone_binary.rs
diff --git a/enclone_args/src/proc_args.rs b/enclone_args/src/proc_args.rs
@@ -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>>();
@@ -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),
@@ -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),
@@ -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",
@@ -674,7 +671,6 @@ pub fn proc_args(ctl: &mut EncloneControl, args: &[String]) -> Result<(), String
         "GEX",
         "HTML",
         "INTERNAL",
-        "BUG_REPORTS",
         "PRE",
         "PREPOST",
         "SOURCE",
@@ -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(),

diff --git a/enclone_args/src/proc_args2.rs b/enclone_args/src/proc_args2.rs
@@ -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() {