clean up some bitrot

nim.cfg

@@ -1,4 +1,5 @@
 -d:noUndefinedBitOpts
+-d:nimNoGetRandom
 --passC:"-mpopcnt"
 --path:"$projectPath/src"
 -d:openmp

somalier.nimble

@@ -10,12 +10,11 @@ license       = "MIT"
 # Dependencies
 
 requires "https://github.com/brentp/zip#dev"
-requires "nim >= 1.2.0", "hts >= 0.3.20", "https://github.com/brentp/pedfile >= 0.0.3", "https://github.com/brentp/hileup", "argparse==0.10.1", "lapper", "arraymancer#head"
+requires "nim >= 1.2.0", "hts >= 0.3.20", "https://github.com/brentp/pedfile >= 0.0.3", "https://github.com/brentp/hileup", "argparse >=0.10.1 & < 0.10.2", "lapper", "arraymancer#head"
 requires "https://github.com/brentp/slivar#head"
 srcDir = "src"
 
-#bin = @["./somalier"]
-#bin = @["somalier"]
+bin = @["somalier"]
 
 task test, "run the tests":
   exec "nim c  -d:useSysAssert -d:useGcAssert --lineDir:on --debuginfo -r tests/test_groups"

src/somalierpkg/ancestry.nim

@@ -174,9 +174,9 @@ proc ancestry_main*() =
     t_proj = T * res.components
     X = ctx.variable t_proj
 
-  network ctx, AncestryNet:
+  network AncestryNet:
     layers:
-      x: Input([1, t_proj.shape[1]])
+      #x: Input([1, t_proj.shape[1]])
       fc1: Linear(t_proj.shape[1], nHidden)
       classifier: Linear(nHidden, nOut)
 

src/somalierpkg/relate.nim

@@ -595,14 +595,14 @@ proc remove_spurious_parent_ids(final:var relation_matrices, L:SampleLooker, sta
 proc add_siblings(final:var relation_matrices, stats: seq[Stat4], gt_counts: array[5, seq[uint16]], L:var SampleLooker) =
   for sample_name, sib_names in L.sib_pairs:
     let isample = L.sample_table[sample_name]
-    let iset = sib_names.toSet
+    let iset = sib_names.toHashSet
     let i = isample.i
     if i >= 0 and not gt_counts.high_quality(i): continue
     var ipids = [isample.paternal_id, isample.maternal_id]
     let parent_order = ["dad", "mom"]
     for sn in sib_names:
 
-      let jset = L.sib_pairs.getOrDefault(sn, @[]).toSet
+      let jset = L.sib_pairs.getOrDefault(sn, @[]).toHashSet
       # require that they share the same siblings
       if iset.symmetricDifference(jset).len != 2:
         continue
@@ -924,7 +924,7 @@ proc rel_main*() =
   opts.extracted.update_with_glob
 
   stderr.write_line &"[somalier] starting read of {opts.extracted.len} samples"
-  if opts.extracted.len == 0 or (opts.extracted.len == 1 and not existsFile(opts.extracted[0])):
+  if opts.extracted.len == 0 or (opts.extracted.len == 1 and not fileExists(opts.extracted[0])):
     echo p.help
     quit "[somalier] specify at least 1 extracted somalier file"
   var