fixed some bugs and added generic flag parsing

deps/asset_init.jl

@@ -74,7 +74,7 @@ open(joinpath(@__DIR__, "mpirunflags.jl"), "w") do wf
                     symbols = [Symbol(name)]
                 end
                 for symbol in symbols
-                    writefbodyline(wf, 1,"""ExecFlag(Symbol("$symbol"), "$name", $type, "$description", nothing),""")
+                    writefbodyline(wf, 1,"""ExecFlag(Symbol("$symbol"), "$name", $type, "$description", nothing, 1),""")
                 end
             end
         end

src/fileio.jl

@@ -163,7 +163,8 @@ function writeexec(f, exec::Exec)
     direxec = joinpath(exec.dir, exec.exec)
     write(f, "$direxec")
     for flag in exec.flags
-        write(f, " -$(flag.symbol)")
+
+        write(f, " $(join(fill('-', flag.minus_count)))$(flag.symbol)")
         if !isa(flag.value, AbstractString)
             for v in flag.value
                 write(f," $v")
@@ -249,7 +250,7 @@ Writes all the input files and job file that are linked to a DFJob.
 Kwargs will be passed down to various writetojob functions.
 """
 function writejobfiles(job::DFJob; kwargs...)
-    rm.(joinpath.(Ref(job.local_dir), searchdir(job.local_dir, ".in")))
+    # rm.(joinpath.(Ref(job.local_dir), searchdir(job.local_dir, ".in")))
     open(joinpath(job.local_dir, "job.tt"), "w") do f
         write(f, "#!/bin/bash\n")
         write_job_name(f, job)
@@ -291,7 +292,8 @@ function read_job_line(line)
     #TODO This is not really nice, we don't handle execs that are unparseable...
     #     Not sure how we can actually do this
     for s in spl
-        if any(occursin.(allexecs(), (s,)))
+        d, e = splitdir(s)
+        if e ∈ allexecs()
             push!(exec_and_flags, s => SubString[])
         elseif !isempty(exec_and_flags)
         # else
@@ -316,12 +318,34 @@ function read_job_line(line)
 	        output = "elk.out"
             push!(execs, Exec(efile, dir))
         else
-            push!(execs, Exec(efile, dir))
+            push!(execs, Exec(efile, dir, parse_generic_flags(flags)))
         end
     end
     return execs, input, output, run
 end
 
+function parse_generic_flags(flags::Vector{<:SubString})
+    out = ExecFlag[]
+    f = :none
+    c = 1
+    for s in flags
+        if s[1] == '-'
+            c = count(isequal('-'), s)
+            f = Symbol(strip(s, '-'))
+        else
+            v = tryparse(Int, s)
+            if v === nothing
+                v = tryparse(Float64, s)
+                if v === nothing
+                    v = s
+                end
+            end
+            push!(out, ExecFlag(f => v, c))
+        end
+    end
+    return out
+end
+
 # TODO: make this work again
 # function read_job_filenames(job_file::String)
 #     input_files = String[]

src/types.jl

@@ -56,18 +56,20 @@ mutable struct ExecFlag
     typ        ::Type
     description::String
     value
+    minus_count::Int
 end
 Base.:(==)(e1::ExecFlag, e2::ExecFlag) =
     all(x -> getfield(e1, x) == getfield(e2, x), (:symbol, :value))
 
-ExecFlag(e::ExecFlag, value) = ExecFlag(e.symbol, e.name, e.typ, e.description, value)
-ExecFlag(p::Pair{Symbol, T}) where T = ExecFlag(first(p), String(first(p)), T, "", last(p))
+ExecFlag(e::ExecFlag, value) = ExecFlag(e.symbol, e.name, e.typ, e.description, value, 1)
+ExecFlag(p::Pair{Symbol, T}) where T = ExecFlag(first(p), String(first(p)), T, "", last(p), 1)
+ExecFlag(p::Pair{Symbol, T}, count::Int) where T = ExecFlag(first(p), String(first(p)), T, "", last(p), count)
 
 const QE_EXECFLAGS = ExecFlag[
-    ExecFlag(:nk, "kpoint-pools", Int, "groups k-point parallelization into nk processor pools", 0),
-    ExecFlag(:ntg, "task-groups", Int, "FFT task groups", 0),
-    ExecFlag(:ndiag, "diag", Int, "Number of processes for linear algebra", 0),
-    ExecFlag(:ni, "images", Int, "Number of processes used for the images", 0)
+    ExecFlag(:nk, "kpoint-pools", Int, "groups k-point parallelization into nk processor pools", 0, 1),
+    ExecFlag(:ntg, "task-groups", Int, "FFT task groups", 0, 1),
+    ExecFlag(:ndiag, "diag", Int, "Number of processes for linear algebra", 0, 1),
+    ExecFlag(:ni, "images", Int, "Number of processes used for the images", 0, 1)
 ]
 
 qeexecflag(flag::AbstractString) = getfirst(x -> x.name==flag, QE_EXECFLAGS)
@@ -85,7 +87,7 @@ function parse_qeexecflags(line::Vector{<:AbstractString})
 end
 
 const WAN_EXECFLAGS = ExecFlag[
-    ExecFlag(:pp, "preprocess", Nothing, "Whether or not to preprocess the wannier input", nothing),
+    ExecFlag(:pp, "preprocess", Nothing, "Whether or not to preprocess the wannier input", nothing, 1),
 ]
 
 wan_execflag(flag::AbstractString) = getfirst(x -> x.name==flag, WAN_EXECFLAGS)
@@ -181,7 +183,7 @@ function parse_mpi_flags(line::Vector{<:SubString})
     eflags
 end
 
-const RUN_EXECS = ["mpirun", "mpi", "mpiexec", "srun"]
+const RUN_EXECS = ["mpirun", "mpiexec", "srun"]
 allexecs() = vcat(RUN_EXECS, QE_EXECS, WAN_EXECS, ELK_EXECS)
 parseable_execs() = vcat(QE_EXECS, WAN_EXECS, ELK_EXECS)
 has_parseable_exec(l::String) = occursin(">", l) && any(occursin.(parseable_execs(), (l,)))