added Job registry and selection

Project.toml

@@ -16,6 +16,7 @@ LinearAlgebra = "37e2e46d-f89d-539d-b4ee-838fcccc9c8e"
 Media = "e89f7d12-3494-54d1-8411-f7d8b9ae1f27"
 NearestNeighbors = "b8a86587-4115-5ab1-83bc-aa920d37bbce"
 Parameters = "d96e819e-fc66-5662-9728-84c9c7592b0a"
+REPL = "3fa0cd96-eef1-5676-8a61-b3b8758bbffb"
 RecipesBase = "3cdcf5f2-1ef4-517c-9805-6587b60abb01"
 Reexport = "189a3867-3050-52da-a836-e630ba90ab69"
 Requires = "ae029012-a4dd-5104-9daa-d747884805df"

deps/build.jl

@@ -8,6 +8,10 @@ if !ispath(abspath(first(DEPOT_PATH), "config","DFControl", "user_defaults.jl"))
     end
 end
 
+if !ispath(abspath(first(DEPOT_PATH), "config","DFControl", "job_registry.txt"))
+    touch(abspath(first(DEPOT_PATH), "config","DFControl", "job_registry.txt"))
+end
+
 relpath = x -> joinpath(@__DIR__, x)
 
 pythonpath = relpath("python2")

src/DFControl.jl

@@ -1,4 +1,10 @@
 module DFControl
+    const CONFIG_DIR = occursin("cache", first(Base.DEPOT_PATH)) ?
+                       abspath(Base.DEPOT_PATH[2], "config","DFControl") :
+                       abspath(Base.DEPOT_PATH[1], "config","DFControl")
+
+    config_path(path...) = joinpath(CONFIG_DIR, path...)
+
     using LinearAlgebra
     using Statistics
     using Media
@@ -22,8 +28,9 @@ module DFControl
 
 	using NearestNeighbors
     using Crayons
-
-
+    import REPL
+    using REPL.TerminalMenus
+
     abstract type Package end
     struct Wannier90 <: Package end
     struct QE        <: Package end
@@ -71,20 +78,19 @@ module DFControl
     const dfprint = print
     include("display/overloads.jl")
     using Requires
+
+
+    const JOB_REGISTRY = String[]
+
     function __init__()
         @require Juno = "e5e0dc1b-0480-54bc-9374-aad01c23163d" include("display/printing_juno.jl")
         @require Glimpse = "f6e19d58-12a4-5927-8606-ac30a9ce9b69" include("display/glimpse.jl")
 		merge!(Unitful.basefactors, localunits)
 		Unitful.register(@__MODULE__)
+		global JOB_REGISTRY = readlines(config_path("job_registry.txt"))
     end
 
     const pythonpath = Sys.iswindows() ? joinpath(depsdir, "python2", "python") : joinpath(dirname(@__DIR__), "deps", "python2", "bin", "python")
     const cif2cellpath = Sys.iswindows() ? joinpath(depsdir, "python2", "Scripts", "cif2cell") : joinpath(dirname(@__DIR__), "deps", "python2", "bin", "cif2cell")
-#     if isfile(joinpath(dirname(@__FILE__),"..","deps","deps.jl"))
-#       include(joinpath(dirname(@__FILE__),"..","deps","deps.jl"))
-#     else
-#       error("DFControl not properly installed. Please run Pkg.build(\"DFControl\")")
-# end
-    # include("precompile.jl")
-    # _precompile_()
+
 end

src/defaults.jl

@@ -1,6 +1,7 @@
 "File with all the user defaults inside it"
 # const default_file = abspath(homedir(),".julia","config","DFControl", "user_defaults.jl")
-const default_file = occursin("cache", first(Base.DEPOT_PATH)) ? abspath(Base.DEPOT_PATH[2], "config","DFControl", "user_defaults.jl") : abspath(Base.DEPOT_PATH[1], "config","DFControl", "user_defaults.jl")
+const default_file = config_path("user_defaults.jl")
+
 const default_pseudodirs = Dict{Symbol, String}()
 const default_pseudos = Dict{Symbol, Dict{Symbol, Vector{Pseudo}}}()
 const default_jobheader = [""]
@@ -41,7 +42,6 @@ function removedefault_pseudodir(pseudo_symbol::Symbol)
     if haskey(default_pseudodirs, pseudo_symbol)
         delete!(default_pseudodirs, pseudo_symbol)
         rm_expr_lhs(default_file, :(default_pseudodirs[$(QuoteNode(pseudo_symbol))]))
-        # removedefault_pseudos(pseudo_symbol)
     end
 end
 

src/fileio.jl

@@ -429,7 +429,7 @@ function read_job_inputs(job_file::String)
 	    error("Something went wrong and no valid structures could be read from input files.")
     end
     outstruct = mergestructures(structures)
-    return (name=name, header=header, inputs=inputs, structure=outstruct, server_dir=serverdir)
+    return (name=name, inputs=inputs, structure=outstruct, header=header, server_dir=serverdir)
 end
 
 #---------------------------END GENERAL SECTION-------------------#

src/job.jl

@@ -1,4 +1,37 @@
-#here all the different input structures for the different calculations go
+function write_job_registry()
+    open(config_path("job_registry.txt"), "w") do f
+        for j in JOB_REGISTRY
+            write(f, "$j\n")
+        end
+    end
+end
+
+function cleanup_job_registry()
+    stale_ids = findall(!ispath, JOB_REGISTRY)
+    if stale_ids !== nothing
+        jobs_to_remove = JOB_REGISTRY[stale_ids] 
+        message = "Removing $(length(jobs_to_remove)) stale jobs (job folder removed) from the registry:\n"
+        for j in jobs_to_remove
+            message *= "\t$j\n"
+        end
+        @warn message
+        deleteat!(JOB_REGISTRY, stale_ids)
+    end
+    write_job_registry()
+end
+
+function maybe_register_job(abspath::String)
+    if !ispath(abspath)
+        push!(JOB_REGISTRY, abspath)
+    else
+        jid = findfirst(isequal(abspath), JOB_REGISTRY)
+        if jid === nothing
+            push!(JOB_REGISTRY, abspath)
+        end
+    end
+    write_job_registry()
+end
+
 #TODO should we also create a config file for each job with stuff like server etc? and other config things,
 #      which if not supplied could contain the default stuff?
 """
@@ -13,13 +46,15 @@ Represents a full DFT job with multiple input files and calculations.
     server_dir   ::String = ""
     header       ::Vector{String} = getdefault_jobheader()
     metadata     ::Dict = Dict()
+    # version      ::Int = 1
     function DFJob(name, structure, calculations, local_dir, server, server_dir, header, metadata)
         if !isabspath(local_dir)
             local_dir = abspath(local_dir)
         end
         if isempty(structure.name)
             structure.name = split(name, "_")[1]
         end
+        maybe_register_job(local_dir)
         return new(name, structure, calculations, local_dir, server, server_dir, header, metadata)
     end
 end
@@ -66,12 +101,31 @@ function DFJob(job::DFJob, flagstoset...; cell_=copy(cell(job)), atoms_=copy(ato
 end
 
 """
-    DFJob(job_dir::String, job_fuzzy = "job"; kwargs...)
+    DFJob(job_dir::String; job_fuzzy = "job", kwargs...)
 
-Loads and returns a local DFJob. kwargs will be passed to the constructor.
+Loads and returns a local DFJob.
+If `job_dir` is not a valid path the JOB_REGISTRY will be scanned for a job with matching directory.
+The kwargs will be passed to the `DFJob` constructor.
 """
-DFJob(job_dir::String, job_fuzzy="job"; kwargs...) =
-    DFJob(;merge(merge((local_dir=job_dir,), read_job_inputs(joinpath(job_dir, searchdir(job_dir, job_fuzzy)[1]))), kwargs)...)
+function DFJob(job_dir::String; job_fuzzy="job", kwargs...)
+    if ispath(job_dir)
+        real_path = job_dir
+    else
+        matching_jobs = filter(x -> occursin(job_dir, x), JOB_REGISTRY)
+        if length(matching_jobs) == 1
+            real_path = matching_jobs[1]
+        else
+            menu = RadioMenu(matching_jobs)
+            choice = request("Multiple matching jobs were found, choose one:", menu)
+            if choice != -1
+                real_path = matching_jobs[choice]
+            else
+                return
+            end
+        end
+    end
+    return DFJob(;merge(merge((local_dir=real_path,), read_job_inputs(joinpath(real_path, searchdir(real_path, job_fuzzy)[1]))), kwargs)...)
+end        
 
 name(job) = job.name
 #-------------------BEGINNING GENERAL SECTION-------------#

src/qe/fileio.jl

@@ -787,6 +787,10 @@ function qe_read_input(filename; execs=[Exec("pw.x")], run=true, structure_name=
             ids = parse.(Int, _s[2:end])
             typ = flagtype(QE, exec, sym)
             v = replace(v, "d" => "e")
+            if typ === Nothing
+                @warn "Flag $f in file $filename not found in allowed flags for $(exec.exec)"
+                continue
+            end
             parsedval = parse.((eltype(typ),), split(v))
             if !haskey(parsed_flags, sym)
                 if typ <: AbstractMatrix