make tests pass and everything work

src/DFControl.jl

@@ -51,6 +51,10 @@ module DFControl
     export add_calculation!
     export get_run_command
     export change_run_command!
+    export set_runflags!
+    export get_runflags
+    export set_execflags!
+    export get_execflags
     export get_inputs
     export get_input
     export change_filename!

src/fileio.jl

@@ -111,7 +111,6 @@ function writetojob(f, job, input::QEInput)
     return 1
 end
 
-#TODO: no exec runcommand flag support, is it necessary?
 function writetojob(f, job, input::WannierInput)
     run_command = input.run_command
     filename    = input.filename
@@ -219,37 +218,25 @@ function read_job_line(line)
     return run_command, exec, input, output, run
 end
 # TODO: make this work again
-# function read_job_filenames(job_file::String)
-#     input_files = String[]
-#     output_files = String[]
-#     open(job_file, "r") do f
-#         readline(f)
-#         while !eof(f)
-#             line = readline(f)
-#             if isempty(line)
-#                 continue
-#             end
-#             if contains(line, ".x")
-#                 spl = split(line)
-#                 i = find(x -> contains(x, ".x"), spl)[1] + 1
-#                 in_out = strip_split(prod(filter(x -> !contains(x, "-pp"), spl[i:end])), ">")
-#                 if length(in_out) == 2
-#                     push!(input_files,  strip(in_out[1], '<'))
-#                     push!(output_files, in_out[2])
-#                 else
-#                     input_file = strip(in_out[1], '<')
-#                     if contains(line, "wannier90.x") && !contains(line, "pw2wannier90")
-#                         input = splitext(input_file)[1] * ".win"
-#                         output =splitext(input_file)[1] * ".wout"
-#                         !in(output, output_files) && push!(output_files, output)
-#                         !in(input, input_files) && push!(input_files, input)
-#                     end
-#                 end
-#             end
-#         end
-#     end
-#     return input_files, output_files
-# end
+function read_job_filenames(job_file::String)
+    input_files = String[]
+    output_files = String[]
+    open(job_file, "r") do f
+        readline(f)
+        while !eof(f)
+            line = readline(f)
+            if isempty(line)
+                continue
+            end
+            if contains(line, ".x")
+                run_command, exec, input, output, run = read_job_line(line)
+                !in(input,  input_files)  && push!(input_files,  input)
+                !in(output, output_files) && push!(output_files, output)
+            end
+        end
+    end
+    return input_files, output_files
+end
 
 """
     read_job_file(job_file::String)

src/job.jl

@@ -571,32 +571,70 @@ function change_flow!(job::DFJob, should_runs::Union{Dict{String,Bool}, Vector{T
 end
 
 """
-    change_run_command!(job::DFJob, filenames, run_command)
+    change_run_command!(job::DFJob, inputnames, run_command)
 
-Goes through the calculation filenames and sets the run command of the calculation.
+Goes through the job calculations and if it contains one of the inputnames it sets the run command of the calculation.
+Since the `run_command` field has both the command and the flags, this function only changes the command.
+To change the run_command's flags use the function `set_runflags`.
 """
-function change_run_command!(job::DFJob, filenames, run_command)
+function change_run_command!(job::DFJob, inputnames, run_command::String)
     UNDO_JOBS[job.id] = deepcopy(job)
 
-    for calc in get_inputs(job, filenames)
-        calc.run_command = run_command
-        dfprintln("Run command of file '$(calc.filename)' is now: '$(calc.run_command)'")
+    for calc in get_inputs(job, inputnames)
+        calc.run_command = run_command => calc.run_command[2]
+        dfprintln("Run command of file '$(calc.filename)' is now: '$(calc.run_command[1])'")
     end
 
     return job
 end
 
 """
-    get_run_command(job::DFJob, filename)
+    get_run_command(job::DFJob, inputname)
+
+Returns the `run_command` string.
+"""
+function get_run_command(job::DFJob, inputname)
+    for calc in get_inputs(job, inputname)
+        return calc.run_command[1]
+    end
+end
+
+"""
+    set_runflags!(job::DFJob, inputnames, flags...)
+
+Goes through the calculations of the job and if the name contains any of the `inputnames` it sets the run_command flags to the specified ones.
+"""
+function set_runflags!(job::DFJob, inputnames, flags...)
+    calcs = get_inputs(job, inputnames)
+    for calc in calcs
+        for (f,v) in flags
+            calc.run_command[2][f] = v
+        end
+        dfprintln("run flags of calculation $(calc.filename) are now $(calc.run_command[2]).")
+    end
+end
+
+"Returns the run_command flags."
+get_runflags(job::DFJob, inputname) = get_input(job, inputname).run_command[2]
+
+"""
+    set_execflags!(job::DFJob, inputnames, flags...)
 
-Returns the run command for the specified calculation.
+Goes through the calculations of the job and if the name contains any of the `inputnames` it sets the exec flags to the specified ones.
 """
-function get_run_command(job::DFJob, filename)
-    for calc in get_inputs(job, filename)
-        return calc.run_command
+function set_execflags!(job::DFJob, inputnames, flags...)
+    calcs = get_inputs(job, inputnames)
+    for calc in calcs
+        for (f,v) in flags
+            calc.exec[2][f] = v
+        end
+        dfprintln("run flags of calculation $(calc.filename) are now $(calc.exec[2]).")
     end
 end
 
+"Returns the run_command flags."
+get_execflags(job::DFJob, inputname) = get_input(job, inputname).exec[2]
+
 """
     add_block!(job::DFJob, filenames, block::Block)
 
@@ -611,7 +649,6 @@ function add_block!(job::DFJob, filenames, block::Block)
     return job
 end
 
-
 """
     add_data!(job::DFJob, filenames, block_symbol, data, option=:none)
 

src/server_comm.jl

@@ -58,50 +58,57 @@ function pull_file(filepath::String, local_dir::String; server=get_default_serve
     end
 end
 
+
+#TODO: doesn't work for abinit
 """
-    pull_outputs(df_job::DFJob, server="", server_dir="", local_dir=""; job_fuzzy="*job*", extras=String[])
+    pull_outputs(job::DFJob, server="", server_dir="", local_dir=""; job_fuzzy="*job*", extras=String[])
 
 First pulls the job file (specified by job_fuzzy), reads the possible output files and tries to pull them.
 Extra files to pull can be specified by the `extras` keyword, works with fuzzy filenames.
 """
-function pull_outputs(df_job::DFJob, server="", server_dir="", local_dir=""; job_fuzzy="*job*", extras=String[])
-    if df_job.server == "" && server == ""
+function pull_outputs(job::DFJob, server="", server_dir="", local_dir=""; job_fuzzy="*job*", extras=String[])
+    if job.server == "" && server == ""
         error("Error: No job server specified. Please specify it first.")
     elseif server != ""
-        df_job.server = server
+        job.server = server
     end
-    if df_job.server_dir == "" && server_dir == ""
+    if job.server_dir == "" && server_dir == ""
         error("Error: No job server_dir specified. Please specify it first.")
     elseif server_dir != ""
-        df_job.server_dir = server_dir
+        job.server_dir = server_dir
     end
-    if df_job.local_dir == "" && local_dir == ""
+    if job.local_dir == "" && local_dir == ""
         error("Error: No job local/home directory specified. Please specify it first.")
     elseif server != ""
-        df_job.local_dir = local_dir
+        job.local_dir = local_dir
     end
-    if !ispath(df_job.local_dir)
-        mkpath(df_job.local_dir)
+    if !ispath(job.local_dir)
+        mkpath(job.local_dir)
     end
-    pull_server_file(filename) = pull_file(df_job.server, df_job.server_dir, df_job.local_dir, filename)
+    pull_server_file(filename) = pull_file(job.server, job.server_dir, job.local_dir, filename)
 
-    pull_server_file(job_fuzzy)
+    # pull_server_file(job_fuzzy)
 
-    job_file = search_dir(df_job.local_dir, strip(job_fuzzy, '*'))[1]
-    inputs, outputs= read_job_filenames(df_job.local_dir * job_file)
+    # job_file = search_dir(job.local_dir, strip(job_fuzzy, '*'))[1]
+    # inputs, outputs= read_job_filenames(job.local_dir * job_file)
     pulled_outputs = String[]
-    for output in outputs
+    for calc in job.calculations
+        if typeof(calc) == QEInput
+            ofile = splitext(calc.filename)[1] * ".out"
+        elseif typeof(calc) == WannierInput
+            ofile = splitext(calc.filename)[1] * ".wout"
+        end
         try
-            pull_server_file(output)
-            push!(pulled_outputs, output)
+            pull_server_file(ofile)
+            push!(pulled_outputs, ofile)
         end
     end
 
     for fuzzy in extras
         pull_server_file(fuzzy)
-        push!(pulled_outputs, search_dir(df_job.local_dir, strip(fuzzy,'*'))...)
+        push!(pulled_outputs, search_dir(job.local_dir, strip(fuzzy,'*'))...)
     end
-    return df_job.local_dir .* pulled_outputs
+    return job.local_dir .* pulled_outputs
 end
 
 """

test/file_processing_tests.jl

@@ -4,7 +4,7 @@ using DFControl, Base.Test
 scf_input, qestructure = read_qe_input(joinpath(@__DIR__,"../assets/inputs/qe/scf.in"));
 
 bands_input   = read_qe_input(joinpath(@__DIR__,"../assets/inputs/qe/bands.in"))[1];
-projwfc_input = read_qe_input(joinpath(@__DIR__,"../assets/inputs/qe/projwfc.in"), exec="projwfc.x")[1];
+projwfc_input = read_qe_input(joinpath(@__DIR__,"../assets/inputs/qe/projwfc.in"), exec="projwfc.x"=>Dict{Symbol, Any}())[1];
 display(projwfc_input);
 @test get_flag(scf_input, :calculation) == "'scf'";
 @test get_block(scf_input,:k_points).option == :automatic;

test/job_control_tests.jl

@@ -5,7 +5,7 @@ df_job = load_job(test_job_path);
 df_job2 = load_job(joinpath(@__DIR__, test_job_path), new_local_dir="blabla");
 @test df_job2.local_dir    == "blabla/"
 @test length(df_job.calculations) == 7
-@test get_input(df_job, "nscf").run_command == get_run_command(df_job, "nscf")
+@test get_input(df_job, "nscf").run_command[1] == get_run_command(df_job, "nscf")
 @test df_job.local_dir     == test_job_path*"/"
 
 try mkdir(joinpath(test_job_path,"test_dir/")) end

test/test_job/job.tt

@@ -13,6 +13,6 @@ mpirun -np 24 ~/bin/pw.x  <scf.in> scf.out
 mpirun -np 24 ~/bin/pw.x  <bands.in> bands.out
 mpirun -np 24 ~/bin/projwfc.x  <projwfc.in> projwfc.out
 mpirun -np 24 ~/bin/pw.x  <nscf.in> nscf.out
-~/bin/wannier90.x -pp wan
-mpirun -np 24 ~/bin/pw2wannier90.x  <pw2wan.in> pw2wan.out 
-~/bin/wannier90.x  wan
+~/bin/wannier90.x -pp wan.win > wan.wout
+mpirun -np 24 ~/bin/pw2wannier90.x  <pw2wan.in> pw2wan.out
+~/bin/wannier90.x  wan.win > wan.wout