tests pass

README.md

@@ -44,7 +44,7 @@ configure_default_pseudos()
 This will then connect to the server, look through all the defined pseudo sets inside the `default_pseudos` and tries to link for each element, for each set the correct filename.
 To find out the filename of a certain atom for a certain pseudo set, or to check whether your config worked, you can do:
 ```julia
-default_pseudo(:O, :pbesolrel) #again change `pbesolrel` to the set you defined before
+getdefault_pseudo(:O, :pbesolrel) #again change `pbesolrel` to the set you defined before
 ```
 This should return you the filename for the pseudo potential file of Oxygen, `:O`, the format for elements in general is e.g. `:Mn`.
 If multiple pseudos are defined for one set and element, you can specify keyword `pseudo_fuzzy = ...` to pull out the one you want to use.
@@ -64,14 +64,14 @@ When the `job.tt` file gets written upon saving of the `DFJob`, calculations whi
 
 As a quick start to see this in action you can do (Juno is highly recommended, for reading clarity)
 ```julia
-job = load_job(joinpath(Pkg.dir("DFControl"), "test/test_job/"))
+job = DFJob(joinpath(Pkg.dir("DFControl"), "test/test_job/"))
 ```
 
 It will automatically look through the directory for a file which matches the fuzzy `*job*`. This can be specified through kwargs, further info in the documentation and examples.
 
 To do something similar on a directory on a server, you can do
 ```julia
-job = load_server_job("path/to/job/starting_from_home", "local_dir", server=default_server())
+job = load_server_job("path/to/job/starting_from_home", "local_dir", server=getdefault_server())
 ```
 If the `local_dir` doesn't exist it will be first created before pulling the `job` script and the calculations that it read from this file.
 

examples/1createandrun_job_from_cif.jl

@@ -53,7 +53,7 @@ job = DFJob(name, local_dir, "/home/ponet/Downloads/9011998.cif", calculations,
       pseudo_set  = :pbesol,
       pseudo_specifier = pseudo_specifier
      )
-# An additional kwarg is `server=default_server()`, which is set to the server you have defined while following the setup in README.
+# An additional kwarg is `server=getdefault_server()`, which is set to the server you have defined while following the setup in README.
 # This can ofcourse be setd to a different server.
 
 #Now the job can be submitted to the server to run.

examples/2edit_job_resubmit.jl

@@ -18,7 +18,7 @@ setflags!(job, :ecutwfc => 25.0)  #more `Pair{Symbol, Any}`'s can be given as va
 setflags!(job, :ecut_rho => 80.) #won't work, it goes through the QE documentation to find the allowed flags for the input files in the job, and also tries to convert the given value to what it should be.
 
 setflags!(job, :ecutrho => 80., :diagonalization => "'david'")
-#shorthand: stfls!
+#shorthand: setflags!!
 
 #now we might not want to run all the calculations again.
 #one can set the job "flow":

src/DFControl.jl

@@ -49,7 +49,7 @@ module DFControl
     export setflow!
     export add!
     export runcommand
-    export runcommand!
+    export setruncommand!
     export setrunflags!
     export runflags
     export setexecflags!

src/defaults.jl

@@ -92,11 +92,11 @@ function setdefault_server(server::String)
 end
 
 """
-    default_server()
+    getdefault_server()
 
 Returns the default server if it's defined. If it is not defined return "".
 """
-function default_server()
+function getdefault_server()
     if isdefined(:default_server)
         return default_server
     else
@@ -105,11 +105,11 @@ function default_server()
 end
 
 """
-    default_pseudo_dirs()
+    getdefault_pseudo_dirs()
 
 Returns the default pseudo dirs if it's defined. If it is not defined return nothing.
 """
-function default_pseudo_dirs()
+function getdefault_pseudo_dirs()
     if isdefined(:default_pseudo_dirs)
         return default_pseudo_dirs
     else
@@ -122,11 +122,11 @@ function default_pseudo_dir(pseudo_set)
 end
 
 """
-    configure_default_pseudos(server = default_server(), pseudo_dirs=default_pseudo_dirs())
+    configure_default_pseudos(server = getdefault_server(), pseudo_dirs=getdefault_pseudo_dirs())
 
 Reads the specified `default_pseudo_dirs` on the `default_server` and sets up the `default_pseudos` variable, and also adds all the entries to the `user_defaults.jl` file.
 """
-function configure_default_pseudos(server = default_server(), pseudo_dirs=default_pseudo_dirs())
+function configure_default_pseudos(server = getdefault_server(), pseudo_dirs=getdefault_pseudo_dirs())
     if server == ""
         error("Either supply a valid server string or setup a default server through 'setdefault_server!()'.")
     end
@@ -173,11 +173,11 @@ function configure_default_pseudos(server = default_server(), pseudo_dirs=defaul
 end
 
 """
-    default_pseudo(atom::Symbol, pseudo_setname=:default; pseudo_specifier=nothing)
+    getdefault_pseudo(atom::Symbol, pseudo_setname=:default; pseudo_specifier=nothing)
 
 Returns the pseudo potential string linked to the atom.
 """
-function default_pseudo(atom::Symbol, pseudo_setname=:default; pseudo_specifier="")
+function getdefault_pseudo(atom::Symbol, pseudo_setname=:default; pseudo_specifier="")
     if !isnull(tryparse(Int, String(atom)[end:end]))
         pp_atom = Symbol(String(atom)[1:end-1])
     else
@@ -250,7 +250,7 @@ function remove_default_input(input::Symbol)
     end
 end
 
-function default_job_header()
+function getdefault_jobheader()
     if isdefined(:default_job_header)
         return default_job_header
     else

src/fileio.jl

@@ -62,7 +62,7 @@ function write_job_name(f, job::DFJob)
 end
 
 function write_job_header(f, job::DFJob)
-    job_header = job.header == "" ? default_job_header() : job.header
+    job_header = job.header == "" ? getdefault_jobheader() : job.header
     for line in job_header
         if contains(line, "\n")
             write(f, line)
@@ -125,7 +125,7 @@ function writetojob(f, job, input::WannierInput)
 
     pw2wanid = findfirst(x -> x.control[1].name == :inputpp && contains(x.exec.exec, "pw2wannier90"), job.calculations[id+1:end])+id
     pw2wan   = job.calculations[pw2wanid]
-    stfls!(pw2wan, :seedname => "'$(splitext(input.filename)[1])'")
+    setflags!(pw2wan, :seedname => "'$(splitext(input.filename)[1])'")
 
     if !pw2wan.run
         write(f, "#")

src/input.jl

@@ -166,9 +166,9 @@ end
 Returns the specified 'DataBlock'.
 """
 function data(input::DFInput, block_symbol::Symbol)
-    block = block(input, block_symbol)
-    if block != nothing && typeof(block) <: DataBlock
-        return block.data
+    block_ = block(input, block_symbol)
+    if block_ != nothing && typeof(block_) <: DataBlock
+        return block_.data
     else
         error("No `DataBlock` with name '$block_symbol' found. ")
     end
@@ -180,9 +180,9 @@ end
 Returns the block with name `block_symbol`.
 """
 function block(input::Union{AbinitInput, WannierInput}, block_symbol::Symbol)
-    for block in input.data
-        if block.name == block_symbol
-            return block
+    for block_ in input.data
+        if block_.name == block_symbol
+            return block_
         end
     end
     return nothing

src/job.jl

@@ -11,7 +11,7 @@ mutable struct DFJob
     server       ::String
     server_dir   ::String
     header       ::Vector{String}
-    function DFJob(name, structure, calculations, local_dir, server, server_dir, header = default_job_header())
+    function DFJob(name, structure, calculations, local_dir, server, server_dir, header = getdefault_jobheader())
         if local_dir != ""
             local_dir = form_directory(local_dir)
         end
@@ -34,14 +34,14 @@ end
 
 #TODO implement abinit
 function DFJob(job_name, local_dir, structure::AbstractStructure, calculations::Vector, common_flags...;
-                    server=default_server(),
+                    server=getdefault_server(),
                     server_dir="",
                     package=:qe,
                     bin_dir="~/bin/",
                     runcommand=Exec("mpirun", bin_dir, Dict(:np => 24)),
                     pseudo_set=:default,
                     pseudo_specifier="",
-                    header=default_job_header())
+                    header=getdefault_jobheader())
 
     @assert package==:qe "Only implemented for Quantum Espresso!"
     local_dir = form_directory(local_dir)
@@ -131,20 +131,20 @@ function DFJob(job::DFJob, flagstoset...;
         newjob.name = name
     end
 
-    stfls!(newjob, flagstoset...)
+    setflags!!(newjob, flagstoset...)
     return newjob
 end
 
 """
-    DFJob(job_dir::String, T=Float64; job_fuzzy = "job", new_job_name=nothing, new_local_dir=nothing, server=default_server(),server_dir="")
+    DFJob(job_dir::String, T=Float64; job_fuzzy = "job", new_job_name=nothing, new_local_dir=nothing, server=getdefault_server(),server_dir="")
 
 Loads and returns a local DFJob. If local_dir is not specified the job directory will be registered as the local one.
 """
 function DFJob(job_dir::String, T=Float64;
                   job_fuzzy     = "job",
                   new_job_name  = "",
                   new_local_dir = nothing,
-                  server        = default_server(),
+                  server        = getdefault_server(),
                   server_dir    = "")
 
     job_dir = form_directory(job_dir)
@@ -162,11 +162,11 @@ function DFJob(job_dir::String, T=Float64;
 end
 
 """
-    DFJob(server_dir::String, local_dir::String, server=default_server(); job_fuzzy="*job*", new_job_name="")
+    DFJob(server_dir::String, local_dir::String, server=getdefault_server(); job_fuzzy="*job*", new_job_name="")
 
 Pulls a server job to local directory and then loads it. A fuzzy search for the job file will be performed and the found input files will be pulled.
 """
-function DFJob(server_dir::String, local_dir::String, server = default_server();
+function DFJob(server_dir::String, local_dir::String, server = getdefault_server();
                          job_fuzzy    = "*job*",
                          new_job_name = "")
 
@@ -242,7 +242,7 @@ function pulljob(server::String, server_dir::String, local_dir::String; job_fuzz
     end
 end
 
-pulljob(args...; kwargs...) = pulljob(default_server(), args..., kwargs...)
+pulljob(args...; kwargs...) = pulljob(getdefault_server(), args..., kwargs...)
 
 
 """
@@ -362,9 +362,9 @@ Looks through the calculation filenames and returns the value of the specified f
 """
 function flag(job::DFJob, calc_filenames, flag_name::Symbol)
     for calc in inputs(job, calc_filenames)
-        flag = flag(calc, flag_name)
-        if flag != nothing
-            return flag
+        flag_ = flag(calc, flag_name)
+        if flag_ != nothing
+            return flag_
         end
     end
     error("Flag $flag_name not found in any input files.")
@@ -377,9 +377,9 @@ Looks through all the calculations and returns the value of the specified flag.
 """
 function flag(job::DFJob, flag_name::Symbol)
     for calc in job.calculations
-        flag = flag(calc, flag_name)
-        if flag != nothing
-            return flag
+        flag_ = flag(calc, flag_name)
+        if flag_ != nothing
+            return flag_
         end
     end
     error("Flag $flag_name not found in any input files.")
@@ -455,7 +455,7 @@ function setflow!(job::DFJob, should_runs...)
     return job
 end
 
-setflow!(job::DFJob, should_runs::Vector{Bool}) = setflow!(job, [calc.filename => run for (calc, run) in zip(inputs(job), should_runs)]...)
+setflow!(job::DFJob, should_runs::Vector{Bool}) = setflow!(job, [calc.filename => run for (calc, run) in zip(job.calculations, should_runs)]...)
 
 """
     setflow!(job::DFJob, filenames::Array{String,1}, should_run)
@@ -899,9 +899,6 @@ function setlocaldir!(job, dir)
     return job
 end
 
-setserverdir!(job, dir) = setserverdir!(job, dir)
-setlocaldir!(job, dir)  = setlocaldir!(job, dir)
-
 """
 sets the projections of the specified atoms inside the job structure.
 """

src/qe/input.jl

@@ -11,9 +11,9 @@ mutable struct QEDataBlock <: DataBlock
 end
 mutable struct QEInput <: DFInput
     filename       ::String
-    control ::Vector{QEControlBlock}
-    data    ::Vector{QEDataBlock}
-    runcommand    ::Exec
+    control        ::Vector{QEControlBlock}
+    data           ::Vector{QEDataBlock}
+    runcommand     ::Exec
     exec           ::Exec
     run            ::Bool
 end

src/server_comm.jl

@@ -12,11 +12,11 @@ function pull_file(server::String, server_dir::String, local_dir::String, filena
 end
 
 """
-    pull_file(server_dir::String, local_dir::String, filename::String; server=default_server())
+    pull_file(server_dir::String, local_dir::String, filename::String; server=getdefault_server())
 
 Pulls a file from the default server if the default server is specified.
 """
-function pull_file(server_dir::String, local_dir::String, filename::String; server=default_server())
+function pull_file(server_dir::String, local_dir::String, filename::String; server=getdefault_server())
     if server != ""
         run(`scp $(server * ":" * server_dir * filename) $local_dir`)
         pulled_files = search_dir(local_dir, filename)
@@ -29,7 +29,7 @@ function pull_file(server_dir::String, local_dir::String, filename::String; serv
     end
 end
 
-function pull_files(server_dir::String, local_dir::String, filenames::Vector{String}; server=default_server())
+function pull_files(server_dir::String, local_dir::String, filenames::Vector{String}; server=getdefault_server())
     pulled_files = String[]
     for file in filenames
        push!(pulled_files, pull_file(server_dir, local_dir, file; server))
@@ -38,11 +38,11 @@ function pull_files(server_dir::String, local_dir::String, filenames::Vector{Str
 end
 
 """
-    pull_file(filepath::String, local_dir::String; server=default_server(), local_filename=nothing)
+    pull_file(filepath::String, local_dir::String; server=getdefault_server(), local_filename=nothing)
 
 Pulls a file from the default server if the default server is specified.
 """
-function pull_file(filepath::String, local_dir::String; server=default_server(), local_filename=nothing)
+function pull_file(filepath::String, local_dir::String; server=getdefault_server(), local_filename=nothing)
     local_dir = form_directory(local_dir)
     if server != ""
         if local_filename != nothing
@@ -117,11 +117,11 @@ end
 If sbatch is running on server it will return the output of the `qstat` command.
 """
 qstat(server) = run(`ssh -t $server qstat`)
-qstat()       = qstat(default_server())
+qstat()       = qstat(getdefault_server())
 
 """
     watch_qstat(server)
 If sbatch is running on server it will return the output of the `watch qstat` command.
 """
 watch_qstat(server) = run(`ssh -t $server watch qstat`)
-watch_qstat()       = watch_qstat(default_server())
+watch_qstat()       = watch_qstat(getdefault_server())

test/file_processing_tests.jl

@@ -52,14 +52,14 @@ else
 end
 setdefault_pseudo_dir(:default, "/test/test/test");
 @test isdefined(:default_pseudo_dirs)
-@test DFControl.default_pseudo_dirs()[:default] == "/test/test/test"
+@test DFControl.getdefault_pseudo_dirs()[:default] == "/test/test/test"
 remove_default_pseudo_dir(:default);
 @test length(keys(default_pseudo_dirs))==pr_l
 
-pr_s = DFControl.default_server();
+pr_s = DFControl.getdefault_server();
 
 setdefault_server("test/default");
-@test DFControl.default_server() == "test/default"
+@test DFControl.getdefault_server() == "test/default"
 if pr_s != ""
   setdefault_server(pr_s)
 end

test/job_control_tests.jl

@@ -1,8 +1,8 @@
 using DFControl, Base.Test
 
 test_job_path = joinpath(@__DIR__, "test_job")
-df_job = load_job(test_job_path);
-df_job2 = load_job(joinpath(@__DIR__, test_job_path), new_local_dir="blabla");
+df_job = DFJob(test_job_path);
+df_job2 = DFJob(joinpath(@__DIR__, test_job_path), new_local_dir="blabla");
 @test df_job2.local_dir    == "blabla/"
 @test length(df_job.calculations) == 7
 @test input(df_job, "nscf").runcommand.exec == runcommand(df_job, "nscf").exec
@@ -12,7 +12,7 @@ try mkdir(joinpath(test_job_path,"test_dir/")) end
 test_dir = joinpath(test_job_path,"test_dir/")
 df_job.local_dir = test_dir
 save(df_job)
-df_job2 = load_job(test_dir)
+df_job2 = DFJob(test_dir)
 @test begin
   for (i,calc) in enumerate(df_job.calculations)
     calc2 = df_job2.calculations[i]
@@ -63,7 +63,7 @@ setflow!(df_job, "nscf" => true, "bands" => true)
 setflow!(df_job, "pw2wan" => true)
 @test df_job.calculations[end-1].run
 
-runcommand!(df_job, "nscf", Exec("test"))
+setruncommand!(df_job, "nscf", Exec("test"))
 @test runcommand(df_job, "nscf").exec == Exec("test").exec
 
 print_run_command(df_job, "nscf")

test/runtests.jl

@@ -5,7 +5,7 @@ using Base.Test
 
 
 tic()
-@testset "Job control tests" begin include("job_control_tests.jl") end
 @testset "File processing tests" begin include("file_processing_tests.jl") end
+@testset "Job control tests" begin include("job_control_tests.jl") end
 @testset "Plotting tests" begin include("plotting_tests.jl") end
 toc()