Formatting!

Author: louisponet

src/.JuliaFormatter.toml renamed to .JuliaFormatter.toml

@@ -1,15 +1,15 @@
 using BinDeps
-if !ispath(abspath(first(DEPOT_PATH), "config","DFControl"))
-    mkpath(abspath(first(DEPOT_PATH), "config","DFControl"))
+if !ispath(abspath(first(DEPOT_PATH), "config", "DFControl"))
+    mkpath(abspath(first(DEPOT_PATH), "config", "DFControl"))
 end
-if !ispath(abspath(first(DEPOT_PATH), "config","DFControl", "user_defaults.jl"))
-    open(abspath(first(DEPOT_PATH), "config","DFControl", "user_defaults.jl"), "w") do f
-        write(f,"#Generated by DFControl.")
+if !ispath(abspath(first(DEPOT_PATH), "config", "DFControl", "user_defaults.jl"))
+    open(abspath(first(DEPOT_PATH), "config", "DFControl", "user_defaults.jl"), "w") do f
+        return write(f, "#Generated by DFControl.")
     end
 end
 
-if !ispath(abspath(first(DEPOT_PATH), "config","DFControl", "job_registry.txt"))
-    touch(abspath(first(DEPOT_PATH), "config","DFControl", "job_registry.txt"))
+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)
@@ -59,26 +59,31 @@ if !ispath(pythonpath)
         run(`$installer -b -f -p $pythonpath`)
     end
     if Sys.iswindows()
-        run(Cmd(`$installer /S /AddToPath=0 /RegisterPython=0 /D=$pythonpath`, windows_verbatim=true))
+        run(Cmd(`$installer /S /AddToPath=0 /RegisterPython=0 /D=$pythonpath`;
+                windows_verbatim = true))
     end
 
     tarpath = relpath("cif2cell.tar.gz")
     download("https://sourceforge.net/projects/cif2cell/files/latest/download", tarpath)
-    run(unpack_cmd("cif2cell.tar.gz", @__DIR__, ".gz",".tar"))
+    run(unpack_cmd("cif2cell.tar.gz", @__DIR__, ".gz", ".tar"))
     cif2celldir = relpath("cif2cell-1.2.10")
     cd(cif2celldir)
-    pyex = Sys.iswindows() ? joinpath(pythonpath, "python") : joinpath(pythonpath, "bin", "python2")
+    pyex = Sys.iswindows() ? joinpath(pythonpath, "python") :
+           joinpath(pythonpath, "bin", "python2")
     run(`$pyex setup.py install --prefix=$pythonpath`)
     cd("..")
-#stupid urlopen
-    starfile = Sys.iswindows() ? joinpath(pythonpath, "lib", "site-packages", "StarFile.py") : joinpath(pythonpath, "lib", "python2.7", "site-packages", "StarFile.py")
+    #stupid urlopen
+    starfile = Sys.iswindows() ?
+               joinpath(pythonpath, "lib", "site-packages", "StarFile.py") :
+               joinpath(pythonpath, "lib", "python2.7", "site-packages", "StarFile.py")
     starsource = read(starfile, String)
-    starsource = replace(starsource, "filestream = urlopen(filename)"=>"filestream = urlopen('file:' + filename)")
+    starsource = replace(starsource,
+                         "filestream = urlopen(filename)" => "filestream = urlopen('file:' + filename)")
     write(starfile, starsource)
-#
+    #
     rm(tarpath)
-    rm(relpath("cif2cell-1.2.10"), recursive=true)
-    rm(relpath("downloads"), recursive=true)
+    rm(relpath("cif2cell-1.2.10"); recursive = true)
+    rm(relpath("downloads"); recursive = true)
 end
 
 include("asset_init.jl")

deps/asset_init.jl

@@ -1,6 +1,6 @@
 # Based on documentation of DFTK
-import LibGit2
-import Pkg
+using LibGit2: LibGit2
+using Pkg: Pkg
 
 # To manually generate the docs:
 #
@@ -18,17 +18,15 @@ CONTINUOUS_INTEGRATION = get(ENV, "CI", nothing) == "true"
 
 # Python and Julia dependencies needed for running the notebooks
 # PYDEPS = ["ase", "pymatgen"]
-JLDEPS = [
-    Pkg.PackageSpec(url="https://github.com/louisponet/DFControl.jl.git",
-                    rev=LibGit2.head(ROOTPATH)),  # The current DFControl
-]
+JLDEPS = [Pkg.PackageSpec(; url = "https://github.com/louisponet/DFControl.jl.git",
+                          rev = LibGit2.head(ROOTPATH))]
 
 # Setup julia dependencies for docs generation if not yet done
 Pkg.activate(@__DIR__)
 if !isfile(joinpath(@__DIR__, "Manifest.toml"))
-    Pkg.develop(Pkg.PackageSpec(path=ROOTPATH))
+    Pkg.develop(Pkg.PackageSpec(; path = ROOTPATH))
     Pkg.instantiate()
-    Pkg.add(url="https://github.com/kimikage/Documenter.jl", rev="ansicolor")
+    Pkg.add(; url = "https://github.com/kimikage/Documenter.jl", rev = "ansicolor")
 end
 
 # Setup environment for making plots
@@ -44,19 +42,24 @@ using Literate
 # Collect examples from the example index (src/index.md)
 # The chosen examples are taken from the examples/ folder to be processed by Literate
 EXAMPLES = [String(m[1])
-            for m in match.(r"\"(examples/[^\"]+.md)\"",
-                            readlines(joinpath(SRCPATH, "index.md")))
-            if !isnothing(m)]
+            for m in
+                match.(r"\"(examples/[^\"]+.md)\"",
+                       readlines(joinpath(SRCPATH, "index.md"))) if !isnothing(m)]
 
 # Collect files to treat with Literate (i.e. the examples and the .jl files in the docs)
 # The examples go to docs/literate_build/examples, the .jl files stay where they are
-literate_files = NamedTuple{(:src, :dest, :example), Tuple{String, String, Bool}}[(src=joinpath(ROOTPATH, splitext(file)[1] * ".jl"),
-                   dest=joinpath(SRCPATH, "examples"), example=true)
-                  for file in EXAMPLES]
+literate_files = NamedTuple{(:src, :dest, :example),Tuple{String,String,Bool}}[(src = joinpath(ROOTPATH,
+                                                                                               splitext(file)[1] *
+                                                                                               ".jl"),
+                                                                                dest = joinpath(SRCPATH,
+                                                                                                "examples"),
+                                                                                example = true)
+                                                                               for file in
+                                                                                   EXAMPLES]
 for (dir, directories, files) in walkdir(SRCPATH)
     for file in files
         if endswith(file, ".jl")
-            push!(literate_files, (src=joinpath(dir, file), dest=dir, example=false))
+            push!(literate_files, (src = joinpath(dir, file), dest = dir, example = false))
         end
     end
 end
@@ -68,56 +71,44 @@ for file in literate_files
     #                   preprocess=preprocess)
     # Literate.notebook(file.src, file.dest; credit=false,
     #                   execute=CONTINUOUS_INTEGRATION || DEBUG)
-    Literate.markdown(file.src, file.dest; documenter=true, credit=false)
-    Literate.notebook(file.src, file.dest; credit=false,
-                      execute=CONTINUOUS_INTEGRATION || DEBUG)
+    Literate.markdown(file.src, file.dest; documenter = true, credit = false)
+    Literate.notebook(file.src, file.dest; credit = false,
+                      execute = CONTINUOUS_INTEGRATION || DEBUG)
 end
 
 # Generate the docs in BUILDPATH
-makedocs(
-    modules = [DFControl],
-    format = Documenter.HTML(
-        # Use clean URLs, unless built as a "local" build
-        prettyurls = CONTINUOUS_INTEGRATION,
-        canonical = "https://louisponet.github.io/DFControl.jl/stable/",
-        assets = ["assets/favicon.ico"],
-    ),
-    sitename = "DFControl.jl",
-    authors = "Louis Ponet",
-    linkcheck = false,  # TODO
-    linkcheck_ignore = [
-        # Ignore links that point to GitHub's edit pages, as they redirect to the
-        # login screen and cause a warning:
-        r"https://github.com/([A-Za-z0-9_.-]+)/([A-Za-z0-9_.-]+)/edit(.*)",
-    ],
-    pages = [
-        "Home" => "index.md",
-        "Getting started" => Any[
-            "guide/installation.md",
-            "guide/configuration.md",
-            "Basic Tutorial" => "guide/basic_tutorial.md",
-            "Advanced Tutorial" => "guide/advanced_tutorial.md"
-        ],
-        "Usage" => Any[
-            "guide/jobs.md",
-            "guide/calculations.md",
-            "guide/structure.md",
-        ],
-        # "Examples" => EXAMPLES,
-        "api.md",
-        # "publications.md",
-    ],
-    # strict = !DEBUG,
-)
+makedocs(; modules = [DFControl],
+         format = Documenter.HTML(
+                                  # Use clean URLs, unless built as a "local" build
+                                  ; prettyurls = CONTINUOUS_INTEGRATION,
+                                  canonical = "https://louisponet.github.io/DFControl.jl/stable/",
+                                  assets = ["assets/favicon.ico"]),
+         sitename = "DFControl.jl", authors = "Louis Ponet", linkcheck = false,  # TODO
+         linkcheck_ignore = [
+                             # Ignore links that point to GitHub's edit pages, as they redirect to the
+                             # login screen and cause a warning:
+                             r"https://github.com/([A-Za-z0-9_.-]+)/([A-Za-z0-9_.-]+)/edit(.*)"],
+         pages = ["Home" => "index.md",
+                  "Getting started" => Any["guide/installation.md",
+                                           "guide/configuration.md",
+                                           "Basic Tutorial"=>"guide/basic_tutorial.md",
+                                           "Advanced Tutorial"=>"guide/advanced_tutorial.md"],
+                  "Usage" => Any["guide/jobs.md", "guide/calculations.md",
+                                 "guide/structure.md",],
+                  # "Examples" => EXAMPLES,
+                  "api.md"
+                  # "publications.md",
+                  ]
+         # strict = !DEBUG,
+         )
 
 # Dump files for managing dependencies in binder
 if CONTINUOUS_INTEGRATION
     cd(BUILDPATH) do
         open("environment.yml", "w") do io
-            print(io,
-                    """
-                    name: dfcontrol
-                    """)
+            return print(io, """
+                             name: dfcontrol
+                             """)
         end
 
         # Install Julia dependencies into build
@@ -130,16 +121,14 @@ if CONTINUOUS_INTEGRATION
 end
 
 # Deploy docs to gh-pages branch
-deploydocs(
-    repo = "github.com/louisponet/DFControl.jl.git",
-)
+deploydocs(; repo = "github.com/louisponet/DFControl.jl.git")
 
 # Remove generated example files
 if !DEBUG
     for file in literate_files
         base = splitext(basename(file.src))[1]
         for ext in [".ipynb", ".md"]
-            rm(joinpath(file.dest, base * ext), force=true)
+            rm(joinpath(file.dest, base * ext); force = true)
         end
     end
 end

deps/build.jl

@@ -6,35 +6,35 @@
 # in it.
 using DFControl
 
-tjob = DFJob(joinpath(pathof(DFControl), "..","..","docs", "src", "assets", "job"))#hide
-tjob2 = DFJob(joinpath(pathof(DFControl), "..","..", "docs", "src", "assets", "Job2"))#hide
+tjob = DFJob(joinpath(pathof(DFControl), "..", "..", "docs", "src", "assets", "job"))#hide
+tjob2 = DFJob(joinpath(pathof(DFControl), "..", "..", "docs", "src", "assets", "Job2"))#hide
 if false#hide
-global job = DFJob("job")
+    global job = DFJob("job")
 else#hide
-global job = deepcopy(tjob)#hide
-set_localdir!(job, "job"); #hide
-job#hide
+    global job = deepcopy(tjob)#hide
+    set_localdir!(job, "job") #hide
+    job#hide
 end#hide
 
 # Since the job created in the [Basic Tutorial](@ref) was saved in the "job" directory this will work, see the section on [Jobs](@ref) for
 # further details and options on how to load previously saved jobs.
 
 # The next thing we may want to do is to change the directory where the job is running.
 if false#hide
-set_localdir!(job, "Job2", copy=true)
+    set_localdir!(job, "Job2"; copy = true)
 else#hide
-global job = deepcopy(tjob2);#hide
-pop!(job);#hide
-pop!(job);#hide
-job#hide
+    global job = deepcopy(tjob2)#hide
+    pop!(job)#hide
+    pop!(job)#hide
+    job#hide
 end#hide
 # With the `copy=true` flag we let DFControl know that not only to create and set the
 # new directory, but also to copy the previous results and temporary files to the
 # new directory so we don't have to rerun the scf calculation.
 
 # Next we would like to plot the projected density of states.
 # For that we create both an nscf calculation to get a uniform k-grid, and projwfc calculation.
-push!(job, gencalc_nscf(job["scf"], (6,6,6)))
+push!(job, gencalc_nscf(job["scf"], (6, 6, 6)))
 
 # The second argument of gencalc_nscf is the kgrid. When passing a 3-Tuple,
 # the code will assume that an explicit k-grid is requested, which can be verified by
@@ -44,13 +44,13 @@ data(job["nscf"], :k_points)
 # energy window.
 # The arguments are structured as (template, Emin, Emax, deltaE) respectively.
 fermi = readfermi(job)
-push!(job, gencalc_projwfc(job["nscf"], fermi-10, fermi+1, 0.1))
+push!(job, gencalc_projwfc(job["nscf"], fermi - 10, fermi + 1, 0.1))
 # Next we disable the bands calculation and run the new ones.
 job["bands"].run = false
 if false#hide
-submit(job)
+    submit(job)
 else#hide
-global job = deepcopy(tjob2)#hide
+    global job = deepcopy(tjob2)#hide
 end#hide
 
 # ## [Plot Results](@id results_plotting)

docs/make.jl

@@ -12,7 +12,7 @@ using DFControl
 using Downloads
 cif_file = Downloads.download("http://www.crystallography.net/cod/9011998.cif", "Si.cif")
 
-structure = Structure(cif_file, name="Si")
+structure = Structure(cif_file; name = "Si")
 set_pseudos!(structure, :pbesol)
 
 # This assumes that the `:pbesol` pseudopotential set was installed during the
@@ -31,20 +31,18 @@ pw_execs = [Exec("mpirun", "", :np => 4), Exec("pw.x", "/opt/qe/bin/", :nk => 4)
 # Then we create the first calculation for our job, we name it scf, which will be used to reference it later.
 # We also pass the executables to be used and additional flags to be set to the constructor.
 # Afterwards we set the kpoints to be used in the scf calculation.
-scf_calculation = DFCalculation{QE}("scf", :calculation => "scf", execs=pw_execs)
-set_kpoints!(scf_calculation, (6,6,6,1,1,1))
+scf_calculation = DFCalculation{QE}("scf", :calculation => "scf"; execs = pw_execs)
+set_kpoints!(scf_calculation, (6, 6, 6, 1, 1, 1))
 
 # The code recognizes internally that this 6-Tuple corresponds to a
 # `K_POINTS (automatic)` block in QE. Alternatively (leading to an identical final result):
 
-scf_calculation = DFCalculation{QE}("scf", :calculation => "scf",
-                        execs=pw_execs,
-                        data=[InputData(:k_points, :automatic, (6,6,6,1,1,1))])
+scf_calculation = DFCalculation{QE}("scf", :calculation => "scf"; execs = pw_execs,
+                                    data = [InputData(:k_points, :automatic,
+                                                      (6, 6, 6, 1, 1, 1))])
 
 # We can now define our job: 
-job = DFJob("Si", structure, [scf_calculation],
-            :ecutwfc => 20, 
-            :conv_thr => 1e-6,
+job = DFJob("Si", structure, [scf_calculation], :ecutwfc => 20, :conv_thr => 1e-6;
             local_dir = "job")
 
 # Additional calculations would be be added to the list `[scf_calculation]`.
@@ -53,10 +51,10 @@ job = DFJob("Si", structure, [scf_calculation],
 
 # We are now ready to submit the job, which will run in the current working directory
 if false #hide
-submit(job)
+    submit(job)
 else #hide
-global job = DFJob(joinpath(@__DIR__, "../../src/assets/job/"))#hide
-pop!(job); #hide
+    global job = DFJob(joinpath(@__DIR__, "../../src/assets/job/"))#hide
+    pop!(job) #hide
 end #hide
 
 # This will generate and save all calculation files, and the corresponding job script (`job.tt`),
@@ -93,9 +91,10 @@ job
 # Seeing that all is right we submit the job again
 set_localdir!(job, "job"); #hide
 if false #hide
-submit(job)
+    submit(job)
 else #hide
-global job = DFJob(joinpath(pathof(DFControl), "..","..", "docs", "src", "assets", "job"));#hide
+    global job = DFJob(joinpath(pathof(DFControl), "..", "..", "docs", "src", "assets",
+                                "job"))#hide
 end #hide
 
 # We can access the bands through
@@ -106,7 +105,7 @@ bands = outputdata(job["bands"])[:bands];
 # They can be plotted too
 fermi = readfermi(job) # = outputdata(job["scf"])[:fermi]
 using Plots
-plot(bands, fermi=fermi)
+plot(bands; fermi = fermi)
 
 # Since more info (such as the structure) is available in the job,
 # plotting the job leads to a richer plot