Rename project

Author: mfherbst

.github/workflows/CI.yml

@@ -72,6 +72,6 @@ jobs:
         shell: julia --project=docs --color=yes {0}
         run: |
           using Documenter: DocMeta, doctest
-          using PseudoLibraries
-          DocMeta.setdocmeta!(PseudoLibraries, :DocTestSetup, :(using PseudoLibraries); recursive=true)
-          doctest(PseudoLibraries)
+          using PseudoPotentialData
+          DocMeta.setdocmeta!(PseudoPotentialData, :DocTestSetup, :(using PseudoPotentialData); recursive=true)
+          doctest(PseudoPotentialData)

Project.toml

@@ -1,4 +1,4 @@
-name = "PseudoLibraries"
+name = "PseudoPotentialData"
 uuid = "5751a51d-ac76-4487-a056-413ecf6fbe19"
 authors = ["Michael F. Herbst <info@michael-herbst.com> and contributors"]
 version = "0.1.0"

README.md

@@ -1,33 +1,35 @@
-# PseudoLibraries
+# PseudoPotentialData
 
-[![Stable](https://img.shields.io/badge/docs-stable-blue.svg)](https://juliamolsim.github.io/PseudoLibraries.jl/stable/)
-[![Dev](https://img.shields.io/badge/docs-dev-blue.svg)](https://juliamolsim.github.io/PseudoLibraries.jl/dev/)
-[![Build Status](https://github.com/JuliaMolSim/PseudoLibraries.jl/actions/workflows/CI.yml/badge.svg?branch=master)](https://github.com/JuliaMolSim/PseudoLibraries.jl/actions/workflows/CI.yml?query=branch%3Amaster)
-[![Coverage](https://codecov.io/gh/JuliaMolSim/PseudoLibraries.jl/branch/master/graph/badge.svg)](https://codecov.io/gh/JuliaMolSim/PseudoLibraries.jl)
+[![Stable](https://img.shields.io/badge/docs-stable-blue.svg)](https://juliamolsim.github.io/PseudoPotentialData.jl/stable/)
+[![Dev](https://img.shields.io/badge/docs-dev-blue.svg)](https://juliamolsim.github.io/PseudoPotentialData.jl/dev/)
+[![Build Status](https://github.com/JuliaMolSim/PseudoPotentialData.jl/actions/workflows/CI.yml/badge.svg?branch=master)](https://github.com/JuliaMolSim/PseudoPotentialData.jl/actions/workflows/CI.yml?query=branch%3Amaster)
+[![Coverage](https://codecov.io/gh/JuliaMolSim/PseudoPotentialData.jl/branch/master/graph/badge.svg)](https://codecov.io/gh/JuliaMolSim/PseudoPotentialData.jl)
 
 Package providing programmatic access
-to standard pseudopotentials in solid-state calculations.
-In using this library the combination of a string identifier and the element
+to standard pseudopotential data files for solid-state calculations.
+The combination of a string identifier for the
+pseudopotential family and the element
 symbol provides a unique and reproducible mapping to a pseudopotential file.
-Moreover in case the pseudopotential file
-happens to be missing on the computer Julia's artifact system takes
-care to automatically download it as needed.
+In case the pseudopotential data file happens to be missing on the computer
+it will be automatically download as needed.
 
 For example, the following code automatically downloads the pseudopotential
-file of the [stringent pseudodojo](http://www.pseudo-dojo.org/) pseudopotential
-for LDA pseudopotentials (referred to by the identifier `pd_nc_sr_lda_stringent_0.4.1_upf`)
-and places the full path to the downloaded pseudopotential file into the `filename` variable:
+file for silicon of the [stringent pseudodojo](http://www.pseudo-dojo.org/)
+family for LDA pseudopotentials
+(referred to by the identifier `pd_nc_sr_lda_stringent_0.4.1_upf`)
+and places the full path to the downloaded pseudopotential file
+into the `filename` variable:
 
 ```julia
-using PseudoLibraries
+using PseudoPotentialData
 identifier = "pd_nc_sr_lda_stringent_0.4.1_upf"
-library = PseudoLibrary(identifier)
-filename = pseudofile(library, :Si)
+family = PseudoFamily(identifier)
+filename = pseudofile(family, :Si)
 ```
 
 For a list of available identifiers see
 ```julia
-PseudoLibraries.available_identifiers()
+PseudoPotentialData.family_identifiers()
 ```
 More details on the meaning of these keys is given
 in the README of the

docs/Project.toml

@@ -1,3 +1,3 @@
 [deps]
 Documenter = "e30172f5-a6a5-5a46-863b-614d45cd2de4"
-PseudoLibraries = "5751a51d-ac76-4487-a056-413ecf6fbe19"
+PseudoPotentialData = "5751a51d-ac76-4487-a056-413ecf6fbe19"

docs/make.jl

@@ -1,14 +1,14 @@
-using PseudoLibraries
+using PseudoPotentialData
 using Documenter
 
-DocMeta.setdocmeta!(PseudoLibraries, :DocTestSetup, :(using PseudoLibraries); recursive=true)
+DocMeta.setdocmeta!(PseudoPotentialData, :DocTestSetup, :(using PseudoPotentialData); recursive=true)
 
 makedocs(;
-    modules=[PseudoLibraries],
+    modules=[PseudoPotentialData],
     authors="Michael F. Herbst <info@michael-herbst.com> and contributors",
-    sitename="PseudoLibraries.jl",
+    sitename="PseudoPotentialData.jl",
     format=Documenter.HTML(;
-        canonical="https://juliamolsim.github.io/PseudoLibraries.jl",
+        canonical="https://juliamolsim.github.io/PseudoPotentialData.jl",
         edit_link="master",
         assets=String[],
     ),
@@ -18,6 +18,6 @@ makedocs(;
 )
 
 deploydocs(;
-    repo="github.com/JuliaMolSim/PseudoLibraries.jl",
+    repo="github.com/JuliaMolSim/PseudoPotentialData.jl",
     devbranch="master",
 )

docs/src/index.md

@@ -1,11 +1,11 @@
 ```@meta
-CurrentModule = PseudoLibraries
+CurrentModule = PseudoPotentialData
 ```
 
-# PseudoLibraries
+# PseudoPotentialData
 
 Enables programmatic access to
-standard pseudopotential libraries in solid-state calculations.
+standard pseudopotential libraries for solid-state calculations.
 In using this library the combination of a string identifier and the element
 symbol provides a unique and reproducible mapping to a pseudopotential file.
 Moreover in case the pseudopotential file
@@ -20,10 +20,10 @@ for LDA pseudopotentials (referred to by the identifier `pd_nc_sr_lda_stringent_
 and places the full path to the downloaded pseudopotential file into the `filename` variable:
 
 ```@example index-example
-using PseudoLibraries
+using PseudoPotentialData
 identifier = "pd_nc_sr_lda_stringent_0.4.1_upf"
-library = PseudoLibrary(identifier)
-filename = library[:Si]
+family = PseudoFamily(identifier)
+filename = pseudofile(family, :Si)
 ```
 As you see this will be a string such as
 `/home/user/.julia/artifacts/56094b8162385233890d523c827ba06e07566079/Si.upf`,
@@ -34,26 +34,21 @@ It is therefore highly recommended to use the above mechanism
 based on `identfier` and element symbol instead of hard-coding
 the expanded path in user scripts.
 
-An alternative version to achieve the same thing as above is
+For multiple elements you can similarly use
 ```@example index-example
-filename = pseudofile(library, :Si)
-```
-or for multiple elements:
-```@example index-example
-pseudofile.(library, [:C, :Si])
+pseudofile.(family, [:C, :Si])
 ```
 
-Some metadata information is stored in the `library` object:
+Some metadata information is stored in the `family` object:
 ```@example index-example
-library
+family
 ```
 
 For a list of available identifiers see
 ```@example index-example
-PseudoLibraries.available_identifiers()
+PseudoPotentialData.family_identifiers()
 ```
-More details on the meaning of these keys is given
-in the README of thei
+More details on the meaning of these keys is given in the README of the
 [PseudoLibrary](https://github.com/JuliaMolSim/PseudoLibrary/blob/7c4b71a3b9d70a229d757aa6d546ef22b83a85a9/README.md)
 repository.
 
@@ -64,5 +59,5 @@ repository.
 ## Interface
 
 ```@autodocs
-Modules = [PseudoLibraries]
+Modules = [PseudoPotentialData]
 ```

src/PseudoLibraries.jl

@@ -0,0 +1,72 @@
+module PseudoPotentialData
+using Artifacts
+using Compat: @compat
+using LazyArtifacts
+using TOML
+
+export PseudoFamily, pseudofile
+@compat public families
+@compat public family_identifiers
+
+struct PseudoFamily
+    identifier::String
+    # metadata
+    extension::String   # Filename expected as $(symbol).$(extension)
+    functional::String  # DFT functional keyword (or "" if unspecified)
+    version::VersionNumber
+    # TODO More things will probably follow
+    #    - Type of pseudisation (norm-conserving, PAW, ...)
+    #    - References to papers describing these pseudopotentials
+    #    - Elements available
+end
+
+"""
+Construction of a PseudoFamily from a `identifier` representing
+the pseudopotential family to use.
+"""
+function PseudoFamily(identifier::AbstractString)
+    artifact_file = find_artifacts_toml(@__FILE__)
+    @assert !isnothing(artifact_file)
+    meta = artifact_meta(identifier, artifact_file)
+    isnothing(meta) && throw(ArgumentError("Invalid pseudo identifier: $identifier"))
+    PseudoFamily(identifier,
+                 meta["extension"],
+                 meta["functional"],
+                 VersionNumber(meta["version"]))
+end
+
+Base.Broadcast.broadcastable(l::PseudoFamily) = Ref(l)
+
+
+"""Get the list of available pseudopotential family identifiers."""
+function family_identifiers()
+    artifact_file = find_artifacts_toml(@__FILE__)
+    @assert !isnothing(artifact_file)
+    collect(keys(TOML.parsefile(artifact_file)))
+end
+
+"""The list of all known pseudopotential families."""
+const families = map(PseudoFamily, family_identifiers())
+
+
+"""
+Return the directory containing the pseudo files.
+This downloads the artifact if necessary.
+"""
+artifact_directory(family::PseudoFamily) = (@artifact_str "$(family.identifier)")
+
+"""
+Get the full path to the file containing the pseudopotential information
+for a particular element and a particular pseudopotential `family`.
+The family can be specified as an identifier or an object.
+"""
+function pseudofile(family::PseudoFamily, element::Symbol)
+    file = joinpath(artifact_directory(family), "$(element)." * family.extension)
+    isfile(file) || throw(KeyError(element))
+    file
+end
+function pseudofile(family::AbstractString, element::Symbol)
+    pseudofile(PseudoFamily(family), element)
+end
+
+end

src/PseudoPotentialData.jl

@@ -1,32 +1,30 @@
-using PseudoLibraries
+using PseudoPotentialData
 using Test
 
-@testset "PseudoLibraries.jl" begin
-    @testset "Test one library can be loaded" begin
+@testset "PseudoPotentialData.jl" begin
+    @testset "Test one family can be loaded" begin
         identifier = "pd_nc_sr_lda_stringent_0.4.1_upf"
-        library = PseudoLibrary(identifier)
-        @test library.identifier == identifier
-        @test library.extension == "upf"
-        @test library.functional == "lda"
-        @test library.version == v"0.4.1"
+        family = PseudoFamily(identifier)
+        @test family.identifier == identifier
+        @test family.extension  == "upf"
+        @test family.functional == "lda"
+        @test family.version == v"0.4.1"
 
         file = pseudofile("pd_nc_sr_lda_stringent_0.4.1_upf", :Si)
         @test basename(file) == "Si.upf"
-        @test file == pseudofile(library, :Si)
-        @test file == library[:Si]
+        @test file == pseudofile(family, :Si)
 
-        files = pseudofile.(library, [:Si, :Si])
+        files = pseudofile.(family, [:Si, :Si])
         @test all(isequal(file), files)
 
-        @test_throws KeyError library[:Uun]
-        @test_throws KeyError pseudofile(library, :Uun)
-        @test_throws KeyError pseudofile(library, :Uun)
+        @test_throws KeyError pseudofile(family, :Uun)
+        @test_throws KeyError pseudofile(identifier, :Uub)
     end
 
     @testset "Test all libraries can be loaded" begin
-        for identifier in PseudoLibraries.available_identifiers()
-            library = PseudoLibrary(identifier)
-            @test library.identifier == identifier
+        for identifier in PseudoPotentialData.family_identifiers()
+            family = PseudoFamily(identifier)
+            @test family.identifier == identifier
         end
     end
 end