Merge pull request #12 from MineralsCloud:fix

Fix problems left in #11

Artifacts.toml

@@ -22,6 +22,14 @@ lazy = true
     sha256 = "64d7713bb9b1e766a4762d52b4828155b5c26f3a8487c516d0a402e7c04797de"
     url = "https://github.com/MineralsCloud/PseudopotentialArtifacts/raw/main/pslibrary/al.tar.gz"
 
+[all]
+git-tree-sha1 = "0fd60ae0d71a6334be1bd5a5e3e6afe604030b19"
+lazy = true
+
+    [[all.download]]
+    sha256 = "6e182fa335f72db0b9131cb7a613e9ab7cd7e584795ea151532e1cb999e83179"
+    url = "https://github.com/MineralsCloud/PseudopotentialArtifacts/raw/main/pslibrary/all.tar.gz"
+
 [ar]
 git-tree-sha1 = "dafcfdbbde59c25e4b80557d2e4bf35353db4eb5"
 lazy = true

Project.toml

@@ -5,11 +5,11 @@ version = "0.1.1-DEV"
 
 [deps]
 AcuteML = "6b84a0a3-a11a-41fa-a417-e600528de108"
-Artifacts = "56f22d72-fd6d-98f1-02f0-08ddc0907c33"
 DataFrames = "a93c6f00-e57d-5684-b7b6-d8193f3e46c0"
 JLD2 = "033835bb-8acc-5ee8-8aae-3f567f8a3819"
 LazyArtifacts = "4af54fe1-eca0-43a8-85a7-787d91b784e3"
 MLStyle = "d8e11817-5142-5d16-987a-aa16d5891078"
+Pkg = "44cfe95a-1eb2-52ea-b672-e2afdf69b78f"
 Pseudopotentials = "1b2dc2e6-48aa-4f00-b8f4-19d1a71d7a0e"
 REPL = "3fa0cd96-eef1-5676-8a61-b3b8758bbffb"
 

scripts/database.jl

@@ -1,8 +1,8 @@
 using AcuteML: UN, parsehtml, root, nextelement, nodecontent
-using Artifacts:
-    artifact_hash, artifact_exists, create_artifact, archive_artifact, bind_artifact!
 using DataFrames: DataFrame, groupby
 using JLD2: jldsave
+using Pkg.Artifacts:
+    artifact_hash, artifact_exists, create_artifact, archive_artifact, bind_artifact!
 using Pseudopotentials:
     CoreHole, ExchangeCorrelationFunctional, ValenceCoreState, Pseudization
 
@@ -32,7 +32,7 @@ end
 
 function makedb(element::String)
     database = DataFrame(
-        element = [],
+        element = String[],
         rel = Bool[],
         corehole = UN{CoreHole}[],
         xc = UN{ExchangeCorrelationFunctional}[],
@@ -48,11 +48,19 @@ function makedb(element::String)
     return database
 end
 makedb(i::Integer) = makedb(ELEMENTS[i])
+function makedb()
+    data = mapreduce(makedb, append!, ELEMENTS)
+    return groupby(data, :element)
+end
 
 function savedb(file, element)
     database = makedb(element)
     return jldsave(file; database)
 end
+function savedb(file)
+    database = makedb()
+    return jldsave(file; database)
+end
 
 function makeartifact(element::AbstractString)
     element_hash = artifact_hash(element, ARTIFACT_TOML)
@@ -71,6 +79,22 @@ function makeartifact(element::AbstractString)
     end
 end
 makeartifact(i::Integer) = makeartifact(ELEMENTS[i])
+function makeartifact()
+    dir_hash = artifact_hash("all", ARTIFACT_TOML)
+    if dir_hash === nothing || !artifact_exists(dir_hash)
+        dir_hash = create_artifact() do artifact_dir
+            savedb(joinpath(artifact_dir, "all.jld2"))
+        end
+        tar_hash = archive_artifact(dir_hash, "all.tar.gz")
+        bind_artifact!(
+            ARTIFACT_TOML,
+            "all",
+            dir_hash;
+            download_info = [(DATABASE_URL_BASE * "all.tar.gz", tar_hash)],
+            lazy = true,
+        )
+    end
+end
 
 grepvalues(x::UPFFileName) = (
     getfield(x, i) for

src/PSlibrary.jl

@@ -1,13 +1,13 @@
 module PSlibrary
 
-using Artifacts: @artifact_str
 using DataFrames: DataFrame, groupby
 using AcuteML: UN, parsehtml, root, nextelement, nodecontent
 using JLD2: load
 using LazyArtifacts
 using MLStyle: @match
 using Pseudopotentials:
     CoreHole, ExchangeCorrelationFunctional, ValenceCoreState, Pseudization
+using Pkg.Artifacts: @artifact_str
 using REPL.TerminalMenus: RadioMenu, request
 
 using ..UnifiedPseudopotentialFormat: UPFFileName
@@ -132,7 +132,7 @@ function list_elements(pt = true)
     if pt
         println(PERIODIC_TABLE)
     end
-    return groupby(unique!(DATABASE), :element)
+    return loaddb()
 end
 
 """
@@ -143,11 +143,7 @@ List all pseudopotentials in `PSlibrary` for a specific element (abbreviation or
 function list_potentials(element::Union{AbstractString,AbstractChar})
     element = lowercase(string(element))
     @assert element in ELEMENTS "element $element is not recognized!"
-    for meta in _parsehtml(element)
-        parsed = parse(UPFFileName, meta.name)
-        push!(DATABASE, [fieldvalues(parsed)..., meta.src, meta.name])
-    end
-    return list_elements(false)[(uppercasefirst(element),)]
+    return loaddb(element)
 end
 function list_potentials(atomic_number::Integer)
     @assert 1 <= atomic_number <= 94
@@ -191,15 +187,20 @@ function download_potential(name::AbstractString, path)
     df = list_potentials(x.element)
     if name in df.name
         i = findfirst(==(name), df.name)
-        download(df.src[i], path)
+        return download(df.src[i], path)
     else
         throw("potential '$name' is not in the database!")
     end
 end
 
 function loaddb(element::AbstractString)
     artifact_path = joinpath(@artifact_str(element), "$element.jld2")
-    load(artifact_path)["database"]
+    return load(artifact_path)["database"]
+end
+loaddb(i::Integer) = loaddb(ELEMENTS[i])
+function loaddb()
+    artifact_path = joinpath(artifact"all", "all.jld2")
+    return load(artifact_path)["database"]
 end
 
 end