Fix documentation generation, version bump, update deps.

jamesrhester · Jan 3, 2025 · 6e4885a · 6e4885a
1 parent 0317827
commit 6e4885a
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Showing 5 changed files with 12 additions and 10 deletions.
diff --git a/Project.toml b/Project.toml
@@ -1,7 +1,7 @@
 name = "CrystalInfoFramework"
 uuid = "6007d9b0-c6b2-11e8-0510-1d10e825f3f1"
 authors = ["James.Hester <[email protected]>"]
-version = "0.7.0"
+version = "0.8.0"
 
 [deps]
 DataFrames = "a93c6f00-e57d-5684-b7b6-d8193f3e46c0"

diff --git a/docs/Project.toml b/docs/Project.toml
@@ -4,4 +4,4 @@ DataFrames = "a93c6f00-e57d-5684-b7b6-d8193f3e46c0"
 Documenter = "e30172f5-a6a5-5a46-863b-614d45cd2de4"
 
 [compat]
-Documenter = "0.25"
+Documenter = "1.8.0"
diff --git a/docs/make.jl b/docs/make.jl
@@ -10,6 +10,7 @@ makedocs(sitename="CrystalInfoFramework documentation",
              "API" => "api.md"
              ],
          #doctest = :fix
+         warnonly = (:cross_references)
 	  )
 
 deploydocs(

diff --git a/docs/src/api.md b/docs/src/api.md
@@ -14,6 +14,7 @@ haskey(c::Cif,name)
 getindex(c::Cif,n)
 setindex!(c::Cif,v,n)
 show(io::IO,::MIME"text/plain",c::Cif)
+show(io::IO,::MIME"text/cif",c::Cif)
 ```
 
 ## CIF blocks
@@ -89,7 +90,7 @@ get_categories(d::DDLm_Dictionary)
 get_keys_for_cat(d::DDLm_Dictionary,cat;aliases=false)
 get_default(d::DDLm_Dictionary,s)
 lookup_default(dict::DDLm_Dictionary,dataname::String,cp)
-show(io::IO,::MIME"text/cif",ddlm_dic::DDLm_Dictionary)
+show(io::IOContext,::MIME"text/cif",ddlm_dic::DDLm_Dictionary;header="")
 ```
 
 ### DDL2 Dictionaries
@@ -105,6 +106,6 @@ keys(d::DDL2_Dictionary)
 getindex(d::DDL2_Dictionary,k)
 get_categories(d::DDL2_Dictionary)
 get_default(d::DDL2_Dictionary,dataname)
-show(io::IO,::MIME"text/cif",ddl2_dic::DDL2_Dictionary)
+show(io::IOContext,::MIME"text/cif",ddl2_dic::DDL2_Dictionary)
 ```
 
diff --git a/src/cif_output.jl b/src/cif_output.jl
@@ -872,7 +872,7 @@ end
 Write the contents of `c` as a CIF file to `io`, ordering each of
 the CifContainers according to `ordering`.
 """
-show(io::IO,::MIME"text/cif",c::Cif; ordering=[]) = begin
+Base.show(io::IO,::MIME"text/cif",c::Cif; ordering=[]) = begin
 
     for k in keys(c)
         write(io,"data_$k\n")
@@ -953,7 +953,7 @@ Output `ddlm_dic` in CIF format. `header` contains text that will
 be output in a comment box at the top of the file, which will replace
 any header comment stored in `ddlm_dic`.
 """
-show(io::IOContext,::MIME"text/cif",ddlm_dic::DDLm_Dictionary;header="") = begin
+Base.show(io::IOContext,::MIME"text/cif",ddlm_dic::DDLm_Dictionary;header="") = begin
     dicname = ddlm_dic[:dictionary].title[]
     #
     # Header
@@ -1121,7 +1121,7 @@ output layout using the following keywords:
     strict: follow the IUCr layout rules
     
 """
-show(io::IOContext,::MIME"text/cif",ddl2_dic::DDL2_Dictionary) = begin
+Base.show(io::IOContext,::MIME"text/cif",ddl2_dic::DDL2_Dictionary) = begin
     dicname = ddl2_dic[:dictionary].title[]
     write(io,"#")
     write(io,"""
@@ -1158,11 +1158,11 @@ show(io::IOContext,::MIME"text/cif",ddl2_dic::DDL2_Dictionary) = begin
 end
 
 """
-    show(io::IO,::MIME"text/cif",ddl2_dic::AbstractCifDictionary)
+    show(io::IO,::MIME"text/cif",ddl_dic::AbstractCifDictionary;strict=false, kwargs...)
     
 Output `ddl2_dic` to `IO` in CIF format
 """
-show(io::IO,x::MIME"text/cif",ddl2_dic::AbstractCifDictionary;strict=false,kwargs...) = begin
+Base.show(io::IO,x::MIME"text/cif",ddl_dic::AbstractCifDictionary;strict=false,kwargs...) = begin
     ic = IOContext(io,:strict=>strict)
-    show(ic,x,ddl2_dic;kwargs...)
+    show(ic,x,ddl_dic;kwargs...)
 end