combined docstrings and code

src/checklist.jl

@@ -1,7 +1,21 @@
-include("checklist_docstrings.jl")
-
 """
-$docstring_checklist_df
+    PRISMA.checklist_df()::DataFrame
+
+returns a template PRISMA checklist as a `DataFrame`
+
+## Returns
+
+- `DataFrame`: the template dataframe
+
+## Example
+
+```jldoctest
+julia> using PRISMA
+
+julia> isa(checklist_df(), DataFrame)
+true
+```
+
 """
 function checklist_df()::DataFrame
     cols::Vector{String} = [
@@ -425,7 +439,47 @@ function complete_dataframe(paper::AbstractString)::DataFrame
 end
 
 """
-$docstring_checklist
+    PRISMA.checklist(paper::AbstractString)::Checklist
+    PRISMA.checklist(bytes::Vector{UInt8})::Checklist
+
+Returns a completed PRISMA checklist as the type `Checklist`. The `Checklist`
+type includes a completed checklist as a `DataFrame` and the metadata of the
+paper as a `OrderedDict`. The `paper` argument can be a path to a pdf file or
+an array of bytes. This function uses the C++ library `Poppler` via `Poppler_jll`
+to parse the pdf and the natural language processing functionality in Julia via
+[`Transformers.jl`](https://github.com/chengchingwen/Transformers.jl) to 
+find items from the checklist in the paper and populate the 
+`Comments or location in manuscript` and `Yes/No/NA` columns in the `DataFrame` 
+from `checklist_df()`.
+
+The following metadata is parsed from the pdf file and stored in the `OrderedDict` as:
+
+- `"title"`: the title of the paper
+- `"subject"`: the subject of the paper
+- `"author"`: the author of the paper
+- `"creator"`: the creator of the paper
+- `"producer"`: the producer of the paper
+- `"creation date"`: the date the paper was created
+- `"modification date"`: the date the paper was last modified
+- `"pages"`: the number of pages in the paper
+- `"paper size"`: the size of the paper
+- `"paper rotation"`: the rotation of the paper
+- `"file size"`: the size of the pdf file
+- `"optimized"`: whether the pdf was optimized
+- `"pdf version"`: the version of the pdf
+
+All keys and values in the dictionary ar eof type `String`.
+If the parsing fails the value will be an empty string.
+
+## Arguments
+
+- `paper::AbstractString`: a path to a pdf file as a string
+- `bytes::Vector{UInt8}`: the pdf data as an array of bytes
+
+## Returns
+
+- `Checklist`: a completed checklist with the paper's metadata
+
 """
 function checklist(paper::AbstractString)::Checklist
     return Checklist(
@@ -477,22 +531,75 @@ function Base.show(io::IO, ::MIME"text/csv", cl::Checklist)::Nothing
 end
 
 """
-$docstring_checklist_read
+    checklist_read(fn::AbstractString)::DataFrame
+
+reads the template data to a `DataFrame`
+
+## Arguments
+
+- `fn::AbstractString`: the name of the file to read
+
+## Returns
+
+- `DataFrame`: the template dataframe
+
+## Example
+
+```jldoctest
+julia> using PRISMA
+
+julia> checklist_template()
+"checklist.csv"
+
+julia> isa(checklist_read("checklist.csv"), DataFrame)
+true
+```
+
 """
 function checklist_read(fn::AbstractString="checklist.csv")::DataFrame
     return CSV.read(fn, DataFrame)
 end
 
 """
-$docstring_checklist_save
+    checklist_save(out::Any, cl::Checklist)
+    checklist_save(out::Any, df::DataFrame)
+
+saves a `Checklist` as a CSV.
+
+## Arguments
+
+- `out::Any`: Accepts the same types as [`CSV.write`](https://csv.juliadata.org/stable/writing.html#CSV.write)
+- `cl::Checklist`: the checklist to save
+- `df::DataFrame`: the dataframe to save
+
 """
-function checklist_save(fn::AbstractString, cl::Checklist)
-    return CSV.write(fn, cl.dataframe)
+function checklist_save(out::Any, cl::Checklist)
+    return CSV.write(out, cl.dataframe)
+end
+
+function checklist_save(out::Any, df::DataFrame)
+    return CSV.write(out, df)
 end
 
 """
-$docstring_checklist_template
+    checklist_template(out::Any="checklist.csv")
+
+saves a template checklist `DataFrame` as a CSV.
+
+## Arguments
+
+- `out::Any`: Accepts the same types as [`CSV.write`](https://csv.juliadata.org/stable/writing.html#CSV.write)
+
+## Example
+
+```jldoctest
+julia> using PRISMA
+
+julia> checklist_template()
+"checklist.csv"
+```
+
 """
-function checklist_template(fn::AbstractString="checklist.csv")
-    return CSV.write(fn, checklist_df())
+function checklist_template(out::Any="checklist.csv")
+    return CSV.write(out, checklist_df())
 end