Enable documentation creation and specify hosting location (#37)

* Enabled documentation creation in initialize_study

* Added configuration for github_name and updated tests/docs

* Added tests for user input into initialize study

Author: TheCedarPrince

ext/HealthBaseDrWatsonExt.jl

@@ -185,17 +185,44 @@ The study environment remains activated for you to immediately add packages.
 
 - `template::Symbol` - A template option specifying the structure of the the study. Available templates can be found by running `@doc(study_template)`.
 
+- `github_name::String` - the GitHub account you intend to host documentation at. You will need to manually enable the `gh-pages` deployment by going to settings/pages of the GitHub study repo, and choosing as "Source" the `gh-pages` branch. If a name is not specified, a prompt will appear.
+
+# Example
+
+```julia-repl
+julia> initialize_study("Cardiooncology", "Jacob S. Zelko, Jakub Mitura"; github_name = "TheCedarPrince", template=:observational)
+```
 """
-function HealthBase.initialize_study(path, authors = nothing; template::Symbol = :default)
+function HealthBase.initialize_study(path, authors = nothing; github_name = "PutYourGitHubNameHere", template::Symbol = :default)
     tpl = study_template(template).template
     ftg = study_template(template).folders_to_gitignore
 
+    if github_name == "PutYourGitHubNameHere"
+        @warn """
+        `github_name` is not specified. Docs will not be deployed.
+
+        To host the docs online, set the keyword `github_name` with the name of the GitHub account
+        you plan to upload at, and then manually enable the `gh-pages` deployment by going to
+        settings/pages of the GitHub repo, and choosing as "Source" the `gh-pages` branch.
+
+        You can skip this prompt by specifying `github_name` in the function call. For example:
+        `initialize_study("MyStudy", "Carlos", github_name = "JuliaHealth")`
+        """
+
+        print("Enter the name of your GitHub account (leave empty to skip): ")
+        input = readline()
+
+        github_name = isempty(input) ? github_name : input
+    end
+
     initialize_project(
         path;
         authors = authors,
         template = tpl,
         folders_to_gitignore = ftg,
         force = true,
+        add_docs = true,
+        github_name = github_name
     )
     cd(path)
 end

test/drwatsonext.jl

@@ -1,7 +1,25 @@
 cd(@__DIR__)
+
+github_name = "foo"
 path = "test_study"
 
-initialize_study(path; template = :observational)
+@test_warn "" initialize_study(path; template = :llm);
+
+cd("..")
+rm("test_study", recursive = true, force = true)
+
+mktemp() do fname, f
+   write(f, "X")
+   seek(f, 0)
+   redirect_stdin(f) do
+        @test initialize_study(path; template = :llm) == nothing
+   end
+end
+
+cd("..")
+rm("test_study", recursive = true, force = true)
+
+initialize_study(path; github_name = github_name, template = :observational)
 quickactivate(path)
 
 @test cohortsdir() == abspath("data", "cohorts")
@@ -12,7 +30,7 @@ quickactivate(path)
 cd("..")
 rm("test_study", recursive = true, force = true)
 
-initialize_study(path; template = :llm)
+initialize_study(path; github_name = github_name, template = :llm)
 quickactivate(path)
 
 @test corpusdir() == abspath("data", "corpus")
@@ -28,7 +46,7 @@ quickactivate(path)
 cd("..")
 rm("test_study", recursive = true, force = true)
 
-@test_throws ErrorException initialize_study(path; template = :foobar)
+@test_throws ErrorException initialize_study(path; github_name = github_name, template = :foobar)
 
 STUDY_TEMPLATES = Base.get_extension(HealthBase, :HealthBaseDrWatsonExt).STUDY_TEMPLATES