Some code comments

src/Pluto.jl

@@ -36,7 +36,7 @@ import Pkg
 import Scratch
 
 include_dependency("../Project.toml")
-const PLUTO_VERSION = VersionNumber(Pkg.TOML.parsefile(joinpath(ROOT_DIR, "Project.toml"))["version"])
+const PLUTO_VERSION = pkgversion(@__MODULE__)
 const PLUTO_VERSION_STR = "v$(string(PLUTO_VERSION))"
 const JULIA_VERSION_STR = "v$(string(VERSION))"
 

src/analysis/DependencyCache.jl

@@ -1,3 +1,5 @@
+import UUIDs: UUID
+
 """
 Gets a dictionary of all symbols and the respective cells which are dependent on the given cell.
 

src/analysis/MoreAnalysis.jl

@@ -46,13 +46,22 @@ function _find_bound_variables!(found::Set{Symbol}, expr::Any) end
 
 
 "Return the given cells, and all cells that depend on them (recursively)."
-function downstream_recursive(notebook::Notebook, topology::NotebookTopology, from::Union{Vector{Cell},Set{Cell}})::Set{Cell}
+function downstream_recursive(
+    notebook::Notebook,
+    topology::NotebookTopology,
+    from::Union{Vector{Cell},Set{Cell}},
+)::Set{Cell}
     found = Set{Cell}(copy(from))
     _downstream_recursive!(found, notebook, topology, from)
     found
 end
 
-function _downstream_recursive!(found::Set{Cell}, notebook::Notebook, topology::NotebookTopology, from::Vector{Cell})::Nothing
+function _downstream_recursive!(
+    found::Set{Cell},
+    notebook::Notebook,
+    topology::NotebookTopology,
+    from::Vector{Cell},
+)::Nothing
     for cell in from
         one_down = PlutoDependencyExplorer.where_referenced(topology, cell)
         for next in one_down
@@ -68,13 +77,22 @@ end
 
 
 "Return all cells that are depended upon by any of the given cells."
-function upstream_recursive(notebook::Notebook, topology::NotebookTopology, from::Union{Vector{Cell},Set{Cell}})::Set{Cell}
+function upstream_recursive(
+    notebook::Notebook,
+    topology::NotebookTopology,
+    from::Union{Vector{Cell},Set{Cell}},
+)::Set{Cell}
     found = Set{Cell}(copy(from))
     _upstream_recursive!(found, notebook, topology, from)
     found
 end
 
-function _upstream_recursive!(found::Set{Cell}, notebook::Notebook, topology::NotebookTopology, from::Vector{Cell})::Nothing
+function _upstream_recursive!(
+    found::Set{Cell},
+    notebook::Notebook,
+    topology::NotebookTopology,
+    from::Vector{Cell},
+)::Nothing
     for cell in from
         references = topology.nodes[cell].references
         for upstream in PlutoDependencyExplorer.where_assigned(topology, references)

src/analysis/Parse.jl

@@ -1,3 +1,5 @@
+# This is how we go from a String of cell code to a Julia `Expr` that can be executed.
+
 import ExpressionExplorer
 import Markdown
 

src/evaluation/Run.jl

@@ -2,6 +2,7 @@ import REPL: ends_with_semicolon
 import .Configuration
 import .Throttled
 import ExpressionExplorer: is_joined_funcname
+import UUIDs: UUID
 
 """
 Run given cells and all the cells that depend on them, based on the topology information before and after the changes.
@@ -507,9 +508,6 @@ function cells_to_disable_to_resolve_multiple_defs(old::NotebookTopology, new::N
 
 		if length(fellow_assigners_new) > length(fellow_assigners_old)
 			other_definers = setdiff(fellow_assigners_new, (cell,))
-
-			@debug "Solving multiple defs" cell.cell_id cell_id.(other_definers) disjoint(cells, other_definers)
-
 			# we want cell to be the only element of cells that defines this varialbe, i.e. all other definers must have been created previously
 			if disjoint(cells, other_definers)
 				# all fellow cells (including the current cell) should meet some criteria:

src/notebook/Cell.jl

@@ -1,5 +1,8 @@
 import UUIDs: UUID, uuid1
 
+# Hello! 👋 Check out the `Cell` struct.
+
+
 const METADATA_DISABLED_KEY = "disabled"
 const METADATA_SHOW_LOGS_KEY = "show_logs"
 const METADATA_SKIP_AS_SCRIPT_KEY = "skip_as_script"

src/notebook/Export.jl

@@ -94,6 +94,8 @@ function prefetch_statefile_html(statefile_js::AbstractString)
 end
 
 """
+This function takes the `editor.html` file from Pluto's source code, and uses string replacements to insert custom data. By inserting a statefile (and more), you can create an HTML file that will display a notebook when opened: this is how the Static HTML export works.
+
 See [PlutoSliderServer.jl](https://github.com/JuliaPluto/PlutoSliderServer.jl) if you are interested in exporting notebooks programatically.
 """
 function generate_html(;

src/notebook/Notebook.jl

@@ -1,8 +1,9 @@
+# The `Notebook` struct!
+
 import UUIDs: UUID, uuid1
 import .Configuration
 import .PkgCompat: PkgCompat, PkgContext
 import Pkg
-import TOML
 import .Status
 
 const DEFAULT_NOTEBOOK_METADATA = Dict{String, Any}()
@@ -22,7 +23,11 @@ const ProcessStatus = (
     waiting_for_permission="waiting_for_permission",
 )
 
-"Like a [`Diary`](@ref) but more serious. 📓"
+"""
+A Pluto notebook, yay! 📓
+
+This mutable struct is a notebook session. It contains the information loaded from the `.jl` file, the cell outputs, package information, execution metadata and more.
+"""
 Base.@kwdef mutable struct Notebook
     "Cells are ordered in a `Notebook`, and this order can be changed by the user. Cells will always have a constant UUID."
     cells_dict::Dict{UUID,Cell}
@@ -111,15 +116,18 @@ end
 Notebook(cells::Vector{Cell}, path::AbstractString=numbered_until_new(joinpath(new_notebooks_directory(), cutename()))) = Notebook(cells, path, uuid1())
 
 function Base.getproperty(notebook::Notebook, property::Symbol)
+    # This is so that you can do notebook.cells to get all cells as a vector.
     if property == :cells
         _collect_cells(notebook.cells_dict, notebook.cell_order)
+    # This is for Firebasey I think
     elseif property == :cell_inputs
         notebook.cells_dict
     else
         getfield(notebook, property)
     end
 end
 
+# New method for this function with a `Notebook` as input.
 function PlutoDependencyExplorer.topological_order(notebook::Notebook)
     cached = notebook._cached_topological_order
 	if cached === nothing || cached.input_topology !== notebook.topology

src/notebook/path helpers.jl

@@ -190,7 +190,7 @@ end
 const tamepath = abspath ∘ tryexpanduser
 
 "Block until reading the file two times in a row gave the same result."
-function wait_until_file_unchanged(filename::String, timeout::Real, last_contents::String="")::Nothing
+function wait_until_file_unchanged(filename::String, timeout::Real, last_contents::String="-=-=-=-")::Nothing
 	new_contents = try
         read(filename, String)
     catch

src/notebook/saving and loading.jl

@@ -1,4 +1,5 @@
-
+import TOML
+import UUIDs: UUID
 
 const _notebook_header = "### A Pluto.jl notebook ###"
 const _notebook_metadata_prefix = "#> "
@@ -43,7 +44,8 @@ function save_notebook(io::IO, notebook::Notebook)
         end
     end
 
-    # Anything between the version string and the first UUID delimiter will be ignored by the notebook loader.
+    # (Anything between the version string and the first UUID delimiter will be ignored by the notebook loader.)
+    # We insert these two imports because they are also imported by default in the Pluto session. You might use these packages in your code, so we add the imports to the file, so the file can run as a script.
     println(io, "")
     println(io, "using Markdown")
     println(io, "using InteractiveUtils")
@@ -78,15 +80,18 @@ function save_notebook(io::IO, notebook::Notebook)
                 end
             end
         end
+
+        # Do one little string replacement to make it impossible to use the Pluto cell delimiter inside of actual cell code. If this would happen, then the notebook file cannot load correctly. So we just remove it from your code (sorry!)
+        current_code = replace(c.code, _cell_id_delimiter => "# ")
 
         if must_be_commented_in_file(c)
             print(io, _disabled_prefix)
-            print(io, replace(c.code, _cell_id_delimiter => "# "))
+            print(io, current_code)
             print(io, _disabled_suffix)
             print(io, _cell_suffix)
         else
             # write the cell code and prevent collisions with the cell delimiter
-            print(io, replace(c.code, _cell_id_delimiter => "# "))
+            print(io, current_code)
             print(io, _cell_suffix)
         end
     end
@@ -155,7 +160,7 @@ save_notebook(notebook::Notebook) = save_notebook(notebook, notebook.path)
 # LOADING
 ###
 
-function _notebook_metadata!(@nospecialize(io::IO))
+function _read_notebook_metadata!(@nospecialize(io::IO))
     firstline = String(readline(io))::String
 
     if firstline != _notebook_header
@@ -192,7 +197,7 @@ function _notebook_metadata!(@nospecialize(io::IO))
     return notebook_metadata
 end
 
-function _notebook_collected_cells!(@nospecialize(io::IO))
+function _read_notebook_collected_cells!(@nospecialize(io::IO))
     collected_cells = Dict{UUID,Cell}()
     while !eof(io)
         cell_id_str = String(readline(io))
@@ -239,7 +244,7 @@ function _notebook_collected_cells!(@nospecialize(io::IO))
     return collected_cells
 end
 
-function _notebook_cell_order!(@nospecialize(io::IO), collected_cells)
+function _read_notebook_cell_order!(@nospecialize(io::IO), collected_cells)
     cell_order = UUID[]
     while !eof(io)
         cell_id_str = String(readline(io))
@@ -259,7 +264,7 @@ function _notebook_cell_order!(@nospecialize(io::IO), collected_cells)
     return cell_order
 end
 
-function _notebook_nbpkg_ctx(cell_order::Vector{UUID}, collected_cells::Dict{Base.UUID, Cell})
+function _read_notebook_nbpkg_ctx(cell_order::Vector{UUID}, collected_cells::Dict{Base.UUID, Cell})
     read_package =
         _ptoml_cell_id ∈ cell_order &&
         _mtoml_cell_id ∈ cell_order &&
@@ -295,7 +300,7 @@ function _notebook_nbpkg_ctx(cell_order::Vector{UUID}, collected_cells::Dict{Bas
     return nbpkg_ctx
 end
 
-function _notebook_appeared_order!(cell_order::Vector{UUID}, collected_cells::Dict{Base.UUID, Cell})
+function _read_notebook_appeared_order!(cell_order::Vector{UUID}, collected_cells::Dict{Base.UUID, Cell})
     setdiff!(
         union!(
             # don't include cells that only appear in the order, but no code was given
@@ -310,12 +315,12 @@ end
 
 "Load a notebook without saving it or creating a backup; returns a `Notebook`. REMEMBER TO CHANGE THE NOTEBOOK PATH after loading it to prevent it from autosaving and overwriting the original file."
 function load_notebook_nobackup(@nospecialize(io::IO), @nospecialize(path::AbstractString))::Notebook
-    notebook_metadata = _notebook_metadata!(io)
+    notebook_metadata = _read_notebook_metadata!(io)
+    collected_cells = _read_notebook_collected_cells!(io)
+    cell_order = _read_notebook_cell_order!(io, collected_cells)
+    nbpkg_ctx = _read_notebook_nbpkg_ctx(cell_order, collected_cells)
+    appeared_order = _read_notebook_appeared_order!(cell_order, collected_cells)
 
-    collected_cells = _notebook_collected_cells!(io)
-    cell_order = _notebook_cell_order!(io, collected_cells)
-    nbpkg_ctx = _notebook_nbpkg_ctx(cell_order, collected_cells)
-    appeared_order = _notebook_appeared_order!(cell_order, collected_cells)
     appeared_cells_dict = filter(collected_cells) do (k, v)
         k ∈ appeared_order
     end
@@ -336,16 +341,14 @@ end
 # UTILS
 
 function load_notebook_nobackup(path::String)::Notebook
-    local loaded
     open(path, "r") do io
-        loaded = load_notebook_nobackup(io, path)
+        load_notebook_nobackup(io, path)
     end
-    loaded
 end
 
 # BACKUPS
 
-"Create a backup of the given file, load the file as a .jl Pluto notebook, save the loaded notebook, compare the two files, and delete the backup of the newly saved file is equal to the backup."
+"Create a backup of the given file, load the file as a .jl Pluto notebook, save the loaded notebook, compare the two files, and delete the backup of the newly saved file is mostly equal to the backup."
 function load_notebook(path::String; disable_writing_notebook_files::Bool=false)::Notebook
     backup_path = backup_filename(path)
     # local backup_num = 1

src/packages/Packages.jl

@@ -485,9 +485,16 @@ function with_auto_fixes(f::Function, notebook::Notebook)
         @info "Operation failed. Updating registries and trying again..." exception=e
 
         PkgCompat.update_registries(; force=true)
+
+        # TODO: check for resolver errors around stdlibs and fix them by doing `up Statistics`
+
+
+
+
         try
             f()
         catch e
+            # this is identical to Pkg.update, right?
             @warn "Operation failed. Removing Manifest and trying again..." exception=e
 
             reset_nbpkg!(notebook; keep_project=true, save=false, backup=false)

src/packages/PkgCompat.jl

@@ -455,7 +455,7 @@ end
 ###
 
 
-_project_key_order = ["name", "uuid", "keywords", "license", "desc", "deps", "weakdeps", "sources", "extensions", "compat"]
+const _project_key_order = ["name", "uuid", "keywords", "license", "desc", "deps", "weakdeps", "sources", "extensions", "compat"]
 project_key_order(key::String) =
     something(findfirst(x -> x == key, _project_key_order), length(_project_key_order) + 1)
 

src/runner/Loader.jl

@@ -1,4 +1,4 @@
-# The goal of this file is to import PlutoRunner into Main. 
+# The goal of this file is to import PlutoRunner into Main, on the process of the notebook (created by Malt.jl).
 # 
 # This is difficult because PlutoRunner uses standard libraries and packages that are not necessarily available in the standard environment. 
 # 

src/runner/PlutoRunner/src/bonds.jl

@@ -1,5 +1,5 @@
 import Base64
-
+import UUIDs: UUID
 
 const registered_bond_elements = Dict{Symbol, Any}()
 

src/webserver/Dynamic.jl

@@ -427,7 +427,6 @@ function _set_cells_to_queued_in_local_state(client, notebook, cells)
             if haskey(results, cell.cell_id)
                 old = results[cell.cell_id]["queued"]
                 results[cell.cell_id]["queued"] = true
-                @debug "Setting val!" cell.cell_id old
             end
         end
     end

src/webserver/Router.jl

@@ -1,6 +1,6 @@
 
 function http_router_for(session::ServerSession)
-    router = HTTP.Router(default_404)
+    router = HTTP.Router(default_404_response)
     security = session.options.security
 
     function create_serve_onefile(path)

src/webserver/Static.jl

@@ -1,6 +1,5 @@
 import HTTP
 import Markdown: htmlesc
-import UUIDs: UUID
 import Pkg
 import MIMEs
 
@@ -24,7 +23,7 @@ const day = let
     day = 24hour
 end
 
-function default_404(req = nothing)
+function default_404_response(req = nothing)
     HTTP.Response(404, "Not found!")
 end
 
@@ -41,7 +40,7 @@ function asset_response(path; cacheable::Bool=false)
         cacheable && HTTP.setheader(response, "Cache-Control" => "public, max-age=$(30day), immutable")
         response
     else
-        default_404()
+        default_404_response()
     end
 end
 
@@ -73,19 +72,29 @@ function notebook_response(notebook; home_url="./", as_redirect=true)
     end
 end
 
-const found_is_pluto_dev = Ref{Union{Nothing,Bool}}(nothing)
+const found_is_pluto_dev = Ref{Bool}()
+"""
+Is the Pluto package `dev`ed? Returns `false` for normal Pluto installation from the registry.
+"""
 function is_pluto_dev()
-    if found_is_pluto_dev[] !== nothing
+    if isassigned(found_is_pluto_dev)
         return found_is_pluto_dev[]
     end
+
     found_is_pluto_dev[] = try
-        deps = Pkg.dependencies()
+        # is the package located in .julia/packages ?
+        if startswith(pkgdir(@__MODULE__), joinpath(get(DEPOT_PATH, 1, "zzz"), "packages"))
+            false
+        else
+            deps = Pkg.dependencies()
 
-        p_index = findfirst(p -> p.name == "Pluto", deps)
-        p = deps[p_index]
+            p_index = findfirst(p -> p.name == "Pluto", deps)
+            p = deps[p_index]
 
-        p.is_tracking_path
-    catch
+            p.is_tracking_path
+        end
+    catch e
+        @debug "is_pluto_dev failed" e
         false
     end
 end