From 2f7bec90004c0eca33e4ed1375bf5520120dd1f9 Mon Sep 17 00:00:00 2001
From: Phillip Alday <phillip.alday@beacon.bio>
Date: Wed, 29 Jan 2025 09:23:17 -0600
Subject: [PATCH] update docs and Documenter version

---
 docs/Project.toml           |  2 +-
 docs/src/api.md             | 16 +++++++++++++++-
 docs/src/convert-to-onda.md | 10 +++++-----
 3 files changed, 21 insertions(+), 7 deletions(-)

diff --git a/docs/Project.toml b/docs/Project.toml
index 101c2b6..1814eb3 100644
--- a/docs/Project.toml
+++ b/docs/Project.toml
@@ -2,4 +2,4 @@
 Documenter = "e30172f5-a6a5-5a46-863b-614d45cd2de4"
 
 [compat]
-Documenter = "0.26"
+Documenter = "1"
diff --git a/docs/src/api.md b/docs/src/api.md
index 08bfe21..61f0268 100644
--- a/docs/src/api.md
+++ b/docs/src/api.md
@@ -9,7 +9,7 @@ CurrentModule = OndaEDF
 OndaEDF.jl prefers "self-service" import over "automagic", and provides
 functionality to extract
 [`Onda.Samples`](https://beacon-biosignals.github.io/Onda.jl/stable/#Samples-1)
-and [`EDFAnnotationV1`](@ref)s (which extend 
+and [`EDFAnnotationV1`](@ref)s (which extend
 [`Onda.AnnotationV1`](https://beacon-biosignals.github.io/Onda.jl/stable/#Onda.AnnotationV1)s)
 from an `EDF.File`.  These can be written to disk (with
 [`Onda.store`](https://beacon-biosignals.github.io/Onda.jl/stable/#Onda.store) /
@@ -33,9 +33,17 @@ EDFAnnotationV1
 
 ### Import plan table schemas
 
+!!! note "Plan version is dependent on EDF.jl version"
+    The utilized plan version is dependent on the EDF.jl version.
+    For EDF 0.8+, V3 are used, while V2 is used for for EDF 0.7.
+    The change from V2 to V3 reflects the change from [`Int16` to `Int32`
+    in EDF.jl's `samples_per_record`](https://github.com/beacon-biosignals/EDF.jl/releases/tag/v0.8.0).
+
 ```@docs
 PlanV2
+PlanV3
 FilePlanV2
+FilePlanV3
 write_plan
 ```
 
@@ -63,6 +71,12 @@ OndaEDF.promote_encodings
 onda_to_edf
 ```
 
+#### Internal export utilities
+
+```@docs
+OndaEDF.reencode_samples
+```
+
 ## Deprecations
 
 To support deserializing plan tables generated with old versions of OndaEDF +
diff --git a/docs/src/convert-to-onda.md b/docs/src/convert-to-onda.md
index 5d5812e..11527ff 100644
--- a/docs/src/convert-to-onda.md
+++ b/docs/src/convert-to-onda.md
@@ -101,7 +101,7 @@ To break this label specification down:
 - `["emg", "chin"]`: indicates that this specification is for `sensor_type` of `"emg"`, for which `"chin"` is accepted as a non-canonical alternative.
 - `["chin" => ["emg"]]` specifies that there's _one_ possible channel for this sensor type, whose canonical label (used in the output) is `"chin"`, but for which an alternative of `"emg"` is accepted.
 
-This essentially tricks OndaEDF into treating `CHIN EMG` as sensor type of "`CHIN` (alternative for sensor type of `EMG`), and channel label "`EMG` (alternative way to specify `CHIN`)".  For more details on how this matching is carried out, see [`plan_edf_to_onda_samples`](@ref) and [`match_labels`](@ref).
+This essentially tricks OndaEDF into treating `CHIN EMG` as sensor type of "`CHIN` (alternative for sensor type of `EMG`), and channel label "`EMG` (alternative way to specify `CHIN`)".  For more details on how this matching is carried out, see [`plan_edf_to_onda_samples`](@ref) and the internal [`OndaEDF.match_edf_label`](@ref).
 
 #### Preprocess signal headers
 
@@ -117,8 +117,8 @@ edf = EDF.File(my_edf_file_path)
 
 function corrected_header(signal::EDF.Signal)
     header = signal.header
-    return Tables.rowmerge(header; 
-                           label=header.transducer_type, 
+    return Tables.rowmerge(header;
+                           label=header.transducer_type,
                            transducer_type=header.label)
 end
 
@@ -200,7 +200,7 @@ If any errors _were_ encountered, you may need to iterate further.
 
 The final step is to store both the `Onda.Samples` and the executed plan in some persistent storage.
 For storing `Onda.Samples`, see [`Onda.store`](https://beacon-biosignals.github.io/Onda.jl/stable/#Onda.store), which supports serializing LPCM-encoded samples to [any "path-like" type](https://beacon-biosignals.github.io/Onda.jl/stable/#Support-For-Generic-Path-Like-Types) (i.e., anything that provides a method for `write`).
-For storing the plan, use [`OndaEDF.write_plan`](@ref) (or `Legolas.write(file_path, plan, FilePlanV2SchemaVersion())` (see the documentation for [`Legolas.write`](https://beacon-biosignals.github.io/Legolas.jl/stable/#Legolas.write) and [`FilePlanV2`](@ref).
+For storing the plan, use [`OndaEDF.write_plan`](@ref) (or `Legolas.write(file_path, plan, FilePlanV3SchemaVersion())` (see the documentation for [`Legolas.write`](https://beacon-biosignals.github.io/Legolas.jl/stable/#Legolas.write) and [`FilePlanV3`](@ref OndaEDF.FilePlanV3).
 
 ## Batch conversion of many EDFs
 
@@ -262,7 +262,7 @@ function plan_all(edf_paths, files; kwargs...)
         plan = DataFrame(plan)
         # make sure this is the same every time this function is re-run!
         recording = uuid5(NAMESPACE, string(origin_uri))
-        return insertcols!(plan, 
+        return insertcols!(plan,
                            :origin_uri => origin_uri,
                            :recording => recording)
     end