Merge branch 'dev' into main

Manifest.toml

@@ -310,11 +310,11 @@ version = "1.8.0"
 
 [[deps.PlanarLarvae]]
 deps = ["DelimitedFiles", "HDF5", "JSON3", "LinearAlgebra", "MAT", "Meshes", "OrderedCollections", "SHA", "StaticArrays", "Statistics", "StatsBase", "StructTypes"]
-git-tree-sha1 = "f7e528d2ecb7b6ef13aab96fade5b4d0a4c64767"
+git-tree-sha1 = "a5226fa20f6f563a82968a0c4714f3a568b3658d"
 repo-rev = "main"
 repo-url = "https://gitlab.pasteur.fr/nyx/planarlarvae.jl"
 uuid = "c2615984-ef14-4d40-b148-916c85b43307"
-version = "0.9.0"
+version = "0.9.1"
 
 [[deps.Preferences]]
 deps = ["TOML"]

Project.toml

 name = "TaggingBackends"
 uuid = "e551f703-3b82-4335-b341-d497b48d519b"
 authors = ["François Laurent", "Institut Pasteur"]
-version = "0.11.0"
+version = "0.11.1"
 
 [deps]
 Dates = "ade2ca70-3891-5945-98fb-dc099432e06a"

README.md

@@ -171,7 +171,7 @@ Note also that, with the above `export` expression, the `JULIA_PROJECT` environm
 
 To install a backend, taking MaggotUBA-adapter as an example:
 ```
-git clone --depth 1 --single-branch -b 20230111 https://gitlab.pasteur.fr/nyx/MaggotUBA-adapter MaggotUBA
+git clone --depth 1 --single-branch -b 20230129 https://gitlab.pasteur.fr/nyx/MaggotUBA-adapter MaggotUBA
 cd MaggotUBA
 poetry install
 ```

pyproject.toml

 [tool.poetry]
 name = "TaggingBackends"
-version = "0.11"
+version = "0.11.1"
 description = "Backbone for LarvaTagger.jl tagging backends"
 authors = ["François Laurent"]
 

src/LarvaDatasets.jl

@@ -336,6 +336,9 @@ function write_larva_dataset_hdf5(path, counts, files, refs, nsteps_before, nste
         end
         attributes(g)["n_samples"] = sampleid
         # extension
+        if !isnothing(includeall)
+            delete!(counts, includeall)
+        end
         h5["labels"] = collect(keys(counts))
         h5["label_counts"] = collect(values(counts))
         #h5["files"] = [f.source for f in files]