python version numbers all frozen + test testPredictWithConflictingInput

Manifest.toml

@@ -1037,11 +1037,11 @@ version = "0.3.3"
 
 [[deps.PlanarLarvae]]
 deps = ["DelimitedFiles", "HDF5", "JSON3", "LinearAlgebra", "MAT", "Meshes", "OrderedCollections", "Random", "SHA", "StaticArrays", "Statistics", "StatsBase", "StructTypes"]
-git-tree-sha1 = "6b2dc28d56bcef101672cbf2bb784bbd5d88d579"
+git-tree-sha1 = "d964d040e319fe3bd9140e5bf91d648de6acc96f"
 repo-rev = "main"
 repo-url = "https://gitlab.pasteur.fr/nyx/PlanarLarvae.jl"
 uuid = "c2615984-ef14-4d40-b148-916c85b43307"
-version = "0.15.0"
+version = "0.16.0"
 
 [[deps.PlotUtils]]
 deps = ["ColorSchemes", "Colors", "Dates", "PrecompileTools", "Printf", "Random", "Reexport", "Statistics"]

recipes/Dockerfile

@@ -77,6 +77,7 @@ RUN if [ -z $TAGGINGBACKENDS_BRANCH ]; then \
  && git clone --depth 1 --no-tags --single-branch -b $(echo $BACKEND | cut -d/ -f2) https://gitlab.pasteur.fr/nyx/MaggotUBA-adapter MaggotUBA \
  && cd MaggotUBA \
  && rm -rf .git \
+ && (cat requirements.txt | xargs -I % sh -c 'poetry add "%"') \
  && poetry install --only main \
  && poetry add "pynvml==11.4.1" \
  && if [ "$(echo $BACKEND | cut -d/ -f2)" = "main" ] || [ "$(echo $BACKEND | cut -d/ -f2)" = "dev" ]; then \

test/deploy_and_test.sh

@@ -97,7 +97,7 @@ if [ -f ../../LarvaTagger_test_data.tgz ]; then
   #   KEEP_MODEL_FILES=1 ./deploy_and_test.sh
   #   cd LarvaTagger/LarvaTagger.jl
   #   rm -rf test/data/test_train_*
-  #   cp -ra ../MaggotUBA/models/test_train_* test/data/
+  #   cp -Rp ../MaggotUBA/models/test_train_* test/data/
   #   tar zcvf LarvaTagger_test_data.tgz test/data/*
   #   mv LarvaTagger_test_data.tgz ../../
   tar zxvf ../../LarvaTagger_test_data.tgz

test/scenarii.sh

@@ -50,9 +50,10 @@ endTest() {
 
 prepareTestData() {
   tmpdir="$SHUNIT_TMPDIR/$1"
+  shift
   rm -rf "$tmpdir"
   mkdir -p "$tmpdir"
-  for file in sample.spine sample.outline; do
+  for file in sample.spine sample.outline $@; do
     cp "$datapath/$file" "$tmpdir/" || exit 1
   done
   echo $tmpdir
@@ -123,6 +124,33 @@ testPredictDefault() {
   endTest
 }
 
+# requires: sample.spine sample.outline trx.mat original_predictions.label test_train_default/predicted.label
+testPredictWithConflictingInput() {
+  tagger="test_train_default$tagger_suffix"
+  # make test data
+  touch "$datapath/spurious.txt"
+  tmpdir=$(prepareTestData $tagger trx.mat original_predictions.label spurious.txt)
+  # restore the model
+  mkdir -p "$maggotuba/models"
+  rm -rf "$maggotuba/models/$tagger"
+  echo "cp -Rp \"$datapath/$tagger\" \"$maggotuba/models/\""
+  cp -Rp "$datapath/$tagger" "$maggotuba/models/"
+  [ -f "$maggotuba/models/$tagger/clf_config.json" ] || exit 1
+  # run
+  cd "$project_root"
+  echo "\"$larvataggerjl\" predict \"$maggotuba\" $tagger \"$tmpdir\" --debug"
+  "$larvataggerjl" predict "$maggotuba" $tagger "$tmpdir" --debug
+  # compare
+  filename=predicted.label
+  predictions="$tmpdir/$filename"
+  expected_labels="$datapath/$tagger/$filename"
+  assertFalse "\`predict\` failed to generate file $filename" '[ -z "$predictions" ]'
+  assertTrue "\`predict\` failed to reproduce file $filename" '$(cmp "$expected_labels" "$predictions")'
+  # clean up
+  rm -f "$datapath/spurious.txt"
+  endTest
+}
+
 # requires: sample.spine sample.outline original_predictions.label test_train_default/*
 testTrainDefault() {
   tagger="test_train_default$tagger_suffix"
@@ -238,7 +266,7 @@ postTrain() {
   assertTrue "\`train\` failed to reproduce file $enc_weights" '$(cmp "$expected_tagger_dir/$enc_weights" "$enc_weights_path")'
   assertTrue "\`train\` failed to reproduce file $enc_config" '$(cmp "$expected_tagger_dir/$enc_config" "$enc_config_path")'
   assertTrue "\`train\` failed to reproduce file $clf_weights" '$(cmp "$expected_tagger_dir/$clf_weights" "$clf_weights_path")'
-  assertTrue "\`train\` failed to reproduce file $clf_config" '$(cmp "$expected_tagger_dir/$clf_config" "$clf_config_path")'
+  assertTrue "\`train\` failed to reproduce file $clf_config" '[ -z "$(diff "$expected_tagger_dir/$clf_config" "$clf_config_path" | grep -E "^[<>]   " | grep -vE larva_dataset_.*[.]hdf5)" ]'
 
   # test the predictions
   echo "\"$larvataggerjl\" predict \"$maggotuba\" $tagger \"$tmpdir/sample.spine\""