diff --git a/.github/workflows/tests.yaml b/.github/workflows/tests.yaml index 91b44ee5..a8694478 100644 --- a/.github/workflows/tests.yaml +++ b/.github/workflows/tests.yaml @@ -12,7 +12,7 @@ jobs: strategy: matrix: - python-version: [3.6, 3.7, 3.8] + python-version: [3.7, 3.8, 3.9] steps: - uses: actions/checkout@v2 diff --git a/redis_consumer/settings.py b/redis_consumer/settings.py index a33eb8f8..c4bbf6ec 100644 --- a/redis_consumer/settings.py +++ b/redis_consumer/settings.py @@ -92,9 +92,9 @@ METADATA_EXPIRE_TIME = config('METADATA_EXPIRE_TIME', default=30, cast=int) # Tracking settings -TRACKING_MODEL = config('TRACKING_MODEL', default='TrackingModelInf:4', cast=str) +TRACKING_MODEL = config('TRACKING_MODEL', default='NuclearTrackingInf:6', cast=str) CALIBAN_MODEL = config('CALIBAN_MODEL', default=TRACKING_MODEL, cast=str) -NEIGHBORHOOD_ENCODER = config('NEIGHBORHOOD_ENCODER', default='TrackingModelNE:2', cast=str) +NEIGHBORHOOD_ENCODER = config('NEIGHBORHOOD_ENCODER', default='NuclearTrackingNE:6', cast=str) # tracking.cell_tracker settings TODO: can we extract from model_metadata? MAX_DISTANCE = config('MAX_DISTANCE', default=50, cast=int) @@ -115,7 +115,7 @@ # Mesmer model Settings # deprecated model name, use MESMER_MODEL instead. -MULTIPLEX_MODEL = config('MULTIPLEX_MODEL', default='MultiplexSegmentation:5', cast=str) +MULTIPLEX_MODEL = config('MULTIPLEX_MODEL', default='MultiplexSegmentation:9', cast=str) MESMER_MODEL = config('MESMER_MODEL', default=MULTIPLEX_MODEL, cast=str) MESMER_COMPARTMENT = config('MESMER_COMPARTMENT', default='whole-cell') @@ -127,8 +127,8 @@ # Set default models based on label type MODEL_CHOICES = { - 0: config('NUCLEAR_MODEL', default='NuclearSegmentation:5', cast=str), - 1: config('CYTOPLASM_MODEL', default='CytoplasmSegmentation:4', cast=str), + 0: config('NUCLEAR_MODEL', default='NuclearSegmentation:6', cast=str), + 1: config('CYTOPLASM_MODEL', default='CytoplasmSegmentation:5', cast=str), 2: config('PHASE_MODEL', default='PhaseCytoSegmentation:0', cast=str) } diff --git a/requirements-no-deps.txt b/requirements-no-deps.txt index e4ac668d..a41909c8 100644 --- a/requirements-no-deps.txt +++ b/requirements-no-deps.txt @@ -1,3 +1,3 @@ # tensorflow-serving-api installs tensorflow so install # with --no-deps to prevent overwriting tensorflow-cpu -tensorflow-serving-api~=2.5.3 +tensorflow-serving-api~=2.8.0 diff --git a/requirements.txt b/requirements.txt index 7fd72707..c55640d9 100644 --- a/requirements.txt +++ b/requirements.txt @@ -1,9 +1,9 @@ # deepcell packages -deepcell-cpu~=0.11.0 -deepcell-spots~=0.2.1 -deepcell-toolbox~=0.10.3 -deepcell-tracking~=0.5.2 -tensorflow-cpu~=2.5.2 +deepcell-cpu~=0.12.0 +deepcell-spots~=0.3.1 +deepcell-toolbox~=0.11.2 +deepcell-tracking~=0.5.7 +tensorflow-cpu~=2.8.0 tifffile>=2020.9.3 imagecodecs numpy>=1.16.6