diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml index 1481fd8e..95037b0a 100644 --- a/.github/workflows/ci.yml +++ b/.github/workflows/ci.yml @@ -24,7 +24,7 @@ jobs: auto-activate-base: false activate-environment: tiktorch-server-env environment-file: environment.yml - channel-priority: flexible + channel-priority: strict miniforge-variant: Miniforge3 - name: Get the latest commit hash and target ref run: | @@ -51,7 +51,7 @@ jobs: auto-activate-base: false activate-environment: tiktorch-server-env environment-file: environment.yml - channel-priority: flexible + channel-priority: strict miniforge-variant: Miniforge3 - name: conda diagnostics run: | @@ -89,7 +89,7 @@ jobs: with: auto-update-conda: true auto-activate-base: true - channel-priority: flexible + channel-priority: strict miniforge-variant: Miniforge3 - name: install common conda dependencies run: conda install -n base -c conda-forge conda-build setuptools_scm -y @@ -133,7 +133,7 @@ jobs: with: auto-update-conda: true auto-activate-base: true - channel-priority: flexible + channel-priority: strict miniforge-variant: Miniforge3 - name: install common conda dependencies run: conda install -n base -c conda-forge conda-build setuptools_scm -y diff --git a/Makefile b/Makefile index 9dc9c0bf..a0c713d8 100644 --- a/Makefile +++ b/Makefile @@ -1,7 +1,7 @@ SHELL=/bin/bash ROOT_DIR:=$(shell dirname $(realpath $(firstword $(MAKEFILE_LIST)))) TIKTORCH_ENV_NAME ?= tiktorch-server-env -SUBMODULES = ./vendor/core-bioimage-io-python ./vendor/spec-bioimage-io +SUBMODULES = ./vendor/spec-bioimage-io ./vendor/core-bioimage-io-python protos: python -m grpc_tools.protoc -I./proto --python_out=tiktorch/proto/ --grpc_python_out=tiktorch/proto/ ./proto/*.proto diff --git a/environment.yml b/environment.yml index aba40a3f..c968d26b 100644 --- a/environment.yml +++ b/environment.yml @@ -1,13 +1,14 @@ name: tiktorch-server-env channels: - - ilastik-forge - pytorch + - ilastik-forge - conda-forge + - nodefaults dependencies: # - bioimage.spec via submodule # - bioimage.core via submodule - python 3.9.* - - numpy + - numpy >=1.21,<2 - grpcio=1.44 # protobuf 5 requires protoc version > 3.19.0 that requires grpcio >= 1.44 - marshmallow-union - marshmallow=3.12.* @@ -15,7 +16,6 @@ dependencies: - protobuf - pyyaml=5.3.* - requests - - ruamel.yaml - scikit-learn - scipy - typing-extensions @@ -32,17 +32,32 @@ dependencies: - cpuonly # - cudatoolkit >=10.2 # - cudnn - # - tochvision + - torchvision # tensorflow (1.14 is the latest 1.x version on cf) # so far we don't have any 2.x models in the model zoo # tensorflow skipped for now, as it conflicts with grpcio version 1.41 # - tensorflow >=2.9,<3.0 - # convenient to use bioiamgeio.core tools - - imageio + # bioimageio.spec / bioimageio.core dependencies: + - annotated-types >=0.5.0,<1 + - email_validator + - h5py + - imageio >=2.10 + - loguru + - packaging >=17.0 + - pooch >=1.5,<2 + - pydantic >=2.7.0,<2.10 + - pydantic-core + - pydantic-settings >=2.5 + - python-dateutil + - rich + - ruyaml + - tifffile - tqdm - typer + - zipp + # dev stuff - pytest diff --git a/setup.py b/setup.py index d7210962..7aebd69c 100644 --- a/setup.py +++ b/setup.py @@ -32,6 +32,7 @@ "grpcio>=1.31", "numpy<2", # pytorch 2.2.2-py3.9_0 for macos is compiled with numpy 1.* "protobuf", + "pydantic>=2.7.0,<2.10", "pyyaml", "xarray", ],