diff --git a/README.md b/README.md index b5182a8..05cfe98 100644 --- a/README.md +++ b/README.md @@ -11,8 +11,7 @@ It's a companion project to an R-shiny based image annotation app that is not ye Use anaconda or miniconda to create a python environment using the included `environment.yml` ``` -conda create -n cyto_39 python=3.9 -conda env update +conda env create -f environment.yml ``` Please note that this is specifically pinned to python 3.9 due to dependency versions; we make experimental use of the [CEFAS plankton model available through SciVision](https://sci.vision/#/model/resnet50-plankton), which in turn uses an older version of pytorch that isn't packaged above python 3.9. diff --git a/environment.yml b/environment.yml index a23b288..56722dd 100644 --- a/environment.yml +++ b/environment.yml @@ -1,21 +1,20 @@ name: cyto_39 channels: + - pytorch - conda-forge + - defaults dependencies: - - numpy + - python=3.9 + - pytorch=1.10.0 + - mkl=2024.0 + - chromadb=0.5.3 + - intake-xarray + - scikit-image - pandas - - s3fs - - matplotlib + - pytest - python-dotenv - - dask + - s3fs + - pip - pip: - - pytest - - imagecodecs - - intake # for reading scivision - - torch==1.10.0 # install before cefas_scivision; it needs this version - scivision - - scikit-image - - setuptools==69.5.1 # because this bug https://github.com/pytorch/serve/issues/3176 - - tiffile - - git+https://github.com/alan-turing-institute/plankton-cefas-scivision@main # torch version - - chromadb + - git+https://github.com/alan-turing-institute/plankton-cefas-scivision@main diff --git a/pyproject.toml b/pyproject.toml index 8510474..f95fedd 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -3,6 +3,6 @@ name = "cyto_ml" version = "0.1" description = "This package supports the processing and analysis of plankton sample data" readme = "README.md" -requires-python = "<3.10" +requires-python = "==3.9.*" [tool.setuptools] py-modules = []