Modify environment.yml

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.

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

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 = []