Merge pull request #13 from jmarshrossney/qol/conda-env

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 = []