add support for python 3.10

camlab-bioml · Jul 5, 2024 · 1ba9cea · 1ba9cea
1 parent 514bb0e
commit 1ba9cea
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diff --git a/Dockerfile b/Dockerfile
@@ -1,4 +1,4 @@
-FROM python:3.9-slim
+FROM python:3.10-slim
 
 WORKDIR /code
 
@@ -41,4 +41,4 @@ COPY --chown=${USER_UID}:${USER_GID} starling/__init__.py /code/starling/__init_
 
 RUN poetry install --with docs,dev
 
-COPY . .
+COPY --chown=${USER_UID}:${USER_GID} . .
diff --git a/README.md b/README.md
@@ -2,6 +2,7 @@
 
 ![build](https://github.com/camlab-bioml/starling/actions/workflows/main.yml/badge.svg)
 ![](https://img.shields.io/badge/Python-3.9-blue)
+![](https://img.shields.io/badge/Python-3.10-blue)
 
 
 STARLING is a probabilistic model for clustering cells measured with spatial expression assays (e.g. IMC, MIBI, etc...) while accounting for segmentation errors.
@@ -19,7 +20,7 @@ A **tutorial** outlining basic usage is available [here][tutorial].
 
 ## Requirements
 
-Python3.9 is required to run starling. If your current version of python is not 3.9, we recommend using [pyenv](https://github.com/pyenv/pyenv) to install a later version alongside your current one. Alternately, you could use the Docker configuration described below.
+Python 3.9 or 3.10 are required to run starling. If your current version of python is not one of these, we recommend using [pyenv](https://github.com/pyenv/pyenv) to install a compatible version alongside your current one. Alternately, you could use the Docker configuration described below.
 
 ## Installation
 

diff --git a/docs/source/tutorial/getting-started.ipynb b/docs/source/tutorial/getting-started.ipynb
@@ -168,7 +168,7 @@
    "outputs": [],
    "source": [
     "## log training results via tensorboard\n",
-    "log_tb = pl.logging.TensorBoardLogger(save_dir=\"log\")"
+    "log_tb = pl.loggers.TensorBoardLogger(save_dir=\"log\")"
    ]
   },
   {
@@ -228,7 +228,7 @@
     "## train ST\n",
     "st.train_and_fit(\n",
     "    callbacks=[cb_early_stopping],\n",
-    "    #logger=[log_tb],\n",
+    "    logger=[log_tb],\n",
     ")"
    ]
   },

diff --git a/pyproject.toml b/pyproject.toml
@@ -14,7 +14,7 @@ classifiers = [
 license = "See License.txt"
 
 [tool.poetry.dependencies]
-python = "~3.9"
+python = ">= 3.9, < 3.11"
 torch = "1.12.1"
 pytorch-lightning = "2.1.0"
 scanpy = "1.9.5"

diff --git a/tests/test_sanity.py b/tests/test_sanity.py
@@ -1,7 +1,6 @@
 from os.path import dirname, join
 
 import anndata as ad
-import numpy as np
 import pandas as pd
 from lightning_lite import seed_everything
 from pytorch_lightning.callbacks import EarlyStopping