From 4480b535d25d9b8dd2901300f90c6cfd5292c103 Mon Sep 17 00:00:00 2001 From: Jacob Rosenthal Date: Tue, 4 Jan 2022 14:59:25 -0500 Subject: [PATCH 1/2] bump version number --- pathml/_version.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/pathml/_version.py b/pathml/_version.py index 5e62fef5..77ee011d 100644 --- a/pathml/_version.py +++ b/pathml/_version.py @@ -3,4 +3,4 @@ License: GNU GPL 2.0 """ -__version__ = "2.0.dev4" +__version__ = "2.0.2" From 24202085971e19d8f86bb437d5c1279b8fbbe582 Mon Sep 17 00:00:00 2001 From: Jacob Rosenthal Date: Tue, 4 Jan 2022 14:59:47 -0500 Subject: [PATCH 2/2] update Docker instructions --- README.md | 52 ++++++++++++++++++++++++++++++++-------------------- 1 file changed, 32 insertions(+), 20 deletions(-) diff --git a/README.md b/README.md index d344fe94..8d5402ea 100644 --- a/README.md +++ b/README.md @@ -18,14 +18,14 @@ A toolkit for computational pathology and machine learning. **View [documentation](https://pathml.readthedocs.io/en/latest/)** :construction: the `dev` branch is under active development, with experimental features, bug fixes, and refactors that may happen at any time! -Stable versions are available as tagged commits on the `master` branch, or as versioned releases on PyPI +Stable versions are available as tagged releases on GitHub, or as versioned releases on PyPI # Installation There are several ways to install `PathML`: -1. pip install (**recommended for users**) -2. clone repo to local machine and install from source (recommended for developers/contributors) +1. `pip install` from PyPI (**recommended for users**) +2. Clone repo to local machine and install from source (recommended for developers/contributors) 3. Use the PathML Docker container Options (1) and (2) require that you first install all external dependencies: @@ -39,43 +39,43 @@ Download Miniconda [here](https://docs.conda.io/en/latest/miniconda.html) ## Installation option 1: pip install -Create conda environment +Create conda environment: ```` conda create --name pathml python=3.8 conda activate pathml ```` -Install external dependencies (Linux) with [Apt](https://ubuntu.com/server/docs/package-management) +Install external dependencies (Linux) with [Apt](https://ubuntu.com/server/docs/package-management): ```` sudo apt-get install openslide-tools g++ gcc libblas-dev liblapack-dev ```` -Install external dependencies (MacOS) with [Brew](www.brew.sh) +Install external dependencies (MacOS) with [Brew](www.brew.sh): ```` brew install openslide ```` -Install [OpenJDK 8](https://openjdk.java.net/) +Install [OpenJDK 8](https://openjdk.java.net/): ```` conda install openjdk==8.0.152 ```` Optionally install CUDA (instructions [here](#CUDA)) -Install `PathML` +Install `PathML` from PyPI: ```` pip install pathml ```` ## Installation option 2: clone repo and install from source -Clone repo +Clone repo: ```` git clone https://github.com/Dana-Farber-AIOS/pathml.git cd pathml ```` -Create conda environment +Create conda environment: ```` conda env create -f environment.yml conda activate pathml @@ -83,27 +83,39 @@ conda activate pathml Optionally install CUDA (instructions [here](#CUDA)) -Install `PathML`: +Install `PathML` from source: ```` pip install -e . ```` -## Installation option 3: docker +## Installation option 3: Docker -Build the PathML docker container: -```` -docker build -t pathml-analysis . -```` +First, download or build the PathML Docker container: + +- Option A: download PathML container from Docker Hub + ```` + docker pull pathml/pathml:latest + ```` + Optionally specify a tag for a particular version, e.g. `docker pull pathml/pathml:2.0.2`. To view possible tags, + please refer to the [PathML DockerHub page](https://hub.docker.com/r/pathml/pathml). + +- Option B: build docker container from source + ```` + git clone https://github.com/Dana-Farber-AIOS/pathml.git + cd pathml + docker build -t pathml/pathml . + ```` -Connect to the container: +Then connect to the container: ```` -docker run -it -p 8888:8888 pathml-analysis +docker run -it -p 8888:8888 pathml/pathml ```` The above command runs the container, which is configured to spin up a jupyter lab session and expose it on port 8888. -The terminal should display a URL to the jupyter lab session starting with http://127.0.0.1:8888/lab?token=<...>. +The terminal should display a URL to the jupyter lab session starting with `http://127.0.0.1:8888/lab?token=<.....>`. Navigate to that page and you should connect to the jupyter lab session running on the container with the pathml -environment fully configured. +environment fully configured. If a password is requested, copy the string of characters following the `token=` in the +url. Note that the docker container requires extra configurations to use with GPU. Note that these instructions assume that there are no other processes using port 8888.