From 74d9fdbd1d185030bc7c91253eb5cacbf91eda01 Mon Sep 17 00:00:00 2001 From: Wade Schulz Date: Wed, 13 Mar 2024 21:19:44 +0000 Subject: [PATCH 1/2] update gitignore, add environment yml --- .gitignore | 5 ++++- environment.yml | 11 +++++++++++ 2 files changed, 15 insertions(+), 1 deletion(-) create mode 100644 environment.yml diff --git a/.gitignore b/.gitignore index fe5e547..a66f664 100644 --- a/.gitignore +++ b/.gitignore @@ -190,4 +190,7 @@ testingenv/ HPAv18RBGY_wodpl.csv HPAv18/ download_images.py -settings.json \ No newline at end of file +settings.json + +data/ +results/ \ No newline at end of file diff --git a/environment.yml b/environment.yml new file mode 100644 index 0000000..105dd59 --- /dev/null +++ b/environment.yml @@ -0,0 +1,11 @@ +name: cm4ai-hpa + +channels: + - defaults + +dependencies: + - python=3.10 + - pip + + - pip: + - -r requirements.txt \ No newline at end of file From d03a3b99228b8352d9d748bb0795d85d3e022df9 Mon Sep 17 00:00:00 2001 From: Wade Schulz Date: Wed, 13 Mar 2024 21:24:40 +0000 Subject: [PATCH 2/2] update readme to switch to miniconda --- README.adoc | 17 +++++++++++++++-- 1 file changed, 15 insertions(+), 2 deletions(-) diff --git a/README.adoc b/README.adoc index 40148f8..ad7ae85 100755 --- a/README.adoc +++ b/README.adoc @@ -21,16 +21,29 @@ up an issue here on Github or by contacting @cwinsnes. == Installation and Setup NOTE: It is recommended to run the module in a separate virtual environment -such as https://www.anaconda.com/[Anaconda] or +such as https://conda.io/projects/conda/en/latest/user-guide/install/linux.html[miniconda] or https://docs.python.org/3/library/venv.html[venvs] to avoid any issues with package versions. -Installing the required modules for this package can be done through `pip`. +If using miniconda, the environment can be installed by running: +[,bash] +---- +python env create -f environment.yml +---- + +After your environment is created, activate it with: +[,bash] +---- +conda activate cm4ai-hpa +---- + +Or after creating a separate environment, the required modules can be installed with `pip`. [,bash] ---- python -m pip install -r requirements.txt ---- + === Data The model requires the input images to be stored in the following way: