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/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: 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