diff --git a/MIMIC-IV_Example/README.md b/MIMIC-IV_Example/README.md index 5df8c16..cd90e45 100644 --- a/MIMIC-IV_Example/README.md +++ b/MIMIC-IV_Example/README.md @@ -8,7 +8,10 @@ be run from this directory or from the directory in which the files in Step 0.5. ```bash conda create -n MEDS python=3.12 conda activate MEDS -pip install "MEDS_transforms[local_parallelism,slurm_parallelism]" +# Get the latest version of MEDS_transforms from pypi +LATEST_VERSION=$(pip index versions "meds-transforms" 2>/dev/null | egrep -o '([0-9]+\.){2}[0-9]+' | head -n 1) +export VERSION=$LATEST_VERSION # or whatever version you want, at the time of writing this is "0.0.8" +pip install "MEDS_transforms[local_parallelism,slurm_parallelism]==${VERSION}" ``` If you want to profile the time and memory costs of your ETL, also install: `pip install hydra-profiler`. @@ -20,9 +23,7 @@ export MIMICIV_RAW_DIR=??? # set to the directory in which you want to store the export MIMICIV_PRE_MEDS_DIR=??? # set to the directory in which you want to store the intermediate MEDS MIMIC-IV data export MIMICIV_MEDS_COHORT_DIR=??? # set to the directory in which you want to store the final MEDS MIMIC-IV data -export VERSION=0.0.6 # or whatever version you want -# export URL="https://raw.githubusercontent.com/mmcdermott/MEDS_transforms/$VERSION/MIMIC-IV_Example" -export URL="https://raw.githubusercontent.com/mmcdermott/MEDS_transforms/refs/heads/main/MIMIC-IV_Example" +export URL="https://raw.githubusercontent.com/mmcdermott/MEDS_transforms/$VERSION/MIMIC-IV_Example" wget $URL/run.sh wget $URL/pre_MEDS.py