UoI Var

.gitignore

@@ -108,4 +108,31 @@ ENV/
 .vscode
 
 # lbfgs solver stuff
-pyuoi/lbfgs/_lowlevel.c
+_lowlevel.c
+
+*~
+out/
+*.prof
+dataDale/
+*.png
+*.npy
+data/
+model/
+\#*
+*.h5
+.cursor
+*.npz
+old/
+result/
+.bash_history
+.viminfo
+.ipython/
+.jupyter/
+.local/
+.emacs.d/
+.lesshst
+*.aux
+*.toc
+*.out
+.codex
+*.dvi

causal_net/Readme

@@ -0,0 +1,80 @@
+Detailed manual at
+https://docs.google.com/document/d/1Ou98jsFpTR7s3cTf6AQwF92tqd2guwA_cGuvQrm8RSE/edit?usp=sharing
+
+
+IMG=nersc/causal-net:v3   # Mar 28
+IMG=nersc/causal-net:v4   # May 13
+
+ export OMP_NUM_THREADS=2
+ salloc -q interactive -C cpu --image=$IMG -t 4:00:00 -A m2043 -N 1
+
+
+Directory structure to stor real and simulated data
+/global/cfs/cdirs/m2043/causal_inference/dale-gen-sim-may27/input_uoi/
+
+basePath=/global/homes/b/balewski/prjs/bioDataVault2025/causalNet_tmp/
+
+exp_raw/  raw data from experiment
+gen_dale/ daleMatrix+samples for generated network
+input_uoi/  data formatted for UoI
+model_uoi/  UoI fit output
+postproc/ any final analysis
+
+
+A------  dale matrix generator + simulator
+runs on PM w/o image, just load python
+
+
+
+= = = = =   OLD = = = = = = = 
+Deplyting software - for now as root
+Must be repeated for each image start
+
+
+cd pyuoi
+pip install -e .[dev]
+
+cd ../toys/
+
+mkdir 2025_UoI-VAR
+cd  2025_UoI-VAR
+git clone -b uoi-var https://github.com/BouchardLab/pyuoi.git
+
+# build podman image using podman build  -f ubu24-casual-net.dockerfile -t balewski/casual-net:p1 .
+
+
+# start image
+
+IMG=balewski/casual-net:p1
+WORK_DIR=/2025_UoI-VAR
+DATA_VAULT=/shared_volumes/dataVault2025
+
+eval podman run -it  \
+    --volume /shared_volumes/$WORK_DIR:$WORK_DIR \
+    --volume $DATA_VAULT:/dataVault2025 \
+    --workdir $WORK_DIR \
+    $IMG /bin/bash
+
+# inside image
+cd ../pyuoi
+cd /2025_UoI-VAR
+pip install -e .[dev]
+
+python <<EOF
+import matplotlib
+import matplotlib.pyplot as plt
+import numpy as np
+
+from sklearn.linear_model import LinearRegression, LassoCV
+
+from pyuoi.linear_model import *
+from pyuoi.datasets import make_linear_regression
+import pandas as pd
+from scipy.linalg import solve_discrete_lyapunov
+from examples.var_utils import *
+from tqdm import tqdm
+EOF
+
+
+
+