Skip to content

Diff: Revision v2 vs v1 #22

New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Open
moinfar wants to merge 2 commits into
base: revision_v1
Choose a base branch
from
Open

Diff: Revision v2 vs v1 #22

Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
2 commits
Select commit Hold shift + click to select a range
f0d5020
Changes for revision v2
Sep 3, 2025
b80a43b
revert back commented runs
Sep 3, 2025
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
104 changes: 104 additions & 0 deletions envs/scmgca_pip_req_freeze.txt
View file
Open in desktop
Original file line number Diff line number Diff line change
@@ -0,0 +1,104 @@
absl-py==0.15.0
# anndata==0.9.2
astunparse==1.6.3
backcall==0.2.0
cached-property==1.5.2
cachetools==4.2.4
certifi==2021.10.8
charset-normalizer==2.0.12
cloudpickle==1.3.0
cycler==0.11.0
#dataclasses==0.8
decorator==4.4.2
dm-tree==0.1.7
flatbuffers==1.12
future==0.18.2
gast==0.3.3
get_version==2.1
google-auth==1.28.0
google-auth-oauthlib==0.4.4
google-pasta==0.2.0
grpcio==1.34.1
# h5py==3.11.0
hyperopt==0.2.5
idna==3.3
igraph==0.9.11
importlib-metadata==4.8.3
ipython==7.16.3
ipython-genutils==0.2.0
jedi==0.17.2
jgraph==0.2.1
joblib==1.1.0
keras-nightly==2.5.0.dev2021032900
Keras-Preprocessing==1.1.2
kiwisolver==1.3.1
legacy-api-wrap==1.2
leidenalg==0.8.8
llvmlite==0.34.0
lxml==4.8.0
Markdown==3.3.6
matplotlib==3.3.4
natsort==8.1.0
networkx==2.5.1
numba==0.51.2
numexpr==2.7.3
numpy==1.18.1
oauthlib==3.1.0
opt-einsum==3.3.0
packaging==21.3
pandas==1.1.5
parso==0.7.1
patsy==0.5.1
pexpect==4.8.0
pickleshare==0.7.5
Pillow==8.4.0
prompt-toolkit==3.0.29
protobuf==3.19.4
ptyprocess==0.7.0
py4j==0.10.9.7
pyasn1==0.4.8
pyasn1-modules==0.2.8
Pygments==2.12.0
pynndescent==0.5.6
pyparsing==3.0.8
python-dateutil==2.8.2
python-igraph==0.9.11
pytz==2022.1
requests==2.27.1
requests-oauthlib==1.3.1
rsa==4.8
scanpy==1.6.0
scikit-learn==0.24.2
scipy==1.4.1
seaborn==0.11.1
setuptools-scm==6.4.2
sinfo==0.3.4
six==1.15.0
spektral==0.6.1
statsmodels==0.12.2
stdlib-list==0.8.0
tables==3.6.1
tensorboard==2.4.1
tensorboard-plugin-wit==1.8.0
tensorflow==2.3.0
tensorflow-estimator==2.3.0
tensorflow-gpu==2.3.0
tensorflow-probability==0.11.0
termcolor==1.1.0
texttable==1.6.4
threadpoolctl==3.1.0
tomli==1.2.3
tqdm==4.41.1
traitlets==4.3.3
typing-extensions==3.7.4.3
umap-learn==0.4.2
urllib3==1.26.9
wcwidth==0.2.5
Werkzeug==2.0.3
wrapt==1.12.1
xlrd==1.2.0
zipp==3.6.0

seml
#scib-metrics==0.5.1
scMGCA==1.0.7
44 changes: 44 additions & 0 deletions envs/update_requirements.sh
View file
Open in desktop
Original file line number Diff line number Diff line change
@@ -0,0 +1,44 @@
#!/bin/bash

# Check if the requirements file is provided
if [ -z "$1" ]; then
echo "Usage: $0 <path_to_requirements.txt>"
exit 1
fi

REQUIREMENTS_FILE=$1

# Check if the file exists
if [ ! -f "$REQUIREMENTS_FILE" ]; then
echo "Error: File $REQUIREMENTS_FILE does not exist."
exit 1
fi

# Create a temporary file to store updated requirements
UPDATED_FILE=$(mktemp)

# Get the list of installed packages with versions
PIP_FREEZE=$(pip freeze)

# Process each line in the requirements file
while read -r PACKAGE; do
if [[ -z "$PACKAGE" || "$PACKAGE" == \#* ]]; then
# Keep comments and empty lines unchanged
echo "$PACKAGE" >> "$UPDATED_FILE"
else
# Extract the package version from pip freeze
VERSION=$(echo "$PIP_FREEZE" | grep "^${PACKAGE}==" || true)
if [ -n "$VERSION" ]; then
echo "$VERSION" >> "$UPDATED_FILE"
else
echo "# $PACKAGE (not found)" >> "$UPDATED_FILE"
fi
fi
done < "$REQUIREMENTS_FILE"

# Overwrite the original file with the updated content
mv "$UPDATED_FILE" "$REQUIREMENTS_FILE"

echo "Updated $REQUIREMENTS_FILE with versions from pip freeze."


45 changes: 30 additions & 15 deletions notebooks/eval/cleaned/eval_summary.py
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -174,15 +174,19 @@ def get_top_runs(res,param_opt_vals=param_opt_vals,params_opt_map=params_opt_map
# Parse param that was optimised
res = prepare_results(res)

# %%
res['params_opt']

# %%
with open("/home/moinfar/io/csi/tmp/pancreas_metrics.pkl", "wb") as f:
pkl.dump(res, f)

# %%
for path in path_integration + res[res.params_opt.replace(params_opt_map).astype(str).isin(['sysvi', 'sysvi_stable'])].index:
print(path + "/args.pkl", end=" ")
print(path + "/loss*", end=" ")
print(path + "/scib*", end=" ")
print(path, end=" ")
# print(path + "/args.pkl", end=" ")
# print(path + "/loss*", end=" ")
# print(path + "/scib*", end=" ")

# %% [markdown]
# ### Best runs
Expand Down Expand Up @@ -231,9 +235,10 @@ def get_top_runs(res,param_opt_vals=param_opt_vals,params_opt_map=params_opt_map

# %%
for path in path_integration + res[res.params_opt.replace(params_opt_map).astype(str).isin(['vamp_cycle', 'sysvi', 'sysvi_stable'])].index:
print(path + "/args.pkl", end=" ")
print(path + "/loss*", end=" ")
print(path + "/scib*", end=" ")
print(path, end=" ")
# print(path + "/args.pkl", end=" ")
# print(path + "/loss*", end=" ")
# print(path + "/scib*", end=" ")

# %% [markdown]
# ### Best runs
Expand Down Expand Up @@ -288,9 +293,10 @@ def get_top_runs(res,param_opt_vals=param_opt_vals,params_opt_map=params_opt_map

# %%
for path in path_integration + res[res.params_opt.replace(params_opt_map).astype(str).isin(['vamp_cycle', 'sysvi', 'sysvi_stable'])].index:
print(path + "/args.pkl", end=" ")
print(path + "/loss*", end=" ")
print(path + "/scib*", end=" ")
print(path, end=" ")
# print(path + "/args.pkl", end=" ")
# print(path + "/loss*", end=" ")
# print(path + "/scib*", end=" ")

# %% [markdown]
# ### Best runs
Expand Down Expand Up @@ -337,6 +343,13 @@ def get_top_runs(res,param_opt_vals=param_opt_vals,params_opt_map=params_opt_map
with open("/home/moinfar/io/csi/tmp/retatlas_metrics.pkl", "wb") as f:
pkl.dump(res, f)

# %%
for path in path_integration + res[res.params_opt.replace(params_opt_map).astype(str).isin(['sysvi', 'sysvi_stable'])].index:
print(path, end=" ")
# print(path + "/args.pkl", end=" ")
# print(path + "/loss*", end=" ")
# print(path + "/scib*", end=" ")

# %% [markdown]
# ### Best runs

Expand Down Expand Up @@ -384,9 +397,10 @@ def get_top_runs(res,param_opt_vals=param_opt_vals,params_opt_map=params_opt_map

# %%
for path in path_integration + res[res.params_opt.replace(params_opt_map).astype(str).isin(['vamp_cycle', 'sysvi', 'sysvi_stable'])].index:
print(path + "/args.pkl", end=" ")
print(path + "/loss*", end=" ")
print(path + "/scib*", end=" ")
print(path, end=" ")
# print(path + "/args.pkl", end=" ")
# print(path + "/loss*", end=" ")
# print(path + "/scib*", end=" ")

# %% [markdown]
# ### Best runs
Expand Down Expand Up @@ -439,9 +453,10 @@ def get_top_runs(res,param_opt_vals=param_opt_vals,params_opt_map=params_opt_map

# %%
for path in path_integration + res[res.params_opt.replace(params_opt_map).astype(str).isin(['vamp_cycle', 'sysvi', 'sysvi_stable'])].index:
print(path + "/args.pkl", end=" ")
print(path + "/loss*", end=" ")
print(path + "/scib*", end=" ")
print(path, end=" ")
# print(path + "/args.pkl", end=" ")
# print(path + "/loss*", end=" ")
# print(path + "/scib*", end=" ")

# %% [markdown]
# ### Best runs
Expand Down
2 changes: 2 additions & 0 deletions notebooks/eval/cleaned/params_opt_maps.py
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -42,6 +42,8 @@
'harmonypy_theta':'harmonypy_theta',
'sysvi_vamp_cyc_z_distance_cycle_weight_2': 'z_distance_cycle_weight',
'sysvi_vamp_cyc_z_distance_cycle_weight_2_stable': 'z_distance_cycle_weight',
'adv_kappa': 'kappa',
'scmgca_w_a': 'scmgca_w_a',
}


Loading