Skip to content

Repo Cleanup & Effiency Gains #57

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
griffinsharps wants to merge 6 commits into
base: main
Choose a base branch
from
Open

Repo Cleanup & Effiency Gains #57

Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
6 commits
Select commit Hold shift + click to select a range
0aab8e4
Added test file to initiate new PR while other work was going on in t…
Jan 7, 2026
5894646
Updated Methodology section
Jan 8, 2026
ab33514
WIP: end-to-end pipeline update to address memory concerns and valida…
Jan 12, 2026
ff7bbd3
updated uv.lock
Jan 12, 2026
76d87b3
.toml and uv.lock updates
Jan 12, 2026
08aa4ad
Stop tracking legacy archive artifacts
Jan 15, 2026
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
12 changes: 12 additions & 0 deletions .gitignore
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -172,3 +172,15 @@ results/
profiles/
docs/*.html
docs/index_files/

# --- Local junk / scratch artifacts (root) ---
sample*.csv
*.log
Untitled
tl_2023_17_bg.zip

# --- Quarantine area (local) ---
archive_quarantine/

# Legacy artifacts (do not track)
archive/
4 changes: 2 additions & 2 deletions analysis/clustering/euclidean_clustering_k_search.py
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -228,7 +228,7 @@ def predict_and_write_assignments_streaming(

pf = pq.ParquetFile(input_path)
out_schema = pf.schema_arrow.append(pa.field("cluster", pa.int32()))
writer = pq.ParquetWriter(output_path, out_schema, compression="zstd")
writer = pq.ParquetWriter(output_path, out_schema, compression="snappy")

k = int(model.n_clusters)
counts = np.zeros(k, dtype=np.int64)
Expand Down Expand Up @@ -273,7 +273,7 @@ def plot_centroids(centroids: np.ndarray, output_path: Path) -> None:
x = np.arange(n_timepoints)
xlabel = "Time Interval"

fig, ax = plt.subplots(figsize=(12, 6))
_fig, ax = plt.subplots(figsize=(12, 6))
for i in range(k):
ax.plot(x, centroids[i], label=f"Cluster {i}", linewidth=2)

Expand Down
Loading
Loading