Path forward on IO operations

Closed

#785 opened on Apr 11, 2025 34 comments 0 reactions 0 assignees View on GitHub

Nobody has claimed this yet.

Assessment

Difficulty: 5/5
Estimated time: Over a week
Newbie friendliness: 25/100

Issue type: Refactor
Clarity: Needs clarification
Activity status: Stale
Tech stack: numpy, python
Domain: data

Research direction

Start by reading the existing IO implementation and issue #685, which is identified as a prerequisite for replacing CSV comments with JSON outputs. The issue describes multiple possible passes and a future binary-output path, but names no files or tests; completion criteria would need to be narrowed before implementation.

Written by the indexing model from the issue text.

Description

code cleanup help wanted method outputs

This issue serves to document plans that myself, @bob-carpenter, and @mitzimorris have all discussed in person.

Issues:

the existing IO code re-uses very little between the different services.
the existing IO code is slow.
the existing IO code depends on things like the order of comments in the files.

Steps:

Split IO code into two passes. One pass should ignore all comments and use a fast reader like numpy's fromtxt to read in the draws. This can be used for all services. The second pass should deal with the comments. This will be service-specific. This change can be done any time
Replace the second pass of the above with the newer JSON outputs rather than CSV comments. This requires a minimum supported cmdstan version: #685
The first step could later be replaced with some sort of binary output. This would require upstream Stan changes

Dominant language: Python
Stars: 198
Forks: 81
PR merge metrics: No merged PRs in 30d

Contributor guide

Open the contributing guide

First steps

Read the whole issue, then the project's contributing guide.
Comment on the issue to say you are picking it up — it saves two people doing the same work.
Fork the repository and make your change on a branch.
Open a pull request that references the issue number.

Similar issues

slack-gif-creator: validate_gif() multiplies the last frame's duration by the frame count, so reported duration/fps are wrong (1.0s GIF reported as 1.8s) Open

Difficulty 2/5 1-3 hours Newbie friendliness 75/100

anthropics/skills#1811 · 1 comment · Opened Sep 23, 2026
App fails to start with gradio 6 (allowed by `gradio>=5.49.1`) Open

Difficulty 2/5 1-3 hours Newbie friendliness 75/100

speaches-ai/speaches#678 · Opened Sep 23, 2026
ModuleNotFoundError: No module named 'mcp.server.fastmcp'. Open

bug

Difficulty 2/5 1-3 hours Newbie friendliness 75/100

datalayer/mcp-compose#42 · Opened Sep 23, 2026
import spacy fails with ModuleNotFoundError: No module named 'click' Open

Difficulty 2/5 1-3 hours Newbie friendliness 75/100

conda-forge/spacy-feedstock#177 · Opened Sep 23, 2026
humaneval: extract_function_body corrupts a fenced body-only reply, so the same correct code scores INCORRECT fenced and CORRECT unfenced Open

Difficulty 2/5 1-3 hours Newbie friendliness 70/100

UKGovernmentBEIS/inspect_evals#2523 · Opened Sep 23, 2026

More Python issues