From 0ca34ae040a2cabc5c1e26d000f99e113c4e6a6f Mon Sep 17 00:00:00 2001 From: "copilot-swe-agent[bot]" <198982749+Copilot@users.noreply.github.com> Date: Fri, 3 Apr 2026 17:59:14 +0000 Subject: [PATCH 1/2] Initial plan From 17f3c555eccc9cede494b2ed5b38d4041d267546 Mon Sep 17 00:00:00 2001 From: "copilot-swe-agent[bot]" <198982749+Copilot@users.noreply.github.com> Date: Fri, 3 Apr 2026 18:14:55 +0000 Subject: [PATCH 2/2] DM3.2: Add D9 task guide to CONTRIBUTING.md and PR template Agent-Logs-Url: https://github.com/TOTOGT/DM3-lab/sessions/146c3fba-6ca6-4d1f-975d-9f323f6256b5 Co-authored-by: TOTOGT <266586635+TOTOGT@users.noreply.github.com> --- .github/PULL_REQUEST_TEMPLATE.md | 52 +++++++++++++++++++++ CONTRIBUTING.md | 78 +++++++++++++++++++++++++++++++- 2 files changed, 128 insertions(+), 2 deletions(-) create mode 100644 .github/PULL_REQUEST_TEMPLATE.md diff --git a/.github/PULL_REQUEST_TEMPLATE.md b/.github/PULL_REQUEST_TEMPLATE.md new file mode 100644 index 0000000..148fdd2 --- /dev/null +++ b/.github/PULL_REQUEST_TEMPLATE.md @@ -0,0 +1,52 @@ +## D9 Task — PR Checklist + +**Related issue / scoreboard task:** closes # + +**Scoreboard entry:** + +--- + +### What this PR does + + + +--- + +### Checklist + +#### Reproducibility +- [ ] All random seeds are fixed and recorded (pass `--seed ` or equivalent). +- [ ] The exact command used to generate output is pasted below (or in the script header). +- [ ] Output files (`.csv`, `.json`, `.png`) committed to the correct folder (`scripts/out/`, `outputs/`), **or** too large and linked externally with a checksum. + +#### Tests / verification +- [ ] Script runs end-to-end without error on a clean install (`pip install numpy networkx matplotlib`). +- [ ] Numerical results match the expected values stated in the issue (or deviations are explained). +- [ ] Lean proof compiles without `sorry` (if applicable). + +#### Data +- [ ] No raw binary blobs > 10 MB committed; large files use a link + SHA-256 hash. +- [ ] Data sources are cited (FlyWire API URL, paper DOI, etc.). + +#### Formatting (analytic notes) +- [ ] Equations use the agreed LaTeX/Markdown conventions from [CONTRIBUTING.md](https://github.com/TOTOGT/DM3-lab/blob/main/CONTRIBUTING.md). +- [ ] File is named `docs/__.md` (or `.pdf` with matching `.tex` source). + +#### Scoreboard +- [ ] PR title starts with the task ID, e.g. `[D9-42] …`. +- [ ] Scoreboard link or issue reference included above. + +--- + +### Reproduction command + +```bash +# paste the exact command here, e.g.: +# python scripts/collatz_c9_2_sampling.py --N 1000 --M 50 \ +# --window-type dyadic --start 1 --end 1024 \ +# --sample-rate 0.1 --seed 42 --output scripts/out/my_run +``` + +### Notes for reviewers + + diff --git a/CONTRIBUTING.md b/CONTRIBUTING.md index c380021..a90c535 100644 --- a/CONTRIBUTING.md +++ b/CONTRIBUTING.md @@ -1,6 +1,6 @@ # Contributing to AXLE -Thank you for your interest in contributing to the AXLE community! This guide explains how to add files to the repository — including from your **phone or tablet** using the GitHub mobile app. +Thank you for your interest in contributing to the AXLE community! This guide covers both the GitHub file-upload workflow (including from mobile) and the specific conventions for **D9 micro-tasks** — numerical scripts, analytic notes, and reproducible pull requests. --- @@ -61,8 +61,82 @@ You can upload files directly to this repository from your phone without needing --- +## D9 Micro-Task Contributions + +D9 tasks are small, self-contained work items (numerical experiments, analytic notes, Lean proofs) tied to the DM3 scoreboard. Anyone can self-assign a task by commenting on the relevant issue. + +### Running Numerical Scripts + +All scripts live in `/scripts/` and `/simulations/`. Use Python 3.10+. + +**1. Install dependencies** + +```bash +pip install numpy networkx matplotlib +``` + +**2. Run a script** + +```bash +# Example — C9.2 conditional sampling +python scripts/collatz_c9_2_sampling.py \ + --N 1000 --M 50 \ + --window-type dyadic --start 1 --end 1024 \ + --sample-rate 0.1 --seed 42 \ + --output scripts/out/my_run +``` + +Output files (`.csv` and `_summary.json`) are written to `scripts/out/`. Create that directory first if it does not exist: + +```bash +mkdir -p scripts/out +``` + +**3. Reproduce a prior result** + +Always pass `--seed ` to lock the random state. The seed used in any published result must be recorded in the PR description and the corresponding JSON summary file. + +**4. Connectome simulations** + +```bash +python simulations/connectome_loader.py # synthetic fallback, no extra data needed +python simulations/simple_to_operator.py +``` + +Plots are saved to `outputs/` (created automatically). + +--- + +### LaTeX / Formatting Guidelines for Analytic Notes + +Place analytic write-ups in `/docs/` as `.md` files (preferred for version control) or `.pdf` (compiled separately). + +**Markdown with inline math (`.md`)** + +- Use standard GitHub-flavored Markdown. +- Inline math: `` $f(n) = \lfloor n/2 \rfloor$ `` +- Display math: fenced with `$$` on its own line. +- Label every key equation with a bold tag, e.g. `**(Eq. C9.2)**`. + +**LaTeX source (`.tex`)** + +- Keep one `.tex` file per note; compile with `pdflatex` or `lualatex`. +- Use `\label{eq:name}` and `\ref{eq:name}` — never bare equation numbers. +- Preferred packages: `amsmath`, `amssymb`, `hyperref`. +- Avoid custom macros that are not defined in the same file. +- Include a `\bibliographystyle{plain}` entry and a `.bib` file when citing external work. + +**Naming convention** + +``` +docs/__.md +# e.g. docs/collatz_c9_sampling_PG_2026-04.md +``` + +--- + ## Questions? -Open an [Issue](https://github.com/TOTOGT/AXLE/issues) or reach out: +Open an [Issue](https://github.com/TOTOGT/DM3-lab/issues) or reach out: **Contact:** Pablo Grossi | PabloGrossi@hotmail.com | G6 LLC · Newark, NJ · 2026