From 77be23126df49d9ea0f3a21d4886fddc7a683587 Mon Sep 17 00:00:00 2001 From: Sande33p Date: Tue, 20 Oct 2026 09:25:53 +0000 Subject: [PATCH] Give the two flagged endpoint URLs a resolving reference The v0.1.0 review (#2) flagged `proxy.alcf.anl.gov:3128` and `rest.kegg.jp/list/organism` as broken links. Both were already backticked code rather than links -- an HTTP proxy endpoint and a REST endpoint -- so neither was link rot, and both correctly fail a browser GET. But a reader hitting them has nothing to follow, and a link scanner has nothing to resolve. Each now cites a page that does resolve, beside the literal value: the ALCF getting-started docs for the proxy, and the KEGG REST API reference for the endpoint. The values themselves stay, because they are configuration a reader needs. Co-Authored-By: Claude Opus 5 --- docs/applications/kegg_curation_implementation_status.md | 3 ++- docs/platforms/running_on_polaris.md | 6 ++++-- 2 files changed, 6 insertions(+), 3 deletions(-) diff --git a/docs/applications/kegg_curation_implementation_status.md b/docs/applications/kegg_curation_implementation_status.md index 647c0a2..c434c78 100644 --- a/docs/applications/kegg_curation_implementation_status.md +++ b/docs/applications/kegg_curation_implementation_status.md @@ -91,7 +91,8 @@ by every stage to read/write its checkpoint file. ## `kegg_rest.py` — KEGG REST API Client -Thin, direct wrapper around `https://rest.kegg.jp`, using `requests` +Thin, direct wrapper around the [KEGG REST API](https://www.kegg.jp/kegg/rest/keggapi.html) +(`https://rest.kegg.jp`), using `requests` directly rather than the `kegg_pull` PyPI package. **Why not `kegg_pull`**: `kegg_pull` 3.2.3 (latest on PyPI as of diff --git a/docs/platforms/running_on_polaris.md b/docs/platforms/running_on_polaris.md index 189c364..7a96591 100644 --- a/docs/platforms/running_on_polaris.md +++ b/docs/platforms/running_on_polaris.md @@ -210,8 +210,10 @@ Training Zone A: 100%|██████| 30/30 [00:31<00:00, 1.02s/it, loss=8.9 Use anchored excludes (`--exclude='/data'`) when staging the repo to Polaris. - **Outbound network is via proxy.** Set - `HTTP_PROXY=http://proxy.alcf.anl.gov:3128` for HF downloads. The - launcher exports these by default; use `--no-proxy` for offline runs. + `HTTP_PROXY=http://proxy.alcf.anl.gov:3128` for HF downloads (an HTTP + proxy endpoint, not a browsable page — see the + [ALCF getting-started docs](https://docs.alcf.anl.gov/polaris/getting-started/)). + The launcher exports these by default; use `--no-proxy` for offline runs. - **Pre-cache HF models.** Compute nodes go through the proxy too, which is rate-limited and intermittently blocks. Download models on a login node first: