From d2e95c44d63dfef7033891676129ee4ac394d764 Mon Sep 17 00:00:00 2001 From: gwct Date: Thu, 22 Oct 2026 11:36:33 -0400 Subject: [PATCH] Use absolute GitHub links in README so they work on PyPI --- README.md | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/README.md b/README.md index 5be30cb..5db5f97 100644 --- a/README.md +++ b/README.md @@ -20,7 +20,7 @@ This project was developed with significant assistance from large language model `mafutils/lib/bgzf.py` is vendored from [Biopython](https://biopython.org/) (BSD 3-Clause License option) rather than pulled in as a dependency — see the -notice at the top of that file and [`THIRD_PARTY_LICENSES.md`](THIRD_PARTY_LICENSES.md) +notice at the top of that file and [`THIRD_PARTY_LICENSES.md`](https://github.com/harvardinformatics/mafutils/blob/main/THIRD_PARTY_LICENSES.md) for full attribution and license text. ## Installation @@ -110,7 +110,7 @@ If you plan to use `--processes > 1` against compressed input, compress with **No extra dependency for bgzip:** BGZF support is vendored in `mafutils/lib/bgzf.py` rather than depending on the `biopython` package — -see `DEVELOPMENT.md` for why, and [`THIRD_PARTY_LICENSES.md`](THIRD_PARTY_LICENSES.md) +see `DEVELOPMENT.md` for why, and [`THIRD_PARTY_LICENSES.md`](https://github.com/harvardinformatics/mafutils/blob/main/THIRD_PARTY_LICENSES.md) for attribution. ## Index Integrity @@ -297,7 +297,7 @@ bounding box over chunks that are separated, on both strands, or on different scaffolds. For background on these classes, filtering recipes, and an example of building -a per-species BED, see [docs/fetch-outputs.md](docs/fetch-outputs.md). +a per-species BED, see [docs/fetch-outputs.md](https://github.com/harvardinformatics/mafutils/blob/main/docs/fetch-outputs.md). ### `maf_fetch_summary.tsv` @@ -538,4 +538,4 @@ verdict. Exit codes: ## Notes For development setup (installing from a source checkout), running the test -suite, and internal implementation notes, see [`DEVELOPMENT.md`](DEVELOPMENT.md). +suite, and internal implementation notes, see [`DEVELOPMENT.md`](https://github.com/harvardinformatics/mafutils/blob/main/DEVELOPMENT.md).