Update dev docs (#204)

* README: Add links to folders

* Put dev-related sections in contributing guide

… instead of the top-level README (except for the pre-commit.ci badge -
these badges seem to be commonly put at the top of the READMEs for other
repos).

* Remove snakefmt CI job

Snakefmt is now run as a part of pre-commit.ci, so the inclusion here is
redundant.

* Update contributing guide

.github/workflows/ci.yaml

@@ -14,14 +14,3 @@ jobs:
     uses: nextstrain/.github/.github/workflows/pathogen-repo-ci.yaml@4f3074183d6ab612faed84444eefe08a5ded0c69
     with:
       build-dir: phylogenetic
-
-
-  lint:
-    runs-on: ubuntu-latest
-    steps:
-      - uses: actions/checkout@v4
-      - uses: actions/setup-python@v4
-        with:
-          python-version: ~3
-      - run: pip install snakefmt
-      - run: snakefmt --check --compact-diff .

CONTRIBUTING.md

@@ -1,5 +1,25 @@
 # Developer guide
 
+## CI
+
+Checks are automatically run on certain pushed commits for testing and linting
+purposes. Some are defined by [.github/workflows/ci.yaml][] while others are
+configured outside of this repository.
+
+[.github/workflows/ci.yaml]: ./.github/workflows/ci.yaml
+
+## Pre-commit
+
+[pre-commit][] is used for various checks (see [configuration][]).
+
+You can either [install it yourself][] to catch issues before pushing or look
+for the [pre-commit.ci run][] after pushing.
+
+[pre-commit]: https://pre-commit.com/
+[configuration]: ./.pre-commit-config.yaml
+[install it yourself]: https://pre-commit.com/#install
+[pre-commit.ci run]: https://results.pre-commit.ci/repo/github/493877605
+
 ## Snakemake formatting
 
 We use [`snakefmt`](https://github.com/snakemake/snakefmt) to ensure consistency in style across Snakemake files in this project.

README.md

@@ -1,42 +1,14 @@
 # Nextstrain repository for mpox virus
 
+[![pre-commit.ci status](https://results.pre-commit.ci/badge/github/nextstrain/monkeypox/master.svg)](https://results.pre-commit.ci/latest/github/nextstrain/monkeypox/master)
+
 This repository contains two workflows for the analysis of mpox virus (MPXV) data:
 
-- `ingest/` - Download data from GenBank, clean and curate it and upload it to S3
-- `phylogenetic/` - Make phylogenetic trees for nextstrain.org
+- [`ingest/`](./ingest) - Download data from GenBank, clean and curate it and upload it to S3
+- [`phylogenetic/`](./phylogenetic) - Make phylogenetic trees for nextstrain.org
 
 Each folder contains a README.md with more information.
 
-## CI
-
-This repository uses GitHub Actions for CI. The workflows are defined in `.github/workflows/`.
-
-## Development
-
-### Pre-commit
-
-This repository uses [pre-commit](https://pre-commit.com/) to run checks on the code before committing.
-
-To install pre-commit on macOS, run:
-
-```bash
-brew install pre-commit
-```
-
-To install pre-commit on Ubuntu, run:
-
-```bash
-sudo apt install pre-commit
-```
-
-To activate pre-commit, run:
-
-```bash
-pre-commit install
-```
-
-## Development
-
-[![pre-commit.ci status](https://results.pre-commit.ci/badge/github/nextstrain/monkeypox/master.svg)](https://results.pre-commit.ci/latest/github/nextstrain/monkeypox/master)
+## Documentation
 
-This repository can be used with pre-commit to automatically run checks before committing.
+- [Contributor documentation](./CONTRIBUTING.md)