Modernize phylogenetic build [#2]

.github/workflows/pre-commit.yaml

@@ -10,5 +10,5 @@ jobs:
       - uses: actions/checkout@v4
       - uses: actions/setup-python@v5
         with:
-          python-version: "3.12"
+          python-version: "3.11"
       - uses: pre-commit/[email protected]

.gitignore

@@ -1,19 +1,26 @@
 # pipeline output #
-benchmarks/
-data/
-logs/
-results/
+ingest/benchmarks
+ingest/data
+ingest/logs
+ingest/results
+phylogenetic/auspice
+phylogenetic/benchmarks
+phylogenetic/logs
+phylogenetic/results
 
-# snakemake output #
+
+# Snakemake state dir #
 .snakemake
 snakemake_log
 
+
 # For Python #
 *.pyc
 .tox/
 .cache/
 __pycache__/*
 
+
 # OS generated files #
 .DS_Store
 ._*

.pre-commit-config.yaml

@@ -1,7 +1,6 @@
 default_language_version:
   python: python3
-# TODO remove _LEGACY once it's gone
-exclude: '\.(tsv|fasta|gb)$|^ingest/vendored/|^_LEGACY'
+exclude: '\.(tsv|fasta|gb)$|^ingest/vendored/|'
 repos:
   - repo: https://github.com/pre-commit/sync-pre-commit-deps
     rev: v0.0.1

README.md

@@ -3,21 +3,19 @@
 <!-- ##TODO## finish updating this -->
 
 This repository is in the process of being upgraded to follow the
-[pathogen repo
-guide](https://github.com/nextstrain/pathogen-repo-guide/).
+[pathogen repo guide][].
 
 ## Installation
 
-Follow the [standard installation
-instructions](https://docs.nextstrain.org/en/latest/install.html) for
-Nextstrain's suite of software tools.
+Follow the [standard installation instructions][] for Nextstrain's
+suite of software tools.
 
 ## Working on this repo
 
-This repo is configured to use [pre-commit](https://pre-commit.com),
-to help automatically catch common coding errors and syntax issues
-with changes before they are committed to the repo.
-.
+This repo is configured to use [pre-commit][] to help automatically
+catch common coding errors and syntax issues with changes before they
+are committed to the repo.
+
 If you will be writing new code or otherwise working within this repo,
 please do the following to get started:
 
@@ -32,3 +30,7 @@ please do the following to get started:
 Note that these pre-commit checks are also run in a GitHub Action when
 changes are pushed to GitHub, so correcting issues locally will
 prevent extra cycles of correction.
+
+[pathogen repo guide]: https://github.com/nextstrain/pathogen-repo-guide/)
+[pre-commit]: https://pre-commit.com
+[standard installation instructions]: https://docs.nextstrain.org/en/latest/install.html