Add pre commit

.github/workflows/pre-commit.yaml

@@ -0,0 +1,15 @@
+name: pre-commit
+
+on:
+  - push
+  - pull_request
+
+jobs:
+  pre-commit:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+      - uses: actions/setup-python@v5
+        with:
+          python-version: "3.12"
+      - uses: pre-commit/action@v3.0.1

.pre-commit-config.yaml

@@ -0,0 +1,41 @@
+default_language_version:
+  python: python3
+exclude: '\.(tsv|fasta|gb)$|^ingest/vendored/'
+repos:
+  - repo: https://github.com/pre-commit/sync-pre-commit-deps
+    rev: v0.0.1
+    hooks:
+      - id: sync-pre-commit-deps
+  - repo: https://github.com/shellcheck-py/shellcheck-py
+    rev: v0.10.0.1
+    hooks:
+      - id: shellcheck
+  - repo: https://github.com/rhysd/actionlint
+    rev: v1.6.27
+    hooks:
+      - id: actionlint
+        entry: env SHELLCHECK_OPTS='--exclude=SC2027' actionlint
+  - repo: https://github.com/pre-commit/pre-commit-hooks
+    rev: v4.6.0
+    hooks:
+      - id: trailing-whitespace
+      - id: check-ast
+      - id: check-case-conflict
+      - id: check-docstring-first
+      - id: check-json
+      - id: check-executables-have-shebangs
+      - id: check-merge-conflict
+      - id: check-shebang-scripts-are-executable
+      - id: check-symlinks
+      - id: check-toml
+      - id: check-yaml
+      - id: destroyed-symlinks
+      - id: detect-private-key
+      - id: end-of-file-fixer
+      - id: fix-byte-order-marker
+  - repo: https://github.com/astral-sh/ruff-pre-commit
+    # Ruff version.
+    rev: v0.4.6
+    hooks:
+      # Run the linter.
+      - id: ruff

README.md

@@ -5,3 +5,16 @@ Phylogenies of human seasonal coronaviruses.
 Built starting from the [Nextstrain pathogen repository template][].
 
 [Nextstrain pathogen repository template]: https://github.com/nextstrain/pathogen-repo-guide/
+
+## Working on this repo
+
+This repo is configured to use [pre-commit](https://pre-commit.com).
+If you will be writing new code or otherwise working within this repo,
+please do the following to get started:
+
+1. install `pre-commit` by running either `python -m pip install
+   pre-commit` or `brew install pre-commit`, depending on your
+   preferred package management solution
+2. install the local git hooks by running `pre-commit install` from
+   the root of the repo
+3. get to coding!

ingest/config/hku1/annotations.tsv

@@ -1,6 +1,6 @@
-# Manually curated annotations TSV file		
-# The TSV should not have a header and should have exactly three columns:		
-"# id to match existing metadata, field name, and field value"		
-"# If there are multiple annotations for the same id and field, then the last value is used"		
-# Lines starting with '#' are treated as comments		
-# Any '#' after the field value are treated as comments.		
+# Manually curated annotations TSV file
+# The TSV should not have a header and should have exactly three columns:
+# "id to match existing metadata, field name, and field value"
+# "If there are multiple annotations for the same id and field, then the last value is used"
+# Lines starting with '#' are treated as comments
+# Any '#' after the field value are treated as comments.

ingest/config/nl63/annotations.tsv

@@ -1,55 +1,55 @@
-# Manually curated annotations TSV file		
-# The TSV should not have a header and should have exactly three columns:		
-"# id to match existing metadata, field name, and field value"		
-"# If there are multiple annotations for the same id and field, then the last value is used"		
-# Lines starting with '#' are treated as comments		
-# Any '#' after the field value are treated as comments.		
-KF530114.1	country	USA
-KF530113.1	country	USA
-KF530112.1	country	USA
-KF530111.1	country	USA
-KF530110.1	country	USA
-KF530109.1	country	USA
-KF530108.1	country	USA
-KF530107.1	country	USA
-KF530106.1	country	USA
-KF530105.1	country	USA
-KF530104.1	country	USA
-JQ900260.1	country	USA
-JQ900259.1	country	USA
-JQ900258.1	country	USA
-JQ900257.1	country	USA
-JQ900256.1	country	USA
-JQ900255.1	country	USA
-JQ771060.1	country	USA
-JQ771059.1	country	USA
-JQ771058.1	country	USA
-JQ771057.1	country	USA
-JQ771056.1	country	USA
-JQ771055.1	country	USA
-JQ765575.1	country	USA
-JQ765574.1	country	USA
-JQ765573.1	country	USA
-JQ765572.1	country	USA
-JQ765571.1	country	USA
-JQ765570.1	country	USA
-JQ765569.1	country	USA
-JQ765568.1	country	USA
-JQ765567.1	country	USA
-JQ765566.1	country	USA
-JQ765565.1	country	USA
-JQ765564.1	country	USA
-JQ765563.1	country	USA
-LC756668.1	country	Japan
-LC720428.1	country	Japan
-LC687402.1	country	Japan
-LC687401.1	country	Japan
-LC687397.1	country	Japan
-LC687396.1	country	Japan
-LC687395.1	country	Japan
-LC687394.1	country	Japan
-LC654455.1	country	Japan
-LC488390.2	country	Japan
-LC488389.2	country	Japan
-JX104161.1	country	China
-OR266947.1	country	Russia
+# Manually curated annotations TSV file
+# The TSV should not have a header and should have exactly three columns:
+# "id to match existing metadata, field name, and field value"
+# "If there are multiple annotations for the same id and field, then the last value is used"
+# Lines starting with '#' are treated as comments
+# Any '#' after the field value are treated as comments.
+KF530114.1	country	USA
+KF530113.1	country	USA
+KF530112.1	country	USA
+KF530111.1	country	USA
+KF530110.1	country	USA
+KF530109.1	country	USA
+KF530108.1	country	USA
+KF530107.1	country	USA
+KF530106.1	country	USA
+KF530105.1	country	USA
+KF530104.1	country	USA
+JQ900260.1	country	USA
+JQ900259.1	country	USA
+JQ900258.1	country	USA
+JQ900257.1	country	USA
+JQ900256.1	country	USA
+JQ900255.1	country	USA
+JQ771060.1	country	USA
+JQ771059.1	country	USA
+JQ771058.1	country	USA
+JQ771057.1	country	USA
+JQ771056.1	country	USA
+JQ771055.1	country	USA
+JQ765575.1	country	USA
+JQ765574.1	country	USA
+JQ765573.1	country	USA
+JQ765572.1	country	USA
+JQ765571.1	country	USA
+JQ765570.1	country	USA
+JQ765569.1	country	USA
+JQ765568.1	country	USA
+JQ765567.1	country	USA
+JQ765566.1	country	USA
+JQ765565.1	country	USA
+JQ765564.1	country	USA
+JQ765563.1	country	USA
+LC756668.1	country	Japan
+LC720428.1	country	Japan
+LC687402.1	country	Japan
+LC687401.1	country	Japan
+LC687397.1	country	Japan
+LC687396.1	country	Japan
+LC687395.1	country	Japan
+LC687394.1	country	Japan
+LC654455.1	country	Japan
+LC488390.2	country	Japan
+LC488389.2	country	Japan
+JX104161.1	country	China
+OR266947.1	country	Russia

ingest/config/oc43/annotations.tsv

@@ -1,6 +1,6 @@
-# Manually curated annotations TSV file		
-# The TSV should not have a header and should have exactly three columns:		
-"# id to match existing metadata, field name, and field value"		
-"# If there are multiple annotations for the same id and field, then the last value is used"		
-# Lines starting with '#' are treated as comments		
-# Any '#' after the field value are treated as comments.		
+# Manually curated annotations TSV file
+# The TSV should not have a header and should have exactly three columns:
+# "id to match existing metadata, field name, and field value"
+# "If there are multiple annotations for the same id and field, then the last value is used"
+# Lines starting with '#' are treated as comments
+# Any '#' after the field value are treated as comments.

ingest/rules/curate.smk

@@ -46,12 +46,13 @@ rule concat_geolocation_rules:
         """
 
 
-def format_field_map(field_map: dict[str,str]) -> str:
+def format_field_map(field_map: dict[str, str]) -> str:
     """
     Format dict to `"key1"="value1" "key2=value2"...` for use in shell commands.
     """
     return " ".join([f'"{key}"="{value}"' for key, value in field_map.items()])
 
+
 # This curate pipeline is based on existing pipelines for pathogen repos using NCBI data.
 # You may want to add and/or remove steps from the pipeline for custom metadata
 # curation for your pathogen. Note that the curate pipeline is streaming NDJSON

ingest/rules/fetch_from_ncbi.smk

@@ -4,6 +4,7 @@ and outputs them as a single NDJSON file that can be directly fed into the
 curation pipeline.
 """
 
+
 rule fetch_ncbi_dataset_package:
     params:
         ncbi_taxon_id=lambda wildcards: config[wildcards.virus]["ncbi_taxon_id"],

ingest/vendored/transform-genbank-location

@@ -6,6 +6,7 @@ GenBank by verifying that the 'database' field has a value of "GenBank" or "RefS
 
 Outputs the modified record to stdout.
 """
+
 import json
 from sys import stdin, stdout
 

ingest/vendored/transform-strain-names

@@ -5,6 +5,7 @@ stdin. Adds a 'strain' field to the record if it does not already exist.
 
 Outputs the modified records to stdout.
 """
+
 import argparse
 import json
 import re

phylogenetic/config/229e/dropped_strains.txt

@@ -1,3 +1,3 @@
 OK662398.1
 OK625404.1
-MZ712010.1
+MZ712010.1

phylogenetic/config/229e/reference.fasta

@@ -454,4 +454,4 @@ ATCTAGTCTTATACACAATGGTAAGCCAGTGGTAGTAAAGGTATAAGAAATTTGCTACTA
 TGTTACTGAACCTAGGTGAACGCTAGTATAACTCATTACAAATGTGCTGGAGTAATCAAA
 GATCGCATTGACGAGCCAACAATGGAAGAGCCAGTCATTTGTCTTGAGACCTATCTAGTT
 AGTAACTGCTAATGGAACGGTTTCGATATGGATACACAAAAAAAAAAAAAAAAAAAAAAA
-AAAAAAAAAAAAAAAAA
+AAAAAAAAAAAAAAAAA

phylogenetic/config/229e/reference.gb

@@ -439,7 +439,7 @@ FEATURES             Location/Qualifiers
                      AGVVANGVKAKGYPQFAELVPSTAAMLFDSHIVSKESGNTVVLTFTTRVTVPKDHPHL
                      GKFLEELNAFTREMQQHPLLNPSALEFNPSQTSPATAEPVRDEVSIETDIIDEVN"
      3'UTR           26856..27317
-ORIGIN      
+ORIGIN
         1 acttaagtac cttatctatc tacagataga aaagttgctt tttagacttt gtgtctactt
        61 ttctcaacta aacgaaattt ttgctatggc cggcatcttt gatgctggag tcgtagtgta
       121 attgaaattt catttgggtt gcaacagttt ggaagcaagt gctgtgtgtc ctagtctaag
@@ -896,4 +896,4 @@ ORIGIN
     27181 gatcgcattg acgagccaac aatggaagag ccagtcattt gtcttgagac ctatctagtt
     27241 agtaactgct aatggaacgg tttcgatatg gatacacaaa aaaaaaaaaa aaaaaaaaaa
     27301 aaaaaaaaaa aaaaaaa
-//
+//

phylogenetic/config/hku1/reference.fasta

@@ -497,4 +497,4 @@ CTTAATGAGAATGAATCCTAATTCGACACTAGGTGGTAACCCCTCGCTATTATTCGGAAT
 AGGACACTCTCTATCAGAATGAATTCTTGCTGTAATAACAGATAGAGTAGGTTGTTACAG
 ACTATATATTAATTAGTAGAAATTTTATATTTAGACATTTGATTGTTAGAGTAGTTATAA
 GGTTTAGCTGTAGTATAAACGCCTCCGGGAAGAGCTATCAATTGTAGTGTTTAATATATA
-TATTAGTATATGATTGAAATTAATTATAGCCTTTTGGAGGAATTAC
+TATTAGTATATGATTGAAATTAATTATAGCCTTTTGGAGGAATTAC

phylogenetic/config/hku1/reference.gb

@@ -41,7 +41,7 @@ REFERENCE   4  (bases 1 to 29926)
             Hong Kong, China
 COMMENT     REVIEWED REFSEQ: This record has been curated by NCBI staff. The
             reference sequence was derived from AY597011.
-            
+
             On Jan 23, 2006 this sequence version replaced NC_006577.1.
             The mature peptides were designated nsp1 through nsp16 following
             the nomenclature used in the MHV-A59 and SARS-CoV RefSeqs
@@ -608,7 +608,7 @@ FEATURES             Location/Qualifiers
                      QLMVNKSSCYRDGISTISVPAHMPMHPMVNPSKGSSGLLITKLTLLLPPMFRQGILLL
                      KKLSLLGFRLVRFCLKAIMLKAQEGLLLIVDQVHVLNHVDPIIVH"
      3'UTR           28960..29926
-ORIGIN      
+ORIGIN
         1 gagtttgagc gattgacgtt cgtaccgtct atcagcttac gatctcttgt cagatctcat
        61 taaatctaaa ctttttaaac aagattccct gttatccatg cttgtgagtg tggtttaatc
       121 ataatcttgt attttacttt ccacactttt catctctctg ccagtgacgt gttggttgtc
@@ -1108,4 +1108,4 @@ ORIGIN
     29761 actatatatt aattagtaga aattttatat ttagacattt gattgttaga gtagttataa
     29821 ggtttagctg tagtataaac gcctccggga agagctatca attgtagtgt ttaatatata
     29881 tattagtata tgattgaaat taattatagc cttttggagg aattac
-//
+//

phylogenetic/config/nl63/reference.fasta

@@ -458,4 +458,4 @@ ATTAGTTGCAACCCCATGCGTTTAGCGCATGATAAGGGTTTAGTCTTACACACAATGGTA
 GGCCAGTGATAGTAAAGTGTAAGTAATTTGCTATCATATTAACATGTCTAGAGGAAAGTC
 AGAACTTTTTCTGTTTGTGTTGTTGGAGTACTTAAAGATCGCATAGGCGCGCCAACAATG
 GAAGAGCCAACAACATATCTAAAAATGTTTTGTCTGGTACTTGTTAATGATATTGTTTTT
-GATATGGATACAC
+GATATGGATACAC

phylogenetic/config/nl63/reference.gb

@@ -40,7 +40,7 @@ REFERENCE   4  (bases 1 to 27553)
             Amsterdam 1105 AZ, The Netherlands
 COMMENT     PROVISIONAL REFSEQ: This record has not yet been subject to final
             NCBI review. The reference sequence is identical to AY567487.
-            
+
             On Jun 24, 2004 this sequence version replaced NC_005831.1.
             COMPLETENESS: full length.
 FEATURES             Location/Qualifiers
@@ -385,7 +385,7 @@ FEATURES             Location/Qualifiers
      3'UTR           27267..27553
                      /inference="non-experimental evidence, no additional
                      details recorded"
-ORIGIN      
+ORIGIN
         1 cttaaagaat ttttctatct atagatagag aattttctta tttagacttt gtgtctactc
        61 ttctcaacta aacgaaattt ttctagtgct gtcatttgtt atggcagtcc tagtgtaatt
       121 gaaatttcgt caagtttgta aactggttag gcaagtgttg tattttctgt gtctaagcac
@@ -846,4 +846,4 @@ ORIGIN
     27421 agaacttttt ctgtttgtgt tgttggagta cttaaagatc gcataggcgc gccaacaatg
     27481 gaagagccaa caacatatct aaaaatgttt tgtctggtac ttgttaatga tattgttttt
     27541 gatatggata cac
-//
+//

phylogenetic/config/oc43/reference.fasta

@@ -511,4 +511,4 @@ TAACCCCTCGCAGAAAAGTCGAGATAAGGCACTCTCTATCAGAATGGATGTCTTGCTGCT
 ATAATAGATAGAGAAGGTTATAGCAGACTATAGATTAATTAGTTGAAAGTTTTGTGTTGT
 AATGTATAGTGTTGGAGAAAGTGAAAGACTTGCGGAAGTAATTGCCGACAAGTGCCCAAG
 GGAAGAGCCAGCATGTTAAGTTACCACCCAGTAATTAGTAAATGAATGAAGTTAATTATG
-GCCAATTGGAAGAATCAC
+GCCAATTGGAAGAATCAC

phylogenetic/config/oc43/reference.gb

@@ -298,7 +298,7 @@ FEATURES             Location/Qualifiers
                      /translation="MATSVNCCHDGIFTIWEQDRMLKTSTAPILTESTGSLATRLMSI
                      PRLTLSIGTQVAMRLFRLGFRLARYSLRVTILKAQEGLLLIPDLLRAHPAEPLVQDRV
                      VEPILAIEPLPLV"
-ORIGIN      
+ORIGIN
         1 gattgtgagc gatttgcgtg cgtgcatccc gcttcactga tctcttgtta gatctttttg
        61 taatctaaac tttataaaaa catccactcc ctgtaatcta tgcttgtggg cgtagatttt
       121 tcatagtggt gtttatattc atttctgctg ttaacagctt tcagccaggg acgtgttgta
@@ -812,4 +812,4 @@ ORIGIN
     30601 aatgtatagt gttggagaaa gtgaaagact tgcggaagta attgccgaca agtgcccaag
     30661 ggaagagcca gcatgttaag ttaccaccca gtaattagta aatgaatgaa gttaattatg
     30721 gccaattgga agaatcac
-//
+//

phylogenetic/rules/annotate_phylogeny.smk

@@ -1,6 +1,6 @@
 """
 This part of the workflow runs ancestral reconstruction and
-creates additonal annotations for the phylogenetic tree. It expects a
+creates additional annotations for the phylogenetic tree. It expects a
 single Newick tree and any additional files needed to create the
 annotations such as the aligned FASTA and metadata file.