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style: fix gofmt drift and gate formatting in CI #46

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Merged
thanhleviet merged 2 commits into from
Aug 5, 2026
Merged

style: fix gofmt drift and gate formatting in CI #46

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8a663bd
style: apply gofmt to five drifted files
thanhleviet Aug 5, 2026
37992f4
ci: check formatting in the lint job
thanhleviet Aug 5, 2026
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14 changes: 13 additions & 1 deletion .github/workflows/ci.yml
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Original file line number Diff line number Diff line change
Expand Up @@ -82,7 +82,19 @@ jobs:

- uses: actions/setup-go@v5
with:
go-version: "1.23"
# gofmt is a standalone binary and does not follow the toolchain
# switch that go.mod's `go 1.25.0` triggers for go commands, so this
# job pins the version the module requires.
go-version: "1.25"

- name: Format check
run: |
unformatted=$(gofmt -l .)
if [ -n "$unformatted" ]; then
echo "gofmt -w . is needed for:"
echo "$unformatted"
exit 1
fi

- name: Vet
run: go vet ./...
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14 changes: 7 additions & 7 deletions internal/cli/download_cmd.go
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Expand Up @@ -14,14 +14,14 @@ import (

func newDownloadCmd() *cobra.Command {
var (
fromFile string
urlsFile string
singleURL string
outputDir string
parallel int
fromFile string
urlsFile string
singleURL string
outputDir string
parallel int
maxSamples int
dryRun bool
force bool
dryRun bool
force bool
)

cmd := &cobra.Command{
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2 changes: 1 addition & 1 deletion internal/cli/query_cmd.go
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Expand Up @@ -14,8 +14,8 @@ import (

cols "github.com/allthebacteria/atb-cli/internal/columns"
idx "github.com/allthebacteria/atb-cli/internal/index"
pq "github.com/allthebacteria/atb-cli/internal/parquet"
"github.com/allthebacteria/atb-cli/internal/output"
pq "github.com/allthebacteria/atb-cli/internal/parquet"
"github.com/allthebacteria/atb-cli/internal/query"
"github.com/allthebacteria/atb-cli/internal/suggest"
)
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56 changes: 28 additions & 28 deletions internal/index/query.go
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Expand Up @@ -72,40 +72,40 @@ type QueryParams struct {

// userColToSQL maps user-facing column names to SQLite column names.
var userColToSQL = map[string]string{
"sample_accession": "sample_accession",
"run_accession": "run_accession",
"assembly_accession": "assembly_accession",
"sylph_species": "sylph_species",
"hq_filter": "hq_filter",
"asm_fasta_on_osf": "asm_fasta_on_osf",
"dataset": "dataset",
"scientific_name": "scientific_name",
"aws_url": "aws_url",
"osf_tarball_url": "osf_tarball_url",
"total_length": "total_length",
"number": "num_contigs",
"N50": "n50",
"N90": "n90",
"sample_accession": "sample_accession",
"run_accession": "run_accession",
"assembly_accession": "assembly_accession",
"sylph_species": "sylph_species",
"hq_filter": "hq_filter",
"asm_fasta_on_osf": "asm_fasta_on_osf",
"dataset": "dataset",
"scientific_name": "scientific_name",
"aws_url": "aws_url",
"osf_tarball_url": "osf_tarball_url",
"total_length": "total_length",
"number": "num_contigs",
"N50": "n50",
"N90": "n90",
"Completeness_General": "completeness",
"Contamination": "contamination",
"Genome_Size": "genome_size",
"GC_Content": "gc_content",
"mlst_scheme": "mlst_scheme",
"mlst_st": "mlst_st",
"mlst_status": "mlst_status",
"mlst_score": "mlst_score",
"mlst_alleles": "mlst_alleles",
"Contamination": "contamination",
"Genome_Size": "genome_size",
"GC_Content": "gc_content",
"mlst_scheme": "mlst_scheme",
"mlst_st": "mlst_st",
"mlst_status": "mlst_status",
"mlst_score": "mlst_score",
"mlst_alleles": "mlst_alleles",
}

// sqlToUserCol is the reverse mapping, used when building result maps.
var sqlToUserCol = map[string]string{
"num_contigs": "number",
"n50": "N50",
"n90": "N90",
"completeness": "Completeness_General",
"num_contigs": "number",
"n50": "N50",
"n90": "N90",
"completeness": "Completeness_General",
"contamination": "Contamination",
"genome_size": "Genome_Size",
"gc_content": "GC_Content",
"genome_size": "Genome_Size",
"gc_content": "GC_Content",
}

// allSQLCols is the full list of columns in SELECT order.
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8 changes: 4 additions & 4 deletions internal/query/executor_test.go
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Expand Up @@ -294,10 +294,10 @@ func TestParseCollectionDate(t *testing.T) {
return t
}
cases := []struct {
in string
wantOK bool
wantStart time.Time
wantEnd time.Time
in string
wantOK bool
wantStart time.Time
wantEnd time.Time
}{
{"2020-05-15", true, d("2020-05-15"), d("2020-05-15")},
{"2020-05", true, d("2020-05-01"), d("2020-05-31")},
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6 changes: 3 additions & 3 deletions internal/selfupdate/selfupdate.go
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Expand Up @@ -14,9 +14,9 @@ import (
)

const (
repo = "allthebacteria/atb-cli"
checkInterval = 24 * time.Hour
stateFileName = "update-state.json"
repo = "allthebacteria/atb-cli"
checkInterval = 24 * time.Hour
stateFileName = "update-state.json"
)

type Release struct {
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