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Add progress bar configuration and conditional display

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This commit introduces a new configuration module `obidefault` to manage progress bar settings, allowing users to disable progress bars via a `--no-progressbar` option. It updates various packages to conditionally display progress bars based on this new configuration, improving user experience by providing control over progress bar output. The changes also include improvements to progress bar handling in several packages, ensuring they are only displayed when appropriate (e.g., when stderr is a terminal and stdout is not piped).
This commit is contained in:
Eric Coissac
2026-02-08 16:13:27 +01:00
parent b2d16721f0
commit 1a28d5ed64
11 changed files with 193 additions and 125 deletions
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34
pkg/obicorazick/worker.go
View File

@@ -14,35 +14,39 @@ func AhoCorazickWorker(slot string, patterns []string) obiseq.SeqWorker {
sizebatch:=10000000
nmatcher := len(patterns) / sizebatch + 1
log.Infof("Building AhoCorasick %d matcher for %d patterns in slot %s",
log.Infof("Building AhoCorasick %d matcher for %d patterns in slot %s",
nmatcher, len(patterns), slot)
if nmatcher == 0 {
log.Errorln("No patterns provided")
}
matchers := make([]*ahocorasick.Matcher, nmatcher)
ieme := make(chan int)
ieme := make(chan int)
mutex := &sync.WaitGroup{}
npar := min(obidefault.ParallelWorkers(), nmatcher)
mutex.Add(npar)
pbopt := make([]progressbar.Option, 0, 5)
pbopt = append(pbopt,
progressbar.OptionSetWriter(os.Stderr),
progressbar.OptionSetWidth(15),
progressbar.OptionShowCount(),
progressbar.OptionShowIts(),
progressbar.OptionSetDescription("Building AhoCorasick matcher..."),
)
var bar *progressbar.ProgressBar
if obidefault.ProgressBar() {
pbopt := make([]progressbar.Option, 0, 5)
pbopt = append(pbopt,
progressbar.OptionSetWriter(os.Stderr),
progressbar.OptionSetWidth(15),
progressbar.OptionShowCount(),
progressbar.OptionShowIts(),
progressbar.OptionSetDescription("Building AhoCorasick matcher..."),
)
bar := progressbar.NewOptions(nmatcher, pbopt...)
bar.Add(0)
bar = progressbar.NewOptions(nmatcher, pbopt...)
}
builder := func() {
for i := range ieme {
for i := range ieme {
matchers[i] = ahocorasick.CompileStrings(patterns[i*sizebatch:min((i+1)*sizebatch,len(patterns))])
bar.Add(1)
if bar != nil {
bar.Add(1)
}
}
mutex.Done()
}

19
pkg/obidefault/progressbar.go Normal file
View File

@@ -0,0 +1,19 @@
package obidefault
var __no_progress_bar__ = false
func ProgressBar() bool {
return !__no_progress_bar__
}
func NoProgressBar() bool {
return __no_progress_bar__
}
func SetNoProgressBar(b bool) {
__no_progress_bar__ = b
}
func NoProgressBarPtr() *bool {
return &__no_progress_bar__
}

14
pkg/obiiter/speed.go
View File

@@ -5,18 +5,30 @@ import (
"os"
"time"
"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obidefault"
"github.com/schollz/progressbar/v3"
)
func (iterator IBioSequence) Speed(message string, size ...int) IBioSequence {
// If the STDERR is redicted and doesn't end up to a terminal
// If the progress bar is disabled via --no-progressbar option
if !obidefault.ProgressBar() {
return iterator
}
// If the STDERR is redirected and doesn't end up to a terminal
// No progress bar is printed.
o, _ := os.Stderr.Stat()
if (o.Mode() & os.ModeCharDevice) != os.ModeCharDevice {
return iterator
}
// If stdout is piped, no progress bar is printed.
oo, _ := os.Stdout.Stat()
if (oo.Mode() & os.ModeNamedPipe) == os.ModeNamedPipe {
return iterator
}
newIter := MakeIBioSequence()
newIter.Add(1)

24
pkg/obikmer/kmermap.go
View File

@@ -5,6 +5,7 @@ import (
"sort"
"unsafe"
"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obidefault"
"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obifp"
"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obilog"
"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obiseq"
@@ -267,20 +268,23 @@ func NewKmerMap[T obifp.FPUint[T]](
}
n := len(sequences)
pbopt := make([]progressbar.Option, 0, 5)
pbopt = append(pbopt,
progressbar.OptionSetWriter(os.Stderr),
progressbar.OptionSetWidth(15),
progressbar.OptionShowCount(),
progressbar.OptionShowIts(),
progressbar.OptionSetDescription("Indexing kmers"),
)
var bar *progressbar.ProgressBar
if obidefault.ProgressBar() {
pbopt := make([]progressbar.Option, 0, 5)
pbopt = append(pbopt,
progressbar.OptionSetWriter(os.Stderr),
progressbar.OptionSetWidth(15),
progressbar.OptionShowCount(),
progressbar.OptionShowIts(),
progressbar.OptionSetDescription("Indexing kmers"),
)
bar := progressbar.NewOptions(n, pbopt...)
bar = progressbar.NewOptions(n, pbopt...)
}
for i, sequence := range sequences {
kmap.Push(sequence, maxoccurs)
if i%100 == 0 {
if bar != nil && i%100 == 0 {
bar.Add(100)
}
}

114
pkg/obitools/obiclean/graph.go
View File

@@ -13,6 +13,7 @@ import (
log "github.com/sirupsen/logrus"
"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obialign"
"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obidefault"
"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obiutils"
"github.com/schollz/progressbar/v3"
)
@@ -69,16 +70,18 @@ func EmpiricalDistCsv(filename string, data [][]Ratio, compressed bool) {
}
defer destfile.Close()
pbopt := make([]progressbar.Option, 0, 5)
pbopt = append(pbopt,
progressbar.OptionSetWriter(os.Stderr),
progressbar.OptionSetWidth(15),
progressbar.OptionShowIts(),
progressbar.OptionSetPredictTime(true),
progressbar.OptionSetDescription("[Save CSV stat ratio file]"),
)
bar := progressbar.NewOptions(len(data), pbopt...)
var bar *progressbar.ProgressBar
if obidefault.ProgressBar() {
pbopt := make([]progressbar.Option, 0, 5)
pbopt = append(pbopt,
progressbar.OptionSetWriter(os.Stderr),
progressbar.OptionSetWidth(15),
progressbar.OptionShowIts(),
progressbar.OptionSetPredictTime(true),
progressbar.OptionSetDescription("[Save CSV stat ratio file]"),
)
bar = progressbar.NewOptions(len(data), pbopt...)
}
fmt.Fprintln(destfile, "Sample,Origin_id,Origin_status,Origin,Mutant,Origin_Weight,Mutant_Weight,Origin_Count,Mutant_Count,Position,Origin_length,A,C,G,T")
for code, dist := range data {
@@ -101,7 +104,9 @@ func EmpiricalDistCsv(filename string, data [][]Ratio, compressed bool) {
ratio.T,
)
}
bar.Add(1)
if bar != nil {
bar.Add(1)
}
}
}
@@ -116,7 +121,7 @@ func Gml(seqs *[]*seqPCR, sample string, statThreshold int) string {
directed 1
{{range $index, $data:= .}}
{{ if or $data.Edges (gt $data.SonCount 0)}}
node [ id {{$index}}
node [ id {{$index}}
graphics [
type "{{ Shape $data.Count }}"
fill "{{ if and (gt $data.SonCount 0) (not $data.Edges)}}#0000FF{{ else }}#00FF00{{ end }}"
@@ -130,15 +135,15 @@ func Gml(seqs *[]*seqPCR, sample string, statThreshold int) string {
{{range $index, $data:= .}}
{{range $i, $edge:= $data.Edges}}
edge [ source {{$index}}
target {{$edge.Father}}
edge [ source {{$index}}
target {{$edge.Father}}
color "{{ if gt (index $data.Edges $i).Dist 1 }}#FF0000{{ else }}#00FF00{{ end }}"
label "{{(index $data.Edges $i).Dist}}"
]
{{ end }}
{{ end }}
]
]
`
tmpl, err := digraphTpl.Funcs(template.FuncMap{
@@ -181,16 +186,18 @@ func SaveGMLGraphs(dirname string,
}
}
pbopt := make([]progressbar.Option, 0, 5)
pbopt = append(pbopt,
progressbar.OptionSetWriter(os.Stderr),
progressbar.OptionSetWidth(15),
progressbar.OptionShowIts(),
progressbar.OptionSetPredictTime(true),
progressbar.OptionSetDescription("[Save GML Graph files]"),
)
bar := progressbar.NewOptions(len(samples), pbopt...)
var bar *progressbar.ProgressBar
if obidefault.ProgressBar() {
pbopt := make([]progressbar.Option, 0, 5)
pbopt = append(pbopt,
progressbar.OptionSetWriter(os.Stderr),
progressbar.OptionSetWidth(15),
progressbar.OptionShowIts(),
progressbar.OptionSetPredictTime(true),
progressbar.OptionSetDescription("[Save GML Graph files]"),
)
bar = progressbar.NewOptions(len(samples), pbopt...)
}
for name, seqs := range samples {
@@ -204,7 +211,9 @@ func SaveGMLGraphs(dirname string,
file.WriteString(Gml(seqs, name, statThreshold))
file.Close()
bar.Add(1)
if bar != nil {
bar.Add(1)
}
}
}
@@ -495,37 +504,44 @@ func BuildSeqGraph(samples map[string]*[]*seqPCR,
npairs += nseq * (nseq - 1) / 2
}
pbopt := make([]progressbar.Option, 0, 5)
pbopt = append(pbopt,
progressbar.OptionSetWriter(os.Stderr),
progressbar.OptionSetWidth(15),
progressbar.OptionShowIts(),
progressbar.OptionSetPredictTime(true),
progressbar.OptionSetDescription("[One error graph]"),
)
bar := progressbar.NewOptions(npairs, pbopt...)
for _, seqs := range samples {
np := buildSamplePairs(seqs, workers)
bar.Add(np)
}
if maxError > 1 {
pbopt = make([]progressbar.Option, 0, 5)
var bar *progressbar.ProgressBar
if obidefault.ProgressBar() {
pbopt := make([]progressbar.Option, 0, 5)
pbopt = append(pbopt,
progressbar.OptionSetWriter(os.Stderr),
progressbar.OptionSetWidth(15),
progressbar.OptionShowIts(),
progressbar.OptionSetPredictTime(true),
progressbar.OptionSetDescription("[Adds multiple errors]"),
progressbar.OptionSetDescription("[One error graph]"),
)
bar = progressbar.NewOptions(npairs, pbopt...)
}
for _, seqs := range samples {
np := extendSimilarityGraph(seqs, maxError, workers)
for _, seqs := range samples {
np := buildSamplePairs(seqs, workers)
if bar != nil {
bar.Add(np)
}
}
if maxError > 1 {
if obidefault.ProgressBar() {
pbopt := make([]progressbar.Option, 0, 5)
pbopt = append(pbopt,
progressbar.OptionSetWriter(os.Stderr),
progressbar.OptionSetWidth(15),
progressbar.OptionShowIts(),
progressbar.OptionSetPredictTime(true),
progressbar.OptionSetDescription("[Adds multiple errors]"),
)
bar = progressbar.NewOptions(npairs, pbopt...)
}
for _, seqs := range samples {
np := extendSimilarityGraph(seqs, maxError, workers)
if bar != nil {
bar.Add(np)
}
}
}
}

5
pkg/obitools/obiconvert/options.go
View File

@@ -31,7 +31,6 @@ var __output_in_json__ = false
var __output_fastjson_format__ = false
var __output_fastobi_format__ = false
var __no_progress_bar__ = false
var __skip_empty__ = false
var __skip_on_error__ = false
@@ -82,7 +81,7 @@ func InputOptionSet(options *getoptions.GetOpt) {
}
func OutputModeOptionSet(options *getoptions.GetOpt, compressed bool) {
options.BoolVar(&__no_progress_bar__, "no-progressbar", false,
options.BoolVar(obidefault.NoProgressBarPtr(), "no-progressbar", obidefault.NoProgressBar(),
options.Description("Disable the progress bar printing"))
if compressed {
@@ -233,7 +232,7 @@ func CLIProgressBar() bool {
oo, _ := os.Stdout.Stat()
toPipe := (oo.Mode() & os.ModeNamedPipe) == os.ModeNamedPipe
return onTerminal && !toPipe && !__no_progress_bar__
return onTerminal && !toPipe && obidefault.ProgressBar()
}
func CLIOutPutFileName() string {

4
pkg/obitools/obiconvert/sequence_reader.go
View File

@@ -210,9 +210,7 @@ func CLIReadBioSequences(filenames ...string) (obiiter.IBioSequence, error) {
}
if CLIProgressBar() {
iterator = iterator.Speed("Reading sequences")
}
iterator = iterator.Speed("Reading sequences")
return iterator, nil
}

4
pkg/obitools/obicsv/obicsv.go
View File

@@ -12,9 +12,7 @@ import (
func CLIWriteSequenceCSV(iterator obiiter.IBioSequence,
terminalAction bool, filenames ...string) *obiitercsv.ICSVRecord {
if obiconvert.CLIProgressBar() {
iterator = iterator.Speed("Writing CSV")
}
iterator = iterator.Speed("Writing CSV")
opts := make([]WithOption, 0, 10)

50
pkg/obitools/obilandmark/obilandmark.go
View File

@@ -42,16 +42,19 @@ func MapOnLandmarkSequences(library obiseq.BioSequenceSlice, landmark_idx []int,
seqworld := obiutils.Make2DArray[float64](library_size, n_landmark)
pbopt := make([]progressbar.Option, 0, 5)
pbopt = append(pbopt,
progressbar.OptionSetWriter(os.Stderr),
progressbar.OptionSetWidth(15),
progressbar.OptionShowCount(),
progressbar.OptionShowIts(),
progressbar.OptionSetDescription("[Sequence mapping]"),
)
var bar *progressbar.ProgressBar
if obidefault.ProgressBar() {
pbopt := make([]progressbar.Option, 0, 5)
pbopt = append(pbopt,
progressbar.OptionSetWriter(os.Stderr),
progressbar.OptionSetWidth(15),
progressbar.OptionShowCount(),
progressbar.OptionShowIts(),
progressbar.OptionSetDescription("[Sequence mapping]"),
)
bar := progressbar.NewOptions(library_size, pbopt...)
bar = progressbar.NewOptions(library_size, pbopt...)
}
waiting := sync.WaitGroup{}
waiting.Add(nworkers)
@@ -66,7 +69,9 @@ func MapOnLandmarkSequences(library obiseq.BioSequenceSlice, landmark_idx []int,
match, lalign := obialign.FastLCSScore(landmark, seq, -1, &buffer)
coord[j] = float64(lalign - match)
}
bar.Add(1)
if bar != nil {
bar.Add(1)
}
}
waiting.Done()
}
@@ -170,23 +175,26 @@ func CLISelectLandmarkSequences(iterator obiiter.IBioSequence) obiiter.IBioSeque
taxa.Set(i, taxon)
}
pbopt := make([]progressbar.Option, 0, 5)
pbopt = append(pbopt,
progressbar.OptionSetWriter(os.Stderr),
progressbar.OptionSetWidth(15),
progressbar.OptionShowCount(),
progressbar.OptionShowIts(),
progressbar.OptionSetDescription("[Sequence Indexing]"),
)
var bar2 *progressbar.ProgressBar
if obidefault.ProgressBar() {
pbopt := make([]progressbar.Option, 0, 5)
pbopt = append(pbopt,
progressbar.OptionSetWriter(os.Stderr),
progressbar.OptionSetWidth(15),
progressbar.OptionShowCount(),
progressbar.OptionShowIts(),
progressbar.OptionSetDescription("[Sequence Indexing]"),
)
bar := progressbar.NewOptions(len(library), pbopt...)
bar2 = progressbar.NewOptions(len(library), pbopt...)
}
for i, seq := range library {
idx := obirefidx.GeomIndexSesquence(i, library, taxa, taxo)
seq.SetOBITagGeomRefIndex(idx)
if i%10 == 0 {
bar.Add(10)
if bar2 != nil && i%10 == 0 {
bar2.Add(10)
}
}
}

25
pkg/obitools/obirefidx/famlilyindexing.go
View File

@@ -207,16 +207,19 @@ func IndexFamilyDB(iterator obiiter.IBioSequence) obiiter.IBioSequence {
log.Infof("Done. Found %d clusters", clusters.Len())
pbopt := make([]progressbar.Option, 0, 5)
pbopt = append(pbopt,
progressbar.OptionSetWriter(os.Stderr),
progressbar.OptionSetWidth(15),
progressbar.OptionShowCount(),
progressbar.OptionShowIts(),
progressbar.OptionSetDescription("Cluster indexing"),
)
var bar *progressbar.ProgressBar
if obidefault.ProgressBar() {
pbopt := make([]progressbar.Option, 0, 5)
pbopt = append(pbopt,
progressbar.OptionSetWriter(os.Stderr),
progressbar.OptionSetWidth(15),
progressbar.OptionShowCount(),
progressbar.OptionShowIts(),
progressbar.OptionSetDescription("Cluster indexing"),
)
bar := progressbar.NewOptions(len(clusters), pbopt...)
bar = progressbar.NewOptions(len(clusters), pbopt...)
}
limits := make(chan [2]int)
waiting := sync.WaitGroup{}
@@ -233,7 +236,9 @@ func IndexFamilyDB(iterator obiiter.IBioSequence) obiiter.IBioSequence {
for i := l[0]; i < l[1]; i++ {
idx := IndexSequence(i, clusters, &kcluster, taxa, taxonomy)
clusters[i].SetOBITagRefIndex(idx)
bar.Add(1)
if bar != nil {
bar.Add(1)
}
}
}

25
pkg/obitools/obirefidx/obirefidx.go
View File

@@ -239,16 +239,19 @@ func IndexReferenceDB(iterator obiiter.IBioSequence) obiiter.IBioSequence {
log.Info("done")
pbopt := make([]progressbar.Option, 0, 5)
pbopt = append(pbopt,
progressbar.OptionSetWriter(os.Stderr),
progressbar.OptionSetWidth(15),
progressbar.OptionShowCount(),
progressbar.OptionShowIts(),
progressbar.OptionSetDescription("[Sequence Processing]"),
)
var bar *progressbar.ProgressBar
if obidefault.ProgressBar() {
pbopt := make([]progressbar.Option, 0, 5)
pbopt = append(pbopt,
progressbar.OptionSetWriter(os.Stderr),
progressbar.OptionSetWidth(15),
progressbar.OptionShowCount(),
progressbar.OptionShowIts(),
progressbar.OptionSetDescription("[Sequence Processing]"),
)
bar := progressbar.NewOptions(len(references), pbopt...)
bar = progressbar.NewOptions(len(references), pbopt...)
}
limits := make(chan [2]int)
indexed := obiiter.MakeIBioSequence()
@@ -267,7 +270,9 @@ func IndexReferenceDB(iterator obiiter.IBioSequence) obiiter.IBioSequence {
iref := references[i].Copy()
iref.SetOBITagRefIndex(idx)
sl = append(sl, iref)
bar.Add(1)
if bar != nil {
bar.Add(1)
}
}
indexed.Push(obiiter.MakeBioSequenceBatch(source, l[0]/10, sl))
}