Change path of the obitools pkg

Former-commit-id: 311cbf8df3b990b393c6f4885d62e74564423b65
2025-12-08 08:40:26 +00:00 · 2023-11-29 12:14:37 +01:00
parent 72ad84c2d4
commit 8d77cc4133
122 changed files with 1004 additions and 544 deletions
--- a/pkg/obiformats/batch_of_files_reader.go
+++ b/pkg/obiformats/batch_of_files_reader.go
@@ -3,8 +3,8 @@ package obiformats
 import (
 	"log"

-	"git.metabarcoding.org/lecasofts/go/obitools/pkg/obiiter"
-	"git.metabarcoding.org/lecasofts/go/obitools/pkg/obiutils"
+	"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obiiter"
+	"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obiutils"
 )

 func ReadSequencesBatchFromFiles(filenames []string,
@@ -48,8 +48,6 @@ func ReadSequencesBatchFromFiles(filenames []string,

 				log.Printf("Start reading of file : %s", filename)

-				
-
 				for iter.Next() {
 					batch := iter.Get()
 					batchiter.Push(batch.Reorder(nextCounter()))
--- a/pkg/obiformats/batch_reader_type.go
+++ b/pkg/obiformats/batch_reader_type.go
@@ -1,5 +1,5 @@
 package obiformats

-import "git.metabarcoding.org/lecasofts/go/obitools/pkg/obiiter"
+import "git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obiiter"

 type IBatchReader func(string, ...WithOption) (obiiter.IBioSequence, error)
--- a/pkg/obiformats/csv_writer.go
+++ b/pkg/obiformats/csv_writer.go
@@ -9,10 +9,10 @@ import (
 	"sync"
 	"time"

-	"git.metabarcoding.org/lecasofts/go/obitools/pkg/obiiter"
-	"git.metabarcoding.org/lecasofts/go/obitools/pkg/obioptions"
-	"git.metabarcoding.org/lecasofts/go/obitools/pkg/obiseq"
-	"git.metabarcoding.org/lecasofts/go/obitools/pkg/obiutils"
+	"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obiiter"
+	"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obioptions"
+	"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obiseq"
+	"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obiutils"
 	log "github.com/sirupsen/logrus"
 )

--- a/pkg/obiformats/dispatcher.go
+++ b/pkg/obiformats/dispatcher.go
@@ -10,7 +10,7 @@ import (

 	log "github.com/sirupsen/logrus"

-	"git.metabarcoding.org/lecasofts/go/obitools/pkg/obiiter"
+	"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obiiter"
 )

 type SequenceBatchWriterToFile func(iterator obiiter.IBioSequence,
--- a/pkg/obiformats/ecopcr_read.go
+++ b/pkg/obiformats/ecopcr_read.go
@@ -13,9 +13,9 @@ import (

 	log "github.com/sirupsen/logrus"

-	"git.metabarcoding.org/lecasofts/go/obitools/pkg/obiiter"
-	"git.metabarcoding.org/lecasofts/go/obitools/pkg/obiseq"
-	"git.metabarcoding.org/lecasofts/go/obitools/pkg/obiutils"
+	"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obiiter"
+	"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obiseq"
+	"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obiutils"
 )

 type __ecopcr_file__ struct {
--- a/pkg/obiformats/embl_read.go
+++ b/pkg/obiformats/embl_read.go
@@ -10,9 +10,9 @@ import (

 	log "github.com/sirupsen/logrus"

-	"git.metabarcoding.org/lecasofts/go/obitools/pkg/obiiter"
-	"git.metabarcoding.org/lecasofts/go/obitools/pkg/obiseq"
-	"git.metabarcoding.org/lecasofts/go/obitools/pkg/obiutils"
+	"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obiiter"
+	"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obiseq"
+	"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obiutils"
 )

 var _FileChunkSize = 1 << 28
--- a/pkg/obiformats/empty_file.go
+++ b/pkg/obiformats/empty_file.go
@@ -1,6 +1,6 @@
 package obiformats

-import "git.metabarcoding.org/lecasofts/go/obitools/pkg/obiiter"
+import "git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obiiter"

 func ReadEmptyFile(options ...WithOption) (obiiter.IBioSequence, error) {
 	out := obiiter.MakeIBioSequence()
--- a/pkg/obiformats/fastaseq_read.go
+++ b/pkg/obiformats/fastaseq_read.go
@@ -7,10 +7,10 @@ import (
 	"os"
 	"path"

-	"git.metabarcoding.org/lecasofts/go/obitools/pkg/obiiter"
-	"git.metabarcoding.org/lecasofts/go/obitools/pkg/obioptions"
-	"git.metabarcoding.org/lecasofts/go/obitools/pkg/obiseq"
-	"git.metabarcoding.org/lecasofts/go/obitools/pkg/obiutils"
+	"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obiiter"
+	"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obioptions"
+	"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obiseq"
+	"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obiutils"
 	"golang.org/x/exp/slices"

 	log "github.com/sirupsen/logrus"
--- a/pkg/obiformats/fastqseq_read.go
+++ b/pkg/obiformats/fastqseq_read.go
@@ -6,10 +6,10 @@ import (
 	"os"
 	"path"

-	"git.metabarcoding.org/lecasofts/go/obitools/pkg/obiiter"
-	"git.metabarcoding.org/lecasofts/go/obitools/pkg/obioptions"
-	"git.metabarcoding.org/lecasofts/go/obitools/pkg/obiseq"
-	"git.metabarcoding.org/lecasofts/go/obitools/pkg/obiutils"
+	"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obiiter"
+	"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obioptions"
+	"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obiseq"
+	"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obiutils"
 	log "github.com/sirupsen/logrus"
 	"golang.org/x/exp/slices"
 )
--- a/pkg/obiformats/fastseq_header.go
+++ b/pkg/obiformats/fastseq_header.go
@@ -3,8 +3,8 @@ package obiformats
 import (
 	"strings"

-	"git.metabarcoding.org/lecasofts/go/obitools/pkg/obiiter"
-	"git.metabarcoding.org/lecasofts/go/obitools/pkg/obiseq"
+	"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obiiter"
+	"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obiseq"
 )

 // ParseGuessedFastSeqHeader parses the guessed fast sequence header.
--- a/pkg/obiformats/fastseq_interface.go
+++ b/pkg/obiformats/fastseq_interface.go
@@ -1,5 +1,5 @@
 package obiformats

-import "git.metabarcoding.org/lecasofts/go/obitools/pkg/obiseq"
+import "git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obiseq"

 type FormatHeader func(sequence *obiseq.BioSequence) string
--- a/pkg/obiformats/fastseq_json_header.go
+++ b/pkg/obiformats/fastseq_json_header.go
@@ -6,8 +6,8 @@ import (

 	log "github.com/sirupsen/logrus"

-	"git.metabarcoding.org/lecasofts/go/obitools/pkg/obiseq"
-	"git.metabarcoding.org/lecasofts/go/obitools/pkg/obiutils"
+	"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obiseq"
+	"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obiutils"
 	"github.com/goccy/go-json"
 )

--- a/pkg/obiformats/fastseq_obi_header.go
+++ b/pkg/obiformats/fastseq_obi_header.go
@@ -9,8 +9,8 @@ import (
 	"strconv"
 	"strings"

-	"git.metabarcoding.org/lecasofts/go/obitools/pkg/obiseq"
-	"git.metabarcoding.org/lecasofts/go/obitools/pkg/obiutils"
+	"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obiseq"
+	"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obiutils"
 	"github.com/goccy/go-json"
 )

--- a/pkg/obiformats/fastseq_read.go
+++ b/pkg/obiformats/fastseq_read.go
@@ -14,10 +14,10 @@ import (

 	log "github.com/sirupsen/logrus"

-	"git.metabarcoding.org/lecasofts/go/obitools/pkg/obiiter"
-	"git.metabarcoding.org/lecasofts/go/obitools/pkg/obioptions"
-	"git.metabarcoding.org/lecasofts/go/obitools/pkg/obiseq"
-	"git.metabarcoding.org/lecasofts/go/obitools/pkg/obiutils"
+	"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obiiter"
+	"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obioptions"
+	"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obiseq"
+	"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obiutils"
 )

 func _FastseqReader(source string,
--- a/pkg/obiformats/fastseq_write_fasta.go
+++ b/pkg/obiformats/fastseq_write_fasta.go
@@ -12,9 +12,9 @@ import (

 	log "github.com/sirupsen/logrus"

-	"git.metabarcoding.org/lecasofts/go/obitools/pkg/obiiter"
-	"git.metabarcoding.org/lecasofts/go/obitools/pkg/obiseq"
-	"git.metabarcoding.org/lecasofts/go/obitools/pkg/obiutils"
+	"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obiiter"
+	"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obiseq"
+	"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obiutils"
 )

 // min returns the minimum of two integers.
--- a/pkg/obiformats/fastseq_write_fastq.go
+++ b/pkg/obiformats/fastseq_write_fastq.go
@@ -10,10 +10,10 @@ import (

 	log "github.com/sirupsen/logrus"

-	"git.metabarcoding.org/lecasofts/go/obitools/pkg/obiiter"
-	"git.metabarcoding.org/lecasofts/go/obitools/pkg/obioptions"
-	"git.metabarcoding.org/lecasofts/go/obitools/pkg/obiseq"
-	"git.metabarcoding.org/lecasofts/go/obitools/pkg/obiutils"
+	"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obiiter"
+	"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obioptions"
+	"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obiseq"
+	"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obiutils"
 )

 // The function FormatFastq takes a BioSequence object, a quality shift value, and a header formatter
--- a/pkg/obiformats/genbank_read.go
+++ b/pkg/obiformats/genbank_read.go
@@ -11,9 +11,9 @@ import (

 	log "github.com/sirupsen/logrus"

-	"git.metabarcoding.org/lecasofts/go/obitools/pkg/obiiter"
-	"git.metabarcoding.org/lecasofts/go/obitools/pkg/obiseq"
-	"git.metabarcoding.org/lecasofts/go/obitools/pkg/obiutils"
+	"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obiiter"
+	"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obiseq"
+	"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obiutils"
 )

 type gbstate int
--- a/pkg/obiformats/json_writer.go
+++ b/pkg/obiformats/json_writer.go
@@ -11,9 +11,9 @@ import (
 	"sync"
 	"time"

-	"git.metabarcoding.org/lecasofts/go/obitools/pkg/obiiter"
-	"git.metabarcoding.org/lecasofts/go/obitools/pkg/obiseq"
-	"git.metabarcoding.org/lecasofts/go/obitools/pkg/obiutils"
+	"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obiiter"
+	"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obiseq"
+	"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obiutils"
 	log "github.com/sirupsen/logrus"
 )

--- a/pkg/obiformats/ncbitaxdump/read.go
+++ b/pkg/obiformats/ncbitaxdump/read.go
@@ -12,7 +12,7 @@ import (

 	log "github.com/sirupsen/logrus"

-	"git.metabarcoding.org/lecasofts/go/obitools/pkg/obitax"
+	"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obitax"
 )

 func loadNodeTable(reader io.Reader, taxonomy *obitax.Taxonomy) {
--- a/pkg/obiformats/ngsfilter_read.go
+++ b/pkg/obiformats/ngsfilter_read.go
@@ -6,8 +6,8 @@ import (
 	"io"
 	"strings"

-	"git.metabarcoding.org/lecasofts/go/obitools/pkg/obingslibrary"
-	"git.metabarcoding.org/lecasofts/go/obitools/pkg/obiseq"
+	"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obingslibrary"
+	"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obiseq"
 )

 func _readLines(reader io.Reader) []string {
--- a/pkg/obiformats/options.go
+++ b/pkg/obiformats/options.go
@@ -1,8 +1,8 @@
 package obiformats

 import (
-	"git.metabarcoding.org/lecasofts/go/obitools/pkg/obioptions"
-	"git.metabarcoding.org/lecasofts/go/obitools/pkg/obiseq"
+	"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obioptions"
+	"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obiseq"
 )

 type __options__ struct {
--- a/pkg/obiformats/universal_read.go
+++ b/pkg/obiformats/universal_read.go
@@ -11,8 +11,8 @@ import (

 	log "github.com/sirupsen/logrus"

-	"git.metabarcoding.org/lecasofts/go/obitools/pkg/obiiter"
-	"git.metabarcoding.org/lecasofts/go/obitools/pkg/obiutils"
+	"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obiiter"
+	"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obiutils"
 )

 // OBIMimeTypeGuesser is a function that takes an io.Reader as input and guesses the MIME type of the data.
--- a/pkg/obiformats/universal_write.go
+++ b/pkg/obiformats/universal_write.go
@@ -7,7 +7,7 @@ import (

 	log "github.com/sirupsen/logrus"

-	"git.metabarcoding.org/lecasofts/go/obitools/pkg/obiiter"
+	"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obiiter"
 )

 func WriteSequence(iterator obiiter.IBioSequence,