mirror of
https://github.com/metabarcoding/obitools4.git
synced 2025-06-29 16:20:46 +00:00
Every small changes to include into Release 4.0.4
Former-commit-id: b2a48c5b5c471f072785e02d4bb0f149a09cdf6f
This commit is contained in:
3
Makefile
3
Makefile
@ -45,6 +45,9 @@ obitools: $(patsubst %,$(OBITOOLS_PREFIX)%,$(OBITOOLS))
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update-deps:
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go get -u ./...
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test:
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$(GOTEST) ./...
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man:
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make -C doc man
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obibook:
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@ -2,6 +2,15 @@
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## Latest changes
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### Becareful
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GO 1.21.0 is out, and it includes new functionalities which are used in the OBITools4 code.
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If you use the recommanded method for compiling OBITools on your computer, their is no problem,
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as the script always load the latest GO version. If you rely on you personnal GO install, please
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think to update.
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## August 27th, 2023. Release 4.0.4
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### Bugs
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- Patch a bug in the install-script for correctly follow download redirection.
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@ -13,6 +22,8 @@
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- Comparison algorithms in `obitag` and `obirefidx` take more advantage of the data structure to limit the number of alignments
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actually computed. This increase a bit the speed of both the software. `obirefidx` is nevertheless still too slow
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compared to my expectation.
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- Switch to a parallel version of the gzip library, allowing for high speed compress and
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decompress operation on files.
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### New feature
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32
cmd/obitools/obilandmark/main.go
Normal file
32
cmd/obitools/obilandmark/main.go
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@ -0,0 +1,32 @@
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package main
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import (
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"os"
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log "github.com/sirupsen/logrus"
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"git.metabarcoding.org/lecasofts/go/obitools/pkg/obiiter"
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"git.metabarcoding.org/lecasofts/go/obitools/pkg/obitools/obiconvert"
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"git.metabarcoding.org/lecasofts/go/obitools/pkg/obitools/obilandmark"
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"git.metabarcoding.org/lecasofts/go/obitools/pkg/obioptions"
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)
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func main() {
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optionParser := obioptions.GenerateOptionParser(obilandmark.OptionSet)
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_, args := optionParser(os.Args)
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fs, err := obiconvert.CLIReadBioSequences(args...)
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if err != nil {
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log.Errorf("Cannot open file (%v)", err)
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os.Exit(1)
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}
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indexed := obilandmark.CLISelectLandmarkSequences(fs)
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obiconvert.CLIWriteBioSequences(indexed, true)
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obiiter.WaitForLastPipe()
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}
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@ -53,8 +53,13 @@ func main() {
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references := obitag.CLIRefDB()
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var identified obiiter.IBioSequence
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identified := obitag.CLIAssignTaxonomy(fs,references,taxo)
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if obitag.CLIGeometricMode() {
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identified = obitag.CLIGeomAssignTaxonomy(fs, references, taxo)
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} else {
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identified = obitag.CLIAssignTaxonomy(fs, references, taxo)
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}
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obiconvert.CLIWriteBioSequences(identified, true)
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obiiter.WaitForLastPipe()
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22
go.mod
22
go.mod
@ -6,25 +6,29 @@ require (
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github.com/DavidGamba/go-getoptions v0.27.0
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github.com/PaesslerAG/gval v1.2.2
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github.com/barkimedes/go-deepcopy v0.0.0-20220514131651-17c30cfc62df
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github.com/chen3feng/stl4go v0.1.1
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github.com/daichi-m/go18ds v1.12.1
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github.com/goccy/go-json v0.10.2
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github.com/klauspost/pgzip v1.2.5
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github.com/klauspost/pgzip v1.2.6
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github.com/rrethy/ahocorasick v1.0.0
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github.com/schollz/progressbar/v3 v3.13.1
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github.com/sirupsen/logrus v1.9.0
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github.com/sirupsen/logrus v1.9.3
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github.com/stretchr/testify v1.7.0
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github.com/tevino/abool/v2 v2.1.0
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golang.org/x/exp v0.0.0-20230321023759-10a507213a29
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gonum.org/v1/gonum v0.12.0
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golang.org/x/exp v0.0.0-20230817173708-d852ddb80c63
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gonum.org/v1/gonum v0.14.0
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scientificgo.org/special v0.0.0
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)
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require (
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github.com/chen3feng/stl4go v0.1.1 // indirect
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github.com/klauspost/compress v1.16.3 // indirect
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github.com/mattn/go-runewidth v0.0.14 // indirect
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github.com/davecgh/go-spew v1.1.1 // indirect
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github.com/klauspost/compress v1.16.7 // indirect
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github.com/mattn/go-runewidth v0.0.15 // indirect
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github.com/mitchellh/colorstring v0.0.0-20190213212951-d06e56a500db // indirect
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github.com/pmezard/go-difflib v1.0.0 // indirect
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github.com/rivo/uniseg v0.4.4 // indirect
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github.com/shopspring/decimal v1.3.1 // indirect
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golang.org/x/sys v0.6.0 // indirect
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golang.org/x/term v0.6.0 // indirect
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golang.org/x/sys v0.11.0 // indirect
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golang.org/x/term v0.11.0 // indirect
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gopkg.in/yaml.v3 v3.0.0-20200313102051-9f266ea9e77c // indirect
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)
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30
go.sum
30
go.sum
@ -16,13 +16,14 @@ github.com/davecgh/go-spew v1.1.1/go.mod h1:J7Y8YcW2NihsgmVo/mv3lAwl/skON4iLHjSs
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github.com/goccy/go-json v0.10.2 h1:CrxCmQqYDkv1z7lO7Wbh2HN93uovUHgrECaO5ZrCXAU=
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github.com/goccy/go-json v0.10.2/go.mod h1:6MelG93GURQebXPDq3khkgXZkazVtN9CRI+MGFi0w8I=
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github.com/k0kubun/go-ansi v0.0.0-20180517002512-3bf9e2903213/go.mod h1:vNUNkEQ1e29fT/6vq2aBdFsgNPmy8qMdSay1npru+Sw=
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github.com/klauspost/compress v1.16.3 h1:XuJt9zzcnaz6a16/OU53ZjWp/v7/42WcR5t2a0PcNQY=
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github.com/klauspost/compress v1.16.3/go.mod h1:ntbaceVETuRiXiv4DpjP66DpAtAGkEQskQzEyD//IeE=
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github.com/klauspost/pgzip v1.2.5 h1:qnWYvvKqedOF2ulHpMG72XQol4ILEJ8k2wwRl/Km8oE=
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github.com/klauspost/pgzip v1.2.5/go.mod h1:Ch1tH69qFZu15pkjo5kYi6mth2Zzwzt50oCQKQE9RUs=
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github.com/klauspost/compress v1.16.7 h1:2mk3MPGNzKyxErAw8YaohYh69+pa4sIQSC0fPGCFR9I=
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github.com/klauspost/compress v1.16.7/go.mod h1:ntbaceVETuRiXiv4DpjP66DpAtAGkEQskQzEyD//IeE=
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github.com/klauspost/pgzip v1.2.6 h1:8RXeL5crjEUFnR2/Sn6GJNWtSQ3Dk8pq4CL3jvdDyjU=
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github.com/klauspost/pgzip v1.2.6/go.mod h1:Ch1tH69qFZu15pkjo5kYi6mth2Zzwzt50oCQKQE9RUs=
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github.com/mattn/go-isatty v0.0.17/go.mod h1:kYGgaQfpe5nmfYZH+SKPsOc2e4SrIfOl2e/yFXSvRLM=
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github.com/mattn/go-runewidth v0.0.14 h1:+xnbZSEeDbOIg5/mE6JF0w6n9duR1l3/WmbinWVwUuU=
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github.com/mattn/go-runewidth v0.0.14/go.mod h1:Jdepj2loyihRzMpdS35Xk/zdY8IAYHsh153qUoGf23w=
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github.com/mattn/go-runewidth v0.0.15 h1:UNAjwbU9l54TA3KzvqLGxwWjHmMgBUVhBiTjelZgg3U=
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github.com/mattn/go-runewidth v0.0.15/go.mod h1:Jdepj2loyihRzMpdS35Xk/zdY8IAYHsh153qUoGf23w=
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github.com/mitchellh/colorstring v0.0.0-20190213212951-d06e56a500db h1:62I3jR2EmQ4l5rM/4FEfDWcRD+abF5XlKShorW5LRoQ=
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github.com/mitchellh/colorstring v0.0.0-20190213212951-d06e56a500db/go.mod h1:l0dey0ia/Uv7NcFFVbCLtqEBQbrT4OCwCSKTEv6enCw=
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github.com/pmezard/go-difflib v1.0.0 h1:4DBwDE0NGyQoBHbLQYPwSUPoCMWR5BEzIk/f1lZbAQM=
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@ -36,24 +37,27 @@ github.com/schollz/progressbar/v3 v3.13.1 h1:o8rySDYiQ59Mwzy2FELeHY5ZARXZTVJC7iH
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github.com/schollz/progressbar/v3 v3.13.1/go.mod h1:xvrbki8kfT1fzWzBT/UZd9L6GA+jdL7HAgq2RFnO6fQ=
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github.com/shopspring/decimal v1.3.1 h1:2Usl1nmF/WZucqkFZhnfFYxxxu8LG21F6nPQBE5gKV8=
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github.com/shopspring/decimal v1.3.1/go.mod h1:DKyhrW/HYNuLGql+MJL6WCR6knT2jwCFRcu2hWCYk4o=
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github.com/sirupsen/logrus v1.9.0 h1:trlNQbNUG3OdDrDil03MCb1H2o9nJ1x4/5LYw7byDE0=
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github.com/sirupsen/logrus v1.9.0/go.mod h1:naHLuLoDiP4jHNo9R0sCBMtWGeIprob74mVsIT4qYEQ=
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github.com/sirupsen/logrus v1.9.3 h1:dueUQJ1C2q9oE3F7wvmSGAaVtTmUizReu6fjN8uqzbQ=
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github.com/sirupsen/logrus v1.9.3/go.mod h1:naHLuLoDiP4jHNo9R0sCBMtWGeIprob74mVsIT4qYEQ=
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github.com/stretchr/objx v0.1.0/go.mod h1:HFkY916IF+rwdDfMAkV7OtwuqBVzrE8GR6GFx+wExME=
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github.com/stretchr/testify v1.3.0/go.mod h1:M5WIy9Dh21IEIfnGCwXGc5bZfKNJtfHm1UVUgZn+9EI=
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github.com/stretchr/testify v1.7.0 h1:nwc3DEeHmmLAfoZucVR881uASk0Mfjw8xYJ99tb5CcY=
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github.com/stretchr/testify v1.7.0/go.mod h1:6Fq8oRcR53rry900zMqJjRRixrwX3KX962/h/Wwjteg=
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github.com/tevino/abool/v2 v2.1.0 h1:7w+Vf9f/5gmKT4m4qkayb33/92M+Um45F2BkHOR+L/c=
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github.com/tevino/abool/v2 v2.1.0/go.mod h1:+Lmlqk6bHDWHqN1cbxqhwEAwMPXgc8I1SDEamtseuXY=
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golang.org/x/exp v0.0.0-20230321023759-10a507213a29 h1:ooxPy7fPvB4kwsA2h+iBNHkAbp/4JxTSwCmvdjEYmug=
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golang.org/x/exp v0.0.0-20230321023759-10a507213a29/go.mod h1:CxIveKay+FTh1D0yPZemJVgC/95VzuuOLq5Qi4xnoYc=
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golang.org/x/exp v0.0.0-20230817173708-d852ddb80c63 h1:m64FZMko/V45gv0bNmrNYoDEq8U5YUhetc9cBWKS1TQ=
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golang.org/x/exp v0.0.0-20230817173708-d852ddb80c63/go.mod h1:0v4NqG35kSWCMzLaMeX+IQrlSnVE/bqGSyC2cz/9Le8=
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golang.org/x/sys v0.0.0-20220715151400-c0bba94af5f8/go.mod h1:oPkhp1MJrh7nUepCBck5+mAzfO9JrbApNNgaTdGDITg=
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golang.org/x/sys v0.0.0-20220811171246-fbc7d0a398ab/go.mod h1:oPkhp1MJrh7nUepCBck5+mAzfO9JrbApNNgaTdGDITg=
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golang.org/x/sys v0.6.0 h1:MVltZSvRTcU2ljQOhs94SXPftV6DCNnZViHeQps87pQ=
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golang.org/x/sys v0.6.0/go.mod h1:oPkhp1MJrh7nUepCBck5+mAzfO9JrbApNNgaTdGDITg=
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golang.org/x/term v0.6.0 h1:clScbb1cHjoCkyRbWwBEUZ5H/tIFu5TAXIqaZD0Gcjw=
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golang.org/x/sys v0.11.0 h1:eG7RXZHdqOJ1i+0lgLgCpSXAp6M3LYlAo6osgSi0xOM=
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golang.org/x/sys v0.11.0/go.mod h1:oPkhp1MJrh7nUepCBck5+mAzfO9JrbApNNgaTdGDITg=
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golang.org/x/term v0.6.0/go.mod h1:m6U89DPEgQRMq3DNkDClhWw02AUbt2daBVO4cn4Hv9U=
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gonum.org/v1/gonum v0.12.0 h1:xKuo6hzt+gMav00meVPUlXwSdoEJP46BR+wdxQEFK2o=
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gonum.org/v1/gonum v0.12.0/go.mod h1:73TDxJfAAHeA8Mk9mf8NlIppyhQNo5GLTcYeqgo2lvY=
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golang.org/x/term v0.11.0 h1:F9tnn/DA/Im8nCwm+fX+1/eBwi4qFjRT++MhtVC4ZX0=
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golang.org/x/term v0.11.0/go.mod h1:zC9APTIj3jG3FdV/Ons+XE1riIZXG4aZ4GTHiPZJPIU=
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gonum.org/v1/gonum v0.14.0 h1:2NiG67LD1tEH0D7kM+ps2V+fXmsAnpUeec7n8tcr4S0=
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gonum.org/v1/gonum v0.14.0/go.mod h1:AoWeoz0becf9QMWtE8iWXNXc27fK4fNeHNf/oMejGfU=
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gopkg.in/check.v1 v0.0.0-20161208181325-20d25e280405 h1:yhCVgyC4o1eVCa2tZl7eS0r+SDo693bJlVdllGtEeKM=
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gopkg.in/check.v1 v0.0.0-20161208181325-20d25e280405/go.mod h1:Co6ibVJAznAaIkqp8huTwlJQCZ016jof/cbN4VW5Yz0=
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gopkg.in/yaml.v3 v3.0.0-20200313102051-9f266ea9e77c h1:dUUwHk2QECo/6vqA44rthZ8ie2QXMNeKRTHCNY2nXvo=
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gopkg.in/yaml.v3 v3.0.0-20200313102051-9f266ea9e77c/go.mod h1:K4uyk7z7BCEPqu6E+C64Yfv1cQ7kz7rIZviUmN+EgEM=
|
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Block a user