mirror of
https://github.com/metabarcoding/obitools4.git
synced 2025-06-29 16:20:46 +00:00
adds a rule to update packages and push the corresponding updates module files
Former-commit-id: 1ffa805e74571f9d970dcb185f187dd586c1a190
This commit is contained in:
5
Makefile
5
Makefile
@ -42,6 +42,9 @@ all: obitools
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packages: $(patsubst %,pkg-%,$(PACKAGES))
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obitools: $(patsubst %,$(OBITOOLS_PREFIX)%,$(OBITOOLS))
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update-deps:
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go get -u ./...
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man:
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make -C doc man
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obibook:
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@ -61,4 +64,4 @@ $(foreach P,$(PACKAGE_DIRS),$(eval $(call MAKE_PKG_RULE,$(P))))
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$(foreach P,$(OBITOOLS_DIRS),$(eval $(call MAKE_OBITOOLS_RULE,$(P))))
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.PHONY: all packages obitools man obibook doc
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.PHONY: all packages obitools man obibook doc update-deps
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@ -1,10 +1,27 @@
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# OBITools release notes
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## On going changes
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## Ongoing changes
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### New features
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- Add the possibility for looking pattern with indels. This has been added to `obimultiplex`
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through the `--with-indels` option.
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### Enhancement
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- Add support for IUPAC DNA code into the DNA sequence LCS computation and an end free gap mode.
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This impact `obitag` and `obimultiplex` in the `--with-indels` mode.
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- Print the synopsis of the command when an error is done by the user at typing the command
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### Corrected bugs
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- Better managment of non existing files. The produced error message is not yet perfectly clear.
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- Better management of non-existing files. The produced error message is not yet perfectly clear.
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- Patch a bug leading with some programs to crash because of : "*empty batch pushed on the channel*"
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- Patch a bug when directory names are used as input data name preventing the system to actually
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analyze the collected files.
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- Make the `--help` or `-h` options working when mandatory options are declared
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- In `obimultiplex` correct a bug leading to a wrong report of the count of reverse mismatch for
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sequences in reverse direction.
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## March 7th, 2023. Release 4.0.1
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29
go.mod
29
go.mod
@ -3,27 +3,28 @@ module git.metabarcoding.org/lecasofts/go/obitools
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go 1.18
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require (
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cloudeng.io/algo v0.0.0-20220721000539-f9fe69fddaf6
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github.com/DavidGamba/go-getoptions v0.25.3
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github.com/PaesslerAG/gval v1.1.2
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cloudeng.io/algo v0.0.0-20230314235058-45ee90f9cff7
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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/goccy/go-json v0.9.4
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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/rrethy/ahocorasick v1.0.0
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github.com/schollz/progressbar/v3 v3.8.6
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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/tevino/abool/v2 v2.0.1
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gonum.org/v1/gonum v0.11.0
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github.com/tevino/abool/v2 v2.1.0
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gonum.org/v1/gonum v0.12.0
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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/klauspost/compress v1.15.9 // indirect
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github.com/mattn/go-runewidth v0.0.13 // 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/mitchellh/colorstring v0.0.0-20190213212951-d06e56a500db // indirect
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github.com/rivo/uniseg v0.2.0 // indirect
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golang.org/x/crypto v0.0.0-20220131195533-30dcbda58838 // indirect
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golang.org/x/exp v0.0.0-20230306221820-f0f767cdffd6 // indirect
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golang.org/x/sys v0.1.0 // indirect
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golang.org/x/term v0.0.0-20210927222741-03fcf44c2211 // 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/crypto v0.7.0 // indirect
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golang.org/x/exp v0.0.0-20230321023759-10a507213a29 // 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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)
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33
go.sum
33
go.sum
@ -1,12 +1,19 @@
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cloudeng.io/algo v0.0.0-20220721000539-f9fe69fddaf6 h1:9vMtasELP9mg/w0tI4gkfdTkc5hDf8fP1CT9w4L/RN4=
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cloudeng.io/algo v0.0.0-20220721000539-f9fe69fddaf6/go.mod h1:dgJhQ6JXLysnBQG09/5Q56rwJfgyKXlnDbKzko9MhdA=
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cloudeng.io/algo v0.0.0-20230314235058-45ee90f9cff7 h1:6Hs98DsbNfToC85+irVtbFmW8/UGP/lO6mbTpZW08EI=
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cloudeng.io/algo v0.0.0-20230314235058-45ee90f9cff7/go.mod h1:80eC8gNGsJP8ZBw+xCIh1kIpt77az1W7fJ+zqLRiE64=
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cloudeng.io/errors v0.0.7 h1:GqFEwQrkOhoaF3Nla8tDzHhFwzYYHWmRmGkf4Ag2zGM=
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cloudeng.io/errors v0.0.8 h1:WEpTcAYnL2wsPm0qfMpXRupoO61DahxbD4doPKbsaGY=
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dmitri.shuralyov.com/gpu/mtl v0.0.0-20190408044501-666a987793e9/go.mod h1:H6x//7gZCb22OMCxBHrMx7a5I7Hp++hsVxbQ4BYO7hU=
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github.com/BurntSushi/xgb v0.0.0-20160522181843-27f122750802/go.mod h1:IVnqGOEym/WlBOVXweHU+Q+/VP0lqqI8lqeDx9IjBqo=
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github.com/DavidGamba/go-getoptions v0.25.3 h1:lSPcMkwWvVZU05C+Uz4DKnKN5wz4bcD1QvJ/QHCRexo=
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github.com/DavidGamba/go-getoptions v0.25.3/go.mod h1:qLaLSYeQ8sUVOfKuu5JT5qKKS3OCwyhkYSJnoG+ggmo=
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github.com/DavidGamba/go-getoptions v0.27.0 h1:hldKJSwO9SwvR+z9pe6ojhEcYECrRiO/bar9B7MnBKA=
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github.com/DavidGamba/go-getoptions v0.27.0/go.mod h1:qLaLSYeQ8sUVOfKuu5JT5qKKS3OCwyhkYSJnoG+ggmo=
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github.com/PaesslerAG/gval v1.1.2 h1:EROKxV4/fAKWb0Qoj7NOxmHZA7gcpjOV9XgiRZMRCUU=
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github.com/PaesslerAG/gval v1.1.2/go.mod h1:Fa8gfkCmUsELXgayr8sfL/sw+VzCVoa03dcOcR/if2w=
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github.com/PaesslerAG/gval v1.2.2 h1:Y7iBzhgE09IGTt5QgGQ2IdaYYYOU134YGHBThD+wm9E=
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github.com/PaesslerAG/gval v1.2.2/go.mod h1:XRFLwvmkTEdYziLdaCeCa5ImcGVrfQbeNUbVR+C6xac=
|
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github.com/PaesslerAG/jsonpath v0.1.0 h1:gADYeifvlqK3R3i2cR5B4DGgxLXIPb3TRTH1mGi0jPI=
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github.com/PaesslerAG/jsonpath v0.1.0/go.mod h1:4BzmtoM/PI8fPO4aQGIusjGxGir2BzcV0grWtFzq1Y8=
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github.com/barkimedes/go-deepcopy v0.0.0-20220514131651-17c30cfc62df h1:GSoSVRLoBaFpOOds6QyY1L8AX7uoY+Ln3BHc22W40X0=
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@ -17,24 +24,37 @@ github.com/davecgh/go-spew v1.1.1/go.mod h1:J7Y8YcW2NihsgmVo/mv3lAwl/skON4iLHjSs
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github.com/go-gl/glfw v0.0.0-20190409004039-e6da0acd62b1/go.mod h1:vR7hzQXu2zJy9AVAgeJqvqgH9Q5CA+iKCZ2gyEVpxRU=
|
||||
github.com/goccy/go-json v0.9.4 h1:L8MLKG2mvVXiQu07qB6hmfqeSYQdOnqPot2GhsIwIaI=
|
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github.com/goccy/go-json v0.9.4/go.mod h1:6MelG93GURQebXPDq3khkgXZkazVtN9CRI+MGFi0w8I=
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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 v1.15.9 h1:wKRjX6JRtDdrE9qwa4b/Cip7ACOshUI4smpCQanqjSY=
|
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github.com/klauspost/compress v1.15.9/go.mod h1:PhcZ0MbTNciWF3rruxRgKxI5NkcHHrHUDtV4Yw2GlzU=
|
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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/mattn/go-isatty v0.0.14/go.mod h1:7GGIvUiUoEMVVmxf/4nioHXj79iQHKdU27kJ6hsGG94=
|
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github.com/mattn/go-isatty v0.0.17/go.mod h1:kYGgaQfpe5nmfYZH+SKPsOc2e4SrIfOl2e/yFXSvRLM=
|
||||
github.com/mattn/go-runewidth v0.0.13 h1:lTGmDsbAYt5DmK6OnoV7EuIF1wEIFAcxld6ypU4OSgU=
|
||||
github.com/mattn/go-runewidth v0.0.13/go.mod h1:Jdepj2loyihRzMpdS35Xk/zdY8IAYHsh153qUoGf23w=
|
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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=
|
||||
github.com/mitchellh/colorstring v0.0.0-20190213212951-d06e56a500db h1:62I3jR2EmQ4l5rM/4FEfDWcRD+abF5XlKShorW5LRoQ=
|
||||
github.com/mitchellh/colorstring v0.0.0-20190213212951-d06e56a500db/go.mod h1:l0dey0ia/Uv7NcFFVbCLtqEBQbrT4OCwCSKTEv6enCw=
|
||||
github.com/pmezard/go-difflib v1.0.0 h1:4DBwDE0NGyQoBHbLQYPwSUPoCMWR5BEzIk/f1lZbAQM=
|
||||
github.com/pmezard/go-difflib v1.0.0/go.mod h1:iKH77koFhYxTK1pcRnkKkqfTogsbg7gZNVY4sRDYZ/4=
|
||||
github.com/rivo/uniseg v0.2.0 h1:S1pD9weZBuJdFmowNwbpi7BJ8TNftyUImj/0WQi72jY=
|
||||
github.com/rivo/uniseg v0.2.0/go.mod h1:J6wj4VEh+S6ZtnVlnTBMWIodfgj8LQOQFoIToxlJtxc=
|
||||
github.com/rivo/uniseg v0.4.4 h1:8TfxU8dW6PdqD27gjM8MVNuicgxIjxpm4K7x4jp8sis=
|
||||
github.com/rivo/uniseg v0.4.4/go.mod h1:FN3SvrM+Zdj16jyLfmOkMNblXMcoc8DfTHruCPUcx88=
|
||||
github.com/rrethy/ahocorasick v1.0.0 h1:YKkCB+E5PXc0xmLfMrWbfNht8vG9Re97IHSWZk/Lk8E=
|
||||
github.com/rrethy/ahocorasick v1.0.0/go.mod h1:nq8oScE7Vy1rOppoQxpQiiDmPHuKCuk9rXrNcxUV3R0=
|
||||
github.com/schollz/progressbar/v3 v3.8.6 h1:QruMUdzZ1TbEP++S1m73OqRJk20ON11m6Wqv4EoGg8c=
|
||||
github.com/schollz/progressbar/v3 v3.8.6/go.mod h1:W5IEwbJecncFGBvuEh4A7HT1nZZ6WNIL2i3qbnI0WKY=
|
||||
github.com/schollz/progressbar/v3 v3.13.1 h1:o8rySDYiQ59Mwzy2FELeHY5ZARXZTVJC7iHD6PEFUiE=
|
||||
github.com/schollz/progressbar/v3 v3.13.1/go.mod h1:xvrbki8kfT1fzWzBT/UZd9L6GA+jdL7HAgq2RFnO6fQ=
|
||||
github.com/shopspring/decimal v1.3.1 h1:2Usl1nmF/WZucqkFZhnfFYxxxu8LG21F6nPQBE5gKV8=
|
||||
github.com/shopspring/decimal v1.3.1/go.mod h1:DKyhrW/HYNuLGql+MJL6WCR6knT2jwCFRcu2hWCYk4o=
|
||||
github.com/sirupsen/logrus v1.8.1 h1:dJKuHgqk1NNQlqoA6BTlM1Wf9DOH3NBjQyu0h9+AZZE=
|
||||
github.com/sirupsen/logrus v1.8.1/go.mod h1:yWOB1SBYBC5VeMP7gHvWumXLIWorT60ONWic61uBYv0=
|
||||
github.com/sirupsen/logrus v1.9.0 h1:trlNQbNUG3OdDrDil03MCb1H2o9nJ1x4/5LYw7byDE0=
|
||||
@ -47,15 +67,21 @@ github.com/stretchr/testify v1.7.0 h1:nwc3DEeHmmLAfoZucVR881uASk0Mfjw8xYJ99tb5Cc
|
||||
github.com/stretchr/testify v1.7.0/go.mod h1:6Fq8oRcR53rry900zMqJjRRixrwX3KX962/h/Wwjteg=
|
||||
github.com/tevino/abool/v2 v2.0.1 h1:OF7FC5V5z3yAWyixbc32ecEzrgAJCsPkVOsPM2qoZPI=
|
||||
github.com/tevino/abool/v2 v2.0.1/go.mod h1:+Lmlqk6bHDWHqN1cbxqhwEAwMPXgc8I1SDEamtseuXY=
|
||||
github.com/tevino/abool/v2 v2.1.0 h1:7w+Vf9f/5gmKT4m4qkayb33/92M+Um45F2BkHOR+L/c=
|
||||
github.com/tevino/abool/v2 v2.1.0/go.mod h1:+Lmlqk6bHDWHqN1cbxqhwEAwMPXgc8I1SDEamtseuXY=
|
||||
golang.org/x/crypto v0.0.0-20190308221718-c2843e01d9a2/go.mod h1:djNgcEr1/C05ACkg1iLfiJU5Ep61QUkGW8qpdssI0+w=
|
||||
golang.org/x/crypto v0.0.0-20190510104115-cbcb75029529/go.mod h1:yigFU9vqHzYiE8UmvKecakEJjdnWj3jj499lnFckfCI=
|
||||
golang.org/x/crypto v0.0.0-20220131195533-30dcbda58838 h1:71vQrMauZZhcTVK6KdYM+rklehEEwb3E+ZhaE5jrPrE=
|
||||
golang.org/x/crypto v0.0.0-20220131195533-30dcbda58838/go.mod h1:IxCIyHEi3zRg3s0A5j5BB6A9Jmi73HwBIUl50j+osU4=
|
||||
golang.org/x/crypto v0.7.0 h1:AvwMYaRytfdeVt3u6mLaxYtErKYjxA2OXjJ1HHq6t3A=
|
||||
golang.org/x/crypto v0.7.0/go.mod h1:pYwdfH91IfpZVANVyUOhSIPZaFoJGxTFbZhFTx+dXZU=
|
||||
golang.org/x/exp v0.0.0-20190306152737-a1d7652674e8/go.mod h1:CJ0aWSM057203Lf6IL+f9T1iT9GByDxfZKAQTCR3kQA=
|
||||
golang.org/x/exp v0.0.0-20191002040644-a1355ae1e2c3 h1:n9HxLrNxWWtEb1cA950nuEEj3QnKbtsCJ6KjcgisNUs=
|
||||
golang.org/x/exp v0.0.0-20191002040644-a1355ae1e2c3/go.mod h1:NOZ3BPKG0ec/BKJQgnvsSFpcKLM5xXVWnvZS97DWHgE=
|
||||
golang.org/x/exp v0.0.0-20230306221820-f0f767cdffd6 h1:3p+wVC0x0TCIPgd3LCQlpgVlEtjziEC5v42w7+B8t8M=
|
||||
golang.org/x/exp v0.0.0-20230306221820-f0f767cdffd6/go.mod h1:CxIveKay+FTh1D0yPZemJVgC/95VzuuOLq5Qi4xnoYc=
|
||||
golang.org/x/exp v0.0.0-20230321023759-10a507213a29 h1:ooxPy7fPvB4kwsA2h+iBNHkAbp/4JxTSwCmvdjEYmug=
|
||||
golang.org/x/exp v0.0.0-20230321023759-10a507213a29/go.mod h1:CxIveKay+FTh1D0yPZemJVgC/95VzuuOLq5Qi4xnoYc=
|
||||
golang.org/x/image v0.0.0-20190227222117-0694c2d4d067/go.mod h1:kZ7UVZpmo3dzQBMxlp+ypCbDeSB+sBbTgSJuh5dn5js=
|
||||
golang.org/x/image v0.0.0-20190802002840-cff245a6509b/go.mod h1:FeLwcggjj3mMvU+oOTbSwawSJRM1uh48EjtB4UJZlP0=
|
||||
golang.org/x/mobile v0.0.0-20190719004257-d2bd2a29d028/go.mod h1:E/iHnbuqvinMTCcRqshq8CkpyQDoeVncDDYHnLhea+o=
|
||||
@ -76,11 +102,16 @@ golang.org/x/sys v0.0.0-20220128215802-99c3d69c2c27/go.mod h1:oPkhp1MJrh7nUepCBc
|
||||
golang.org/x/sys v0.0.0-20220715151400-c0bba94af5f8/go.mod h1:oPkhp1MJrh7nUepCBck5+mAzfO9JrbApNNgaTdGDITg=
|
||||
golang.org/x/sys v0.0.0-20220722155257-8c9f86f7a55f h1:v4INt8xihDGvnrfjMDVXGxw9wrfxYyCjk0KbXjhR55s=
|
||||
golang.org/x/sys v0.0.0-20220722155257-8c9f86f7a55f/go.mod h1:oPkhp1MJrh7nUepCBck5+mAzfO9JrbApNNgaTdGDITg=
|
||||
golang.org/x/sys v0.0.0-20220811171246-fbc7d0a398ab/go.mod h1:oPkhp1MJrh7nUepCBck5+mAzfO9JrbApNNgaTdGDITg=
|
||||
golang.org/x/sys v0.1.0 h1:kunALQeHf1/185U1i0GOB/fy1IPRDDpuoOOqRReG57U=
|
||||
golang.org/x/sys v0.1.0/go.mod h1:oPkhp1MJrh7nUepCBck5+mAzfO9JrbApNNgaTdGDITg=
|
||||
golang.org/x/sys v0.6.0 h1:MVltZSvRTcU2ljQOhs94SXPftV6DCNnZViHeQps87pQ=
|
||||
golang.org/x/sys v0.6.0/go.mod h1:oPkhp1MJrh7nUepCBck5+mAzfO9JrbApNNgaTdGDITg=
|
||||
golang.org/x/term v0.0.0-20201126162022-7de9c90e9dd1/go.mod h1:bj7SfCRtBDWHUb9snDiAeCFNEtKQo2Wmx5Cou7ajbmo=
|
||||
golang.org/x/term v0.0.0-20210927222741-03fcf44c2211 h1:JGgROgKl9N8DuW20oFS5gxc+lE67/N3FcwmBPMe7ArY=
|
||||
golang.org/x/term v0.0.0-20210927222741-03fcf44c2211/go.mod h1:jbD1KX2456YbFQfuXm/mYQcufACuNUgVhRMnK/tPxf8=
|
||||
golang.org/x/term v0.6.0 h1:clScbb1cHjoCkyRbWwBEUZ5H/tIFu5TAXIqaZD0Gcjw=
|
||||
golang.org/x/term v0.6.0/go.mod h1:m6U89DPEgQRMq3DNkDClhWw02AUbt2daBVO4cn4Hv9U=
|
||||
golang.org/x/text v0.3.0/go.mod h1:NqM8EUOU14njkJ3fqMW+pc6Ldnwhi/IjpwHt7yyuwOQ=
|
||||
golang.org/x/text v0.3.6/go.mod h1:5Zoc/QRtKVWzQhOtBMvqHzDpF6irO9z98xDceosuGiQ=
|
||||
golang.org/x/tools v0.0.0-20180917221912-90fa682c2a6e/go.mod h1:n7NCudcB/nEzxVGmLbDWY5pfWTLqBcC2KZ6jyYvM4mQ=
|
||||
@ -88,6 +119,8 @@ golang.org/x/tools v0.0.0-20190927191325-030b2cf1153e/go.mod h1:b+2E5dAYhXwXZwtn
|
||||
golang.org/x/xerrors v0.0.0-20190717185122-a985d3407aa7/go.mod h1:I/5z698sn9Ka8TeJc9MKroUUfqBBauWjQqLJ2OPfmY0=
|
||||
gonum.org/v1/gonum v0.11.0 h1:f1IJhK4Km5tBJmaiJXtk/PkL4cdVX6J+tGiM187uT5E=
|
||||
gonum.org/v1/gonum v0.11.0/go.mod h1:fSG4YDCxxUZQJ7rKsQrj0gMOg00Il0Z96/qMA4bVQhA=
|
||||
gonum.org/v1/gonum v0.12.0 h1:xKuo6hzt+gMav00meVPUlXwSdoEJP46BR+wdxQEFK2o=
|
||||
gonum.org/v1/gonum v0.12.0/go.mod h1:73TDxJfAAHeA8Mk9mf8NlIppyhQNo5GLTcYeqgo2lvY=
|
||||
gopkg.in/check.v1 v0.0.0-20161208181325-20d25e280405/go.mod h1:Co6ibVJAznAaIkqp8huTwlJQCZ016jof/cbN4VW5Yz0=
|
||||
gopkg.in/yaml.v3 v3.0.0-20200313102051-9f266ea9e77c/go.mod h1:K4uyk7z7BCEPqu6E+C64Yfv1cQ7kz7rIZviUmN+EgEM=
|
||||
scientificgo.org/special v0.0.0 h1:P6WJkECo6tgtvZAEfNXl+KEB9ReAatjKAeX8U07mjSc=
|
||||
|
||||
Reference in New Issue
Block a user