Merge pull request #79 from kjsanger/devel

Update dependencies and changelog

CHANGELOG.md

@@ -6,6 +6,33 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 ## [Unreleased] - [![Unit tests](https://github.com/wtsi-npg/valet/actions/workflows/run-tests.yml/badge.svg)](https://github.com/wtsi-npg/valet/actions/workflows/run-tests.yml)
 
+### Added
+
+- Add Github Actions test workflow
+- Improve recognition of files to be processed and archived
+- Add support for TSV files.
+- Add support for compressing CSV files.
+- Add new all ONT-specific paths to the exclusion list.
+- Add the /data/laboratory WSI-specific path to the exclusion list.
+- Add iRODS 4.2.8 support
+
+### Removed
+
+- Remove iRODS 4.1.12 support
+
+### Changed
+
+- Relocate repository from github.com/kjsanger to github.com/wtsi-npg
+
+- Bump github.com/wtsi-npg/extendo/v2 from 2.2.0 to 2.4.0
+- Bump github.com/wtsi-npg/logshim from to 1.1.0 to 1.3.0
+- Bump github.com/wtsi-npg/logshim-zerolog from 1.1.0 to 1.3.0
+- Bump github.com/klauspost/pgzip from 1.2.1 to 1.2.5
+- Bump github.com/onsi/ginkgo from 1.12.3 to 1.16.1
+- Bump github.com/onsi/gomega from 1.10.1 to 1.11.0
+- Bump github.com/rs/zerolog from 1.19.1 to 1.21.0
+- Bump github.com/spf13/cobra from 0.0.5 to 0.0.7
+
 ## [1.4.0] - 2020-09-14
 
 ### Added
@@ -26,7 +53,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 ### Changed
 
-- Bump github.com/wtsi-npg//extendo from 2.0.0 to 2.1.0
+- Bump github.com/wtsi-npg/extendo from 2.0.0 to 2.1.0
 - Bump github.com/stretchr/testify from 1.5.1 to 1.6.0
 - Bump github.com/onsi/ginkgo from 1.12.0 to 1.12.2
 
@@ -43,7 +70,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 - Improve verbose level logging for consistency and information.
 - Add to default paths to ignore in the data root.
 
-- Bump github.com/wtsi-npg//extendo from 1.1.0 to 2.0.0
+- Bump github.com/wtsi-npg/extendo from 1.1.0 to 2.0.0
 - Bump github.com/onsi/ginkgo from 1.10.3 to 1.12.0
 - Bump github.com/onsi/gomega from 1.7.1 to 1.9.0
 
@@ -68,7 +95,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 ## Changed
 
-- Bump github.com/wtsi-npg//extendo from 1.0.0 to 1.1.0
+- Bump github.com/wtsi-npg/extendo from 1.0.0 to 1.1.0
 - Bump github.com/onsi/gomega from 1.5.0 to 1.7.1
 - Bump github.com/onsi/ginkgo from 1.8.0 to 1.10.3
 - Bump github.com/rs/zerolog from 1.14.3 to 1.17.2

go.mod

@@ -1,6 +1,6 @@
 module github.com/wtsi-npg/valet
 
-go 1.14
+go 1.16
 
 require (
 	github.com/klauspost/compress v1.9.1 // indirect
@@ -11,10 +11,10 @@ require (
 	github.com/rs/zerolog v1.21.0
 	github.com/spf13/cobra v0.0.7
 	github.com/stretchr/testify v1.7.0
-	github.com/wtsi-npg/extendo/v2 v2.3.0
+	github.com/wtsi-npg/extendo/v2 v2.4.0
 	github.com/wtsi-npg/fsnotify v1.4.8-0.20190705153444-45ca73e9793a
-	github.com/wtsi-npg/logshim v1.2.0
-	github.com/wtsi-npg/logshim-zerolog v1.2.0
+	github.com/wtsi-npg/logshim v1.3.0
+	github.com/wtsi-npg/logshim-zerolog v1.3.0
 	golang.org/x/crypto v0.0.0-20200622213623-75b288015ac9
 )
 

go.sum

@@ -83,12 +83,10 @@ github.com/nxadm/tail v1.4.8/go.mod h1:+ncqLTQzXmGhMZNUePPaPqPvBxHAIsmXswZKocGu+
 github.com/oklog/ulid v1.3.1/go.mod h1:CirwcVhetQ6Lv90oh/F+FBtV6XMibvdAFo93nm5qn4U=
 github.com/onsi/ginkgo v1.6.0/go.mod h1:lLunBs/Ym6LB5Z9jYTR76FiuTmxDTDusOGeTQH+WWjE=
 github.com/onsi/ginkgo v1.12.1/go.mod h1:zj2OWP4+oCPe1qIXoGWkgMRwljMUYCdkwsT2108oapk=
-github.com/onsi/ginkgo v1.15.0/go.mod h1:hF8qUzuuC8DJGygJH3726JnCZX4MYbRB8yFfISqnKUg=
 github.com/onsi/ginkgo v1.16.1 h1:foqVmeWDD6yYpK+Yz3fHyNIxFYNxswxqNFjSKe+vI54=
 github.com/onsi/ginkgo v1.16.1/go.mod h1:CObGmKUOKaSC0RjmoAK7tKyn4Azo5P2IWuoMnvwxz1E=
 github.com/onsi/gomega v1.7.1/go.mod h1:XdKZgCCFLUoM/7CFJVPcG8C1xQ1AJ0vpAezJrB7JYyY=
 github.com/onsi/gomega v1.10.1/go.mod h1:iN09h71vgCQne3DLsj+A5owkum+a2tYe+TOCB1ybHNo=
-github.com/onsi/gomega v1.10.5/go.mod h1:gza4q3jKQJijlu05nKWRCW/GavJumGt8aNRxWg7mt48=
 github.com/onsi/gomega v1.11.0 h1:+CqWgvj0OZycCaqclBD1pxKHAU+tOkHmQIWvDHq2aug=
 github.com/onsi/gomega v1.11.0/go.mod h1:azGKhqFUon9Vuj0YmTfLSmx0FUwqXYSTl5re8lQLTUg=
 github.com/pelletier/go-toml v1.2.0/go.mod h1:5z9KED0ma1S8pY6P1sdut58dfprrGBbd/94hg7ilaic=
@@ -109,8 +107,6 @@ github.com/prometheus/procfs v0.0.0-20190507164030-5867b95ac084/go.mod h1:TjEm7z
 github.com/prometheus/tsdb v0.7.1/go.mod h1:qhTCs0VvXwvX/y3TZrWD7rabWM+ijKTux40TwIPHuXU=
 github.com/rogpeppe/fastuuid v0.0.0-20150106093220-6724a57986af/go.mod h1:XWv6SoW27p1b0cqNHllgS5HIMJraePCO15w5zCzIWYg=
 github.com/rs/xid v1.2.1/go.mod h1:+uKXf+4Djp6Md1KODXJxgGQPKngRmWyn10oCKFzNHOQ=
-github.com/rs/zerolog v1.17.2/go.mod h1:9nvC1axdVrAHcu/s9taAVfBuIdTZLVQmKQyvrUjF5+I=
-github.com/rs/zerolog v1.19.0/go.mod h1:IzD0RJ65iWH0w97OQQebJEvTZYvsCUm9WVLWBQrJRjo=
 github.com/rs/zerolog v1.21.0 h1:Q3vdXlfLNT+OftyBHsU0Y445MD+8m8axjKgf2si0QcM=
 github.com/rs/zerolog v1.21.0/go.mod h1:ZPhntP/xmq1nnND05hhpAh2QMhSsA4UN3MGZ6O2J3hM=
 github.com/russross/blackfriday/v2 v2.0.1/go.mod h1:+Rmxgy9KzJVeS9/2gXHxylqXiyQDYRxCVz55jmeOWTM=
@@ -134,18 +130,19 @@ github.com/stretchr/testify v1.7.0 h1:nwc3DEeHmmLAfoZucVR881uASk0Mfjw8xYJ99tb5Cc
 github.com/stretchr/testify v1.7.0/go.mod h1:6Fq8oRcR53rry900zMqJjRRixrwX3KX962/h/Wwjteg=
 github.com/tmc/grpc-websocket-proxy v0.0.0-20190109142713-0ad062ec5ee5/go.mod h1:ncp9v5uamzpCO7NfCPTXjqaC+bZgJeR0sMTm6dMHP7U=
 github.com/ugorji/go v1.1.4/go.mod h1:uQMGLiO92mf5W77hV/PUCpI3pbzQx3CRekS0kk+RGrc=
-github.com/wtsi-npg/extendo/v2 v2.3.0 h1:sKlABJFbFtuQB2LOmlBTX4oMbhfAM7HbdreMU81YeRc=
-github.com/wtsi-npg/extendo/v2 v2.3.0/go.mod h1:K0EdJrVoWbZbJAYiUxiSzaemYXzfKXwO36nNYCM1mHM=
+github.com/wtsi-npg/extendo/v2 v2.4.0 h1:rbBbVklHGoobwQiovcfs1d7znaniBVlempgBAL0uEUI=
+github.com/wtsi-npg/extendo/v2 v2.4.0/go.mod h1:/mi30w9nekV6fYUGb1T7zvX3Kspy9HQKh2IzSQIJIOw=
 github.com/wtsi-npg/fsnotify v1.4.8-0.20190705153444-45ca73e9793a h1:LmzJGJXUS8U69eZ08MjwKwii8mos8630pV3aSZRdmc0=
 github.com/wtsi-npg/fsnotify v1.4.8-0.20190705153444-45ca73e9793a/go.mod h1:/ux2ROeuYmj0JshWH6r5f+gvLIJP2ZbMutVFrW6/8Pg=
 github.com/wtsi-npg/logshim v1.2.0 h1:d9y9XvBRkYB2bUsN07zGJWhGCu13PKoxIxQE97Q9aZw=
 github.com/wtsi-npg/logshim v1.2.0/go.mod h1:1JRn1t/rlx1/oAtv3LOcshcpjDDvHGHCK8p8ua0Hrss=
-github.com/wtsi-npg/logshim-zerolog v1.2.0 h1:b1HpB1h8OO9XBg/m9r6ycmHRUDNZLnpTmfjWrhmeaT4=
-github.com/wtsi-npg/logshim-zerolog v1.2.0/go.mod h1:xyahqnZDG2utxSUAQKYjgEdzQz74wfPY7+JttEie41k=
+github.com/wtsi-npg/logshim v1.3.0 h1:J4JIzWrEVC6RghSdnhadjviOwAwQ4BUqG7hveqxrisY=
+github.com/wtsi-npg/logshim v1.3.0/go.mod h1:O1IqtDB3IiWuIpEE42IznMkJD8d++UFp40gBSjps3ac=
+github.com/wtsi-npg/logshim-zerolog v1.3.0 h1:7BoTUhTKtBwuduc+8mCcsYVWCAptqFY1CT1Y3pSjoaw=
+github.com/wtsi-npg/logshim-zerolog v1.3.0/go.mod h1:yWGzgCuHUkg1tcKcF0DBKi2laec69EIUMkXl77P2yII=
 github.com/xiang90/probing v0.0.0-20190116061207-43a291ad63a2/go.mod h1:UETIi67q53MR2AWcXfiuqkDkRtnGDLqkBTpCHuJHxtU=
 github.com/xordataexchange/crypt v0.0.3-0.20170626215501-b2862e3d0a77/go.mod h1:aYKd//L2LvnjZzWKhF00oedf4jCCReLcmhLdhm1A27Q=
 github.com/yuin/goldmark v1.2.1/go.mod h1:3hX8gzYuyVAZsxl0MRgGTJEmQBFcNTphYh9decYSb74=
-github.com/zenazn/goji v0.9.0/go.mod h1:7S9M489iMyHBNxwZnk9/EHS098H4/F6TATF2mIxtB1Q=
 go.etcd.io/bbolt v1.3.2/go.mod h1:IbVyRI1SCnLcuJnV2u8VeU0CEYM7e686BmAb1XKL+uU=
 go.uber.org/atomic v1.4.0/go.mod h1:gD2HeocX3+yG+ygLZcrzQJaqmWj9AIm7n08wl/qW/PE=
 go.uber.org/multierr v1.1.0/go.mod h1:wR5kodmAFQ0UK8QlbwjlSNy0Z68gJhDJUG5sjR94q/0=
@@ -199,7 +196,6 @@ golang.org/x/tools v0.0.0-20180221164845-07fd8470d635/go.mod h1:n7NCudcB/nEzxVGm
 golang.org/x/tools v0.0.0-20180917221912-90fa682c2a6e/go.mod h1:n7NCudcB/nEzxVGmLbDWY5pfWTLqBcC2KZ6jyYvM4mQ=
 golang.org/x/tools v0.0.0-20190114222345-bf090417da8b/go.mod h1:n7NCudcB/nEzxVGmLbDWY5pfWTLqBcC2KZ6jyYvM4mQ=
 golang.org/x/tools v0.0.0-20190311212946-11955173bddd/go.mod h1:LCzVGOaR6xXOjkQ3onu1FJEFr0SW1gC7cKk1uF8kGRs=
-golang.org/x/tools v0.0.0-20190828213141-aed303cbaa74/go.mod h1:b+2E5dAYhXwXZwtnZ6UAqBI28+e2cm9otk0dWdXHAEo=
 golang.org/x/tools v0.0.0-20191119224855-298f0cb1881e/go.mod h1:b+2E5dAYhXwXZwtnZ6UAqBI28+e2cm9otk0dWdXHAEo=
 golang.org/x/tools v0.0.0-20201224043029-2b0845dc783e/go.mod h1:emZCQorbCU4vsT4fOWvOPXz4eW1wZW4PmDk9uLelYpA=
 golang.org/x/tools v0.1.0/go.mod h1:xkSsbof2nBLbhDlRMhhhyNLN/zl3eTqcnHD5viDpcZ0=