Merge pull request #105 from wtsi-npg/devel

Merge devel to master for release

.github/workflows/run-tests.yml

@@ -17,16 +17,19 @@ jobs:
 
     strategy:
       matrix:
-        go: [ "1.16" ]
-        baton: [ "2.1.0" ]
-        experimental: [false]
         include:
-          - irods: "4.2.7"
+          # iRODS 4.2.10 clients vs 4.2.7 server
+          - go: "1.17"
+            irods: "4.2.10"
             server_image: "wsinpg/ub-16.04-irods-4.2.7:latest"
+            baton: "3.1.0"
+            experimental: false
+          # iRODS 4.2.10 clients vs 4.2.10 server
+          - go: "1.17"
+            irods: "4.2.10"
+            server_image: "wsinpg/ub-18.04-irods-4.2.10:latest"
+            baton: "3.1.0"
             experimental: false
-          - irods: "4.2.8"
-            server_image: "wsinpg/ub-18.04-irods-4.2.8:latest"
-            experimental: true
 
     services:
       irods:
@@ -53,14 +56,13 @@ jobs:
 
         conda config --set auto_update_conda False
         conda config --prepend channels "$WSI_CONDA_CHANNEL"
-        conda config --append channels conda-forge
         conda info
 
     - name: "Install iRODS clients"
       run: |
         conda create -y -n "$CONDA_TEST_ENVIRONMENT"
-        conda install -y -n "$CONDA_TEST_ENVIRONMENT" "irods-icommands ==${{ matrix.irods }}"
-        conda install -y -n "$CONDA_TEST_ENVIRONMENT" "baton ==${{ matrix.baton }}"
+        conda install -y -n "$CONDA_TEST_ENVIRONMENT" "irods-icommands=${{ matrix.irods }}"
+        conda install -y -n "$CONDA_TEST_ENVIRONMENT" "baton=${{ matrix.baton }}"
 
     - name: "Configure iRODS clients"
       run: |
@@ -74,7 +76,7 @@ jobs:
             "irods_user_name": "irods",
             "irods_zone_name": "testZone",
             "irods_home": "/testZone/home/irods",
-            "irods_default_resource": "testResc"
+            "irods_default_resource": "replResc"
         }
         EOF
 

CHANGELOG.md

@@ -8,17 +8,46 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 ### 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.
+### Changed
+
+## [1.6.0] - 2022-01-10
+
+### Added
+
+- Support for adding iRODS metadata for PromethION-24 runs.
+- Support for BAM files.
+- support for BED files (compressed).
+- iRODS 4.2.10 support.
+
+### Changed
+
+- Build with Go.1.17
+
+- Bump github.com/rs/zerolog from 1.21.0 to 1.26.1
+- Bump github.com/onsi/ginkgo from 1.16.2 to 1.16.5
+- Bump github.com/onsi/gomega from 1.11.0 to 1.17.0
+- Bump github.com/spf13/cobra from 0.0.7 to 1.3.0
+
+### Removed
+
+- Travis CI configuration.
+- PromethION beta report parsing tests and unused test data.
+
+## [1.5.0] - 2021-04-15
+
+### Added
+
+- Github Actions test workflow.
+- Improve recognition of files to be processed and archived.
+- Support for TSV files.
+- Support for compressing CSV files.
+- Add 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
+- iRODS 4.2.8 support.
 
 ### Removed
 
-- Remove iRODS 4.1.12 support
+- RODS 4.1.12 support.
 
 ### Changed
 
@@ -88,13 +117,14 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 - Checksum creation improvements using tee'ing to avoid re-reading data.
 - Make the size of the client pool equal to the number of threads.
-- Use pgzip implementation.
 - Gzip compression of fastq and txt files.
 - Enhancements to FilePath for handling compressed files.
 - Find paths immediately, then at intervals.
 
 ## Changed
 
+- Use pgzip implementation.
+
 - 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

go.mod

@@ -1,15 +1,15 @@
 module github.com/wtsi-npg/valet
 
-go 1.16
+go 1.17
 
 require (
 	github.com/klauspost/compress v1.9.1 // indirect
 	github.com/klauspost/pgzip v1.2.5
-	github.com/onsi/ginkgo v1.16.1
-	github.com/onsi/gomega v1.11.0
+	github.com/onsi/ginkgo v1.16.5
+	github.com/onsi/gomega v1.17.0
 	github.com/pkg/errors v0.9.1
-	github.com/rs/zerolog v1.21.0
-	github.com/spf13/cobra v0.0.7
+	github.com/rs/zerolog v1.26.0
+	github.com/spf13/cobra v1.2.1
 	github.com/stretchr/testify v1.7.0
 	github.com/wtsi-npg/extendo/v2 v2.4.0
 	github.com/wtsi-npg/fsnotify v1.4.8-0.20190705153444-45ca73e9793a
@@ -18,4 +18,19 @@ require (
 	golang.org/x/crypto v0.0.0-20200622213623-75b288015ac9
 )
 
+require (
+	github.com/davecgh/go-spew v1.1.1 // indirect
+	github.com/fsnotify/fsnotify v1.4.9 // indirect
+	github.com/inconshreveable/mousetrap v1.0.0 // indirect
+	github.com/nxadm/tail v1.4.8 // indirect
+	github.com/pmezard/go-difflib v1.0.0 // indirect
+	github.com/spf13/pflag v1.0.5 // indirect
+	golang.org/x/net v0.0.0-20210805182204-aaa1db679c0d // indirect
+	golang.org/x/sys v0.0.0-20210809222454-d867a43fc93e // indirect
+	golang.org/x/text v0.3.6 // indirect
+	gopkg.in/tomb.v1 v1.0.0-20141024135613-dd632973f1e7 // indirect
+	gopkg.in/yaml.v2 v2.4.0 // indirect
+	gopkg.in/yaml.v3 v3.0.0-20210107192922-496545a6307b // indirect
+)
+
 // replace github.com/wtsi-npg/extendo/v2 => ../extendo