Merge pull request #292 from wtsi-npg/devel

pull from devel to master to create Release 3.21.0

.github/workflows/run-tests.yml

@@ -21,19 +21,34 @@ jobs:
         include:
           - perl: "5.22.4"
             irods: "4.2.7"
-            client_image: "ghcr.io/wtsi-npg/ub-18.04-irods-clients-4.2.11:latest"
+            client_image: "ghcr.io/wtsi-npg/ub-16.04-irods-clients-4.2.7:latest"
             server_image: "ghcr.io/wtsi-npg/ub-16.04-irods-4.2.7:latest"
             experimental: false
           - perl: "5.22.4"
             irods: "4.2.11"
             client_image: "ghcr.io/wtsi-npg/ub-18.04-irods-clients-4.2.11:latest"
             server_image: "ghcr.io/wtsi-npg/ub-18.04-irods-4.2.11:latest"
             experimental: false
+          - perl: "5.34.1"
+            irods: "4.2.11"
+            client_image: "ghcr.io/wtsi-npg/ub-18.04-irods-clients-4.2.11:latest"
+            server_image: "ghcr.io/wtsi-npg/ub-18.04-irods-4.2.11:latest"
+            experimental: false
           - perl: "5.22.4"
             irods: "4.2.12"
             client_image: "ghcr.io/wtsi-npg/ub-18.04-irods-clients-4.2.12:latest"
             server_image: "ghcr.io/wtsi-npg/ub-18.04-irods-4.2.12:latest"
             experimental: false
+          - perl: "5.22.4"
+            irods: "4.3.1"
+            client_image: "ghcr.io/wtsi-npg/ub-22.04-irods-clients-4.3.1:latest"
+            server_image: "ghcr.io/wtsi-npg/ub-22.04-irods-4.3.1:latest"
+            experimental: false
+          - perl: "5.22.4"
+            irods: "4.3.0"
+            client_image: "ghcr.io/wtsi-npg/ub-22.04-irods-clients-4.3-nightly:latest"
+            server_image: "ghcr.io/wtsi-npg/ub-22.04-irods-4.3-nightly:latest"
+            experimental: true
 
     services:
       irods-server:
@@ -49,6 +64,13 @@ jobs:
           --health-retries 6
 
     steps:
+      - name: "Set environmental variables based on other environmental variables"
+        run: |
+          echo "SINGULARITY_CACHEDIR=$HOME/.singularity-cache" >> $GITHUB_ENV
+          # '~' in SINGULARITY_CACHEDIR value (from say a env: section in this YAML) is not expanded by
+          # singularity so that paths used are misleading/unclear
+
+
       - uses: actions/checkout@v3
 
       - name: "Install OS dependencies"
@@ -74,24 +96,21 @@ jobs:
       - name: "Cache Singularity images"
         uses: actions/cache@v3
         with:
-          path: ${{ github.workspace }}/.singularity-cache
+          path: ${{ env.SINGULARITY_CACHEDIR }}
           key: ${{ runner.os }}-singularity
 
       - name: "Install iRODS client wrappers"
         env:
           DOCKER_IMAGE: ${{ matrix.client_image }}
-          PREFIX: ${{ github.workspace }}
-          SINGULARITY_CACHEDIR: ${{ github.workspace }}/.singularity-cache
         run: |
           # Use -s option for the wrappers to enable re-usable service instances
-          singularity exec docker://$DOCKER_IMAGE singularity-wrapper -s -p $PREFIX install
-          echo "$PREFIX/bin" >> $GITHUB_PATH
+          # Install is to HOME rather than workspace to avoid clashes with repo e.g. in bin/
+          singularity exec docker://$DOCKER_IMAGE singularity-wrapper -s -p $HOME/.local install
+          echo "$HOME/.local/bin" >> $GITHUB_PATH
 
       - name: "Configure iRODS clients"
         env:
           DOCKER_IMAGE: ${{ matrix.client_image }}
-          PREFIX: ${{ github.workspace }}
-          SINGULARITY_CACHEDIR: ${{ github.workspace }}/.singularity-cache
         run: |
           mkdir -p "$HOME/.irods"
           cat <<'EOF' > "$HOME/.irods/irods_environment.json"

Changes

@@ -1,3 +1,15 @@
+Release 3.21.0
+
+ - Add iRODS 4.3.1 Ubuntu 22.04 as a required test target
+ - Handle optional rodsadmin group
+ - Update test matrix iRODS versions
+     Remove the combination of 4.2.11 clients with a 4.2.7 server
+     Add the combination of 4.2.7 clients with a 4.2.7 server
+     Add the combination of 4.3-nightly clients with a 4.3-nightly server
+ - GHA: move irods client deployment and singularity cache to HOME
+   instead of workspace/ repo checkout dir.
+ - Add Perl 5.34 to CI matrix
+
 Release 3.20.0
  - Add iquest wrapper
 

t/lib/WTSI/NPG/iRODS/GroupAdminTest.pm

@@ -20,7 +20,7 @@ my $have_admin_rights =
 my $group_prefix = 'ss_';
 
 # Groups to be added to the test iRODS
-my @irods_groups = map { $group_prefix . $_ } (0 .. 100);
+my @irods_groups = map { $group_prefix . $_ } (0 .. 5);
 my @irods_users = qw(user_foo user_bar);
 
 my $test_irods = WTSI::NPG::iRODS->new(environment          => \%ENV,
@@ -76,8 +76,9 @@ sub lg : Test(5) {
       skip 'No admin rights to create test groups', 2;
     }
 
-    my @observed_groups = sort $iga->lg;
-    my @expected_groups = sort ('public', 'rodsadmin', @irods_groups);
+    # Ignore the rodsadmin group as it is not present in iRODS >4.3.0
+    my @observed_groups = sort grep { $_ ne 'rodsadmin' } $iga->lg;
+    my @expected_groups = sort ('public', @irods_groups);
     is_deeply(\@observed_groups, \@expected_groups, 'Expected groups found') or
       diag explain \@observed_groups;
 

t/lib/WTSI/NPG/iRODSTest.pm

@@ -231,14 +231,14 @@ sub list_groups : Test(1) {
   my $irods = WTSI::NPG::iRODS->new(environment          => \%ENV,
                                     strict_baton_version => 0);
 
-  ok(grep { /^rodsadmin$/ } $irods->list_groups, 'Listed the rodsadmin group');
+  ok(grep { /^public/ } $irods->list_groups, 'Listed the public group');
 }
 
 sub group_exists : Test(2) {
   my $irods = WTSI::NPG::iRODS->new(environment          => \%ENV,
                                     strict_baton_version => 0);
 
-  ok($irods->group_exists('rodsadmin'), 'The rodsadmin group exists');
+  ok($irods->group_exists('public'), 'The public group exists');
   ok(!$irods->group_exists('no_such_group'), 'An absent group does not exist');
 }