Merge branch 'master' into 32-add-a-fat-jar-release

.github/workflows/build.yml

@@ -6,6 +6,13 @@ on:
       - '!refs/tags/.*'
     tags-ignore:
       - '*'
+  pull_request:
+    types: [opened, reopened, synchronize]
+    branches:
+      - '*'
+      - '!refs/tags/.*'
+    tags-ignore:
+      - '*'
 jobs:
   build:
     name: Wave on ${{ matrix.os }}

VERSION

@@ -1 +1 @@
-1.0.0
+1.1.1

app/build.gradle

@@ -1,8 +1,8 @@
 plugins {
     id 'io.seqera.wave.cli.java-application-conventions'
     id 'groovy'
-    id 'org.graalvm.buildtools.native' version '0.9.24'
     id 'com.github.johnrengelman.shadow' version '7.1.2'
+    id 'org.graalvm.buildtools.native' version '0.9.28'
 }
 
 java {
@@ -22,7 +22,7 @@ repositories {
 
 dependencies {
     implementation 'io.seqera:wave-api:0.5.0'
-    implementation 'io.seqera:wave-utils:0.7.8'
+    implementation 'io.seqera:wave-utils:0.8.0'
     implementation 'info.picocli:picocli:4.6.1'
     implementation 'com.squareup.moshi:moshi:1.14.0'
     implementation 'com.squareup.moshi:moshi-adapters:1.14.0'

app/src/main/java/io/seqera/wave/cli/App.java

@@ -366,9 +366,6 @@ protected void validateArgs() {
         if( !isEmpty(platform) && !VALID_PLATFORMS.contains(platform) )
             throw new IllegalCliArgumentException(String.format("Unsupported container platform: '%s'", platform));
 
-        if( singularity && !isEmpty(platform) && platform.contains("arm64") )
-            throw new IllegalCliArgumentException("Options --platform is currently not supported by Singularity native build");
-
     }
 
     protected Client client() {

app/src/main/java/io/seqera/wave/cli/Client.java

@@ -18,7 +18,9 @@
 package io.seqera.wave.cli;
 
 import java.io.IOException;
+import java.net.MalformedURLException;
 import java.net.URI;
+import java.net.URL;
 import java.net.http.HttpClient;
 import java.net.http.HttpRequest;
 import java.net.http.HttpResponse;
@@ -146,11 +148,20 @@ protected HttpResponse<String> httpSend(HttpRequest req)  {
         });
     }
 
+    protected String protocol(String endpoint) {
+        if( StringUtils.isEmpty(endpoint) )
+            return "https://";
+        try {
+            return new URL(endpoint).getProtocol() + "://";
+        } catch (MalformedURLException e) {
+            throw new RuntimeException("Invalid endpoint URL: " + endpoint, e);
+        }
+    }
 
     protected URI imageToManifestUri(String image) {
         final int p = image.indexOf('/');
         if( p==-1 ) throw new IllegalArgumentException("Invalid container name: "+image);
-        final String result = "https://" + image.substring(0,p) + "/v2" + image.substring(p).replace(":","/manifests/");
+        final String result = protocol(endpoint) + image.substring(0,p) + "/v2" + image.substring(p).replace(":","/manifests/");
         return URI.create(result);
     }
 

app/src/main/resources/META-INF/build-info.properties

@@ -16,5 +16,5 @@
 #
 
 name=wave-cli
-version=0.7.0
+version=1.1.0
 commitId=unknown

app/src/test/groovy/io/seqera/wave/cli/AppCondaOptsTest.groovy

@@ -136,6 +136,7 @@ class AppCondaOptsTest extends Specification {
                     && micromamba install -y -n base conda-forge::procps-ng \\
                     && micromamba clean -a -y
                 USER root
+                ENV PATH="$MAMBA_ROOT_PREFIX/bin:$PATH"
                 '''.stripIndent()
         and:
         new String(req.condaFile.decodeBase64()) == CONDA_RECIPE
@@ -162,6 +163,7 @@ class AppCondaOptsTest extends Specification {
                     && micromamba install -y -n base conda-forge::procps-ng \\   
                     && micromamba clean -a -y
                 USER root
+                ENV PATH="$MAMBA_ROOT_PREFIX/bin:$PATH"
                 '''.stripIndent()
         and:
         new String(req.condaFile.decodeBase64()) == '''\
@@ -192,6 +194,7 @@ class AppCondaOptsTest extends Specification {
                     && micromamba install -y -n base conda-forge::procps-ng \\
                     && micromamba clean -a -y
                 USER root
+                ENV PATH="$MAMBA_ROOT_PREFIX/bin:$PATH"
                 '''.stripIndent()
         and:
         req.condaFile == null
@@ -222,6 +225,7 @@ class AppCondaOptsTest extends Specification {
                     && micromamba install -y -n base conda-forge::procps-ng \\
                     && micromamba clean -a -y
                 USER root
+                ENV PATH="$MAMBA_ROOT_PREFIX/bin:$PATH"
                 RUN one
                 RUN two
                 '''.stripIndent()

app/src/test/groovy/io/seqera/wave/cli/AppTest.groovy

@@ -210,18 +210,25 @@ class AppTest extends Specification {
         noExceptionThrown()
     }
 
-    def 'should not allow platform arm64  with singularity' () {
+    def 'should allow platform arm64 with singularity' () {
         given:
         def app = new App()
-        String[] args = ['--singularity', "--platform", 'linux/arm64', '-i', 'ubuntu', '--freeze', '--build-repo', 'docker.io/foo',  '--tower-token', 'xyz']
+        String[] args = [ '--singularity', "--platform", 'linux/arm64',  '-i', 'ubuntu', '--freeze', '--build-repo', 'docker.io/foo',  '--tower-token', 'xyz']
 
         when:
         new CommandLine(app).parseArgs(args)
         and:
         app.validateArgs()
 
         then:
-        def e = thrown(IllegalCliArgumentException)
-        e.message == "Options --platform is currently not supported by Singularity native build"
+        noExceptionThrown()
+        and:
+        app.@platform == 'linux/arm64'
+        app.@image == 'ubuntu'
+        app.@singularity
+        app.@freeze
+        app.@buildRepository == 'docker.io/foo'
+        app.@towerToken == 'xyz'
     }
+
 }

app/src/test/groovy/io/seqera/wave/cli/ClientTest.groovy

@@ -0,0 +1,43 @@
+/*
+ * Copyright 2023, Seqera Labs
+ *
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ *
+ *     http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ *
+ */
+
+package io.seqera.wave.cli
+
+import spock.lang.Specification
+import spock.lang.Unroll
+
+/**
+ *
+ * @author Paolo Di Tommaso <[email protected]>
+ */
+class ClientTest extends Specification {
+
+    @Unroll
+    def 'should get endpoint protocol' () {
+        given:
+        def client = new Client()
+        expect:
+        client.protocol(ENDPOINT) == EXPECTED
+
+        where:
+        ENDPOINT            | EXPECTED
+        null                | 'https://'
+        'http://foo'        | 'http://'
+        'https://bar.com'   | 'https://'
+
+    }
+}

changelog.txt

@@ -1,4 +1,15 @@
 WAVE CLI CHANGE-LOG
 ===================
+1.1.1 - 30 Nov 2023
+- Fix invalid protol prefix with await option [d37faca1]
+- Fix execute CI tests on pull requests (#44) [5e236b0a]
+- Fix error when a context file path is longer than 100 chars (#26) [d8eed21b]
+- Bump org.graalvm.buildtools.native to 0.9.28 (#40) [244be075]
+- Bump gradle 8.4 (#39) [399f0b22]
+
+1.1.0 - 10 Nov 2023
+- Add ability to specify platform for Singularity build [c19727a5]
+- Improve err handling for missing files [98df6ea3]
+
 1.0.0 - 16 Oct 2023
 - Initial release

gradle/wrapper/gradle-wrapper.properties

@@ -17,7 +17,7 @@
 
 distributionBase=GRADLE_USER_HOME
 distributionPath=wrapper/dists
-distributionUrl=https\://services.gradle.org/distributions/gradle-8.2.1-bin.zip
+distributionUrl=https\://services.gradle.org/distributions/gradle-8.4-bin.zip
 networkTimeout=10000
 zipStoreBase=GRADLE_USER_HOME
 zipStorePath=wrapper/dists