Actions build

.github/workflows/ant.yml

@@ -0,0 +1,20 @@
+---
+name: Build with Ant
+
+on: [push, pull_request]
+
+jobs:
+  build:
+    strategy:
+      matrix:
+        java: [1.8, 11]
+        os: [ubuntu-latest, windows-latest]
+    runs-on: ${{ matrix.os }}
+    steps:
+      - uses: actions/checkout@v2
+      - name: Set up JDK ${{ matrix.java }}
+        uses: actions/setup-java@v1
+        with:
+          java-version: ${{ matrix.java }}
+      - name: Build with Ant
+        run: ./tools/test-build ant

.github/workflows/maven.yml

@@ -0,0 +1,20 @@
+---
+name: Build with Maven
+
+on: [push, pull_request]
+
+jobs:
+  build:
+    strategy:
+      matrix:
+        java: [1.8, 11]
+        os: [ubuntu-latest, windows-latest]
+    runs-on: ${{ matrix.os }}
+    steps:
+      - uses: actions/checkout@v2
+      - name: Set up JDK ${{ matrix.java }}
+        uses: actions/setup-java@v1
+        with:
+          java-version: ${{ matrix.java }}
+      - name: Build with Maven
+        run: ./tools/test-build maven

components/formats-api/src/loci/formats/in/DynamicMetadataOptions.java

@@ -516,9 +516,7 @@ public void loadOptions(String optionsFile, ArrayList<String> availableOptionKey
   public static String getMetadataOptionsFile(String id) {
     Location f = new Location(id);
     if (f != null && f.getParent() != null) {
-      String p = f.getParent();
-      String n = f.getName();
-      return new Location(p, n + ".bfoptions").getAbsolutePath();
+      return new Location(id + ".bfoptions").getAbsolutePath();
     }
     return null;
   }

components/formats-api/test/loci/formats/utests/DynamicMetadataOptionsTest.java

@@ -42,6 +42,7 @@
 import static org.testng.Assert.assertEquals;
 import static org.testng.Assert.assertNull;
 
+import loci.common.Location;
 import loci.formats.in.DynamicMetadataOptions;
 import loci.formats.in.MetadataLevel;
 
@@ -372,6 +373,11 @@ public void testIsValidate() {
 
   @Test(dataProvider = "optionFiles")
   public void testGetMetadataOptionsFile(String source, String target) {
+    source = source.replace('/', File.separatorChar);
+    if (target != null) {
+      target = target.replace('/', File.separatorChar);
+      target = (new Location(target)).getAbsolutePath();
+    }
     assertEquals(DynamicMetadataOptions.getMetadataOptionsFile(source), target);
   }
 

components/formats-api/test/loci/formats/utests/FormatToolsTest.java

@@ -32,6 +32,7 @@
 
 package loci.formats.utests;
 
+import java.io.File;
 import loci.common.Constants;
 import loci.formats.FormatTools;
 
@@ -44,6 +45,7 @@
 import org.testng.annotations.Test;
 
 
+
 /**
  * Unit tests for {@link loci.formats.FormatTools}.
  */
@@ -262,6 +264,13 @@ public void testParseLength(String value, String unit, Length length) {
 
   @Test(dataProvider = "fileLists")
   public void testGetRequiredDirectories(String[] files, int number) {
-    assertEquals(number, FormatTools.getRequiredDirectories(files));
+    String[] newfiles = null;
+    if (files != null) {
+      newfiles = new String[files.length];
+      for (int i = 0; i < files.length; i++) {
+        newfiles[i] = files[i].replace('/', File.separatorChar);
+      }
+    }
+    assertEquals(number, FormatTools.getRequiredDirectories(newfiles));
   }
 }

components/formats-bsd/src/loci/formats/UpgradeChecker.java

@@ -64,6 +64,9 @@ public class UpgradeChecker {
   // -- Constants --
 
   /** Version number of the latest stable release. */
+  /**
+   * @deprecated  As of release 6.6.0
+   */
   public static final String STABLE_VERSION = "6.5.1";
 
   /** Location of the OME continuous integration server. */
@@ -85,7 +88,7 @@ public class UpgradeChecker {
    * Location of the JAR artifacts for the stable releases.
    */
   public static final String STABLE_BUILD =
-    "http://downloads.openmicroscopy.org/bio-formats/" +  STABLE_VERSION + "/artifacts/";
+    "http://downloads.openmicroscopy.org/bio-formats/latest/artifacts/";
 
   /** Name of the ueber tools JAR. */
   public static final String TOOLS = "bioformats_package.jar";

tools/bump_maven_version.py

@@ -9,7 +9,7 @@
 
 def check_version_format(version):
     """Check format of version number"""
-    pattern = '^[0-9]+[\.][0-9]+[\.][0-9]+(\-.+)*$'
+    pattern = r'^[0-9]+[\.][0-9]+[\.][0-9]+(\-.+)*$'
     return re.match(pattern, version) is not None
 
 
@@ -18,6 +18,7 @@ def check_version_format(version):
     ".*<artifactId>pom-bio-formats</artifactId>\n"
     ".*<version>).*(</version>)")
 
+
 class Replacer(object):
 
     def __init__(self, old_group="ome", new_group="ome"):
@@ -76,7 +77,7 @@ def bump_stable_version(self, version):
     ns = parser.parse_args()
 
     if not check_version_format(ns.version):
-        print "Invalid version format"
+        print("Invalid version format")
         sys.exit(1)
 
     replacer = Replacer(old_group=ns.old_group, new_group=ns.new_group)

tools/source-archive.py

@@ -6,10 +6,8 @@
 import os
 from subprocess import call
 import sys
-import time
 import zipfile
 import tarfile
-import StringIO
 import platform
 
 # This script archives the base tree and repacks it into a single zip which is
@@ -163,7 +161,7 @@
     basetar.close()
     try:
         call(['xz', "%s/%s.tar" % (options.target, prefix)])
-    except:
+    except Exception:
         # This is expected to fail on Windows when xz is unavailable,
         # but is always an error on all other platforms.
         if platform.system() != 'Windows':