From a5f0b79b5949bc7751782cec73e89349d8461316 Mon Sep 17 00:00:00 2001
From: Jean-Marie Burel <j.burel@dundee.ac.uk>
Date: Wed, 14 Oct 2020 11:45:40 +0100
Subject: [PATCH 01/20] add issue

---
 .github/workflows/main.yml | 40 ++++++++++++++++++++++++++++++++++++++
 1 file changed, 40 insertions(+)
 create mode 100644 .github/workflows/main.yml

diff --git a/.github/workflows/main.yml b/.github/workflows/main.yml
new file mode 100644
index 00000000000..1e22f3b0298
--- /dev/null
+++ b/.github/workflows/main.yml
@@ -0,0 +1,40 @@
+---
+name: Publish packages
+
+on:
+  push:
+    tags:
+      - 'v*'
+
+jobs:
+  build:
+    runs-on: ubuntu-latest
+
+    steps:
+      - uses: actions/checkout@v2
+      - name: Set up JDK 1.8
+        uses: actions/setup-java@v1
+        with:
+          java-version: 1.8
+      - name: Create Release
+        id: create_release
+        uses: actions/create-release@v1
+        env: 
+          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+        with:
+          tag_name: ${{ github.ref }}
+          release_name: Release ${{ github.ref }}
+          draft: false
+          prerelease: false
+      - name: Upload Release Assets
+        run: |
+          set -x
+          assets=()
+          for asset in ./artifacts/*.jar; do
+            assets+=("-a" "$asset")
+          done
+          tag_name="${GITHUB_REF##*/}"
+          hub release create "${assets[@]}" -m "$tag_name" "$tag_name"
+        env: 
+          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+

From dedba6d39a26ac9b3e554c3d07381b38ae6dd78e Mon Sep 17 00:00:00 2001
From: Jean-Marie Burel <j.burel@dundee.ac.uk>
Date: Wed, 14 Oct 2020 11:54:08 +0100
Subject: [PATCH 02/20] rename

---
 .github/workflows/{main.yml => release.yml} | 0
 1 file changed, 0 insertions(+), 0 deletions(-)
 rename .github/workflows/{main.yml => release.yml} (100%)

diff --git a/.github/workflows/main.yml b/.github/workflows/release.yml
similarity index 100%
rename from .github/workflows/main.yml
rename to .github/workflows/release.yml

From 1b122a2d3c1b046bf7f0de5e40446c6d721b5dda Mon Sep 17 00:00:00 2001
From: Jean-Marie Burel <j.burel@dundee.ac.uk>
Date: Wed, 14 Oct 2020 12:00:05 +0100
Subject: [PATCH 03/20] build with ant and maven

---
 .github/workflows/main.yml | 21 +++++++++++++++++++++
 1 file changed, 21 insertions(+)
 create mode 100644 .github/workflows/main.yml

diff --git a/.github/workflows/main.yml b/.github/workflows/main.yml
new file mode 100644
index 00000000000..cf2de47f461
--- /dev/null
+++ b/.github/workflows/main.yml
@@ -0,0 +1,21 @@
+---
+name: Publish packages
+
+on: [push]
+
+jobs:
+  build:
+    runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        java: [1.8, 11]
+    steps:
+      - uses: actions/checkout@v2
+      - name: Set up JDK 1.8
+        uses: actions/setup-java@v1
+        with:
+          java-version: ${{ matrix.java }}
+      - name: Build with Maven
+        run: ./tools/test-build maven
+      - name: Build with Ant
+        run: ./tools/test-build ant

From 65a6d407a6ae37f82998d31c01885bde926a3403 Mon Sep 17 00:00:00 2001
From: Jean-Marie Burel <j.burel@dundee.ac.uk>
Date: Wed, 14 Oct 2020 12:11:53 +0100
Subject: [PATCH 04/20] change name

---
 .github/workflows/main.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/main.yml b/.github/workflows/main.yml
index cf2de47f461..79b4ac3f223 100644
--- a/.github/workflows/main.yml
+++ b/.github/workflows/main.yml
@@ -11,7 +11,7 @@ jobs:
         java: [1.8, 11]
     steps:
       - uses: actions/checkout@v2
-      - name: Set up JDK 1.8
+      - name: Set up JDK ${{ matrix.java }}
         uses: actions/setup-java@v1
         with:
           java-version: ${{ matrix.java }}

From 8b1c1f2cba2dca0090b6428655ca6dd620b8229a Mon Sep 17 00:00:00 2001
From: Jean-Marie Burel <j.burel@dundee.ac.uk>
Date: Wed, 14 Oct 2020 12:39:19 +0100
Subject: [PATCH 05/20] upload artifacts

---
 .github/workflows/release.yml | 18 +++++-------------
 1 file changed, 5 insertions(+), 13 deletions(-)

diff --git a/.github/workflows/release.yml b/.github/workflows/release.yml
index 1e22f3b0298..f062c5a228f 100644
--- a/.github/workflows/release.yml
+++ b/.github/workflows/release.yml
@@ -12,21 +12,13 @@ jobs:
 
     steps:
       - uses: actions/checkout@v2
-      - name: Set up JDK 1.8
+      - name: Set up JDK 11
         uses: actions/setup-java@v1
         with:
-          java-version: 1.8
-      - name: Create Release
-        id: create_release
-        uses: actions/create-release@v1
-        env: 
-          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
-        with:
-          tag_name: ${{ github.ref }}
-          release_name: Release ${{ github.ref }}
-          draft: false
-          prerelease: false
-      - name: Upload Release Assets
+          java-version: 11
+      - name: Build artifacts
+        run: ./tools/test-build ant
+      - name: Create and Upload Release Assets
         run: |
           set -x
           assets=()

From 354dcd9ba05ce1871322c60f2bbd22b39537541b Mon Sep 17 00:00:00 2001
From: Jean-Marie Burel <j.burel@dundee.ac.uk>
Date: Wed, 14 Oct 2020 14:07:10 +0100
Subject: [PATCH 06/20] add matrix

---
 .github/workflows/main.yml | 7 ++++---
 1 file changed, 4 insertions(+), 3 deletions(-)

diff --git a/.github/workflows/main.yml b/.github/workflows/main.yml
index 79b4ac3f223..7ba1e33a7e9 100644
--- a/.github/workflows/main.yml
+++ b/.github/workflows/main.yml
@@ -1,14 +1,15 @@
 ---
-name: Publish packages
+name: Build with Maven and Ant
 
-on: [push]
+on: [push, pull_request]
 
 jobs:
   build:
-    runs-on: ubuntu-latest
     strategy:
       matrix:
         java: [1.8, 11]
+        os: [ubuntu-latest]
+    runs-on: ${{ matrix.os }}
     steps:
       - uses: actions/checkout@v2
       - name: Set up JDK ${{ matrix.java }}

From 90ecc9f789f8f1edacb3331f1040c107acf18296 Mon Sep 17 00:00:00 2001
From: Jean-Marie Burel <j.burel@dundee.ac.uk>
Date: Wed, 14 Oct 2020 14:07:21 +0100
Subject: [PATCH 07/20] change name

---
 .github/workflows/release.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/release.yml b/.github/workflows/release.yml
index f062c5a228f..12df6535f50 100644
--- a/.github/workflows/release.yml
+++ b/.github/workflows/release.yml
@@ -1,5 +1,5 @@
 ---
-name: Publish packages
+name: Build and publish packages
 
 on:
   push:

From d1e1ab09fa0dd1bb76ca4cc6dca4ceed996513d4 Mon Sep 17 00:00:00 2001
From: Jean-Marie Burel <j.burel@dundee.ac.uk>
Date: Wed, 14 Oct 2020 15:20:02 +0100
Subject: [PATCH 08/20] make py3 compatible

---
 tools/source-archive.py | 4 +---
 1 file changed, 1 insertion(+), 3 deletions(-)

diff --git a/tools/source-archive.py b/tools/source-archive.py
index 1a6e7b50315..85544543af7 100755
--- a/tools/source-archive.py
+++ b/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':

From e755122da973a434403569543cd2ed5cf250a201 Mon Sep 17 00:00:00 2001
From: Jean-Marie Burel <j.burel@dundee.ac.uk>
Date: Wed, 14 Oct 2020 15:37:00 +0100
Subject: [PATCH 09/20] generate sha256

---
 .github/workflows/release.yml | 9 +++++++--
 1 file changed, 7 insertions(+), 2 deletions(-)

diff --git a/.github/workflows/release.yml b/.github/workflows/release.yml
index 12df6535f50..557a133f5e4 100644
--- a/.github/workflows/release.yml
+++ b/.github/workflows/release.yml
@@ -17,14 +17,19 @@ jobs:
         with:
           java-version: 11
       - name: Build artifacts
-        run: ./tools/test-build ant
+        run: |
+          ./tools/test-build ant
+          ant release
       - name: Create and Upload Release Assets
         run: |
           set -x
           assets=()
-          for asset in ./artifacts/*.jar; do
+          touch SHASUMS
+          for asset in ./artifacts/*; do
             assets+=("-a" "$asset")
+            sha256sum $asset >> SHASUMS
           done
+          assets+=("-a" SHASUMS)
           tag_name="${GITHUB_REF##*/}"
           hub release create "${assets[@]}" -m "$tag_name" "$tag_name"
         env: 

From b099cb256f7c6b7352c3b4cc51f3c5b6e30caaf9 Mon Sep 17 00:00:00 2001
From: Jean-Marie Burel <j.burel@dundee.ac.uk>
Date: Wed, 14 Oct 2020 16:24:46 +0100
Subject: [PATCH 10/20] add filename in shasums

---
 .github/workflows/release.yml | 5 ++++-
 1 file changed, 4 insertions(+), 1 deletion(-)

diff --git a/.github/workflows/release.yml b/.github/workflows/release.yml
index 557a133f5e4..8f87d065755 100644
--- a/.github/workflows/release.yml
+++ b/.github/workflows/release.yml
@@ -27,7 +27,10 @@ jobs:
           touch SHASUMS
           for asset in ./artifacts/*; do
             assets+=("-a" "$asset")
-            sha256sum $asset >> SHASUMS
+            filename=$(basename -- "$asset")
+            value=$(sha256sum $asset)
+            IFS=' ' read -r -a array <<< "$value"
+            echo "${array[0]} $filename" >> SHASUMS
           done
           assets+=("-a" SHASUMS)
           tag_name="${GITHUB_REF##*/}"

From cd54f1a88a44bc19231e58e7b2b991fdd253ac6f Mon Sep 17 00:00:00 2001
From: Jean-Marie Burel <j.burel@dundee.ac.uk>
Date: Wed, 14 Oct 2020 20:08:48 +0100
Subject: [PATCH 11/20] add md5

---
 .github/workflows/release.yml | 9 +++++++--
 1 file changed, 7 insertions(+), 2 deletions(-)

diff --git a/.github/workflows/release.yml b/.github/workflows/release.yml
index 8f87d065755..b20389f94e3 100644
--- a/.github/workflows/release.yml
+++ b/.github/workflows/release.yml
@@ -25,14 +25,19 @@ jobs:
           set -x
           assets=()
           touch SHASUMS
+          touch MD5
           for asset in ./artifacts/*; do
             assets+=("-a" "$asset")
             filename=$(basename -- "$asset")
-            value=$(sha256sum $asset)
-            IFS=' ' read -r -a array <<< "$value"
+            sha=$(sha256sum $asset)
+            IFS=' ' read -r -a array <<< "$sha"
             echo "${array[0]} $filename" >> SHASUMS
+            md5=$(md5sum $asset)
+            IFS=' ' read -r -a array <<< "$md5"
+            echo "${array[0]} $filename" >> MD5
           done
           assets+=("-a" SHASUMS)
+          assets+=("-a" MD5)
           tag_name="${GITHUB_REF##*/}"
           hub release create "${assets[@]}" -m "$tag_name" "$tag_name"
         env: 

From 2b1d2e6555a630a886d556379be73b44e6e72086 Mon Sep 17 00:00:00 2001
From: Jean-Marie Burel <j.burel@dundee.ac.uk>
Date: Wed, 14 Oct 2020 21:30:51 +0100
Subject: [PATCH 12/20] check windows

---
 .github/workflows/main.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/main.yml b/.github/workflows/main.yml
index 7ba1e33a7e9..45180404b21 100644
--- a/.github/workflows/main.yml
+++ b/.github/workflows/main.yml
@@ -8,7 +8,7 @@ jobs:
     strategy:
       matrix:
         java: [1.8, 11]
-        os: [ubuntu-latest]
+        os: [ubuntu-latest, windows-2016]
     runs-on: ${{ matrix.os }}
     steps:
       - uses: actions/checkout@v2

From a3563d43d9bed5683d1b19ba8a896d83775267ac Mon Sep 17 00:00:00 2001
From: Jean-Marie Burel <j.burel@dundee.ac.uk>
Date: Wed, 14 Oct 2020 21:45:36 +0100
Subject: [PATCH 13/20] adjust tests

---
 .../test/loci/formats/utests/FormatToolsTest.java     | 11 ++++++++++-
 1 file changed, 10 insertions(+), 1 deletion(-)

diff --git a/components/formats-api/test/loci/formats/utests/FormatToolsTest.java b/components/formats-api/test/loci/formats/utests/FormatToolsTest.java
index fea83375b26..08460bbbdc8 100644
--- a/components/formats-api/test/loci/formats/utests/FormatToolsTest.java
+++ b/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));
   }
 }

From 2c7b054ecaf7b59f93c735eeaec703696299995b Mon Sep 17 00:00:00 2001
From: Jean-Marie Burel <j.burel@dundee.ac.uk>
Date: Wed, 14 Oct 2020 22:03:19 +0100
Subject: [PATCH 14/20] using windows-latest

---
 .github/workflows/main.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/main.yml b/.github/workflows/main.yml
index 45180404b21..3a7759e766f 100644
--- a/.github/workflows/main.yml
+++ b/.github/workflows/main.yml
@@ -8,7 +8,7 @@ jobs:
     strategy:
       matrix:
         java: [1.8, 11]
-        os: [ubuntu-latest, windows-2016]
+        os: [ubuntu-latest, windows-latest]
     runs-on: ${{ matrix.os }}
     steps:
       - uses: actions/checkout@v2

From 6e309bd098574eb44ed72c4f3424d205f767368d Mon Sep 17 00:00:00 2001
From: Jean-Marie Burel <j.burel@dundee.ac.uk>
Date: Thu, 15 Oct 2020 08:25:11 +0100
Subject: [PATCH 15/20] generate the docs

---
 .github/workflows/release.yml | 1 +
 1 file changed, 1 insertion(+)

diff --git a/.github/workflows/release.yml b/.github/workflows/release.yml
index b20389f94e3..f6471141a5f 100644
--- a/.github/workflows/release.yml
+++ b/.github/workflows/release.yml
@@ -20,6 +20,7 @@ jobs:
         run: |
           ./tools/test-build ant
           ant release
+          ant docs
       - name: Create and Upload Release Assets
         run: |
           set -x

From 3316c1f8a72facf9b11f1084e87218229f301005 Mon Sep 17 00:00:00 2001
From: Jean-Marie Burel <j.burel@dundee.ac.uk>
Date: Thu, 15 Oct 2020 14:25:43 +0100
Subject: [PATCH 16/20] make py3 compatible

---
 tools/bump_maven_version.py | 5 +++--
 1 file changed, 3 insertions(+), 2 deletions(-)

diff --git a/tools/bump_maven_version.py b/tools/bump_maven_version.py
index ae143167dd3..56256323b98 100755
--- a/tools/bump_maven_version.py
+++ b/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)

From ec4e40e00f2ce833ae54fbc21f3a97303de82356 Mon Sep 17 00:00:00 2001
From: Jean-Marie Burel <j.burel@dundee.ac.uk>
Date: Thu, 15 Oct 2020 17:10:42 +0100
Subject: [PATCH 17/20] change url

---
 components/formats-bsd/src/loci/formats/UpgradeChecker.java | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/components/formats-bsd/src/loci/formats/UpgradeChecker.java b/components/formats-bsd/src/loci/formats/UpgradeChecker.java
index f487f0820d6..b7a0ef4df85 100644
--- a/components/formats-bsd/src/loci/formats/UpgradeChecker.java
+++ b/components/formats-bsd/src/loci/formats/UpgradeChecker.java
@@ -85,7 +85,7 @@ 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/";
 
   /** Name of the ueber tools JAR. */
   public static final String TOOLS = "bioformats_package.jar";

From 03df3980f9f86a242d5bd2c9512cc65175bf8850 Mon Sep 17 00:00:00 2001
From: Jean-Marie Burel <j.burel@dundee.ac.uk>
Date: Tue, 27 Oct 2020 15:34:11 +0000
Subject: [PATCH 18/20] fix url

---
 components/formats-bsd/src/loci/formats/UpgradeChecker.java | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/components/formats-bsd/src/loci/formats/UpgradeChecker.java b/components/formats-bsd/src/loci/formats/UpgradeChecker.java
index b7a0ef4df85..4c8aedb2ee2 100644
--- a/components/formats-bsd/src/loci/formats/UpgradeChecker.java
+++ b/components/formats-bsd/src/loci/formats/UpgradeChecker.java
@@ -85,7 +85,7 @@ public class UpgradeChecker {
    * Location of the JAR artifacts for the stable releases.
    */
   public static final String STABLE_BUILD =
-    "http://downloads.openmicroscopy.org/bio-formats/";
+    "http://downloads.openmicroscopy.org/bio-formats/latest/artifacts/";
 
   /** Name of the ueber tools JAR. */
   public static final String TOOLS = "bioformats_package.jar";

From 9713aee7c8f6a9b10d487b8fea66118d100392a4 Mon Sep 17 00:00:00 2001
From: Jean-Marie Burel <j.burel@dundee.ac.uk>
Date: Tue, 27 Oct 2020 15:39:12 +0000
Subject: [PATCH 19/20] add deprecated

---
 components/formats-bsd/src/loci/formats/UpgradeChecker.java | 3 +++
 1 file changed, 3 insertions(+)

diff --git a/components/formats-bsd/src/loci/formats/UpgradeChecker.java b/components/formats-bsd/src/loci/formats/UpgradeChecker.java
index 4c8aedb2ee2..57c5de64c69 100644
--- a/components/formats-bsd/src/loci/formats/UpgradeChecker.java
+++ b/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. */

From 5556451c133a936d15fcf90089dc17f41c4c9c8e Mon Sep 17 00:00:00 2001
From: Jean-Marie Burel <j.burel@dundee.ac.uk>
Date: Mon, 2 Nov 2020 20:18:29 +0000
Subject: [PATCH 20/20] remove file not used

---
 .appveyor.yml | 35 -----------------------------------
 1 file changed, 35 deletions(-)
 delete mode 100644 .appveyor.yml

diff --git a/.appveyor.yml b/.appveyor.yml
deleted file mode 100644
index e33500d44fe..00000000000
--- a/.appveyor.yml
+++ /dev/null
@@ -1,35 +0,0 @@
-environment:
-  AV_PROJECTS: 'c:\projects'
-  AV_BF_M2: 'c:\projects\m2'
-  AV_BF_SOURCE: 'c:\projects\bioformats'
-
-# Note that only Oracle JDK is provided.
-  matrix:
-    - java: 11
-      build: maven
-    - java: 1.8
-      build: maven
-    - java: 1.8
-      build: ant
-      ant_version: 1.10.1
-
-cache:
-  - '%AV_BF_M2% -> appveyor.yml'
-
-os: 'Visual Studio 2015'
-clone_folder: '%AV_BF_SOURCE%'
-clone_depth: 5
-platform: x64
-
-init:
-  - git config --global core.autocrlf input
-  - if [%build%] == [ant] appveyor-retry cinst -y ant --version %ant_version%
-  - refreshenv
-  - 'if [%java%] == [1.8] set "JAVA_HOME=C:\Program Files\Java\jdk1.8.0"'
-  - 'if [%java%] == [11] set "JAVA_HOME=C:\Program Files\Java\jdk11"'
-  - PATH=%JAVA_HOME%\bin;%PATH%
-  - 'if [%build%] == [maven] set "MAVEN_OPTS=-Dmaven.repo.local=%AV_BF_M2%"'
-  - 'if [%build%] == [ant] set "ANT_OPTS=-Dmaven.repo.local=%AV_BF_M2%"'
-
-build_script:
-  - tools\test-build %build%