Fiji archive file changed to .zip

[wdlingit]

A minor change that Fiji archive files changed to *.zip and no more *.tar.gz

[github-actions]

Updated software Fiji-20240605-1417.eb

Diff against Fiji-2.14.0-Java-11.eb

easybuild/easyconfigs/f/Fiji/Fiji-2.14.0-Java-11.eb

diff --git a/easybuild/easyconfigs/f/Fiji/Fiji-2.14.0-Java-11.eb b/easybuild/easyconfigs/f/Fiji/Fiji-20240605-1417.eb
index 6e3f4cddae..b3cf00d3a4 100644
--- a/easybuild/easyconfigs/f/Fiji/Fiji-2.14.0-Java-11.eb
+++ b/easybuild/easyconfigs/f/Fiji/Fiji-20240605-1417.eb
@@ -1,8 +1,7 @@
 easyblock = 'PackedBinary'
 
 name = 'Fiji'
-version = '2.14.0'
-versionsuffix = '-Java-%(javaver)s'
+version = '20240605-1417'
 
 homepage = 'https://fiji.sc/'
 description = """Fiji is an image processing package—a 'batteries-included' distribution of
@@ -11,28 +10,31 @@ This release is based on ImageJ-2.1.0 and Fiji-2.1.1"""
 
 toolchain = SYSTEM
 
-source_urls = ['https://downloads.imagej.net/fiji/releases/%(version)s']
-sources = ['%(namelower)s-%(version)s-nojre.zip']
-checksums = ['1dcf6efd7a2c99b70ab921bea3b9e7c74ef99acf35b9857199de7f9c424187db']
+source_urls = ['https://downloads.imagej.net/%(namelower)s/archive/%(version)s']
+sources = [{
+    'download_filename': '%(namelower)s-nojre.zip',
+    'filename': '%(namelower)s-nojre-%(version)s.zip',
+}]
+checksums = ['d9329f79f548db1d74143146215b02f18a005549e57847cf8df3bedb2905ab12']
 
-dependencies = [('Java', '11', '', SYSTEM)]
+dependencies = [('Java', '1.8', '', SYSTEM)]
 
 postinstallcmds = [
     # Remove binaries for other platforms
     'rm %(installdir)s/{ImageJ-win32.exe,ImageJ-win64.exe}',
     # Enable any update site (edit existing site with same parameters to enable it)
     # Full list at https://imagej.github.io/list-of-update-sites/
-    '%(installdir)s/ImageJ-linux64 --default-gc --java-home "$EBROOTJAVA/lib/server/" --headless'
-    ' --update edit-update-site "ImageScience" https://sites.imagej.net/ImageScience/',
-    '%(installdir)s/ImageJ-linux64 --default-gc --java-home "$EBROOTJAVA/lib/server/" --headless'
-    ' --update edit-update-site "3D ImageJ Suite" https://sites.imagej.net/Tboudier/',
-    '%(installdir)s/ImageJ-linux64 --default-gc --java-home "$EBROOTJAVA/lib/server/" --headless'
-    ' --update edit-update-site "ilastik" https://sites.imagej.net/Ilastik/',
+    '%(installdir)s/ImageJ-linux64 --headless --update edit-update-site "ImageScience"'
+    ' https://sites.imagej.net/ImageScience/',
+    '%(installdir)s/ImageJ-linux64 --headless --update edit-update-site "3D ImageJ Suite"'
+    ' https://sites.imagej.net/Tboudier/',
+    '%(installdir)s/ImageJ-linux64 --headless --update edit-update-site "ilastik"'
+    ' https://sites.imagej.net/Ilastik/',
     # Add a new update site
     # '%(installdir)s/ImageJ-linux64 --headless --update add-update-site "New Name"'
     # ' https://site.url/NewName/',
     # Update the installation
-    '%(installdir)s/ImageJ-linux64 --default-gc --java-home "$EBROOTJAVA/lib/server/" --headless --update update',
+    '%(installdir)s/ImageJ-linux64 --headless --update update',
 ]
 
 sanity_check_paths = {
@@ -44,9 +46,6 @@ modloadmsg = """
 Additional plugins can be installed in your $HOME/.plugins folder or requested to user support
 Use ImageJ/Fiji in headless mode in your scripts with the command `ImageJ-linux64 --headless`
 More information at https://imagej.net/Headless
-Also for Fiji 2.14.0 the arguments `--default-gc --java-home "$EBROOTJAVA/lib/server/"`
-should always be used when running `ImageJ-linux64` commands to avoid errors like:
-`Could not load Java library` and `Unrecognized option: -Xincgc`.
 """
 
 moduleclass = 'vis'

Diff against Fiji-2.9.0-Java-8.eb

easybuild/easyconfigs/f/Fiji/Fiji-2.9.0-Java-8.eb

diff --git a/easybuild/easyconfigs/f/Fiji/Fiji-2.9.0-Java-8.eb b/easybuild/easyconfigs/f/Fiji/Fiji-20240605-1417.eb
index a025352372..b3cf00d3a4 100644
--- a/easybuild/easyconfigs/f/Fiji/Fiji-2.9.0-Java-8.eb
+++ b/easybuild/easyconfigs/f/Fiji/Fiji-20240605-1417.eb
@@ -1,21 +1,23 @@
 easyblock = 'PackedBinary'
 
 name = 'Fiji'
-version = '2.9.0'
-versionsuffix = '-Java-%(javaver)s'
+version = '20240605-1417'
 
-homepage = 'https://fiji.sc'
+homepage = 'https://fiji.sc/'
 description = """Fiji is an image processing package—a 'batteries-included' distribution of
  ImageJ, bundling a lot of plugins which facilitate scientific image analysis.
 This release is based on ImageJ-2.1.0 and Fiji-2.1.1"""
 
 toolchain = SYSTEM
 
-source_urls = ['https://downloads.imagej.net/fiji/releases/%(version)s/']
-sources = ['fiji-%(version)s-nojre.zip']
-checksums = ['970fb80cf2a4fe8bfcecc2cc9a8617b9ab28f19fbe229ea6ae2f7f42674c8a42']
+source_urls = ['https://downloads.imagej.net/%(namelower)s/archive/%(version)s']
+sources = [{
+    'download_filename': '%(namelower)s-nojre.zip',
+    'filename': '%(namelower)s-nojre-%(version)s.zip',
+}]
+checksums = ['d9329f79f548db1d74143146215b02f18a005549e57847cf8df3bedb2905ab12']
 
-dependencies = [('Java', '8', '', SYSTEM)]
+dependencies = [('Java', '1.8', '', SYSTEM)]
 
 postinstallcmds = [
     # Remove binaries for other platforms

Diff against Fiji-2.9.0-Java-1.8.eb

easybuild/easyconfigs/f/Fiji/Fiji-2.9.0-Java-1.8.eb

diff --git a/easybuild/easyconfigs/f/Fiji/Fiji-2.9.0-Java-1.8.eb b/easybuild/easyconfigs/f/Fiji/Fiji-20240605-1417.eb
index c655cd1654..b3cf00d3a4 100644
--- a/easybuild/easyconfigs/f/Fiji/Fiji-2.9.0-Java-1.8.eb
+++ b/easybuild/easyconfigs/f/Fiji/Fiji-20240605-1417.eb
@@ -1,19 +1,21 @@
 easyblock = 'PackedBinary'
 
 name = 'Fiji'
-version = '2.9.0'
-versionsuffix = '-Java-%(javaver)s'
+version = '20240605-1417'
 
-homepage = 'https://fiji.sc'
+homepage = 'https://fiji.sc/'
 description = """Fiji is an image processing package—a 'batteries-included' distribution of
  ImageJ, bundling a lot of plugins which facilitate scientific image analysis.
 This release is based on ImageJ-2.1.0 and Fiji-2.1.1"""
 
 toolchain = SYSTEM
 
-source_urls = ['https://downloads.imagej.net/fiji/releases/%(version)s/']
-sources = ['fiji-%(version)s-nojre.zip']
-checksums = ['970fb80cf2a4fe8bfcecc2cc9a8617b9ab28f19fbe229ea6ae2f7f42674c8a42']
+source_urls = ['https://downloads.imagej.net/%(namelower)s/archive/%(version)s']
+sources = [{
+    'download_filename': '%(namelower)s-nojre.zip',
+    'filename': '%(namelower)s-nojre-%(version)s.zip',
+}]
+checksums = ['d9329f79f548db1d74143146215b02f18a005549e57847cf8df3bedb2905ab12']
 
 dependencies = [('Java', '1.8', '', SYSTEM)]
 

[Micket]

I think we should using this. Their github do tag releases:
https://github.com/fiji/fiji/tags
https://github.com/fiji/fiji/archive/refs/tags/fiji-2.16.0.tar.gz

so they do have actual version numbers

[Micket]

1.8 is the old Oracle java, please avoid using it. Based on earlier PRs, at least JAva 11 should work for this software. So, maybe 11 or 17?