[ImageJ-devel] ImgLib2 release underway -- plus a question

Curtis Rueden ctrueden at wisc.edu
Tue Oct 28 16:56:58 CDT 2014

Hi everyone,

Earlier this month, LOCI hosted an ImgLib2 hackathon in Madison, with the
goal of finally getting the ImgLib2 core library out of beta. We have been
working through the ramifications of that release for the past week and a
half, but some issues have arisen that complicate matters.

So, this mail is a quick status update on where we are at, and a question
for the community. An official release announcement for ImgLib2 will come
soon, as soon as the issues in question have been fully resolved.

Release status:
- Can always be seen at http://status.imagej.net/
- See the P.S. below for a complete rundown as of this writing.

On to the question. It is technical and Maven-centric, so if you don't care
about that, then feel free to stop reading here.

Background: when preparing for the ImgLib2 release, we decided to
restructure the dependency hierarchy of a couple of components. In
particular, the imglib2-meta component moved into imagej-common. This is

* ImgLib2 now represents the N-dimensional core
* ImageJ (specifically: imagej-common) provides metadata-rich extensions to
that core, built on the SciJava Common plugin framework
* The SCIFIO library provides I/O capabilities also driven by SciJava
Common, built on the metadata-rich image structures of ImageJ.

More details at the newly minted page: http://imagej.net/Architecture

This restructuring exacerbated an already-known problem: the hierarchy of
organizational parent POMs does not, and cannot, match the core library
dependency hierarchy above. Or to put another way: the imagej, imglib2 and
scifio organizations (on GitHub) each have projects that utilize components
from the other two organizations; e.g.:

* https://github.com/imagej/imagej, which provides the top-level ImageJ
application itself depending on both ImgLib2 and SCIFIO libraries
* https://github.com/imglib/imglib2-tutorials, which uses SCIFIO for image
I/O and ImageJ1 for displaying images
* https://github.com/scifio/scifio, which utilizes data structures from
ImgLib2 and ImageJ Common.

Hence, these three organizations are fundamentally interdependent.

One function of the pom-scijava parent (
https://github.com/scijava/pom-scijava) has been to act as a "Bill of
Materials" defining all the component versions which are intended to be
used together. Recently, we factored out a separate Bill of Materials for
each of the three organizations. But then we realized that due to the
interdependence explained above, each of the three parent POMs (pom-imagej,
pom-imglib2 and pom-scifio) needed to inherit the BOMs of all three

Like Java, Maven POMs support only single inheritance. But they do support
a limited form of composition via an "import scope" which allows you to
import the managed dependency versions from a non-parent POM. We tried to
do this, creating three new artifacts -- bom-imagej, bom-imagej and
bom-scifio -- and having each of the three POM parents import all three of
the bom artifacts. But I am sorry to say that after trying it in anger, it
has been a failed experiment. The import scope _only_ supports managed
versions, not properties and not profiles. So we lost access to the version
properties (which are occasionally extremely useful) as well as the dev
profiles (which make it easier to couple the latest versions of multiple
components together for local development). It also locks out the
possibility of any other shared configuration between the projects of the
three affected organizations.

Yesterday and today, we (dscho, hinerm and myself) discussed three
potential solutions to the problem; see the chatlogs [1] for some gory

The solution we converged upon is to put the shared configuration of
pom-imagej, pom-imglib2 and pom-scifio into pom-imagej, and have
pom-imglib2 and pom-scifio now extend pom-imagej instead of pom-scijava
directly. (pom-imagej would still extend pom-scijava, of course.)

We like it because it isolates the version management of those three "core
SciJava orgs" into its own place (rather than "polluting" pom-scijava
directly), but without the need to create yet another potentially confusing
parent POM ("pom-imagej-imglib2-scifio-shared-configuration-and-bom").

The question for the community -- especially Tobias, Stephan P. & Stephan
S. -- is: do you agree? Or do you have any better ideas?

If everyone is OK with it, I will push ahead and complete this work.
Current topic branches are at:

* https://github.com/imagej/pom-imagej/compare/imagej-is-da-bom
* https://github.com/imglib/pom-imglib2/compare/imagej-is-da-bom
* https://github.com/scifio/pom-scifio/compare/imagej-is-da-bom



P.S. Here is the complete rundown of components:

The following components are released:

* imglib2 2.0.1
* imglib2-algorithm 0.1.0
* imglib2-algorithm-fft 0.1.0
* imglib2-algorithm-gpl 0.1.0
* imglib2-ij 2.0.0-beta-27
* imglib2-realtransform 2.0.0-beta-27
* imagej-common 0.10.0
* scifio 0.17.0

The following components are not done yet:

* imglib2-script 0.1.0
* imglib2-tests
* imglib2-tutorials

(Note that for tests and tutorials, it is just a matter of updating the
master branch, since we will never cut Maven release of those.)

* imagej-ops 0.6.0
* imagej-plugins-commands 0.3.0
* imagej-ui-swing 0.8.0
* scifio-ome-xml 0.10.0

And probably others that will become obvious as we proceed further along.

Lastly, each of the following components has an "imglib2-release" branch
which is ostensibly complete but still has build or test failures:

* imglib2-tests
* imglib2-script
* imagej-ops
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