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Decoupling

We are in the process of getting rid of submodules and separating our code into smaller repositories. Why? And why should developers and users care?

The OME development workflow has been following a single, integrated approach for the last couple of years. This means that all components of the OME stack, including OMERO and Bio-Formats are versioned globally and released simultaneously. The only notable exception to this rule is the OME Data Model which is released on its own release cycle to be consumed by major versions of Bio-Formats and OMERO.

While such a global approach can simplify both internal and external communication to a certain extent, it does have several limitations for developers and users. For example, the increasingly-frequent security vulnerabilities (see the recent blog post about the Java security issue) usually require one of our software components to be released with a very fast turnaround without modifying other components. A second example is the release of urgent bug fixes or support for new file formats in Bio-Formats. In the current approach, these updates are held back until a full release of OMERO and Bio-Formats is ready, delaying access and use by a very large community. A single release cycle across all components also does not scale with the diversity, the needs and the size of our user community.

Starting with the 5.1.3 release, we are separating our various software, both at the codebase and release level. We call this process decoupling. This follows a development pattern adopted by other open-source softwares - see for example http://imagej.net/Architecture.

The first concrete application of decoupling is Bio-Formats which had been included as a Git submodule of the OMERO source code since 2011. As of OMERO 5.1.3, Bio-Formats is now treated as any other dependency of OMERO, like Hibernate or Spring. This means:

  • Bio-Formats is now released independently of OMERO as was the case for Bio-Formats 5.1.3 and OMERO 5.1.3.
  • Bio-Formats source code is no longer embedded either directly or via a submodule.
  • Bio-Formats is no longer built as part of the OMERO build system. Instead, the JARs are referenced by their version and consumed from the OME artifactory as part of the build.

Bio-Formats decoupling comes at some cost, it increases the testing burden and the complexity of our build system, but delivers important benefits to the communities that use Bio-Formats such as ImageJ, Fiji, CellProfiler, KNIME, Icy, Matlab, and others.

In the near future, other components of OMERO and Bio-Formats may undergo the same split process. Amongst potential decoupling candidates are:

  • all C++ projects for both OMERO and Bio-Formats
  • all Bio-Formats and OMERO code generation
  • OME documentation

We hope this change is useful for the community. One of the great things about open source software is the ability to learn, change, and adapt, especially as we integrate feedback from the community. We welcome comments from users and developers, and any ideas on how we can continue to improve the tools we deliver.