Description
We want to add JPMS module descriptors to the core ImgLib2 artefacts. This issue tracks overall progress on this.
Which repos should be included in this effort?
Which repos should become imglib2 modules (vs. just being updated to use the modularized jars)?
Here is a list of the proj
C075
ects currently in the imglib2 Github org:
$ gh repo list imglib --no-archived
NAME DESCRIPTION
imglib/.github ImgLib organization profile
imglib/dotfiles Configuration files for ImgLib2 resources
imglib/imglib2 A generic next-generation Java library for image processing
imglib/imglib2-advanced-workshop ImgLib2 Advanced Workshop
imglib/imglib2-algorithm Image processing algorithms for ImgLib2
imglib/imglib2-algorithm-fft Fast Fourier Transform routine for ImgLib2
imglib/imglib2-algorithm-gpl Image processing algorithms for ImgLib2 (GPL-licensed)
imglib/imglib2-blog ImgLib2 news and tutorials
imglib/imglib2-cache Cache interfaces and java.lang.ref based implementation.
imglib/imglib2-cache-examples Examples that illustrate imglib2-cache and cached images
imglib/imglib2-cache-python
imglib/imglib2-ij Translation between ImgLib & ImageJ data structures (both 1.x and 2)
imglib/imglib2-imglyb
imglib/imglib2-introductory-workshop ImgLib2 Introductory Workshop
imglib/imglib2-jmh
imglib/imglib2-mesh Proposal for a Java mesh library
imglib/imglib2-realtransform
imglib/imglib2-roi Regions of interest (ROIs) and labelings for ImgLib2
imglib/imglib2-roi-io
imglib/imglib2-tests ImgLib tests that are not bound to specific ImgLib projects
imglib/imglib2-tutorials Examples how to work with ImgLib2
imglib/imglib2-unsafe
imglib/imglib2-www Landing page for imglib2/BDV projects
imglib/imglyb Connecting Java/ImgLib2 + Python/NumPy
imglib/imglyb-bdv Bdv extensions for imglyb
imglib/imglyb-examples
imglib/imglyb-learnathon
Of these, the following are potential candidates for modularization:
(The others are non-Java repositories)
NAME DESCRIPTION
imglib/imglib2 A generic next-generation Java library for image processing
imglib/imglib2-advanced-workshop ImgLib2 Advanced Workshop
imglib/imglib2-algorithm Image processing algorithms for ImgLib2
imglib/imglib2-algorithm-fft Fast Fourier Transform routine for ImgLib2
imglib/imglib2-algorithm-gpl Image processing algorithms for ImgLib2 (GPL-licensed)
imglib/imglib2-cache Cache interfaces and java.lang.ref based implementation.
imglib/imglib2-cache-examples Examples that illustrate imglib2-cache and cached images
imglib/imglib2-cache-python
imglib/imglib2-ij Translation between ImgLib & ImageJ data structures (both 1.x and 2)
imglib/imglib2-imglyb
imglib/imglib2-introductory-workshop ImgLib2 Introductory Workshop
imglib/imglib2-jmh
imglib/imglib2-mesh Proposal for a Java mesh library
imglib/imglib2-realtransform
imglib/imglib2-roi Regions of interest (ROIs) and labelings for ImgLib2
imglib/imglib2-roi-io
imglib/imglib2-tests ImgLib tests that are not bound to specific ImgLib projects
imglib/imglib2-tutorials Examples how to work with ImgLib2
imglib/imglib2-unsafe
Of these repositories, the following contain test or example code.
They don't have released artefacts or dependants.
They should be kept working, but do not need to be modularized themselves.
NAME DESCRIPTION
imglib/imglib2-advanced-workshop ImgLib2 Advanced Workshop
imglib/imglib2-cache-examples Examples that illustrate imglib2-cache and cached images
imglib/imglib2-introductory-workshop ImgLib2 Introductory Workshop
imglib/imglib2-jmh
imglib/imglib2-tests ImgLib tests that are not bound to specific ImgLib projects
imglib/imglib2-tutorials Examples how to work with ImgLib2
The following are related to imglyb (Python bindings).
They should be included in the modularization, but they will probably have no (Java) dependants.
NAME DESCRIPTION
imglib/imglib2-cache-python
imglib/imglib2-imglyb
imglib/imglib2-unsafe
That means we will focus on the following repos first:
NAME DESCRIPTION
imglib/imglib2 A generic next-generation Java library for image processing
imglib/imglib2-algorithm Image processing algorithms for ImgLib2
imglib/imglib2-algorithm-fft Fast Fourier Transform routine for ImgLib2
imglib/imglib2-algorithm-gpl Image processing algorithms for ImgLib2 (GPL-licensed)
imglib/imglib2-cache Cache interfaces and java.lang.ref based implementation.
imglib/imglib2-ij Translation between ImgLib & ImageJ data structures (both 1.x and 2)
imglib/imglib2-mesh Proposal for a Java mesh library
imglib/imglib2-realtransform
imglib/imglib2-roi Regions of interest (ROIs) and labelings for ImgLib2
imglib/imglib2-roi-io
Split packages
At the very minimum, we have to fix instances where the same package is used in two different artefacts.
JPMS disallows splitting packages over module boundaries.
The following split packages exist currently in the core imglib2 repos:
| package | projects |
|---|---|
net.imglib2.type.numeric |
imglib2-unsafe, imglib2 |
net.imglib2.type.numeric.complex |
imglib2-unsafe, imglib2 |
net.imglib2.type.numeric.real |
imglib2-unsafe, imglib2 |
net.imglib2.type |
imglib2-unsafe, imglib2 |
net.imglib2.display.projector |
imglib2-ij, imglib2 |
net.imglib2.img.basictypeaccess |
imglib2-unsafe, imglib2 |
net.imglib2.img |
imglib2-ij, imglib2-unsafe, imglib2 |
net.imglib2.type.numeric.integer |
imglib2-unsafe, imglib2 |
net.imglib2.algorithm.region |
imglib2-algorithm-gpl, imglib2-algorithm |
net.imglib2.algorithm.math |
imglib2-algorithm-gpl, imglib2-algorithm |
net.imglib2.algorithm.fft2 |
imglib2-algorithm-fft, imglib2-algorithm-gpl |
Repo name vs. Automatic module name vs. Package prefix
Before we add module descriptors, we can already decide on module names using the
<package-name> property in the POM of the respective project.
Via pom-scijava, this property is used to set the Automatic-Module-Name property in the jar's MANIFEST.mf.
This will then be used by the JPMS when the plain jars are put on the module path.
Ideally, project name, module name, and package prefix should all match:
If the repo is called imglib2-ij then all the classes should be in packages with prefix net.imglib2.ij.
And the automatic module name should also be net.imglib2.ij
The following is a list of the current automatic module names and package prefixes.
Problems, where they don't match up are highlighted.
| project | automatic module name | package prefix |
|---|---|---|
| imglib2 | net.imglib2 |
net.imglib2 |
| imglib2-algorithm | net.imglib2.algorithm |
net.imglib2 |
| imglib2-algorithm-fft | net.imglib2.algorithm.fft2 | net.imglib2.algorithm.fft2 |
| imglib2-algorithm-gpl | net.imglib2.algorithm | net.imglib2.algorithm |
| imglib2-cache | net.imglib2.cache |
net.imglib2.cache |
| imglib2-ij | net.imglib2.img | net.imglib2 |
| imglib2-mesh | net.imglib2.mesh |
net.imglib2.mesh |
| imglib2-realtransform | net.imglib2.realtransform |
net.imglib2.realtransform |
| imglib2-roi | net.imglib2.roi |
net.imglib2 |
| imglib2-roi-io | net.imglib2.roi.io |
net.imglib2.roi.io.labeling |
| imglib2-cache-python | net.imglib2.cache.python |
net.imglib2.cache.python |
| imglib2-imglyb | net.imglib2.python |
net.imglib2.python |
| imglib2-unsafe | UNDEFINED | net.imglib2 |
Resolving these problems will also resolve split packages.
First steps
We'll start by fixing imglib2-ij. imglib/imglib2-ij#37
To update dependent projects, we need tooling to
- Find all occurrences of specific classes, and update package names.
- Create PRs to the dependent projects.
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