Update superdsm: Fix compatibility with Biocontainers (#178)

* Fix biocontainers compatibility

* Trigger CI

* Update .shed.yml to trigger CI

* [skip-ci] Reset `@VERSION_SUFFIX@`

* Use cleaner solution

* Fix linting

* Add code comment explaining the change

* Remove blank lines

Author: kostrykin

tools/superdsm/.shed.yml

@@ -4,5 +4,5 @@ description: Globally optimal segmentation method based on superadditivity and d
 long_description: Globally optimal segmentation method based on superadditivity and deformable shape models for cell nuclei in 2-D fluorescence microscopy images.
 name: superdsm
 owner: imgteam
-homepage_url: https://github.com/bmcv
+homepage_url: https://superdsm.readthedocs.io
 remote_repository_url: https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/superdsm/

tools/superdsm/run-superdsm.py

@@ -86,10 +86,12 @@ def flatten_dict(d, sep='/'):
     import superdsm.io
     import superdsm.render
 
-    ray.init(num_cpus=num_processes, log_to_driver=True)
-
-    with tempfile.TemporaryDirectory() as tmpdirname:
+    # The explicit `dir` and `prefix` is to avoid breaking the 107 byte limit for socket paths in Biocontainers
+    # See for details: https://github.com/BMCV/galaxy-image-analysis/pull/178
+    with tempfile.TemporaryDirectory(dir='/tmp', prefix='superdsm') as tmpdirname:
         tmpdir = pathlib.Path(tmpdirname)
+        ray.init(num_cpus=num_processes, log_to_driver=True, _temp_dir=str(tmpdir / 'ray'))
+
         img_ext = imghdr.what(args.image)
         img_filepath = tmpdir / f'input.{img_ext}'
         shutil.copy(str(args.image), img_filepath)