Bugfix

* removed .travis.yml since we don't use them anymore
* added ilastik.IlastikHeader class, which was implied but absent >:(
* fixed github workflow by removing py27 and py35 and quote py3.10
* version bump: v0.6.0.dev1

.github/workflows/python-package.yml

@@ -15,7 +15,7 @@ jobs:
     runs-on: ubuntu-latest
     strategy:
       matrix:
-        python-version: [3.6, 3.7, 3.8, 3.9, 3.10]
+        python-version: [3.6, 3.7, 3.8, 3.9, '3.10']
 
     steps:
     - uses: actions/checkout@v2

CHANGELOG.md

@@ -1,5 +1,13 @@
 #Changes by release
 
+## [0.6.0.dev1] - 2022-09-02
+
+Bugfixes
+
+* removed .travis.yml since we don't use them anymore
+* added ilastik.IlastikHeader class, which was implied but absent >:(
+* fixed github workflow by removing py27 and py35 and quote py3.10
+
 ## [0.6.0.dev0] - 2022-09-01
 
 * dropped support for Python2.7; requires Python3.6+

sfftk/__init__.py

@@ -3,5 +3,5 @@
 
 BASE_DIR = os.path.dirname(__file__)
 
-SFFTK_VERSION = 'v0.6.0.dev0'
+SFFTK_VERSION = 'v0.6.0.dev1'
 

sfftk/formats/ilastik.py

@@ -13,6 +13,11 @@
 from ..readers import ilastikreader
 
 
+class IlastikHeader:
+    def __init__(self, segmentation):
+        self._segmentation = segmentation
+
+
 class IlastikSegment(object):
     """Segment"""
 

sfftk/test_data/sff/v0.8/output_emd_1181.json

@@ -45,15 +45,15 @@
       "id": 15559,
       "parent_id": 0,
       "biological_annotation": {
-        "name": "chart hydrometers trackers",
-        "description": "Nascetur minim dolore voluptua odio, leo minulla dictumst cum ornare elitvivamus. Sociis felissed.",
-        "number_of_instances": 366,
+        "name": "slit factories fire",
+        "description": "Felis ea nec consetetur lobortis, nulla pulvinar sociosqu. Invidunt egestasmauris venenatis integer nullam elit, luptatum euismod elitnunc doming.",
+        "number_of_instances": 587,
         "external_references": [
           {
             "id": 0,
-            "resource": "powders",
-            "url": "conn",
-            "accession": "icing",
+            "resource": "contents",
+            "url": "parameter",
+            "accession": "destinations",
             "label": null,
             "description": null
           }

sfftk/test_data/sff/v0.8/output_emd_1181.sff

@@ -28,12 +28,12 @@
     <segment_list>
         <segment id="15559" parent_id="0">
             <biological_annotation>
-                <name>hip pear transmission</name>
-                <description>Sedfusce enimnulla volutpatut purus, ridiculus nisi accumsan autem. Bibendumfusce phasellus.</description>
+                <name>combatants limitation alternation</name>
+                <description>Facilisisat neque. Sadipscing ametduis conubia.</description>
                 <external_references>
-                    <ref id="0" resource="highline" url="trunk" accession="birth"/>
+                    <ref id="0" resource="buoys" url="laboratories" accession="verbs"/>
                 </external_references>
-                <number_of_instances>89</number_of_instances>
+                <number_of_instances>982</number_of_instances>
             </biological_annotation>
             <colour>
                 <red>0.921817600727081</red>

sfftk/unittests/test_formats.py

@@ -115,6 +115,7 @@ def test_am_read(self):
     def test_ilastik_read(self):
         """Read an ilastik (.h5) segmentation"""
         self.read_ilastik()
+        self.assertIsInstance(self.ilastik_segmentation.header, ilastik.IlastikHeader)
         self.assertIsInstance(list(self.ilastik_segmentation.segments), list)
         self.assertIsInstance(list(self.ilastik_segmentation.segments)[0], ilastik.IlastikSegment)