Massive refactoring, added SVG export, added names tracks, added converter batch mode, update README, updated years in license text.

AxisAlexNT · AxisAlexNT · commit 296a85cf65b1 · 2026-02-23T05:58:09.000+04:00
diff --git a/LICENSE b/LICENSE
@@ -1,6 +1,6 @@
 MIT License
 
-Copyright (c) 2021-2024 Aleksandr Serdiukov, Anton Zamyatin, Aleksandr Sinitsyn, Vitalii Dravgelis and Computer Technologies Laboratory ITMO University team.
+Copyright (c) 2021-2026 Aleksandr Serdiukov, Anton Zamyatin, Aleksandr Sinitsyn, Vitalii Dravgelis and Computer Technologies Laboratory ITMO University team.
 
 Permission is hereby granted, free of charge, to any person obtaining a copy
 of this software and associated documentation files (the "Software"), to deal
diff --git a/doc/hict.api.ContactMatrixFacet.html b/doc/hict.api.ContactMatrixFacet.html
@@ -1,7 +1,7 @@
 <!--
   ~ MIT License
   ~
-  ~ Copyright (c) 2021-2024. Aleksandr Serdiukov, Anton Zamyatin, Aleksandr Sinitsyn, Vitalii Dravgelis and Computer Technologies Laboratory ITMO University team.
+  ~ Copyright (c) 2021-2026. Aleksandr Serdiukov, Anton Zamyatin, Aleksandr Sinitsyn, Vitalii Dravgelis and Computer Technologies Laboratory ITMO University team.
   ~
   ~ Permission is hereby granted, free of charge, to any person obtaining a copy
   ~ of this software and associated documentation files (the "Software"), to deal
diff --git a/hict/__init__.py b/hict/__init__.py
@@ -1,6 +1,6 @@
 #  MIT License
 #
-#  Copyright (c) 2021-2024. Aleksandr Serdiukov, Anton Zamyatin, Aleksandr Sinitsyn, Vitalii Dravgelis and Computer Technologies Laboratory ITMO University team.
+#  Copyright (c) 2021-2026. Aleksandr Serdiukov, Anton Zamyatin, Aleksandr Sinitsyn, Vitalii Dravgelis and Computer Technologies Laboratory ITMO University team.
 #
 #  Permission is hereby granted, free of charge, to any person obtaining a copy
 #  of this software and associated documentation files (the "Software"), to deal
diff --git a/hict/api/ContactMatrixFacet.py b/hict/api/ContactMatrixFacet.py
@@ -1,6 +1,6 @@
 #  MIT License
 #
-#  Copyright (c) 2021-2024. Aleksandr Serdiukov, Anton Zamyatin, Aleksandr Sinitsyn, Vitalii Dravgelis and Computer Technologies Laboratory ITMO University team.
+#  Copyright (c) 2021-2026. Aleksandr Serdiukov, Anton Zamyatin, Aleksandr Sinitsyn, Vitalii Dravgelis and Computer Technologies Laboratory ITMO University team.
 #
 #  Permission is hereby granted, free of charge, to any person obtaining a copy
 #  of this software and associated documentation files (the "Software"), to deal
diff --git a/hict/api/__init__.py b/hict/api/__init__.py
@@ -1,6 +1,6 @@
 #  MIT License
 #
-#  Copyright (c) 2021-2024. Aleksandr Serdiukov, Anton Zamyatin, Aleksandr Sinitsyn, Vitalii Dravgelis and Computer Technologies Laboratory ITMO University team.
+#  Copyright (c) 2021-2026. Aleksandr Serdiukov, Anton Zamyatin, Aleksandr Sinitsyn, Vitalii Dravgelis and Computer Technologies Laboratory ITMO University team.
 #
 #  Permission is hereby granted, free of charge, to any person obtaining a copy
 #  of this software and associated documentation files (the "Software"), to deal
diff --git a/hict/core/AGPProcessor.py b/hict/core/AGPProcessor.py
@@ -1,6 +1,6 @@
 #  MIT License
 #
-#  Copyright (c) 2021-2024. Aleksandr Serdiukov, Anton Zamyatin, Aleksandr Sinitsyn, Vitalii Dravgelis and Computer Technologies Laboratory ITMO University team.
+#  Copyright (c) 2021-2026. Aleksandr Serdiukov, Anton Zamyatin, Aleksandr Sinitsyn, Vitalii Dravgelis and Computer Technologies Laboratory ITMO University team.
 #
 #  Permission is hereby granted, free of charge, to any person obtaining a copy
 #  of this software and associated documentation files (the "Software"), to deal
diff --git a/hict/core/FASTAProcessor.py b/hict/core/FASTAProcessor.py
@@ -1,6 +1,6 @@
 #  MIT License
 #
-#  Copyright (c) 2021-2024. Aleksandr Serdiukov, Anton Zamyatin, Aleksandr Sinitsyn, Vitalii Dravgelis and Computer Technologies Laboratory ITMO University team.
+#  Copyright (c) 2021-2026. Aleksandr Serdiukov, Anton Zamyatin, Aleksandr Sinitsyn, Vitalii Dravgelis and Computer Technologies Laboratory ITMO University team.
 #
 #  Permission is hereby granted, free of charge, to any person obtaining a copy
 #  of this software and associated documentation files (the "Software"), to deal
diff --git a/hict/core/__init__.py b/hict/core/__init__.py
@@ -1,6 +1,6 @@
 #  MIT License
 #
-#  Copyright (c) 2021-2024. Aleksandr Serdiukov, Anton Zamyatin, Aleksandr Sinitsyn, Vitalii Dravgelis and Computer Technologies Laboratory ITMO University team.
+#  Copyright (c) 2021-2026. Aleksandr Serdiukov, Anton Zamyatin, Aleksandr Sinitsyn, Vitalii Dravgelis and Computer Technologies Laboratory ITMO University team.
 #
 #  Permission is hereby granted, free of charge, to any person obtaining a copy
 #  of this software and associated documentation files (the "Software"), to deal
diff --git a/hict/core/chunked_file.py b/hict/core/chunked_file.py
@@ -1,6 +1,6 @@
 #  MIT License
 #
-#  Copyright (c) 2021-2024. Aleksandr Serdiukov, Anton Zamyatin, Aleksandr Sinitsyn, Vitalii Dravgelis and Computer Technologies Laboratory ITMO University team.
+#  Copyright (c) 2021-2026. Aleksandr Serdiukov, Anton Zamyatin, Aleksandr Sinitsyn, Vitalii Dravgelis and Computer Technologies Laboratory ITMO University team.
 #
 #  Permission is hereby granted, free of charge, to any person obtaining a copy
 #  of this software and associated documentation files (the "Software"), to deal
diff --git a/hict/core/common.py b/hict/core/common.py
@@ -1,6 +1,6 @@
 #  MIT License
 #
-#  Copyright (c) 2021-2024. Aleksandr Serdiukov, Anton Zamyatin, Aleksandr Sinitsyn, Vitalii Dravgelis and Computer Technologies Laboratory ITMO University team.
+#  Copyright (c) 2021-2026. Aleksandr Serdiukov, Anton Zamyatin, Aleksandr Sinitsyn, Vitalii Dravgelis and Computer Technologies Laboratory ITMO University team.
 #
 #  Permission is hereby granted, free of charge, to any person obtaining a copy
 #  of this software and associated documentation files (the "Software"), to deal
diff --git a/hict/core/contig_tree.py b/hict/core/contig_tree.py
@@ -1,6 +1,6 @@
 #  MIT License
 #
-#  Copyright (c) 2021-2024. Aleksandr Serdiukov, Anton Zamyatin, Aleksandr Sinitsyn, Vitalii Dravgelis and Computer Technologies Laboratory ITMO University team.
+#  Copyright (c) 2021-2026. Aleksandr Serdiukov, Anton Zamyatin, Aleksandr Sinitsyn, Vitalii Dravgelis and Computer Technologies Laboratory ITMO University team.
 #
 #  Permission is hereby granted, free of charge, to any person obtaining a copy
 #  of this software and associated documentation files (the "Software"), to deal
diff --git a/hict/core/scaffold_tree.py b/hict/core/scaffold_tree.py
@@ -1,6 +1,6 @@
 #  MIT License
 #
-#  Copyright (c) 2021-2024. Aleksandr Serdiukov, Anton Zamyatin, Aleksandr Sinitsyn, Vitalii Dravgelis and Computer Technologies Laboratory ITMO University team.
+#  Copyright (c) 2021-2026. Aleksandr Serdiukov, Anton Zamyatin, Aleksandr Sinitsyn, Vitalii Dravgelis and Computer Technologies Laboratory ITMO University team.
 #
 #  Permission is hereby granted, free of charge, to any person obtaining a copy
 #  of this software and associated documentation files (the "Software"), to deal
diff --git a/hict/util/__init__.py b/hict/util/__init__.py
@@ -1,6 +1,6 @@
 #  MIT License
 #
-#  Copyright (c) 2021-2024. Aleksandr Serdiukov, Anton Zamyatin, Aleksandr Sinitsyn, Vitalii Dravgelis and Computer Technologies Laboratory ITMO University team.
+#  Copyright (c) 2021-2026. Aleksandr Serdiukov, Anton Zamyatin, Aleksandr Sinitsyn, Vitalii Dravgelis and Computer Technologies Laboratory ITMO University team.
 #
 #  Permission is hereby granted, free of charge, to any person obtaining a copy
 #  of this software and associated documentation files (the "Software"), to deal
diff --git a/hict/util/h5helpers.py b/hict/util/h5helpers.py
@@ -1,6 +1,6 @@
 #  MIT License
 #
-#  Copyright (c) 2021-2024. Aleksandr Serdiukov, Anton Zamyatin, Aleksandr Sinitsyn, Vitalii Dravgelis and Computer Technologies Laboratory ITMO University team.
+#  Copyright (c) 2021-2026. Aleksandr Serdiukov, Anton Zamyatin, Aleksandr Sinitsyn, Vitalii Dravgelis and Computer Technologies Laboratory ITMO University team.
 #
 #  Permission is hereby granted, free of charge, to any person obtaining a copy
 #  of this software and associated documentation files (the "Software"), to deal
diff --git a/hict/util/matrix_visualise.py b/hict/util/matrix_visualise.py
@@ -1,6 +1,6 @@
 #  MIT License
 #
-#  Copyright (c) 2021-2024. Aleksandr Serdiukov, Anton Zamyatin, Aleksandr Sinitsyn, Vitalii Dravgelis and Computer Technologies Laboratory ITMO University team.
+#  Copyright (c) 2021-2026. Aleksandr Serdiukov, Anton Zamyatin, Aleksandr Sinitsyn, Vitalii Dravgelis and Computer Technologies Laboratory ITMO University team.
 #
 #  Permission is hereby granted, free of charge, to any person obtaining a copy
 #  of this software and associated documentation files (the "Software"), to deal
diff --git a/hict/util/persistence/__init__.py b/hict/util/persistence/__init__.py
@@ -1,6 +1,6 @@
 #  MIT License
 #
-#  Copyright (c) 2021-2024. Aleksandr Serdiukov, Anton Zamyatin, Aleksandr Sinitsyn, Vitalii Dravgelis and Computer Technologies Laboratory ITMO University team.
+#  Copyright (c) 2021-2026. Aleksandr Serdiukov, Anton Zamyatin, Aleksandr Sinitsyn, Vitalii Dravgelis and Computer Technologies Laboratory ITMO University team.
 #
 #  Permission is hereby granted, free of charge, to any person obtaining a copy
 #  of this software and associated documentation files (the "Software"), to deal
diff --git a/hict/util/persistence/counter.py b/hict/util/persistence/counter.py
@@ -1,6 +1,6 @@
 #  MIT License
 #
-#  Copyright (c) 2021-2024. Aleksandr Serdiukov, Anton Zamyatin, Aleksandr Sinitsyn, Vitalii Dravgelis and Computer Technologies Laboratory ITMO University team.
+#  Copyright (c) 2021-2026. Aleksandr Serdiukov, Anton Zamyatin, Aleksandr Sinitsyn, Vitalii Dravgelis and Computer Technologies Laboratory ITMO University team.
 #
 #  Permission is hereby granted, free of charge, to any person obtaining a copy
 #  of this software and associated documentation files (the "Software"), to deal
diff --git a/hict/util/persistence/exceptions.py b/hict/util/persistence/exceptions.py
@@ -1,6 +1,6 @@
 #  MIT License
 #
-#  Copyright (c) 2021-2024. Aleksandr Serdiukov, Anton Zamyatin, Aleksandr Sinitsyn, Vitalii Dravgelis and Computer Technologies Laboratory ITMO University team.
+#  Copyright (c) 2021-2026. Aleksandr Serdiukov, Anton Zamyatin, Aleksandr Sinitsyn, Vitalii Dravgelis and Computer Technologies Laboratory ITMO University team.
 #
 #  Permission is hereby granted, free of charge, to any person obtaining a copy
 #  of this software and associated documentation files (the "Software"), to deal
diff --git a/hict/util/persistence/versioned.py b/hict/util/persistence/versioned.py
@@ -1,6 +1,6 @@
 #  MIT License
 #
-#  Copyright (c) 2021-2024. Aleksandr Serdiukov, Anton Zamyatin, Aleksandr Sinitsyn, Vitalii Dravgelis and Computer Technologies Laboratory ITMO University team.
+#  Copyright (c) 2021-2026. Aleksandr Serdiukov, Anton Zamyatin, Aleksandr Sinitsyn, Vitalii Dravgelis and Computer Technologies Laboratory ITMO University team.
 #
 #  Permission is hereby granted, free of charge, to any person obtaining a copy
 #  of this software and associated documentation files (the "Software"), to deal
diff --git a/run_tests.sh b/run_tests.sh
@@ -2,7 +2,7 @@
 #
 # MIT License
 #
-# Copyright (c) 2021-2024. Aleksandr Serdiukov, Anton Zamyatin, Aleksandr Sinitsyn, Vitalii Dravgelis and Computer Technologies Laboratory ITMO University team.
+# Copyright (c) 2021-2026. Aleksandr Serdiukov, Anton Zamyatin, Aleksandr Sinitsyn, Vitalii Dravgelis and Computer Technologies Laboratory ITMO University team.
 #
 # Permission is hereby granted, free of charge, to any person obtaining a copy
 # of this software and associated documentation files (the "Software"), to deal
diff --git a/setup.py b/setup.py
@@ -1,6 +1,6 @@
 #  MIT License
 #
-#  Copyright (c) 2021-2024. Aleksandr Serdiukov, Anton Zamyatin, Aleksandr Sinitsyn, Vitalii Dravgelis and Computer Technologies Laboratory ITMO University team.
+#  Copyright (c) 2021-2026. Aleksandr Serdiukov, Anton Zamyatin, Aleksandr Sinitsyn, Vitalii Dravgelis and Computer Technologies Laboratory ITMO University team.
 #
 #  Permission is hereby granted, free of charge, to any person obtaining a copy
 #  of this software and associated documentation files (the "Software"), to deal
diff --git a/tests/__init__.py b/tests/__init__.py
@@ -1,6 +1,6 @@
 #  MIT License
 #
-#  Copyright (c) 2021-2024. Aleksandr Serdiukov, Anton Zamyatin, Aleksandr Sinitsyn, Vitalii Dravgelis and Computer Technologies Laboratory ITMO University team.
+#  Copyright (c) 2021-2026. Aleksandr Serdiukov, Anton Zamyatin, Aleksandr Sinitsyn, Vitalii Dravgelis and Computer Technologies Laboratory ITMO University team.
 #
 #  Permission is hereby granted, free of charge, to any person obtaining a copy
 #  of this software and associated documentation files (the "Software"), to deal
diff --git a/tests/test_CompareWithCooler.py b/tests/test_CompareWithCooler.py
@@ -1,6 +1,6 @@
 #  MIT License
 #
-#  Copyright (c) 2021-2024. Aleksandr Serdiukov, Anton Zamyatin, Aleksandr Sinitsyn, Vitalii Dravgelis and Computer Technologies Laboratory ITMO University team.
+#  Copyright (c) 2021-2026. Aleksandr Serdiukov, Anton Zamyatin, Aleksandr Sinitsyn, Vitalii Dravgelis and Computer Technologies Laboratory ITMO University team.
 #
 #  Permission is hereby granted, free of charge, to any person obtaining a copy
 #  of this software and associated documentation files (the "Software"), to deal
diff --git a/tests/test_ContigTreeSplitMergeProperties.py b/tests/test_ContigTreeSplitMergeProperties.py
@@ -1,6 +1,6 @@
 #  MIT License
 #
-#  Copyright (c) 2021-2024. Aleksandr Serdiukov, Anton Zamyatin, Aleksandr Sinitsyn, Vitalii Dravgelis and Computer Technologies Laboratory ITMO University team.
+#  Copyright (c) 2021-2026. Aleksandr Serdiukov, Anton Zamyatin, Aleksandr Sinitsyn, Vitalii Dravgelis and Computer Technologies Laboratory ITMO University team.
 #
 #  Permission is hereby granted, free of charge, to any person obtaining a copy
 #  of this software and associated documentation files (the "Software"), to deal
diff --git a/tests/test_ScaffoldTree.py b/tests/test_ScaffoldTree.py
@@ -1,6 +1,6 @@
 #  MIT License
 #
-#  Copyright (c) 2021-2024. Aleksandr Serdiukov, Anton Zamyatin, Aleksandr Sinitsyn, Vitalii Dravgelis and Computer Technologies Laboratory ITMO University team.
+#  Copyright (c) 2021-2026. Aleksandr Serdiukov, Anton Zamyatin, Aleksandr Sinitsyn, Vitalii Dravgelis and Computer Technologies Laboratory ITMO University team.
 #
 #  Permission is hereby granted, free of charge, to any person obtaining a copy
 #  of this software and associated documentation files (the "Software"), to deal
diff --git a/tests/test_pickling.py b/tests/test_pickling.py
@@ -1,6 +1,6 @@
 #  MIT License
 #
-#  Copyright (c) 2021-2024. Aleksandr Serdiukov, Anton Zamyatin, Aleksandr Sinitsyn, Vitalii Dravgelis and Computer Technologies Laboratory ITMO University team.
+#  Copyright (c) 2021-2026. Aleksandr Serdiukov, Anton Zamyatin, Aleksandr Sinitsyn, Vitalii Dravgelis and Computer Technologies Laboratory ITMO University team.
 #
 #  Permission is hereby granted, free of charge, to any person obtaining a copy
 #  of this software and associated documentation files (the "Software"), to deal

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`@@ -1,7 +1,7 @@`
`1`	`1`	`<!--`
`2`	`2`	`~ MIT License`
`3`	`3`	`~`
`4`		`- ~ Copyright (c) 2021-2024. Aleksandr Serdiukov, Anton Zamyatin, Aleksandr Sinitsyn, Vitalii Dravgelis and Computer Technologies Laboratory ITMO University team.`
	`4`	`+ ~ Copyright (c) 2021-2026. Aleksandr Serdiukov, Anton Zamyatin, Aleksandr Sinitsyn, Vitalii Dravgelis and Computer Technologies Laboratory ITMO University team.`
`5`	`5`	`~`
`6`	`6`	`~ Permission is hereby granted, free of charge, to any person obtaining a copy`
`7`	`7`	`~ of this software and associated documentation files (the "Software"), to deal`
Original file line number	Diff line number	Diff line change
`@@ -1,6 +1,6 @@`
`1`	`1`	`# MIT License`
`2`	`2`	`#`
`3`		`-# Copyright (c) 2021-2024. Aleksandr Serdiukov, Anton Zamyatin, Aleksandr Sinitsyn, Vitalii Dravgelis and Computer Technologies Laboratory ITMO University team.`
	`3`	`+# Copyright (c) 2021-2026. Aleksandr Serdiukov, Anton Zamyatin, Aleksandr Sinitsyn, Vitalii Dravgelis and Computer Technologies Laboratory ITMO University team.`
`4`	`4`	`#`
`5`	`5`	`# Permission is hereby granted, free of charge, to any person obtaining a copy`
`6`	`6`	`# of this software and associated documentation files (the "Software"), to deal`