From 81a78e16e237aafab2d05ba4a82a0802affc76f7 Mon Sep 17 00:00:00 2001
From: Rupert Nash <r.nash@epcc.ed.ac.uk>
Date: Tue, 18 Jun 2024 14:07:54 +0100
Subject: [PATCH] Update for dependencies removing deprecations...

---
 .../converters/ExtractedPropertyUnstructuredGridReader.py    | 2 +-
 python-tools/hlb/parsers/extraction.py                       | 2 +-
 python-tools/hlb/parsers/geometry/BaseSite.pyx               | 2 +-
 python-tools/hlb/parsers/geometry/freeing.py                 | 2 +-
 python-tools/hlb/parsers/geometry/generic.py                 | 2 +-
 python-tools/tox.ini                                         | 5 ++---
 6 files changed, 7 insertions(+), 8 deletions(-)

diff --git a/python-tools/hlb/converters/ExtractedPropertyUnstructuredGridReader.py b/python-tools/hlb/converters/ExtractedPropertyUnstructuredGridReader.py
index d86277883..c37a63aee 100644
--- a/python-tools/hlb/converters/ExtractedPropertyUnstructuredGridReader.py
+++ b/python-tools/hlb/converters/ExtractedPropertyUnstructuredGridReader.py
@@ -118,7 +118,7 @@ def _CreateSkeleton(self, input_ug):
         selectors.AddNode(selector)
 
         # Perform the selection
-        extractSelection = vtk.vtkExtractSelectedIds()
+        extractSelection = vtk.vtkExtractSelection()
         extractSelection.SetInputData(0, input_ug)
         extractSelection.SetInputData(1, selectors)
         extractSelection.Update()
diff --git a/python-tools/hlb/parsers/extraction.py b/python-tools/hlb/parsers/extraction.py
index 0742d86d4..9689360a5 100644
--- a/python-tools/hlb/parsers/extraction.py
+++ b/python-tools/hlb/parsers/extraction.py
@@ -289,7 +289,7 @@ def _DetermineTimes(self):
             times[iT] = xdrlib.Unpacker(timeBuf).unpack_uhyper()
             continue
 
-        assert np.alltrue(
+        assert np.all(
             np.argsort(times) == np.arange(len(times))
         ), "Times in extraction file are not monotonically increasing!"
         self.times = times
diff --git a/python-tools/hlb/parsers/geometry/BaseSite.pyx b/python-tools/hlb/parsers/geometry/BaseSite.pyx
index 47c801bdf..d452c882d 100644
--- a/python-tools/hlb/parsers/geometry/BaseSite.pyx
+++ b/python-tools/hlb/parsers/geometry/BaseSite.pyx
@@ -28,7 +28,7 @@ cdef public enum:
     WALL_NORMAL_AVAILABLE = 1
 
 cdef class BaseSite:
-    def __init__(self, block, np.ndarray[np.int_t] sgIdx):
+    def __init__(self, block, np.ndarray[np.int64_t] sgIdx):
         self.GetBlock = weakref.ref(block)
         self.Index = sgIdx
         self.IntersectionType = None
diff --git a/python-tools/hlb/parsers/geometry/freeing.py b/python-tools/hlb/parsers/geometry/freeing.py
index 481a10ffb..fbc43b01a 100644
--- a/python-tools/hlb/parsers/geometry/freeing.py
+++ b/python-tools/hlb/parsers/geometry/freeing.py
@@ -102,7 +102,7 @@ def OnBlockProcessed(self, bIdx):
                     self.OnBlockNeighboursProcessed(nIdx)
                     pass
                 continue
-            if np.alltrue(self.IsBlockDone):
+            if np.all(self.IsBlockDone):
                 self.OnAllBlocksProcessed()
 
         return
diff --git a/python-tools/hlb/parsers/geometry/generic.py b/python-tools/hlb/parsers/geometry/generic.py
index 3cc36caee..d13a3b13f 100644
--- a/python-tools/hlb/parsers/geometry/generic.py
+++ b/python-tools/hlb/parsers/geometry/generic.py
@@ -21,7 +21,7 @@ def __init__(self, shape):
         """shape is the number of elements along each dimension of the
         array."""
 
-        self.shape = np.array(shape).squeeze()
+        self.shape = np.array(shape, dtype=int).squeeze()
         self.ndim = len(self.shape)
         self._conv = np.array(
             [np.prod(self.shape[i:]) for i in range(1, self.ndim + 1)], dtype=int
diff --git a/python-tools/tox.ini b/python-tools/tox.ini
index 17d75c13e..ff5ad6e8e 100644
--- a/python-tools/tox.ini
+++ b/python-tools/tox.ini
@@ -1,14 +1,13 @@
 [tox]
-envlist = py36,py37,py38,py39,py10
+envlist = py38,py39,py310,py311
 isolated_build = true
 
 [gh-actions]
 python =
-    3.6: py36
-    3.7: py37
     3.8: py38
     3.9: py39
     3.10: py310
+    3.11: py311
 
 [testenv]
 deps = -rtest-requirements.txt