Merging dev into release

.github/workflows/bump-version.yml

@@ -46,7 +46,16 @@ jobs:
       - name: Merge release back into dev
         if: github.ref == 'refs/heads/release'
         run: |
-          git fetch origin dev
-          git checkout dev
-          git merge --no-ff origin/release -m "maint: merge release into dev [skip bump]"
+          # Fetch both branches after the release bump.  In particular, the
+          # origin/release ref checked out by actions/checkout can otherwise
+          # still point at the pre-bump commit.
+          git fetch origin dev release
+          git checkout -B dev origin/dev
+
+          # Keep the release version when the version edits conflict.  Other
+          # non-conflicting development changes on dev are retained.
+          git merge --no-ff -X theirs origin/release \
+            -m "maint: merge release into dev [skip bump]"
+
+          uvx bump-my-version bump pre_n --no-tag
           git push origin dev

.gitignore

@@ -163,3 +163,4 @@ openpnm/core/.DS_Store
 *.DS_Store
 *.nblink
 .idea
+.leankg

pyproject.toml

@@ -1,6 +1,6 @@
 [project]
 name = "openpnm"
-version = "3.6.3"
+version = "3.6.3-dev1"
 description = "A framework for conducting pore network modeling simulations of multiphase transport in porous materials"
 authors = [{ name = "OpenPNM Team", email = "jgostick@gmail.com" }]
 maintainers = [
@@ -220,7 +220,7 @@ path = "src/openpnm/__version__.py"
 packages = ["src/openpnm"]
 
 [tool.bumpversion]
-current_version = "3.6.3"
+current_version = "3.6.3-dev1"
 parse = """(?x)
     (?P<major>0|[1-9]\\d*)\\.
     (?P<minor>0|[1-9]\\d*)\\.

src/openpnm/_skgraph/queries/_funcs.py

@@ -357,7 +357,7 @@ def find_neighbor_nodes(network, inds, flatten=True, include_input=False, logic=
     if len(rows) == 0:
         return []
     n_nodes = am.shape[0]
-    neighbors = am_coo.col[np.in1d(am_coo.row, nodes)]
+    neighbors = am_coo.col[np.isin(am_coo.row, nodes)]
     if logic in ["or", "union", "any"]:
         neighbors = np.unique(neighbors)
     elif logic in ["xor", "exclusive_or"]:

src/openpnm/_skgraph/simulations/_percolation.py

@@ -227,9 +227,9 @@ def remove_isolated_clusters(labels, inlets):
     # Remove cluster numbers == -1, if any
     inv_clusters = inv_clusters[inv_clusters >= 0]
     # Find all pores in invading clusters
-    p_invading = np.in1d(labels.site_labels, inv_clusters)
+    p_invading = np.isin(labels.site_labels, inv_clusters)
     labels.site_labels[~p_invading] = -1
-    t_invading = np.in1d(labels.bond_labels, inv_clusters)
+    t_invading = np.isin(labels.bond_labels, inv_clusters)
     labels.bond_labels[~t_invading] = -1
     return labels
 
@@ -268,5 +268,5 @@ def ispercolating(conns, occupied, inlets, outlets):
     outs = np.unique(clusters.site_labels[outlets])
     if outs[0] == -1:
         outs = outs[1:]
-    hits = np.in1d(ins, outs)
+    hits = np.isin(ins, outs)
     return np.any(hits)

src/openpnm/network/_network.py

@@ -816,7 +816,7 @@ def find_nearby_pores(self, pores, r, flatten=False, include_input=False):
         Pn = np.unique(temp).astype(np.int64)
         # Remove inputs if necessary
         if include_input is False:
-            Pn = Pn[~np.in1d(Pn, pores)]
+            Pn = Pn[~np.isin(Pn, pores)]
         # Convert list of lists to a list of ndarrays
         if flatten is False:
             if len(Pn) == 0:  # Deal with no nearby neighbors

src/openpnm/topotools/_perctools.py

@@ -89,7 +89,7 @@ def find_isolated_clusters(network, mask, inlets):
         connected to the given ``inlets``.
     """
     labels = find_clusters(network=network, mask=mask)
-    isolated = np.in1d(labels.pore_labels, labels.pore_labels[inlets], invert=True)
+    isolated = np.isin(labels.pore_labels, labels.pore_labels[inlets], invert=True)
     isolated = np.where(isolated)[0]
     return isolated
 

tests/unit/models/misc/MiscTest.py

@@ -108,7 +108,7 @@ def test_from_neighbor_throats_min(self):
                            propname='pore.seed',
                            prop='throat.seed',
                            mode='min')
-        assert np.all(np.in1d(self.net['pore.seed'], self.net['throat.seed']))
+        assert np.all(np.isin(self.net['pore.seed'], self.net['throat.seed']))
         assert np.isclose(self.net['throat.seed'].mean(), 0.5)
         assert np.isclose(self.net['pore.seed'].mean(), 0.16454849498327762)
 
@@ -121,7 +121,7 @@ def test_from_neighbor_throats_max(self):
                            propname='pore.seed',
                            prop='throat.seed',
                            mode='max')
-        assert np.all(np.in1d(self.net['pore.seed'], self.net['throat.seed']))
+        assert np.all(np.isin(self.net['pore.seed'], self.net['throat.seed']))
         assert np.isclose(self.net['throat.seed'].mean(), 0.5)
         assert np.isclose(self.net['pore.seed'].mean(), 0.8595317725752508)
 

tests/unit/network/GenericNetworkTest.py

@@ -179,7 +179,7 @@ def test_find_nearby_pores_distance_2_flattened_include_input(self):
         a = self.net.find_nearby_pores(pores=[0, 1], r=2,
                                        flatten=True, include_input=True)
         assert np.size(a) == 17
-        assert np.all(np.in1d([0, 1], a))
+        assert np.all(np.isin([0, 1], a))
 
     def test_get_incidence_matrix(self):
         net = op.network.Demo([4, 4, 1])