From 31f3b2077a3f6b8b3a83c23bbaea3e5b93880937 Mon Sep 17 00:00:00 2001
From: Martin Fleischmann <martin@martinfleischmann.net>
Date: Sat, 6 Apr 2024 23:43:29 +0200
Subject: [PATCH 1/7] GAL Graph IO

---
 libpysal/graph/base.py              | 36 ++++++++++++++++++-
 libpysal/graph/io/_gal.py           | 54 +++++++++++++++++++++++++++++
 libpysal/graph/{ => io}/_parquet.py |  0
 3 files changed, 89 insertions(+), 1 deletion(-)
 create mode 100644 libpysal/graph/io/_gal.py
 rename libpysal/graph/{ => io}/_parquet.py (100%)

diff --git a/libpysal/graph/base.py b/libpysal/graph/base.py
index abbd0033d..ff029d07e 100644
--- a/libpysal/graph/base.py
+++ b/libpysal/graph/base.py
@@ -16,7 +16,6 @@
 )
 from ._kernel import _distance_band, _kernel
 from ._matching import _spatial_matching
-from ._parquet import _read_parquet, _to_parquet
 from ._plotting import _explore_graph, _plot
 from ._set_ops import SetOpsMixin
 from ._spatial_lag import _lag_spatial
@@ -27,6 +26,8 @@
     _resolve_islands,
     _sparse_to_arrays,
 )
+from .io._gal import _read_gal, _to_gal
+from .io._parquet import _read_parquet, _to_parquet
 
 ALLOWED_TRANSFORMATIONS = ("O", "B", "R", "D", "V", "C")
 
@@ -1259,6 +1260,22 @@ def to_parquet(self, path, **kwargs):
         """
         _to_parquet(self, path, **kwargs)
 
+    def to_gal(self, path):
+        """Save Graph to a GAL file
+
+        Graph is serialized to the GAL file format.
+
+        Parameters
+        ----------
+        path : str
+            path to the GAL file
+
+        See also
+        --------
+        read_gal
+        """
+        _to_gal(self, path)
+
     def to_networkx(self):
         """Convert Graph to a ``networkx`` graph.
 
@@ -1614,3 +1631,20 @@ def read_parquet(path, **kwargs):
     """
     adjacency, transformation = _read_parquet(path, **kwargs)
     return Graph(adjacency, transformation, is_sorted=True)
+
+
+def read_gal(path):
+    """Read Graph from a GAL file
+
+    Parameters
+    ----------
+    path : str
+        path to a file
+
+    Returns
+    -------
+    Graph
+        deserialized Graph
+    """
+    neighbors = _read_gal(path)
+    return Graph.from_dicts(neighbors)
diff --git a/libpysal/graph/io/_gal.py b/libpysal/graph/io/_gal.py
new file mode 100644
index 000000000..e010ddb5d
--- /dev/null
+++ b/libpysal/graph/io/_gal.py
@@ -0,0 +1,54 @@
+def _read_gal(path):
+    """Read GAL weights to Graph object
+
+    Parameters
+    ----------
+    path : str
+        path to GAL file
+
+    Returns
+    -------
+    dict
+        neighbors dict
+    """
+    with open(path) as file:
+        neighbors = {}
+
+        # handle case where more than n is specified in first line
+        header = file.readline().strip().split()
+        header_n = len(header)
+        n = int(header[0])
+
+        if header_n > 1:
+            n = int(header[1])
+
+        for _ in range(n):
+            id_, _ = file.readline().strip().split()
+            neighbors_i = file.readline().strip().split()
+            neighbors[id_] = neighbors_i
+    return neighbors
+
+
+def _to_gal(graph_obj, path):
+    """Write GAL weights to Graph object
+
+    Parameters
+    ----------
+    path : str
+        path to GAL file
+    neighbors : dict
+        neighbors dict
+    """
+    grouper = graph_obj._adjacency.groupby(level=0, sort=False)
+
+    with open(path, "w") as file:
+        file.write(f"{graph_obj.n}\n")
+
+        for ix, chunk in grouper:
+            if ix in graph_obj.isolates:
+                neighbors = []
+            else:
+                neighbors = chunk.index.get_level_values("neighbor").tolist()
+
+            file.write(f"{ix} {len(neighbors)}\n")
+            file.write(" ".join(neighbors) + "\n")
diff --git a/libpysal/graph/_parquet.py b/libpysal/graph/io/_parquet.py
similarity index 100%
rename from libpysal/graph/_parquet.py
rename to libpysal/graph/io/_parquet.py

From fa74d6ef5af7e52c20bf98c55d33b4295655cfe8 Mon Sep 17 00:00:00 2001
From: Martin Fleischmann <martin@martinfleischmann.net>
Date: Sun, 7 Apr 2024 23:36:46 +0200
Subject: [PATCH 2/7] GWT

---
 libpysal/graph/__init__.py |  2 +-
 libpysal/graph/base.py     | 34 ++++++++++++++++++++++++++++++++++
 libpysal/graph/io/_gal.py  |  4 ++--
 libpysal/graph/io/_gwt.py  | 38 ++++++++++++++++++++++++++++++++++++++
 4 files changed, 75 insertions(+), 3 deletions(-)
 create mode 100644 libpysal/graph/io/_gwt.py

diff --git a/libpysal/graph/__init__.py b/libpysal/graph/__init__.py
index 5e0c34c35..69bf59f0a 100644
--- a/libpysal/graph/__init__.py
+++ b/libpysal/graph/__init__.py
@@ -1 +1 @@
-from .base import Graph, read_parquet  # noqa
+from .base import Graph, read_parquet, read_gal, read_gwt  # noqa
diff --git a/libpysal/graph/base.py b/libpysal/graph/base.py
index ff029d07e..dd3a55ab4 100644
--- a/libpysal/graph/base.py
+++ b/libpysal/graph/base.py
@@ -27,6 +27,7 @@
     _sparse_to_arrays,
 )
 from .io._gal import _read_gal, _to_gal
+from .io._gwt import _read_gwt, _to_gwt
 from .io._parquet import _read_parquet, _to_parquet
 
 ALLOWED_TRANSFORMATIONS = ("O", "B", "R", "D", "V", "C")
@@ -1276,6 +1277,22 @@ def to_gal(self, path):
         """
         _to_gal(self, path)
 
+    def to_gwt(self, path):
+        """Save Graph to a GWT file
+
+        Graph is serialized to the GWT file format.
+
+        Parameters
+        ----------
+        path : str
+            path to the GWT file
+
+        See also
+        --------
+        read_gwt
+        """
+        _to_gwt(self, path)
+
     def to_networkx(self):
         """Convert Graph to a ``networkx`` graph.
 
@@ -1648,3 +1665,20 @@ def read_gal(path):
     """
     neighbors = _read_gal(path)
     return Graph.from_dicts(neighbors)
+
+
+def read_gwt(path):
+    """Read Graph from a GWT file
+
+    Parameters
+    ----------
+    path : str
+        path to a file
+
+    Returns
+    -------
+    Graph
+        deserialized Graph
+    """
+    head, tail, weight = _read_gwt(path)
+    return Graph.from_arrays(head, tail, weight)
diff --git a/libpysal/graph/io/_gal.py b/libpysal/graph/io/_gal.py
index e010ddb5d..a0d43b688 100644
--- a/libpysal/graph/io/_gal.py
+++ b/libpysal/graph/io/_gal.py
@@ -34,10 +34,10 @@ def _to_gal(graph_obj, path):
 
     Parameters
     ----------
+    graph_obj : Graph
+        Graph object
     path : str
         path to GAL file
-    neighbors : dict
-        neighbors dict
     """
     grouper = graph_obj._adjacency.groupby(level=0, sort=False)
 
diff --git a/libpysal/graph/io/_gwt.py b/libpysal/graph/io/_gwt.py
new file mode 100644
index 000000000..8b47ee528
--- /dev/null
+++ b/libpysal/graph/io/_gwt.py
@@ -0,0 +1,38 @@
+import pandas as pd
+
+
+def _read_gwt(path):
+    """
+    Read GWT weights to Graph object
+
+    Parameters
+    ----------
+    path : str
+        path to GWT file
+
+    Returns
+    -------
+    tuple
+        focal, neighbor, weight arrays
+    """
+    adjacency = pd.read_csv(path, sep=r"\s+", skiprows=1, header=None)
+    return adjacency[0].values, adjacency[1].values, adjacency[2].values
+
+
+def _to_gwt(graph_obj, path):
+    """
+    Write GWT weights to Graph object
+
+    Parameters
+    ----------
+    graph_obj : Graph
+        Graph object
+    path : str
+        path to GAL file
+    """
+    adj = graph_obj._adjacency.reset_index()
+    adj["focal"] = adj["focal"].astype(str).str.replace(" ", "_")
+    adj["neighbor"] = adj["neighbor"].astype(str).str.replace(" ", "_")
+    with open(path, "w") as file:
+        file.write(f"0 {graph_obj.n} Unknown Unknown\n")
+    adj.to_csv(path, sep=" ", header=False, index=False, mode="a", float_format="%.7f")

From e8db7751ee0188431a0c8a328a6cec7bb0fe52d2 Mon Sep 17 00:00:00 2001
From: Martin Fleischmann <martin@martinfleischmann.net>
Date: Mon, 20 May 2024 21:31:44 +0200
Subject: [PATCH 3/7] tests + necessary bugfixes

---
 libpysal/graph/_contiguity.py     |  8 ++++++--
 libpysal/graph/_utils.py          | 18 ++++++++++--------
 libpysal/graph/base.py            |  3 +++
 libpysal/graph/io/_gal.py         | 12 +++++++++++-
 libpysal/graph/tests/test_base.py | 26 ++++++++++++++++++++++++++
 5 files changed, 56 insertions(+), 11 deletions(-)

diff --git a/libpysal/graph/_contiguity.py b/libpysal/graph/_contiguity.py
index c28b3104b..76bb83500 100644
--- a/libpysal/graph/_contiguity.py
+++ b/libpysal/graph/_contiguity.py
@@ -77,8 +77,12 @@ def _vertex_set_intersection(geoms, rook=True, ids=None, by_perimeter=False):
         nexus_names = {ids[ix] for ix in nexus}
         for geom_ix in nexus:
             gid = ids[geom_ix]
-            graph[gid] |= nexus_names
-            graph[gid].remove(gid)
+            graph[gid].update(nexus_names)
+
+    for idx in ids:
+        graph[idx].remove(idx)
+
+    # return graph
 
     heads, tails, weights = _neighbor_dict_to_edges(graph)
 
diff --git a/libpysal/graph/_utils.py b/libpysal/graph/_utils.py
index 8cab2f674..9d40685b7 100644
--- a/libpysal/graph/_utils.py
+++ b/libpysal/graph/_utils.py
@@ -109,13 +109,15 @@ def _neighbor_dict_to_edges(neighbors, weights=None):
     that the any self-loops have a weight of zero.
     """
     idxs = pd.Series(neighbors).explode()
-    with warnings.catch_warnings():
-        warnings.filterwarnings(
-            "ignore",
-            "Downcasting object dtype arrays on .fillna, .ffill, .bfill ",
-            FutureWarning,
-        )
-        idxs = idxs.fillna(pd.Series(idxs.index, index=idxs.index))  # self-loops
+    isolates = idxs.isna()
+    if isolates.any():
+        with warnings.catch_warnings():
+            warnings.filterwarnings(
+                "ignore",
+                "Downcasting object dtype arrays on .fillna, .ffill, .bfill ",
+                FutureWarning,
+            )
+            idxs = idxs.fillna(pd.Series(idxs.index, index=idxs.index))  # self-loops
     heads, tails = idxs.index.values, idxs.values
     tails = tails.astype(heads.dtype)
     if weights is not None:
@@ -130,7 +132,7 @@ def _neighbor_dict_to_edges(neighbors, weights=None):
             data_array = pd.to_numeric(data_array)
     else:
         data_array = np.ones(idxs.shape[0], dtype=int)
-        data_array[heads == tails] = 0
+        data_array[isolates] = 0
     return heads, tails, data_array
 
 
diff --git a/libpysal/graph/base.py b/libpysal/graph/base.py
index dd3a55ab4..6a8598039 100644
--- a/libpysal/graph/base.py
+++ b/libpysal/graph/base.py
@@ -1653,6 +1653,9 @@ def read_parquet(path, **kwargs):
 def read_gal(path):
     """Read Graph from a GAL file
 
+    The reader tries to infer the dtype of IDs. In case of unsuccessful
+    casting to int, it will fall back to string.
+
     Parameters
     ----------
     path : str
diff --git a/libpysal/graph/io/_gal.py b/libpysal/graph/io/_gal.py
index a0d43b688..0042de911 100644
--- a/libpysal/graph/io/_gal.py
+++ b/libpysal/graph/io/_gal.py
@@ -1,3 +1,6 @@
+import contextlib
+
+
 def _read_gal(path):
     """Read GAL weights to Graph object
 
@@ -26,6 +29,11 @@ def _read_gal(path):
             id_, _ = file.readline().strip().split()
             neighbors_i = file.readline().strip().split()
             neighbors[id_] = neighbors_i
+
+    # try casting to ints to ensure loss-less roundtrip of integer node ids
+    with contextlib.suppress(ValueError):
+        neighbors = {int(k): list(map(int, v)) for k, v in neighbors.items()}
+
     return neighbors
 
 
@@ -48,7 +56,9 @@ def _to_gal(graph_obj, path):
             if ix in graph_obj.isolates:
                 neighbors = []
             else:
-                neighbors = chunk.index.get_level_values("neighbor").tolist()
+                neighbors = (
+                    chunk.index.get_level_values("neighbor").astype(str).tolist()
+                )
 
             file.write(f"{ix} {len(neighbors)}\n")
             file.write(" ".join(neighbors) + "\n")
diff --git a/libpysal/graph/tests/test_base.py b/libpysal/graph/tests/test_base.py
index f5b83724c..cd24885e6 100644
--- a/libpysal/graph/tests/test_base.py
+++ b/libpysal/graph/tests/test_base.py
@@ -824,6 +824,32 @@ def test_parquet(self):
             g_pandas = graph.read_parquet(path)
             assert self.g_str == g_pandas
 
+    def test_gal(self):
+        with tempfile.TemporaryDirectory() as tmpdir:
+            path = os.path.join(tmpdir, "g_int.gal")
+            g_int = self.g_int.transform("b")
+            g_int.to_gal(path)
+            g_int_ = graph.read_gal(path)
+            assert g_int == g_int_
+
+            path = os.path.join(tmpdir, "g_str.gal")
+            g_str = self.g_str.transform("b")
+            g_str.to_gal(path)
+            g_str_ = graph.read_gal(path)
+            assert g_str == g_str_
+
+    def test_gwt(self):
+        with tempfile.TemporaryDirectory() as tmpdir:
+            path = os.path.join(tmpdir, "g_int.gwt")
+            self.g_int.to_gwt(path)
+            g_int = graph.read_gwt(path)
+            assert self.g_int == g_int
+
+            path = os.path.join(tmpdir, "g_str.gwt")
+            self.g_str.to_gwt(path)
+            g_str = graph.read_gwt(path)
+            assert self.g_str == g_str
+
     def test_getitem(self):
         expected = pd.Series(
             [1, 0.5, 0.5],

From 402ece500dc0d2d502fe7aa006a3105bde31c640 Mon Sep 17 00:00:00 2001
From: Martin Fleischmann <martin@martinfleischmann.net>
Date: Mon, 20 May 2024 21:34:02 +0200
Subject: [PATCH 4/7] allow full path imports

---
 libpysal/__init__.py   | 2 +-
 libpysal/graph/base.py | 7 +++++++
 2 files changed, 8 insertions(+), 1 deletion(-)

diff --git a/libpysal/__init__.py b/libpysal/__init__.py
index 72ddee53a..8b49fb0ec 100644
--- a/libpysal/__init__.py
+++ b/libpysal/__init__.py
@@ -24,7 +24,7 @@
 import contextlib
 from importlib.metadata import PackageNotFoundError, version
 
-from . import cg, examples, io, weights
+from . import cg, examples, graph, io, weights
 
 with contextlib.suppress(PackageNotFoundError):
     __version__ = version("libpysal")
diff --git a/libpysal/graph/base.py b/libpysal/graph/base.py
index 6a8598039..c9d673b28 100644
--- a/libpysal/graph/base.py
+++ b/libpysal/graph/base.py
@@ -40,6 +40,13 @@
 Levi John Wolf (levi.john.wolf@gmail.com)
 """
 
+__all__ = [
+    "Graph",
+    "read_parquet",
+    "read_gal",
+    "read_gwt",
+]
+
 
 class Graph(SetOpsMixin):
     """Graph class encoding spatial weights matrices

From e9d5da4ba23af96be10e43848e18ddfc4f2eb3e2 Mon Sep 17 00:00:00 2001
From: Martin Fleischmann <martin@martinfleischmann.net>
Date: Mon, 20 May 2024 21:53:45 +0200
Subject: [PATCH 5/7] compat

---
 libpysal/graph/_utils.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/libpysal/graph/_utils.py b/libpysal/graph/_utils.py
index 9d40685b7..ea957fc80 100644
--- a/libpysal/graph/_utils.py
+++ b/libpysal/graph/_utils.py
@@ -132,7 +132,7 @@ def _neighbor_dict_to_edges(neighbors, weights=None):
             data_array = pd.to_numeric(data_array)
     else:
         data_array = np.ones(idxs.shape[0], dtype=int)
-        data_array[isolates] = 0
+        data_array[isolates.values] = 0
     return heads, tails, data_array
 
 

From f014971544034f296324693974c5443b9cf79e25 Mon Sep 17 00:00:00 2001
From: Martin Fleischmann <martin@martinfleischmann.net>
Date: Mon, 20 May 2024 22:24:22 +0200
Subject: [PATCH 6/7] pull the latest tobler

---
 ci/312-dev.yaml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/ci/312-dev.yaml b/ci/312-dev.yaml
index 5bf7585d5..5f0995470 100644
--- a/ci/312-dev.yaml
+++ b/ci/312-dev.yaml
@@ -10,7 +10,6 @@ dependencies:
   # testing
   - codecov
   - matplotlib
-  - tobler
   - h3-py
   - pytest
   - pytest-cov
@@ -39,4 +38,5 @@ dependencies:
       - xarray
       - git+https://github.com/geopandas/geopandas.git@main
       - git+https://github.com/shapely/shapely.git@main
+      - git+https://github.com/pysal/tobler.git@main
       - pulp

From ef6bfdca868d16f8a79d578af2ae89d87fa3ea2e Mon Sep 17 00:00:00 2001
From: Martin Fleischmann <martin@martinfleischmann.net>
Date: Mon, 27 May 2024 16:15:42 +0200
Subject: [PATCH 7/7] cleanup

---
 libpysal/graph/_contiguity.py | 2 --
 1 file changed, 2 deletions(-)

diff --git a/libpysal/graph/_contiguity.py b/libpysal/graph/_contiguity.py
index 76bb83500..deed456db 100644
--- a/libpysal/graph/_contiguity.py
+++ b/libpysal/graph/_contiguity.py
@@ -82,8 +82,6 @@ def _vertex_set_intersection(geoms, rook=True, ids=None, by_perimeter=False):
     for idx in ids:
         graph[idx].remove(idx)
 
-    # return graph
-
     heads, tails, weights = _neighbor_dict_to_edges(graph)
 
     if by_perimeter: