From 41767a26027f3f5802f0370572ce936deb408952 Mon Sep 17 00:00:00 2001
From: Dongdong Tian <seisman.info@gmail.com>
Date: Fri, 22 Sep 2023 13:23:22 +0800
Subject: [PATCH 01/15] Figure.savefig: Support generating GeoTIFF file (with
 extension '.tiff')

---
 pygmt/figure.py | 32 +++++++++++++++++++++-----------
 1 file changed, 21 insertions(+), 11 deletions(-)

diff --git a/pygmt/figure.py b/pygmt/figure.py
index f8b631e7102..a511855f3b7 100644
--- a/pygmt/figure.py
+++ b/pygmt/figure.py
@@ -257,12 +257,19 @@ def savefig(
         """
         Save the figure to a file.
 
-        This method implements a matplotlib-like interface for
-        :meth:`pygmt.Figure.psconvert`.
+        Supported file formats and their extensions:
 
-        Supported formats: PNG (``.png``), JPEG (``.jpg`` or ``.jpeg``),
-        PDF (``.pdf``), BMP (``.bmp``), TIFF (``.tif``), EPS (``.eps``), and
-        KML (``.kml``). The KML output generates a companion PNG file.
+        - PNG (``.png``)
+        - JPEG (``.jpg`` or ``.jpeg``)
+        - PDF (``.pdf``)
+        - BMP (``.bmp``)
+        - TIFF (``.tif`` or `.tiff`)
+        - EPS (``.eps``)
+        - KML (``.kml``)
+
+        For TIFF format, ``.tiff`` generates a GeoTIFF file with embedded
+        georeferencing information and a companion world file. For KML format,
+        a companion PNG file is also generated.
 
         You can pass in any keyword arguments that
         :meth:`pygmt.Figure.psconvert` accepts.
@@ -279,8 +286,8 @@ def savefig(
             If ``True``, will crop the figure canvas (page) to the plot area.
         anti_alias: bool
             If ``True``, will use anti-aliasing when creating raster images
-            (PNG, JPG, TIFF). More specifically, it passes arguments ``t2``
-            and ``g2`` to the ``anti_aliasing`` parameter of
+            (BMP, PNG, JPEG and TIFF). More specifically, it passes arguments
+            ``t2`` and ``g2`` to the ``anti_aliasing`` parameter of
             :meth:`pygmt.Figure.psconvert`. Ignored if creating vector
             graphics.
         show: bool
@@ -307,9 +314,14 @@ def savefig(
         fname = Path(fname)
         prefix, suffix = fname.with_suffix("").as_posix(), fname.suffix
         ext = suffix[1:].lower()  # Remove the . and normalize to lowercase
-        # alias jpeg to jpg
-        if ext == "jpeg":
+
+        if ext == "jpeg":  # Alias jpeg to jpg
             ext = "jpg"
+        elif ext == "tiff":  # Alias tif to tiff and make it a GeoTIFF
+            ext = "tif"
+            kwargs["W"] = "+g"
+        elif ext == "kml":
+            kwargs["W"] = "+k"
 
         if ext not in fmts:
             if ext == "ps":
@@ -328,8 +340,6 @@ def savefig(
         if anti_alias:
             kwargs["Qt"] = 2
             kwargs["Qg"] = 2
-        if ext == "kml":
-            kwargs["W"] = "+k"
 
         self.psconvert(prefix=prefix, fmt=fmt, crop=crop, **kwargs)
 

From cd9918fe42de4238b96ba0797504bf9fa7f03d36 Mon Sep 17 00:00:00 2001
From: Dongdong Tian <seisman.info@gmail.com>
Date: Fri, 22 Sep 2023 13:35:16 +0800
Subject: [PATCH 02/15] Test the .tiff extension

---
 pygmt/tests/test_figure.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/pygmt/tests/test_figure.py b/pygmt/tests/test_figure.py
index f01df85f942..b7b97ed507f 100644
--- a/pygmt/tests/test_figure.py
+++ b/pygmt/tests/test_figure.py
@@ -83,7 +83,7 @@ def test_figure_savefig_exists():
     fig = Figure()
     fig.basemap(region="10/70/-300/800", projection="X3i/5i", frame="af")
     prefix = "test_figure_savefig_exists"
-    for fmt in "png pdf jpg jpeg bmp eps tif PNG JPG JPEG Png".split():
+    for fmt in "png pdf jpg jpeg bmp eps tif tiff PNG JPG JPEG Png".split():
         fname = ".".join([prefix, fmt])
         fig.savefig(fname)
 

From f2348ccb68642e0ac9b0c7ae7361af3b3753a36b Mon Sep 17 00:00:00 2001
From: Dongdong Tian <seisman.info@gmail.com>
Date: Fri, 22 Sep 2023 22:44:07 +0800
Subject: [PATCH 03/15] GeoTIFF doesn't need the -T option

---
 pygmt/figure.py | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/pygmt/figure.py b/pygmt/figure.py
index a511855f3b7..65cc6432ef3 100644
--- a/pygmt/figure.py
+++ b/pygmt/figure.py
@@ -308,6 +308,7 @@ def savefig(
             "bmp": "b",
             "eps": "e",
             "tif": "t",
+            "tiff": None,  # GeoTIFF doesn't need the -T option
             "kml": "g",
         }
 
@@ -317,10 +318,9 @@ def savefig(
 
         if ext == "jpeg":  # Alias jpeg to jpg
             ext = "jpg"
-        elif ext == "tiff":  # Alias tif to tiff and make it a GeoTIFF
-            ext = "tif"
+        elif ext == "tiff":  # GeoTIFF
             kwargs["W"] = "+g"
-        elif ext == "kml":
+        elif ext == "kml":  # KML
             kwargs["W"] = "+k"
 
         if ext not in fmts:

From 921912d842c5414c37aa8f592b70afdd96a5d2a0 Mon Sep 17 00:00:00 2001
From: Dongdong Tian <seisman.info@gmail.com>
Date: Fri, 22 Sep 2023 23:01:50 +0800
Subject: [PATCH 04/15] Add a new test to check if .tiff is a GeoTIFF file

---
 pygmt/tests/test_figure.py | 40 ++++++++++++++++++++++++++++++++++++++
 1 file changed, 40 insertions(+)

diff --git a/pygmt/tests/test_figure.py b/pygmt/tests/test_figure.py
index b7b97ed507f..5a8c5c390ed 100644
--- a/pygmt/tests/test_figure.py
+++ b/pygmt/tests/test_figure.py
@@ -92,6 +92,46 @@ def test_figure_savefig_exists():
         fname.unlink()
 
 
+def test_figure_savefig_geotiff():
+    """
+    Make sure the extension .tiff generates a GeoTIFF file.
+    """
+    fig = Figure()
+    fig.basemap(region=[0, 10, 0, 10], projection="M10c", frame=True)
+
+    # save as GeoTIFF
+    geofname = Path("test_figure_savefig_geotiff.tiff")
+    fig.savefig(geofname)
+
+    assert geofname.exists()
+    # Is a GeoTIFF file
+    try:
+        import rioxarray
+
+        with rioxarray.open_rasterio(geofname) as xds:
+            assert xds.rio.crs is not None
+    except ImportError:
+        pass
+    geofname.unlink()
+
+    # save as TIFF
+    fname = Path("test_figure_savefig_geotiff.tif")
+    fig.savefig(fname)
+    assert fname.exists()
+    # Is a normal TIFF file
+    try:
+        import rioxarray
+        from rasterio.errors import NotGeoreferencedWarning
+
+        with pytest.warns(expected_warning=NotGeoreferencedWarning) as record:
+            with rioxarray.open_rasterio(fname) as xds:
+                assert xds.rio.crs is None
+            assert len(record) == 1
+    except ImportError:
+        pass
+    fname.unlink()
+
+
 def test_figure_savefig_directory_nonexists():
     """
     Make sure that Figure.savefig() raises a FileNotFoundError when the parent

From a83862f14c897471032f457ce7ba485453f04c9b Mon Sep 17 00:00:00 2001
From: Dongdong Tian <seisman.info@gmail.com>
Date: Fri, 22 Sep 2023 23:21:16 +0800
Subject: [PATCH 05/15] Revert the changes in test_figure_savefig_exists

---
 pygmt/tests/test_figure.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/pygmt/tests/test_figure.py b/pygmt/tests/test_figure.py
index 5a8c5c390ed..a0d3fafbc8b 100644
--- a/pygmt/tests/test_figure.py
+++ b/pygmt/tests/test_figure.py
@@ -83,7 +83,7 @@ def test_figure_savefig_exists():
     fig = Figure()
     fig.basemap(region="10/70/-300/800", projection="X3i/5i", frame="af")
     prefix = "test_figure_savefig_exists"
-    for fmt in "png pdf jpg jpeg bmp eps tif tiff PNG JPG JPEG Png".split():
+    for fmt in "png pdf jpg jpeg bmp eps tif PNG JPG JPEG Png".split():
         fname = ".".join([prefix, fmt])
         fig.savefig(fname)
 

From 51c8dbe6cc66cb942ebb6b201d2a72e750d13201 Mon Sep 17 00:00:00 2001
From: Dongdong Tian <seisman.info@gmail.com>
Date: Fri, 22 Sep 2023 23:27:29 +0800
Subject: [PATCH 06/15] Simplify the test

---
 pygmt/tests/test_figure.py | 25 ++++++++++++-------------
 1 file changed, 12 insertions(+), 13 deletions(-)

diff --git a/pygmt/tests/test_figure.py b/pygmt/tests/test_figure.py
index a0d3fafbc8b..cb01ffbbbb4 100644
--- a/pygmt/tests/test_figure.py
+++ b/pygmt/tests/test_figure.py
@@ -94,7 +94,8 @@ def test_figure_savefig_exists():
 
 def test_figure_savefig_geotiff():
     """
-    Make sure the extension .tiff generates a GeoTIFF file.
+    Make sure .tif generates a normal TIFF file and .tiff generates a GeoTIFF
+    file.
     """
     fig = Figure()
     fig.basemap(region=[0, 10, 0, 10], projection="M10c", frame=True)
@@ -102,33 +103,31 @@ def test_figure_savefig_geotiff():
     # save as GeoTIFF
     geofname = Path("test_figure_savefig_geotiff.tiff")
     fig.savefig(geofname)
-
     assert geofname.exists()
-    # Is a GeoTIFF file
-    try:
-        import rioxarray
+    assert geofname.with_suffix(".pgw").exists()  # The companion world file
 
-        with rioxarray.open_rasterio(geofname) as xds:
-            assert xds.rio.crs is not None
-    except ImportError:
-        pass
-    geofname.unlink()
-
-    # save as TIFF
+    # Save as TIFF
     fname = Path("test_figure_savefig_geotiff.tif")
     fig.savefig(fname)
     assert fname.exists()
-    # Is a normal TIFF file
+
+    # Check is a TIFF is georeferenced or not
     try:
         import rioxarray
         from rasterio.errors import NotGeoreferencedWarning
 
+        # GeoTIFF
+        with rioxarray.open_rasterio(geofname) as xds:
+            assert xds.rio.crs is not None
+        # TIFF
         with pytest.warns(expected_warning=NotGeoreferencedWarning) as record:
             with rioxarray.open_rasterio(fname) as xds:
                 assert xds.rio.crs is None
             assert len(record) == 1
     except ImportError:
         pass
+    geofname.unlink()
+    geofname.with_suffix(".pgw").unlink()
     fname.unlink()
 
 

From cf771cc8c4459174be118711e3e8d5b9a810e959 Mon Sep 17 00:00:00 2001
From: Dongdong Tian <seisman.info@gmail.com>
Date: Fri, 22 Sep 2023 23:32:20 +0800
Subject: [PATCH 07/15] Fix a linting issue

---
 pygmt/tests/test_figure.py | 1 +
 1 file changed, 1 insertion(+)

diff --git a/pygmt/tests/test_figure.py b/pygmt/tests/test_figure.py
index cb01ffbbbb4..e1706c311a0 100644
--- a/pygmt/tests/test_figure.py
+++ b/pygmt/tests/test_figure.py
@@ -113,6 +113,7 @@ def test_figure_savefig_geotiff():
 
     # Check is a TIFF is georeferenced or not
     try:
+        # pylint: disable=import-outside-toplevel
         import rioxarray
         from rasterio.errors import NotGeoreferencedWarning
 

From 3303ba4ce139f1cf14c39638a0f3f9dd1b7978c5 Mon Sep 17 00:00:00 2001
From: Dongdong Tian <seisman.info@gmail.com>
Date: Sun, 24 Sep 2023 17:56:43 +0800
Subject: [PATCH 08/15] Fix typos
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit

Co-authored-by: Yvonne Fröhlich <94163266+yvonnefroehlich@users.noreply.github.com>
---
 pygmt/figure.py            | 10 +++++-----
 pygmt/tests/test_figure.py |  4 ++--
 2 files changed, 7 insertions(+), 7 deletions(-)

diff --git a/pygmt/figure.py b/pygmt/figure.py
index 65cc6432ef3..47a52405014 100644
--- a/pygmt/figure.py
+++ b/pygmt/figure.py
@@ -263,7 +263,7 @@ def savefig(
         - JPEG (``.jpg`` or ``.jpeg``)
         - PDF (``.pdf``)
         - BMP (``.bmp``)
-        - TIFF (``.tif`` or `.tiff`)
+        - TIFF (``.tif`` or ``.tiff``)
         - EPS (``.eps``)
         - KML (``.kml``)
 
@@ -286,10 +286,10 @@ def savefig(
             If ``True``, will crop the figure canvas (page) to the plot area.
         anti_alias: bool
             If ``True``, will use anti-aliasing when creating raster images
-            (BMP, PNG, JPEG and TIFF). More specifically, it passes arguments
-            ``t2`` and ``g2`` to the ``anti_aliasing`` parameter of
-            :meth:`pygmt.Figure.psconvert`. Ignored if creating vector
-            graphics.
+            (BMP, PNG, JPEG, and TIFF). More specifically, it passes the
+            arguments ``"t2"`` and ``"g2"`` to the ``anti_aliasing``
+            parameter of :meth:`pygmt.Figure.psconvert`. Ignored if
+            creating vector graphics.
         show: bool
             If ``True``, will open the figure in an external viewer.
         dpi : int
diff --git a/pygmt/tests/test_figure.py b/pygmt/tests/test_figure.py
index e1706c311a0..89ab04508b8 100644
--- a/pygmt/tests/test_figure.py
+++ b/pygmt/tests/test_figure.py
@@ -100,7 +100,7 @@ def test_figure_savefig_geotiff():
     fig = Figure()
     fig.basemap(region=[0, 10, 0, 10], projection="M10c", frame=True)
 
-    # save as GeoTIFF
+    # Save as GeoTIFF
     geofname = Path("test_figure_savefig_geotiff.tiff")
     fig.savefig(geofname)
     assert geofname.exists()
@@ -111,7 +111,7 @@ def test_figure_savefig_geotiff():
     fig.savefig(fname)
     assert fname.exists()
 
-    # Check is a TIFF is georeferenced or not
+    # Check if a TIFF is georeferenced or not
     try:
         # pylint: disable=import-outside-toplevel
         import rioxarray

From 4fd2f50c874c5b09cb09539c1fe745123dbac296 Mon Sep 17 00:00:00 2001
From: Dongdong Tian <seisman.info@gmail.com>
Date: Mon, 25 Sep 2023 07:38:25 +0800
Subject: [PATCH 09/15] Apply suggestions from code review

Co-authored-by: Wei Ji <23487320+weiji14@users.noreply.github.com>
---
 pygmt/figure.py            | 3 ++-
 pygmt/tests/test_figure.py | 2 +-
 2 files changed, 3 insertions(+), 2 deletions(-)

diff --git a/pygmt/figure.py b/pygmt/figure.py
index 47a52405014..fa739293a6c 100644
--- a/pygmt/figure.py
+++ b/pygmt/figure.py
@@ -263,7 +263,8 @@ def savefig(
         - JPEG (``.jpg`` or ``.jpeg``)
         - PDF (``.pdf``)
         - BMP (``.bmp``)
-        - TIFF (``.tif`` or ``.tiff``)
+        - TIFF (``.tif``)
+        - GeoTIFF (``.tiff``)
         - EPS (``.eps``)
         - KML (``.kml``)
 
diff --git a/pygmt/tests/test_figure.py b/pygmt/tests/test_figure.py
index 89ab04508b8..0341bdc3060 100644
--- a/pygmt/tests/test_figure.py
+++ b/pygmt/tests/test_figure.py
@@ -107,7 +107,7 @@ def test_figure_savefig_geotiff():
     assert geofname.with_suffix(".pgw").exists()  # The companion world file
 
     # Save as TIFF
-    fname = Path("test_figure_savefig_geotiff.tif")
+    fname = Path("test_figure_savefig_tiff.tif")
     fig.savefig(fname)
     assert fname.exists()
 

From 252514b429577d952807fb516e4826280ef9816e Mon Sep 17 00:00:00 2001
From: Dongdong Tian <seisman.info@gmail.com>
Date: Wed, 4 Oct 2023 17:39:55 +0800
Subject: [PATCH 10/15] Delete the .pgw if exists

---
 pygmt/figure.py            | 17 ++++++++++-------
 pygmt/tests/test_figure.py |  4 ++--
 2 files changed, 12 insertions(+), 9 deletions(-)

diff --git a/pygmt/figure.py b/pygmt/figure.py
index fa739293a6c..5c4217ed00d 100644
--- a/pygmt/figure.py
+++ b/pygmt/figure.py
@@ -268,9 +268,7 @@ def savefig(
         - EPS (``.eps``)
         - KML (``.kml``)
 
-        For TIFF format, ``.tiff`` generates a GeoTIFF file with embedded
-        georeferencing information and a companion world file. For KML format,
-        a companion PNG file is also generated.
+        For KML format, a companion PNG file is also generated.
 
         You can pass in any keyword arguments that
         :meth:`pygmt.Figure.psconvert` accepts.
@@ -287,10 +285,10 @@ def savefig(
             If ``True``, will crop the figure canvas (page) to the plot area.
         anti_alias: bool
             If ``True``, will use anti-aliasing when creating raster images
-            (BMP, PNG, JPEG, and TIFF). More specifically, it passes the
-            arguments ``"t2"`` and ``"g2"`` to the ``anti_aliasing``
-            parameter of :meth:`pygmt.Figure.psconvert`. Ignored if
-            creating vector graphics.
+            (BMP, PNG, JPEG, TIFF, and GeoTIFF). More specifically, it passes
+            the arguments ``"t2"`` and ``"g2"`` to the ``anti_aliasing``
+            parameter of :meth:`pygmt.Figure.psconvert`. Ignored if creating
+            vector graphics.
         show: bool
             If ``True``, will open the figure in an external viewer.
         dpi : int
@@ -344,6 +342,11 @@ def savefig(
 
         self.psconvert(prefix=prefix, fmt=fmt, crop=crop, **kwargs)
 
+        # Remove the .pgw world file if exists
+        # See upstream fix https://github.com/GenericMappingTools/gmt/pull/7865
+        if ext == "tiff" and fname.with_suffix(".pgw").exists():
+            fname.with_suffix(".pgw").unlink()
+
         # Rename if file extension doesn't match the input file suffix
         if ext != suffix[1:]:
             fname.with_suffix("." + ext).rename(fname)
diff --git a/pygmt/tests/test_figure.py b/pygmt/tests/test_figure.py
index 0341bdc3060..2b5df7060e3 100644
--- a/pygmt/tests/test_figure.py
+++ b/pygmt/tests/test_figure.py
@@ -104,7 +104,8 @@ def test_figure_savefig_geotiff():
     geofname = Path("test_figure_savefig_geotiff.tiff")
     fig.savefig(geofname)
     assert geofname.exists()
-    assert geofname.with_suffix(".pgw").exists()  # The companion world file
+    # The .pgw should not exist
+    assert not geofname.with_suffix(".pgw").exists()
 
     # Save as TIFF
     fname = Path("test_figure_savefig_tiff.tif")
@@ -128,7 +129,6 @@ def test_figure_savefig_geotiff():
     except ImportError:
         pass
     geofname.unlink()
-    geofname.with_suffix(".pgw").unlink()
     fname.unlink()
 
 

From 44bfcfe93a286a8d26906d217bffe594df3bd5b5 Mon Sep 17 00:00:00 2001
From: Dongdong Tian <seisman.info@gmail.com>
Date: Mon, 9 Oct 2023 10:10:27 +0800
Subject: [PATCH 11/15] Improve the comment about removing .pgw file

Co-authored-by: Wei Ji <23487320+weiji14@users.noreply.github.com>
---
 pygmt/figure.py | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/pygmt/figure.py b/pygmt/figure.py
index 5c4217ed00d..23b0b2e6272 100644
--- a/pygmt/figure.py
+++ b/pygmt/figure.py
@@ -342,7 +342,8 @@ def savefig(
 
         self.psconvert(prefix=prefix, fmt=fmt, crop=crop, **kwargs)
 
-        # Remove the .pgw world file if exists
+        # Remove the .pgw world file if exists 
+        # Not necessary after GMT 6.5.0.
         # See upstream fix https://github.com/GenericMappingTools/gmt/pull/7865
         if ext == "tiff" and fname.with_suffix(".pgw").exists():
             fname.with_suffix(".pgw").unlink()

From e7c2b36cd87812ce7b061f6302a8718917d48ad8 Mon Sep 17 00:00:00 2001
From: Dongdong Tian <seisman.info@gmail.com>
Date: Mon, 9 Oct 2023 14:55:54 +0800
Subject: [PATCH 12/15] Check bounds in the test

Co-authored-by: Wei Ji <23487320+weiji14@users.noreply.github.com>
---
 pygmt/tests/test_figure.py | 14 ++++++++++++++
 1 file changed, 14 insertions(+)

diff --git a/pygmt/tests/test_figure.py b/pygmt/tests/test_figure.py
index 2b5df7060e3..53ef898bfd7 100644
--- a/pygmt/tests/test_figure.py
+++ b/pygmt/tests/test_figure.py
@@ -121,10 +121,24 @@ def test_figure_savefig_geotiff():
         # GeoTIFF
         with rioxarray.open_rasterio(geofname) as xds:
             assert xds.rio.crs is not None
+npt.assert_allclose(
+                actual=xds.rio.bounds(),
+                desired=(
+                    -667728.5869475466,
+                    6356999.491390044,
+                    594269.0244906943,
+                    8381540.2498699855,
+                ),
+            )
+            assert xds.rio.shape == (2149, 1340)
         # TIFF
         with pytest.warns(expected_warning=NotGeoreferencedWarning) as record:
             with rioxarray.open_rasterio(fname) as xds:
                 assert xds.rio.crs is None
+                npt.assert_allclose(
+                    actual=xds.rio.bounds(), desired=(0.0, 0.0, 1331.0, 1257.0)
+                )
+                assert xds.rio.shape == (1257, 1331)
             assert len(record) == 1
     except ImportError:
         pass

From 26837e84dd532acc22993a6b45cab8f2ede919fc Mon Sep 17 00:00:00 2001
From: Dongdong Tian <seisman.info@gmail.com>
Date: Mon, 9 Oct 2023 14:57:05 +0800
Subject: [PATCH 13/15] Fix typos and linting issues

---
 pygmt/figure.py            | 2 +-
 pygmt/tests/test_figure.py | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/pygmt/figure.py b/pygmt/figure.py
index 23b0b2e6272..93e2d70340d 100644
--- a/pygmt/figure.py
+++ b/pygmt/figure.py
@@ -342,7 +342,7 @@ def savefig(
 
         self.psconvert(prefix=prefix, fmt=fmt, crop=crop, **kwargs)
 
-        # Remove the .pgw world file if exists 
+        # Remove the .pgw world file if exists
         # Not necessary after GMT 6.5.0.
         # See upstream fix https://github.com/GenericMappingTools/gmt/pull/7865
         if ext == "tiff" and fname.with_suffix(".pgw").exists():
diff --git a/pygmt/tests/test_figure.py b/pygmt/tests/test_figure.py
index 53ef898bfd7..35a406d7ea4 100644
--- a/pygmt/tests/test_figure.py
+++ b/pygmt/tests/test_figure.py
@@ -121,7 +121,7 @@ def test_figure_savefig_geotiff():
         # GeoTIFF
         with rioxarray.open_rasterio(geofname) as xds:
             assert xds.rio.crs is not None
-npt.assert_allclose(
+            npt.assert_allclose(
                 actual=xds.rio.bounds(),
                 desired=(
                     -667728.5869475466,

From 71611dfd617c870cd3bdaf0ff84b07213427befd Mon Sep 17 00:00:00 2001
From: Dongdong Tian <seisman.info@gmail.com>
Date: Wed, 18 Oct 2023 14:26:30 +0800
Subject: [PATCH 14/15] Fix the bounds and shape for geotiff files

---
 pygmt/tests/test_figure.py | 10 +++++-----
 1 file changed, 5 insertions(+), 5 deletions(-)

diff --git a/pygmt/tests/test_figure.py b/pygmt/tests/test_figure.py
index 35a406d7ea4..814f13335d7 100644
--- a/pygmt/tests/test_figure.py
+++ b/pygmt/tests/test_figure.py
@@ -124,13 +124,13 @@ def test_figure_savefig_geotiff():
             npt.assert_allclose(
                 actual=xds.rio.bounds(),
                 desired=(
-                    -667728.5869475466,
-                    6356999.491390044,
-                    594269.0244906943,
-                    8381540.2498699855,
+                    -661136.0621116752,
+                    -54631.82709660966,
+                    592385.4459661598,
+                    1129371.7360144067,
                 ),
             )
-            assert xds.rio.shape == (2149, 1340)
+            assert xds.rio.shape == (1257, 1331)
         # TIFF
         with pytest.warns(expected_warning=NotGeoreferencedWarning) as record:
             with rioxarray.open_rasterio(fname) as xds:

From 6a1caa355155e04e7e139ea9e88bac84111eb0a0 Mon Sep 17 00:00:00 2001
From: Dongdong Tian <seisman.info@gmail.com>
Date: Tue, 24 Oct 2023 21:13:28 +0800
Subject: [PATCH 15/15] Check Affine transformation

Co-authored-by: Wei Ji <23487320+weiji14@users.noreply.github.com>
---
 pygmt/tests/test_figure.py | 12 ++++++++++++
 1 file changed, 12 insertions(+)

diff --git a/pygmt/tests/test_figure.py b/pygmt/tests/test_figure.py
index 814f13335d7..4969aad0fb0 100644
--- a/pygmt/tests/test_figure.py
+++ b/pygmt/tests/test_figure.py
@@ -117,6 +117,7 @@ def test_figure_savefig_geotiff():
         # pylint: disable=import-outside-toplevel
         import rioxarray
         from rasterio.errors import NotGeoreferencedWarning
+        from rasterio.transform import Affine
 
         # GeoTIFF
         with rioxarray.open_rasterio(geofname) as xds:
@@ -131,6 +132,14 @@ def test_figure_savefig_geotiff():
                 ),
             )
             assert xds.rio.shape == (1257, 1331)
+            assert xds.rio.transform() == Affine(
+                a=941.789262267344,
+                b=0.0,
+                c=-661136.0621116752,
+                d=0.0,
+                e=-941.92805338983,
+                f=1129371.7360144067,
+            )
         # TIFF
         with pytest.warns(expected_warning=NotGeoreferencedWarning) as record:
             with rioxarray.open_rasterio(fname) as xds:
@@ -139,6 +148,9 @@ def test_figure_savefig_geotiff():
                     actual=xds.rio.bounds(), desired=(0.0, 0.0, 1331.0, 1257.0)
                 )
                 assert xds.rio.shape == (1257, 1331)
+                assert xds.rio.transform() == Affine(
+                    a=1.0, b=0.0, c=0.0, d=0.0, e=1.0, f=0.0
+                )
             assert len(record) == 1
     except ImportError:
         pass