From 3a5d6da334d4dd89a39ebe5cd783247f9d6520e1 Mon Sep 17 00:00:00 2001
From: Wei Ji <23487320+weiji14@users.noreply.github.com>
Date: Thu, 21 Nov 2024 14:28:18 +1300
Subject: [PATCH 01/15] Use uv package manager to test lowest versions in
 ci_tests_legacy.yaml

Using uv's --resolution lowest-direct to install the lowest compatible versions for all direct Python dependencies (required and optional) listed in the pyproject.toml file.
---
 .github/workflows/ci_tests_legacy.yaml | 37 ++++++++++----------------
 1 file changed, 14 insertions(+), 23 deletions(-)

diff --git a/.github/workflows/ci_tests_legacy.yaml b/.github/workflows/ci_tests_legacy.yaml
index 5ac5dcedbbc..3de6c99ce5d 100644
--- a/.github/workflows/ci_tests_legacy.yaml
+++ b/.github/workflows/ci_tests_legacy.yaml
@@ -1,8 +1,8 @@
-# Test PyGMT with GMT legacy versions on Linux/macOS/Windows
+# Test PyGMT with GMT legacy versions and old Python dependencies on Linux/macOS/Windows
 #
-# This workflow runs regular PyGMT tests with GMT legacy versions. Due to the minor
-# baseline image changes between GMT versions, the workflow only runs the tests but
-# doesn't do image comparisons.
+# This workflow runs regular PyGMT tests with GMT legacy versions and old versions of
+# all optional Python dependencies. Due to the minor baseline image changes between GMT
+# versions, the workflow only runs the tests but doesn't do image comparisons.
 #
 # It is scheduled to run every Tuesday on the main branch.
 #
@@ -62,23 +62,6 @@ jobs:
             python=3.10
             gmt=${{ matrix.gmt_version }}
             ghostscript<10
-            numpy
-            pandas
-            xarray
-            netCDF4
-            packaging
-            contextily
-            geopandas
-            ipython
-            pyarrow
-            rioxarray
-            sphinx-gallery
-            make
-            pip
-            python-build
-            pytest
-            pytest-doctestplus
-            pytest-mpl
 
       # Download cached remote files (artifacts) from GitHub
       - name: Download remote data from GitHub
@@ -95,10 +78,18 @@ jobs:
         env:
           GH_TOKEN: ${{ github.token }}
 
+      # Install uv package manager
+      - name: Install uv
+        uses: astral-sh/setup-uv@v3
+
       # Install the package that we want to test
       - name: Install the package
-        run: make install
+        run: |
+          uv run --with pip==23 --resolution lowest-direct --all-extras --dev make install
+          uv pip list
 
       # Run the tests but skip images
       - name: Run tests
-        run: make test_no_images PYTEST_EXTRA="-r P"
+        run: uv run --with pytest==8 --resolution lowest-direct --all-extras --dev make test_no_images PYTEST_EXTRA="-r P"
+        env:
+          GMT_LIBRARY_PATH: $CONDA_PREFIX/lib

From f3039641a5dde5b46bf923f512734ef3aa8ea18c Mon Sep 17 00:00:00 2001
From: Wei Ji <23487320+weiji14@users.noreply.github.com>
Date: Thu, 21 Nov 2024 14:29:04 +1300
Subject: [PATCH 02/15] Temporarily enable ci_tests_legacy.yaml

---
 .github/workflows/ci_tests_legacy.yaml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/ci_tests_legacy.yaml b/.github/workflows/ci_tests_legacy.yaml
index 3de6c99ce5d..e1a292dad03 100644
--- a/.github/workflows/ci_tests_legacy.yaml
+++ b/.github/workflows/ci_tests_legacy.yaml
@@ -12,7 +12,7 @@ on:
   # push:
   #   branches: [ main ]
   # Uncomment the 'pull_request' line below to trigger the workflow in PR
-  # pull_request:
+  pull_request:
     # types: [ready_for_review]
     # paths:
     #  - 'pygmt/**'

From 3f6909d0105580158a911f18fa9e18c1ba1f5910 Mon Sep 17 00:00:00 2001
From: Wei Ji <23487320+weiji14@users.noreply.github.com>
Date: Thu, 21 Nov 2024 14:44:37 +1300
Subject: [PATCH 03/15] Pin to netCDF>=1.7

Need to get more recent version with a binary wheel, otherwise will need to compile from source.
---
 pyproject.toml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/pyproject.toml b/pyproject.toml
index 8400da80625..04886c6d1be 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -33,7 +33,7 @@ dependencies = [
     "numpy>=1.24",
     "pandas>=2.0",
     "xarray>=2023.04",
-    "netCDF4",
+    "netCDF4>=1.7",
     "packaging",
 ]
 dynamic = ["version"]

From 788fc461e6fa73415761ab791f1fa3f250717f70 Mon Sep 17 00:00:00 2001
From: Wei Ji <23487320+weiji14@users.noreply.github.com>
Date: Thu, 21 Nov 2024 14:51:53 +1300
Subject: [PATCH 04/15] Pin contextily>=1, IPython>=8, pyarrow>=14

Pin major versions for optional dependencies that are not on version 0.x. Using a reasonable major version released in the past year or two.
---
 pyproject.toml | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/pyproject.toml b/pyproject.toml
index 04886c6d1be..8bea1e75bfe 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -40,10 +40,10 @@ dynamic = ["version"]
 
 [project.optional-dependencies]
 all = [
-    "contextily",
+    "contextily>=1",
     "geopandas",
-    "IPython",  # 'ipython' is not the correct module name.
-    "pyarrow",
+    "IPython>=8",  # 'ipython' is not the correct module name.
+    "pyarrow>=14",
     "rioxarray",
 ]
 

From 4139f4e2b177bc89688d35d6f1b0b768251cab1f Mon Sep 17 00:00:00 2001
From: Wei Ji <23487320+weiji14@users.noreply.github.com>
Date: Thu, 21 Nov 2024 14:57:19 +1300
Subject: [PATCH 05/15] Pin geopandas>=0.14, rioxarray>=0.14

Pin minor versions of optional dependencies that are still on v0.x.
---
 pyproject.toml | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/pyproject.toml b/pyproject.toml
index 8bea1e75bfe..63edd180f62 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -41,10 +41,10 @@ dynamic = ["version"]
 [project.optional-dependencies]
 all = [
     "contextily>=1",
-    "geopandas",
+    "geopandas>=0.14",
     "IPython>=8",  # 'ipython' is not the correct module name.
     "pyarrow>=14",
-    "rioxarray",
+    "rioxarray>=0.14",
 ]
 
 [project.urls]

From 12630755aba4b1274a5e088df08ce2ef198d2d02 Mon Sep 17 00:00:00 2001
From: Wei Ji <23487320+weiji14@users.noreply.github.com>
Date: Thu, 21 Nov 2024 15:16:10 +1300
Subject: [PATCH 06/15] Add --color=yes to test_no_images addopts

Xref #3330
---
 Makefile | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/Makefile b/Makefile
index 4494f2996c3..2dd8243f95d 100644
--- a/Makefile
+++ b/Makefile
@@ -55,7 +55,7 @@ doctest: _runtest
 # run tests without image comparisons
 # run pytest without the --mpl option to disable image comparisons
 # use '-o addopts' to override 'addopts' settings in pyproject.toml file
-test_no_images: PYTEST_ARGS=-o addopts="--verbose --durations=0 --durations-min=0.2 --doctest-modules"
+test_no_images: PYTEST_ARGS=-o addopts="--verbose --color=yes --durations=0 --durations-min=0.2 --doctest-modules"
 test_no_images: _runtest
 
 format:

From d1fa38d2393c613af8ef4149744beb6e7681683e Mon Sep 17 00:00:00 2001
From: Wei Ji <23487320+weiji14@users.noreply.github.com>
Date: Thu, 21 Nov 2024 15:24:43 +1300
Subject: [PATCH 07/15] Pin packaging>=22.0

Fix `TypeError: canonicalize_version() got an unexpected keyword argument 'strip_trailing_zero'` when running `pip install --no-deps -e .`, xref https://github.com/pypa/setuptools/issues/4501
---
 pyproject.toml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/pyproject.toml b/pyproject.toml
index 63edd180f62..02acde598e7 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -34,7 +34,7 @@ dependencies = [
     "pandas>=2.0",
     "xarray>=2023.04",
     "netCDF4>=1.7",
-    "packaging",
+    "packaging>=22.0",
 ]
 dynamic = ["version"]
 

From 1c69406e3ee9dbee35ea9424230d55c0c120d363 Mon Sep 17 00:00:00 2001
From: Wei Ji <23487320+weiji14@users.noreply.github.com>
Date: Thu, 21 Nov 2024 15:40:03 +1300
Subject: [PATCH 08/15] Test with pytest-mpl and pytest-doctestplus

---
 .github/workflows/ci_tests_legacy.yaml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/ci_tests_legacy.yaml b/.github/workflows/ci_tests_legacy.yaml
index e1a292dad03..b583e9ba748 100644
--- a/.github/workflows/ci_tests_legacy.yaml
+++ b/.github/workflows/ci_tests_legacy.yaml
@@ -90,6 +90,6 @@ jobs:
 
       # Run the tests but skip images
       - name: Run tests
-        run: uv run --with pytest==8 --resolution lowest-direct --all-extras --dev make test_no_images PYTEST_EXTRA="-r P"
+        run: uv run --with pytest==8,pytest-mpl==0.17,pytest-doctestplus==1.2 --resolution lowest-direct --all-extras --dev make test_no_images PYTEST_EXTRA="-r P"
         env:
           GMT_LIBRARY_PATH: $CONDA_PREFIX/lib

From 3b7b777d3046d0762e067367d8d87e6123db4c9a Mon Sep 17 00:00:00 2001
From: Wei Ji <23487320+weiji14@users.noreply.github.com>
Date: Thu, 21 Nov 2024 16:12:36 +1300
Subject: [PATCH 09/15] Install into uv venv

Create a proper virtualenv, and activate that virtualenv before installing pygmt and running pytest.
---
 .github/workflows/ci_tests_legacy.yaml | 6 +++++-
 1 file changed, 5 insertions(+), 1 deletion(-)

diff --git a/.github/workflows/ci_tests_legacy.yaml b/.github/workflows/ci_tests_legacy.yaml
index b583e9ba748..ded4472b2ea 100644
--- a/.github/workflows/ci_tests_legacy.yaml
+++ b/.github/workflows/ci_tests_legacy.yaml
@@ -85,11 +85,15 @@ jobs:
       # Install the package that we want to test
       - name: Install the package
         run: |
+          uv venv
+          source .venv/bin/activate
           uv run --with pip==23 --resolution lowest-direct --all-extras --dev make install
           uv pip list
 
       # Run the tests but skip images
       - name: Run tests
-        run: uv run --with pytest==8,pytest-mpl==0.17,pytest-doctestplus==1.2 --resolution lowest-direct --all-extras --dev make test_no_images PYTEST_EXTRA="-r P"
+        run: |
+          source .venv/bin/activate
+          uv run --with pytest==8,pytest-mpl==0.17,pytest-doctestplus==1.2 --resolution lowest-direct --all-extras --dev make test_no_images PYTEST_EXTRA="-r P"
         env:
           GMT_LIBRARY_PATH: $CONDA_PREFIX/lib

From 6120bbe31a78ad8df5a005f983d3378e08756396 Mon Sep 17 00:00:00 2001
From: Wei Ji <23487320+weiji14@users.noreply.github.com>
Date: Fri, 22 Nov 2024 12:00:19 +1300
Subject: [PATCH 10/15] Pin contextily>=1.2

So that xyzservices is also installed by default and `from xyzservices import TileProvider` can work. See https://github.com/geopandas/contextily/pull/183
---
 pyproject.toml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/pyproject.toml b/pyproject.toml
index 02acde598e7..3504543902e 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -40,7 +40,7 @@ dynamic = ["version"]
 
 [project.optional-dependencies]
 all = [
-    "contextily>=1",
+    "contextily>=1.2",
     "geopandas>=0.14",
     "IPython>=8",  # 'ipython' is not the correct module name.
     "pyarrow>=14",

From 3299229ef398ae1e6d7365e7591b781d12f05835 Mon Sep 17 00:00:00 2001
From: Wei Ji <23487320+weiji14@users.noreply.github.com>
Date: Fri, 22 Nov 2024 12:19:15 +1300
Subject: [PATCH 11/15] Pin pyarrow>=16

So that `pyarrow.array(..., dtype="string_view")` will work. See https://github.com/apache/arrow/pull/39652 when this was added.
---
 pyproject.toml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/pyproject.toml b/pyproject.toml
index 3504543902e..c680a77c17f 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -43,7 +43,7 @@ all = [
     "contextily>=1.2",
     "geopandas>=0.14",
     "IPython>=8",  # 'ipython' is not the correct module name.
-    "pyarrow>=14",
+    "pyarrow>=16",
     "rioxarray>=0.14",
 ]
 

From 7d542a91040787d8ed81bab050d16b931b5ab9df Mon Sep 17 00:00:00 2001
From: Wei Ji <23487320+weiji14@users.noreply.github.com>
Date: Fri, 22 Nov 2024 15:25:32 +1300
Subject: [PATCH 12/15] Update wording on ci_tests_legacy.yaml header comment

---
 .github/workflows/ci_tests_legacy.yaml | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/.github/workflows/ci_tests_legacy.yaml b/.github/workflows/ci_tests_legacy.yaml
index ded4472b2ea..716032b6045 100644
--- a/.github/workflows/ci_tests_legacy.yaml
+++ b/.github/workflows/ci_tests_legacy.yaml
@@ -1,8 +1,8 @@
 # Test PyGMT with GMT legacy versions and old Python dependencies on Linux/macOS/Windows
 #
 # This workflow runs regular PyGMT tests with GMT legacy versions and old versions of
-# all optional Python dependencies. Due to the minor baseline image changes between GMT
-# versions, the workflow only runs the tests but doesn't do image comparisons.
+# all optional and required Python dependencies. Due to minor baseline image changes
+# between GMT versions, the workflow runs the tests but doesn't do image comparisons.
 #
 # It is scheduled to run every Tuesday on the main branch.
 #

From 4733bda9e710061e79acafc771f8d0b1e32100e8 Mon Sep 17 00:00:00 2001
From: Wei Ji <23487320+weiji14@users.noreply.github.com>
Date: Fri, 22 Nov 2024 21:56:56 +1300
Subject: [PATCH 13/15] Pin pyarrow>=13 and use pytest.mark.skipif on
 string_view type test

Lower pyarrow pin from 16 to 13, and added a skipif pytest marker to the `test_to_numpy_pyarrow_array_pyarrow_dtypes_string[string_view]` unit test to not run when pyarrow<16 is installed. Setting a pin on pyarrow>=13 so that datetime64 unit preservation is handled, xref https://github.com/apache/arrow/issues/33321.
---
 pygmt/tests/test_clib_to_numpy.py | 9 ++++++++-
 pyproject.toml                    | 2 +-
 2 files changed, 9 insertions(+), 2 deletions(-)

diff --git a/pygmt/tests/test_clib_to_numpy.py b/pygmt/tests/test_clib_to_numpy.py
index 02b65062da8..88845d31f2a 100644
--- a/pygmt/tests/test_clib_to_numpy.py
+++ b/pygmt/tests/test_clib_to_numpy.py
@@ -10,6 +10,7 @@
 import pandas as pd
 import pytest
 from packaging.version import Version
+from pygmt._show_versions import _get_module_version
 from pygmt.clib.conversion import _to_numpy
 from pygmt.helpers.testing import skip_if_no
 
@@ -323,7 +324,13 @@ def test_to_numpy_pyarrow_array_pyarrow_dtypes_numeric_with_na(dtype, expected_d
         "utf8",  # alias for string
         "large_string",
         "large_utf8",  # alias for large_string
-        "string_view",
+        pytest.param(
+            "string_view",
+            marks=pytest.mark.skipif(
+                Version(_get_module_version("pyarrow")) < Version("16"),
+                reason="string_view type was added since pyarrow 16",
+            ),
+        ),
     ],
 )
 def test_to_numpy_pyarrow_array_pyarrow_dtypes_string(dtype):
diff --git a/pyproject.toml b/pyproject.toml
index c680a77c17f..88cc042848c 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -43,7 +43,7 @@ all = [
     "contextily>=1.2",
     "geopandas>=0.14",
     "IPython>=8",  # 'ipython' is not the correct module name.
-    "pyarrow>=16",
+    "pyarrow>=13",
     "rioxarray>=0.14",
 ]
 

From 52c78fa378aafa1463abbcf2a98216fde114fcfa Mon Sep 17 00:00:00 2001
From: Wei Ji <23487320+weiji14@users.noreply.github.com>
Date: Tue, 3 Dec 2024 12:56:24 +1300
Subject: [PATCH 14/15] Remove unused import _get_module_version

---
 pygmt/tests/test_clib_to_numpy.py | 1 -
 1 file changed, 1 deletion(-)

diff --git a/pygmt/tests/test_clib_to_numpy.py b/pygmt/tests/test_clib_to_numpy.py
index bed8b32247f..64db3ea6547 100644
--- a/pygmt/tests/test_clib_to_numpy.py
+++ b/pygmt/tests/test_clib_to_numpy.py
@@ -10,7 +10,6 @@
 import pandas as pd
 import pytest
 from packaging.version import Version
-from pygmt._show_versions import _get_module_version
 from pygmt.clib.conversion import _to_numpy
 from pygmt.helpers.testing import skip_if_no
 

From af01f751853ad650ec82ccaefd68cbf93d98889a Mon Sep 17 00:00:00 2001
From: Wei Ji <23487320+weiji14@users.noreply.github.com>
Date: Fri, 3 Jan 2025 11:20:43 +1300
Subject: [PATCH 15/15] Bump astral-sh/setup-uv from 3 to 5.1.0

Bumps [astral-sh/setup-uv](https://github.com/astral-sh/setup-uv) from 3to 5.1.0.
- [Release notes](https://github.com/astral-sh/setup-uv/releases)
- [Commits](https://github.com/astral-sh/setup-uv/compare/v3...v5.1.0)

Includes auto activate venv when python-version is set, xref https://github.com/astral-sh/setup-uv/pull/194
---
 .github/workflows/ci_tests_legacy.yaml | 10 ++++------
 1 file changed, 4 insertions(+), 6 deletions(-)

diff --git a/.github/workflows/ci_tests_legacy.yaml b/.github/workflows/ci_tests_legacy.yaml
index 8abb317f9a1..f0c91592a3f 100644
--- a/.github/workflows/ci_tests_legacy.yaml
+++ b/.github/workflows/ci_tests_legacy.yaml
@@ -80,20 +80,18 @@ jobs:
 
       # Install uv package manager
       - name: Install uv
-        uses: astral-sh/setup-uv@v3
+        uses: astral-sh/setup-uv@v5.1.0
+        with:
+          python-version: 3.11
 
       # Install the package that we want to test
       - name: Install the package
         run: |
-          uv venv
-          source .venv/bin/activate
           uv run --with pip==23 --resolution lowest-direct --all-extras --dev make install
           uv pip list
 
       # Run the tests but skip images
       - name: Run tests
-        run: |
-          source .venv/bin/activate
-          uv run --with pytest==8,pytest-mpl==0.17,pytest-doctestplus==1.2 --resolution lowest-direct --all-extras --dev make test_no_images PYTEST_EXTRA="-r P"
+        run: uv run --with pytest==8,pytest-mpl==0.17,pytest-doctestplus==1.2 --resolution lowest-direct --all-extras --dev make test_no_images PYTEST_EXTRA="-r P"
         env:
           GMT_LIBRARY_PATH: $CONDA_PREFIX/lib