From 32d92d79b9f736b32dabdd7a1d63cafcb4d37486 Mon Sep 17 00:00:00 2001
From: Wei Ji <23487320+weiji14@users.noreply.github.com>
Date: Sat, 23 Dec 2023 19:44:31 +1300
Subject: [PATCH 01/39] Setup Continuous Benchmarking workflow with
 pytest-codspeed

Measuring the execution speed of tests to track performance of PyGMT functions over time. Using pytest-codspeed, see https://docs.codspeed.io/benchmarks/python#running-the-benchmarks-in-your-ci. Decorated a couple of unit tests with @pytest.mark.benchmark to see if the benchmarking works.
---
 .github/workflows/benchmarks.yml | 73 ++++++++++++++++++++++++++++++++
 pygmt/tests/test_blockm.py       |  1 +
 pygmt/tests/test_grd2xyz.py      |  1 +
 3 files changed, 75 insertions(+)
 create mode 100644 .github/workflows/benchmarks.yml

diff --git a/.github/workflows/benchmarks.yml b/.github/workflows/benchmarks.yml
new file mode 100644
index 00000000000..b8a94753ff8
--- /dev/null
+++ b/.github/workflows/benchmarks.yml
@@ -0,0 +1,73 @@
+# Run performance benchmarks
+#
+# Continuous benchmarking using pytest-codspeed. Measures the execution speed
+# of tests marked with @pytest.mark.benchmark decorator.
+
+name: Benchmarks
+
+on:
+  # Run on pushes to the main branch
+  push:
+    branches: [ main ]
+  # Uncomment the 'pull_request' line below to trigger the workflow in PR
+  pull_request:
+  # `workflow_dispatch` allows CodSpeed to trigger backtest
+  # performance analysis in order to generate initial data.
+  workflow_dispatch:
+
+concurrency:
+  group: ${{ github.workflow }}-${{ github.ref }}
+  cancel-in-progress: ${{ github.ref != 'refs/heads/main' }}
+
+jobs:
+  benchmarks:
+    runs-on: ubuntu-22.04
+    defaults:
+      run:
+        shell: bash -l {0}
+
+    steps:
+      # Checkout current git repository
+      - name: Checkout
+        uses: actions/checkout@v4.1.1
+
+      # Install Micromamba with conda-forge dependencies
+      - name: Setup Micromamba
+        uses: mamba-org/setup-micromamba@v1.7.3
+        with:
+          environment-name: pygmt
+          condarc: |
+            channels:
+              - conda-forge
+              - nodefaults
+          cache-downloads: true
+          cache-environment: true
+          create-args: >-
+            python=3.12
+            gmt=6.4.0
+            numpy=${{ matrix.numpy-version }}
+            pandas
+            xarray
+            netCDF4
+            packaging
+            pytest
+            pytest-benchmark
+
+      # Install dependencies from PyPI
+      - name: Install dependencies
+        run: |
+          python -m pip install pytest-codspeed
+
+      # Show installed pkg information for postmortem diagnostic
+      - name: List installed packages
+        run: micromamba list
+
+      # Install the package that we want to test
+      - name: Install the package
+        run: make install
+
+      # Run the benchmark tests
+      - name: Run benchmarks
+        uses: CodSpeedHQ/action@v2.0.2
+        with:
+          run: make test PYTEST_EXTRA="-r P --codspeed"
diff --git a/pygmt/tests/test_blockm.py b/pygmt/tests/test_blockm.py
index c75de7673c0..9b4acb95cd6 100644
--- a/pygmt/tests/test_blockm.py
+++ b/pygmt/tests/test_blockm.py
@@ -22,6 +22,7 @@ def fixture_dataframe():
     return load_sample_data(name="bathymetry")
 
 
+@pytest.mark.benchmark
 def test_blockmean_input_dataframe(dataframe):
     """
     Run blockmean by passing in a pandas.DataFrame as input.
diff --git a/pygmt/tests/test_grd2xyz.py b/pygmt/tests/test_grd2xyz.py
index d53993388c2..2cd555d6d5f 100644
--- a/pygmt/tests/test_grd2xyz.py
+++ b/pygmt/tests/test_grd2xyz.py
@@ -20,6 +20,7 @@ def fixture_grid():
     return load_static_earth_relief()
 
 
+@pytest.mark.benchmark
 def test_grd2xyz(grid):
     """
     Make sure grd2xyz works as expected.

From 2fabfb873a3ae1e64788a444bb807b17f8d57f97 Mon Sep 17 00:00:00 2001
From: Wei Ji <23487320+weiji14@users.noreply.github.com>
Date: Sat, 23 Dec 2023 19:53:49 +1300
Subject: [PATCH 02/39] Try fetching all history for setuptools-scm

---
 .github/workflows/benchmarks.yml | 3 +++
 1 file changed, 3 insertions(+)

diff --git a/.github/workflows/benchmarks.yml b/.github/workflows/benchmarks.yml
index b8a94753ff8..4e34709075f 100644
--- a/.github/workflows/benchmarks.yml
+++ b/.github/workflows/benchmarks.yml
@@ -30,6 +30,9 @@ jobs:
       # Checkout current git repository
       - name: Checkout
         uses: actions/checkout@v4.1.1
+        with:
+          # fetch all history so that setuptools-scm works
+          fetch-depth: 0
 
       # Install Micromamba with conda-forge dependencies
       - name: Setup Micromamba

From bf5499c96198dbd9cadb94b076eab1f1979c7786 Mon Sep 17 00:00:00 2001
From: Wei Ji <23487320+weiji14@users.noreply.github.com>
Date: Sat, 23 Dec 2023 20:02:33 +1300
Subject: [PATCH 03/39] List installed packages after make install step

To debug why import pygmt doesn't work.
---
 .github/workflows/benchmarks.yml | 8 ++++----
 1 file changed, 4 insertions(+), 4 deletions(-)

diff --git a/.github/workflows/benchmarks.yml b/.github/workflows/benchmarks.yml
index 4e34709075f..37b10a785a4 100644
--- a/.github/workflows/benchmarks.yml
+++ b/.github/workflows/benchmarks.yml
@@ -61,14 +61,14 @@ jobs:
         run: |
           python -m pip install pytest-codspeed
 
-      # Show installed pkg information for postmortem diagnostic
-      - name: List installed packages
-        run: micromamba list
-
       # Install the package that we want to test
       - name: Install the package
         run: make install
 
+      # Show installed pkg information for postmortem diagnostic
+      - name: List installed packages
+        run: micromamba list
+
       # Run the benchmark tests
       - name: Run benchmarks
         uses: CodSpeedHQ/action@v2.0.2

From fde104800d4ff495ba0f03241949f891195eabe8 Mon Sep 17 00:00:00 2001
From: Wei Ji <23487320+weiji14@users.noreply.github.com>
Date: Sat, 23 Dec 2023 20:14:07 +1300
Subject: [PATCH 04/39] Try bash -el -c which python

Might need to launch into the correct shell first. Also running pip list to double check if dependencies are installed ok.
---
 .github/workflows/benchmarks.yml | 8 ++++++--
 1 file changed, 6 insertions(+), 2 deletions(-)

diff --git a/.github/workflows/benchmarks.yml b/.github/workflows/benchmarks.yml
index 37b10a785a4..6043c238ba7 100644
--- a/.github/workflows/benchmarks.yml
+++ b/.github/workflows/benchmarks.yml
@@ -67,10 +67,14 @@ jobs:
 
       # Show installed pkg information for postmortem diagnostic
       - name: List installed packages
-        run: micromamba list
+        run: |
+          micromamba list
+          pip list
 
       # Run the benchmark tests
       - name: Run benchmarks
         uses: CodSpeedHQ/action@v2.0.2
         with:
-          run: make test PYTEST_EXTRA="-r P --codspeed"
+          run: |
+            bash -el -c which python
+            make test PYTEST_EXTRA="-r P --codspeed"

From f39abfb683bccdb8f4ce5fb8dd4b8e12aa004041 Mon Sep 17 00:00:00 2001
From: Wei Ji <23487320+weiji14@users.noreply.github.com>
Date: Sat, 23 Dec 2023 20:40:15 +1300
Subject: [PATCH 05/39] Try using mostly PyPI packages, with GMT from
 conda-forge

Seeing if it's possible to avoid using conda shell.
---
 .github/workflows/benchmarks.yml | 16 +++++++---------
 1 file changed, 7 insertions(+), 9 deletions(-)

diff --git a/.github/workflows/benchmarks.yml b/.github/workflows/benchmarks.yml
index 6043c238ba7..94bde3755fe 100644
--- a/.github/workflows/benchmarks.yml
+++ b/.github/workflows/benchmarks.yml
@@ -48,18 +48,12 @@ jobs:
           create-args: >-
             python=3.12
             gmt=6.4.0
-            numpy=${{ matrix.numpy-version }}
-            pandas
-            xarray
-            netCDF4
-            packaging
-            pytest
-            pytest-benchmark
 
       # Install dependencies from PyPI
       - name: Install dependencies
         run: |
-          python -m pip install pytest-codspeed
+          python -m pip install numpy pandas xarray netCDF4 packaging \
+                                pytest pytest-benchmark pytest-codspeed
 
       # Install the package that we want to test
       - name: Install the package
@@ -70,11 +64,15 @@ jobs:
         run: |
           micromamba list
           pip list
+          which gmt
+          echo ${{ github.workspace }}
 
       # Run the benchmark tests
       - name: Run benchmarks
         uses: CodSpeedHQ/action@v2.0.2
         with:
           run: |
-            bash -el -c which python
+            python -m pip list
             make test PYTEST_EXTRA="-r P --codspeed"
+        env:
+          GMT_LIBRARY_PATH: ${{ github.workspace }}/micromamba/envs/pygmt/lib/

From 6eddb0bdebea2ef695135dfbf3792f943b7ee90d Mon Sep 17 00:00:00 2001
From: Wei Ji <23487320+weiji14@users.noreply.github.com>
Date: Sat, 23 Dec 2023 20:49:20 +1300
Subject: [PATCH 06/39] Just install pygmt and dependencies in the benchmark
 step

Do everything in the same shell, but point to the GMT installation in /home/runner/micromamba/envs/pygmt/lib/
---
 .github/workflows/benchmarks.yml | 17 ++++-------------
 1 file changed, 4 insertions(+), 13 deletions(-)

diff --git a/.github/workflows/benchmarks.yml b/.github/workflows/benchmarks.yml
index 94bde3755fe..38a84b24859 100644
--- a/.github/workflows/benchmarks.yml
+++ b/.github/workflows/benchmarks.yml
@@ -49,21 +49,10 @@ jobs:
             python=3.12
             gmt=6.4.0
 
-      # Install dependencies from PyPI
-      - name: Install dependencies
-        run: |
-          python -m pip install numpy pandas xarray netCDF4 packaging \
-                                pytest pytest-benchmark pytest-codspeed
-
-      # Install the package that we want to test
-      - name: Install the package
-        run: make install
-
       # Show installed pkg information for postmortem diagnostic
       - name: List installed packages
         run: |
           micromamba list
-          pip list
           which gmt
           echo ${{ github.workspace }}
 
@@ -72,7 +61,9 @@ jobs:
         uses: CodSpeedHQ/action@v2.0.2
         with:
           run: |
-            python -m pip list
+            python -m pip install numpy pandas xarray netCDF4 packaging \
+                                  pytest pytest-benchmark pytest-codspeed
+            make install
             make test PYTEST_EXTRA="-r P --codspeed"
         env:
-          GMT_LIBRARY_PATH: ${{ github.workspace }}/micromamba/envs/pygmt/lib/
+          GMT_LIBRARY_PATH: /home/runner/micromamba/envs/pygmt/lib/

From 7d431b4de0c3da5bc83f29d236fbc870c4846d03 Mon Sep 17 00:00:00 2001
From: Wei Ji <23487320+weiji14@users.noreply.github.com>
Date: Sat, 23 Dec 2023 20:57:38 +1300
Subject: [PATCH 07/39] Install setuptools

Try to prevent `ERROR: Project file:///home/runner/work/pygmt/pygmt has a 'pyproject.toml' and its build backend is missing the 'build_editable' hook. Since it does not have a 'setup.py' nor a 'setup.cfg', it cannot be installed in editable mode. Consider using a build backend that supports PEP 660`.
---
 .github/workflows/benchmarks.yml | 4 +++-
 1 file changed, 3 insertions(+), 1 deletion(-)

diff --git a/.github/workflows/benchmarks.yml b/.github/workflows/benchmarks.yml
index 38a84b24859..ccfb8e20261 100644
--- a/.github/workflows/benchmarks.yml
+++ b/.github/workflows/benchmarks.yml
@@ -62,7 +62,9 @@ jobs:
         with:
           run: |
             python -m pip install numpy pandas xarray netCDF4 packaging \
-                                  pytest pytest-benchmark pytest-codspeed
+                                  pytest pytest-benchmark pytest-codspeed \
+                                  setuptools
+            python -m pip list
             make install
             make test PYTEST_EXTRA="-r P --codspeed"
         env:

From b527c9d54aaeab599684748950bd017c81c5b213 Mon Sep 17 00:00:00 2001
From: Wei Ji <23487320+weiji14@users.noreply.github.com>
Date: Sat, 23 Dec 2023 21:01:45 +1300
Subject: [PATCH 08/39] Upgrade version of pip and setuptools

Need newer setuptools greater than 64.
---
 .github/workflows/benchmarks.yml | 10 ++++------
 1 file changed, 4 insertions(+), 6 deletions(-)

diff --git a/.github/workflows/benchmarks.yml b/.github/workflows/benchmarks.yml
index ccfb8e20261..cc0f1df7d01 100644
--- a/.github/workflows/benchmarks.yml
+++ b/.github/workflows/benchmarks.yml
@@ -51,19 +51,17 @@ jobs:
 
       # Show installed pkg information for postmortem diagnostic
       - name: List installed packages
-        run: |
-          micromamba list
-          which gmt
-          echo ${{ github.workspace }}
+        run: micromamba list
 
       # Run the benchmark tests
       - name: Run benchmarks
         uses: CodSpeedHQ/action@v2.0.2
         with:
           run: |
-            python -m pip install numpy pandas xarray netCDF4 packaging \
+            python -m pip install -U pip
+            python -m pip install -U numpy pandas xarray netCDF4 packaging \
                                   pytest pytest-benchmark pytest-codspeed \
-                                  setuptools
+                                  'setuptools>64'
             python -m pip list
             make install
             make test PYTEST_EXTRA="-r P --codspeed"

From 31a7567b23fd15d8b563f3f495e34ba23e515861 Mon Sep 17 00:00:00 2001
From: Wei Ji <23487320+weiji14@users.noreply.github.com>
Date: Sat, 23 Dec 2023 21:06:11 +1300
Subject: [PATCH 09/39] Try plain setuptools

Action might not like the single quotes.
---
 .github/workflows/benchmarks.yml | 5 ++---
 1 file changed, 2 insertions(+), 3 deletions(-)

diff --git a/.github/workflows/benchmarks.yml b/.github/workflows/benchmarks.yml
index cc0f1df7d01..2161a5e7452 100644
--- a/.github/workflows/benchmarks.yml
+++ b/.github/workflows/benchmarks.yml
@@ -58,10 +58,9 @@ jobs:
         uses: CodSpeedHQ/action@v2.0.2
         with:
           run: |
-            python -m pip install -U pip
             python -m pip install -U numpy pandas xarray netCDF4 packaging \
-                                  pytest pytest-benchmark pytest-codspeed \
-                                  'setuptools>64'
+                                  pip pytest pytest-benchmark pytest-codspeed \
+                                  setuptools
             python -m pip list
             make install
             make test PYTEST_EXTRA="-r P --codspeed"

From 5ca4565c95635117ef324dd0b9d8d459daece24f Mon Sep 17 00:00:00 2001
From: Wei Ji <23487320+weiji14@users.noreply.github.com>
Date: Sat, 23 Dec 2023 21:21:19 +1300
Subject: [PATCH 10/39] Try to find GMT install path

Should be /home/runner/micromamba/envs/pygmt/lib/, but don't know what's happening in the CodSpeedHQ/action shell.
---
 .github/workflows/benchmarks.yml | 1 +
 1 file changed, 1 insertion(+)

diff --git a/.github/workflows/benchmarks.yml b/.github/workflows/benchmarks.yml
index 2161a5e7452..7109dfb69be 100644
--- a/.github/workflows/benchmarks.yml
+++ b/.github/workflows/benchmarks.yml
@@ -63,6 +63,7 @@ jobs:
                                   setuptools
             python -m pip list
             make install
+            which gmt
             make test PYTEST_EXTRA="-r P --codspeed"
         env:
           GMT_LIBRARY_PATH: /home/runner/micromamba/envs/pygmt/lib/

From 1ad03e94261deb646438e571f91704df75cee21b Mon Sep 17 00:00:00 2001
From: Wei Ji <23487320+weiji14@users.noreply.github.com>
Date: Sat, 23 Dec 2023 21:34:57 +1300
Subject: [PATCH 11/39] Try installing GMT with bundled conda

Maybe best to use the bundled conda with GitHub Actions?
---
 .github/workflows/benchmarks.yml | 33 ++++++++++++++------------------
 1 file changed, 14 insertions(+), 19 deletions(-)

diff --git a/.github/workflows/benchmarks.yml b/.github/workflows/benchmarks.yml
index 7109dfb69be..52e80af1ac4 100644
--- a/.github/workflows/benchmarks.yml
+++ b/.github/workflows/benchmarks.yml
@@ -34,26 +34,22 @@ jobs:
           # fetch all history so that setuptools-scm works
           fetch-depth: 0
 
-      # Install Micromamba with conda-forge dependencies
-      - name: Setup Micromamba
-        uses: mamba-org/setup-micromamba@v1.7.3
+      # Install Miniconda with conda-forge dependencies
+      - name: Setup Miniconda
+        uses: conda-incubator/setup-miniconda@v3.0.1
         with:
-          environment-name: pygmt
-          condarc: |
-            channels:
-              - conda-forge
-              - nodefaults
-          cache-downloads: true
-          cache-environment: true
-          create-args: >-
-            python=3.12
-            gmt=6.4.0
+          activate-environment: pygmt
+          python-version: '3.12'
+          channels: conda-forge,nodefaults
+          channel-priority: strict
 
-      # Show installed pkg information for postmortem diagnostic
-      - name: List installed packages
-        run: micromamba list
+      # Install GMT from conda-forge
+      - name: Install GMT
+        run: |
+          conda install --solver=libmamba gmt=6.4.0
+          which gmt
 
-      # Run the benchmark tests
+      # Install dependencies from PyPI and run the benchmark tests
       - name: Run benchmarks
         uses: CodSpeedHQ/action@v2.0.2
         with:
@@ -63,7 +59,6 @@ jobs:
                                   setuptools
             python -m pip list
             make install
-            which gmt
             make test PYTEST_EXTRA="-r P --codspeed"
         env:
-          GMT_LIBRARY_PATH: /home/runner/micromamba/envs/pygmt/lib/
+          GMT_LIBRARY_PATH: /home/runner/miniconda/envs/pygmt/lib/

From 1b67ca7b482d030bbad0017cf229278445ac46d5 Mon Sep 17 00:00:00 2001
From: Wei Ji <23487320+weiji14@users.noreply.github.com>
Date: Sat, 23 Dec 2023 21:37:30 +1300
Subject: [PATCH 12/39] Update GMT_LIBRARY_PATH to
 /usr/share/miniconda/envs/pygmt/lib

New place where GMT is installed by miniconda.
---
 .github/workflows/benchmarks.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/benchmarks.yml b/.github/workflows/benchmarks.yml
index 52e80af1ac4..60a568316e4 100644
--- a/.github/workflows/benchmarks.yml
+++ b/.github/workflows/benchmarks.yml
@@ -61,4 +61,4 @@ jobs:
             make install
             make test PYTEST_EXTRA="-r P --codspeed"
         env:
-          GMT_LIBRARY_PATH: /home/runner/miniconda/envs/pygmt/lib/
+          GMT_LIBRARY_PATH: /usr/share/miniconda/envs/pygmt/lib/

From 6d2fb3266f50c1dcd69283fc5a77529911471634 Mon Sep 17 00:00:00 2001
From: Wei Ji <23487320+weiji14@users.noreply.github.com>
Date: Sun, 24 Dec 2023 16:20:49 +1300
Subject: [PATCH 13/39] List contents of /usr/share/miniconda/envs/pygmt/lib/

See if libgmt.so is in this folder.
---
 .github/workflows/benchmarks.yml | 1 +
 1 file changed, 1 insertion(+)

diff --git a/.github/workflows/benchmarks.yml b/.github/workflows/benchmarks.yml
index 60a568316e4..5e9258c96c4 100644
--- a/.github/workflows/benchmarks.yml
+++ b/.github/workflows/benchmarks.yml
@@ -54,6 +54,7 @@ jobs:
         uses: CodSpeedHQ/action@v2.0.2
         with:
           run: |
+            ls -lh /usr/share/miniconda/envs/pygmt/lib/
             python -m pip install -U numpy pandas xarray netCDF4 packaging \
                                   pip pytest pytest-benchmark pytest-codspeed \
                                   setuptools

From 8bb16659fe792b8a38ceeeead3267e683553674e Mon Sep 17 00:00:00 2001
From: Wei Ji <23487320+weiji14@users.noreply.github.com>
Date: Sun, 24 Dec 2023 16:30:41 +1300
Subject: [PATCH 14/39] Back to installing dependencies with conda instead of
 pip

Trying to workaround `Error loading GMT shared library at '/usr/share/miniconda/envs/pygmt/lib/libgmt.so'.
  /lib/x86_64-linux-gnu/libcrypto.so.3: version `OPENSSL_3.2.0' not found (required by /usr/share/miniconda/envs/pygmt/lib/././libssl.so.3)`
---
 .github/workflows/benchmarks.yml | 13 +++++--------
 1 file changed, 5 insertions(+), 8 deletions(-)

diff --git a/.github/workflows/benchmarks.yml b/.github/workflows/benchmarks.yml
index 5e9258c96c4..ed72049f1d9 100644
--- a/.github/workflows/benchmarks.yml
+++ b/.github/workflows/benchmarks.yml
@@ -43,11 +43,12 @@ jobs:
           channels: conda-forge,nodefaults
           channel-priority: strict
 
-      # Install GMT from conda-forge
-      - name: Install GMT
+      # Install GMT and dependencies from conda-forge
+      - name: Install dependencies
         run: |
-          conda install --solver=libmamba gmt=6.4.0
-          which gmt
+          conda install --solver=libmamba gmt=6.4.0 \
+                        numpy pandas xarray netCDF4 packaging \
+                        pytest pytest-benchmark pytest-codspeed setuptools
 
       # Install dependencies from PyPI and run the benchmark tests
       - name: Run benchmarks
@@ -55,10 +56,6 @@ jobs:
         with:
           run: |
             ls -lh /usr/share/miniconda/envs/pygmt/lib/
-            python -m pip install -U numpy pandas xarray netCDF4 packaging \
-                                  pip pytest pytest-benchmark pytest-codspeed \
-                                  setuptools
-            python -m pip list
             make install
             make test PYTEST_EXTRA="-r P --codspeed"
         env:

From 351f8f2370656ff0eeaae4974953ee9a479a7cc4 Mon Sep 17 00:00:00 2001
From: Wei Ji <23487320+weiji14@users.noreply.github.com>
Date: Sun, 24 Dec 2023 16:34:09 +1300
Subject: [PATCH 15/39] Still need to install pytest-codspeed from PyPI

Missing conda-forge package for pytest-codspeed.
---
 .github/workflows/benchmarks.yml | 5 ++++-
 1 file changed, 4 insertions(+), 1 deletion(-)

diff --git a/.github/workflows/benchmarks.yml b/.github/workflows/benchmarks.yml
index ed72049f1d9..f8812655881 100644
--- a/.github/workflows/benchmarks.yml
+++ b/.github/workflows/benchmarks.yml
@@ -46,9 +46,12 @@ jobs:
       # Install GMT and dependencies from conda-forge
       - name: Install dependencies
         run: |
+          which conda
+          echo $CONDA
           conda install --solver=libmamba gmt=6.4.0 \
                         numpy pandas xarray netCDF4 packaging \
-                        pytest pytest-benchmark pytest-codspeed setuptools
+                        pytest pytest-benchmark setuptools
+          $CONDA/bin/python -m pip install pytest-codspeed
 
       # Install dependencies from PyPI and run the benchmark tests
       - name: Run benchmarks

From e66497354fa7658c98d583b3859488513b761175 Mon Sep 17 00:00:00 2001
From: Wei Ji <23487320+weiji14@users.noreply.github.com>
Date: Sun, 24 Dec 2023 16:38:38 +1300
Subject: [PATCH 16/39] Activate base environment rather than pygmt environment

---
 .github/workflows/benchmarks.yml | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/.github/workflows/benchmarks.yml b/.github/workflows/benchmarks.yml
index f8812655881..97849d44bf0 100644
--- a/.github/workflows/benchmarks.yml
+++ b/.github/workflows/benchmarks.yml
@@ -38,7 +38,8 @@ jobs:
       - name: Setup Miniconda
         uses: conda-incubator/setup-miniconda@v3.0.1
         with:
-          activate-environment: pygmt
+          auto-activate-base: true
+          activate-environment: ""  # base environment
           python-version: '3.12'
           channels: conda-forge,nodefaults
           channel-priority: strict

From 992f914151001900952e93e0aeb6b078dd044f66 Mon Sep 17 00:00:00 2001
From: Wei Ji <23487320+weiji14@users.noreply.github.com>
Date: Sun, 24 Dec 2023 16:41:16 +1300
Subject: [PATCH 17/39] Just use default python from setup-miniconda

Instead of setting Python 3.12 explicitly.
---
 .github/workflows/benchmarks.yml | 1 -
 1 file changed, 1 deletion(-)

diff --git a/.github/workflows/benchmarks.yml b/.github/workflows/benchmarks.yml
index 97849d44bf0..04476fe1cc6 100644
--- a/.github/workflows/benchmarks.yml
+++ b/.github/workflows/benchmarks.yml
@@ -40,7 +40,6 @@ jobs:
         with:
           auto-activate-base: true
           activate-environment: ""  # base environment
-          python-version: '3.12'
           channels: conda-forge,nodefaults
           channel-priority: strict
 

From 2d38ecb4352b90223754549539df6d84063332dd Mon Sep 17 00:00:00 2001
From: Wei Ji <23487320+weiji14@users.noreply.github.com>
Date: Sun, 24 Dec 2023 16:45:38 +1300
Subject: [PATCH 18/39] Install setuptools via PyPI and use GMT_LIBRARY_PATH
 from base env

---
 .github/workflows/benchmarks.yml | 8 ++++----
 1 file changed, 4 insertions(+), 4 deletions(-)

diff --git a/.github/workflows/benchmarks.yml b/.github/workflows/benchmarks.yml
index 04476fe1cc6..c41eb49d261 100644
--- a/.github/workflows/benchmarks.yml
+++ b/.github/workflows/benchmarks.yml
@@ -50,16 +50,16 @@ jobs:
           echo $CONDA
           conda install --solver=libmamba gmt=6.4.0 \
                         numpy pandas xarray netCDF4 packaging \
-                        pytest pytest-benchmark setuptools
-          $CONDA/bin/python -m pip install pytest-codspeed
+                        pytest pytest-benchmarks
+          $CONDA/bin/python -m pip install pytest-codspeed setuptools
 
       # Install dependencies from PyPI and run the benchmark tests
       - name: Run benchmarks
         uses: CodSpeedHQ/action@v2.0.2
         with:
           run: |
-            ls -lh /usr/share/miniconda/envs/pygmt/lib/
+            ls -lh /usr/share/miniconda/lib/
             make install
             make test PYTEST_EXTRA="-r P --codspeed"
         env:
-          GMT_LIBRARY_PATH: /usr/share/miniconda/envs/pygmt/lib/
+          GMT_LIBRARY_PATH: /usr/share/miniconda/lib/

From 44533a54bc28e4286eed5ff94843a427f14ed9fc Mon Sep 17 00:00:00 2001
From: Wei Ji <23487320+weiji14@users.noreply.github.com>
Date: Sun, 24 Dec 2023 16:48:10 +1300
Subject: [PATCH 19/39] Typo

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

diff --git a/.github/workflows/benchmarks.yml b/.github/workflows/benchmarks.yml
index c41eb49d261..aba804e8755 100644
--- a/.github/workflows/benchmarks.yml
+++ b/.github/workflows/benchmarks.yml
@@ -50,7 +50,7 @@ jobs:
           echo $CONDA
           conda install --solver=libmamba gmt=6.4.0 \
                         numpy pandas xarray netCDF4 packaging \
-                        pytest pytest-benchmarks
+                        pytest pytest-benchmark
           $CONDA/bin/python -m pip install pytest-codspeed setuptools
 
       # Install dependencies from PyPI and run the benchmark tests

From f0aba1a3bd07f2a0c08bd40a69460fd001c7eddc Mon Sep 17 00:00:00 2001
From: Wei Ji <23487320+weiji14@users.noreply.github.com>
Date: Sun, 24 Dec 2023 16:52:14 +1300
Subject: [PATCH 20/39] Still need to upgrade setuptools version

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

diff --git a/.github/workflows/benchmarks.yml b/.github/workflows/benchmarks.yml
index aba804e8755..d47a4eb78d9 100644
--- a/.github/workflows/benchmarks.yml
+++ b/.github/workflows/benchmarks.yml
@@ -51,7 +51,7 @@ jobs:
           conda install --solver=libmamba gmt=6.4.0 \
                         numpy pandas xarray netCDF4 packaging \
                         pytest pytest-benchmark
-          $CONDA/bin/python -m pip install pytest-codspeed setuptools
+          $CONDA/bin/python -m pip install -U pytest-codspeed setuptools
 
       # Install dependencies from PyPI and run the benchmark tests
       - name: Run benchmarks

From c5a8338d059689b871a79d99824a38f7d99f001d Mon Sep 17 00:00:00 2001
From: Wei Ji <23487320+weiji14@users.noreply.github.com>
Date: Sun, 24 Dec 2023 16:59:18 +1300
Subject: [PATCH 21/39] Try using conda's python rather than system python

---
 .github/workflows/benchmarks.yml | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/.github/workflows/benchmarks.yml b/.github/workflows/benchmarks.yml
index d47a4eb78d9..57f742d2034 100644
--- a/.github/workflows/benchmarks.yml
+++ b/.github/workflows/benchmarks.yml
@@ -59,7 +59,8 @@ jobs:
         with:
           run: |
             ls -lh /usr/share/miniconda/lib/
-            make install
+            which python
+            $CONDA/bin/python -m pip install --no-deps -e .
             make test PYTEST_EXTRA="-r P --codspeed"
         env:
           GMT_LIBRARY_PATH: /usr/share/miniconda/lib/

From c4cef5caa3a8815fe67f85b659cdfc9a85105ca4 Mon Sep 17 00:00:00 2001
From: Wei Ji <23487320+weiji14@users.noreply.github.com>
Date: Sun, 24 Dec 2023 17:06:17 +1300
Subject: [PATCH 22/39] Run tests with conda python instead of system python

Don't use `make test`, which seems to use the system python in `/usr/bin/python` rather than `/usr/share/miniconda/bin/python`.
---
 .github/workflows/benchmarks.yml | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/.github/workflows/benchmarks.yml b/.github/workflows/benchmarks.yml
index 57f742d2034..f4da48a9c10 100644
--- a/.github/workflows/benchmarks.yml
+++ b/.github/workflows/benchmarks.yml
@@ -59,8 +59,8 @@ jobs:
         with:
           run: |
             ls -lh /usr/share/miniconda/lib/
-            which python
             $CONDA/bin/python -m pip install --no-deps -e .
-            make test PYTEST_EXTRA="-r P --codspeed"
+            $CONDA/bin/python -c "import pygmt; pygmt.show_versions()"
+            PYGMT_USE_EXTERNAL_DISPLAY="false" pytest -r P --codspeed
         env:
           GMT_LIBRARY_PATH: /usr/share/miniconda/lib/

From b91c1dff15c9128b4c559c92b56874639d3084b6 Mon Sep 17 00:00:00 2001
From: Wei Ji <23487320+weiji14@users.noreply.github.com>
Date: Sun, 24 Dec 2023 17:12:26 +1300
Subject: [PATCH 23/39] Actually use conda python to run pytest

Also split the PyGMT build step into a separate step, now that we're confident all the packages are installed using conda's python/pip.
---
 .github/workflows/benchmarks.yml | 8 +++++---
 1 file changed, 5 insertions(+), 3 deletions(-)

diff --git a/.github/workflows/benchmarks.yml b/.github/workflows/benchmarks.yml
index f4da48a9c10..b2a8455d14d 100644
--- a/.github/workflows/benchmarks.yml
+++ b/.github/workflows/benchmarks.yml
@@ -53,14 +53,16 @@ jobs:
                         pytest pytest-benchmark
           $CONDA/bin/python -m pip install -U pytest-codspeed setuptools
 
+      # Install the package that we want to test
+      - name: Install the package
+        run: $CONDA/bin/python -m pip install --no-deps -e .
+
       # Install dependencies from PyPI and run the benchmark tests
       - name: Run benchmarks
         uses: CodSpeedHQ/action@v2.0.2
         with:
           run: |
-            ls -lh /usr/share/miniconda/lib/
-            $CONDA/bin/python -m pip install --no-deps -e .
             $CONDA/bin/python -c "import pygmt; pygmt.show_versions()"
-            PYGMT_USE_EXTERNAL_DISPLAY="false" pytest -r P --codspeed
+            PYGMT_USE_EXTERNAL_DISPLAY="false" $CONDA/bin/python -m pytest -r P --codspeed
         env:
           GMT_LIBRARY_PATH: /usr/share/miniconda/lib/

From a566eb818501c109e332387ff9799d8f0243671b Mon Sep 17 00:00:00 2001
From: Wei Ji <23487320+weiji14@users.noreply.github.com>
Date: Sun, 24 Dec 2023 17:16:56 +1300
Subject: [PATCH 24/39] Install pytest-mpl from conda-forge

Also tidy up some stray bits
---
 .github/workflows/benchmarks.yml | 6 ++----
 1 file changed, 2 insertions(+), 4 deletions(-)

diff --git a/.github/workflows/benchmarks.yml b/.github/workflows/benchmarks.yml
index b2a8455d14d..9dfd59b56ef 100644
--- a/.github/workflows/benchmarks.yml
+++ b/.github/workflows/benchmarks.yml
@@ -46,18 +46,16 @@ jobs:
       # Install GMT and dependencies from conda-forge
       - name: Install dependencies
         run: |
-          which conda
-          echo $CONDA
           conda install --solver=libmamba gmt=6.4.0 \
                         numpy pandas xarray netCDF4 packaging \
-                        pytest pytest-benchmark
+                        pytest pytest-benchmark pytest-mpl
           $CONDA/bin/python -m pip install -U pytest-codspeed setuptools
 
       # Install the package that we want to test
       - name: Install the package
         run: $CONDA/bin/python -m pip install --no-deps -e .
 
-      # Install dependencies from PyPI and run the benchmark tests
+      # Run the benchmark tests
       - name: Run benchmarks
         uses: CodSpeedHQ/action@v2.0.2
         with:

From 3df918ff093fab65a63b5151a533ff06dae822eb Mon Sep 17 00:00:00 2001
From: Wei Ji <23487320+weiji14@users.noreply.github.com>
Date: Sun, 24 Dec 2023 17:27:15 +1300
Subject: [PATCH 25/39] Run pytest with --pyargs pygmt

Try to avoid collecting tests in the examples/ folder.
---
 .github/workflows/benchmarks.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/benchmarks.yml b/.github/workflows/benchmarks.yml
index 9dfd59b56ef..c2c21686ec7 100644
--- a/.github/workflows/benchmarks.yml
+++ b/.github/workflows/benchmarks.yml
@@ -61,6 +61,6 @@ jobs:
         with:
           run: |
             $CONDA/bin/python -c "import pygmt; pygmt.show_versions()"
-            PYGMT_USE_EXTERNAL_DISPLAY="false" $CONDA/bin/python -m pytest -r P --codspeed
+            PYGMT_USE_EXTERNAL_DISPLAY="false" $CONDA/bin/python -m pytest -r P --pyargs pygmt --codspeed
         env:
           GMT_LIBRARY_PATH: /usr/share/miniconda/lib/

From 4a0af5e259c202c017b4a8bb292cb70d5eef6248 Mon Sep 17 00:00:00 2001
From: Wei Ji <23487320+weiji14@users.noreply.github.com>
Date: Sun, 24 Dec 2023 17:46:57 +1300
Subject: [PATCH 26/39] Pin to Python 3.12

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

diff --git a/.github/workflows/benchmarks.yml b/.github/workflows/benchmarks.yml
index c2c21686ec7..6d55b6cfebe 100644
--- a/.github/workflows/benchmarks.yml
+++ b/.github/workflows/benchmarks.yml
@@ -46,7 +46,7 @@ jobs:
       # Install GMT and dependencies from conda-forge
       - name: Install dependencies
         run: |
-          conda install --solver=libmamba gmt=6.4.0 \
+          conda install --solver=libmamba gmt=6.4.0 python=3.12 \
                         numpy pandas xarray netCDF4 packaging \
                         pytest pytest-benchmark pytest-mpl
           $CONDA/bin/python -m pip install -U pytest-codspeed setuptools

From cd6884aa254f1bb2357f7e04ebf05aa492c8548d Mon Sep 17 00:00:00 2001
From: Wei Ji <23487320+weiji14@users.noreply.github.com>
Date: Sun, 24 Dec 2023 17:52:39 +1300
Subject: [PATCH 27/39] Try using CodSpeedHQ/action@v2 instead of 2.0.2

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

diff --git a/.github/workflows/benchmarks.yml b/.github/workflows/benchmarks.yml
index 6d55b6cfebe..dccc91ab2ca 100644
--- a/.github/workflows/benchmarks.yml
+++ b/.github/workflows/benchmarks.yml
@@ -57,7 +57,7 @@ jobs:
 
       # Run the benchmark tests
       - name: Run benchmarks
-        uses: CodSpeedHQ/action@v2.0.2
+        uses: CodSpeedHQ/action@v2
         with:
           run: |
             $CONDA/bin/python -c "import pygmt; pygmt.show_versions()"

From 1b9316ff5b9a86ce00d362b5ced2fca873abbac2 Mon Sep 17 00:00:00 2001
From: Wei Ji <23487320+weiji14@users.noreply.github.com>
Date: Sun, 24 Dec 2023 21:15:53 +1300
Subject: [PATCH 28/39] Add shield.io badge for CodSpeed

---
 README.rst | 3 +++
 1 file changed, 3 insertions(+)

diff --git a/README.rst b/README.rst
index 9c013253999..a56aee69c13 100644
--- a/README.rst
+++ b/README.rst
@@ -22,6 +22,9 @@ PyGMT
 .. image:: https://codecov.io/gh/GenericMappingTools/pygmt/branch/main/graph/badge.svg?token=78Fu4EWstx
     :alt: Test coverage status
     :target: https://app.codecov.io/gh/GenericMappingTools/pygmt
+.. image:: https://img.shields.io/endpoint?url=https://codspeed.io/badge.json
+    :alt: CodSpeed Performance Benchmarks
+    :target: https://codspeed.io/GenericMappingTools/pygmt
 .. image:: https://img.shields.io/pypi/pyversions/pygmt.svg?style=flat-square
     :alt: Compatible Python versions.
     :target: https://pypi.python.org/pypi/pygmt

From 37015d750d1b332e781bdb6659c7a14090cc4005 Mon Sep 17 00:00:00 2001
From: Wei Ji <23487320+weiji14@users.noreply.github.com>
Date: Mon, 25 Dec 2023 00:01:56 +1300
Subject: [PATCH 29/39] Set CODSPEED_TOKEN

Co-authored-by: Dongdong Tian <seisman.info@gmail.com>
---
 .github/workflows/benchmarks.yml | 1 +
 1 file changed, 1 insertion(+)

diff --git a/.github/workflows/benchmarks.yml b/.github/workflows/benchmarks.yml
index dccc91ab2ca..7363e521226 100644
--- a/.github/workflows/benchmarks.yml
+++ b/.github/workflows/benchmarks.yml
@@ -59,6 +59,7 @@ jobs:
       - name: Run benchmarks
         uses: CodSpeedHQ/action@v2
         with:
+          token: ${{ secrets.CODSPEED_TOKEN }}
           run: |
             $CONDA/bin/python -c "import pygmt; pygmt.show_versions()"
             PYGMT_USE_EXTERNAL_DISPLAY="false" $CONDA/bin/python -m pytest -r P --pyargs pygmt --codspeed

From f11520675fc4bb1ac74d8ae1f38c9650b6f51dd0 Mon Sep 17 00:00:00 2001
From: Wei Ji <23487320+weiji14@users.noreply.github.com>
Date: Mon, 25 Dec 2023 00:10:14 +1300
Subject: [PATCH 30/39] Revert setup CODSPEED_TOKEN

---
 .github/workflows/benchmarks.yml | 1 -
 1 file changed, 1 deletion(-)

diff --git a/.github/workflows/benchmarks.yml b/.github/workflows/benchmarks.yml
index 7363e521226..dccc91ab2ca 100644
--- a/.github/workflows/benchmarks.yml
+++ b/.github/workflows/benchmarks.yml
@@ -59,7 +59,6 @@ jobs:
       - name: Run benchmarks
         uses: CodSpeedHQ/action@v2
         with:
-          token: ${{ secrets.CODSPEED_TOKEN }}
           run: |
             $CONDA/bin/python -c "import pygmt; pygmt.show_versions()"
             PYGMT_USE_EXTERNAL_DISPLAY="false" $CONDA/bin/python -m pytest -r P --pyargs pygmt --codspeed

From c92fcb27597d4a4a803de2c9fb1fe08d75491699 Mon Sep 17 00:00:00 2001
From: Wei Ji <23487320+weiji14@users.noreply.github.com>
Date: Mon, 25 Dec 2023 11:50:04 +1300
Subject: [PATCH 31/39] Document benchmarks.yml workflow in docs/maintenance.md

---
 doc/maintenance.md | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/doc/maintenance.md b/doc/maintenance.md
index cc861eba5b2..f0615c556dd 100644
--- a/doc/maintenance.md
+++ b/doc/maintenance.md
@@ -104,6 +104,8 @@ workflow files for more details.
 12. `format-command.yml`: Format the codes using slash command
 13. `dvc-diff.yml`: Report changes in test images
 14. `slash-command-dispatch.yml`: Support slash commands in pull requests
+15. `benchmarks.yml`: Benchmarks the execution speed of tests to track performance of PyGMT functions
+
 
 ## Continuous Documentation
 

From c8d19656a4d5396b44ab48103eab2bbb52f02b91 Mon Sep 17 00:00:00 2001
From: Wei Ji <23487320+weiji14@users.noreply.github.com>
Date: Mon, 25 Dec 2023 11:52:26 +1300
Subject: [PATCH 32/39] Run benchmarks when a release is published

---
 .github/workflows/benchmarks.yml | 3 +++
 1 file changed, 3 insertions(+)

diff --git a/.github/workflows/benchmarks.yml b/.github/workflows/benchmarks.yml
index dccc91ab2ca..85364bd2e69 100644
--- a/.github/workflows/benchmarks.yml
+++ b/.github/workflows/benchmarks.yml
@@ -14,6 +14,9 @@ on:
   # `workflow_dispatch` allows CodSpeed to trigger backtest
   # performance analysis in order to generate initial data.
   workflow_dispatch:
+  release:
+    types:
+      - published
 
 concurrency:
   group: ${{ github.workflow }}-${{ github.ref }}

From 7bf09b9f9c7bf20ebace952542ed8e339bd3986f Mon Sep 17 00:00:00 2001
From: Wei Ji <23487320+weiji14@users.noreply.github.com>
Date: Mon, 25 Dec 2023 11:53:40 +1300
Subject: [PATCH 33/39] Add benchmarks.yml to bump_gmt_checklist.md

---
 .github/ISSUE_TEMPLATE/bump_gmt_checklist.md | 1 +
 1 file changed, 1 insertion(+)

diff --git a/.github/ISSUE_TEMPLATE/bump_gmt_checklist.md b/.github/ISSUE_TEMPLATE/bump_gmt_checklist.md
index 014c093a886..146d9f42c04 100644
--- a/.github/ISSUE_TEMPLATE/bump_gmt_checklist.md
+++ b/.github/ISSUE_TEMPLATE/bump_gmt_checklist.md
@@ -19,6 +19,7 @@ assignees: ''
 - [ ] Bump the GMT version in CI (1 PR)
   - [ ] Update `environment.yml`
   - [ ] Update `ci/requirements/docs.yml`
+  - [ ] Update `.github/workflows/benchmarks.yml`
   - [ ] Update `.github/workflows/cache_data.yaml`
   - [ ] Update `.github/workflows/ci_doctests.yaml`
   - [ ] Update `.github/workflows/ci_docs.yml`

From 31eb3da573c85c35d4429e5debd3f48c1714c23d Mon Sep 17 00:00:00 2001
From: Wei Ji <23487320+weiji14@users.noreply.github.com>
Date: Mon, 25 Dec 2023 11:55:14 +1300
Subject: [PATCH 34/39] Pin to CodSpeedHQ/action@v2.0.2

Co-Authored-By: Dongdong Tian <seisman.info@gmail.com>
---
 .github/workflows/benchmarks.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/benchmarks.yml b/.github/workflows/benchmarks.yml
index 85364bd2e69..35f8e125413 100644
--- a/.github/workflows/benchmarks.yml
+++ b/.github/workflows/benchmarks.yml
@@ -60,7 +60,7 @@ jobs:
 
       # Run the benchmark tests
       - name: Run benchmarks
-        uses: CodSpeedHQ/action@v2
+        uses: CodSpeedHQ/action@v2.0.2
         with:
           run: |
             $CONDA/bin/python -c "import pygmt; pygmt.show_versions()"

From 9c04e3fd75d4088cfca3436897e430a07178eada Mon Sep 17 00:00:00 2001
From: Wei Ji <23487320+weiji14@users.noreply.github.com>
Date: Mon, 25 Dec 2023 12:45:11 +1300
Subject: [PATCH 35/39] Only benchmark test_basemap for now

Remove markers for test_blockmean_input_dataframe and test_grd2xyz.
---
 pygmt/tests/test_basemap.py | 1 +
 pygmt/tests/test_blockm.py  | 1 -
 pygmt/tests/test_grd2xyz.py | 1 -
 3 files changed, 1 insertion(+), 2 deletions(-)

diff --git a/pygmt/tests/test_basemap.py b/pygmt/tests/test_basemap.py
index a78d909cd40..69f6bacf8a5 100644
--- a/pygmt/tests/test_basemap.py
+++ b/pygmt/tests/test_basemap.py
@@ -5,6 +5,7 @@
 from pygmt import Figure
 
 
+@pytest.mark.benchmark
 @pytest.mark.mpl_image_compare
 def test_basemap():
     """
diff --git a/pygmt/tests/test_blockm.py b/pygmt/tests/test_blockm.py
index 9b4acb95cd6..c75de7673c0 100644
--- a/pygmt/tests/test_blockm.py
+++ b/pygmt/tests/test_blockm.py
@@ -22,7 +22,6 @@ def fixture_dataframe():
     return load_sample_data(name="bathymetry")
 
 
-@pytest.mark.benchmark
 def test_blockmean_input_dataframe(dataframe):
     """
     Run blockmean by passing in a pandas.DataFrame as input.
diff --git a/pygmt/tests/test_grd2xyz.py b/pygmt/tests/test_grd2xyz.py
index 2cd555d6d5f..d53993388c2 100644
--- a/pygmt/tests/test_grd2xyz.py
+++ b/pygmt/tests/test_grd2xyz.py
@@ -20,7 +20,6 @@ def fixture_grid():
     return load_static_earth_relief()
 
 
-@pytest.mark.benchmark
 def test_grd2xyz(grid):
     """
     Make sure grd2xyz works as expected.

From f45b727ce0c389d022398314a84464b4977cb330 Mon Sep 17 00:00:00 2001
From: Wei Ji <23487320+weiji14@users.noreply.github.com>
Date: Mon, 25 Dec 2023 12:55:01 +1300
Subject: [PATCH 36/39] Preprend $CONDA/bin to $GITHUB_PATH

See https://docs.github.com/en/actions/using-workflows/workflow-commands-for-github-actions#adding-a-system-path and https://github.com/actions/starter-workflows/blob/c31fe3d5d44d7cb4c912f4c3213f7b4610f13ea2/ci/python-package-conda.yml#L19-L20
---
 .github/workflows/benchmarks.yml | 11 +++++++----
 1 file changed, 7 insertions(+), 4 deletions(-)

diff --git a/.github/workflows/benchmarks.yml b/.github/workflows/benchmarks.yml
index 35f8e125413..fdbb16252c3 100644
--- a/.github/workflows/benchmarks.yml
+++ b/.github/workflows/benchmarks.yml
@@ -49,21 +49,24 @@ jobs:
       # Install GMT and dependencies from conda-forge
       - name: Install dependencies
         run: |
+          # $CONDA is an environment variable pointing to the root of the miniconda directory
+          # Preprend $CONDA/bin to $PATH so that conda's python is used over system python
+          echo $CONDA/bin >> $GITHUB_PATH
           conda install --solver=libmamba gmt=6.4.0 python=3.12 \
                         numpy pandas xarray netCDF4 packaging \
                         pytest pytest-benchmark pytest-mpl
-          $CONDA/bin/python -m pip install -U pytest-codspeed setuptools
+          python -m pip install -U pytest-codspeed setuptools
 
       # Install the package that we want to test
       - name: Install the package
-        run: $CONDA/bin/python -m pip install --no-deps -e .
+        run: python -m pip install --no-deps -e .
 
       # Run the benchmark tests
       - name: Run benchmarks
         uses: CodSpeedHQ/action@v2.0.2
         with:
           run: |
-            $CONDA/bin/python -c "import pygmt; pygmt.show_versions()"
-            PYGMT_USE_EXTERNAL_DISPLAY="false" $CONDA/bin/python -m pytest -r P --pyargs pygmt --codspeed
+            python -c "import pygmt; pygmt.show_versions()"
+            PYGMT_USE_EXTERNAL_DISPLAY="false" python -m pytest -r P --pyargs pygmt --codspeed
         env:
           GMT_LIBRARY_PATH: /usr/share/miniconda/lib/

From 514564927753b6f6e4aed6e2a38643bc7fbdd678 Mon Sep 17 00:00:00 2001
From: Wei Ji <23487320+weiji14@users.noreply.github.com>
Date: Mon, 25 Dec 2023 13:00:06 +1300
Subject: [PATCH 37/39] Use make commands instead of calling $CONDA/bin/python

The default Python used now should be the conda one instead of the system one.
---
 .github/workflows/benchmarks.yml | 6 ++----
 1 file changed, 2 insertions(+), 4 deletions(-)

diff --git a/.github/workflows/benchmarks.yml b/.github/workflows/benchmarks.yml
index fdbb16252c3..dfb324d240c 100644
--- a/.github/workflows/benchmarks.yml
+++ b/.github/workflows/benchmarks.yml
@@ -59,14 +59,12 @@ jobs:
 
       # Install the package that we want to test
       - name: Install the package
-        run: python -m pip install --no-deps -e .
+        run: make install
 
       # Run the benchmark tests
       - name: Run benchmarks
         uses: CodSpeedHQ/action@v2.0.2
         with:
-          run: |
-            python -c "import pygmt; pygmt.show_versions()"
-            PYGMT_USE_EXTERNAL_DISPLAY="false" python -m pytest -r P --pyargs pygmt --codspeed
+          run: make test PYTEST_EXTRA="-r P --codspeed"
         env:
           GMT_LIBRARY_PATH: /usr/share/miniconda/lib/

From 0a254f88748f2e1a6b6cc1e49612830eb6408e32 Mon Sep 17 00:00:00 2001
From: Wei Ji <23487320+weiji14@users.noreply.github.com>
Date: Mon, 25 Dec 2023 13:12:15 +1300
Subject: [PATCH 38/39] Revert back to using python -m pytest

Default `make test` requires the use of pytest-cov and pytest-doctestplus
---
 .github/workflows/benchmarks.yml | 4 +++-
 1 file changed, 3 insertions(+), 1 deletion(-)

diff --git a/.github/workflows/benchmarks.yml b/.github/workflows/benchmarks.yml
index dfb324d240c..c9b93da6c54 100644
--- a/.github/workflows/benchmarks.yml
+++ b/.github/workflows/benchmarks.yml
@@ -65,6 +65,8 @@ jobs:
       - name: Run benchmarks
         uses: CodSpeedHQ/action@v2.0.2
         with:
-          run: make test PYTEST_EXTRA="-r P --codspeed"
+          run: |
+            python -c "import pygmt; pygmt.show_versions()"
+            PYGMT_USE_EXTERNAL_DISPLAY="false" python -m pytest -r P --pyargs pygmt --codspeed
         env:
           GMT_LIBRARY_PATH: /usr/share/miniconda/lib/

From dedfa7af7250762f473a81928a609b04198d11b1 Mon Sep 17 00:00:00 2001
From: Wei Ji <23487320+weiji14@users.noreply.github.com>
Date: Mon, 25 Dec 2023 18:55:20 +1300
Subject: [PATCH 39/39] Only run when non-test PyGMT source files and
 benchmarks.yml is modified

Trigger the benchmark run when files in `pygmt/clib`, `pygmt/datasets`, `pygmt/helpers`, `pygmt/src` and `pygmt/*.py` are modified (i.e. except `pygmt/tests/**`), and also when .github/workflows/benchmarks.yml is modified.
---
 .github/workflows/benchmarks.yml | 9 ++++++++-
 1 file changed, 8 insertions(+), 1 deletion(-)

diff --git a/.github/workflows/benchmarks.yml b/.github/workflows/benchmarks.yml
index c9b93da6c54..2b562e9aa46 100644
--- a/.github/workflows/benchmarks.yml
+++ b/.github/workflows/benchmarks.yml
@@ -9,8 +9,15 @@ on:
   # Run on pushes to the main branch
   push:
     branches: [ main ]
-  # Uncomment the 'pull_request' line below to trigger the workflow in PR
+    paths:
+      - 'pygmt/**/*.py'
+      - '!pygmt/tests/**'
+      - '.github/workflows/benchmarks.yml'
   pull_request:
+    paths:
+      - 'pygmt/**/*.py'
+      - '!pygmt/tests/**'
+      - '.github/workflows/benchmarks.yml'
   # `workflow_dispatch` allows CodSpeed to trigger backtest
   # performance analysis in order to generate initial data.
   workflow_dispatch: