From 2be42de684e588acb6190d9c85bd04a46d0663c3 Mon Sep 17 00:00:00 2001
From: Frank Malatino <frank.malatino@noaa.gov>
Date: Tue, 5 May 2026 11:54:31 -0400
Subject: [PATCH 01/45] Roman changes from branch
 romanc:romanc/pyfms-monitor-ci

---
 .github/workflows/unit_tests.yaml             | 24 +++++++++++++++----
 .../monitor/diag_manager_monitor.md           |  3 +++
 mkdocs.yml                                    |  1 +
 ndsl/optional_imports.py                      |  5 ++++
 pyproject.toml                                |  2 ++
 tests/monitor/__init__.py                     |  0
 tests/{ => monitor}/test_dm_monitor_cubed.py  |  0
 tests/{ => monitor}/test_dm_monitor_single.py |  0
 tests/{ => monitor}/test_netcdf_monitor.py    |  0
 tests/{ => monitor}/test_zarr_monitor.py      |  0
 10 files changed, 31 insertions(+), 4 deletions(-)
 create mode 100644 docs/docstrings/monitor/diag_manager_monitor.md
 create mode 100644 tests/monitor/__init__.py
 rename tests/{ => monitor}/test_dm_monitor_cubed.py (100%)
 rename tests/{ => monitor}/test_dm_monitor_single.py (100%)
 rename tests/{ => monitor}/test_netcdf_monitor.py (100%)
 rename tests/{ => monitor}/test_zarr_monitor.py (100%)

diff --git a/.github/workflows/unit_tests.yaml b/.github/workflows/unit_tests.yaml
index 0e7aa421..0ecdf218 100644
--- a/.github/workflows/unit_tests.yaml
+++ b/.github/workflows/unit_tests.yaml
@@ -19,7 +19,18 @@ jobs:
     strategy:
       matrix:
         python-version: ['3.11', '3.12', '3.13']
-    name: Python ${{ matrix.python-version }}
+        extra: ['test,zarr']
+        marker-serial: ['not parallel and not gpu and not pyfms']
+        marker-parallel: ['parallel and not gpu and not pyfms']
+        include:
+          # add pyfms tests for 3.12
+          - extra: 'test,pyfms'
+            marker-serial: 'pyfms and not parallel'
+            marker-parallel: 'pyfms and parallel'
+            python-version: '3.12'
+      # don't cancel other jobs if one fails
+      fail-fast: false
+    name: Python ${{ matrix.python-version }}${{ contains(matrix.extra, 'pyfms') && ' (pyFMS)' || '' }}
     steps:
       - name: Checkout repository
         uses: actions/checkout@v6
@@ -32,16 +43,21 @@ jobs:
           python-version: ${{ matrix.python-version }}
 
       - name: Install mpi (MPICH flavor)
+        if: ${{!contains(matrix.extra, 'pyfms')}}
         run: pip3 install mpich
 
+      - name: Install pyFMS dependencies (includes system MPI)
+        if: contains(matrix.extra, 'pyfms')
+        run: sudo apt-get install libopenmpi-dev netcdf-bin libnetcdf-dev libnetcdff-dev nco libyaml-dev diffutils
+
       - name: Install Python packages
-        run: pip3 install .[test,zarr]
+        run: pip3 install .[${{matrix.extra}}]
 
       - name: Run serial cpu tests
-        run: coverage run --rcfile=pyproject.toml -m pytest -m "not parallel and not gpu" tests
+        run: coverage run --rcfile=pyproject.toml -m pytest -m "${{matrix.marker-serial}}" tests
 
       - name: Run parallel cpu tests
-        run: mpiexec -np 6 coverage run --rcfile=pyproject.toml -m mpi4py -m pytest -m "parallel and not gpu" tests
+        run: mpiexec -np 6 coverage run --rcfile=pyproject.toml -m mpi4py -m pytest -m "${{matrix.marker-parallel}}" tests
 
       - name: Output code coverage
         run: |
diff --git a/docs/docstrings/monitor/diag_manager_monitor.md b/docs/docstrings/monitor/diag_manager_monitor.md
new file mode 100644
index 00000000..b377bdfa
--- /dev/null
+++ b/docs/docstrings/monitor/diag_manager_monitor.md
@@ -0,0 +1,3 @@
+# diag_manager_monitor
+
+::: monitor.diag_manager_monitor
\ No newline at end of file
diff --git a/mkdocs.yml b/mkdocs.yml
index 62b3fbcf..b19fc02a 100644
--- a/mkdocs.yml
+++ b/mkdocs.yml
@@ -75,6 +75,7 @@ nav:
           - "subtile_grid_sizer": docstrings/initialization/subtile_grid_sizer.md
       - monitor:
           - "convert": docstrings/monitor/convert.md
+          - "diag_manager_monitor": docstrings/monitor/diag_manager_monitor.md
           - "netcdf_monitor": docstrings/monitor/netcdf_monitor.md
           - "protocol": docstrings/monitor/protocol.md
           - "zarr_monitor": docstrings/monitor/zarr_monitor.md
diff --git a/ndsl/optional_imports.py b/ndsl/optional_imports.py
index 4cc81ea6..af2ec8d0 100644
--- a/ndsl/optional_imports.py
+++ b/ndsl/optional_imports.py
@@ -17,6 +17,11 @@ def __call__(self, *args: Any, **kwargs: dict) -> None:
 except ModuleNotFoundError as err:
     zarr = RaiseWhenAccessed(err)
 
+try:
+    import pyfms
+except ModuleNotFoundError as err:
+    pyfms = RaiseWhenAccessed(err)
+
 try:
     import cupy
 except ImportError:
diff --git a/pyproject.toml b/pyproject.toml
index 8bce607f..1a7ff3dc 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -124,6 +124,8 @@ module = [
 markers = [
   # tests running on a cpu (e.g. with cupy)
   "gpu",
+  # tests relying on the optional pyFMS dependency
+  "pyfms",
   # tests relying on at least two MPI processes
   "parallel",
   # tests relying on the optional zarr dependency
diff --git a/tests/monitor/__init__.py b/tests/monitor/__init__.py
new file mode 100644
index 00000000..e69de29b
diff --git a/tests/test_dm_monitor_cubed.py b/tests/monitor/test_dm_monitor_cubed.py
similarity index 100%
rename from tests/test_dm_monitor_cubed.py
rename to tests/monitor/test_dm_monitor_cubed.py
diff --git a/tests/test_dm_monitor_single.py b/tests/monitor/test_dm_monitor_single.py
similarity index 100%
rename from tests/test_dm_monitor_single.py
rename to tests/monitor/test_dm_monitor_single.py
diff --git a/tests/test_netcdf_monitor.py b/tests/monitor/test_netcdf_monitor.py
similarity index 100%
rename from tests/test_netcdf_monitor.py
rename to tests/monitor/test_netcdf_monitor.py
diff --git a/tests/test_zarr_monitor.py b/tests/monitor/test_zarr_monitor.py
similarity index 100%
rename from tests/test_zarr_monitor.py
rename to tests/monitor/test_zarr_monitor.py

From 055148458119712e55f1444a3769ed0e524e84a4 Mon Sep 17 00:00:00 2001
From: Frank Malatino <frank.malatino@noaa.gov>
Date: Tue, 5 May 2026 12:06:43 -0400
Subject: [PATCH 02/45] Linting

---
 .github/workflows/unit_tests.yaml               | 4 ++--
 docs/docstrings/monitor/diag_manager_monitor.md | 2 +-
 2 files changed, 3 insertions(+), 3 deletions(-)

diff --git a/.github/workflows/unit_tests.yaml b/.github/workflows/unit_tests.yaml
index 0ecdf218..89bbc7bf 100644
--- a/.github/workflows/unit_tests.yaml
+++ b/.github/workflows/unit_tests.yaml
@@ -5,8 +5,8 @@ on:
   pull_request: # ... a PR is opened / updated
   merge_group: # ... the PR is added to the merge queue
   push:
-    branches:
-      - main # ... when merging into the main branch
+    # branches:
+    #   - main # ... when merging into the main branch
 
 # cancel running jobs if theres a newer push
 concurrency:
diff --git a/docs/docstrings/monitor/diag_manager_monitor.md b/docs/docstrings/monitor/diag_manager_monitor.md
index b377bdfa..36b92e81 100644
--- a/docs/docstrings/monitor/diag_manager_monitor.md
+++ b/docs/docstrings/monitor/diag_manager_monitor.md
@@ -1,3 +1,3 @@
 # diag_manager_monitor
 
-::: monitor.diag_manager_monitor
\ No newline at end of file
+::: monitor.diag_manager_monitor

From 319320bad74204946aba069e93e0b3ac96997b50 Mon Sep 17 00:00:00 2001
From: Frank Malatino <frank.malatino@noaa.gov>
Date: Tue, 5 May 2026 12:19:16 -0400
Subject: [PATCH 03/45] Fixing apt-get update in pyFMS workflow

---
 .github/workflows/unit_tests.yaml | 4 +++-
 1 file changed, 3 insertions(+), 1 deletion(-)

diff --git a/.github/workflows/unit_tests.yaml b/.github/workflows/unit_tests.yaml
index 89bbc7bf..b077b83c 100644
--- a/.github/workflows/unit_tests.yaml
+++ b/.github/workflows/unit_tests.yaml
@@ -48,7 +48,9 @@ jobs:
 
       - name: Install pyFMS dependencies (includes system MPI)
         if: contains(matrix.extra, 'pyfms')
-        run: sudo apt-get install libopenmpi-dev netcdf-bin libnetcdf-dev libnetcdff-dev nco libyaml-dev diffutils
+        run: |
+          sudo apt-get update --fix-missing 
+          sudo apt-get install libopenmpi-dev netcdf-bin libnetcdf-dev libnetcdff-dev nco libyaml-dev diffutils
 
       - name: Install Python packages
         run: pip3 install .[${{matrix.extra}}]

From 9e05a012cf7594b714070043c4570e46e2ca91f7 Mon Sep 17 00:00:00 2001
From: Frank Malatino <frank.malatino@noaa.gov>
Date: Tue, 5 May 2026 12:41:41 -0400
Subject: [PATCH 04/45] Using open_dataset instead of open_mfdataset in
 diag_manager monitor tests

---
 tests/monitor/test_dm_monitor_cubed.py  | 2 +-
 tests/monitor/test_dm_monitor_single.py | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/tests/monitor/test_dm_monitor_cubed.py b/tests/monitor/test_dm_monitor_cubed.py
index a1ec8c59..79b4d426 100644
--- a/tests/monitor/test_dm_monitor_cubed.py
+++ b/tests/monitor/test_dm_monitor_cubed.py
@@ -203,7 +203,7 @@ def test_dm_monitor():
     pe = MPIComm()._comm.Get_rank() + 1
     filename = "diag_manager_cubed_sphere.tile" + str(pe) + ".nc"
     assert Path(filename).exists()
-    ds = xr.open_mfdataset(filename, decode_times=True)
+    ds = xr.open_dataset(filename, decode_times=True)
     assert "var1" in ds
     np.testing.assert_array_equal(ds["var1"].shape, (ntimesteps, ny, nx))
     assert "var2" in ds
diff --git a/tests/monitor/test_dm_monitor_single.py b/tests/monitor/test_dm_monitor_single.py
index f8c86328..f5411aca 100644
--- a/tests/monitor/test_dm_monitor_single.py
+++ b/tests/monitor/test_dm_monitor_single.py
@@ -220,7 +220,7 @@ def test_dm_monitor_single_tile():
 
     # check output!
     assert Path("diag_manager_single_tile.nc").exists()
-    ds = xr.open_mfdataset("diag_manager_single_tile.nc", decode_times=True)
+    ds = xr.open_dataset("diag_manager_single_tile.nc", decode_times=True)
     assert "var_2d" in ds
     np.testing.assert_array_equal(ds["var_2d"].shape, (ntimesteps, nx, ny))
     assert ds["var_2d"].dims == ("time", "y", "x")

From c67041a39db9dd5a811074cfb38bcd0719ee1f65 Mon Sep 17 00:00:00 2001
From: Frank Malatino <frank.malatino@noaa.gov>
Date: Tue, 5 May 2026 12:47:56 -0400
Subject: [PATCH 05/45] Matching romanc version of tests

---
 tests/monitor/test_dm_monitor_cubed.py  | 12 +++++-------
 tests/monitor/test_dm_monitor_single.py | 12 +++++-------
 2 files changed, 10 insertions(+), 14 deletions(-)

diff --git a/tests/monitor/test_dm_monitor_cubed.py b/tests/monitor/test_dm_monitor_cubed.py
index 79b4d426..546647e4 100644
--- a/tests/monitor/test_dm_monitor_cubed.py
+++ b/tests/monitor/test_dm_monitor_cubed.py
@@ -21,9 +21,7 @@
 )
 from ndsl.config import Backend
 from ndsl.initialization import SubtileGridSizer
-
-
-pyfms = pytest.importorskip("pyfms")
+from ndsl.optional_imports import pyfms
 
 
 # init fms mpi and set up a simple domain
@@ -52,7 +50,7 @@ def fms_mpp_init():
     return domain_id
 
 
-def _create_input(reduction: str = "none"):
+def _create_input(reduction: str = "none") -> None:
     diag_config = {
         "title": "ndsl_diag_manager_test",
         "base_date": "1 1 1 0 0 0",
@@ -89,9 +87,9 @@ def _create_input(reduction: str = "none"):
 
 
 # Simple test, uses a lat/lon grid and (1, npes) layout
+@pytest.mark.pyfms
 @pytest.mark.parallel
-def test_dm_monitor():
-
+def test_dm_monitor() -> None:
     npes = MPIComm()._comm.Get_size()
     if npes % 6 != 0:
         raise RuntimeError("this test requires npes to be a multiple of 6 to run")
@@ -223,4 +221,4 @@ def test_dm_monitor():
     np.testing.assert_array_equal(ds["var2"].values[1, :, :, :], 4)
     np.testing.assert_array_equal(ds["var2"].values[2, :, :, :], 6)
 
-    pyfms.fms.end()
+    pyfms.fms.end()
\ No newline at end of file
diff --git a/tests/monitor/test_dm_monitor_single.py b/tests/monitor/test_dm_monitor_single.py
index f5411aca..661d904a 100644
--- a/tests/monitor/test_dm_monitor_single.py
+++ b/tests/monitor/test_dm_monitor_single.py
@@ -22,12 +22,10 @@
 )
 from ndsl.config import Backend
 from ndsl.initialization import SubtileGridSizer
+from ndsl.optional_imports import pyfms
 
 
-pyfms = pytest.importorskip("pyfms")
-
-
-def _create_input(reduction: str = "none"):
+def _create_input() -> None:
     diag_config = {
         "title": "ndsl_diag_manager_test",
         "base_date": "2 1 1 1 1 1",
@@ -63,10 +61,10 @@ def _create_input(reduction: str = "none"):
         f.write(text_content)
 
 
-def test_dm_monitor_single_tile():
+@pytest.mark.pyfms
+def test_dm_monitor_single_tile() -> None:
     # mpi info
     npes = MPIComm()._comm.Get_size()
-    pe = MPIComm()._comm.Get_rank()
     # tile parameters for quantities/domains
     nx = 8
     ny = 8
@@ -246,4 +244,4 @@ def test_dm_monitor_single_tile():
         ds["var_3d"].values[2, :, :, :], var3_global.transpose()
     )
 
-    pyfms.fms.end()
+    pyfms.fms.end()
\ No newline at end of file

From 7a15106640c201abbad522b0185ee1f628dc108e Mon Sep 17 00:00:00 2001
From: Frank Malatino <frank.malatino@noaa.gov>
Date: Tue, 5 May 2026 12:48:44 -0400
Subject: [PATCH 06/45] Linting

---
 .github/workflows/unit_tests.yaml       | 2 +-
 tests/monitor/test_dm_monitor_cubed.py  | 2 +-
 tests/monitor/test_dm_monitor_single.py | 2 +-
 3 files changed, 3 insertions(+), 3 deletions(-)

diff --git a/.github/workflows/unit_tests.yaml b/.github/workflows/unit_tests.yaml
index b077b83c..5f0a19ba 100644
--- a/.github/workflows/unit_tests.yaml
+++ b/.github/workflows/unit_tests.yaml
@@ -49,7 +49,7 @@ jobs:
       - name: Install pyFMS dependencies (includes system MPI)
         if: contains(matrix.extra, 'pyfms')
         run: |
-          sudo apt-get update --fix-missing 
+          sudo apt-get update --fix-missing
           sudo apt-get install libopenmpi-dev netcdf-bin libnetcdf-dev libnetcdff-dev nco libyaml-dev diffutils
 
       - name: Install Python packages
diff --git a/tests/monitor/test_dm_monitor_cubed.py b/tests/monitor/test_dm_monitor_cubed.py
index 546647e4..5fa2bd82 100644
--- a/tests/monitor/test_dm_monitor_cubed.py
+++ b/tests/monitor/test_dm_monitor_cubed.py
@@ -221,4 +221,4 @@ def test_dm_monitor() -> None:
     np.testing.assert_array_equal(ds["var2"].values[1, :, :, :], 4)
     np.testing.assert_array_equal(ds["var2"].values[2, :, :, :], 6)
 
-    pyfms.fms.end()
\ No newline at end of file
+    pyfms.fms.end()
diff --git a/tests/monitor/test_dm_monitor_single.py b/tests/monitor/test_dm_monitor_single.py
index 661d904a..2671437c 100644
--- a/tests/monitor/test_dm_monitor_single.py
+++ b/tests/monitor/test_dm_monitor_single.py
@@ -244,4 +244,4 @@ def test_dm_monitor_single_tile() -> None:
         ds["var_3d"].values[2, :, :, :], var3_global.transpose()
     )
 
-    pyfms.fms.end()
\ No newline at end of file
+    pyfms.fms.end()

From 0521b8a000c0f0d3d48d4c0294a62603c25f80b8 Mon Sep 17 00:00:00 2001
From: Frank Malatino <frank.malatino@noaa.gov>
Date: Tue, 5 May 2026 13:00:13 -0400
Subject: [PATCH 07/45] Looking at pip list in unit_tests

---
 .github/workflows/unit_tests.yaml | 4 +++-
 1 file changed, 3 insertions(+), 1 deletion(-)

diff --git a/.github/workflows/unit_tests.yaml b/.github/workflows/unit_tests.yaml
index 5f0a19ba..c8290116 100644
--- a/.github/workflows/unit_tests.yaml
+++ b/.github/workflows/unit_tests.yaml
@@ -53,7 +53,9 @@ jobs:
           sudo apt-get install libopenmpi-dev netcdf-bin libnetcdf-dev libnetcdff-dev nco libyaml-dev diffutils
 
       - name: Install Python packages
-        run: pip3 install .[${{matrix.extra}}]
+        run: |
+          pip3 install .[${{matrix.extra}}]
+          pip3 list
 
       - name: Run serial cpu tests
         run: coverage run --rcfile=pyproject.toml -m pytest -m "${{matrix.marker-serial}}" tests

From fc4b13d5b984928f596fb3e6dbc93ed55b8d2ce3 Mon Sep 17 00:00:00 2001
From: Frank Malatino <frank.malatino@noaa.gov>
Date: Tue, 5 May 2026 13:26:55 -0400
Subject: [PATCH 08/45] Checking non-pip installed netcdf version

---
 .github/workflows/unit_tests.yaml | 1 +
 1 file changed, 1 insertion(+)

diff --git a/.github/workflows/unit_tests.yaml b/.github/workflows/unit_tests.yaml
index c8290116..81317146 100644
--- a/.github/workflows/unit_tests.yaml
+++ b/.github/workflows/unit_tests.yaml
@@ -56,6 +56,7 @@ jobs:
         run: |
           pip3 install .[${{matrix.extra}}]
           pip3 list
+          nc-config --version
 
       - name: Run serial cpu tests
         run: coverage run --rcfile=pyproject.toml -m pytest -m "${{matrix.marker-serial}}" tests

From c410f2233b32d45fea3f93e519a3c5ace53585fe Mon Sep 17 00:00:00 2001
From: Frank Malatino <frank.malatino@noaa.gov>
Date: Tue, 5 May 2026 13:41:45 -0400
Subject: [PATCH 09/45] Print statements to debug dm_monitor single test

---
 .github/workflows/unit_tests.yaml       |  6 ++----
 tests/monitor/test_dm_monitor_single.py | 18 ++++++++++++++++++
 2 files changed, 20 insertions(+), 4 deletions(-)

diff --git a/.github/workflows/unit_tests.yaml b/.github/workflows/unit_tests.yaml
index 81317146..3f68df2a 100644
--- a/.github/workflows/unit_tests.yaml
+++ b/.github/workflows/unit_tests.yaml
@@ -55,14 +55,12 @@ jobs:
       - name: Install Python packages
         run: |
           pip3 install .[${{matrix.extra}}]
-          pip3 list
-          nc-config --version
 
       - name: Run serial cpu tests
-        run: coverage run --rcfile=pyproject.toml -m pytest -m "${{matrix.marker-serial}}" tests
+        run: coverage run --rcfile=pyproject.toml -m pytest -s -m "${{matrix.marker-serial}}" tests
 
       - name: Run parallel cpu tests
-        run: mpiexec -np 6 coverage run --rcfile=pyproject.toml -m mpi4py -m pytest -m "${{matrix.marker-parallel}}" tests
+        run: mpiexec -np 6 coverage run --rcfile=pyproject.toml -m mpi4py -m pytest -s -m "${{matrix.marker-parallel}}" tests
 
       - name: Output code coverage
         run: |
diff --git a/tests/monitor/test_dm_monitor_single.py b/tests/monitor/test_dm_monitor_single.py
index 2671437c..1c4c8028 100644
--- a/tests/monitor/test_dm_monitor_single.py
+++ b/tests/monitor/test_dm_monitor_single.py
@@ -77,10 +77,17 @@ def test_dm_monitor_single_tile() -> None:
     layout_ndsl = (npes, 1)  # flipped to match fms domain decomposition
     global_indices = [0, nx - 1, 0, ny - 1]
 
+    print("")
+    print("INITIALIZED ALL VARIABLES")
+
     _create_input()
 
+    print("PASSED CALL TO _CREATE_INPUT")
+
     pyfms.fms.init(localcomm=MPIComm()._comm.py2f(), calendar_type=pyfms.fms.NOLEAP)
 
+    print("pyFMS initialized")
+
     domain = pyfms.mpp_domains.define_domains(
         global_indices=global_indices,
         layout=layout_fms,
@@ -92,6 +99,8 @@ def test_dm_monitor_single_tile() -> None:
         io_layout=io_layout,
     )
 
+    print("Domains defined")
+
     if npes > 1:
         rank = MPIComm()._comm.Get_rank()
         print(f"intializing partitioner/communicator rank {rank} of {npes}")
@@ -119,12 +128,16 @@ def test_dm_monitor_single_tile() -> None:
     )
     quantity_factory = QuantityFactory(sizer, backend=backend)
 
+    print("NDSL stuff created")
+
     # set up for diag manager for before the main loop, need to set timestep + end_time and register all axes and fields
     monitor = DiagManagerMonitor(domain_id=domain_id)
     start = datetime(2, 1, 1, 1, 1, 1)
     step = timedelta(seconds=3600)
     end = start + ntimesteps * step
 
+    print("diag_manager Monitor created")
+
     monitor.set_timestep(step)
     monitor.set_end_time(end)
 
@@ -182,6 +195,8 @@ def test_dm_monitor_single_tile() -> None:
     assert "var_2d" in monitor.fields
     assert "var_3d" in monitor.fields
 
+    print("Checks on monitor field registers done")
+
     # set up data to send for diagnostics
     var2_global = np.empty(shape=(nx, ny), dtype=np.float64)
     var3_global = np.empty(shape=(nx, ny, nz), dtype=np.float64)
@@ -216,9 +231,12 @@ def test_dm_monitor_single_tile() -> None:
     # cleanup writes and closes the file
     monitor.cleanup()
 
+    print("Monitor cleaned up")
+
     # check output!
     assert Path("diag_manager_single_tile.nc").exists()
     ds = xr.open_dataset("diag_manager_single_tile.nc", decode_times=True)
+    print("Dataset opened through xarray")
     assert "var_2d" in ds
     np.testing.assert_array_equal(ds["var_2d"].shape, (ntimesteps, nx, ny))
     assert ds["var_2d"].dims == ("time", "y", "x")

From 6cd2d282a16e01f286df281c5aa14f4e0cacbb35 Mon Sep 17 00:00:00 2001
From: Frank Malatino <frank.malatino@noaa.gov>
Date: Tue, 5 May 2026 14:45:59 -0400
Subject: [PATCH 10/45] Commenting out xarray Dataset accessing calls in
 test_dm_monitor_single

---
 tests/monitor/test_dm_monitor_single.py | 54 ++++++++++++-------------
 1 file changed, 27 insertions(+), 27 deletions(-)

diff --git a/tests/monitor/test_dm_monitor_single.py b/tests/monitor/test_dm_monitor_single.py
index 1c4c8028..d7e271d1 100644
--- a/tests/monitor/test_dm_monitor_single.py
+++ b/tests/monitor/test_dm_monitor_single.py
@@ -234,32 +234,32 @@ def test_dm_monitor_single_tile() -> None:
     print("Monitor cleaned up")
 
     # check output!
-    assert Path("diag_manager_single_tile.nc").exists()
-    ds = xr.open_dataset("diag_manager_single_tile.nc", decode_times=True)
-    print("Dataset opened through xarray")
-    assert "var_2d" in ds
-    np.testing.assert_array_equal(ds["var_2d"].shape, (ntimesteps, nx, ny))
-    assert ds["var_2d"].dims == ("time", "y", "x")
-    assert ds["var_2d"].attrs["units"] == "muntin"
-    assert ds["var_3d"].dims == ("time", "z", "y", "x")
-    assert ds["var_3d"].attrs["units"] == "muntin"
-    assert ds["time"].shape == (ntimesteps,)
-    assert ds["time"].dims == ("time",)
-    assert ds["time"].values[0] == cftime.DatetimeNoLeap(2, 1, 1, 2, 1, 1)
-    assert ds["time"].values[1] == cftime.DatetimeNoLeap(2, 1, 1, 3, 1, 1)
-    assert ds["time"].values[2] == cftime.DatetimeNoLeap(2, 1, 1, 4, 1, 1)
-    np.testing.assert_array_equal(ds["var_2d"].values[0, :, :], var2_global.transpose())
-    np.testing.assert_array_equal(ds["var_2d"].values[1, :, :], var2_global.transpose())
-    np.testing.assert_array_equal(ds["var_2d"].values[2, :, :], var2_global.transpose())
-    # data is transposed when passed into fortran
-    np.testing.assert_array_equal(
-        ds["var_3d"].values[0, :, :, :], var3_global.transpose()
-    )
-    np.testing.assert_array_equal(
-        ds["var_3d"].values[1, :, :, :], var3_global.transpose()
-    )
-    np.testing.assert_array_equal(
-        ds["var_3d"].values[2, :, :, :], var3_global.transpose()
-    )
+    # assert Path("diag_manager_single_tile.nc").exists()
+    # ds = xr.open_dataset("diag_manager_single_tile.nc", decode_times=True)
+    # print("Dataset opened through xarray")
+    # assert "var_2d" in ds
+    # np.testing.assert_array_equal(ds["var_2d"].shape, (ntimesteps, nx, ny))
+    # assert ds["var_2d"].dims == ("time", "y", "x")
+    # assert ds["var_2d"].attrs["units"] == "muntin"
+    # assert ds["var_3d"].dims == ("time", "z", "y", "x")
+    # assert ds["var_3d"].attrs["units"] == "muntin"
+    # assert ds["time"].shape == (ntimesteps,)
+    # assert ds["time"].dims == ("time",)
+    # assert ds["time"].values[0] == cftime.DatetimeNoLeap(2, 1, 1, 2, 1, 1)
+    # assert ds["time"].values[1] == cftime.DatetimeNoLeap(2, 1, 1, 3, 1, 1)
+    # assert ds["time"].values[2] == cftime.DatetimeNoLeap(2, 1, 1, 4, 1, 1)
+    # np.testing.assert_array_equal(ds["var_2d"].values[0, :, :], var2_global.transpose())
+    # np.testing.assert_array_equal(ds["var_2d"].values[1, :, :], var2_global.transpose())
+    # np.testing.assert_array_equal(ds["var_2d"].values[2, :, :], var2_global.transpose())
+    # # data is transposed when passed into fortran
+    # np.testing.assert_array_equal(
+    #     ds["var_3d"].values[0, :, :, :], var3_global.transpose()
+    # )
+    # np.testing.assert_array_equal(
+    #     ds["var_3d"].values[1, :, :, :], var3_global.transpose()
+    # )
+    # np.testing.assert_array_equal(
+    #     ds["var_3d"].values[2, :, :, :], var3_global.transpose()
+    # )
 
     pyfms.fms.end()

From 0131b9715ced008ee0491f8fecffd484e57803d3 Mon Sep 17 00:00:00 2001
From: Frank Malatino <frank.malatino@noaa.gov>
Date: Tue, 5 May 2026 14:53:47 -0400
Subject: [PATCH 11/45] Adding back in assert of Path in test_dm_monitor_single

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

diff --git a/tests/monitor/test_dm_monitor_single.py b/tests/monitor/test_dm_monitor_single.py
index d7e271d1..b5559cb1 100644
--- a/tests/monitor/test_dm_monitor_single.py
+++ b/tests/monitor/test_dm_monitor_single.py
@@ -234,7 +234,7 @@ def test_dm_monitor_single_tile() -> None:
     print("Monitor cleaned up")
 
     # check output!
-    # assert Path("diag_manager_single_tile.nc").exists()
+    assert Path("diag_manager_single_tile.nc").exists()
     # ds = xr.open_dataset("diag_manager_single_tile.nc", decode_times=True)
     # print("Dataset opened through xarray")
     # assert "var_2d" in ds

From 7715c0ca5724fcbafd6cf615ff38cbdd8c6a6aee Mon Sep 17 00:00:00 2001
From: Frank Malatino <frank.malatino@noaa.gov>
Date: Thu, 7 May 2026 11:09:00 -0400
Subject: [PATCH 12/45] Moving through dm_monitor_single

---
 .github/workflows/unit_tests.yaml       | 2 +-
 tests/monitor/test_dm_monitor_single.py | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/.github/workflows/unit_tests.yaml b/.github/workflows/unit_tests.yaml
index 3f68df2a..d606442b 100644
--- a/.github/workflows/unit_tests.yaml
+++ b/.github/workflows/unit_tests.yaml
@@ -60,7 +60,7 @@ jobs:
         run: coverage run --rcfile=pyproject.toml -m pytest -s -m "${{matrix.marker-serial}}" tests
 
       - name: Run parallel cpu tests
-        run: mpiexec -np 6 coverage run --rcfile=pyproject.toml -m mpi4py -m pytest -s -m "${{matrix.marker-parallel}}" tests
+        run: mpiexec -np 6 --oversubscribe coverage run --rcfile=pyproject.toml -m mpi4py -m pytest -s -m "${{matrix.marker-parallel}}" tests
 
       - name: Output code coverage
         run: |
diff --git a/tests/monitor/test_dm_monitor_single.py b/tests/monitor/test_dm_monitor_single.py
index b5559cb1..fbc09348 100644
--- a/tests/monitor/test_dm_monitor_single.py
+++ b/tests/monitor/test_dm_monitor_single.py
@@ -235,7 +235,7 @@ def test_dm_monitor_single_tile() -> None:
 
     # check output!
     assert Path("diag_manager_single_tile.nc").exists()
-    # ds = xr.open_dataset("diag_manager_single_tile.nc", decode_times=True)
+    ds = xr.open_dataset("diag_manager_single_tile.nc", decode_times=True)
     # print("Dataset opened through xarray")
     # assert "var_2d" in ds
     # np.testing.assert_array_equal(ds["var_2d"].shape, (ntimesteps, nx, ny))

From 98c48040aa160449bcb9f914be6f46488fc7dce8 Mon Sep 17 00:00:00 2001
From: Frank Malatino <frank.malatino@noaa.gov>
Date: Thu, 7 May 2026 11:20:59 -0400
Subject: [PATCH 13/45] ALways install mpich and checking xarray call without
 time decode

---
 .github/workflows/unit_tests.yaml       | 6 +++---
 tests/monitor/test_dm_monitor_single.py | 3 ++-
 2 files changed, 5 insertions(+), 4 deletions(-)

diff --git a/.github/workflows/unit_tests.yaml b/.github/workflows/unit_tests.yaml
index d606442b..66482b51 100644
--- a/.github/workflows/unit_tests.yaml
+++ b/.github/workflows/unit_tests.yaml
@@ -43,18 +43,18 @@ jobs:
           python-version: ${{ matrix.python-version }}
 
       - name: Install mpi (MPICH flavor)
-        if: ${{!contains(matrix.extra, 'pyfms')}}
+        # if: ${{!contains(matrix.extra, 'pyfms')}}
         run: pip3 install mpich
 
       - name: Install pyFMS dependencies (includes system MPI)
         if: contains(matrix.extra, 'pyfms')
         run: |
           sudo apt-get update --fix-missing
-          sudo apt-get install libopenmpi-dev netcdf-bin libnetcdf-dev libnetcdff-dev nco libyaml-dev diffutils
+          sudo apt-get install netcdf-bin libnetcdf-dev libnetcdff-dev nco libyaml-dev diffutils
 
       - name: Install Python packages
         run: |
-          pip3 install .[${{matrix.extra}}]
+          pip3 install -v .[${{matrix.extra}}]
 
       - name: Run serial cpu tests
         run: coverage run --rcfile=pyproject.toml -m pytest -s -m "${{matrix.marker-serial}}" tests
diff --git a/tests/monitor/test_dm_monitor_single.py b/tests/monitor/test_dm_monitor_single.py
index fbc09348..a2facf40 100644
--- a/tests/monitor/test_dm_monitor_single.py
+++ b/tests/monitor/test_dm_monitor_single.py
@@ -235,7 +235,8 @@ def test_dm_monitor_single_tile() -> None:
 
     # check output!
     assert Path("diag_manager_single_tile.nc").exists()
-    ds = xr.open_dataset("diag_manager_single_tile.nc", decode_times=True)
+    # ds = xr.open_dataset("diag_manager_single_tile.nc", decode_times=True)
+    ds = xr.open_dataset("diag_manager_single_tile.nc")
     # print("Dataset opened through xarray")
     # assert "var_2d" in ds
     # np.testing.assert_array_equal(ds["var_2d"].shape, (ntimesteps, nx, ny))

From 4238aae8495716e2afbf696595b2b16475e09323 Mon Sep 17 00:00:00 2001
From: Frank Malatino <frank.malatino@noaa.gov>
Date: Thu, 7 May 2026 11:24:33 -0400
Subject: [PATCH 14/45] Always installing pyfms dependencies

---
 .github/workflows/unit_tests.yaml | 12 ++++++------
 1 file changed, 6 insertions(+), 6 deletions(-)

diff --git a/.github/workflows/unit_tests.yaml b/.github/workflows/unit_tests.yaml
index 66482b51..76d39f10 100644
--- a/.github/workflows/unit_tests.yaml
+++ b/.github/workflows/unit_tests.yaml
@@ -42,19 +42,19 @@ jobs:
         with:
           python-version: ${{ matrix.python-version }}
 
-      - name: Install mpi (MPICH flavor)
-        # if: ${{!contains(matrix.extra, 'pyfms')}}
-        run: pip3 install mpich
+      # - name: Install mpi (MPICH flavor)
+      #   if: ${{!contains(matrix.extra, 'pyfms')}}
+      #   run: pip3 install mpich
 
       - name: Install pyFMS dependencies (includes system MPI)
-        if: contains(matrix.extra, 'pyfms')
+        # if: contains(matrix.extra, 'pyfms')
         run: |
           sudo apt-get update --fix-missing
-          sudo apt-get install netcdf-bin libnetcdf-dev libnetcdff-dev nco libyaml-dev diffutils
+          sudo apt-get install libopenmpi-dev netcdf-bin libnetcdf-dev libnetcdff-dev nco libyaml-dev diffutils
 
       - name: Install Python packages
         run: |
-          pip3 install -v .[${{matrix.extra}}]
+          pip3 install .[${{matrix.extra}}]
 
       - name: Run serial cpu tests
         run: coverage run --rcfile=pyproject.toml -m pytest -s -m "${{matrix.marker-serial}}" tests

From c2a34c9826c50d4414205d402765e667e7ab3904 Mon Sep 17 00:00:00 2001
From: Frank Malatino <frank.malatino@noaa.gov>
Date: Thu, 7 May 2026 11:25:06 -0400
Subject: [PATCH 15/45] Verbose pip install

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

diff --git a/.github/workflows/unit_tests.yaml b/.github/workflows/unit_tests.yaml
index 76d39f10..4309c1ba 100644
--- a/.github/workflows/unit_tests.yaml
+++ b/.github/workflows/unit_tests.yaml
@@ -54,7 +54,7 @@ jobs:
 
       - name: Install Python packages
         run: |
-          pip3 install .[${{matrix.extra}}]
+          pip3 install -v .[${{matrix.extra}}]
 
       - name: Run serial cpu tests
         run: coverage run --rcfile=pyproject.toml -m pytest -s -m "${{matrix.marker-serial}}" tests

From 2b83d845d8436085ed37103fc9d3baa41c7f4f35 Mon Sep 17 00:00:00 2001
From: Frank Malatino <frank.malatino@noaa.gov>
Date: Thu, 7 May 2026 13:12:38 -0400
Subject: [PATCH 16/45] Using dask scheduler to avoid race condition

---
 tests/monitor/test_dm_monitor_single.py | 55 +++++++++++++------------
 1 file changed, 28 insertions(+), 27 deletions(-)

diff --git a/tests/monitor/test_dm_monitor_single.py b/tests/monitor/test_dm_monitor_single.py
index a2facf40..89ba325d 100644
--- a/tests/monitor/test_dm_monitor_single.py
+++ b/tests/monitor/test_dm_monitor_single.py
@@ -11,6 +11,7 @@
 import pytest
 import xarray as xr
 import yaml
+import dask
 
 from ndsl import (
     DiagManagerMonitor,
@@ -235,32 +236,32 @@ def test_dm_monitor_single_tile() -> None:
 
     # check output!
     assert Path("diag_manager_single_tile.nc").exists()
-    # ds = xr.open_dataset("diag_manager_single_tile.nc", decode_times=True)
-    ds = xr.open_dataset("diag_manager_single_tile.nc")
-    # print("Dataset opened through xarray")
-    # assert "var_2d" in ds
-    # np.testing.assert_array_equal(ds["var_2d"].shape, (ntimesteps, nx, ny))
-    # assert ds["var_2d"].dims == ("time", "y", "x")
-    # assert ds["var_2d"].attrs["units"] == "muntin"
-    # assert ds["var_3d"].dims == ("time", "z", "y", "x")
-    # assert ds["var_3d"].attrs["units"] == "muntin"
-    # assert ds["time"].shape == (ntimesteps,)
-    # assert ds["time"].dims == ("time",)
-    # assert ds["time"].values[0] == cftime.DatetimeNoLeap(2, 1, 1, 2, 1, 1)
-    # assert ds["time"].values[1] == cftime.DatetimeNoLeap(2, 1, 1, 3, 1, 1)
-    # assert ds["time"].values[2] == cftime.DatetimeNoLeap(2, 1, 1, 4, 1, 1)
-    # np.testing.assert_array_equal(ds["var_2d"].values[0, :, :], var2_global.transpose())
-    # np.testing.assert_array_equal(ds["var_2d"].values[1, :, :], var2_global.transpose())
-    # np.testing.assert_array_equal(ds["var_2d"].values[2, :, :], var2_global.transpose())
-    # # data is transposed when passed into fortran
-    # np.testing.assert_array_equal(
-    #     ds["var_3d"].values[0, :, :, :], var3_global.transpose()
-    # )
-    # np.testing.assert_array_equal(
-    #     ds["var_3d"].values[1, :, :, :], var3_global.transpose()
-    # )
-    # np.testing.assert_array_equal(
-    #     ds["var_3d"].values[2, :, :, :], var3_global.transpose()
-    # )
+    with dask.config.set(scheduler='synchronous'):
+        ds = xr.open_dataset("diag_manager_single_tile.nc", decode_times=True)
+    print("Dataset opened through xarray")
+    assert "var_2d" in ds
+    np.testing.assert_array_equal(ds["var_2d"].shape, (ntimesteps, nx, ny))
+    assert ds["var_2d"].dims == ("time", "y", "x")
+    assert ds["var_2d"].attrs["units"] == "muntin"
+    assert ds["var_3d"].dims == ("time", "z", "y", "x")
+    assert ds["var_3d"].attrs["units"] == "muntin"
+    assert ds["time"].shape == (ntimesteps,)
+    assert ds["time"].dims == ("time",)
+    assert ds["time"].values[0] == cftime.DatetimeNoLeap(2, 1, 1, 2, 1, 1)
+    assert ds["time"].values[1] == cftime.DatetimeNoLeap(2, 1, 1, 3, 1, 1)
+    assert ds["time"].values[2] == cftime.DatetimeNoLeap(2, 1, 1, 4, 1, 1)
+    np.testing.assert_array_equal(ds["var_2d"].values[0, :, :], var2_global.transpose())
+    np.testing.assert_array_equal(ds["var_2d"].values[1, :, :], var2_global.transpose())
+    np.testing.assert_array_equal(ds["var_2d"].values[2, :, :], var2_global.transpose())
+    # data is transposed when passed into fortran
+    np.testing.assert_array_equal(
+        ds["var_3d"].values[0, :, :, :], var3_global.transpose()
+    )
+    np.testing.assert_array_equal(
+        ds["var_3d"].values[1, :, :, :], var3_global.transpose()
+    )
+    np.testing.assert_array_equal(
+        ds["var_3d"].values[2, :, :, :], var3_global.transpose()
+    )
 
     pyfms.fms.end()

From 531828cdf702881322ac629cc20cb8bd928aebda Mon Sep 17 00:00:00 2001
From: Frank Malatino <frank.malatino@noaa.gov>
Date: Thu, 7 May 2026 13:24:20 -0400
Subject: [PATCH 17/45] Removing debugging print statements

---
 tests/monitor/test_dm_monitor_single.py | 17 -----------------
 1 file changed, 17 deletions(-)

diff --git a/tests/monitor/test_dm_monitor_single.py b/tests/monitor/test_dm_monitor_single.py
index 89ba325d..c8f69dc9 100644
--- a/tests/monitor/test_dm_monitor_single.py
+++ b/tests/monitor/test_dm_monitor_single.py
@@ -78,17 +78,10 @@ def test_dm_monitor_single_tile() -> None:
     layout_ndsl = (npes, 1)  # flipped to match fms domain decomposition
     global_indices = [0, nx - 1, 0, ny - 1]
 
-    print("")
-    print("INITIALIZED ALL VARIABLES")
-
     _create_input()
 
-    print("PASSED CALL TO _CREATE_INPUT")
-
     pyfms.fms.init(localcomm=MPIComm()._comm.py2f(), calendar_type=pyfms.fms.NOLEAP)
 
-    print("pyFMS initialized")
-
     domain = pyfms.mpp_domains.define_domains(
         global_indices=global_indices,
         layout=layout_fms,
@@ -100,8 +93,6 @@ def test_dm_monitor_single_tile() -> None:
         io_layout=io_layout,
     )
 
-    print("Domains defined")
-
     if npes > 1:
         rank = MPIComm()._comm.Get_rank()
         print(f"intializing partitioner/communicator rank {rank} of {npes}")
@@ -129,16 +120,12 @@ def test_dm_monitor_single_tile() -> None:
     )
     quantity_factory = QuantityFactory(sizer, backend=backend)
 
-    print("NDSL stuff created")
-
     # set up for diag manager for before the main loop, need to set timestep + end_time and register all axes and fields
     monitor = DiagManagerMonitor(domain_id=domain_id)
     start = datetime(2, 1, 1, 1, 1, 1)
     step = timedelta(seconds=3600)
     end = start + ntimesteps * step
 
-    print("diag_manager Monitor created")
-
     monitor.set_timestep(step)
     monitor.set_end_time(end)
 
@@ -196,8 +183,6 @@ def test_dm_monitor_single_tile() -> None:
     assert "var_2d" in monitor.fields
     assert "var_3d" in monitor.fields
 
-    print("Checks on monitor field registers done")
-
     # set up data to send for diagnostics
     var2_global = np.empty(shape=(nx, ny), dtype=np.float64)
     var3_global = np.empty(shape=(nx, ny, nz), dtype=np.float64)
@@ -232,8 +217,6 @@ def test_dm_monitor_single_tile() -> None:
     # cleanup writes and closes the file
     monitor.cleanup()
 
-    print("Monitor cleaned up")
-
     # check output!
     assert Path("diag_manager_single_tile.nc").exists()
     with dask.config.set(scheduler='synchronous'):

From 26eeaad05af150955773ea3c1b5a82979cac878a Mon Sep 17 00:00:00 2001
From: Frank Malatino <frank.malatino@noaa.gov>
Date: Thu, 7 May 2026 13:46:29 -0400
Subject: [PATCH 18/45] Linting and removing commented sections

---
 .github/workflows/unit_tests.yaml       | 7 +------
 tests/monitor/test_dm_monitor_single.py | 4 ++--
 2 files changed, 3 insertions(+), 8 deletions(-)

diff --git a/.github/workflows/unit_tests.yaml b/.github/workflows/unit_tests.yaml
index 4309c1ba..e3632ef7 100644
--- a/.github/workflows/unit_tests.yaml
+++ b/.github/workflows/unit_tests.yaml
@@ -42,12 +42,7 @@ jobs:
         with:
           python-version: ${{ matrix.python-version }}
 
-      # - name: Install mpi (MPICH flavor)
-      #   if: ${{!contains(matrix.extra, 'pyfms')}}
-      #   run: pip3 install mpich
-
-      - name: Install pyFMS dependencies (includes system MPI)
-        # if: contains(matrix.extra, 'pyfms')
+      - name: Install dependencies
         run: |
           sudo apt-get update --fix-missing
           sudo apt-get install libopenmpi-dev netcdf-bin libnetcdf-dev libnetcdff-dev nco libyaml-dev diffutils
diff --git a/tests/monitor/test_dm_monitor_single.py b/tests/monitor/test_dm_monitor_single.py
index c8f69dc9..490112c4 100644
--- a/tests/monitor/test_dm_monitor_single.py
+++ b/tests/monitor/test_dm_monitor_single.py
@@ -7,11 +7,11 @@
 from pathlib import Path
 
 import cftime
+import dask
 import numpy as np
 import pytest
 import xarray as xr
 import yaml
-import dask
 
 from ndsl import (
     DiagManagerMonitor,
@@ -219,7 +219,7 @@ def test_dm_monitor_single_tile() -> None:
 
     # check output!
     assert Path("diag_manager_single_tile.nc").exists()
-    with dask.config.set(scheduler='synchronous'):
+    with dask.config.set(scheduler="synchronous"):
         ds = xr.open_dataset("diag_manager_single_tile.nc", decode_times=True)
     print("Dataset opened through xarray")
     assert "var_2d" in ds

From 5186f80aa8c3e93ec49b9e0705cba6cf4273b4d0 Mon Sep 17 00:00:00 2001
From: Frank Malatino <frank.malatino@noaa.gov>
Date: Fri, 8 May 2026 09:28:05 -0400
Subject: [PATCH 19/45] Addressing comments from PR 459: removing use of dask
 scheduler

---
 .github/workflows/unit_tests.yaml       | 20 +++++++++++---------
 tests/monitor/test_dm_monitor_single.py |  9 +++++----
 2 files changed, 16 insertions(+), 13 deletions(-)

diff --git a/.github/workflows/unit_tests.yaml b/.github/workflows/unit_tests.yaml
index e3632ef7..143026f2 100644
--- a/.github/workflows/unit_tests.yaml
+++ b/.github/workflows/unit_tests.yaml
@@ -5,8 +5,8 @@ on:
   pull_request: # ... a PR is opened / updated
   merge_group: # ... the PR is added to the merge queue
   push:
-    # branches:
-    #   - main # ... when merging into the main branch
+    branches:
+      - main # ... when merging into the main branch
 
 # cancel running jobs if theres a newer push
 concurrency:
@@ -42,20 +42,22 @@ jobs:
         with:
           python-version: ${{ matrix.python-version }}
 
-      - name: Install dependencies
-        run: |
-          sudo apt-get update --fix-missing
-          sudo apt-get install libopenmpi-dev netcdf-bin libnetcdf-dev libnetcdff-dev nco libyaml-dev diffutils
+      - name: Install MPI
+        if: ${{!contains(matrix.extra, 'pyfms')}}
+        run: pip3 install mpich
+
+      - name: Install pyFMS dependencies (includes system MPI)
+        if: contains(matrix.extra, 'pyfms')
+        run: sudo apt-get install mpich libmpich-dev netcdf-bin libnetcdf-dev libnetcdff-dev nco libyaml-dev diffutils
 
       - name: Install Python packages
-        run: |
-          pip3 install -v .[${{matrix.extra}}]
+        run: pip3 install -v .[${{matrix.extra}}]
 
       - name: Run serial cpu tests
         run: coverage run --rcfile=pyproject.toml -m pytest -s -m "${{matrix.marker-serial}}" tests
 
       - name: Run parallel cpu tests
-        run: mpiexec -np 6 --oversubscribe coverage run --rcfile=pyproject.toml -m mpi4py -m pytest -s -m "${{matrix.marker-parallel}}" tests
+        run: mpiexec -np 6 coverage run --rcfile=pyproject.toml -m mpi4py -m pytest -s -m "${{matrix.marker-parallel}}" tests
 
       - name: Output code coverage
         run: |
diff --git a/tests/monitor/test_dm_monitor_single.py b/tests/monitor/test_dm_monitor_single.py
index 490112c4..6b2e2255 100644
--- a/tests/monitor/test_dm_monitor_single.py
+++ b/tests/monitor/test_dm_monitor_single.py
@@ -7,7 +7,8 @@
 from pathlib import Path
 
 import cftime
-import dask
+
+# import dask
 import numpy as np
 import pytest
 import xarray as xr
@@ -219,9 +220,9 @@ def test_dm_monitor_single_tile() -> None:
 
     # check output!
     assert Path("diag_manager_single_tile.nc").exists()
-    with dask.config.set(scheduler="synchronous"):
-        ds = xr.open_dataset("diag_manager_single_tile.nc", decode_times=True)
-    print("Dataset opened through xarray")
+    MPIComm()._comm.Barrier()
+    # with dask.config.set(scheduler="synchronous"):
+    ds = xr.open_dataset("diag_manager_single_tile.nc", decode_times=True)
     assert "var_2d" in ds
     np.testing.assert_array_equal(ds["var_2d"].shape, (ntimesteps, nx, ny))
     assert ds["var_2d"].dims == ("time", "y", "x")

From 0e2e1240eea7a5db6259a5ccff33051d1e29e110 Mon Sep 17 00:00:00 2001
From: Frank Malatino <frank.malatino@noaa.gov>
Date: Fri, 8 May 2026 09:36:25 -0400
Subject: [PATCH 20/45] Doing sudo apt-get update just for pyfms install

---
 .github/workflows/unit_tests.yaml | 4 +++-
 1 file changed, 3 insertions(+), 1 deletion(-)

diff --git a/.github/workflows/unit_tests.yaml b/.github/workflows/unit_tests.yaml
index 143026f2..f634de05 100644
--- a/.github/workflows/unit_tests.yaml
+++ b/.github/workflows/unit_tests.yaml
@@ -48,7 +48,9 @@ jobs:
 
       - name: Install pyFMS dependencies (includes system MPI)
         if: contains(matrix.extra, 'pyfms')
-        run: sudo apt-get install mpich libmpich-dev netcdf-bin libnetcdf-dev libnetcdff-dev nco libyaml-dev diffutils
+        run: |
+          sudo apt-get update 
+          sudo apt-get install mpich libmpich-dev netcdf-bin libnetcdf-dev libnetcdff-dev nco libyaml-dev diffutils
 
       - name: Install Python packages
         run: pip3 install -v .[${{matrix.extra}}]

From b6933b0ed5bead2c4f2401abc837a6e80f161c85 Mon Sep 17 00:00:00 2001
From: Frank Malatino <frank.malatino@noaa.gov>
Date: Fri, 8 May 2026 09:50:16 -0400
Subject: [PATCH 21/45] Trying with h5netcdf engine in xarray open_dataset for
 single dm_monitor test

---
 .github/workflows/unit_tests.yaml       | 2 +-
 tests/monitor/test_dm_monitor_single.py | 4 +++-
 2 files changed, 4 insertions(+), 2 deletions(-)

diff --git a/.github/workflows/unit_tests.yaml b/.github/workflows/unit_tests.yaml
index f634de05..766a72ea 100644
--- a/.github/workflows/unit_tests.yaml
+++ b/.github/workflows/unit_tests.yaml
@@ -49,7 +49,7 @@ jobs:
       - name: Install pyFMS dependencies (includes system MPI)
         if: contains(matrix.extra, 'pyfms')
         run: |
-          sudo apt-get update 
+          sudo apt-get update
           sudo apt-get install mpich libmpich-dev netcdf-bin libnetcdf-dev libnetcdff-dev nco libyaml-dev diffutils
 
       - name: Install Python packages
diff --git a/tests/monitor/test_dm_monitor_single.py b/tests/monitor/test_dm_monitor_single.py
index 6b2e2255..d918af3e 100644
--- a/tests/monitor/test_dm_monitor_single.py
+++ b/tests/monitor/test_dm_monitor_single.py
@@ -222,7 +222,9 @@ def test_dm_monitor_single_tile() -> None:
     assert Path("diag_manager_single_tile.nc").exists()
     MPIComm()._comm.Barrier()
     # with dask.config.set(scheduler="synchronous"):
-    ds = xr.open_dataset("diag_manager_single_tile.nc", decode_times=True)
+    ds = xr.open_dataset(
+        "diag_manager_single_tile.nc", decode_times=True, engine="h5netcdf", chunks={}
+    )
     assert "var_2d" in ds
     np.testing.assert_array_equal(ds["var_2d"].shape, (ntimesteps, nx, ny))
     assert ds["var_2d"].dims == ("time", "y", "x")

From 6681da92c899debca4c5a960caa2419dfcf16a59 Mon Sep 17 00:00:00 2001
From: Frank Malatino <frank.malatino@noaa.gov>
Date: Fri, 8 May 2026 09:57:20 -0400
Subject: [PATCH 22/45] Using threading.Lock to resolve issue in open_dataset
 loading

---
 tests/monitor/test_dm_monitor_single.py | 8 +++-----
 1 file changed, 3 insertions(+), 5 deletions(-)

diff --git a/tests/monitor/test_dm_monitor_single.py b/tests/monitor/test_dm_monitor_single.py
index d918af3e..eab1767a 100644
--- a/tests/monitor/test_dm_monitor_single.py
+++ b/tests/monitor/test_dm_monitor_single.py
@@ -3,12 +3,11 @@
 with data gathered from any other processors.
 """
 
+import threading
 from datetime import datetime, timedelta
 from pathlib import Path
 
 import cftime
-
-# import dask
 import numpy as np
 import pytest
 import xarray as xr
@@ -220,10 +219,9 @@ def test_dm_monitor_single_tile() -> None:
 
     # check output!
     assert Path("diag_manager_single_tile.nc").exists()
-    MPIComm()._comm.Barrier()
-    # with dask.config.set(scheduler="synchronous"):
+    lock = threading.Lock()
     ds = xr.open_dataset(
-        "diag_manager_single_tile.nc", decode_times=True, engine="h5netcdf", chunks={}
+        "diag_manager_single_tile.nc", decode_times=True, chunks={}, lock=lock
     )
     assert "var_2d" in ds
     np.testing.assert_array_equal(ds["var_2d"].shape, (ntimesteps, nx, ny))

From b4034983bc25345921186ff22ceb5f5ff87e68e2 Mon Sep 17 00:00:00 2001
From: Frank Malatino <frank.malatino@noaa.gov>
Date: Fri, 8 May 2026 11:06:19 -0400
Subject: [PATCH 23/45] Using pip list to check versions installed via pip in
 unit tests

---
 .github/workflows/unit_tests.yaml | 4 +++-
 1 file changed, 3 insertions(+), 1 deletion(-)

diff --git a/.github/workflows/unit_tests.yaml b/.github/workflows/unit_tests.yaml
index 766a72ea..9da3cfc7 100644
--- a/.github/workflows/unit_tests.yaml
+++ b/.github/workflows/unit_tests.yaml
@@ -53,7 +53,9 @@ jobs:
           sudo apt-get install mpich libmpich-dev netcdf-bin libnetcdf-dev libnetcdff-dev nco libyaml-dev diffutils
 
       - name: Install Python packages
-        run: pip3 install -v .[${{matrix.extra}}]
+        run: |
+          pip3 install -v .[${{matrix.extra}}]
+          pip3 list
 
       - name: Run serial cpu tests
         run: coverage run --rcfile=pyproject.toml -m pytest -s -m "${{matrix.marker-serial}}" tests

From ea986fc719122a11759b2aa096db867374ad1381 Mon Sep 17 00:00:00 2001
From: Frank Malatino <frank.malatino@noaa.gov>
Date: Fri, 8 May 2026 12:17:41 -0400
Subject: [PATCH 24/45] Updating allowed version of netcdf4

---
 setup.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/setup.py b/setup.py
index ec9dc341..76bdf06e 100644
--- a/setup.py
+++ b/setup.py
@@ -15,7 +15,7 @@ def local_pkg(name: str, relative_path: str) -> str:
     "cftime",
     "xarray>=2025.01.2",  # datatree + fixes
     "f90nml>=1.1.0",
-    "netcdf4==1.7.2",
+    "netcdf4>=1.7.2",
     "scipy",  # restart capacities only
     "h5netcdf",  # for xarray
     "h5py",  # for h5netcdf >= 1.8

From bd5a5b96d2ed9973221c2ea1292eb01b4b480072 Mon Sep 17 00:00:00 2001
From: Frank Malatino <frank.malatino@noaa.gov>
Date: Fri, 8 May 2026 12:31:32 -0400
Subject: [PATCH 25/45] Removing chunks={} from open_dataset call

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

diff --git a/tests/monitor/test_dm_monitor_single.py b/tests/monitor/test_dm_monitor_single.py
index eab1767a..e846c642 100644
--- a/tests/monitor/test_dm_monitor_single.py
+++ b/tests/monitor/test_dm_monitor_single.py
@@ -221,7 +221,7 @@ def test_dm_monitor_single_tile() -> None:
     assert Path("diag_manager_single_tile.nc").exists()
     lock = threading.Lock()
     ds = xr.open_dataset(
-        "diag_manager_single_tile.nc", decode_times=True, chunks={}, lock=lock
+        "diag_manager_single_tile.nc", decode_times=True, lock=lock
     )
     assert "var_2d" in ds
     np.testing.assert_array_equal(ds["var_2d"].shape, (ntimesteps, nx, ny))

From c3a1baa60aa31357b80209455524ee0b865b8f16 Mon Sep 17 00:00:00 2001
From: Frank Malatino <frank.malatino@noaa.gov>
Date: Fri, 8 May 2026 13:12:08 -0400
Subject: [PATCH 26/45] Checking if python 3.12 is causing breakage

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

diff --git a/.github/workflows/unit_tests.yaml b/.github/workflows/unit_tests.yaml
index 9da3cfc7..03172e88 100644
--- a/.github/workflows/unit_tests.yaml
+++ b/.github/workflows/unit_tests.yaml
@@ -27,7 +27,7 @@ jobs:
           - extra: 'test,pyfms'
             marker-serial: 'pyfms and not parallel'
             marker-parallel: 'pyfms and parallel'
-            python-version: '3.12'
+            python-version: '3.11'
       # don't cancel other jobs if one fails
       fail-fast: false
     name: Python ${{ matrix.python-version }}${{ contains(matrix.extra, 'pyfms') && ' (pyFMS)' || '' }}

From 0cf5946df945fa7b725da3b4847f6b0db8247df6 Mon Sep 17 00:00:00 2001
From: Frank Malatino <frank.malatino@noaa.gov>
Date: Fri, 8 May 2026 13:13:05 -0400
Subject: [PATCH 27/45] Linting

---
 tests/monitor/test_dm_monitor_single.py | 4 +---
 1 file changed, 1 insertion(+), 3 deletions(-)

diff --git a/tests/monitor/test_dm_monitor_single.py b/tests/monitor/test_dm_monitor_single.py
index e846c642..dab29659 100644
--- a/tests/monitor/test_dm_monitor_single.py
+++ b/tests/monitor/test_dm_monitor_single.py
@@ -220,9 +220,7 @@ def test_dm_monitor_single_tile() -> None:
     # check output!
     assert Path("diag_manager_single_tile.nc").exists()
     lock = threading.Lock()
-    ds = xr.open_dataset(
-        "diag_manager_single_tile.nc", decode_times=True, lock=lock
-    )
+    ds = xr.open_dataset("diag_manager_single_tile.nc", decode_times=True, lock=lock)
     assert "var_2d" in ds
     np.testing.assert_array_equal(ds["var_2d"].shape, (ntimesteps, nx, ny))
     assert ds["var_2d"].dims == ("time", "y", "x")

From d6cf6c01d2247f4f87a6f27f41374dbb2bc5d5b5 Mon Sep 17 00:00:00 2001
From: Frank Malatino <frank.malatino@noaa.gov>
Date: Fri, 8 May 2026 13:27:39 -0400
Subject: [PATCH 28/45] Using netcdf4 directly over xarray

---
 .github/workflows/unit_tests.yaml       |  2 +-
 tests/monitor/test_dm_monitor_single.py | 62 ++++++++++++++-----------
 2 files changed, 36 insertions(+), 28 deletions(-)

diff --git a/.github/workflows/unit_tests.yaml b/.github/workflows/unit_tests.yaml
index 03172e88..9da3cfc7 100644
--- a/.github/workflows/unit_tests.yaml
+++ b/.github/workflows/unit_tests.yaml
@@ -27,7 +27,7 @@ jobs:
           - extra: 'test,pyfms'
             marker-serial: 'pyfms and not parallel'
             marker-parallel: 'pyfms and parallel'
-            python-version: '3.11'
+            python-version: '3.12'
       # don't cancel other jobs if one fails
       fail-fast: false
     name: Python ${{ matrix.python-version }}${{ contains(matrix.extra, 'pyfms') && ' (pyFMS)' || '' }}
diff --git a/tests/monitor/test_dm_monitor_single.py b/tests/monitor/test_dm_monitor_single.py
index dab29659..3ab24b72 100644
--- a/tests/monitor/test_dm_monitor_single.py
+++ b/tests/monitor/test_dm_monitor_single.py
@@ -10,9 +10,12 @@
 import cftime
 import numpy as np
 import pytest
-import xarray as xr
 import yaml
 
+# import dask
+# import xarray as xr
+from netCDF4 import Dataset
+
 from ndsl import (
     DiagManagerMonitor,
     LocalComm,
@@ -219,31 +222,36 @@ def test_dm_monitor_single_tile() -> None:
 
     # check output!
     assert Path("diag_manager_single_tile.nc").exists()
-    lock = threading.Lock()
-    ds = xr.open_dataset("diag_manager_single_tile.nc", decode_times=True, lock=lock)
-    assert "var_2d" in ds
-    np.testing.assert_array_equal(ds["var_2d"].shape, (ntimesteps, nx, ny))
-    assert ds["var_2d"].dims == ("time", "y", "x")
-    assert ds["var_2d"].attrs["units"] == "muntin"
-    assert ds["var_3d"].dims == ("time", "z", "y", "x")
-    assert ds["var_3d"].attrs["units"] == "muntin"
-    assert ds["time"].shape == (ntimesteps,)
-    assert ds["time"].dims == ("time",)
-    assert ds["time"].values[0] == cftime.DatetimeNoLeap(2, 1, 1, 2, 1, 1)
-    assert ds["time"].values[1] == cftime.DatetimeNoLeap(2, 1, 1, 3, 1, 1)
-    assert ds["time"].values[2] == cftime.DatetimeNoLeap(2, 1, 1, 4, 1, 1)
-    np.testing.assert_array_equal(ds["var_2d"].values[0, :, :], var2_global.transpose())
-    np.testing.assert_array_equal(ds["var_2d"].values[1, :, :], var2_global.transpose())
-    np.testing.assert_array_equal(ds["var_2d"].values[2, :, :], var2_global.transpose())
-    # data is transposed when passed into fortran
-    np.testing.assert_array_equal(
-        ds["var_3d"].values[0, :, :, :], var3_global.transpose()
-    )
-    np.testing.assert_array_equal(
-        ds["var_3d"].values[1, :, :, :], var3_global.transpose()
-    )
-    np.testing.assert_array_equal(
-        ds["var_3d"].values[2, :, :, :], var3_global.transpose()
-    )
+    # lock = threading.Lock()
+    # ds = xr.open_dataset("diag_manager_single_tile.nc", decode_times=True, lock=lock)
+    ds = Dataset("diag_manager_single_tile.nc")
+    assert "var_2d" in ds.variables
+    var2 = ds.variables["var_2d"]
+    assert var2.shape == (ntimesteps, ny, nx)
+    assert var2.units == "muntin"
+    # assert "var_2d" in ds
+    # np.testing.assert_array_equal(ds["var_2d"].shape, (ntimesteps, nx, ny))
+    # assert ds["var_2d"].dims == ("time", "y", "x")
+    # assert ds["var_2d"].attrs["units"] == "muntin"
+    # assert ds["var_3d"].dims == ("time", "z", "y", "x")
+    # assert ds["var_3d"].attrs["units"] == "muntin"
+    # assert ds["time"].shape == (ntimesteps,)
+    # assert ds["time"].dims == ("time",)
+    # assert ds["time"].values[0] == cftime.DatetimeNoLeap(2, 1, 1, 2, 1, 1)
+    # assert ds["time"].values[1] == cftime.DatetimeNoLeap(2, 1, 1, 3, 1, 1)
+    # assert ds["time"].values[2] == cftime.DatetimeNoLeap(2, 1, 1, 4, 1, 1)
+    # np.testing.assert_array_equal(ds["var_2d"].values[0, :, :], var2_global.transpose())
+    # np.testing.assert_array_equal(ds["var_2d"].values[1, :, :], var2_global.transpose())
+    # np.testing.assert_array_equal(ds["var_2d"].values[2, :, :], var2_global.transpose())
+    # # data is transposed when passed into fortran
+    # np.testing.assert_array_equal(
+    #     ds["var_3d"].values[0, :, :, :], var3_global.transpose()
+    # )
+    # np.testing.assert_array_equal(
+    #     ds["var_3d"].values[1, :, :, :], var3_global.transpose()
+    # )
+    # np.testing.assert_array_equal(
+    #     ds["var_3d"].values[2, :, :, :], var3_global.transpose()
+    # )
 
     pyfms.fms.end()

From ab22f589cf38d7e5064d87b1f3ffbacc90410245 Mon Sep 17 00:00:00 2001
From: Frank Malatino <frank.malatino@noaa.gov>
Date: Fri, 8 May 2026 14:07:18 -0400
Subject: [PATCH 29/45] Bring all asserts back into test_dm_monitor_single.py

---
 tests/monitor/test_dm_monitor_single.py | 58 ++++++++++---------------
 1 file changed, 24 insertions(+), 34 deletions(-)

diff --git a/tests/monitor/test_dm_monitor_single.py b/tests/monitor/test_dm_monitor_single.py
index 3ab24b72..bc9e4a55 100644
--- a/tests/monitor/test_dm_monitor_single.py
+++ b/tests/monitor/test_dm_monitor_single.py
@@ -3,7 +3,6 @@
 with data gathered from any other processors.
 """
 
-import threading
 from datetime import datetime, timedelta
 from pathlib import Path
 
@@ -11,10 +10,7 @@
 import numpy as np
 import pytest
 import yaml
-
-# import dask
-# import xarray as xr
-from netCDF4 import Dataset
+from netCDF4 import Dataset, num2date
 
 from ndsl import (
     DiagManagerMonitor,
@@ -222,36 +218,30 @@ def test_dm_monitor_single_tile() -> None:
 
     # check output!
     assert Path("diag_manager_single_tile.nc").exists()
-    # lock = threading.Lock()
-    # ds = xr.open_dataset("diag_manager_single_tile.nc", decode_times=True, lock=lock)
     ds = Dataset("diag_manager_single_tile.nc")
     assert "var_2d" in ds.variables
-    var2 = ds.variables["var_2d"]
-    assert var2.shape == (ntimesteps, ny, nx)
-    assert var2.units == "muntin"
-    # assert "var_2d" in ds
-    # np.testing.assert_array_equal(ds["var_2d"].shape, (ntimesteps, nx, ny))
-    # assert ds["var_2d"].dims == ("time", "y", "x")
-    # assert ds["var_2d"].attrs["units"] == "muntin"
-    # assert ds["var_3d"].dims == ("time", "z", "y", "x")
-    # assert ds["var_3d"].attrs["units"] == "muntin"
-    # assert ds["time"].shape == (ntimesteps,)
-    # assert ds["time"].dims == ("time",)
-    # assert ds["time"].values[0] == cftime.DatetimeNoLeap(2, 1, 1, 2, 1, 1)
-    # assert ds["time"].values[1] == cftime.DatetimeNoLeap(2, 1, 1, 3, 1, 1)
-    # assert ds["time"].values[2] == cftime.DatetimeNoLeap(2, 1, 1, 4, 1, 1)
-    # np.testing.assert_array_equal(ds["var_2d"].values[0, :, :], var2_global.transpose())
-    # np.testing.assert_array_equal(ds["var_2d"].values[1, :, :], var2_global.transpose())
-    # np.testing.assert_array_equal(ds["var_2d"].values[2, :, :], var2_global.transpose())
-    # # data is transposed when passed into fortran
-    # np.testing.assert_array_equal(
-    #     ds["var_3d"].values[0, :, :, :], var3_global.transpose()
-    # )
-    # np.testing.assert_array_equal(
-    #     ds["var_3d"].values[1, :, :, :], var3_global.transpose()
-    # )
-    # np.testing.assert_array_equal(
-    #     ds["var_3d"].values[2, :, :, :], var3_global.transpose()
-    # )
+    assert "time" in ds.variables
+    assert "var_3d" in ds.variables
+    var2_ds = ds.variables["var_2d"]
+    time_var = ds.variables["time"]
+    var3_ds = ds.variables["var_3d"]
+    np.testing.assert_array_equal(var2_ds.shape, (ntimesteps, nx, ny))
+    assert var2_ds.dimensions == ("time", "y", "x")
+    assert var2_ds.units == "muntin"
+    assert var3_ds.dimensions == ("time", "z", "y", "x")
+    assert var3_ds.units == "muntin"
+    assert time_var.shape == (ntimesteps,)
+    assert time_var.dimensions == ("time",)
+    dates = num2date(time_var[:], units=time_var.units, calendar=time_var.calendar)
+    assert dates[0] == cftime.DatetimeNoLeap(2, 1, 1, 2, 1, 1)
+    assert dates[1] == cftime.DatetimeNoLeap(2, 1, 1, 3, 1, 1)
+    assert dates[2] == cftime.DatetimeNoLeap(2, 1, 1, 4, 1, 1)
+    np.testing.assert_array_equal(var2_ds[0, :, :], var2_global.transpose())
+    np.testing.assert_array_equal(var2_ds[1, :, :], var2_global.transpose())
+    np.testing.assert_array_equal(var2_ds[2, :, :], var2_global.transpose())
+    # data is transposed when passed into fortran
+    np.testing.assert_array_equal(var3_ds[0, :, :, :], var3_global.transpose())
+    np.testing.assert_array_equal(var3_ds[1, :, :, :], var3_global.transpose())
+    np.testing.assert_array_equal(var3_ds[2, :, :, :], var3_global.transpose())
 
     pyfms.fms.end()

From 528f21f0a301defe0b8ca0c5bfa9175e033b0916 Mon Sep 17 00:00:00 2001
From: Frank Malatino <frank.malatino@noaa.gov>
Date: Fri, 8 May 2026 14:21:06 -0400
Subject: [PATCH 30/45] Adding option for parallel pyfms tests vs non in
 unit_tests workflow

---
 .github/workflows/unit_tests.yaml | 8 ++++++--
 1 file changed, 6 insertions(+), 2 deletions(-)

diff --git a/.github/workflows/unit_tests.yaml b/.github/workflows/unit_tests.yaml
index 9da3cfc7..cbb68435 100644
--- a/.github/workflows/unit_tests.yaml
+++ b/.github/workflows/unit_tests.yaml
@@ -50,17 +50,21 @@ jobs:
         if: contains(matrix.extra, 'pyfms')
         run: |
           sudo apt-get update
-          sudo apt-get install mpich libmpich-dev netcdf-bin libnetcdf-dev libnetcdff-dev nco libyaml-dev diffutils
+          sudo apt-get install libopenmpi-dev netcdf-bin libnetcdf-dev libnetcdff-dev nco libyaml-dev diffutils
 
       - name: Install Python packages
         run: |
           pip3 install -v .[${{matrix.extra}}]
-          pip3 list
 
       - name: Run serial cpu tests
         run: coverage run --rcfile=pyproject.toml -m pytest -s -m "${{matrix.marker-serial}}" tests
 
+      - name: Run parallel cpu tests for pyFMS
+        if: contains(matrix.extra, 'pyfms')
+        run: mpiexec -np 6 --oversubscribe coverage run --rcfile=pyproject.toml -m mpi4py -m pytest -s -m "${{matrix.marker-parallel}}" tests
+
       - name: Run parallel cpu tests
+        if: ${{!contains(matrix.extra, 'pyfms')}}
         run: mpiexec -np 6 coverage run --rcfile=pyproject.toml -m mpi4py -m pytest -s -m "${{matrix.marker-parallel}}" tests
 
       - name: Output code coverage

From 877fd63c7c72b729de210ff46c7039b8e9c98516 Mon Sep 17 00:00:00 2001
From: Frank Malatino <frank.malatino@noaa.gov>
Date: Fri, 8 May 2026 14:34:28 -0400
Subject: [PATCH 31/45] Using netcdf4 over xarray in test_dm_monitor_cubed.py

---
 tests/monitor/test_dm_monitor_cubed.py | 42 ++++++++++++++------------
 1 file changed, 23 insertions(+), 19 deletions(-)

diff --git a/tests/monitor/test_dm_monitor_cubed.py b/tests/monitor/test_dm_monitor_cubed.py
index 5fa2bd82..e1bdb557 100644
--- a/tests/monitor/test_dm_monitor_cubed.py
+++ b/tests/monitor/test_dm_monitor_cubed.py
@@ -8,8 +8,8 @@
 import cftime
 import numpy as np
 import pytest
-import xarray as xr
 import yaml
+from netCDF4 import Dataset, num2date
 
 from ndsl import (
     CubedSphereCommunicator,
@@ -201,24 +201,28 @@ def test_dm_monitor() -> None:
     pe = MPIComm()._comm.Get_rank() + 1
     filename = "diag_manager_cubed_sphere.tile" + str(pe) + ".nc"
     assert Path(filename).exists()
-    ds = xr.open_dataset(filename, decode_times=True)
-    assert "var1" in ds
-    np.testing.assert_array_equal(ds["var1"].shape, (ntimesteps, ny, nx))
-    assert "var2" in ds
-    np.testing.assert_array_equal(ds["var2"].shape, (ntimesteps, nz, ny, nx))
-    assert ds["var1"].dims == ("time", "y", "x")
-    assert ds["var2"].dims == ("time", "z", "y", "x")
-    assert ds["time"].shape == (ntimesteps,)
-    assert ds["time"].dims == ("time",)
-    assert ds["time"].values[0] == cftime.DatetimeNoLeap(1, 1, 1, 0, 0, 15)
-    assert ds["time"].values[1] == cftime.DatetimeNoLeap(1, 1, 1, 0, 0, 30)
-    assert ds["time"].values[2] == cftime.DatetimeNoLeap(1, 1, 1, 0, 0, 45)
+    ds = Dataset(filename)
+    assert "var1" in ds.variables
+    var1_ds = ds.variables["var1"]
+    np.testing.assert_array_equal(var1_ds.shape, (ntimesteps, ny, nx))
+    assert "var2" in ds.variables
+    var2_ds = ds.variables["var2"]
+    np.testing.assert_array_equal(var2_ds.shape, (ntimesteps, nz, ny, nx))
+    assert var1_ds.dimensions == ("time", "y", "x")
+    assert var2_ds.dimensions == ("time", "z", "y", "x")
+    time_var = ds["time"]
+    dates = num2date(time_var[:], units=time_var.units, calendar=time_var.calendar)
+    assert time_var.shape == (ntimesteps,)
+    assert time_var.dimensions == ("time",)
+    assert dates[0] == cftime.DatetimeNoLeap(1, 1, 1, 0, 0, 15)
+    assert dates[1] == cftime.DatetimeNoLeap(1, 1, 1, 0, 0, 30)
+    assert dates[2] == cftime.DatetimeNoLeap(1, 1, 1, 0, 0, 45)
     # data is just the timestep number
-    np.testing.assert_array_equal(ds["var1"].values[0, :, :], 1)
-    np.testing.assert_array_equal(ds["var1"].values[1, :, :], 2)
-    np.testing.assert_array_equal(ds["var1"].values[2, :, :], 3)
-    np.testing.assert_array_equal(ds["var2"].values[0, :, :, :], 2)
-    np.testing.assert_array_equal(ds["var2"].values[1, :, :, :], 4)
-    np.testing.assert_array_equal(ds["var2"].values[2, :, :, :], 6)
+    np.testing.assert_array_equal(var1_ds[0, :, :], 1)
+    np.testing.assert_array_equal(var1_ds[1, :, :], 2)
+    np.testing.assert_array_equal(var1_ds[2, :, :], 3)
+    np.testing.assert_array_equal(var2_ds[0, :, :, :], 2)
+    np.testing.assert_array_equal(var2_ds[1, :, :, :], 4)
+    np.testing.assert_array_equal(var2_ds[2, :, :, :], 6)
 
     pyfms.fms.end()

From e6c365f87d5d0770b88c8d597251d82badd9f98e Mon Sep 17 00:00:00 2001
From: Frank Malatino <frank.malatino@noaa.gov>
Date: Mon, 11 May 2026 09:55:36 -0400
Subject: [PATCH 32/45] Removing script mode for pip install in unit_tests
 workflow

---
 .github/workflows/unit_tests.yaml | 3 +--
 1 file changed, 1 insertion(+), 2 deletions(-)

diff --git a/.github/workflows/unit_tests.yaml b/.github/workflows/unit_tests.yaml
index cbb68435..2cfd67a4 100644
--- a/.github/workflows/unit_tests.yaml
+++ b/.github/workflows/unit_tests.yaml
@@ -53,8 +53,7 @@ jobs:
           sudo apt-get install libopenmpi-dev netcdf-bin libnetcdf-dev libnetcdff-dev nco libyaml-dev diffutils
 
       - name: Install Python packages
-        run: |
-          pip3 install -v .[${{matrix.extra}}]
+        run: pip3 install -v .[${{matrix.extra}}]
 
       - name: Run serial cpu tests
         run: coverage run --rcfile=pyproject.toml -m pytest -s -m "${{matrix.marker-serial}}" tests

From af1d2a55ce90c9c278c312215f03db2df1928b80 Mon Sep 17 00:00:00 2001
From: Frank Malatino <frank.malatino@noaa.gov>
Date: Mon, 11 May 2026 14:40:31 -0400
Subject: [PATCH 33/45] Addressing PR 459 comments, removing -s flag, no
 apt-get update, single parallel test run

---
 .github/workflows/unit_tests.yaml | 19 ++++++++++---------
 setup.py                          |  2 +-
 2 files changed, 11 insertions(+), 10 deletions(-)

diff --git a/.github/workflows/unit_tests.yaml b/.github/workflows/unit_tests.yaml
index 2cfd67a4..f7c75796 100644
--- a/.github/workflows/unit_tests.yaml
+++ b/.github/workflows/unit_tests.yaml
@@ -48,23 +48,24 @@ jobs:
 
       - name: Install pyFMS dependencies (includes system MPI)
         if: contains(matrix.extra, 'pyfms')
-        run: |
-          sudo apt-get update
-          sudo apt-get install libopenmpi-dev netcdf-bin libnetcdf-dev libnetcdff-dev nco libyaml-dev diffutils
+        run: sudo apt-get install libopenmpi-dev netcdf-bin libnetcdf-dev libnetcdff-dev nco libyaml-dev diffutils
 
       - name: Install Python packages
-        run: pip3 install -v .[${{matrix.extra}}]
+        run: pip3 install .[${{matrix.extra}}]
 
       - name: Run serial cpu tests
         run: coverage run --rcfile=pyproject.toml -m pytest -s -m "${{matrix.marker-serial}}" tests
 
-      - name: Run parallel cpu tests for pyFMS
-        if: contains(matrix.extra, 'pyfms')
-        run: mpiexec -np 6 --oversubscribe coverage run --rcfile=pyproject.toml -m mpi4py -m pytest -s -m "${{matrix.marker-parallel}}" tests
+      # - name: Run parallel cpu tests for pyFMS
+      #   if: contains(matrix.extra, 'pyfms')
+      #   run: mpiexec -np 6 --oversubscribe coverage run --rcfile=pyproject.toml -m mpi4py -m pytest -m "${{matrix.marker-parallel}}" tests
+
+      # - name: Run parallel cpu tests
+      #   if: ${{!contains(matrix.extra, 'pyfms')}}
+      #   run: mpiexec -np 6 coverage run --rcfile=pyproject.toml -m mpi4py -m pytest -m "${{matrix.marker-parallel}}" tests
 
       - name: Run parallel cpu tests
-        if: ${{!contains(matrix.extra, 'pyfms')}}
-        run: mpiexec -np 6 coverage run --rcfile=pyproject.toml -m mpi4py -m pytest -s -m "${{matrix.marker-parallel}}" tests
+        run: mpiexec -np 6 coverage run --rcfile=pyproject.toml -m mpi4py -m pytest -m "${{matrix.marker-parallel}}" tests
 
       - name: Output code coverage
         run: |
diff --git a/setup.py b/setup.py
index 76bdf06e..ec9dc341 100644
--- a/setup.py
+++ b/setup.py
@@ -15,7 +15,7 @@ def local_pkg(name: str, relative_path: str) -> str:
     "cftime",
     "xarray>=2025.01.2",  # datatree + fixes
     "f90nml>=1.1.0",
-    "netcdf4>=1.7.2",
+    "netcdf4==1.7.2",
     "scipy",  # restart capacities only
     "h5netcdf",  # for xarray
     "h5py",  # for h5netcdf >= 1.8

From d18e647963e37ab5a8dc39f87e36fe6bd9131c21 Mon Sep 17 00:00:00 2001
From: Frank Malatino <frank.malatino@noaa.gov>
Date: Mon, 11 May 2026 14:47:51 -0400
Subject: [PATCH 34/45] Using --fix-missing to try to amend broken install for
 pyfms

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

diff --git a/.github/workflows/unit_tests.yaml b/.github/workflows/unit_tests.yaml
index f7c75796..cc3f7ba4 100644
--- a/.github/workflows/unit_tests.yaml
+++ b/.github/workflows/unit_tests.yaml
@@ -48,7 +48,7 @@ jobs:
 
       - name: Install pyFMS dependencies (includes system MPI)
         if: contains(matrix.extra, 'pyfms')
-        run: sudo apt-get install libopenmpi-dev netcdf-bin libnetcdf-dev libnetcdff-dev nco libyaml-dev diffutils
+        run: sudo apt-get install -y --fix-missing libopenmpi-dev netcdf-bin libnetcdf-dev libnetcdff-dev nco libyaml-dev diffutils
 
       - name: Install Python packages
         run: pip3 install .[${{matrix.extra}}]

From 424760da9ef218b2664715d0f2a5ad0f47f9c89b Mon Sep 17 00:00:00 2001
From: Frank Malatino <frank.malatino@noaa.gov>
Date: Mon, 11 May 2026 15:04:08 -0400
Subject: [PATCH 35/45] Using update for pyfms install to check that other
 changes are working

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

diff --git a/.github/workflows/unit_tests.yaml b/.github/workflows/unit_tests.yaml
index cc3f7ba4..86570b6a 100644
--- a/.github/workflows/unit_tests.yaml
+++ b/.github/workflows/unit_tests.yaml
@@ -48,7 +48,7 @@ jobs:
 
       - name: Install pyFMS dependencies (includes system MPI)
         if: contains(matrix.extra, 'pyfms')
-        run: sudo apt-get install -y --fix-missing libopenmpi-dev netcdf-bin libnetcdf-dev libnetcdff-dev nco libyaml-dev diffutils
+        run: sudo apt-get update && install -y libopenmpi-dev netcdf-bin libnetcdf-dev libnetcdff-dev nco libyaml-dev diffutils
 
       - name: Install Python packages
         run: pip3 install .[${{matrix.extra}}]

From 62b21c0c1a4576a602100ded52c34445a21ba9d9 Mon Sep 17 00:00:00 2001
From: Frank Malatino <frank.malatino@noaa.gov>
Date: Mon, 11 May 2026 15:05:36 -0400
Subject: [PATCH 36/45] Removing -y flag from pyfms dependency install

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

diff --git a/.github/workflows/unit_tests.yaml b/.github/workflows/unit_tests.yaml
index 86570b6a..70073b04 100644
--- a/.github/workflows/unit_tests.yaml
+++ b/.github/workflows/unit_tests.yaml
@@ -48,7 +48,7 @@ jobs:
 
       - name: Install pyFMS dependencies (includes system MPI)
         if: contains(matrix.extra, 'pyfms')
-        run: sudo apt-get update && install -y libopenmpi-dev netcdf-bin libnetcdf-dev libnetcdff-dev nco libyaml-dev diffutils
+        run: sudo apt-get update && install libopenmpi-dev netcdf-bin libnetcdf-dev libnetcdff-dev nco libyaml-dev diffutils
 
       - name: Install Python packages
         run: pip3 install .[${{matrix.extra}}]

From ac125d171c6aa210421467ab3077a5870a0d036d Mon Sep 17 00:00:00 2001
From: Frank Malatino <frank.malatino@noaa.gov>
Date: Mon, 11 May 2026 15:08:56 -0400
Subject: [PATCH 37/45] Using script mode for pyfms dependency install

---
 .github/workflows/unit_tests.yaml | 4 +++-
 1 file changed, 3 insertions(+), 1 deletion(-)

diff --git a/.github/workflows/unit_tests.yaml b/.github/workflows/unit_tests.yaml
index 70073b04..ba36816f 100644
--- a/.github/workflows/unit_tests.yaml
+++ b/.github/workflows/unit_tests.yaml
@@ -48,7 +48,9 @@ jobs:
 
       - name: Install pyFMS dependencies (includes system MPI)
         if: contains(matrix.extra, 'pyfms')
-        run: sudo apt-get update && install libopenmpi-dev netcdf-bin libnetcdf-dev libnetcdff-dev nco libyaml-dev diffutils
+        run: |
+          sudo apt-get update 
+          sudo apt-get install libopenmpi-dev netcdf-bin libnetcdf-dev libnetcdff-dev nco libyaml-dev diffutils
 
       - name: Install Python packages
         run: pip3 install .[${{matrix.extra}}]

From 9d85b3481f033cc6fd24f5e8b5a3ed6c124cf1ee Mon Sep 17 00:00:00 2001
From: Frank Malatino <frank.malatino@noaa.gov>
Date: Mon, 11 May 2026 15:18:19 -0400
Subject: [PATCH 38/45] Moving back to using separate parallel test runs in
 unit tests

---
 .github/workflows/unit_tests.yaml | 13 +++++--------
 1 file changed, 5 insertions(+), 8 deletions(-)

diff --git a/.github/workflows/unit_tests.yaml b/.github/workflows/unit_tests.yaml
index ba36816f..0a1be7bb 100644
--- a/.github/workflows/unit_tests.yaml
+++ b/.github/workflows/unit_tests.yaml
@@ -49,7 +49,7 @@ jobs:
       - name: Install pyFMS dependencies (includes system MPI)
         if: contains(matrix.extra, 'pyfms')
         run: |
-          sudo apt-get update 
+          sudo apt-get update
           sudo apt-get install libopenmpi-dev netcdf-bin libnetcdf-dev libnetcdff-dev nco libyaml-dev diffutils
 
       - name: Install Python packages
@@ -58,15 +58,12 @@ jobs:
       - name: Run serial cpu tests
         run: coverage run --rcfile=pyproject.toml -m pytest -s -m "${{matrix.marker-serial}}" tests
 
-      # - name: Run parallel cpu tests for pyFMS
-      #   if: contains(matrix.extra, 'pyfms')
-      #   run: mpiexec -np 6 --oversubscribe coverage run --rcfile=pyproject.toml -m mpi4py -m pytest -m "${{matrix.marker-parallel}}" tests
-
-      # - name: Run parallel cpu tests
-      #   if: ${{!contains(matrix.extra, 'pyfms')}}
-      #   run: mpiexec -np 6 coverage run --rcfile=pyproject.toml -m mpi4py -m pytest -m "${{matrix.marker-parallel}}" tests
+      - name: Run parallel cpu tests for pyFMS
+        if: contains(matrix.extra, 'pyfms')
+        run: mpiexec -np 6 --oversubscribe coverage run --rcfile=pyproject.toml -m mpi4py -m pytest -m "${{matrix.marker-parallel}}" tests
 
       - name: Run parallel cpu tests
+        if: ${{!contains(matrix.extra, 'pyfms')}}
         run: mpiexec -np 6 coverage run --rcfile=pyproject.toml -m mpi4py -m pytest -m "${{matrix.marker-parallel}}" tests
 
       - name: Output code coverage

From cb49a53e61897a94b612760e15c784928eeeb855 Mon Sep 17 00:00:00 2001
From: Frank Malatino <frank.malatino@noaa.gov>
Date: Mon, 11 May 2026 17:05:31 -0400
Subject: [PATCH 39/45] Always using openmpi in unit_tests workflow

---
 .github/workflows/unit_tests.yaml | 9 ++-------
 1 file changed, 2 insertions(+), 7 deletions(-)

diff --git a/.github/workflows/unit_tests.yaml b/.github/workflows/unit_tests.yaml
index 0a1be7bb..e7aa7ae4 100644
--- a/.github/workflows/unit_tests.yaml
+++ b/.github/workflows/unit_tests.yaml
@@ -44,7 +44,7 @@ jobs:
 
       - name: Install MPI
         if: ${{!contains(matrix.extra, 'pyfms')}}
-        run: pip3 install mpich
+        run: pip3 install openmpi
 
       - name: Install pyFMS dependencies (includes system MPI)
         if: contains(matrix.extra, 'pyfms')
@@ -58,13 +58,8 @@ jobs:
       - name: Run serial cpu tests
         run: coverage run --rcfile=pyproject.toml -m pytest -s -m "${{matrix.marker-serial}}" tests
 
-      - name: Run parallel cpu tests for pyFMS
-        if: contains(matrix.extra, 'pyfms')
-        run: mpiexec -np 6 --oversubscribe coverage run --rcfile=pyproject.toml -m mpi4py -m pytest -m "${{matrix.marker-parallel}}" tests
-
       - name: Run parallel cpu tests
-        if: ${{!contains(matrix.extra, 'pyfms')}}
-        run: mpiexec -np 6 coverage run --rcfile=pyproject.toml -m mpi4py -m pytest -m "${{matrix.marker-parallel}}" tests
+        run: mpiexec -np 6 --oversubscribe coverage run --rcfile=pyproject.toml -m mpi4py -m pytest -m "${{matrix.marker-parallel}}" tests
 
       - name: Output code coverage
         run: |

From dae409499f52461eac02881acb5615b9e57d6df4 Mon Sep 17 00:00:00 2001
From: Frank Malatino <frank.malatino@noaa.gov>
Date: Tue, 12 May 2026 10:29:10 -0400
Subject: [PATCH 40/45] Removing -s flag from serial cpu unit tests

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

diff --git a/.github/workflows/unit_tests.yaml b/.github/workflows/unit_tests.yaml
index e7aa7ae4..46d3ca53 100644
--- a/.github/workflows/unit_tests.yaml
+++ b/.github/workflows/unit_tests.yaml
@@ -56,7 +56,7 @@ jobs:
         run: pip3 install .[${{matrix.extra}}]
 
       - name: Run serial cpu tests
-        run: coverage run --rcfile=pyproject.toml -m pytest -s -m "${{matrix.marker-serial}}" tests
+        run: coverage run --rcfile=pyproject.toml -m pytest -m "${{matrix.marker-serial}}" tests
 
       - name: Run parallel cpu tests
         run: mpiexec -np 6 --oversubscribe coverage run --rcfile=pyproject.toml -m mpi4py -m pytest -m "${{matrix.marker-parallel}}" tests

From ae26ded422df8d9d686857cf4008079ef4fe23e0 Mon Sep 17 00:00:00 2001
From: Frank Malatino <frank.malatino@noaa.gov>
Date: Thu, 14 May 2026 11:09:43 -0400
Subject: [PATCH 41/45] Trying with chunks set to None in xarray open_dataset
 to skip Dask

---
 tests/monitor/test_dm_monitor_single.py | 78 +++++++++++++++++--------
 1 file changed, 53 insertions(+), 25 deletions(-)

diff --git a/tests/monitor/test_dm_monitor_single.py b/tests/monitor/test_dm_monitor_single.py
index bc9e4a55..6ea4ca9a 100644
--- a/tests/monitor/test_dm_monitor_single.py
+++ b/tests/monitor/test_dm_monitor_single.py
@@ -11,6 +11,7 @@
 import pytest
 import yaml
 from netCDF4 import Dataset, num2date
+import xarray as xr
 
 from ndsl import (
     DiagManagerMonitor,
@@ -216,32 +217,59 @@ def test_dm_monitor_single_tile() -> None:
     # cleanup writes and closes the file
     monitor.cleanup()
 
-    # check output!
+    # # check output!
+    # assert Path("diag_manager_single_tile.nc").exists()
+    # ds = Dataset("diag_manager_single_tile.nc")
+    # assert "var_2d" in ds.variables
+    # assert "time" in ds.variables
+    # assert "var_3d" in ds.variables
+    # var2_ds = ds.variables["var_2d"]
+    # time_var = ds.variables["time"]
+    # var3_ds = ds.variables["var_3d"]
+    # np.testing.assert_array_equal(var2_ds.shape, (ntimesteps, nx, ny))
+    # assert var2_ds.dimensions == ("time", "y", "x")
+    # assert var2_ds.units == "muntin"
+    # assert var3_ds.dimensions == ("time", "z", "y", "x")
+    # assert var3_ds.units == "muntin"
+    # assert time_var.shape == (ntimesteps,)
+    # assert time_var.dimensions == ("time",)
+    # dates = num2date(time_var[:], units=time_var.units, calendar=time_var.calendar)
+    # assert dates[0] == cftime.DatetimeNoLeap(2, 1, 1, 2, 1, 1)
+    # assert dates[1] == cftime.DatetimeNoLeap(2, 1, 1, 3, 1, 1)
+    # assert dates[2] == cftime.DatetimeNoLeap(2, 1, 1, 4, 1, 1)
+    # np.testing.assert_array_equal(var2_ds[0, :, :], var2_global.transpose())
+    # np.testing.assert_array_equal(var2_ds[1, :, :], var2_global.transpose())
+    # np.testing.assert_array_equal(var2_ds[2, :, :], var2_global.transpose())
+    # # data is transposed when passed into fortran
+    # np.testing.assert_array_equal(var3_ds[0, :, :, :], var3_global.transpose())
+    # np.testing.assert_array_equal(var3_ds[1, :, :, :], var3_global.transpose())
+    # np.testing.assert_array_equal(var3_ds[2, :, :, :], var3_global.transpose())
+
     assert Path("diag_manager_single_tile.nc").exists()
-    ds = Dataset("diag_manager_single_tile.nc")
-    assert "var_2d" in ds.variables
-    assert "time" in ds.variables
-    assert "var_3d" in ds.variables
-    var2_ds = ds.variables["var_2d"]
-    time_var = ds.variables["time"]
-    var3_ds = ds.variables["var_3d"]
-    np.testing.assert_array_equal(var2_ds.shape, (ntimesteps, nx, ny))
-    assert var2_ds.dimensions == ("time", "y", "x")
-    assert var2_ds.units == "muntin"
-    assert var3_ds.dimensions == ("time", "z", "y", "x")
-    assert var3_ds.units == "muntin"
-    assert time_var.shape == (ntimesteps,)
-    assert time_var.dimensions == ("time",)
-    dates = num2date(time_var[:], units=time_var.units, calendar=time_var.calendar)
-    assert dates[0] == cftime.DatetimeNoLeap(2, 1, 1, 2, 1, 1)
-    assert dates[1] == cftime.DatetimeNoLeap(2, 1, 1, 3, 1, 1)
-    assert dates[2] == cftime.DatetimeNoLeap(2, 1, 1, 4, 1, 1)
-    np.testing.assert_array_equal(var2_ds[0, :, :], var2_global.transpose())
-    np.testing.assert_array_equal(var2_ds[1, :, :], var2_global.transpose())
-    np.testing.assert_array_equal(var2_ds[2, :, :], var2_global.transpose())
+    ds = xr.open_dataset("diag_manager_single_tile.nc", decode_times=True, chunks=None)
+    assert "var_2d" in ds
+    np.testing.assert_array_equal(ds["var_2d"].shape, (ntimesteps, nx, ny))
+    assert ds["var_2d"].dims == ("time", "y", "x")
+    assert ds["var_2d"].attrs["units"] == "muntin"
+    assert ds["var_3d"].dims == ("time", "z", "y", "x")
+    assert ds["var_3d"].attrs["units"] == "muntin"
+    assert ds["time"].shape == (ntimesteps,)
+    assert ds["time"].dims == ("time",)
+    assert ds["time"].values[0] == cftime.DatetimeNoLeap(2, 1, 1, 2, 1, 1)
+    assert ds["time"].values[1] == cftime.DatetimeNoLeap(2, 1, 1, 3, 1, 1)
+    assert ds["time"].values[2] == cftime.DatetimeNoLeap(2, 1, 1, 4, 1, 1)
+    np.testing.assert_array_equal(ds["var_2d"].values[0, :, :], var2_global.transpose())
+    np.testing.assert_array_equal(ds["var_2d"].values[1, :, :], var2_global.transpose())
+    np.testing.assert_array_equal(ds["var_2d"].values[2, :, :], var2_global.transpose())
     # data is transposed when passed into fortran
-    np.testing.assert_array_equal(var3_ds[0, :, :, :], var3_global.transpose())
-    np.testing.assert_array_equal(var3_ds[1, :, :, :], var3_global.transpose())
-    np.testing.assert_array_equal(var3_ds[2, :, :, :], var3_global.transpose())
+    np.testing.assert_array_equal(
+        ds["var_3d"].values[0, :, :, :], var3_global.transpose()
+    )
+    np.testing.assert_array_equal(
+        ds["var_3d"].values[1, :, :, :], var3_global.transpose()
+    )
+    np.testing.assert_array_equal(
+        ds["var_3d"].values[2, :, :, :], var3_global.transpose()
+    )
 
     pyfms.fms.end()

From 08c557374040d482da55aaff53f74669549a800c Mon Sep 17 00:00:00 2001
From: Frank Malatino <frank.malatino@noaa.gov>
Date: Thu, 14 May 2026 11:19:48 -0400
Subject: [PATCH 42/45] Checking decode_times use within xarray open_dataset
 failure

---
 tests/monitor/test_dm_monitor_single.py | 50 ++++++++++++-------------
 1 file changed, 25 insertions(+), 25 deletions(-)

diff --git a/tests/monitor/test_dm_monitor_single.py b/tests/monitor/test_dm_monitor_single.py
index 6ea4ca9a..c901e6fc 100644
--- a/tests/monitor/test_dm_monitor_single.py
+++ b/tests/monitor/test_dm_monitor_single.py
@@ -246,30 +246,30 @@ def test_dm_monitor_single_tile() -> None:
     # np.testing.assert_array_equal(var3_ds[2, :, :, :], var3_global.transpose())
 
     assert Path("diag_manager_single_tile.nc").exists()
-    ds = xr.open_dataset("diag_manager_single_tile.nc", decode_times=True, chunks=None)
-    assert "var_2d" in ds
-    np.testing.assert_array_equal(ds["var_2d"].shape, (ntimesteps, nx, ny))
-    assert ds["var_2d"].dims == ("time", "y", "x")
-    assert ds["var_2d"].attrs["units"] == "muntin"
-    assert ds["var_3d"].dims == ("time", "z", "y", "x")
-    assert ds["var_3d"].attrs["units"] == "muntin"
-    assert ds["time"].shape == (ntimesteps,)
-    assert ds["time"].dims == ("time",)
-    assert ds["time"].values[0] == cftime.DatetimeNoLeap(2, 1, 1, 2, 1, 1)
-    assert ds["time"].values[1] == cftime.DatetimeNoLeap(2, 1, 1, 3, 1, 1)
-    assert ds["time"].values[2] == cftime.DatetimeNoLeap(2, 1, 1, 4, 1, 1)
-    np.testing.assert_array_equal(ds["var_2d"].values[0, :, :], var2_global.transpose())
-    np.testing.assert_array_equal(ds["var_2d"].values[1, :, :], var2_global.transpose())
-    np.testing.assert_array_equal(ds["var_2d"].values[2, :, :], var2_global.transpose())
-    # data is transposed when passed into fortran
-    np.testing.assert_array_equal(
-        ds["var_3d"].values[0, :, :, :], var3_global.transpose()
-    )
-    np.testing.assert_array_equal(
-        ds["var_3d"].values[1, :, :, :], var3_global.transpose()
-    )
-    np.testing.assert_array_equal(
-        ds["var_3d"].values[2, :, :, :], var3_global.transpose()
-    )
+    ds = xr.open_dataset("diag_manager_single_tile.nc", chunks=None)
+    # assert "var_2d" in ds
+    # np.testing.assert_array_equal(ds["var_2d"].shape, (ntimesteps, nx, ny))
+    # assert ds["var_2d"].dims == ("time", "y", "x")
+    # assert ds["var_2d"].attrs["units"] == "muntin"
+    # assert ds["var_3d"].dims == ("time", "z", "y", "x")
+    # assert ds["var_3d"].attrs["units"] == "muntin"
+    # assert ds["time"].shape == (ntimesteps,)
+    # assert ds["time"].dims == ("time",)
+    # assert ds["time"].values[0] == cftime.DatetimeNoLeap(2, 1, 1, 2, 1, 1)
+    # assert ds["time"].values[1] == cftime.DatetimeNoLeap(2, 1, 1, 3, 1, 1)
+    # assert ds["time"].values[2] == cftime.DatetimeNoLeap(2, 1, 1, 4, 1, 1)
+    # np.testing.assert_array_equal(ds["var_2d"].values[0, :, :], var2_global.transpose())
+    # np.testing.assert_array_equal(ds["var_2d"].values[1, :, :], var2_global.transpose())
+    # np.testing.assert_array_equal(ds["var_2d"].values[2, :, :], var2_global.transpose())
+    # # data is transposed when passed into fortran
+    # np.testing.assert_array_equal(
+    #     ds["var_3d"].values[0, :, :, :], var3_global.transpose()
+    # )
+    # np.testing.assert_array_equal(
+    #     ds["var_3d"].values[1, :, :, :], var3_global.transpose()
+    # )
+    # np.testing.assert_array_equal(
+    #     ds["var_3d"].values[2, :, :, :], var3_global.transpose()
+    # )
 
     pyfms.fms.end()

From 8c5107b8704e2283807d360fe45eb25cbac9eed2 Mon Sep 17 00:00:00 2001
From: Frank Malatino <frank.malatino@noaa.gov>
Date: Thu, 14 May 2026 11:28:37 -0400
Subject: [PATCH 43/45] Again checking decode_times in open_dataset and
 checking xarray version

---
 .github/workflows/unit_tests.yaml       | 4 +++-
 tests/monitor/test_dm_monitor_single.py | 2 +-
 2 files changed, 4 insertions(+), 2 deletions(-)

diff --git a/.github/workflows/unit_tests.yaml b/.github/workflows/unit_tests.yaml
index 46d3ca53..60a25404 100644
--- a/.github/workflows/unit_tests.yaml
+++ b/.github/workflows/unit_tests.yaml
@@ -53,7 +53,9 @@ jobs:
           sudo apt-get install libopenmpi-dev netcdf-bin libnetcdf-dev libnetcdff-dev nco libyaml-dev diffutils
 
       - name: Install Python packages
-        run: pip3 install .[${{matrix.extra}}]
+        run: |
+          pip3 install .[${{matrix.extra}}]
+          pip3 list
 
       - name: Run serial cpu tests
         run: coverage run --rcfile=pyproject.toml -m pytest -m "${{matrix.marker-serial}}" tests
diff --git a/tests/monitor/test_dm_monitor_single.py b/tests/monitor/test_dm_monitor_single.py
index c901e6fc..2631ab39 100644
--- a/tests/monitor/test_dm_monitor_single.py
+++ b/tests/monitor/test_dm_monitor_single.py
@@ -246,7 +246,7 @@ def test_dm_monitor_single_tile() -> None:
     # np.testing.assert_array_equal(var3_ds[2, :, :, :], var3_global.transpose())
 
     assert Path("diag_manager_single_tile.nc").exists()
-    ds = xr.open_dataset("diag_manager_single_tile.nc", chunks=None)
+    ds = xr.open_dataset("diag_manager_single_tile.nc", decode_times=False, chunks=None)
     # assert "var_2d" in ds
     # np.testing.assert_array_equal(ds["var_2d"].shape, (ntimesteps, nx, ny))
     # assert ds["var_2d"].dims == ("time", "y", "x")

From 8a7776081122f1370ecf6efc07286dbe86e2e55f Mon Sep 17 00:00:00 2001
From: Frank Malatino <frank.malatino@noaa.gov>
Date: Thu, 14 May 2026 12:22:05 -0400
Subject: [PATCH 44/45] Reverting changes back to netcdf direct access in
 test_dm_monitor_single

---
 tests/monitor/test_dm_monitor_single.py | 80 ++++++++-----------------
 1 file changed, 26 insertions(+), 54 deletions(-)

diff --git a/tests/monitor/test_dm_monitor_single.py b/tests/monitor/test_dm_monitor_single.py
index 2631ab39..bc9e4a55 100644
--- a/tests/monitor/test_dm_monitor_single.py
+++ b/tests/monitor/test_dm_monitor_single.py
@@ -11,7 +11,6 @@
 import pytest
 import yaml
 from netCDF4 import Dataset, num2date
-import xarray as xr
 
 from ndsl import (
     DiagManagerMonitor,
@@ -217,59 +216,32 @@ def test_dm_monitor_single_tile() -> None:
     # cleanup writes and closes the file
     monitor.cleanup()
 
-    # # check output!
-    # assert Path("diag_manager_single_tile.nc").exists()
-    # ds = Dataset("diag_manager_single_tile.nc")
-    # assert "var_2d" in ds.variables
-    # assert "time" in ds.variables
-    # assert "var_3d" in ds.variables
-    # var2_ds = ds.variables["var_2d"]
-    # time_var = ds.variables["time"]
-    # var3_ds = ds.variables["var_3d"]
-    # np.testing.assert_array_equal(var2_ds.shape, (ntimesteps, nx, ny))
-    # assert var2_ds.dimensions == ("time", "y", "x")
-    # assert var2_ds.units == "muntin"
-    # assert var3_ds.dimensions == ("time", "z", "y", "x")
-    # assert var3_ds.units == "muntin"
-    # assert time_var.shape == (ntimesteps,)
-    # assert time_var.dimensions == ("time",)
-    # dates = num2date(time_var[:], units=time_var.units, calendar=time_var.calendar)
-    # assert dates[0] == cftime.DatetimeNoLeap(2, 1, 1, 2, 1, 1)
-    # assert dates[1] == cftime.DatetimeNoLeap(2, 1, 1, 3, 1, 1)
-    # assert dates[2] == cftime.DatetimeNoLeap(2, 1, 1, 4, 1, 1)
-    # np.testing.assert_array_equal(var2_ds[0, :, :], var2_global.transpose())
-    # np.testing.assert_array_equal(var2_ds[1, :, :], var2_global.transpose())
-    # np.testing.assert_array_equal(var2_ds[2, :, :], var2_global.transpose())
-    # # data is transposed when passed into fortran
-    # np.testing.assert_array_equal(var3_ds[0, :, :, :], var3_global.transpose())
-    # np.testing.assert_array_equal(var3_ds[1, :, :, :], var3_global.transpose())
-    # np.testing.assert_array_equal(var3_ds[2, :, :, :], var3_global.transpose())
-
+    # check output!
     assert Path("diag_manager_single_tile.nc").exists()
-    ds = xr.open_dataset("diag_manager_single_tile.nc", decode_times=False, chunks=None)
-    # assert "var_2d" in ds
-    # np.testing.assert_array_equal(ds["var_2d"].shape, (ntimesteps, nx, ny))
-    # assert ds["var_2d"].dims == ("time", "y", "x")
-    # assert ds["var_2d"].attrs["units"] == "muntin"
-    # assert ds["var_3d"].dims == ("time", "z", "y", "x")
-    # assert ds["var_3d"].attrs["units"] == "muntin"
-    # assert ds["time"].shape == (ntimesteps,)
-    # assert ds["time"].dims == ("time",)
-    # assert ds["time"].values[0] == cftime.DatetimeNoLeap(2, 1, 1, 2, 1, 1)
-    # assert ds["time"].values[1] == cftime.DatetimeNoLeap(2, 1, 1, 3, 1, 1)
-    # assert ds["time"].values[2] == cftime.DatetimeNoLeap(2, 1, 1, 4, 1, 1)
-    # np.testing.assert_array_equal(ds["var_2d"].values[0, :, :], var2_global.transpose())
-    # np.testing.assert_array_equal(ds["var_2d"].values[1, :, :], var2_global.transpose())
-    # np.testing.assert_array_equal(ds["var_2d"].values[2, :, :], var2_global.transpose())
-    # # data is transposed when passed into fortran
-    # np.testing.assert_array_equal(
-    #     ds["var_3d"].values[0, :, :, :], var3_global.transpose()
-    # )
-    # np.testing.assert_array_equal(
-    #     ds["var_3d"].values[1, :, :, :], var3_global.transpose()
-    # )
-    # np.testing.assert_array_equal(
-    #     ds["var_3d"].values[2, :, :, :], var3_global.transpose()
-    # )
+    ds = Dataset("diag_manager_single_tile.nc")
+    assert "var_2d" in ds.variables
+    assert "time" in ds.variables
+    assert "var_3d" in ds.variables
+    var2_ds = ds.variables["var_2d"]
+    time_var = ds.variables["time"]
+    var3_ds = ds.variables["var_3d"]
+    np.testing.assert_array_equal(var2_ds.shape, (ntimesteps, nx, ny))
+    assert var2_ds.dimensions == ("time", "y", "x")
+    assert var2_ds.units == "muntin"
+    assert var3_ds.dimensions == ("time", "z", "y", "x")
+    assert var3_ds.units == "muntin"
+    assert time_var.shape == (ntimesteps,)
+    assert time_var.dimensions == ("time",)
+    dates = num2date(time_var[:], units=time_var.units, calendar=time_var.calendar)
+    assert dates[0] == cftime.DatetimeNoLeap(2, 1, 1, 2, 1, 1)
+    assert dates[1] == cftime.DatetimeNoLeap(2, 1, 1, 3, 1, 1)
+    assert dates[2] == cftime.DatetimeNoLeap(2, 1, 1, 4, 1, 1)
+    np.testing.assert_array_equal(var2_ds[0, :, :], var2_global.transpose())
+    np.testing.assert_array_equal(var2_ds[1, :, :], var2_global.transpose())
+    np.testing.assert_array_equal(var2_ds[2, :, :], var2_global.transpose())
+    # data is transposed when passed into fortran
+    np.testing.assert_array_equal(var3_ds[0, :, :, :], var3_global.transpose())
+    np.testing.assert_array_equal(var3_ds[1, :, :, :], var3_global.transpose())
+    np.testing.assert_array_equal(var3_ds[2, :, :, :], var3_global.transpose())
 
     pyfms.fms.end()

From b6631f8129f289844ac71e3f8b3657e642e48d73 Mon Sep 17 00:00:00 2001
From: Frank Malatino <frank.malatino@noaa.gov>
Date: Wed, 20 May 2026 11:46:25 -0400
Subject: [PATCH 45/45] Removing pip list debug command from unit_tests
 workflow

---
 .github/workflows/unit_tests.yaml | 4 +---
 1 file changed, 1 insertion(+), 3 deletions(-)

diff --git a/.github/workflows/unit_tests.yaml b/.github/workflows/unit_tests.yaml
index 60a25404..46d3ca53 100644
--- a/.github/workflows/unit_tests.yaml
+++ b/.github/workflows/unit_tests.yaml
@@ -53,9 +53,7 @@ jobs:
           sudo apt-get install libopenmpi-dev netcdf-bin libnetcdf-dev libnetcdff-dev nco libyaml-dev diffutils
 
       - name: Install Python packages
-        run: |
-          pip3 install .[${{matrix.extra}}]
-          pip3 list
+        run: pip3 install .[${{matrix.extra}}]
 
       - name: Run serial cpu tests
         run: coverage run --rcfile=pyproject.toml -m pytest -m "${{matrix.marker-serial}}" tests