Test fixes

README.md

@@ -13,9 +13,8 @@ simulations by automating commonly performed tasks.
 
 See [documentation](https://e3sm-project.github.io/zppy) for more details.
 
-- Run `python -m unittest discover -s tests -p "test_*.py"` to run all tests.
-- Run `python -m unittest tests/test_*.py` to run only unit tests.
-- Run `python -m unittest tests/integration/test_*.py` to run only integration tests (on server).
+- Run `pytest tests/test_*.py` to run only unit tests.
+- Run `pytest tests/integration/test_*.py` to run only integration tests (on server).
 
 ## License
 

docs/source/dev_guide/new_glb_plot.rst

@@ -10,4 +10,4 @@ Note that unlike E3SM Diags and MPAS-Analysis which are packages called by ``zpp
 - In `coupled_global.py <https://github.com/E3SM-Project/zppy/blob/main/zppy/templates/coupled_global.py>`_: Add variables under "# Variables to extract". Add the code for your new plot under "Plotting functions"; the name of your function should start with ``plot_``. In ``PLOT_DICT``, add ``"function name without plot_" : function name``.
 - If this plot should be added to the defaults, then complete this step: for ``plot_names`` under ``[global_time_series]`` in `default.ini <https://github.com/E3SM-Project/zppy/blob/main/zppy/templates/default.ini>`_, add the function name without plot to the string.
 - Optionally, after making your edits, you can run ``pre-commit run --all-files`` to clean up your code and check for any obvious errors.
-- Run the `integration tests <https://e3sm-project.github.io/zppy/_build/html/main/dev_guide/testing.html#integration-tests>`_ and examine the differences from the expected files. If they match what you expect, update the expected files following "Commands to run to replace outdated expected files" on the machine-specific directions. (The commands to run all the integration tests are ``pip install .`` followed by ``python -u -m unittest tests/integration/test_*.py``).
+- Run the `integration tests <https://e3sm-project.github.io/zppy/_build/html/main/dev_guide/testing.html#integration-tests>`_ and examine the differences from the expected files. If they match what you expect, update the expected files following "Commands to run to replace outdated expected files" on the machine-specific directions. (The commands to run all the integration tests are ``pip install .`` followed by ``pytest tests/integration/test_*.py``).

docs/source/dev_guide/release_testing.rst

@@ -83,7 +83,7 @@ Testing directions for making a release
         * Compy: ``source /share/apps/E3SM/conda_envs/load_latest_e3sm_unified_compy.sh``
         * Perlmutter: ``source /global/common/software/e3sm/anaconda_envs/load_latest_e3sm_unified_pm-cpu.sh``
 
-7. Run the unit tests with ``python -u -m unittest tests/test_*.py``.
+7. Run the unit tests with ``pytest tests/test_*.py``.
 
     a. test dev (run before making a new zppy RC):
 
@@ -107,7 +107,7 @@ Testing directions for making a release
     * `Compy <https://github.com/E3SM-Project/zppy/blob/main/tests/integration/generated/directions_compy.md>`_
     * `Perlmutter <https://github.com/E3SM-Project/zppy/blob/main/tests/integration/generated/directions_pm-cpu.md>`_
 
-9. Run the integration tests with ``python -u -m unittest tests/integration/test_*.py``. Note that ``test_complete_run.py`` takes approximately 75 minutes to run on Compy.
+9. Run the integration tests with ``pytest tests/integration/test_*.py``. Note that ``test_complete_run.py`` takes approximately 75 minutes to run on Compy.
 
     a. test dev (run before making a new zppy RC):
 

docs/source/dev_guide/testing.rst

@@ -10,7 +10,7 @@ Run all unit tests by doing the following:
     .. code::
 
         pip install . # Install your changes (`python -m pip install .` also works)
-        python -u -m unittest tests/test_*.py # Run all unit tests
+        pytest tests/test_*.py # Run all unit tests
 
 Integration tests
 =================
@@ -24,7 +24,7 @@ Run all integration tests by doing the following:
 
         pip install . # Install your changes (`python -m pip install .` also works)
 
-        python -u -m unittest tests/integration/test_*.py # Run all integration tests
+        pytest tests/integration/test_*.py # Run all integration tests
 
 Automated tests
 ===============

docs/source/dev_guide/tutorial_testing_e3sm_unified.rst

@@ -368,5 +368,5 @@ Run the unit tests and integration tests on Chrysalis:
     git fetch upstream
     git rebase upstream/main
     <ENVIRONMENT_COMMANDS> # Load the appropriate environment
-    python -u -m unittest tests/test_*.py # Run unit tests
-    python -u -m unittest tests/integration/test_*.py # Run integration tests
+    pytest tests/test_*.py # Run unit tests
+    pytest tests/integration/test_*.py # Run integration tests

tests/integration/generated/directions_chrysalis.md

@@ -38,7 +38,7 @@ Changing `UNIQUE_ID` allows you to simultaneously run jobs
 launched from `zppy` on different branches,
 without worrying about overwriting results.
 
-NOTE: Actually running the tests (e.g., `python -u -m unittest tests/integration/test_*.py`)
+NOTE: Actually running the tests (e.g., `pytest tests/integration/test_*.py`)
 can not be done from two different branches simultaneously
 (since files in the `zppy` directory rather than an external directory get changed).
 

tests/integration/generated/test_min_case_global_time_series_comprehensive_v3_setup_only_chrysalis.cfg

@@ -0,0 +1,64 @@
+[default]
+case = "v3.LR.historical_0051"
+constraint = ""
+dry_run = "False"
+environment_commands = ""
+fail_on_dependency_skip = True
+guess_path_parameters = False
+guess_section_parameters = False
+input = /lcrc/group/e3sm2/ac.wlin/E3SMv3/v3.LR.historical_0051
+input_subdir = archive/atm/hist
+mapping_file = "map_ne30pg2_to_cmip6_180x360_aave.20200201.nc"
+output = "/lcrc/group/e3sm/ac.forsyth2/zppy_min_case_global_time_series_comprehensive_v3_setup_only_output/unique_id/v3.LR.historical_0051"
+partition = "debug"
+qos = "regular"
+www = "/lcrc/group/e3sm/public_html/diagnostic_output/ac.forsyth2/zppy_min_case_global_time_series_comprehensive_v3_setup_only_www/unique_id"
+years = "1985:1989:2",
+
+[ts]
+active = True
+e3sm_to_cmip_environment_commands = ""
+walltime = "00:30:00"
+
+  [[ atm_monthly_glb ]]
+  # Note global average won't work for 3D variables.
+  frequency = "monthly"
+  input_files = "eam.h0"
+  input_subdir = "archive/atm/hist"
+  mapping_file = "glb"
+  years = "1985:1995:5",
+
+  [[ lnd_monthly_glb ]]
+  frequency = "monthly"
+  input_files = "elm.h0"
+  input_subdir = "archive/lnd/hist"
+  mapping_file = "glb"
+  vars = "FSH,RH2M,LAISHA,LAISUN,QINTR,QOVER,QRUNOFF,QSOIL,QVEGE,QVEGT,SOILWATER_10CM,TSA,H2OSNO,TOTLITC,CWDC,SOIL1C,SOIL2C,SOIL3C,SOIL4C,WOOD_HARVESTC,TOTVEGC,NBP,GPP,AR,HR"
+  years = "1985:1995:5",
+
+[mpas_analysis]
+active = True
+anomalyRefYear = 1985
+climo_years = "1985-1989", "1990-1995",
+enso_years = "1985-1989", "1990-1995",
+mesh = "IcoswISC30E3r5"
+parallelTaskCount = 6
+partition = "compute"
+qos = "regular"
+shortTermArchive = True
+ts_years = "1985-1989", "1985-1995",
+walltime = "00:30:00"
+
+# (This cfg is the setup portion only)
+# [global_time_series]
+# active = True
+# climo_years = "1985-1989", "1990-1995",
+# environment_commands = "source <INSERT PATH TO CONDA>/conda.sh; conda activate <INSERT ENV NAME>"
+# experiment_name = "v3.LR.historical_0051"
+# figstr = "v3.LR.historical_0051"
+# moc_file=mocTimeSeries_1985-1995.nc
+# plots_lnd = "FSH,RH2M,LAISHA,LAISUN,QINTR,QOVER,QRUNOFF,QSOIL,QVEGE,QVEGT,SOILWATER_10CM,TSA,H2OSNO,TOTLITC,CWDC,SOIL1C,SOIL2C,SOIL3C,SOIL4C,WOOD_HARVESTC,TOTVEGC,NBP,GPP,AR,HR"
+# ts_num_years = 5
+# ts_years = "1985-1989", "1985-1995",
+# walltime = "00:30:00"
+# years = "1985-1995",

tests/integration/generated/update_bash_generation_expected_files_chrysalis.sh

@@ -7,4 +7,4 @@ rm -rf /lcrc/group/e3sm/public_html/zppy_test_resources/expected_bash_files
 # You can just move (i.e., not copy) the output since re-running this test will re-generate the output.
 mv test_bash_generation_output/post/scripts /lcrc/group/e3sm/public_html/zppy_test_resources/expected_bash_files
 # Rerun test
-python -u -m unittest tests/integration/test_bash_generation.py
+pytest tests/integration/test_bash_generation.py

tests/integration/generated/update_campaign_expected_files_chrysalis.sh

@@ -13,4 +13,4 @@ do
 done
 
 # Rerun test
-python -m unittest tests/integration/test_campaign.py
+pytest tests/integration/test_campaign.py

tests/integration/generated/update_defaults_expected_files_chrysalis.sh

@@ -8,4 +8,4 @@ mkdir -p /lcrc/group/e3sm/public_html/zppy_test_resources/test_defaults_expected
 # You can just move (i.e., not copy) the output since re-running this test will re-generate the output.
 mv test_defaults_output/post/scripts/*.settings /lcrc/group/e3sm/public_html/zppy_test_resources/test_defaults_expected_files
 # Rerun test
-python -u -m unittest tests/integration/test_defaults.py
+pytest tests/integration/test_defaults.py

tests/integration/generated/update_weekly_expected_files_chrysalis.sh

@@ -27,4 +27,4 @@ do
 done
 
 # Rerun test
-python -u -m unittest tests/integration/test_weekly.py
+pytest tests/integration/test_weekly.py

tests/integration/template_directions.md

@@ -38,7 +38,7 @@ Changing `UNIQUE_ID` allows you to simultaneously run jobs
 launched from `zppy` on different branches,
 without worrying about overwriting results.
 
-NOTE: Actually running the tests (e.g., `python -u -m unittest tests/integration/test_*.py`)
+NOTE: Actually running the tests (e.g., `pytest tests/integration/test_*.py`)
 can not be done from two different branches simultaneously
 (since files in the `zppy` directory rather than an external directory get changed).
 

tests/integration/template_min_case_global_time_series_comprehensive_v3_setup_only.cfg

@@ -0,0 +1,64 @@
+[default]
+case = "#expand case_name#"
+constraint = "#expand constraint#"
+dry_run = "#expand dry_run#"
+environment_commands = "#expand environment_commands#"
+fail_on_dependency_skip = True
+guess_path_parameters = False
+guess_section_parameters = False
+input = /lcrc/group/e3sm2/ac.wlin/E3SMv3/#expand case_name#
+input_subdir = archive/atm/hist
+mapping_file = "map_ne30pg2_to_cmip6_180x360_aave.20200201.nc"
+output = "#expand user_output#zppy_min_case_global_time_series_comprehensive_v3_setup_only_output/#expand unique_id#/#expand case_name#"
+partition = "#expand partition_short#"
+qos = "#expand qos_short#"
+www = "#expand user_www#zppy_min_case_global_time_series_comprehensive_v3_setup_only_www/#expand unique_id#"
+years = "1985:1989:2",
+
+[ts]
+active = True
+e3sm_to_cmip_environment_commands = "#expand e3sm_to_cmip_environment_commands#"
+walltime = "00:30:00"
+
+  [[ atm_monthly_glb ]]
+  # Note global average won't work for 3D variables.
+  frequency = "monthly"
+  input_files = "eam.h0"
+  input_subdir = "archive/atm/hist"
+  mapping_file = "glb"
+  years = "1985:1995:5",
+
+  [[ lnd_monthly_glb ]]
+  frequency = "monthly"
+  input_files = "elm.h0"
+  input_subdir = "archive/lnd/hist"
+  mapping_file = "glb"
+  vars = "FSH,RH2M,LAISHA,LAISUN,QINTR,QOVER,QRUNOFF,QSOIL,QVEGE,QVEGT,SOILWATER_10CM,TSA,H2OSNO,TOTLITC,CWDC,SOIL1C,SOIL2C,SOIL3C,SOIL4C,WOOD_HARVESTC,TOTVEGC,NBP,GPP,AR,HR"
+  years = "1985:1995:5",
+
+[mpas_analysis]
+active = True
+anomalyRefYear = 1985
+climo_years = "1985-1989", "1990-1995",
+enso_years = "1985-1989", "1990-1995",
+mesh = "IcoswISC30E3r5"
+parallelTaskCount = 6
+partition = "#expand partition_long#"
+qos = "#expand qos_long#"
+shortTermArchive = True
+ts_years = "1985-1989", "1985-1995",
+walltime = "#expand mpas_analysis_walltime#"
+
+# (This cfg is the setup portion only)
+# [global_time_series]
+# active = True
+# climo_years = "1985-1989", "1990-1995",
+# environment_commands = "#expand global_time_series_environment_commands#"
+# experiment_name = "#expand case_name#"
+# figstr = "#expand case_name#"
+# moc_file=mocTimeSeries_1985-1995.nc
+# plots_lnd = "FSH,RH2M,LAISHA,LAISUN,QINTR,QOVER,QRUNOFF,QSOIL,QVEGE,QVEGT,SOILWATER_10CM,TSA,H2OSNO,TOTLITC,CWDC,SOIL1C,SOIL2C,SOIL3C,SOIL4C,WOOD_HARVESTC,TOTVEGC,NBP,GPP,AR,HR"
+# ts_num_years = 5
+# ts_years = "1985-1989", "1985-1995",
+# walltime = "00:30:00"
+# years = "1985-1995",

tests/integration/template_update_bash_generation_expected_files.sh

@@ -7,4 +7,4 @@ rm -rf #expand expected_dir#expected_bash_files
 # You can just move (i.e., not copy) the output since re-running this test will re-generate the output.
 mv test_bash_generation_output/post/scripts #expand expected_dir#expected_bash_files
 # Rerun test
-python -u -m unittest tests/integration/test_bash_generation.py
+pytest tests/integration/test_bash_generation.py

tests/integration/template_update_campaign_expected_files.sh

@@ -13,4 +13,4 @@ do
 done
 
 # Rerun test
-python -m unittest tests/integration/test_campaign.py
+pytest tests/integration/test_campaign.py

tests/integration/template_update_defaults_expected_files.sh

@@ -8,4 +8,4 @@ mkdir -p #expand expected_dir#test_defaults_expected_files
 # You can just move (i.e., not copy) the output since re-running this test will re-generate the output.
 mv test_defaults_output/post/scripts/*.settings #expand expected_dir#test_defaults_expected_files
 # Rerun test
-python -u -m unittest tests/integration/test_defaults.py
+pytest tests/integration/test_defaults.py

tests/integration/template_update_weekly_expected_files.sh

@@ -27,4 +27,4 @@ do
 done
 
 # Rerun test
-python -u -m unittest tests/integration/test_weekly.py
+pytest tests/integration/test_weekly.py

tests/integration/test_bash_generation.py

@@ -1,25 +1,16 @@
 import os
-import unittest
 
 from tests.integration.utils import get_expansions
 
 
-class TestBashGeneration(unittest.TestCase):
-    def test_bash_generation(self):
-        # cfg is not machine-specific
-        self.assertEqual(
-            os.system("zppy -c tests/integration/test_bash_generation.cfg"), 0
+def test_bash_generation():
+    # cfg is not machine-specific
+    assert os.system("zppy -c tests/integration/test_bash_generation.cfg") == 0
+    expected_dir = get_expansions()["expected_dir"]
+    assert (
+        os.system(
+            f"diff -bur -I 'templateDir' test_bash_generation_output/post/scripts {expected_dir}expected_bash_files"
         )
-        expected_dir = get_expansions()["expected_dir"]
-        self.assertEqual(
-            os.system(
-                f"diff -bur -I 'templateDir' test_bash_generation_output/post/scripts {expected_dir}expected_bash_files"
-            ),
-            0,
-        )
-        self.assertEqual(os.system("rm -r test_bash_generation_output"), 0)
-
-
-if __name__ == "__main__":
-    # Run from top level of repo
-    unittest.main()
+        == 0
+    )
+    assert os.system("rm -r test_bash_generation_output") == 0