Fix docs, tests

.github/workflows/ci.yml

@@ -21,34 +21,36 @@ jobs:
     - name: Install dependencies
       run: |
         python -m pip install --upgrade pip wheel
-        pip install -r dev-requirements.txt
-        pip install -e .[R,julia]
+        pip install -e .[dev,julia]
     - name: Setup Apptainer
       uses: eWaterCycle/setup-apptainer@v2
       with:
         apptainer-version: 1.1.9
     - name: Pull Docker image
       run: docker pull ewatercycle/walrus-grpc4bmi:v0.3.1
-    - name: Cache Apptainer image
-      id: cache-apptainer-image
-      uses: actions/cache@v3
-      with:
-        path: ~/.apptainer
-        key: apptainer-image
-    - name: Pull Apptainer image
-      if: steps.cache-apptainer-image.outputs.cache-hit != 'true'
-      run: apptainer pull docker://ewatercycle/walrus-grpc4bmi:v0.3.1
     - uses: r-lib/actions/setup-r@v2
       with:
-        install-r: false
+        install-r: true
     - name: Install R dependencies
       run: |
         Rscript -e "install.packages('remotes')"
         Rscript -e "install.packages('R6')"
+    - name: Install rpy2 (first requires R to be available).
+      run: |
+        pip install -e .[R]
     - name: Install Julia
       uses: julia-actions/setup-julia@v1
       with:
         version: '^1.9'
+    - name: Cache Apptainer image
+      id: cache-apptainer-image
+      uses: actions/cache@v3
+      with:
+        path: ~/.apptainer
+        key: apptainer-image
+    - name: Pull Apptainer image
+      if: steps.cache-apptainer-image.outputs.cache-hit != 'true'
+      run: apptainer pull docker://ewatercycle/walrus-grpc4bmi:v0.3.1
     - name: Test with pytest
       run: |
         pytest -vv --cov=grpc4bmi --cov-report xml

README.md

@@ -180,7 +180,7 @@ python3 -m venv .venv
 . venv/bin/activate
 # Make sure latest pip and wheel are install
 pip install -U pip wheel
-pip install -r dev-requirements.txt
+pip install -e .[dev]
 # For R integration also install the R extras with
 pip install -e .[R]
 # For building docs (cd docs && make html) also install the docs extras with

docs/conf.py

@@ -33,7 +33,7 @@
 extensions = ['sphinx.ext.autodoc', 'sphinx.ext.viewcode',
               'sphinx.ext.napoleon', 'sphinx.ext.intersphinx',
               'sphinx.ext.autosectionlabel',
-              'sphinxarg.ext', 'sphinxcontrib.apidoc',
+              'sphinxarg.ext', 'sphinx.ext.apidoc',
               'sphinx_copybutton', 'sphinxcontrib.jquery',
               ]
 
@@ -175,7 +175,7 @@
 ]
 
 intersphinx_mapping = {
-    'https://docs.python.org/': None,
+    'python': ('https://docs.python.org/', None),
     'numpy': ('http://docs.scipy.org/doc/numpy', None),
     "bmipy": ("https://bmi.readthedocs.io/en/latest/", None),
 }

pyproject.toml

@@ -48,6 +48,7 @@ dev = [
     "nbconvert",
     "ipykernel",
     "nbformat",
+    "bmi-heat@git+https://github.com/csdms/bmi-example-python",
 ]
 docs = [
     "sphinx",

test/test_apptainer.py

@@ -29,7 +29,7 @@ def test_too_old(self, test_input: str, error_class: Type[ApptainerVersionExcept
         with pytest.raises(error_class, match=expected):
             check_apptainer_version_string(test_input)
 
-IMAGE_NAME = "docker://ewatercycle/walrus-grpc4bmi:v0.2.0"
+IMAGE_NAME = "docker://ewatercycle/walrus-grpc4bmi:v0.3.1"
 
 @pytest.fixture
 def walrus_model(tmp_path, walrus_input):

test/test_client.py

@@ -110,7 +110,10 @@ def test_initialize_with_nonstring():
     assert client is not None
     with pytest.raises(TypeError, match='bad argument type for built-in operation'):
         client.initialize(42)
-    client.finalize()
+    try:  # Can't finalize model which is not initialized.
+        client.finalize()
+    except MyRpcError as err:
+        assert "has no attribute '_model'" in str(err)
     del client
 
 
@@ -132,7 +135,7 @@ def test_update_until():
 
 
 def test_get_time_unit():
-    client, local = make_bmi_classes()
+    client, local = make_bmi_classes(True)
     assert client.get_time_units() == local.get_time_units()
     client.finalize()
     del client
@@ -819,18 +822,18 @@ class TestCreateGrpcChannel:
     def test_defaults(self):
         with BmiClient.create_grpc_channel() as channel:
             target = channel._channel.target()
-            assert target == b'localhost:50051'
+            assert target == b'dns:///localhost:50051'
 
     def test_custom(self):
         with BmiClient.create_grpc_channel(51234, 'somehost') as channel:
             target = channel._channel.target()
-            assert target == b'somehost:51234'
+            assert target == b'dns:///somehost:51234'
 
     def test_same_port_twice(self):
         port = 51235
         with BmiClient.create_grpc_channel(port) as channel1, BmiClient.create_grpc_channel(port) as channel2:
-            assert channel1._channel.target() == b'localhost:51235'
-            assert channel2._channel.target() == b'localhost:51235'
+            assert channel1._channel.target() == b'dns:///localhost:51235'
+            assert channel2._channel.target() == b'dns:///localhost:51235'
 
 class TestModelWithItemSizeZeroAndVarTypeFloat32:
     name = 'plate_surface__temperature'

test/test_julia.py

@@ -55,7 +55,7 @@ def model(self, cfg_file):
             ("get_input_var_names", tuple(), ["plate_surface__temperature"]),
             ("get_output_var_names", tuple(), ["plate_surface__temperature"]),
             ("get_start_time", tuple(), 0.0),
-            ("get_end_time", tuple(), np.Inf),
+            ("get_end_time", tuple(), np.inf),
             ("get_time_step", tuple(), 0.25),
             ("get_time_units", tuple(), "s"),
             ("get_var_type", ["plate_surface__temperature"], "float64"),

test/test_legacy_server.py

@@ -86,7 +86,7 @@ def test_update():
 
 
 def test_get_time_unit():
-    server, local = make_bmi_classes()
+    server, local = make_bmi_classes(True)
     assert server.getTimeUnits(None, None).units == make_string(local.get_time_units())
     server.finalize(None, None)
     del server

test/test_memoized.py

@@ -83,9 +83,11 @@ def test_nonmemoized_methods(mut_name, mut_args):
         mot = getattr(client, mut_name)
 
         mot(*mut_args)
-        mot(*mut_args)
-
-        assert mock_method.call_count == 2
+        if mut_name != "finalize":
+            mot(*mut_args)
+            assert mock_method.call_count == 2
+        else:
+            assert mock_method.call_count == 1
 
 
 def test_initialize_clears_cache():

test/test_optionaldest.py

@@ -50,7 +50,7 @@ def test_methods_with_optional_dest(orig_model, method_name, method_args, expect
     [
         (BmiHeat(), 'update', tuple()),
         (BmiHeat(), 'update_until', [2]),
-        (BmiHeat(), 'finalize', tuple()),
+        # (BmiHeat(), 'finalize', tuple()),  # Can't test finalize: double finalize not allowed.
         (BmiHeat(), 'get_current_time', tuple()),
         (BmiHeat(), 'get_component_name', tuple()),
         (BmiHeat(), 'get_input_item_count', tuple()),

test/test_server.py

@@ -111,7 +111,7 @@ def test_update():
 
 
 def test_get_time_unit():
-    server, local = make_bmi_classes()
+    server, local = make_bmi_classes(True)
     assert server.getTimeUnits(None, None).units == make_string(local.get_time_units())
     server.finalize(None, None)
     del server

test/test_subproc.py

@@ -65,7 +65,7 @@ def test_update():
 
 
 def test_get_time_unit():
-    client, local = make_bmi_classes()
+    client, local = make_bmi_classes(True)
     assert client.get_time_units() == local.get_time_units()
     client.finalize()
     del client