Merge pull request #139 from eWaterCycle/drop-typeguard-apptainer-ver…

…sion

Drop typeguard + backport apptainer version

.github/workflows/ci.yml

@@ -64,7 +64,7 @@ jobs:
       - name: Install grpc
         uses: ewatercycle/setup-grpc@v4
         with:
-          grpc-version: 1.27.2
+          grpc-version: 1.47.3
       - name: Copy grpc to system default
         run: |
           sudo rsync -a $GRPC_ROOT/ /usr/local

grpc4bmi/bmi_client_apptainer.py

@@ -8,7 +8,6 @@
 
 from packaging.specifiers import SpecifierSet
 from packaging.version import Version
-from typeguard import check_argument_types, qualified_name
 
 from grpc4bmi.bmi_grpc_client import BmiClient
 from grpc4bmi.exceptions import ApptainerVersionException, DeadContainerException
@@ -17,7 +16,7 @@
 
 def check_apptainer_version_string(version_output: str) -> bool:
     version = version_output.split(' ').pop()
-    local_version = Version(version)
+    local_version = Version(version.replace('.el', ''))
     if local_version not in SpecifierSet(SUPPORTED_APPTAINER_VERSIONS):
         raise ApptainerVersionException(f'Unsupported version ({version_output}) of apptainer found, '
                                         f'supported versions {SUPPORTED_APPTAINER_VERSIONS}')
@@ -197,11 +196,6 @@ class BmiClientApptainer(BmiClient):
     def __init__(self, image: str, work_dir: str, input_dirs: Iterable[str] = tuple(), delay=0, timeout=None,
                  capture_logs=True,
                  ):
-        assert check_argument_types()
-        if type(input_dirs) == str:
-            msg = f'type of argument "input_dirs" must be collections.abc.Iterable; ' \
-                  f'got {qualified_name(input_dirs)} instead'
-            raise TypeError(msg)
         check_apptainer_version()
         host = 'localhost'
         port = BmiClient.get_unique_port(host)

grpc4bmi/bmi_client_docker.py

@@ -4,7 +4,6 @@
 from typing import Iterable
 
 import docker
-from typeguard import check_argument_types, qualified_name
 
 from grpc4bmi.bmi_grpc_client import BmiClient
 from grpc4bmi.exceptions import DeadContainerException
@@ -50,11 +49,6 @@ def __init__(self, image: str, work_dir: str, image_port=50051, host=None,
                  input_dirs: Iterable[str] = tuple(),
                  user=os.getuid(), remove=False, delay=5,
                  timeout=None):
-        assert check_argument_types()
-        if type(input_dirs) == str:
-            msg = f'type of argument "input_dirs" must be collections.abc.Iterable; ' \
-                  f'got {qualified_name(input_dirs)} instead'
-            raise TypeError(msg)
         port = BmiClient.get_unique_port()
         client = docker.from_env()
         volumes = {}

grpc4bmi/bmi_client_singularity.py

@@ -8,7 +8,6 @@
 
 from packaging.specifiers import SpecifierSet
 from packaging.version import Version
-from typeguard import check_argument_types, qualified_name
 
 from grpc4bmi.bmi_grpc_client import BmiClient
 from grpc4bmi.exceptions import ApptainerVersionException, DeadContainerException, SingularityVersionException
@@ -18,7 +17,7 @@
 
 def check_singularity_version_string(version_output: str) -> bool:
     (app, _, version) = version_output.split(' ')
-    local_version = Version(version)
+    local_version = Version(version.replace('.el', ''))
     if app == 'singularity' and local_version not in SpecifierSet(SUPPORTED_SINGULARITY_VERSIONS):
         raise SingularityVersionException(f'Unsupported version ({version_output}) of singularity found, '
                                           f'supported versions {SUPPORTED_SINGULARITY_VERSIONS}')
@@ -200,11 +199,6 @@ class BmiClientSingularity(BmiClient):
     def __init__(self, image: str, work_dir: str, input_dirs: Iterable[str] = tuple(), delay=0, timeout=None,
                  capture_logs=True,
                  ):
-        assert check_argument_types()
-        if type(input_dirs) == str:
-            msg = f'type of argument "input_dirs" must be collections.abc.Iterable; ' \
-                  f'got {qualified_name(input_dirs)} instead'
-            raise TypeError(msg)
         check_singularity_version()
         host = 'localhost'
         port = BmiClient.get_unique_port(host)

grpc4bmi/bmi_grpc_client.py

@@ -8,7 +8,6 @@
 import basic_modeling_interface.bmi as bmi
 import grpc
 import numpy
-from typeguard import check_argument_types
 
 from . import bmi_pb2, bmi_pb2_grpc
 from .constants import GRPC_MAX_MESSAGE_LENGTH
@@ -57,7 +56,6 @@ def get_unique_port(host=None):
             return int(s.getsockname()[1])
 
     def initialize(self, filename: Optional[str]):
-        assert check_argument_types()
         fname = "" if filename is None else filename
         self.stub.initialize(bmi_pb2.InitializeRequest(config_file=fname))
 

setup.py

@@ -11,7 +11,7 @@ def read(fname):
 
 
 setup(name="grpc4bmi",
-      version="0.2.16",
+      version="0.2.17",
       author="Gijs van den Oord",
       author_email="[email protected]",
       description="Run your BMI implementation in a separate process and expose it as BMI-python with GRPC",
@@ -33,7 +33,6 @@ def read(fname):
           "docker",
           "basic-modeling-interface",
           "packaging",
-          "typeguard",
       ],
       extras_require={
           'R': ['rpy2'],

test/test_apptainer.py

@@ -13,6 +13,8 @@ class Test_check_apptainer_version_string:
         ('apptainer version 1.0.3'),
         ('apptainer version 1.1.0-rc.3'),
         ('apptainer version 1.1.2'),
+        # From snellius cluster at SURF.
+        ('apptainer version 1.1.5-2.el8'),
     ])
     def test_ok(self, test_input: str):
         result = check_apptainer_version_string(test_input)
@@ -63,19 +65,6 @@ def test_same_inputdir_and_workdir(self, tmp_path):
         with pytest.raises(ValueError, match=match):
             BmiClientApptainer(image=IMAGE_NAME, input_dirs=(some_dir,), work_dir=some_dir)
 
-    def test_workdir_as_number(self):
-        with pytest.raises(TypeError, match='must be str'):
-            BmiClientApptainer(image=IMAGE_NAME, work_dir=42)
-
-    def test_inputdirs_as_str(self, tmp_path):
-        some_dir = str(tmp_path)
-        with pytest.raises(TypeError, match='must be collections.abc.Iterable; got str instead'):
-            BmiClientApptainer(image=IMAGE_NAME, input_dirs='old type', work_dir=some_dir)
-
-    def test_inputdirs_as_number(self, tmp_path):
-        some_dir = str(tmp_path)
-        with pytest.raises(TypeError, match='must be collections.abc.Iterable; got int instead'):
-            BmiClientApptainer(image=IMAGE_NAME, input_dirs=42, work_dir=some_dir)
 
 
 

test/test_client.py

@@ -68,15 +68,6 @@ def test_initialize():
     del client
 
 
-def test_initialize_with_nonstring():
-    client, local = make_bmi_classes(False)
-    assert client is not None
-    with pytest.raises(TypeError, match='got int instead'):
-        client.initialize(42)
-    client.finalize()
-    del client
-
-
 def test_update():
     client, local = make_bmi_classes(True)
     client.update()

test/test_docker.py

@@ -93,20 +93,6 @@ def test_same_inputdir_and_workdir(self, tmp_path):
         with pytest.raises(ValueError, match=match):
             BmiClientDocker(image=walrus_docker_image, image_port=55555, input_dirs=(some_dir,), work_dir=some_dir)
 
-    def test_workdir_as_number(self):
-        with pytest.raises(TypeError, match='must be str'):
-            BmiClientDocker(image=walrus_docker_image, work_dir=42)
-
-    def test_inputdirs_as_str(self, tmp_path):
-        some_dir = str(tmp_path)
-        with pytest.raises(TypeError, match='must be collections.abc.Iterable; got str instead'):
-            BmiClientDocker(image=walrus_docker_image, input_dirs='old type', work_dir=some_dir)
-
-    def test_inputdirs_as_number(self, tmp_path):
-        some_dir = str(tmp_path)
-        with pytest.raises(TypeError, match='must be collections.abc.Iterable; got int instead'):
-            BmiClientDocker(image=walrus_docker_image, input_dirs=42, work_dir=some_dir)
-
     def test_logs(self, walrus_model, capfd):
         logs = walrus_model.logs()
 

test/test_singularity.py

@@ -163,20 +163,6 @@ def test_with_config_inside_image(self, walrus_model_with_config_inside_image):
         # After initialization and update the forcings have been read from the scratch dir
         assert len(model.get_value('Q')) == 1
 
-    def test_workdir_as_number(self):
-        with pytest.raises(TypeError, match='must be str'):
-            BmiClientSingularity(image=IMAGE_NAME, work_dir=42)
-
-    def test_inputdirs_as_str(self, tmp_path):
-        some_dir = str(tmp_path)
-        with pytest.raises(TypeError, match='must be collections.abc.Iterable; got str instead'):
-            BmiClientSingularity(image=IMAGE_NAME, input_dirs='old type', work_dir=some_dir)
-
-    def test_inputdirs_as_number(self, tmp_path):
-        some_dir = str(tmp_path)
-        with pytest.raises(TypeError, match='must be collections.abc.Iterable; got int instead'):
-            BmiClientSingularity(image=IMAGE_NAME, input_dirs=42, work_dir=some_dir)
-
 
 class TestRedirectOutput:
     EXPECTED = 'Hello from Docker!'
@@ -230,6 +216,8 @@ class Test_check_singularity_version_string:
         ('apptainer version 1.0.3'),
         ('apptainer version 1.1.0-rc.3'),
         ('apptainer version 1.1.2'),
+        # From snellius cluster at SURF.
+        ('apptainer version 1.1.5-2.el8'),
     ])
     def test_ok(self, test_input: str):
         result = check_singularity_version_string(test_input)