fixes in context and tests

Author: denisri

capsul/config/test/test_config.py

@@ -33,6 +33,7 @@ def test_single_configuration(self):
         user_file = osp.join(self.tmp_dir, "user_conf.json")
         conf_dict = {
             "builtin": {
+                "config_modules": ["spm", "matlab"],
                 "database": "builtin",
                 "persistent": True,
                 "start_workers": default_engine_start_workers,
@@ -57,6 +58,7 @@ def test_single_configuration(self):
             json.dump(conf_dict, f)
         app_config = ApplicationConfiguration("single_conf", user_file=user_file)
         self.maxDiff = 2500
+
         self.assertEqual(
             app_config.asdict(),
             {
@@ -80,6 +82,7 @@ def test_single_configuration(self):
     def test_config_as_dict(self):
         conf_dict = {
             "builtin": {
+                "config_modules": ["spm", "matlab"],
                 "database": "builtin",
                 "persistent": True,
                 "start_workers": default_engine_start_workers,
@@ -157,6 +160,7 @@ def test_config_merge(self):
         }
         merged_conf_dict = {
             "builtin": {
+                "config_modules": ["spm", "matlab"],
                 "database": "builtin",
                 "persistent": True,
                 "start_workers": default_engine_start_workers,

capsul/execution_context.py

@@ -21,17 +21,17 @@
 
 
 class ExecutionContext(Controller):
-    python_modules: list[str]
-    config_modules: list[str]
+    python_modules: list[str] = field(type=list[str], default_factory=list)
+    config_modules: list[str] = field(type=list[str], default_factory=list)
     dataset: OpenKeyDictController[Dataset]
 
     def __init__(self, config=None, executable=None, activate_modules=True):
         super().__init__()
         if config:
-            python_modules = config.get("python_modules", ())
+            python_modules = config.get("python_modules", [])
             for m in python_modules:
                 importlib.import_module(m)
-            config_modules = config.get("config_modules", ())
+            config_modules = config.get("config_modules", [])
             self.config_modules = config_modules
             for m in config_modules:
                 # The following function loads the appropriate module

capsul/in_context/afni.py

@@ -32,7 +32,7 @@ def set_env_from_config(execution_context):
     Set environment variables FSLDIR, FSL_CONFIG, FSL_PREFIX according to the
     execution context configuration.
     """
-    afni_mod = getattr(execution_context, "afni")
+    afni_mod = getattr(execution_context, "afni", None)
     if afni_mod:
         if afni_mod.directory is not undefined:
             os.environ["AFNIPATH"] = afni_mod.directory

capsul/in_context/ants.py

@@ -32,7 +32,7 @@ def set_env_from_config(execution_context):
     Set environment variables FSLDIR, FSL_CONFIG, FSL_PREFIX according to the
     execution context configuration.
     """
-    ants_mod = getattr(execution_context, "ants")
+    ants_mod = getattr(execution_context, "ants", None)
     if ants_mod:
         if ants_mod.directory is not undefined:
             os.environ["ANTSPATH"] = ants_mod.directory

capsul/in_context/freesurfer.py

@@ -30,7 +30,7 @@ def set_env_from_config(execution_context):
     Set environment variables FSLDIR, FSL_CONFIG, FSL_PREFIX according to the
     execution context configuration.
     """
-    fs_mod = getattr(execution_context, "freesurfer")
+    fs_mod = getattr(execution_context, "freesurfer", None)
     if fs_mod:
         if fs_mod.setup_script is not undefined:
             os.environ["FREESURFER_HOME"] = osp.dirname(fs_mod.setup_script)

capsul/in_context/fsl.py

@@ -51,7 +51,7 @@ def set_env_from_config(execution_context):
     Set environment variables FSLDIR, FSL_CONFIG, FSL_PREFIX according to the
     execution context configuration.
     """
-    fsl_mod = getattr(execution_context, "fsl")
+    fsl_mod = getattr(execution_context, "fsl", None)
     if fsl_mod:
         if fsl_mod.directory is not undefined:
             os.environ["FSLDIR"] = fsl_mod.directory

capsul/in_context/matlab.py

@@ -14,7 +14,7 @@ def set_env_from_config(execution_context):
     Set environment variables according to the
     execution context configuration.
     """
-    matlab_mod = getattr(execution_context, "matlab")
+    matlab_mod = getattr(execution_context, "matlab", None)
     if matlab_mod:
         if matlab_mod.executable is not undefined:
             os.environ["MATLAB_EXECUTABLE"] = matlab_mod.executable

capsul/in_context/mrtrix.py

@@ -19,7 +19,7 @@ def set_env_from_config(execution_context):
     Set environment variables according to the
     execution context configuration.
     """
-    mrtrix_mod = getattr(execution_context, "mrtrix")
+    mrtrix_mod = getattr(execution_context, "mrtrix", None)
     if mrtrix_mod:
         if mrtrix_mod.directory is not undefined:
             os.environ["MRTRIXPATH"] = mrtrix_mod.directory

capsul/in_context/spm.py

@@ -16,7 +16,7 @@ def set_env_from_config(execution_context):
     Set environment variables according to the
     execution context configuration.
     """
-    spm_mod = getattr(execution_context, "spm")
+    spm_mod = getattr(execution_context, "spm", None)
     if spm_mod:
         if spm_mod.directory is not undefined:
             os.environ["SPM_DIRECTORY"] = spm_mod.directory

capsul/test/test_fake_morphologist.py

@@ -205,6 +205,7 @@ def test_fake_morphologist_config(self):
                 }
             },
             "builtin": {
+                "config_modules": ["spm", "matlab"],
                 "database": "builtin",
                 "persistent": True,
                 "start_workers": default_engine_start_workers,
@@ -242,7 +243,7 @@ def test_fake_morphologist_config(self):
                 #'config_modules': ['capsul.test.test_fake_morphologist'],
             },
         }
-        print("\nconfig:", self.capsul.config.asdict(), "\n")
+        # print("\nconfig:", self.capsul.config.asdict(), "\n")
         self.assertEqual(self.capsul.config.asdict(), expected_config)
 
         engine = self.capsul.engine()
@@ -256,6 +257,8 @@ def test_fake_morphologist_config(self):
         context = engine.execution_context(morphologist)
         expected_context = {
             #'config_modules': ['capsul.test.test_fake_morphologist'],
+            "config_modules": ["spm", "matlab"],
+            "python_modules": [],
             "dataset": {
                 "input": {
                     "path": str(self.tmp / "bids"),

capsul/test/test_tiny_morphologist.py

@@ -499,6 +499,7 @@ def test_tiny_morphologist_config(self):
         context = engine.execution_context(tiny_morphologist)
         expected_context = {
             "config_modules": ["capsul.test.test_tiny_morphologist"],
+            "python_modules": [],
             "dataset": {
                 "input": {
                     "path": str(self.tmp / "bids"),