adding test

.gitignore

 .vscode*
+.pdm*
 pypelines/__pycache__*
 tests/__pycache__*
 *.egg-info*
@@ -9,3 +10,6 @@ dist/*
 notebooks/pipelines_tests/*
 notebooks/*.log
 build*
+.coverage
+coverage*
+pytest_results*

pyproject.toml

@@ -25,14 +25,59 @@ requires-python = ">=3.10"
 license = { text = "MIT" }
 dynamic = ["version"]
 
-[project.optional-dependencies]
-celery = ["celery>=5.3.5", "alyx_connector>=2.1.5"]
-
 [project.urls]
 homepage = "https://gitlab.pasteur.fr/haisslab/data-management/pypelines"
 repository = "https://gitlab.pasteur.fr/haisslab/data-management/pypelines"
 documentation = "https://gitlab.pasteur.fr/haisslab/data-management/pypelines"
 
+[project.optional-dependencies]
+celery = ["celery>=5.3.5", "alyx_connector>=2.1.5"]
+
+
+[tool.pdm.dev-dependencies]
+dev = ["pytest>=8.3.2", "pytest-cov>=5.0.0"]
+
+[tool.pytest.ini_options]
+addopts = "--pdbcls=IPython.terminal.debugger:TerminalPdb --cov-report xml --cov --junitxml=pytest_results.xml"
+testpaths = ["tests"]
+
+
 [tool.pdm.version]
 source = "file"
 path = "src/pypelines/__init__.py"
+
+[tool.black]
+preview = true
+line-length = 120
+
+[tool.flake8]
+max-line-length = 120
+ignore = [
+    "F401",
+    "F403",
+    "F841",
+    "E401",
+    "E265",
+    "E704",
+    "E266",
+    "E203",
+    "E712",
+    "W503",
+    "W605",
+]
+
+[tool.pyright]
+reportGeneralTypeIssues = "information"
+reportOptionalMemberAccess = "information"
+reportMissingImports = "information"
+reportMissingModuleSource = "information"
+reportInvalidStringEscapeSequence = "information"
+reportOptionalOperand = "none"
+reportOptionalSubscript = "none"
+reportOptionalIterable = "none"
+reportAttributeAccessIssue = "information"
+
+typeCheckingMode = "basic"
+
+include = ["src", "tests"]
+exclude = ["**/__pycache__"]

src/pypelines/__init__.py

-__version__ = "0.0.68"
+__version__ = "0.0.70"
 
 from . import loggs
 from .pipes import *

src/pypelines/pipelines.py

@@ -10,11 +10,7 @@ if TYPE_CHECKING:
     from .graphs import PipelineGraph
 
 
-class BasePipelineType(Protocol):
-    def __getattr__(self, name: str) -> "BasePipe": ...
-
-
-class Pipeline(BasePipelineType):
+class Pipeline:
     pipes: Dict[str, "BasePipe"]
     runner_backend_class = BaseTaskBackend
 
@@ -108,6 +104,11 @@ class Pipeline(BasePipelineType):
 
         self.resolved = True
 
+    def __getattr__(self, name: str) -> "BasePipe":
+        if name in self.pipes:
+            return self.pipes[name]
+        raise AttributeError(f"'Pipeline' object has no attribute '{name}'")
+
     def get_requirement_stack(
         self, instance: "BaseStep", names: bool = False, max_recursion: int = 100
     ) -> List["BaseStep"]:

tests/test_core.py

+import pytest
+
+# for testing on local version, instead of installed version,
+# this may not be desired as testing uninstalled may not catch issues that occur after installation is performed
+# comment the next three lines to test installed version
+# import sys
+# from pathlib import Path
+# sys.path.append(str(Path(__file__).resolve().parent / "src"))
+
+from pypelines import examples
+from pypelines.sessions import Session
+
+from pypelines import Pipeline, stepmethod, BaseStep
+from pypelines.pickle_backend import PicklePipe
+
+
+@pytest.fixture
+def test_class_based_pypeline():
+
+    pipeline = Pipeline("test_class_based")
+
+    @pipeline.register_pipe
+    class MyPipe(PicklePipe):
+        class Steps:
+            def my_step(self, session, extra=""):
+                return 1
+
+            my_step.requires = []
+
+    return pipeline
+
+
+@pytest.fixture
+def test_method_based_pypeline():
+
+    pipeline = Pipeline("test_method_based")
+
+    @pipeline.register_pipe
+    class MyPipe(PicklePipe):
+
+        @stepmethod(requires=[])
+        def my_step(self, session, extra=""):
+            return 1
+
+
+def test_pypeline_creation(test_class_based_pypeline):
+    assert isinstance(test_class_based_pypeline.MyPipe.my_step, BaseStep)
+    assert hasattr(test_class_based_pypeline.MyPipe.my_step, "generate")
+    assert hasattr(test_class_based_pypeline.MyPipe.my_step, "load")
+    assert hasattr(test_class_based_pypeline.MyPipe.my_step, "save")

tests/tests.py

-import unittest
-
-# for testing on local version, instead of installed version,
-# this may not be desired as testing uninstalled may not catch issues that occur after installation is performed
-# comment the next three lines to test installed version
-# import sys
-# from pathlib import Path
-# sys.path.append(str(Path(__file__).resolve().parent / "src"))
-
-from pypelines import examples
-from pypelines.sessions import Session
-
-
-class TestVersions(unittest.TestCase):
-    def setUp(self):
-        self.pipeline = examples.example_pipeline
-        self.session = Session(subject="test_subject", date="2023-10-10", number=0, path="C:/test", auto_path=True)
-        print(self.session.alias)
-
-    def test_pipeline_generate(self):
-        self.assertEqual(
-            self.pipeline.ExamplePipe.example_step1.generate(self.session, "bonjour"),
-            {"argument1": "bonjour", "optionnal_argument2": 23},
-        )
-
-
-if __name__ == "__main__":
-    unittest.main()