Backlog and new issues fixes (#21)

1.    Fix some badges in README and docs (hopefully now for real)
2.    Typing fixes
3.   Update of pre-commit ruff version
      a. Changes necessary with this change
4.    Fix weights not correctly passed to external python functions with NURBS representation
5.    Fix change of signature for splinepy io functions
6.    Rename function `get_control_points` to `get_parameter_values`

.github/workflows/pre_commit.yml

@@ -10,5 +10,8 @@ jobs:
     runs-on: ubuntu-latest
     steps:
     - uses: actions/checkout@v3
-    - uses: actions/setup-python@v3
+    - name: Setup python
+      uses: actions/setup-python@v3
+      with:
+          python-version: '3.11'
     - uses: pre-commit/[email protected]

.pre-commit-config.yaml

@@ -1,10 +1,10 @@
 # See https://pre-commit.com for more information
 # See https://pre-commit.com/hooks.html for more hooks
 default_language_version:
-    python: python3.10
+    python: python3.11
 repos:
 -   repo: https://github.com/pre-commit/pre-commit-hooks
-    rev: v3.2.0
+    rev: v5.0.0
     hooks:
     -   id: end-of-file-fixer
     -   id: check-yaml
@@ -19,12 +19,8 @@ repos:
     -   id: detect-private-key
     -   id: end-of-file-fixer
     -   id: mixed-line-ending
--   repo: https://github.com/psf/black
-    rev: 23.7.0
-    hooks:
-      - id: black
--   repo: https://github.com/astral-sh/ruff-pre-commit
-    # Ruff version.
-    rev: v0.0.291
-    hooks:
-      - id: ruff
+- repo: https://github.com/astral-sh/ruff-pre-commit
+  rev: v0.9.1
+  hooks:
+    - id: ruff
+      args: [--fix, --exit-non-zero-on-fix]

README.md

@@ -1,6 +1,6 @@
 # Reinforcement Learning based Shape Optimization (ReLeSO)
 
-[![GitHub Workflow Status (with event)](https://img.shields.io/github/actions/workflow/status/tataratat/releso/pypi_upload)](https://github.com/tataratat/releso)
+[![pypi_upload](https://github.com/tataratat/releso/actions/workflows/build_and_upload_wheels.yml/badge.svg)](https://github.com/tataratat/releso)
 [![Read the docs](https://readthedocs.org/projects/releso/badge/?version=latest)](https://releso.readthedocs.io/en/latest/?badge=latest)
 [![PyPI - Version](https://img.shields.io/pypi/v/releso)](https://pypi.org/project/releso/)
 [![Python Versions](https://img.shields.io/pypi/pyversions/releso)](https://pypi.org/project/releso/)
@@ -10,7 +10,7 @@ Releso is a Library/Framework for
 Reinforcement Learning based Shape Optimization. Please look into the
 Documentation for information on how it works. The instruction on how the
 documentation can be built is given below as well as the instruction on how the
-package can be installed.  
+package can be installed.
 Alternatively, it can be installed from `pip` via `pip install releso`.
 
 

docs/source/index.rst

@@ -8,7 +8,7 @@ Reinforcement Learning based Shape Optimization (ReLeSO)
 |Build Status| |Documentation Status|
 |PyPI| |Python| |License|
 
-.. |Build Status| image:: https://img.shields.io/github/actions/workflow/status/tataratat/releso/pypi_upload
+.. |Build Status| image:: https://github.com/tataratat/releso/actions/workflows/build_and_upload_wheels.yml/badge.svg
    :target: https://github.com/tataratat/releso
    :alt: PyPI - Version
 

examples/nutils_converging_channel_incremental.hjson

@@ -25,7 +25,7 @@
                 // "control_points": [[0.0,0.0],[0.5,0.0],[1.0,0.0],[0.0,0.2],[0.5,0.2],[1.0,0.2],[0.0,0.4],[0.5,0.4],[1.0,0.4]]
             },
             "mesh": {
-                "path": "examples/2DChannelTria.msh",
+                "path": "2DChannelTria.msh",
                 "dimensions": 2
             },
             "discrete_actions": true,
@@ -39,7 +39,7 @@
                     "run_on_reset": true,
                     "use_communication_interface": true,
                     "working_directory": "./",
-                    "python_file_path": "examples/poiseuille_flow_channel_shear_thinning.py",
+                    "python_file_path": "poiseuille_flow_channel_shear_thinning.py",
                     "add_step_information": true,
                     "additional_observations": 3
                 }

pyproject.toml

@@ -37,7 +37,7 @@ repository = "https://github.com/clemens-fricke/releso.git"
 
 [project.optional-dependencies]
 all = [
-    "splinepy[all]",
+    "splinepy[all]>=0.1.2",
     "torchvision",
 ]
 test = [
@@ -50,7 +50,7 @@ docs = [
     "sphinx-jsonschema",
 ]
 dev = [
-    "splinepy[all]",
+    "splinepy[all]>=0.1.2",
     "torchvision",
     "pytest",
     "pytest-cov",
@@ -82,6 +82,10 @@ line-length = 79
 
 [tool.ruff]
 line-length = 79
+preview = true
+exclude = ["examples", "tests/samples"]
+
+[tool.lint]
 # Adding "ANN" would be really nice, but is to much work currently.
 # Adding "PT" would be nice, for pytest naming convention.
 # Adding "SIM" would be nice, but is to much work currently.
@@ -90,18 +94,16 @@ select = [
     "ISC", "ICN", "PIE", "T20", "PYI", "Q", "RSE", "TID", "TCH", "INT", "PD",
     "PGH", "TRY", "FLY", "NPY", "PERF", "FURB", "LOG"]
 ignore = ["N818", "TRY003"]
-preview = true
-exclude = ["examples"]
 
-[tool.ruff.per-file-ignores]
+[tool.lint.per-file-ignores]
 "tests/*.py" = ["D", "S", "E", "CPY", "PIE804", "NPY002"]
 "__main__.py" = ["T20"]
 
-[tool.ruff.pydocstyle]
+[tool.lint.pydocstyle]
 convention = "google"
 
 [tool.pytest.ini_options]
-addopts = "--ignore=tests/samples -W ignore::DeprecationWarning"
+addopts = "--ignore=tests/samples --ignore=examples -W ignore::DeprecationWarning"
 markers = [
     "torch_test",
 ]

releso/__version__.py

@@ -2,4 +2,4 @@
 
 Current version.
 """
-version = "0.1.1"
+version = "0.1.2"

releso/agent.py

@@ -77,7 +77,7 @@ class BaseAgent(BaseModel):
     #: with a current timestamp is also added.
     tensorboard_log: Optional[str]
 
-    def get_next_tensorboard_experiment_name(self) -> str:
+    def get_next_tensorboard_experiment_name(self) -> Optional[str]:
         """Return tensorboard experiment name.
 
         Adds a date and time marker to the tensorboard experiment name so that
@@ -231,7 +231,7 @@ def get_agent(
         else:
             raise AgentUnknownException(self.agent_type)
 
-    def get_next_tensorboard_experiment_name(self) -> str:
+    def get_next_tensorboard_experiment_name(self) -> Optional[str]:
         """Return the name of the tensorboard experiment.
 
         The tensorboard experiment name of the original training run if given
@@ -241,7 +241,7 @@ def get_next_tensorboard_experiment_name(self) -> str:
             str: tensorboard experiment name
         """
         if self.tesorboard_run_directory:
-            return self.tesorboard_run_directory
+            return str(self.tesorboard_run_directory) if not None else None
         if self.tensorboard_log is not None:
             return super().get_next_tensorboard_experiment_name()
         return None
@@ -324,7 +324,7 @@ def get_agent(
         self.get_logger().info(f"Using agent of type {self.agent_type}.")
         if normalizer_divisor == 0:
             self.get_logger().warning("Normalizer divisor is 0, will use 1.")
-            normalizer_divisor = 1.0
+            normalizer_divisor = 1
         self.n_steps = max(int(self.n_steps / normalizer_divisor), 1)
         return A2C(env=environment, **self.get_additional_kwargs())
 
@@ -398,7 +398,7 @@ def get_agent(
         self.get_logger().info(f"Using agent of type {self.agent_type}.")
         if normalizer_divisor == 0:
             self.get_logger().warning("Normalizer divisor is 0, will use 1.")
-            normalizer_divisor = 1.0
+            normalizer_divisor = 1
         self.n_steps = max(int(self.n_steps / normalizer_divisor), 1)
         return PPO(env=environment, **self.get_additional_kwargs())
 

releso/base_parser.py

@@ -168,7 +168,7 @@ def save_model(self, file_name: Optional[str] = None) -> str:
         path.parent.mkdir(parents=True, exist_ok=True)
         save_path = path / "model_end.save"
         self._agent.save(save_path)
-        return save_path
+        return str(save_path)
 
     def evaluate_model(
         self,
@@ -242,7 +242,7 @@ def _init():
 
     def _create_validation_environment(
         self, throw_error_if_none: bool = False
-    ) -> Environment:
+    ) -> Optional[Environment]:
         """Creates a validation environment.
 
         Args:

releso/geometry.py

@@ -68,13 +68,13 @@ def setup(self, environment_id: UUID):
         """
         self._actions = self.shape_definition.get_actions()
 
-    def get_control_points(self) -> List[List[float]]:
+    def get_parameter_values(self) -> List[List[float]]:
         """Return all control_points of the spline.
 
         Returns:
             List[List[float]]: Nested list of control_points.
         """
-        return self.shape_definition.get_control_points()
+        return self.shape_definition.get_parameter_values()
 
     def apply_action(self, action: Union[List[float], int]) -> Optional[Any]:
         """Function that applies a given action to the Spline.
@@ -117,7 +117,7 @@ def apply(self) -> Optional[Any]:
         Returns:
             List[List[float]]: Current control points of the shape.
         """
-        return self.get_control_points()
+        return self.get_parameter_values()
 
     def is_geometry_changed(self) -> bool:
         """Checks if the geometry was changed with the previous action apply.

releso/gym_environment.py

@@ -24,10 +24,12 @@
     fix for this problem is currently worked on.
 """
 
-from typing import Any, Dict, List, Tuple, Union
+from typing import Any, List, Union
 
 import gymnasium
 
+from releso.util.types import StepReturnType
+
 
 class GymEnvironment(gymnasium.Env):
     """Environment interface class for the gym environment definition.
@@ -54,9 +56,7 @@ def __init__(self, action_space, observation_space) -> None:
         self.action_space = action_space
         self.observation_space = observation_space
 
-    def step(
-        self, action: Union[int, List[float]]
-    ) -> Tuple[Any, float, bool, Dict[str, Any]]:
+    def step(self, action: Union[int, List[float]]) -> StepReturnType:
         """Dummy function definition for gym interface."""
 
     def reset(self) -> Any:

releso/mesh.py

@@ -119,7 +119,7 @@ def export_mesh(self, mesh: GustafMeshTypes, space_time: bool = False):
             RuntimeError: _description_
         """
         if self.mesh_format == "mixd":
-            mixd.export(mesh, self._export_path_changed, space_time=space_time)
+            mixd.export(self._export_path_changed, mesh, space_time=space_time)
         else:
             raise RuntimeError(
                 f"The requested format {self.mesh_format} is not supported."

releso/shape_parameterization.py

@@ -240,15 +240,16 @@ class ShapeDefinition(BaseModel):
     """Base of shape parameterization, also represents a simple point cloud."""
 
     #: control_points of the shape. These are the base variables used for the
-    #: optimization. Overwrite `get_actions` and `get_control_points` if
+    #: optimization. Overwrite `get_actions` and `get_parameter_values` if
     #: additional optimization variables are needed. See (WIP) NURBSDefinition.
     control_points: List[List[VariableLocation]]
 
     def get_number_of_points(self) -> int:
         """Returns the number of points in the Cube.
 
         Number of control points multiplied by the number of dimensions for
-        each cp.
+        each cp. Assumes that all dimensions have the same number of control
+        points.
 
         Returns:
             int: number of points in the geometry
@@ -297,7 +298,7 @@ def convert_all_control_point_locations_to_variable_locations(
                     ) from None
         return new_list
 
-    def get_control_points(self) -> List[List[float]]:
+    def get_parameter_values(self) -> List[List[float]]:
         """Returns the current positions of all control points.
 
         Returns:
@@ -336,7 +337,7 @@ def get_shape(self) -> Any:
         Returns:
             Any: Shape that is generated.
         """
-        return self.get_control_points()
+        return self.get_parameter_values()
 
     def reset(self) -> None:
         """Resets the shape to the original values."""

releso/spline.py

@@ -300,7 +300,7 @@ def get_shape(self) -> BSpline:
         """
         self.get_logger().debug("Creating BSpline.")
         self.get_logger().debug(
-            f"With control_points: {self.get_control_points()}"
+            f"With control_points: {self.get_parameter_values()}"
         )
 
         return BSpline(
@@ -309,7 +309,7 @@ def get_shape(self) -> BSpline:
                 space_dim.get_knot_vector()
                 for space_dim in self.space_dimensions
             ],
-            self.get_control_points(),
+            self.get_parameter_values(),
         )
 
 
@@ -430,7 +430,7 @@ def get_shape(self) -> NURBS:
                 space_dim.get_knot_vector()
                 for space_dim in self.space_dimensions
             ],
-            self.get_control_points(),
+            self.get_parameter_values()[:-1],
             self.get_weights(),
         )
 
@@ -448,6 +448,20 @@ def get_actions(self) -> List[VariableLocation]:
         # raise RuntimeError(f"Actions: {actions}")
         return actions
 
+
+    def get_parameter_values(self) -> List[List[float]]:
+        """Returns the current positions of all control points with weights as
+        well.
+
+        Returns:
+            List[List[float]]: Positions of all control points.
+        """
+        control_points = super().get_parameter_values()
+        control_points.append(
+            [weight.current_position for weight in self.weights]
+        )
+        return control_points
+
     def reset(self) -> None:
         """Resets the spline to the original shape."""
         super().reset()

releso/util/util_funcs.py

@@ -62,7 +62,7 @@ def which(
     def is_exe(fpath):
         return os.path.isfile(fpath) and os.access(fpath, os.X_OK)
 
-    fpath, fname = os.path.split(program)
+    fpath, _ = os.path.split(program)
     if fpath:
         if is_exe(program):
             return program
@@ -136,17 +136,20 @@ def get_path_extension() -> str:
         # check if slurm task array is running
         if (
             os.getenv("SLURM_ARRAY_TASK_COUNT")
-            and int(os.getenv("SLURM_ARRAY_TASK_COUNT")) > 1
+            and (
+                (tmp_var := os.getenv("SLURM_ARRAY_TASK_COUNT")) is not None
+                and int(tmp_var) > 1
+            )
             and os.getenv("SLURM_ARRAY_JOB_ID")
             and os.getenv("SLURM_ARRAY_TASK_ID")
         ):
             ret_str = (
-                os.getenv("SLURM_ARRAY_JOB_ID")
+                str(os.getenv("SLURM_ARRAY_JOB_ID"))
                 + "/"
-                + os.getenv("SLURM_ARRAY_TASK_ID")
+                + str(os.getenv("SLURM_ARRAY_TASK_ID"))
                 + "_"
                 + ret_str
             )
         elif os.getenv("SLURM_JOB_ID"):  # default slurm job running
-            ret_str += "_" + os.getenv("SLURM_JOB_ID")
+            ret_str += "_" + str(os.getenv("SLURM_JOB_ID"))
     return ret_str

tests/test_base_parser.py

@@ -1,4 +1,5 @@
 from typing import Any, Dict, List, Union
+import pathlib
 
 import pytest
 
@@ -130,6 +131,8 @@ def test_base_parser_validation(
     )
 
     for file_path in file_paths:
+        print(file_path)
+        file_path = pathlib.Path(file_path)
         assert file_path.exists()
         clean_up_provider(
             file_path.parent