Merge pull request #134 from GazzolaLab/update-0.2.4

Update 0.2.4

.github/workflows/main.yml

@@ -19,7 +19,7 @@ jobs:
 
     strategy:
       matrix:
-        os: [ubuntu-latest] # [ubuntu-latest, macos-latest] # Run macos tests if really required, since they charge 10 times more for macos
+        os: [ubuntu-latest, macos-latest] #, windows-latest] # Run macos tests if really required, since they charge 10 times more for macos
         python-version: [3.6, 3.7, 3.8]
 
     # Steps represent a sequence of tasks that will be executed as part of the job

RELEASE.md

@@ -1,5 +1,21 @@
-# Release Note (version 0.2.3)
+# Release Note (version 0.2.4)
+
+## What's Changed
+
+* Refactor EndPointForcesSinusoidal example and test cases by @armantekinalp in https://github.com/GazzolaLab/PyElastica/pull/110
+* Fix save_every condition in ExportCallBack by @mstoelzle in https://github.com/GazzolaLab/PyElastica/pull/125
+* Fix and update contact examples by @armantekinalp in https://github.com/GazzolaLab/PyElastica/pull/109
+* Update rigid body rod contact by @armantekinalp in https://github.com/GazzolaLab/PyElastica/pull/117
+* Update rigid body rod contact friction by @armantekinalp in https://github.com/GazzolaLab/PyElastica/pull/124
+* Update ExportCallback by @skim0119 in https://github.com/GazzolaLab/PyElastica/pull/130
 
+## New Contributors
+
+* @mstoelzle made their first contribution in https://github.com/GazzolaLab/PyElastica/pull/125
+
+---
+
+# Release Note (version 0.2.3)
 
 ## Developer Note
 The major updates are knot theory module added to the Cosserat rod as *mixin*, and muscular snake example is added. 
@@ -8,6 +24,7 @@ The major updates are knot theory module added to the Cosserat rod as *mixin*, a
 - #70: Knot theory module to compute topological quantities.
 - #71: Reorganize rod constructor warning messages and collect messages in log.  
 - #72: Muscular snake example is added.
+
 ---
 
 # Release Note (version 0.2.2)

docs/api/connections.rst

@@ -25,9 +25,9 @@ Compatibility
 =============================== ==== =========== 
 Connection / Contact / Joints   Rod  Rigid Body
 =============================== ==== =========== 
-FreeJoint                       ✅   ✅
+FreeJoint                       ✅   ❌
 ExternalContact                 ✅   ❌
-FixedJoint                      ✅   ✅
+FixedJoint                      ✅   ❌
 HingeJoint                      ✅   ❌
 SelfContact                     ✅   ❌
 =============================== ==== =========== 

docs/api/external_forces.rst

@@ -22,6 +22,7 @@ External force and environmental interaction are represented as force/torque bou
    UniformForces
    UniformTorques
    MuscleTorques
+   EndpointForcesSinusoidal
 
 .. rubric:: Available Interaction
 
@@ -40,11 +41,12 @@ Compatibility
 Forcing                     Rod     Rigid Body
 ========================== ======= ============
 NoForces                    ✅      ✅
-EndpointForces              ✅      ✅
+EndpointForces              ✅      ❌
 GravityForces               ✅      ✅
 UniformForces               ✅      ✅
 UniformTorques              ✅      ✅
 MuscleTorques               ✅      ❌
+EndpointForcesSinusoidal    ✅      ❌
 ========================== ======= ============
 
 ========================== ======= ============
@@ -78,6 +80,9 @@ Built-in External Forces
 .. autoclass:: MuscleTorques
    :special-members: __init__
 
+.. autoclass:: EndpointForcesSinusoidal
+   :special-members: __init__
+
 Built-in Environment Interactions
 ---------------------------------
 .. automodule:: elastica.interaction

elastica/callback_functions.py

@@ -1,10 +1,12 @@
 __doc__ = """ Module contains callback classes to save simulation data for rod-like objects """
 __all__ = ["CallBackBaseClass", "MyCallBack", "ExportCallBack"]
 
-import warnings
 import os
 import sys
 import numpy as np
+import logging
+
+from collections import defaultdict
 
 
 class CallBackBaseClass:
@@ -111,48 +113,61 @@ class ExportCallBack(CallBackBaseClass):
     def __init__(
         self,
         step_skip: int,
-        path: str,
+        filename: str,
+        directory: str,
         method: str,
         initial_file_count: int = 0,
-        save_every: int = 1e8,
+        file_save_interval: int = 1e8,
     ):
         """
-
         Parameters
         ----------
         step_skip : int
-            Collect data at each step_skip steps.
-        path : str
-            Path to save the file. If directories are prepended,
-            they must exist. The filename depends on the method.
-            The path is not expected to include extension.
+            Interval to collect simulation data into buffer.
+            The data will be collected at every `dt * step_skip`
+            interval.
+        filename : str
+            Name of the file without extension. The extension will be
+            determined depend on the method. File will be saved with the
+            name <filename>_<number>.<extension>.
+        directory : str
+            Directory to save the file. If directory doesn't exist, it will
+            be created. During the save, any existing files in this directory
+            could be overwritten.
         method : str
             Method name. Only the name in AVAILABLE_METHOD is
             allowed.
         initial_file_count : int
             Initial file count index that will be appended
-        save_every : int
-            Save the file every save_every steps. (default=1e8)
+        file_save_interval : int
+            Interval, in steps, to export/save collected buffer
+            as file. (default = 1e8)
         """
         # Assertions
         MIN_STEP_SKIP = 100
         if step_skip <= MIN_STEP_SKIP:
-            warnings.warn(f"We recommend step_skip at least {MIN_STEP_SKIP}")
+            logging.warning(
+                f"We recommend (step_skip={step_skip}) at least {MIN_STEP_SKIP}"
+            )
         assert (
             method in ExportCallBack.AVAILABLE_METHOD
         ), f"The exporting method ({method}) is not supported. Please use one of {ExportCallBack.AVAILABLE_METHOD}."
-        assert os.path.exists(path), "The export path does not exist."
+
+        # Create directory
+        if os.path.exists(directory):
+            logging.warning(
+                f"The directory ({directory}) already exists. Previously saved data could be overwritten."
+            )
+        os.makedirs(directory, exist_ok=True)
 
         # Argument Parameters
         self.step_skip = step_skip
-        self.save_path = path
+        self.save_path = os.path.join(directory, filename) + "_{:02d}.{}"
         self.method = method
         self.file_count = initial_file_count
-        self.save_every = save_every
+        self.file_save_interval = file_save_interval
 
         # Data collector
-        from collections import defaultdict
-
         self.buffer = defaultdict(list)
         self.buffer_size = 0
 
@@ -161,16 +176,19 @@ def __init__(
             import pickle
 
             self._pickle = pickle
+            self._ext = "pkl"
         elif method == ExportCallBack.AVAILABLE_METHOD[1]:
             from numpy import savez
 
             self._savez = savez
+            self._ext = "npz"
         elif method == ExportCallBack.AVAILABLE_METHOD[2]:
             import tempfile
             import pickle
 
             self._tempfile = tempfile.NamedTemporaryFile(delete=False)
             self._pickle = pickle
+            self._ext = "pkl"
 
     def make_callback(self, system, time, current_step: int):
         """
@@ -200,14 +218,19 @@ def make_callback(self, system, time, current_step: int):
                 + sys.getsizeof(velocity)
                 + sys.getsizeof(director)
             )
-            if (
-                self.buffer_size > ExportCallBack.FILE_SIZE_CUTOFF
-                or (current_step + 1) % self.save_every == 0
-            ):
-                self._dump()
+
+        if (
+            self.buffer_size > self.FILE_SIZE_CUTOFF
+            or (current_step + 1) % self.file_save_interval == 0
+        ):
+            self._dump()
 
     def _dump(self, **kwargs):
-        file_path = f"{self.save_path}_{self.file_count}.dat"
+        """
+        Dump dictionary buffer (self.buffer) to a file and clear
+        the buffer.
+        """
+        file_path = self.save_path.format(self.file_count, self._ext)
         data = {k: np.array(v) for k, v in self.buffer.items()}
         if self.method == ExportCallBack.AVAILABLE_METHOD[0]:
             # pickle
@@ -224,3 +247,26 @@ def _dump(self, **kwargs):
         self.file_count += 1
         self.buffer_size = 0
         self.buffer.clear()
+
+    def get_last_saved_path(self) -> str:
+        """
+        Return last saved file path. If no file has been saved,
+        return None
+        """
+        if self.file_count == 0:
+            return None
+        else:
+            return self.save_path.format(self.file_count - 1, self._ext)
+
+    def close(self):
+        """
+        Save residual buffer
+        """
+        if self.buffer_size:
+            self._dump()
+
+    def clear(self):
+        """
+        Alias to `close`
+        """
+        self.close()