Added more documentation

Preparing to tag and release

commands.md

@@ -4,3 +4,6 @@ pdoc --html robofish.io robofish.evaluate --html-dir docs --force
 
 ## Code coverage:
 pytest --cov=src --cov-report=html
+
+## Flake
+flake8 --ignore E203 --max-line-length 88

pyproject.toml

 [build-system]
 # Minimum requirements for the build system to execute.
-requires = ["setuptools", "wheel", "pytest", "pandas", "deprecation"]  # PEP 508 specifications.
+requires = ["setuptools", "wheel"]  # PEP 508 specifications.
+
+[flake8]
+max-line-length = 88
+extend-ignore = "E203"

src/robofish/io/validation.py

@@ -334,13 +334,18 @@ def validate_positions_range(world_size, positions, e_name):
 def validate_orientations_length(orientations, e_name):
     ori_lengths = np.linalg.norm(orientations, axis=1)
 
+    # import matplotlib.pyplot as plt
+    #
+    # plt.plot(ori_lengths)
+    # plt.show()
+
     # Check if all orientation lengths are all 1. Different lengths cause warnings.
     assert_validate(
         np.isclose(ori_lengths, 1).all(),
-        "The orientation vectors were not unit vectors. Their length was in the range [%.2f, %.2f] when it should be 1"
+        "The orientation vectors were not unit vectors. Their length was in the range [%.4f, %.4f] when it should be 1"
         % (min(ori_lengths), max(ori_lengths)),
         e_name,
-        strict_validate=False,
+        strict_validate=True,
     )
 
 

tests/robofish/evaluate/test_evaluate.py

+import pytest
+import robofish.evaluate
+from robofish.io import utils
+import numpy as np
+
+
+def test_get_all_poses_from_paths():
+    valid_file_path = utils.full_path(__file__, "../../resources/valid.hdf5")
+    poses, frequency = robofish.evaluate.get_all_poses_from_paths([valid_file_path])
+
+    # (1 input array, 1 file, 2 fishes, 100 timesteps, 4 poses)
+    assert np.array(poses).shape == (1, 1, 2, 100, 4)
+    assert frequency == 25

tests/robofish/io/test_examples.py

 import robofish.io
 from robofish.io import utils
 from pathlib import Path
-from testbook import testbook
+
 import sys
 
 
@@ -29,6 +29,8 @@ def test_example_basic():
 
 # This test can be executed manually. The CI/CD System has issues with testbook.
 def manual_test_example_basic_ipynb():
+    from testbook import testbook
+
     # Executing the notebook should not lead to an exception
     with testbook(str(ipynb_path), execute=True) as tb:
         pass