diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml
index d579b9a074657960670aa4eedd0dcf8c2bc73fed..e9fe349ea93f5abb4e30e39fbdcea9ee1dc81754 100644
--- a/.gitlab-ci.yml
+++ b/.gitlab-ci.yml
@@ -24,6 +24,7 @@ stages:
artifacts:
paths:
- report.xml
+ - htmlcov
expire_in: 1 day
script:
- ./ci/test.py
diff --git a/ci/test.py b/ci/test.py
index c6d90a39d599fc668a6a1ed525c2a940ddeeec4f..cce250734d5cf4fa9724c3155a4714ea22c129e4 100755
--- a/ci/test.py
+++ b/ci/test.py
@@ -34,7 +34,7 @@ if __name__ == "__main__":
"--prompt",
"ci",
".venv",
- ],
+ ]
)
check_call(
@@ -44,9 +44,16 @@ if __name__ == "__main__":
"pip",
"install",
str(sorted(Path("dist").glob("*.whl"))[-1].resolve()),
- ],
+ ]
)
check_call(
- [python_venv_executable(), "-m", "pytest", "--junitxml=report.xml"],
+ [
+ python_venv_executable(),
+ "-m",
+ "pytest",
+ "--junitxml=report.xml",
+ "--cov=src",
+ "--cov-report=html",
+ ]
)
diff --git a/examples/example_basic.ipynb b/examples/example_basic.ipynb
index 5445fe80256a9ee78bc0ae8e3c439135750b41b8..e737a4c023bb58873e9331b73d68a8af40ad8fda 100644
--- a/examples/example_basic.ipynb
+++ b/examples/example_basic.ipynb
@@ -14,155 +14,160 @@
"['fish_1', 'fish_2', 'fish_3', 'obstacle_1', 'robot']\n",
"\n",
"All poses\n",
- "[[[8.86584103e-01 2.35670820e-01 5.41754842e-01 4.49850202e-01]\n",
- " [8.15511882e-01 4.78223324e-01 6.29803419e-01 1.12592392e-01]\n",
- " [1.53732300e-01 7.24954247e-01 9.38574493e-01 4.65665817e-01]\n",
- " [9.10354614e-01 4.47880208e-01 3.81429136e-01 9.67544317e-01]\n",
- " [6.07822955e-01 5.20158827e-01 8.17965686e-01 8.42760384e-01]]\n",
+ "[[[5.56598067e-01 2.42021829e-01 2.45265663e-01 2.95294344e-01]\n",
+ " [9.83367860e-01 4.36241180e-01 5.68063319e-01 8.96367550e-01]\n",
+ " [8.71030211e-01 9.32705551e-02 8.51928890e-01 9.48658109e-01]\n",
+ " ...\n",
+ " [6.94550753e-01 6.52826130e-01 6.08456850e-01 4.88614887e-01]\n",
+ " [4.84500438e-01 1.14949882e-01 6.08556986e-01 7.93362781e-02]\n",
+ " [9.54909027e-01 3.18913072e-01 4.58294243e-01 7.45387852e-01]]\n",
"\n",
- " [[2.29353935e-01 8.80753636e-01 7.94585168e-01 2.22074524e-01]\n",
- " [6.13970399e-01 1.33511815e-02 2.89155185e-01 2.65219092e-01]\n",
- " [6.62197351e-01 6.47982001e-01 9.46004018e-02 6.59599364e-01]\n",
- " [4.86104101e-01 4.23153102e-01 1.39821902e-01 3.11809748e-01]\n",
- " [8.03322852e-01 9.52799857e-01 3.89638603e-01 6.43237352e-01]]\n",
+ " [[7.51943365e-02 9.95502114e-01 5.04003823e-01 8.36720586e-01]\n",
+ " [8.18848014e-01 4.04324770e-01 5.49858093e-01 3.51742476e-01]\n",
+ " [1.66903093e-01 1.78061739e-01 2.81622916e-01 8.88221264e-01]\n",
+ " ...\n",
+ " [7.69020915e-01 6.33118331e-01 4.15713340e-01 4.24170971e-01]\n",
+ " [7.64205098e-01 7.78579533e-01 7.44598091e-01 3.30398619e-01]\n",
+ " [4.45223182e-01 9.25011218e-01 2.36187894e-02 7.62242600e-02]]\n",
"\n",
- " [[9.70978260e-01 6.75936878e-01 6.23196602e-01 8.42264950e-01]\n",
- " [4.07079160e-01 8.46290290e-01 5.64092159e-01 3.56871307e-01]\n",
- " [4.84096229e-01 8.60232174e-01 1.39015794e-01 7.82253265e-01]\n",
- " [1.24170482e-01 2.21511930e-01 8.88282284e-02 4.53450561e-01]\n",
- " [1.28404438e-01 2.87771430e-02 4.57022637e-01 9.80571806e-01]]\n",
+ " [[7.73669600e-01 3.54849041e-01 4.21867281e-01 9.16552365e-01]\n",
+ " [4.73650604e-01 1.79305673e-01 8.38760436e-01 3.96051705e-01]\n",
+ " [2.01547332e-02 8.12301695e-01 2.78097481e-01 8.67732406e-01]\n",
+ " ...\n",
+ " [8.12627971e-01 6.28660858e-01 2.13196307e-01 6.49513781e-01]\n",
+ " [5.58035910e-01 4.63277161e-01 8.21570277e-01 6.79726541e-01]\n",
+ " [7.10023165e-01 5.45146585e-01 8.51007760e-01 9.56029415e-01]]\n",
"\n",
- " [[5.00000000e+01 5.00000000e+01 0.00000000e+00 0.00000000e+00]\n",
+ " [[5.00000000e+01 5.00000000e+01 1.00000000e+00 0.00000000e+00]\n",
" [ nan nan nan nan]\n",
" [ nan nan nan nan]\n",
+ " ...\n",
+ " [ nan nan nan nan]\n",
" [ nan nan nan nan]\n",
" [ nan nan nan nan]]\n",
"\n",
- " [[0.00000000e+00 0.00000000e+00 0.00000000e+00 0.00000000e+00]\n",
- " [0.00000000e+00 0.00000000e+00 0.00000000e+00 0.00000000e+00]\n",
- " [0.00000000e+00 0.00000000e+00 0.00000000e+00 0.00000000e+00]\n",
- " [0.00000000e+00 0.00000000e+00 0.00000000e+00 0.00000000e+00]\n",
- " [ nan nan nan nan]]]\n",
+ " [[5.00000000e+01 5.00000000e+01 5.00000000e+01 5.00000000e+01]\n",
+ " [5.00000000e+01 5.00000000e+01 5.00000000e+01 5.00000000e+01]\n",
+ " [5.00000000e+01 5.00000000e+01 5.00000000e+01 5.00000000e+01]\n",
+ " ...\n",
+ " [5.00000000e+01 5.00000000e+01 5.00000000e+01 5.00000000e+01]\n",
+ " [5.00000000e+01 5.00000000e+01 5.00000000e+01 5.00000000e+01]\n",
+ " [5.00000000e+01 5.00000000e+01 5.00000000e+01 5.00000000e+01]]]\n",
"\n",
"Fish poses\n",
- "[[[0.8865841 0.23567082 0.54175484 0.4498502 ]\n",
- " [0.81551188 0.47822332 0.62980342 0.11259239]\n",
- " [0.1537323 0.72495425 0.93857449 0.46566582]\n",
- " [0.91035461 0.44788021 0.38142914 0.96754432]\n",
- " [0.60782295 0.52015883 0.81796569 0.84276038]]\n",
+ "[[[0.55659807 0.24202183 0.24526566 0.29529434]\n",
+ " [0.98336786 0.43624118 0.56806332 0.89636755]\n",
+ " [0.87103021 0.09327056 0.85192889 0.94865811]\n",
+ " ...\n",
+ " [0.69455075 0.65282613 0.60845685 0.48861489]\n",
+ " [0.48450044 0.11494988 0.60855699 0.07933628]\n",
+ " [0.95490903 0.31891307 0.45829424 0.74538785]]\n",
"\n",
- " [[0.22935393 0.88075364 0.79458517 0.22207452]\n",
- " [0.6139704 0.01335118 0.28915519 0.26521909]\n",
- " [0.66219735 0.647982 0.0946004 0.65959936]\n",
- " [0.4861041 0.4231531 0.1398219 0.31180975]\n",
- " [0.80332285 0.95279986 0.3896386 0.64323735]]\n",
+ " [[0.07519434 0.99550211 0.50400382 0.83672059]\n",
+ " [0.81884801 0.40432477 0.54985809 0.35174248]\n",
+ " [0.16690309 0.17806174 0.28162292 0.88822126]\n",
+ " ...\n",
+ " [0.76902092 0.63311833 0.41571334 0.42417097]\n",
+ " [0.7642051 0.77857953 0.74459809 0.33039862]\n",
+ " [0.44522318 0.92501122 0.02361879 0.07622426]]\n",
"\n",
- " [[0.97097826 0.67593688 0.6231966 0.84226495]\n",
- " [0.40707916 0.84629029 0.56409216 0.35687131]\n",
- " [0.48409623 0.86023217 0.13901579 0.78225327]\n",
- " [0.12417048 0.22151193 0.08882823 0.45345056]\n",
- " [0.12840444 0.02877714 0.45702264 0.98057181]]]\n",
+ " [[0.7736696 0.35484904 0.42186728 0.91655236]\n",
+ " [0.4736506 0.17930567 0.83876044 0.3960517 ]\n",
+ " [0.02015473 0.8123017 0.27809748 0.86773241]\n",
+ " ...\n",
+ " [0.81262797 0.62866086 0.21319631 0.64951378]\n",
+ " [0.55803591 0.46327716 0.82157028 0.67972654]\n",
+ " [0.71002316 0.54514658 0.85100776 0.95602942]]]\n",
"\n",
"File structure\n",
- " version:\t[1 0]\n",
- " world size:\t[100. 100.]\n",
+ " format_url:\thttps://git.imp.fu-berlin.de/bioroboticslab/robofish/track_format/-/releases/1.0\n",
+ " format_version:\t[1 0]\n",
+ " world_size_cm:\t[100. 100.]\n",
"| entities\n",
"|---| fish_1\n",
- "|---|--- type:\tfish\n",
- "|---|--- poses:\t Shape (5, 4)\n",
- "|---|---| time\n",
- "|---|---|--- monotonic points:\t Shape (5,)\n",
+ "|---|--- category:\tfish\n",
+ "|---|--- orientations:\t Shape (1000, 2)\n",
+ "|---|--- positions:\t Shape (1000, 2)\n",
"|---| fish_2\n",
- "|---|--- type:\tfish\n",
- "|---|--- poses:\t Shape (5, 4)\n",
- "|---|---| time\n",
- "|---|---|--- monotonic points:\t Shape (5,)\n",
+ "|---|--- category:\tfish\n",
+ "|---|--- orientations:\t Shape (1000, 2)\n",
+ "|---|--- positions:\t Shape (1000, 2)\n",
"|---| fish_3\n",
- "|---|--- type:\tfish\n",
- "|---|--- poses:\t Shape (5, 4)\n",
- "|---|---| time\n",
- "|---|---|--- monotonic points:\t Shape (5,)\n",
+ "|---|--- category:\tfish\n",
+ "|---|--- orientations:\t Shape (1000, 2)\n",
+ "|---|--- positions:\t Shape (1000, 2)\n",
"|---| obstacle_1\n",
- "|---|--- type:\tobstacle\n",
+ "|---|--- category:\tobstacle\n",
+ "|---|--- orientations:\t Shape (1, 2)\n",
"|---|--- outlines:\t Shape (1, 4, 2)\n",
- "|---|--- poses:\t Shape (1, 4)\n",
- "|---|---| time\n",
+ "|---|--- positions:\t Shape (1, 2)\n",
"|---| robot\n",
- "|---|--- type:\trobot\n",
- "|---|--- poses:\t Shape (4, 4)\n",
- "|---|---| time\n",
- "|---|---|--- monotonic step:\t40\n",
+ "|---|--- category:\trobot\n",
+ "|---|--- orientations:\t Shape (1000, 2)\n",
+ "|---|--- positions:\t Shape (1000, 2)\n",
+ "| samplings\n",
+ "|--- default:\t25 hz\n",
+ "|---| 25 hz\n",
+ "|---|--- frequency_hz:\t25.0\n",
"\n"
]
}
],
"source": [
- "#! /usr/bin/env python3\n",
- "\n",
"import robofish.io\n",
"import numpy as np\n",
- "from pathlib import Path\n",
- "import os\n",
- "\n",
"\n",
- "# Helper function to enable relative paths from this file\n",
- "def full_path(path):\n",
- " return (Path(os.path.abspath(\"__file__\")).parent / path).resolve()\n",
"\n",
- "\n",
- "if __name__ == \"__main__\":\n",
+ "def create_example_file(path):\n",
" # Create a new io file object with a 100x100cm world\n",
- " sf = robofish.io.File(world_size=[100, 100])\n",
+ " sf = robofish.io.File(world_size_cm=[100, 100], frequency_hz=25.0)\n",
"\n",
" # create a simple obstacle, fixed in place, fixed outline\n",
- " obstacle_pose = [[50, 50, 0, 0]]\n",
" obstacle_outline = [[[-10, -10], [-10, 0], [0, 0], [0, -10]]]\n",
" obstacle_name = sf.create_entity(\n",
- " \"obstacle\", poses=obstacle_pose, outlines=obstacle_outline\n",
+ " \"obstacle\", positions=[[50, 50]], orientations=[[0]], outlines=obstacle_outline\n",
" )\n",
"\n",
- " # create a robofish with 100 timesteps and 40ms between the timesteps. If we would not give a name, the name would be generated to be robot_1.\n",
- " robofish_timesteps = 4\n",
- " robofish_poses = np.zeros((robofish_timesteps, 4))\n",
- " sf.create_entity(\"robot\", robofish_poses, name=\"robot\", monotonic_step=40)\n",
+ " # create a robofish with 1000 timesteps. If we would not give a name, the name would be generated to be robot_1.\n",
+ " robofish_timesteps = 1000\n",
+ " robofish_poses = np.ones((robofish_timesteps, 4)) * 50\n",
+ " robot = sf.create_entity(\"robot\", robofish_poses, name=\"robot\")\n",
"\n",
" # create multiple fishes with timestamps. Since we don't specify names, but only the type \"fish\" the fishes will be named [\"fish_1\", \"fish_2\", \"fish_3\"]\n",
" agents = 3\n",
- " timesteps = 5\n",
- " timestamps = np.linspace(0, timesteps + 1, timesteps)\n",
+ " timesteps = 1000\n",
+ " # timestamps = np.linspace(0, timesteps + 1, timesteps)\n",
" agent_poses = np.random.random((agents, timesteps, 4))\n",
"\n",
- " fish_names = sf.create_multiple_entities(\n",
- " \"fish\", agent_poses, monotonic_points=timestamps\n",
- " )\n",
+ " fishes = sf.create_multiple_entities(\"fish\", agent_poses)\n",
"\n",
" # This would throw an exception if the file was invalid\n",
" sf.validate()\n",
"\n",
" # Save file validates aswell\n",
- " example_file = full_path(\"example.hdf5\")\n",
- " sf.save(example_file)\n",
+ "\n",
+ " sf.save_as(path)\n",
"\n",
" # Closing and opening files (just for demonstration)\n",
" sf.close()\n",
- " sf = robofish.io.File(path=example_file)\n",
+ " sf = robofish.io.File(path=path)\n",
"\n",
" print(\"\\nEntity Names\")\n",
" print(sf.entity_names)\n",
"\n",
- " # Get an array with all poses. As the length of poses varies per agent, it\n",
- " # is filled up with nans. The result is not interpolated and the time scales\n",
- " # per agent are different. It is planned to create a warning in the case of\n",
- " # different time scales and have another function, which generates an\n",
- " # interpolated array.\n",
+ " # Get an array with all poses. As the length of poses varies per agent, it is filled up with nans.\n",
" print(\"\\nAll poses\")\n",
- " print(sf.select_poses())\n",
+ " print(sf.entity_poses)\n",
"\n",
" print(\"\\nFish poses\")\n",
- " print(sf.select_poses(lambda e: e.category == \"fish\"))\n",
+ " print(sf.select_entity_poses(lambda e: e.category == \"fish\"))\n",
"\n",
" print(\"\\nFile structure\")\n",
- " print(sf)\n"
+ " print(sf)\n",
+ "\n",
+ "\n",
+ "if __name__ == \"__main__\":\n",
+ " create_example_file(\"example.hdf5\")\n"
]
}
],
@@ -187,4 +192,4 @@
},
"nbformat": 4,
"nbformat_minor": 4
-}
\ No newline at end of file
+}
diff --git a/examples/example_basic.py b/examples/example_basic.py
index dec8e3be1c7997b33b36f9868f0df8b0c6c3fbe6..b9e356c7547a37cdfc66e75f8f93269bb4365a1c 100755
--- a/examples/example_basic.py
+++ b/examples/example_basic.py
@@ -1,7 +1,6 @@
#! /usr/bin/env python3
import robofish.io
-from robofish.io import utils
import numpy as np
diff --git a/setup.py b/setup.py
index 5be2fe4573c17f9dbb776058058ea0e38c4674aa..7999f5ac38332788fb314af928b99b67c06040d7 100644
--- a/setup.py
+++ b/setup.py
@@ -14,9 +14,15 @@ entry_points = {
]
}
+
def source_version():
version_parts = (
- run(["git", "describe", "--tags", "--dirty"], check=True, stdout=PIPE, encoding="utf-8")
+ run(
+ ["git", "describe", "--tags", "--dirty"],
+ check=True,
+ stdout=PIPE,
+ encoding="utf-8",
+ )
.stdout.strip()
.split("-")
)
@@ -36,12 +42,20 @@ def source_version():
return version
+
setup(
name="robofish-io",
version=source_version(),
author="",
author_email="",
- install_requires=["h5py>=3", "numpy", "seaborn", "pandas", "deprecation"],
+ install_requires=[
+ "h5py>=3",
+ "numpy",
+ "seaborn",
+ "pandas",
+ "deprecation",
+ "testbook",
+ ],
classifiers=[
"Development Status :: 3 - Alpha",
"Intended Audience :: Science/Research",
diff --git a/src/robofish/io/entity.py b/src/robofish/io/entity.py
index 8ef557c3d7d0bdcdd010f47055a121ca3452114f..f791a125e2e7ef9f22c539e9b9810061e444de88 100644
--- a/src/robofish/io/entity.py
+++ b/src/robofish/io/entity.py
@@ -98,7 +98,7 @@ class Entity(h5py.Group):
else:
if poses is not None:
- assert poses.shape[1] == 3 or poses.shape[1] == 4
+ assert poses.shape[1] in [3, 4]
positions = poses[:, :2]
orientations = poses[:, 2:]
if orientations is not None and orientations.shape[1] == 1:
diff --git a/tests/robofish/evaluate/test_app_evaluate.py b/tests/robofish/evaluate/test_app_evaluate.py
index 58ca278882b1756830fd66b7a37a4cb823d8199a..2a7fe486a95c961f41f591ea7c8ab533db6b2ccf 100644
--- a/tests/robofish/evaluate/test_app_evaluate.py
+++ b/tests/robofish/evaluate/test_app_evaluate.py
@@ -22,7 +22,7 @@ def test_app_validate():
self.names = None
self.save_path = graphics_out
- # TODO: Get rid of deprecated get_poses function
+ # TODO: Get rid of deprecation
with pytest.warns(DeprecationWarning):
app.evaluate(DummyArgs("speed"))
graphics_out.unlink()
diff --git a/tests/robofish/io/test_examples.py b/tests/robofish/io/test_examples.py
index 1d0379fb1b06448e5f733c3690ff48a4f623592c..deb626a6faa1d3675b00fb7bf18ecff39488022e 100644
--- a/tests/robofish/io/test_examples.py
+++ b/tests/robofish/io/test_examples.py
@@ -1,12 +1,13 @@
import robofish.io
from robofish.io import utils
from pathlib import Path
+from testbook import testbook
import sys
sys.path.append(str(utils.full_path(__file__, "../../../examples/")))
-
+ipynb_path = utils.full_path(__file__, "../../../examples/example_basic.ipynb")
path = utils.full_path(__file__, "../../../examples/tmp_example.hdf5")
if path.exists():
path.unlink()
@@ -24,3 +25,9 @@ def test_example_basic():
example_basic.create_example_file(path)
path.unlink()
+
+
+def test_example_basic_ipynb():
+ # Executing the notebook should not lead to an exception
+ with testbook(str(ipynb_path), execute=True) as tb:
+ pass