Merge branch 'develop' into 'master'

Updated docs

See merge request !17

docs/entity.md

@@ -65,9 +65,9 @@ As described in `robofish.io`, Files and Entities have useful properties.
 
 | Entity function                                  | Description                                                              |
 | ------------------------------------------------ | ------------------------------------------------------------------------ |
-| `robofish.io.entity.Entity.positions`            | Positions as a `(timesteps, 2 (x, y))` arary.                            |
-| `robofish.io.entity.Entity.orientations`         | Orientations as a `(timesteps, 2 (ori_x, ori_y))` arary.                 |
-| `robofish.io.entity.Entity.orientations_rad`     | Orientations as a `(timesteps, 1 (ori_rad))` arary.                      |
+| `robofish.io.entity.Entity.positions`            | Positions as a `(timesteps, 2 (x, y))` array.                            |
+| `robofish.io.entity.Entity.orientations`         | Orientations as a `(timesteps, 2 (ori_x, ori_y))` array.                 |
+| `robofish.io.entity.Entity.orientations_rad`     | Orientations as a `(timesteps, 1 (ori_rad))` array.                      |
 | `robofish.io.entity.Entity.poses`                | Poses as a `(timesteps, 4 (x, y, x_ori, y_ori))` array.                  |
 | `robofish.io.entity.Entity.poses_rad`            | Poses as a `(timesteps, 3(x, y, ori_rad))` array.                        |
 | `robofish.io.entity.Entity.actions_speeds_turns` | Speed and turn as a `(timesteps - 1, 2 (speed_cm/s, turn_rad/s))` array. |

gen_docs.sh

 
 cd "${0%/*}"
 
-pdoc3 --html fish_models --force
-cp -r docs/img/ html/fish_models/
+pdoc3 --html robofish.io --force
+cp -r docs/img/ html/robofish/io

src/robofish/io/entity.py

@@ -151,8 +151,8 @@ class Entity(h5py.Group):
 
     @property
     @deprecation.deprecated(
-        deprecated_in="1.2",
-        removed_in="1.2.4",
+        deprecated_in="0.2",
+        removed_in="0.2.4",
         details="We found that our calculation of 'poses_calc_ori_rad' is flawed and replaced it "
         "Use the original poses ('poses_rad') with tracked orientations instead. "
         "If you see this message and you don't know what to do, update all packages, "
@@ -172,8 +172,8 @@ class Entity(h5py.Group):
 
     @property
     @deprecation.deprecated(
-        deprecated_in="1.2",
-        removed_in="1.2.4",
+        deprecated_in="0.2",
+        removed_in="0.2.4",
         details="We found that our calculation of 'poses_calc_ori' is flawed and replaced it "
         "Use the original poses ('poses') with tracked orientations instead. "
         "If you see this message and you don't know what to do, update all packages, "
@@ -206,8 +206,8 @@ class Entity(h5py.Group):
 
     @property
     @deprecation.deprecated(
-        deprecated_in="1.2",
-        removed_in="1.2.4",
+        deprecated_in="0.2",
+        removed_in="0.2.4",
         details="We found that our calculation of 'speed_turn' is flawed and replaced it "
         "with 'actions_speeds_turns'. The difference in calculation is, that the tracked "
         "orientation is used now which gives the fish the ability to swim backwards. "

src/robofish/io/file.py

@@ -424,8 +424,8 @@ class File(h5py.File):
 
     @property
     @deprecation.deprecated(
-        deprecated_in="1.2",
-        removed_in="1.2.4",
+        deprecated_in="0.2",
+        removed_in="0.2.4",
         details="We found that our calculation of 'poses_calc_ori' is flawed."
         "Please replace it with 'poses' and use the tracked orientation."
         "If you see this message and you don't know what to do, update all packages and if nothing helps, contact Andi.\n"
@@ -436,8 +436,8 @@ class File(h5py.File):
 
     @property
     @deprecation.deprecated(
-        deprecated_in="1.2",
-        removed_in="1.2.4",
+        deprecated_in="0.2",
+        removed_in="0.2.4",
         details="We found that our calculation of 'poses_calc_ori_rad' is flawed."
         "Please replace it with 'poses_rad' and use the tracked orientation."
         "If you see this message and you don't know what to do, update all packages and if nothing helps, contact Andi.\n"
@@ -450,8 +450,8 @@ class File(h5py.File):
 
     @property
     @deprecation.deprecated(
-        deprecated_in="1.2",
-        removed_in="1.2.4",
+        deprecated_in="0.2",
+        removed_in="0.2.4",
         details="We found that our calculation of 'speed_turn' is flawed and replaced it "
         "with 'actions_speeds_turns'. The difference in calculation is, that the tracked "
         "orientation is used now which gives the fish the ability to swim backwards. "

tests/robofish/io/test_entity.py

@@ -36,7 +36,8 @@ def test_entity_turns_speeds():
     There were issues with the calculation of speeds and turns. The corresponding functions were set to be deprecated.
     This test was adapted to have plausible orientations which are used when the speeds and turns are calculated.
     The reconstructed track is not identical to the original track. The reson for this is unknown.
-    TODO: Find the reason, why the reconstructed track differs
+
+    There is an open issue, to check this test again: https://git.imp.fu-berlin.de/bioroboticslab/robofish/io/-/issues/14
     """
 
     f = robofish.io.File(world_size_cm=[100, 100], frequency_hz=25)