Added some doc details

Added buttons to link between docs and code
Changed required h5py version to 3.2.1 to prevent bugs

README.md

@@ -12,6 +12,34 @@
 This repository implements an easy to use interface, to create, save, load, and work with [specification-compliant](https://git.imp.fu-berlin.de/bioroboticslab/robofish/track_format) hdf5 files, containing 2D swarm data. This repository should be used by the different swarm projects to generate comparable standardized files.
 
 
+<a href="http://agerken.de/io/index.html" class="myButton">Documentation</a>
+<style>
+.myButton {
+	background:#3971cc;
+	background-color:#3971cc;
+	border-radius:9px;
+	display:inline-block;
+	cursor:pointer;
+	color:#ffffff;
+	font-family:Arial;
+	font-size:20px;
+	padding:8px 16px;
+	text-decoration:none;
+}
+.myButton:hover {
+	background:#396bd1;
+	background-color:#396bd1;
+  color: #e0e0e0;
+  text-decoration: none;
+}
+.myButton:active {
+	position:relative;
+	top:1px;
+}
+</style>
+
+        
+
 ## Installation
 
 Add our [Artifacts repository](https://git.imp.fu-berlin.de/bioroboticslab/robofish/artifacts) to your pip config and install the packagage.
@@ -21,8 +49,6 @@ python3 -m pip config set global.extra-index-url https://git.imp.fu-berlin.de/ap
 python3 -m pip install robofish-io
 ```
 
-
-
 ## Usage
 We show a simple example below. More examples can be found in ```examples/```
 
@@ -74,13 +100,3 @@ Current modes are:
 - tank_positions
 - trajectories
 - follow_iid
\ No newline at end of file
-
-
-## LICENSE
-
-This work is licensed under LGPL 3.0 (or any later version).
-Individual files contain the following tag instead of the full license text:
-
-`SPDX-License-Identifier: LGPL-3.0-or-later`
-
-This enables machine processing of license information based on the SPDX License Identifiers available here: https://spdx.org/licenses/

docs/entity.md

@@ -54,7 +54,7 @@ nemo.attrs["fish_standard_length_cm"] = 10
 ```
 
 Any attribute is allowed, but some cannonical attributes are prepared:<br>
-`species`: str, `sex`: str, `fish_standard_length_cm`: float
+`species`:`str`, `sex`:`str`, `fish_standard_length_cm`:`float`
 
 
 ## Properties

docs/file.md

@@ -10,8 +10,6 @@ f = robofish.io.File(world_size_cm=[100, 100], frequency_hz=25.0)
 f.save_as("test.hdf5")
 ```
 
----
-
 The File object can also be generated, with a given path. In this case, we work on the file directly. The `with` block ensures, that the file is validated after the block.
 
 ```python
@@ -31,7 +29,7 @@ When opening a file with a path, a mode should be specified to describe how the
 | x    	| Create file, fail if exists            	|
 | a    	| Read/write if exists, create otherwise 	|
 
----
+## Attributes
 
 Attributes of the file can be added, to describe the contents. 
 The attributes can be set like this:
@@ -43,6 +41,5 @@ f.attrs["experiment_issues"] = "All data in this file is made up."
 Any attribute is allowed, but some cannonical attributes are prepared:<br>
 `publication_url, video_url, tracking_software_name, tracking_software_version, tracking_software_url, experiment_setup, experiment_issues`
 
----
-
-All file functions and their documentation can be found at `robofish.io.file.File`.
\ No newline at end of file
+## Properties
+As described in `robofish.io`, all properties of `robofish.io.entity.Entity`s can be accessed by adding the prefix `entity_` to the function.
\ No newline at end of file

docs/img/calc_ori_speed_turn.md

-testtesttest
\ No newline at end of file

docs/index.md

@@ -4,7 +4,8 @@ This package provides you:
 - Preprocessing (orientation calculation, action calculation, raycasting, ...)
 - Quick and easy evaluation of behavior
 - Data, which is interchangable between labs and tools. No conversions required, since units and coordinate systems are standardized.
-- No custom data import, but just `include robofish.io`
+- No custom data import, just `include robofish.io`
+- This package is tested extensively
 
 Features coming up:
 
@@ -12,6 +13,33 @@ Features coming up:
 - Pytorch Datasets directly from `robofish.io` files.
 
 
+<a href="https://git.imp.fu-berlin.de/bioroboticslab/robofish/io" class="myButton">Code</a>
+<style>
+.myButton {
+	background:#3971cc;
+	background-color:#3971cc;
+	border-radius:9px;
+	display:inline-block;
+	cursor:pointer;
+	color:#ffffff;
+	font-family:Arial;
+	font-size:20px;
+	padding:8px 16px;
+	text-decoration:none;
+}
+.myButton:hover {
+	background:#396bd1;
+	background-color:#396bd1;
+  color: #e0e0e0;
+  text-decoration: none;
+}
+.myButton:active {
+	position:relative;
+	top:1px;
+}
+</style>
+
+
 ## Installation
 Add our [Artifacts repository](https://git.imp.fu-berlin.de/bioroboticslab/robofish/artifacts) to your pip config and install the packagage.
 
@@ -22,8 +50,8 @@ python3 -m pip install robofish-io robofish-trackviewer
 
 ## Usage
 
-This documentation is structured to increase in complexity.
-First we'll execute the example from the README. More examples can be found in ```examples/```.
+This documentation is structured with increasing complexity.
+First we'll execute the example from the readme. More examples can be found in ```examples/```.
 
 ```python
 # Create a new robofish io file
@@ -123,7 +151,7 @@ In the same scheme the following properties are available:
 
 
 | File/ Entity function | Description |
-|---------------------------------  |-------------------------------------------------------------------------------------------------------	|
+| --------------------- | ----------- ||
 | *entity_*positions          	    | The positions as a (*entities*, timesteps, 2 (x, y)) arary.                                            	|
 | *entity_*orientations       	    | The orientations as a (*entities*, timesteps, 2 (ori_x, ori_y)) arary.                                 	|
 | *entity_*orientations_rad   	    | The orientations as a (*entities*, timesteps, 1 (ori_rad)) arary.                                      	|
@@ -132,10 +160,26 @@ In the same scheme the following properties are available:
 | *entity_*poses_calc_ori_rad 	    | The poses with calculated orientations as a<br>(*entities*, timesteps - 1, 3 (x, y, calc_ori_rad)) array. |
 | *entity_*speed_turn        	    | The speed and turn as a (*entities*, timesteps - 2, 2 (speed_cm/s, turn_rad/s)) array.                    |
 
-The functions `robofish.io.entity.Entity.poses_calc_ori_rad` and `robofish.io.entity.Entity.speed_turn` are described in detail in `robofish.io.entity`
+All these functions are described in more detail in `robofish.io.entity`.
 
 ## Where to continue?
 We recommend continuing to read advanced options for `robofish.io.file`s and `robofish.io.entity`s.
 Create some files, validate them, look at them in the trackviewer, evaluate them.
 
-If you find bugs or get stuck somewhere, please text `Andi` on Mattermost or by mail (andi.gerken@gmail.com)
\ No newline at end of file
+If you find bugs or get stuck somewhere, please text `Andi` on Mattermost or by mail ([andi.gerken@gmail.com](mailto:andi.gerken@gmail.com))
+
+
+---
+
+## Extended functions
+In the [Track Format Specification](https://git.imp.fu-berlin.de/bioroboticslab/robofish/track_format/uploads/f76d86e7a629ca38f472b8f23234dbb4/RoboFish_Track_Format_-_1.0.pdf) and in this package there are more possibilities, we don't describe explicitly here. If you want to use any of the following features, please ask Andi:
+
+Built in robofish.io and not described:
+- Multiple sampling frequencies
+- Timestamps per timestep
+- Calendar points
+- Outlines
+- Obstacles
+
+Planned in Track Format but not implemented:
+- 3D Tracks
\ No newline at end of file

setup.py

@@ -48,7 +48,7 @@ setup(
     version=source_version(),
     author="",
     author_email="",
-    install_requires=["h5py>=2.10.0", "numpy", "seaborn", "pandas", "deprecation"],
+    install_requires=["h5py>=3.2.1", "numpy", "seaborn", "pandas", "deprecation"],
     classifiers=[
         "Development Status :: 3 - Alpha",
         "Intended Audience :: Science/Research",

src/robofish/io/__init__.py

 # SPDX-License-Identifier: LGPL-3.0-or-later
 
 """
-The Python package `robofish.io` provides a simple interface to create, load, modify, and inspect files containing tracks of swarms.
-The files are saved in the `.hdf5` format and following the [track_format specification](https://git.imp.fu-berlin.de/bioroboticslab/robofish/track_format/uploads/f76d86e7a629ca38f472b8f23234dbb4/RoboFish_Track_Format_-_1.0.pdf).
+The Python package <a href="https://git.imp.fu-berlin.de/bioroboticslab/robofish/io">robofish.io</a> provides a simple interface to create, load, modify, and inspect files containing tracks of swarms.
+The files are saved in the `.hdf5` format and following the [Track Format Specification](https://git.imp.fu-berlin.de/bioroboticslab/robofish/track_format/uploads/f76d86e7a629ca38f472b8f23234dbb4/RoboFish_Track_Format_-_1.0.pdf).
 
 .. include:: ../../../docs/index.md
 """