docs: minor clean-ups

docs/api.md

@@ -403,7 +403,7 @@ NBLAST and related functions:
 
 ### Distances
 
-Functions to calculate Euclidian and geodesic ("along-the-arbor") distances.
+Functions to calculate Euclidean and geodesic ("along-the-arbor") distances.
 
 | Function | Description |
 |----------|-------------|

docs/changelog.md

@@ -11,9 +11,17 @@ For a full list of changes please see the [commits history](https://github.com/n
 {{ navis }}' Github repository.
 
 ## dev
-Date: ongoing
+_Date: ongoing_
 
-This version contains a major internal rework of both [`navis.plot2d`][] and [`navis.plot3d`][] to make them more consistent and easier to use.
+To install the current `dev` version of {{ navis }}:
+
+```shell
+pip uninstall navis -y
+pip install git+https://github.com/navis-org/navis@master
+```
+
+This version contains a major internal rework of both [`navis.plot2d`][] and [`navis.plot3d`][] to make them
+more consistent and easier to use.
 
 ##### Breaking
 - Plotting: the `synapse_layout` parameter was renamed to `cn_layout` (matching e.g. other parameters such as `cn_colors`)
@@ -56,7 +64,7 @@ This version contains a major internal rework of both [`navis.plot2d`][] and [`n
 - [`navis.TreeNeuron.simple][] now correctly drops soma nodes if they aren't root, branch or leaf points themselves
 
 ## Version `1.7.0` { data-toc-label="1.7.0" }
-Date: 25/07/24
+_Date: 25/07/24_
 
 ##### Breaking
 - Plotting: dropped the `cluster` parameter in favor of an improved `color_by` logic (see below)
@@ -81,7 +89,7 @@ Date: 25/07/24
 **Full Changelog**: [v1.6.0...v1.7.0](https://github.com/navis-org/navis/compare/v1.6.0...v1.7.0)
 
 ## Version `1.6.0` { data-toc-label="1.6.0" }
-Date: 07/04/24
+_Date: 07/04/24_
 
 ##### Breaking
 - Dropped support for Python 3.8, per NEP 29
@@ -117,7 +125,7 @@ Date: 07/04/24
 **Full Changelog**: [v1.5.0...v1.6.0](https://github.com/navis-org/navis/compare/v1.5.0...v1.6.0)
 
 ## Version `1.5.0` { data-toc-label="1.5.0" }
-Date: 27/07/23
+_Date: 27/07/23_
 
 ##### Breaking
 - Dropped support for Python 3.7
@@ -140,7 +148,7 @@ Date: 27/07/23
 **Full Changelog**: [v1.4.0...v1.5.0](https://github.com/navis-org/navis/compare/v1.4.0...v1.5.0)
 
 ## Version `1.4.0` { data-toc-label="1.4.0" }
-Date: 21/12/22
+_Date: 21/12/22_
 
 ##### Breaking
 - `navis.flow_centrality` was renamed to `navis.synapse_flow_centrality` and a new non-synaptic `navis.flow_centrality` function was added. This also impacts the `method` parameter in `navis.split_axon_dendrite`!
@@ -163,15 +171,15 @@ Date: 21/12/22
 **Full Changelog**: [v1.3.1...v1.4.0](https://github.com/navis-org/navis/compare/v1.3.1...v1.4.0)
 
 ## Version `1.3.1` { data-toc-label="1.3.1" }
-Date: 10/06/22
+_Date: 10/06/22_
 
 ##### Fixes
 - Various bugs fixed
 
 **Full Changelog**: [v1.3.0...v1.3.1](https://github.com/navis-org/navis/compare/v1.3.0...v1.3.1)
 
 ## Version `1.3.0` { data-toc-label="1.3.0" }
-Date: 10/05/22
+_Date: 10/05/22_
 
 ##### Breaking
 - As of this version `pip install navis` won't install a vispy backend
@@ -193,15 +201,15 @@ Date: 10/05/22
 **Full Changelog**: [v1.2.1...v1.3.0](https://github.com/navis-org/navis/compare/v1.2.1...v1.3.0)
 
 ## Version `1.2.1` { data-toc-label="1.2.1" }
-Date: 25/02/22
+_Date: 25/02/22_
 
 ##### Fixes
 - Hot fix for `navis.split_axon_dendrite`
 
 **Full Changelog**: [v1.2.0...v1.2.1](https://github.com/navis-org/navis/compare/v1.2.0...v1.2.1)
 
 ## Version `1.2.0` { data-toc-label="1.2.0" }
-Date: 24/02/22
+_Date: 24/02/22_
 
 ##### Additions
 - New function: `navis.betweeness_centrality`
@@ -223,7 +231,7 @@ Date: 24/02/22
 **Full Changelog**: [v1.1.0...v1.2.0](https://github.com/navis-org/navis/compare/v1.1.0...v1.2.0)
 
 ## Version `1.1.0` { data-toc-label="1.1.0" }
-Date: 18/11/21
+_Date: 18/11/21_
 
 ##### Additions
 - New function: `navis.sholl_analysis`
@@ -235,7 +243,7 @@ Date: 18/11/21
 **Full Changelog**: [v1.0.0...v1.1.0](https://github.com/navis-org/navis/compare/v1.0.0...v1.1.0)
 
 ## Version `1.0.0` { data-toc-label="1.0.0" }
-Date: 11/11/21
+_Date: 11/11/21_
 
 ##### Breaking
 - `navis.MeshNeuron`: `__getattr__` does not search `trimesh` representation anymore
@@ -322,7 +330,7 @@ Date: 11/11/21
 **Full Changelog**: [v0.6.0...v1.0.0](https://github.com/navis-org/navis/compare/v0.6.0...v1.0.0)
 
 ## Version `0.6.0` { data-toc-label="0.6.0" }
-Date: 12/05/21
+_Date: 12/05/21_
 
 ##### Additions
 - new functions: `navis.prune_at_depth`, `navis.read_rda`, `navis.cell_body_fiber`
@@ -353,7 +361,7 @@ Date: 12/05/21
 **Full Changelog**: [v0.5.3...v0.6.0](https://github.com/navis-org/navis/compare/v0.5.3...v0.6.0)
 
 ## Version `0.5.3` { data-toc-label="0.5.3" }
-Date: 10/04/21
+_Date: 10/04/21_
 
 ##### Additions
 - new functions: `navis.nblast_smart`, `navis.synblast`, `navis.symmetrize_brain`
@@ -374,7 +382,7 @@ Date: 10/04/21
 **Full Changelog**: [v0.5.2...v0.5.3](https://github.com/navis-org/navis/compare/v0.5.2...v0.5.3)
 
 ## Version `0.5.2` { data-toc-label="0.5.2" }
-Date: 02/02/21
+_Date: 02/02/21_
 
 ##### Additions
 - new functions: `navis.xform`, `navis.write_precomputed`
@@ -387,15 +395,15 @@ Date: 02/02/21
 **Full Changelog**: [v0.5.1...v0.5.2](https://github.com/navis-org/navis/compare/v0.5.1...v0.5.2)
 
 ## Version `0.5.1` { data-toc-label="0.5.1" }
-Date: 10/01/21
+_Date: 10/01/21_
 
 ##### Fixes
 - Various under-the-hood improvements and bugfixes
 
 **Full Changelog**: [v0.5.0...v0.5.1](https://github.com/navis-org/navis/compare/v0.5.0...v0.5.1)
 
 ## Version `0.5.0` { data-toc-label="0.5.0" }
-Date: 05/01/21
+_Date: 05/01/21_
 
 ##### Additions
 - new functions for transforming spatial data (locations, neurons, etc) between brain spaces:
@@ -410,31 +418,31 @@ Date: 05/01/21
 **Full Changelog**: [v0.4.3...v0.5.0](https://github.com/navis-org/navis/compare/v0.4.3...v0.5.0)
 
 ## Version `0.4.3` { data-toc-label="0.4.3" }
-Date: 22/12/20
+_Date: 22/12/20_
 
 ##### Fixes
 - Small bugfixes
 
 **Full Changelog**: [v0.4.2...v0.4.3](https://github.com/navis-org/navis/compare/v0.4.2...v0.4.3)
 
 ## Version `0.4.2` { data-toc-label="0.4.2" }
-Date: 22/12/20
+_Date: 22/12/20_
 
 ##### Fixes
 - Small bugfixes
 
 **Full Changelog**: [v0.4.1...v0.4.2](https://github.com/navis-org/navis/compare/v0.4.1...v0.4.2)
 
 ## Version `0.4.1` { data-toc-label="0.4.1" }
-Date: 06/12/20
+_Date: 06/12/20_
 
 ##### Fixes
 - Critical bugfix in NBLAST
 
 **Full Changelog**: [v0.4.0...v0.4.1](https://github.com/navis-org/navis/compare/v0.4.0...v0.4.1)
 
 ## Version `0.4.0` { data-toc-label="0.4.0" }
-Date: 06/12/20
+_Date: 06/12/20_
 
 ##### Additions
 - native implementation of NBLAST: `navis.nblast` and `navis.nblast_allbyall`!
@@ -444,7 +452,7 @@ Date: 06/12/20
 **Full Changelog**: [v0.3.4...v0.4.0](https://github.com/navis-org/navis/compare/v0.3.4...v0.4.0)
 
 ## Version `0.3.4` { data-toc-label="0.3.4" }
-Date: 24/11/20
+_Date: 24/11/20_
 
 ##### Improvements
 - improved `navis.Dotprops`:
@@ -454,7 +462,7 @@ Date: 24/11/20
 **Full Changelog**: [v0.3.3...v0.3.4](https://github.com/navis-org/navis/compare/v0.3.3...v0.3.4)
 
 ## Version `0.3.3` { data-toc-label="0.3.3" }
-Date: 23/11/20
+_Date: 23/11/20_
 
 ##### Additions
 - new module: `models` for modelling networks and neurons
@@ -486,7 +494,7 @@ neuron by custom properties (e.g. by Strahler index or compartment)
 **Full Changelog**: [v0.3.2...v0.3.3](https://github.com/navis-org/navis/compare/v0.3.2...v0.3.3)
 
 ## Version `0.3.2` { data-toc-label="0.3.2" }
-Date: 18/10/20
+_Date: 18/10/20_
 
 ##### Improvements
 - `navis.plot2d` and `navis.plot3d` now accept `trimesh.Trimesh` directly
@@ -498,7 +506,7 @@ Date: 18/10/20
 **Full Changelog**: [v0.3.1...v0.3.2](https://github.com/navis-org/navis/compare/v0.3.1...v0.3.2)
 
 ## Version `0.3.1` { data-toc-label="0.3.1" }
-Date: 07/10/20
+_Date: 07/10/20_
 
 ##### Additions
 - new function `navis.rewire_skeleton`
@@ -519,7 +527,7 @@ Date: 07/10/20
 **Full Changelog**: [v0.3.0...v0.3.1](https://github.com/navis-org/navis/compare/v0.3.0...v0.3.1)
 
 ## Version `0.3.0` { data-toc-label="0.3.0" }
-Date: 06/10/20
+_Date: 06/10/20_
 
 ##### Additions
 - Started module to manipulate mesh data (see e.g. `navis.simplify_mesh`)
@@ -531,7 +539,7 @@ Date: 06/10/20
 **Full Changelog**: [v0.2.3...v0.3.0](https://github.com/navis-org/navis/compare/v0.2.3...v0.3.0)
 
 ## Version `0.2.3` { data-toc-label="0.2.3" }
-Date: 06/09/20
+_Date: 06/09/20_
 
 ##### Additions
 - New Neuron property `.label` that if present will be used for plot legends
@@ -541,7 +549,7 @@ Date: 06/09/20
 - Blender interface: improved scatter plot generation
 
 ## Version `0.2.2` { data-toc-label="0.2.2" }
-Date: 15/08/20
+_Date: 15/08/20_
 
 ##### Additions
 - New `plot3d` parameter: with plotly backend, use `fig` to add data to existing plotly figure
@@ -556,7 +564,7 @@ Date: 15/08/20
 - Various improvements and bug fixes
 
 ## Version `0.2.1` { data-toc-label="0.2.1" }
-Date: 20/04/20
+_Date: 20/04/20_
 
 ##### Additions
 - New `plot3d` parameter: with plotly backend, use `radius=True` plots TreeNeurons with radius
@@ -566,7 +574,7 @@ Date: 20/04/20
 - Various improvements to e.g. `nx2neuron`
 
 ## Version `0.2.0` { data-toc-label="0.2.0" }
-Date: 29/06/20
+_Date: 29/06/20_
 
 ##### Breaking
 - `navis.nx2neuron` now returns a `navis.TreeNeuron` instead of a `DataFrame`
@@ -584,27 +592,27 @@ Date: 29/06/20
 - Fix bugs in `navis.Volume` pickling
 
 ## Version `0.1.16` { data-toc-label="0.1.16" }
-Date: 26/05/20
+_Date: 26/05/20_
 
 ##### Fixes
 - Many small bugfixes
 
 ## Version `0.1.15` { data-toc-label="0.1.15" }
-Date: 15/05/20
+_Date: 15/05/20_
 
 ##### Improvements
 - improvements to R and Blender interface
 - improved loading from SWCs (up to 2x faster)
 - TreeNeurons: allow rerooting by setting the `.root` attribute
 
 ## Version `0.1.14` { data-toc-label="0.1.14" }
-Date: 05/05/20
+_Date: 05/05/20_
 
 ##### Fixes
 - Emergency fixes for critical bugs
 
 ## Version `0.1.13` { data-toc-label="0.1.13" }
-Date: 05/05/20
+_Date: 05/05/20_
 
 ##### Additions
 - new function: `navis.vary_color`
@@ -613,13 +621,13 @@ Date: 05/05/20
 - improvements to Blender interface and various other functions
 
 ## Version `0.1.12` { data-toc-label="0.1.12" }
-Date: 02/04/20
+_Date: 02/04/20_
 
 ##### Imnprovements
 - `navis.Volume` is now sublcass of `trimesh.Trimesh`
 
 ## Version `0.1.11` { data-toc-label="0.1.11" }
-Date: 28/02/20
+_Date: 28/02/20_
 
 ##### Improvements
 - improved `navis.stitch_neurons`: much faster now if you have iGraph
@@ -629,32 +637,32 @@ Date: 28/02/20
 - fixed bugs in `navis.downsample_neuron`
 
 ## Version `0.1.10` { data-toc-label="0.1.10" }
-Date: 24/02/20
+_Date: 24/02/20_
 
 ##### Fixes
 - Fixed bugs in Blender interface introduced in 0.1.9
 
 ## Version `0.1.9` { data-toc-label="0.1.9" }
-Date: 24/02/20
+_Date: 24/02/20_
 
 ##### Fixes
 - Removed hard-coded swapping and translation of axes in the Blender interface
 - Fixed bugs in `navis.stitch_neurons`
 
 ## Version `0.1.8` { data-toc-label="0.1.8" }
-Date: 21/02/20
+_Date: 21/02/20_
 
 ##### Fixes
 - Again lots of fixed bugs
 
 ## Version `0.1.0` { data-toc-label="0.1.0" }
-Date: 23/05/19
+_Date: 23/05/19_
 
 ##### Fixes
 - Many small bugfixes
 
 ## Version `0.0.1` { data-toc-label="0.0.1" }
-Date: 29/01/19
+_Date: 29/01/19_
 
 ##### Fixes
 - First commit, lots to fix.

docs/examples/0_io/plot_02_io_dotprops.py

@@ -76,4 +76,5 @@
 dp
 
 # %%
-# There is no established format to store dotprops. But like all other neuron types in navis, you can pickle data for later (re)use - see the :ref:`pickling tutorial <local_data_pickle_tut>`. See also the :ref:`I/O API reference api_io>`.
+# There is no established format to store dotprops. But like all other neuron types in navis, you can pickle data for later (re)use
+# - see the [pickling tutorial](../plot_04_io_pickle). See also the [I/O API reference](../../../api.md#importexport).