Merge pull request #205 from schlegelp/dev

Update master to 2.0.0
navis-org · Dec 19, 2020 · 173a7e0 · 173a7e0
2 parents 135cb5a + 69c67b7
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diff --git a/.github/workflows/publish-to-pypi.yml b/.github/workflows/publish-to-pypi.yml
@@ -0,0 +1,34 @@
+name: Publish Python 🐍 distributions 📦 to PyPI
+
+on:
+  release:
+    types: [created]
+
+jobs:
+  build-n-publish:
+    name: Build and publish Python 🐍 distributions 📦 to PyPI
+    runs-on: ubuntu-18.04
+    steps:
+    - uses: actions/checkout@master
+    - name: Set up Python 3.7
+      uses: actions/setup-python@v1
+      with:
+        python-version: 3.7
+    - name: Install wheel and setuptools
+      run: >-
+        python -m
+        pip install
+        wheel
+        setuptools
+        --user
+        --upgrade
+    - name: Build a binary wheel and a source tarball
+      run: >-
+        python3
+        setup.py
+        sdist
+        bdist_wheel
+    - name: Publish distribution 📦 to PyPI
+      uses: pypa/gh-action-pypi-publish@master
+      with:
+        password: ${{ secrets.pypi_password }}
diff --git a/.gitignore b/.gitignore
@@ -6,7 +6,7 @@ __pycache__/
 *$py.class
 *.pyc
 
-# Test config 
+# Test config
 /pymaid/tests/config_test.py
 
 # Coverage
@@ -30,7 +30,7 @@ env/
 build/
 generated/
 develop-eggs/
-#dist/
+dist/
 downloads/
 eggs/
 .eggs/

diff --git a/.travis.yml b/.travis.yml
@@ -4,7 +4,7 @@ services:
   - xvfb
 language: python
 python:
-  - "3.6"
+  - "3.7"
 # command to install dependencies
 install:
   - pip install -U pip

diff --git a/README.md b/README.md
@@ -2,28 +2,33 @@
 
 <img src="https://github.com/schlegelp/pyMaid/raw/master/docs/_static/favicon.png" height="30"> pymaid
 ======================================================================================================
-Collection of [Python](http://www.python.org) 3 tools to interface with [CATMAID](https://github.com/catmaid/CATMAID "CATMAID Repo") servers.
-Tested with CATMAID release version 2018.07.19 - if you are working with older versions you may run into issues due to API changes.
+Python-Catmaid - or pymaid - is a collection of [Python](http://www.python.org) 3 tools to interface with [CATMAID](https://github.com/catmaid/CATMAID "CATMAID Repo") servers.
+Tested with CATMAID release version 2020.02.15 - if you are working with older versions you may run into issues due to API changes.
 
 ## Documentation
 Pymaid is on [ReadTheDocs](http://pymaid.readthedocs.io/ "pymaid ReadTheDocs").
 
 ## Features
-
 * fetch data via CATMAID's API
-* custom neuron classes that perform on-demand data fetching
-* interactive 2D (matplotlib) and 3D (vispy or plotly) plotting of neurons
-* virtual neuron surgery: cutting, pruning, rerooting
-* clustering methods (e.g. by connectivity or synapse placement)
-* R bindings (e.g. for libraries [nat](https://github.com/jefferis/nat), [rcatmaid](https://github.com/jefferis/rcatmaid), [elmr](https://github.com/jefferis/elmr), [catnat](https://github.com/alexanderbates/catnat) )
-* interface with NetworkX and iGraph
 * tools to analyse user stats (e.g. time-invested, project history)
-* interface with Blender 3D
+* custom neuron classes that work with [navis](https://navis.readthedocs.io)
+* clustering methods (e.g. by connectivity or synapse placement)
 
 ## Getting started
 See the [documentation](http://pymaid.readthedocs.io/ "PyMaid ReadTheDocs") for detailed installation instructions, tutorials and examples. For the impatient:
 
-`pip install git+git://github.com/schlegelp/pymaid@master`
+```bash
+pip3 install python-catmaid
+```
+
+*Important*: there is a `pymaid` package on PyPI which has _nothing_ to do with
+this pymaid!
+
+To install bleeding edge from Github:
+
+```bash
+pip3 install git+git://github.com/schlegelp/pymaid@master
+```
 
 Alternatively click on the *launch binder* badge above to try out pymaid hosted by [mybinder](https://mybinder.org)!
 
@@ -51,4 +56,3 @@ Schlegel P, Texada MJ, Miroschnikow A, Schoofs A, Hueckesfeld S, Peters M, ... P
 *Quantitative neuroanatomy for connectomics in Drosophila.*
 Schneider-Mizell CM, Gerhard S, Longair M, Kazimiers T, Li, Feng L, Zwart M ... Cardona A.
 [link](https://elifesciences.org/articles/12059)
-
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diff --git a/docs/conf.py b/docs/conf.py
@@ -42,6 +42,8 @@
 
                 'pandas',
 
+                'pint',
+
                 'bpy', 'bmesh',
 
                 'pyoctree',
@@ -148,9 +150,12 @@
     #'sphinx.ext.mathjax', # mathjax is interactive and configurable but can also misbehave when rendering - switched to imgmath instead
     'sphinx.ext.imgmath',
     'matplotlib.sphinxext.plot_directive',
+    'sphinx.ext.intersphinx'
     #'numpydoc'
 ]
 
+intersphinx_mapping = {'navis': ('https://navis.readthedocs.io/en/latest/', None)}
+
 # Include the example source for plots in API docs
 plot_include_source = True
 plot_formats = [("png", 90)]

diff --git a/docs/index.rst b/docs/index.rst
@@ -1,20 +1,18 @@
-pymaid: neuron analysis toolbox
-===============================
+pymaid: a Python-CATMAID interface
+==================================
 
 .. raw:: html
 
    <div class="container-fluid">
       <div class="row">
          <div class="col-lg-6">
 
-Pymaid is a Python library for **visualisation** and **analysis** of **neuron data**
-generated with `CATMAID <http://catmaid.readthedocs.io/en/stable/>`_. It allows you to
-fetch, analyse and plot neuron morpholgy and connectivity from a CATMAID server.
+``pymaid`` (short for "Python-CATMAID") is a Python library for fetching,
+analyzing and visualisating data generated with
+`CATMAID <http://catmaid.readthedocs.io/en/stable/>`_.
 
-The package is stable but I recommend watching its
-`Github repository <https://github.com/schlegelp/PyMaid>`_ for updates.
-Make sure that your ``pymaid.__version__`` is up-to-date and check out the
-:ref:`release notes <whats_new>`.
+``pymaid`` is built on top of `navis <https://navis.readthedocs.io/en/latest/>`_
+and is fully compatible with its functions.
 
 For a brief introduction to the library, you can read the
 :ref:`tutorial <tutorial>`. Visit the
@@ -28,6 +26,10 @@ and bug reports are very welcome and best placed in
 `issues <https://github.com/schlegelp/PyMaid/issues>`_.
 If you have any questions, please don't hesitate: [email protected]
 
+The package is stable but I recommend watching its
+`Github repository <https://github.com/schlegelp/PyMaid>`_ for updates.
+Make sure that your ``pymaid.__version__`` is up-to-date and check out the
+:ref:`release notes <whats_new>`.
 
 .. raw:: html
 
@@ -62,14 +64,10 @@ If you have any questions, please don't hesitate: [email protected]
                </div>
                <div class="panel-body">
 
-* data fetching directly from CATMAID server
-* 2D (matplotlib) and 3D (vispy or plotly) plotting
-* virtual neuron surgery (cutting, stitching, pruning, rerooting)
-* R bindings (e.g. for libraries nat, nat.nblast and elmr)
-* interface with Blender 3D and Cytoscape
-* import/export from/to SWC
-* EM image data processing
-* data snapshots
+* fetch data directly from CATMAID server
+* write data (e.g. annotations, tags, neurons) to the server
+* fully compatible with `navis <https://navis.readthedocs.io/en/latest/>`_
+* high-level functions to analyze e.g. connectivity
 
 .. raw:: html
 
@@ -78,4 +76,3 @@ If you have any questions, please don't hesitate: [email protected]
          </div>
       </div>
    </div>
-