Automated publication (#39)

Reformat and add workflow for publishing to PyPi

.github/workflows/python-publish.yml

@@ -0,0 +1,38 @@
+# This workflow will upload a Python Package using Twine when a release is created
+# For more information see: https://help.github.com/en/actions/language-and-framework-guides/using-python-with-github-actions#publishing-to-package-registries
+
+name: Publish Opexebo to PyPi-Test
+
+on:
+  release:
+    types: [created]
+
+
+jobs:
+  build-and-publish:
+    name: Build and publish Opexebo to PyPi-Test
+    runs-on: ubuntu-latest
+    steps:
+    - uses: actions/checkout@master
+    - name: Set up Python
+      uses: actions/setup-python@v2
+      with:
+        python-version: 3.7
+    - name: Install dependencies
+      run: |
+        python -m pip install --upgrade pip
+        pip install -r dev-requirements.txt
+    - name: Build and publish (test-pypi)
+      env:
+        TWINE_USERNAME: '__token__'
+        TWINE_PASSWORD: ${{ secrets.PYPI_TEST_API_TOKEN }}
+        TWINE_REPOSITORY_URL: https://test.pypi.org/legacy/
+      run: |
+        python setup.py sdist bdist_wheel
+        twine upload dist/* --verbose
+    - name: Build and publish (pypi)
+      env:
+        TWINE_USERNAME: '__token__'
+        TWINE_PASSWORD: ${{ secrets.PYPI_API_TOKEN }}
+      run: |
+        twine upload dist/* --verbose

LICENSE

@@ -1,4 +1,20 @@
-(c) Vadim Frolov, 2018
-(c) Simon Ball, 2019, simon.ball@ntnu.no
+Copyright 2018 Simon Ball, Vadim Frolov, Horst Obenhaus
 
-Kavli institute for systems neuroscience, http://www.ntnu.edu/kavli
+Permission is hereby granted, free of charge, to any person obtaining
+a copy of this software and associated documentation files (the
+"Software"), to deal in the Software without restriction, including
+without limitation the rights to use, copy, modify, merge, publish,
+distribute, sublicense, and/or sell copies of the Software, and to
+permit persons to whom the Software is furnished to do so, subject to
+the following conditions:
+
+The above copyright notice and this permission notice shall be
+included in all copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
+EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF
+MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
+NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE
+LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION
+OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION
+WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.

docs/conf.py

@@ -27,9 +27,9 @@
 author = 'Simon Ball'
 
 # The short X.Y version
-version = '0.5.2'
+version = '0.5.5'
 # The full version, including alpha/beta/rc tags
-release = '0.5.2'
+release = '0.5.5'
 
 
 # -- General configuration ---------------------------------------------------

history.md

@@ -0,0 +1,91 @@
+# History
+
+
+## 0.5.5 (2021-06-01)
+
+* Publish to PyPi
+
+
+## 0.5.2 (2021-04-19)
+
+* Support 1D data in spatial occupancy and ratemap
+* Add Opexebo-specific errors
+* Add automated testing prior to release
+* Add `calculate_speed`
+* Add `egocentric_occupancy`
+* Fixed an edge case error in `accumulate_spatial`
+
+
+## 0.4.3 (2020-02-19)
+
+* Substantial cleanup to `accumulate_spatial`
+  - Function was mathematically correct but confusing, due to the difference between opexebo's standard of `(x, y)` and NumPy's standard of `(y, x)`
+* Added `upsampling`
+* Added `circular_mask`
+* Mandatory keyword arguments have been made positional
+* `peak_search` updated to handle issues with MaskedArrays containing negative values
+* Dcumentation expanded, made Sphinx compatible, and published on ReadTheDocs
+* Further work on BorderScore, still experimental though
+  - Functional for Rectangular arenas
+  - Circular arenas are still WIP, should not be relied upon yet.
+
+
+## 0.4.2 (2020-02-05)
+
+* Speedscore modified substantially
+  - Adaptive filtering added, allowing the user to specify an upper speed as a bandwidth
+  - Adaptive filtering adjusted to behave more sensibly in the case of small bin sizes
+  - Speeds are smoothed before correlating
+* Spatial cross correlation added
+* General `bin_number` to `bin_size` code refactored to make future development more consistent
+* Assorted unit tests added, including run-once code removed for speed
+* Fix errors associated with `>` where applied to MaskedArrays (which, unlike ndarrays, do not correctly obey  the symbol)
+
+
+## 0.4.0 (2019-12-10)
+
+* Ratemaps updated to handle walk filter (signature now requires providing animal speeds)
+* Angular occupancy coverage calculation corrected
+* circular arenas now handled in Spatial Occupancy
+* Population Vector Correlation added
+
+
+## 0.3.5 (2019-11-18)
+
+* Assorted bugfixes to HDtuning
+* Gridscore to handle NaNs more gracefully
+
+
+## 0.3.4 (2019-20-25)
+
+* `sep` made an optional dependency
+* Alternative, non `sep` based code uses `skimage`
+* Attempting to use `sep` if not installed with raise an error
+
+
+## 0.3.2 (2019-09-20)
+
+* Consistent calculating of bin numbers when histogramming
+
+
+## 0.3.0 (2019-08-27)
+
+* Third development release
+* Improve NaN handling throughout by moving to MaskedArrays
+* Fix Angular handling to function in seconds instead of frames
+* Remove matplotlib from requirements
+
+
+## 0.2.0 
+
+* Second development release
+  - Implementation of time-map -> rate-map -> (acorr, gridness score)
+  - Implementation of rate-map stats, grid stats
+  - Implementation of angular-map -> tuning-curve -> head direction score, stats.
+  - Non-production-ready implementation of border-score, speed-score. 
+
+
+## 0.1.0 (2018-08-30)
+
+* First development release
+  - Implementation of gridness score, autocorrelogram, place-field detection

opexebo/__init__.py

@@ -19,4 +19,4 @@
 
 __author__ = """Simon Ball"""
 __email__ = 'simon.ball@ntnu.no'
-__version__ = '0.5.2'
+__version__ = '0.5.5'

readme.md

@@ -1,43 +1,27 @@
 # opexebo
 
-
 [![Build Status](https://travis-ci.com/kavli-ntnu/opexebo.svg?branch=master&status=passed)](https://travis-ci.com/kavli-ntnu/opexebo)
 [![codecov](https://codecov.io/gh/kavli-ntnu/opexebo/branch/master/graph/badge.svg)](https://codecov.io/gh/kavli-ntnu/opexebo)
 [![Documentation Status](https://readthedocs.org/projects/opexebo/badge/?version=latest)](https://opexebo.readthedocs.io/en/latest/?badge=latest)
 
+This library provides various analysis tools written by and for the Moser group  at the [Kavli Institute](https://www.ntnu.edu/kavli) in Trondheim. 
 
+The package contains a mixture of translations of the older MatLab based [Behavioural Neurology Toolbox](https://bitbucket.org/cnc-ntnu/bnt), and other functions written only in Python 3, as part of the transition towards providing open access to research code. 
 
-Collections of code in use in the Moser Group at the [Kavli Institute](https://www.ntnu.edu/kavli) in Trondheim
 
 ### Documentation
 
 Specifications and documentation for `opexebo` are available on [Read the Docs](https://opexebo.readthedocs.io/en/latest/).
 
-### Installation
 
+### Installation
 
-Install by using pip:
+Install with pip:
 
-```bash
-pip install git+https://github.com/kavli-ntnu/opexebo.git -U
 ```
-
-A specific revision, branch, tag, or release an be installed with the @ modifier::
-
-```bash
-pip install git+https://github.com/kavli-ntnu/opexebo.git@v0.3.3
+pip install opexebo
 ```
 
-Installing in this way requires having `git`, this can be acquired from::
-
-    https://git-scm.com/download/win
-
-Opexebo has an optional dependency, `sep`, that is not installed by default. To be able to install it, you require a C++ compiler installed on your system. On Linux, `gcc` will do the job. On Windows, the the Microsoft Visual C++ Build Tools fulfil the same role (https://www.microsoft.com/en-us/download/details.aspx?id=48159). To force installation of all optional dependencies, append `#egg[full]` to the install command, for example::
-
-    pip install git+https://github.com/kavli-ntnu/opexebo.git@v0.3.3#egg[full]
-
-
-
-
-​    
+Opexebo has an optional dependency, `sep`, that is not installed by default. To be able to install it, you require a C++ compiler installed on your system. On Linux, `gcc` will do the job. On Windows, the the Microsoft Visual C++ Build Tools fulfil the same role (https://www.microsoft.com/en-us/download/details.aspx?id=48159). To force installation of all optional dependencies, append `[full]` to the install command, for example:
 
+    pip install opexebo[full]

setup.cfg

@@ -1,5 +1,5 @@
 [bumpversion]
-current_version = 0.5.2
+current_version = 0.5.5
 commit = False
 tag = False
 
@@ -36,4 +36,3 @@ release = 0.2.0
 source-dir = 'docs'
 
 [aliases]
-

setup.py

@@ -8,7 +8,7 @@
 with open('readme.md') as readme_file:
     readme = readme_file.read()
 
-with open('HISTORY.rst') as history_file:
+with open('history.md') as history_file:
     history = history_file.read()
 
 here = path.abspath(path.dirname(__file__))
@@ -24,26 +24,28 @@
 test_requirements = [ ]
 
 setup(
+    name='opexebo',
+    description="Collection of python code in Kavli lab.",
+    long_description=readme + '\n\n' + history,
+    long_description_content_type="text/markdown",
+    url='https://github.com/kavli-ntnu/opexebo',
     author="Simon Ball",
     author_email='simon.ball@ntnu.no',
     classifiers=[
+        "License :: OSI Approved :: MIT License",
         'Development Status :: 4 - Beta',
         'Intended Audience :: Developers',
         'Natural Language :: English',
-        'Programming Language :: Python :: 3'
+        'Programming Language :: Python :: 3',
         'Programming Language :: Python :: 3.6',
         'Programming Language :: Python :: 3.7',
         'Programming Language :: Python :: 3.8',
     ],
-    description="Collection of python code in Kavli lab.",
     install_requires=requirements,
     extras_require={"full": optional_requirements},
-    long_description=readme + '\n\n' + history,
     include_package_data=True,
     keywords='neuroscience kavli gridscore',
-    name='opexebo',
     packages=find_packages(include=['opexebo*']),
-    url='https://github.com/kavli-ntnu/opexebo',
-    version='0.5.2',
+    version='0.5.5',
     zip_safe=False,
 )