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Reformat and add workflow for publishing to PyPi
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# 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 | ||
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name: Publish Opexebo to PyPi-Test | ||
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on: | ||
release: | ||
types: [created] | ||
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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 |
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(c) Vadim Frolov, 2018 | ||
(c) Simon Ball, 2019, simon.ball@ntnu.no | ||
Copyright 2018 Simon Ball, Vadim Frolov, Horst Obenhaus | ||
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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: | ||
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The above copyright notice and this permission notice shall be | ||
included in all copies or substantial portions of the Software. | ||
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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. |
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# History | ||
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## 0.5.5 (2021-06-01) | ||
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* Publish to PyPi | ||
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## 0.5.2 (2021-04-19) | ||
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* 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` | ||
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## 0.4.3 (2020-02-19) | ||
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* 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. | ||
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## 0.4.2 (2020-02-05) | ||
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* 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) | ||
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## 0.4.0 (2019-12-10) | ||
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* 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 | ||
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## 0.3.5 (2019-11-18) | ||
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* Assorted bugfixes to HDtuning | ||
* Gridscore to handle NaNs more gracefully | ||
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## 0.3.4 (2019-20-25) | ||
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* `sep` made an optional dependency | ||
* Alternative, non `sep` based code uses `skimage` | ||
* Attempting to use `sep` if not installed with raise an error | ||
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## 0.3.2 (2019-09-20) | ||
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* Consistent calculating of bin numbers when histogramming | ||
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## 0.3.0 (2019-08-27) | ||
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* 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 | ||
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## 0.2.0 | ||
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* 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. | ||
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## 0.1.0 (2018-08-30) | ||
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* First development release | ||
- Implementation of gridness score, autocorrelogram, place-field detection |
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__author__ = """Simon Ball""" | ||
__email__ = 'simon.ball@ntnu.no' | ||
__version__ = '0.5.2' | ||
__version__ = '0.5.5' |
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# opexebo | ||
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[![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) | ||
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This library provides various analysis tools written by and for the Moser group at the [Kavli Institute](https://www.ntnu.edu/kavli) in Trondheim. | ||
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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. | ||
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Collections of code in use in the Moser Group at the [Kavli Institute](https://www.ntnu.edu/kavli) in Trondheim | ||
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### Documentation | ||
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Specifications and documentation for `opexebo` are available on [Read the Docs](https://opexebo.readthedocs.io/en/latest/). | ||
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### Installation | ||
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### Installation | ||
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Install by using pip: | ||
Install with pip: | ||
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```bash | ||
pip install git+https://github.com/kavli-ntnu/opexebo.git -U | ||
``` | ||
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A specific revision, branch, tag, or release an be installed with the @ modifier:: | ||
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```bash | ||
pip install git+https://github.com/kavli-ntnu/opexebo.git@v0.3.3 | ||
pip install opexebo | ||
``` | ||
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Installing in this way requires having `git`, this can be acquired from:: | ||
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https://git-scm.com/download/win | ||
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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:: | ||
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pip install git+https://github.com/kavli-ntnu/opexebo.git@v0.3.3#egg[full] | ||
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| ||
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: | ||
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pip install opexebo[full] |
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