Add infra files

.all-contributorsrc

@@ -0,0 +1,47 @@
+{
+  "files": [
+    "README.md"
+  ],
+  "imageSize": 100,
+  "commit": false,
+  "contributors": [
+    {
+      "login": "CesarCaballeroGaudes",
+      "name": "Cesar Caballero Gaudes",
+      "avatar_url": "https://avatars1.githubusercontent.com/u/7611340?v=4",
+      "profile": "https://github.com/CesarCaballeroGaudes",
+      "contributions": [
+        "code",
+        "data",
+        "ideas"
+      ]
+    },
+    {
+      "login": "rmarkello",
+      "name": "Ross Markello",
+      "avatar_url": "https://avatars0.githubusercontent.com/u/14265705?v=4",
+      "profile": "http://rossmarkello.com",
+      "contributions": [
+        "infra"
+      ]
+    },
+    {
+      "login": "smoia",
+      "name": "Stefano Moia",
+      "avatar_url": "https://avatars3.githubusercontent.com/u/35300580?v=4",
+      "profile": "https://github.com/smoia",
+      "contributions": [
+        "data",
+        "infra",
+        "projectManagement",
+        "doc"
+      ]
+    }
+  ],
+  "contributorsPerLine": 5,
+  "projectName": "phys2denoise",
+  "projectOwner": "physiopy",
+  "repoType": "github",
+  "repoHost": "https://github.com",
+  "skipCi": true
+}

.gitattributes

@@ -0,0 +1,4 @@
+phys2bids/_version.py export-subst
+
+*.py eol=lf
+*.rst eol=lf

.gitignore

@@ -1,3 +1,4 @@
+### PTYHON
 # Byte-compiled / optimized / DLL files
 __pycache__/
 *.py[cod]
@@ -47,7 +48,6 @@ htmlcov/
 nosetests.xml
 coverage.xml
 *.cover
-*.py,cover
 .hypothesis/
 .pytest_cache/
 
@@ -91,12 +91,8 @@ ipython_config.py
 #   install all needed dependencies.
 #Pipfile.lock
 
-# PEP 582; used by e.g. github.com/David-OConnor/pyflow
-__pypackages__/
-
-# Celery stuff
+# celery beat schedule file
 celerybeat-schedule
-celerybeat.pid
 
 # SageMath parsed files
 *.sage.py
@@ -127,3 +123,5 @@ dmypy.json
 
 # Pyre type checker
 .pyre/
+
+.vscode/

.requires.yml

@@ -0,0 +1,7 @@
+version: 1.0
+requirements:
+  - requirements.txt
+  - setup.py
+  - tox.ini
+  - path: /requirements.txt
+    parser: python/pip

.travis.yml

@@ -0,0 +1,78 @@
+language: python
+sudo: false
+dist: bionic
+services:
+  - xvfb
+notifications:
+  email: change
+
+python:
+  - 3.6
+  - 3.7
+
+env:
+  matrix:
+    - CHECK_TYPE=linting
+    - CHECK_TYPE=docdoctest
+    - CHECK_TYPE=test
+  global:
+    - INSTALL_TYPE=setup
+
+matrix:
+  include:
+    - python: 3.6
+      env:
+        - INSTALL_TYPE=sdist
+        - CHECK_TYPE=test
+    - python: 3.6
+      env:
+        - INSTALL_TYPE=wheel
+        - CHECK_TYPE=test
+
+before_install:
+  - python -m pip install --upgrade pip
+  - if [ "${CHECK_TYPE}" == "linting" ]; then
+      pip install flake8;
+    fi
+  - if [ "${CHECK_TYPE}" == "test" ]; then
+      pip install "pytest>=3.6" pytest-cov coverage coveralls codecov;
+    fi
+  - if [ "${CHECK_TYPE}" == "docdoctest" ]; then
+      pip install "sphinx>2.0" sphinx_rtd_theme pandas sphinx-argparse;
+    fi
+
+install:
+    if [ "${INSTALL_TYPE}" == "setup" ]; then
+      python setup.py install;
+    elif [ "${INSTALL_TYPE}" == "sdist" ]; then
+      python setup.py sdist;
+      pip install dist/*.tar.gz;
+    elif [ "${INSTALL_TYPE}" == "wheel" ]; then
+      python setup.py bdist_wheel;
+      pip install dist/*.whl;
+    else
+      false;
+    fi
+
+script:
+  - |
+    if [ "${CHECK_TYPE}" == "linting" ]; then
+      flake8 phys2denoise;
+    elif [ "${CHECK_TYPE}" == "docdoctest" ]; then
+      cd docs;
+      pip install -r ./requirements.txt;
+      make html;
+      make doctest;
+    elif [ "${CHECK_TYPE}" == "test" ]; then
+      mkdir for_testing && cd for_testing;
+      cp ../setup.cfg ./;
+      args="--doctest-modules --cov-report term-missing --cov=phys2denoise --pyargs"
+      python -m pytest ${args} phys2denoise;
+    else
+      false;
+    fi
+
+after_success:
+  - if [ "${CHECK_TYPE}" == "test" ]; then
+      coveralls; codecov;
+    fi

MANIFEST.in

@@ -0,0 +1,7 @@
+include README.* LICENSE setup* MANIFEST.in requirements.txt
+recursive-include phys2denoise/data *
+recursive-include phys2denoise/heuristics *
+recursive-include phys2denoise/tests/data *
+
+include versioneer.py
+include phys2denoise/_version.py

README.md

@@ -1,2 +1,73 @@
-# phys2denoise
-A collection of scripts to prepare physiological denoise
+<a name="readme"></a>
+<!-- <img alt="Phys2BIDS" src="https://github.com/physiopy/phys2bids/blob/master/docs/_static/phys2bids_logo1280×640.png" height="150"> -->
+
+phys2denoise
+============
+
+<!-- [![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.3653153.svg)](https://doi.org/10.5281/zenodo.3653153) -->
+<!-- [![Build Status](https://travis-ci.org/physiopy/phys2bids.svg?branch=master)](https://travis-ci.org/physiopy/phys2bids) -->
+<!-- [![Join the chat at https://gitter.im/phys2bids/community](https://badges.gitter.im/phys2bids/community.svg)](https://gitter.im/phys2bids/community?utm_source=badge&utm_medium=badge&utm_campaign=pr-badge&utm_content=badge) -->
+<!-- [![Documentation Status](https://readthedocs.org/projects/phys2bids/badge/?version=latest)](https://phys2bids.readthedocs.io/en/latest/?badge=latest) -->
+<!-- [![Requirements Status](https://requires.io/github/physiopy/phys2bids/requirements.svg?branch=master)](https://requires.io/github/physiopy/phys2bids/requirements/?branch=master) -->
+<!-- [![codecov](https://codecov.io/gh/physiopy/phys2bids/branch/master/graph/badge.svg)](https://codecov.io/gh/physiopy/phys2bids) -->
+<!-- ALL-CONTRIBUTORS-BADGE:START - Do not remove or modify this section -->
+<!-- [![All Contributors](https://img.shields.io/badge/all_contributors-11-orange.svg?style=flat)](#contributors-) -->
+<!-- ALL-CONTRIBUTORS-BADGE:END -->
+
+<!-- ``phys2denoise`` is a python3 library meant to format physiological files in BIDS. -->
+<!-- It was born for AcqKnowledge files (BIOPAC), and at the moment it supports -->
+<!-- ``.acq`` files as well as ``.txt`` files obtained by labchart -->
+<!-- (ADInstruments). -->
+<!-- It doesn't support physiological files recorded with the MRI, as you can find a software for it [here](https://github.com/tarrlab/physio2bids). -->
+<!--  -->
+<!-- If you use ``phy2bids`` in your work, please cite it with the zenodo DOI as: -->
+<!--  -->
+<!-- >The phys2bids contributors, Daniel Alcalá, Apoorva Ayyagari, Molly Bright, César Caballero-Gaudes, Vicente Ferrer Gallardo, Soichi Hayashi, Ross Markello, Stefano Moia, Rachael Stickland, Eneko Uruñuela, & Kristina Zvolanek (2020, February 6). physiopy/phys2bids: BIDS formatting of physiological recordings v1.3.0-beta (Version v1.3.0-beta). Zenodo. http://doi.org/10.5281/zenodo.3653153 -->
+<!--  -->
+<!-- [Read the latest documentation](https://phys2bids.readthedocs.io/en/latest/) for more information on phys2bids! -->
+<!--  -->
+<!-- Shortcuts: -->
+<!-- - [Requirements](https://phys2bids.readthedocs.io/en/latest/installation.html#requirements) -->
+<!-- - [Installation](https://phys2bids.readthedocs.io/en/latest/installation.html#linux-and-mac-installation) -->
+<!-- - [Usage](https://phys2bids.readthedocs.io/en/latest/cli.html) -->
+<!-- - [How to use phys2bids](https://phys2bids.readthedocs.io/en/latest/howto.html) -->
+<!-- - [Contributing to phys2bids](https://phys2bids.readthedocs.io/en/latest/contributing.html) -->
+<!-- - [Developer installation](https://phys2bids.readthedocs.io/en/latest/contributing.html#linux-and-mac-developer-installation) -->
+<!-- - [**Contributor guide**](https://phys2bids.readthedocs.io/en/latest/contributorfile.html) -->
+<!-- - [**Code of Conduct**](https://phys2bids.readthedocs.io/en/latest/conduct.html) -->
+
+**The project is currently under development**.
+Any suggestion/bug report is welcome! Feel free to open an issue.
+
+This project follows the [all-contributors](https://github.com/all-contributors/all-contributors) specification. Contributions of any kind welcome!
+
+## Contributors ✨
+
+Thanks goes to these wonderful people ([emoji key](https://allcontributors.org/docs/en/emoji-key)):
+
+<!-- ALL-CONTRIBUTORS-LIST:START - Do not remove or modify this section -->
+<!-- prettier-ignore-start -->
+<!-- markdownlint-disable -->
+
+
+<!-- markdownlint-enable -->
+<!-- prettier-ignore-end -->
+<!-- ALL-CONTRIBUTORS-LIST:END -->
+
+
+License
+-------
+
+Copyright 2019, The Phys2BIDS community.
+
+Licensed under the Apache License, Version 2.0 (the "License");
+you may not use this file except in compliance with the License.
+You may obtain a copy of the License at
+
+http://www.apache.org/licenses/LICENSE-2.0
+
+Unless required by applicable law or agreed to in writing, software
+distributed under the License is distributed on an "AS IS" BASIS,
+WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+See the License for the specific language governing permissions and
+limitations under the License.

codecov.yml

@@ -0,0 +1,35 @@
+codecov:
+  branch: master
+  strict_yaml_branch: master
+  require_ci_to_pass: yes
+  bot: "codecov-io"
+  ci:
+    - "travis.org"
+  max_report_age: 48
+  disable_default_path_fixes: no
+
+coverage:
+  precision: 2
+  round: down
+  range: "60...90"
+
+parsers:
+  gcov:
+    branch_detection:
+      conditional: yes
+      loop: yes
+      method: no
+      macro: no
+
+ignore:
+  - "docs"
+  - "phys2denoise/_version.py"
+  - "**/__init__.py"
+  - "**/**/__init__.py"
+  - "phys2denoise/tests"
+  - "phys2denoise/heuristics"
+
+comment:
+  layout: "reach,diff,flags,tree"
+  behavior: default
+  require_changes: no

phys2denoise/__init__.py

@@ -0,0 +1,4 @@
+
+from ._version import get_versions
+__version__ = get_versions()['version']
+del get_versions