Separate docs packages.

.editorconfig

@@ -0,0 +1,37 @@
+# EditorConfig helps developers define and maintain consistent coding styles between different editors and IDEs
+# More information at https://EditorConfig.org
+
+root = true
+
+# Unix-style newlines with a newline ending every file
+[*]
+end_of_line = lf
+insert_final_newline = true
+trim_trailing_whitespace = true
+charset = utf-8
+indent_style = space
+
+# Python: PEP8 defines 4 spaces for indentation
+[*.{py,java,r,R,sh}]
+indent_size = 4
+
+# The JSON files contain newlines inconsistently
+[*.json]
+indent_size = 2
+insert_final_newline = false
+
+[*.{md,Rmd,rst}]
+trim_trailing_whitespace = false
+indent_size = 2
+
+# Tabs matter for Makefile and .gitmodules
+[{makefile*,Makefile*,*.mk,*.mak,*.makefile,*.Makefile,GNUmakefile,BSDmakefile,make.bat,Makevars*,*.gitmodules}]
+indent_style = tab
+insert_final_newline = false
+
+# Placeholder files
+[{*.gitkeep,__init__.py}]
+insert_final_newline = false
+
+[{LICENSE, VERSION*, requirements*}]
+insert_final_newline = false

.github/ISSUE_TEMPLATE/bug-report.md

@@ -0,0 +1,18 @@
+---
+name: "\U0001F41B Bug report"
+about: Create a report to help us improve
+
+---
+
+<!--
+Thank you for reporting a possible bug in tsfel.
+
+If possible, please provide code that demonstrates the problem, keeping it as
+simple and free of external dependencies as you can.
+-->
+
+* **Version**:
+* **Platform**:
+* **Subsystem**:
+
+<!-- Please provide more details below this comment. -->

.github/ISSUE_TEMPLATE/config.yml

@@ -0,0 +1 @@
+blank_issues_enabled: false

.github/ISSUE_TEMPLATE/feature-request.md

@@ -0,0 +1,20 @@
+---
+name: "\U0001F680 Feature request"
+about: Suggest an idea for this project
+
+---
+
+<!--
+Thank you for suggesting an idea to make tsfel better.
+
+Please fill in as much of the template below as you're able.
+-->
+
+**Is your feature request related to a problem? Please describe.**
+Please describe the problem you are trying to solve.
+
+**Describe the solution you'd like**
+Please describe the desired behavior.
+
+**Describe alternatives you've considered**
+Please describe alternative solutions or features you have considered.

.github/release-drafter.yml

@@ -0,0 +1,27 @@
+categories:
+  - title: ':boom: Breaking Changes'
+    label: 'breaking'
+  - title: ':package: Build System'
+    label: 'build'
+  - title: ':construction_worker: Continuous Integration'
+    label: 'ci'
+  - title: ':books: Documentation'
+    label: 'documentation'
+  - title: ':rocket: Features'
+    label: 'enhancement'
+  - title: ':beetle: Fixes'
+    label: 'bug'
+  - title: ':racehorse: Performance'
+    label: 'performance'
+  - title: ':hammer: Refactoring'
+    label: 'refactoring'
+  - title: ':fire: Removals and Deprecations'
+    label: 'removal'
+  - title: ':lipstick: Style'
+    label: 'style'
+  - title: ':rotating_light: Testing'
+    label: 'testing'
+template: |
+  ## What’s Changed
+
+  $CHANGES

.github/workflows/codeql.yml

@@ -0,0 +1,37 @@
+name: "CodeQL"
+
+on:
+  push:
+    branches: [ master ]
+  pull_request:
+    branches: [ master ]
+  schedule:
+    - cron: '43 5 * * 0'
+
+jobs:
+  analyze:
+    name: Analyze
+    runs-on: ubuntu-latest
+    permissions:
+      actions: read
+      contents: read
+      security-events: write
+
+    strategy:
+      fail-fast: false
+      matrix:
+        language: [ 'python' ]
+
+    steps:
+    - name: Checkout repository
+      uses: actions/checkout@v3
+      with:
+        ref: ${{ github.head_ref }}
+
+    - name: Initialize CodeQL
+      uses: github/codeql-action/init@v1
+      with:
+        languages: ${{ matrix.language }}
+
+    - name: Perform CodeQL Analysis
+      uses: github/codeql-action/analyze@v1

.github/workflows/dlint.yml

@@ -0,0 +1,11 @@
+name: Dlint
+on: [push, pull_request]
+jobs:
+    dlint:
+        runs-on: ubuntu-latest
+        name: Dlint
+        steps:
+            - uses: actions/checkout@v3
+              with:
+                ref: ${{ github.head_ref }}
+            - uses: dlint-py/dlint-action@master

.github/workflows/release-drafter.yml

@@ -0,0 +1,12 @@
+name: Release Drafter
+on:
+  push:
+    branches:
+      - master
+jobs:
+  draft_release:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: release-drafter/[email protected]
+        env:
+          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}

.github/workflows/tests.yaml

@@ -0,0 +1,44 @@
+name: "Tests"
+
+on:
+  push:
+  pull_request:
+    types: [opened, synchronize, reopened]
+
+jobs:
+  test:
+    name: Run template tests
+    strategy:
+      max-parallel: 4
+      fail-fast: false
+      matrix:
+        python-version: ['3.7', '3.8', '3.9']
+        platform: ['ubuntu-18.04', 'ubuntu-20.04', 'macos-latest', 'windows-latest']
+    runs-on: ${{ matrix.platform }}
+    timeout-minutes: 30
+
+    steps:
+    - name: Git Checkout
+      uses: actions/checkout@v3
+      with:
+        ref: ${{ github.head_ref }}
+    - name: Extract branch name
+      run: echo running on branch ${GITHUB_REF##*/}
+    - name: Set up Python ${{ matrix.python-version }}
+      uses: actions/setup-python@v3
+      with:
+        python-version: ${{ matrix.python-version }}
+    - name: Install dependencies
+      run: |
+        python -VV
+        python -m pip install --upgrade pip setuptools
+        pip install -r requirements/requirements.txt
+        pip install -r requirements/requirements-test.txt
+        python -m pip install .
+    - name: Check numpy and scipy flags
+      run: |
+        python -c "import numpy as np; np.show_config()"
+        python -c "import scipy as sp; sp.show_config()"
+    - name: Run pytest
+      run: |
+        python -m pytest -vvv tests

.gitignore

@@ -91,6 +91,9 @@ celerybeat-schedule
 # Environments
 .env
 .venv
+.venv-dev
+.venv-test
+.venv-docs
 env/
 venv/
 ENV/
@@ -115,12 +118,14 @@ dmypy.json
 # Pyre type checker
 .pyre/
 .idea/
+
+# Notebooks
 notebooks/UCI HAR Dataset
 notebooks/__MACOSX
 notebooks/CorrelationReport.html
 notebooks/orange_input_test.csv
 notebooks/orange_input_train.csv
 notebooks/UCI HAR Dataset.zip
 
-
-
+# Test outputs
+output/

.pre-commit-config.yaml

@@ -0,0 +1,101 @@
+---
+##########################################################################################
+#                                                                                        #
+#                       Pre-commit configuration file                                    #
+#                                                                                        #
+#                                                                                        #
+# See https://pre-commit.com for more information                                        #
+# See https://pre-commit.com/hooks.html for more hooks                                   #
+#                                                                                        #
+# To install the git pre-commit hook run:                                                #
+#   pre-commit install                                                                   #
+#   pre-commit autoupdate                                                                #
+# To update the pre-commit hooks run:                                                    #
+#   pre-commit install-hooks                                                             #
+#   pre-commit install --hook-type commit-msg                                            #
+# To run all hooks against current changes in your repository                            #
+#   pre-commit run --all-files                                                           #
+# If you wish to execute an individual hook use pre-commit run <hook_id>. Example:       #
+#   pre-commit run black                                                                 #
+#                                                                                        #
+##########################################################################################
+default_language_version:
+    python: python3
+default_stages: [commit, push]
+fail_fast: false
+repos:
+    - repo: https://github.com/pre-commit/pre-commit-hooks
+      rev: v4.1.0
+      hooks:
+          - id: fix-byte-order-marker
+            name: fix-byte-order-marker
+            description: removes UTF-8 byte order marker
+          - id: trailing-whitespace
+            name: trailing-whitespace
+            description: Trims trailing whitespace
+            args: [--markdown-linebreak-ext=md]
+          - id: end-of-file-fixer
+            name: end-of-file-fixer
+            description: Makes sure files end in a newline and only a newline.
+          - id: check-json
+            name: check-json
+            description: Attempts to load all json files to verify syntax.
+          - id: check-toml
+            name: check-toml
+            description: Attempts to load all TOML files to verify syntax.
+          - id: check-symlinks
+            name: check-symlinks
+            description: Checks for symlinks which do not point to anything.
+          - id: check-added-large-files
+            name: check-added-large-files
+            description: Prevent giant files from being committed.
+          - id: check-case-conflict
+            name: check-case-conflict
+            description: Check for files with names that would conflict on a case-insensitive filesystem like MacOS HFS+ or Windows FAT
+          - id: end-of-file-fixer
+            name: end-of-file-fixer
+            description: Makes sure files end in a newline and only a newline.
+          - id: mixed-line-ending
+            name: mixed-line-ending
+            description: Replaces or checks mixed line ending.
+          - id: check-ast
+            name: check-ast
+            description: Simply check whether files parse as valid python.
+          - id: debug-statements
+            name: debug-statements
+            description: Check for debugger imports and py37+ breakpoint() calls in python source.
+          - id: detect-aws-credentials
+            name: detect-aws-credentials
+            description: Checks for the existence of AWS/Minio secrets that you have set up.
+            args: [--allow-missing-credentials]
+          - id: detect-private-key
+            name: detect-private-key
+            description: Checks for the existence of private keys.
+          - id: requirements-txt-fixer
+            name: requirements-txt-fixer
+            description: Sorts entries in requirements.txt and removes incorrect entries
+    - repo: https://github.com/psf/black
+      rev: 22.3.0
+      hooks:
+          - id: black
+            description: The uncompromising Python code formatter
+    - repo: https://github.com/PyCQA/isort
+      rev: 5.10.1
+      hooks:
+          - id: isort
+            description: Library to sort imports.
+    - repo: https://github.com/asottile/pyupgrade
+      rev: v2.31.1
+      hooks:
+          - id: pyupgrade
+            args: [--py36-plus]
+    - repo: https://github.com/nbQA-dev/nbQA
+      rev: 1.3.1
+      hooks:
+          - id: nbqa-isort
+            additional_dependencies: [isort]
+          - id: nbqa-pyupgrade
+            additional_dependencies: [pyupgrade]
+            args: [--py36-plus]
+          - id: nbqa-black
+            additional_dependencies: [black]

AUTHORS.rst

@@ -2,7 +2,7 @@ Authors
 ==========
 This package is being developed and maintained by `Fraunhofer AICOS <https://www.aicos.fraunhofer.pt/en/home.html>`_.
 
-.. image:: imgs/fhp_logo.png
+.. image:: docs/imgs/fhp_logo.png
     :align: center
     :scale: 25 %
     :alt: FhP-AICOS

MANIFEST.in

@@ -0,0 +1,2 @@
+include LICENSE.txt
+include requirements/*.txt

README.md

@@ -7,14 +7,12 @@
 
 # Time Series Feature Extraction Library
 ## Intuitive time series feature extraction
-This repository hosts the **TSFEL - Time Series Feature Extraction Library** python package. TSFEL assists researchers on exploratory feature extraction tasks on time series without requiring significant programming effort.
+This repository hosts the **TSFEL - Time Series Feature Extraction Library** python package. TSFEL assists researchers on
+exploratory feature extraction tasks on time series without requiring significant programming effort.
 
-Users can interact with TSFEL using two methods:
-##### Online
-It does not requires installation as it relies on Google Colabs and a user interface provided by Google Sheets
 
-##### Offline
-Advanced users can take full potential of TSFEL by installing as a python package
+## Installation
+
 ```python
 pip install tsfel
 ```
@@ -40,10 +38,10 @@ import pandas as pd
 df = pd.read_csv('Dataset.txt')
 
 # Retrieves a pre-defined feature configuration file to extract all available features
-cfg = tsfel.get_features_by_domain()
+cfg = tsfel.feature_extraction.features_settings.get_features_by_domain()
 
 # Extract features
-X = tsfel.time_series_features_extractor(cfg, df)
+X = tsfel.feature_extraction.calc_features.time_series_features_extractor(cfg, df)
 ```
 
 ## Available features
@@ -129,4 +127,7 @@ When using TSFEL please cite the following publication:
 Barandas, Marília and Folgado, Duarte, et al. "*TSFEL: Time Series Feature Extraction Library.*" SoftwareX 11 (2020). [https://doi.org/10.1016/j.softx.2020.100456](https://doi.org/10.1016/j.softx.2020.100456)
 
 ## Acknowledgements
-We would like to acknowledge the financial support obtained from the project Total Integrated and Predictive Manufacturing System Platform for Industry 4.0, co-funded by Portugal 2020, framed under the COMPETE 2020 (Operational Programme  Competitiveness and Internationalization) and European Regional Development Fund (ERDF) from European Union (EU), with operation code POCI-01-0247-FEDER-038436.
+We would like to acknowledge the financial support obtained from the project Total Integrated and Predictive Manufacturing
+System Platform for Industry 4.0, co-funded by Portugal 2020, framed under the COMPETE 2020 (Operational Programme
+Competitiveness and Internationalization) and European Regional Development Fund (ERDF) from European Union (EU),
+with operation code POCI-01-0247-FEDER-038436.