Merge branch 'fathon-dev'

stfbnc · Jan 10, 2021 · 99fb113 · 99fb113
2 parents f0408fc + d85db8f
commit 99fb113
Show file tree

Hide file tree

Showing 60 changed files with 675 additions and 581 deletions.
diff --git a/.appveyor.yml b/.appveyor.yml
@@ -0,0 +1,56 @@
+branches:
+  only:
+    - master
+
+environment:
+  global:
+    PYTHON: "C:\\Python37-x64"
+    PYTHON_VERSION: "3.7.x"
+    PYTHON_ARCH: "64"
+    CIBW_BUILD_VERBOSITY: 1
+    CIBW_TEST_REQUIRES: pytest
+    CIBW_TEST_COMMAND: "pytest %APPVEYOR_BUILD_FOLDER%\\tests"
+    CIBW_BEFORE_BUILD: "python -m pip install -r requirements.txt"
+
+  matrix:
+    - CIBW_BUILD: "cp35-win_amd64"
+    - CIBW_BUILD: "cp36-win_amd64"
+    - CIBW_BUILD: "cp37-win_amd64"
+    - CIBW_BUILD: "cp38-win_amd64"
+    - CIBW_BUILD: "cp39-win_amd64"
+
+stack: python 3.7
+
+init:
+  - cmd: PATH=%PYTHON%;%PYTHON%\Scripts;%PATH%
+
+install:
+  ### GSL ###
+  - cd C:\Tools\vcpkg
+  - git pull
+  - .\bootstrap-vcpkg.bat
+  - .\vcpkg integrate install
+  - .\vcpkg.exe install gsl:x64-windows-static
+  - md %APPVEYOR_BUILD_FOLDER%\fathon\3rd_party\gsl\include
+  - xcopy C:\Tools\vcpkg\packages\gsl_x64-windows-static\include %APPVEYOR_BUILD_FOLDER%\fathon\3rd_party\gsl\include /f /s /e
+  - md %APPVEYOR_BUILD_FOLDER%\fathon\3rd_party\gsl\lib
+  - xcopy C:\Tools\vcpkg\packages\gsl_x64-windows-static\lib %APPVEYOR_BUILD_FOLDER%\fathon\3rd_party\gsl\lib /f /s /e
+  ### PYTHON ###
+  - "python -m pip install --upgrade pip"
+  - "python -m pip install --upgrade cibuildwheel"
+  - "python -m pip install --upgrade twine"
+
+build_script:
+  - cd %APPVEYOR_BUILD_FOLDER%
+  - "python --version"
+  - "python -c \"import struct; print(struct.calcsize('P') * 8)\""
+  - "python -m pip --version"
+  - "python -m twine --version"
+  - "python -m cibuildwheel --output-dir wheelhouse"
+  - dir wheelhouse
+  - ps: >-
+      if ($env:PYPI_UPLOAD -eq "test") {
+        python -m twine upload --skip-existing wheelhouse\* --repository-url https://test.pypi.org/legacy/ -u $env:TEST_PYPI_USR -p $env:TEST_PYPI_PWD
+      } elseif ($env:PYPI_UPLOAD -eq "release") {
+        python -m twine upload --skip-existing wheelhouse\* -u $env:PYPI_USR -p $env:PYPI_PWD
+      }
diff --git a/.travis.yml b/.travis.yml
@@ -11,20 +11,70 @@ env:
 
 matrix:
   include:
-    # ===== Linux ======
-    #- name: "Python 3.7 on Linux"
-    #  env:
-    #    - CIBW_BUILD="cp35-manylinux* cp36-manylinux* cp37-manylinux* cp38-manylinux*"
-    #    - CIBW_SKIP: "*-manylinux_i686"
-    #  language: python
-    #  dist: xenial
-    #  sudo: required
-    #  python: "3.7"
-    #  services:
-    #    - docker
-    # ===== Linux ======
-    - name: "Python 3.7 on Linux"
+    ##### Linux #####
+    ##### ARM #####
+    ### 3.5 ###
+    - name: "Python 3.5 on Linux arm64"
+      arch:
+        - arm64
       env:
+        - CIBW_MANYLINUX_AARCH64_IMAGE: manylinux2014
+        - CIBW_BUILD="cp35-manylinux*"
+        - CIBW_SKIP: "*-manylinux_i686"
+      language: python
+      dist: xenial
+      sudo: required
+      python: "3.7"
+      services:
+        - docker
+    ### 3.6 ###
+    - name: "Python 3.6 on Linux arm64"
+      arch:
+        - arm64
+      env:
+        - CIBW_MANYLINUX_AARCH64_IMAGE: manylinux2014
+        - CIBW_BUILD="cp36-manylinux*"
+        - CIBW_SKIP: "*-manylinux_i686"
+      language: python
+      dist: xenial
+      sudo: required
+      python: "3.7"
+      services:
+        - docker
+    ### 3.7 ###
+    - name: "Python 3.7 on Linux arm64"
+      arch:
+        - arm64
+      env:
+        - CIBW_MANYLINUX_AARCH64_IMAGE: manylinux2014
+        - CIBW_BUILD="cp37-manylinux*"
+        - CIBW_SKIP: "*-manylinux_i686"
+      language: python
+      dist: xenial
+      sudo: required
+      python: "3.7"
+      services:
+        - docker
+    ### 3.8 ###
+    - name: "Python 3.8 on Linux arm64"
+      arch:
+        - arm64
+      env:
+        - CIBW_MANYLINUX_AARCH64_IMAGE: manylinux2014
+        - CIBW_BUILD="cp38-manylinux*"
+        - CIBW_SKIP: "*-manylinux_i686"
+      language: python
+      dist: xenial
+      sudo: required
+      python: "3.7"
+      services:
+        - docker
+    ### 3.9 ###
+    - name: "Python 3.9 on Linux arm64"
+      arch:
+        - arm64
+      env:
+        - CIBW_MANYLINUX_AARCH64_IMAGE: manylinux2014
         - CIBW_BUILD="cp39-manylinux*"
         - CIBW_SKIP: "*-manylinux_i686"
       language: python
@@ -33,27 +83,108 @@ matrix:
       python: "3.7"
       services:
         - docker
-    # ======= macOS ========
-    #- name: "Python 3.7 on macOS 10.14 (1)"
-    #  env:
-    #    - CIBW_BUILD="cp35-macosx* cp36-macosx*"
-    #  os: osx
-    #  osx_image: xcode10.2
-    #  language: shell
-    # ======= macOS ========
-    #- name: "Python 3.7 on macOS 10.14 (2)"
-    #  env:
-    #    - CIBW_BUILD="cp37-macosx* cp38-macosx*"
-    #  os: osx
-    #  osx_image: xcode10.2
-    #  language: shell
-    # ======= macOS ========
-    #- name: "Python 3.7 on macOS 10.14 (3)"
-    #  env:
-    #    - CIBW_BUILD="cp39-macosx*"
-    #  os: osx
-    #  osx_image: xcode10.2
-    #  language: shell
+    ##### x86_64 #####
+    ### 3.5 ###
+    - name: "Python 3.5 on Linux amd64"
+      arch:
+        - amd64
+      env:
+        - CIBW_BUILD="cp35-manylinux*"
+        - CIBW_SKIP: "*-manylinux_i686"
+      language: python
+      dist: xenial
+      sudo: required
+      python: "3.7"
+      services:
+        - docker
+    ### 3.6 ###
+    - name: "Python 3.6 on Linux amd64"
+      arch:
+        - amd64
+      env:
+        - CIBW_BUILD="cp36-manylinux*"
+        - CIBW_SKIP: "*-manylinux_i686"
+      language: python
+      dist: xenial
+      sudo: required
+      python: "3.7"
+      services:
+        - docker
+    ### 3.7 ###
+    - name: "Python 3.7 on Linux amd64"
+      arch:
+        - amd64
+      env:
+        - CIBW_BUILD="cp37-manylinux*"
+        - CIBW_SKIP: "*-manylinux_i686"
+      language: python
+      dist: xenial
+      sudo: required
+      python: "3.7"
+      services:
+        - docker
+    ### 3.8 ###
+    - name: "Python 3.8 on Linux amd64"
+      arch:
+        - amd64
+      env:
+        - CIBW_BUILD="cp38-manylinux*"
+        - CIBW_SKIP: "*-manylinux_i686"
+      language: python
+      dist: xenial
+      sudo: required
+      python: "3.7"
+      services:
+        - docker
+    ### 3.9 ###
+    - name: "Python 3.9 on Linux amd64"
+      arch:
+        - amd64
+      env:
+        - CIBW_BUILD="cp39-manylinux*"
+        - CIBW_SKIP: "*-manylinux_i686"
+      language: python
+      dist: xenial
+      sudo: required
+      python: "3.7"
+      services:
+        - docker
+    ##### macOS #####
+    ### 3.5 ###
+    - name: "Python 3.5 on macOS 10.14"
+      env:
+        - CIBW_BUILD="cp35-macosx*"
+      os: osx
+      osx_image: xcode10.2
+      language: shell
+    ### 3.6 ###
+    - name: "Python 3.6 on macOS 10.14"
+      env:
+        - CIBW_BUILD="cp36-macosx*"
+      os: osx
+      osx_image: xcode10.2
+      language: shell
+    ### 3.7 ###
+    - name: "Python 3.7 on macOS 10.14"
+      env:
+        - CIBW_BUILD="cp37-macosx*"
+      os: osx
+      osx_image: xcode10.2
+      language: shell
+    ### 3.8 ###
+    - name: "Python 3.8 on macOS 10.14"
+      env:
+        - CIBW_BUILD="cp38-macosx*"
+      os: osx
+      osx_image: xcode10.2
+      language: shell
+    ### 3.9 ###
+    - name: "Python 3.9 on macOS 10.14"
+      env:
+        - CIBW_BUILD="cp39-macosx*"
+      os: osx
+      osx_image: xcode10.2
+      language: shell
 
 before_install:
   - python3 --version
@@ -70,4 +201,8 @@ script:
     elif [ "$TRAVIS_OS_NAME" = "osx" ]; then
       pip install twine;
     fi
-  - twine upload --skip-existing wheelhouse/* -u ${PYPI_USR} -p ${PYPI_PWD}
+  - if [ "$PYPI_UPLOAD" = "test" ]; then
+      twine upload --skip-existing wheelhouse/* --repository-url https://test.pypi.org/legacy/ -u ${TEST_PYPI_USR} -p ${TEST_PYPI_PWD};
+    elif [ "$PYPI_UPLOAD" = "release" ]; then
+      twine upload --skip-existing wheelhouse/* -u ${PYPI_USR} -p ${PYPI_PWD};
+    fi
diff --git a/README.md b/README.md
@@ -1,13 +1,11 @@
-# fathon [![Build Status](https://travis-ci.org/stfbnc/fathon.svg?branch=master)](https://travis-ci.org/stfbnc/fathon)
+# fathon [![Build Status](https://travis-ci.org/stfbnc/fathon.svg?branch=master)](https://travis-ci.org/stfbnc/fathon)[![Build status](https://ci.appveyor.com/api/projects/status/tl2a8c84bbvxu37p?svg=true)](https://ci.appveyor.com/project/stfbnc/fathon)
 
 [![Issues](https://img.shields.io/github/issues-raw/stfbnc/fathon.svg?maxAge=25000)](https://github.com/stfbnc/fathon/issues) [![GitHub stars](https://img.shields.io/github/stars/stfbnc/fathon.svg?style=social&label=Stars&style=plastic)]() [![GitHub forks](https://img.shields.io/github/forks/stfbnc/fathon.svg?style=social&label=Fork&style=plastic)]() [![Python 3.5+](https://img.shields.io/badge/python-3.5+-blue.svg)](https://www.python.org/)
 
 [![DOI](https://zenodo.org/badge/214290119.svg)](https://zenodo.org/badge/latestdoi/214290119) [![DOI](https://joss.theoj.org/papers/10.21105/joss.01828/status.svg)](https://doi.org/10.21105/joss.01828)
 
 
 
-:warning::warning: At the moment, `fathon` is only available for Linux (64 bit) and macOS :warning::warning:
-
 `fathon` is a python package for DFA (*Detrended Fluctuation Analysis*) and related algorithms.
 
 It is mostly written in Cython and C in order to speed up computations.
@@ -27,8 +25,13 @@ It is mostly written in Cython and C in order to speed up computations.
 
 ### Prerequisites
 
-- Python 3.5 or higher
+| Linux i686 |    Linux x86_64    |    Linux ARM64     |    macOS x86_64    | Windows 32bit |    Windows 64bit    |
+| :--------: | :----------------: | :----------------: | :----------------: | :-----------: | :-----------------: |
+|    :x:     | :white_check_mark: | :white_check_mark: | :white_check_mark: |      :x:      | :white_check_mark:* |
+
+<sub>*It is possible that OpenMP was not activated during compilation, so `fathon` could run slower on Windows compared to macOS and Linux</sub>
 
+- Python 3.5 or higher
  - numpy (version >= 1.15)
  - Cython
 
@@ -60,10 +63,14 @@ Bianchi, S., (2020). fathon: A Python package for a fast computation of  detrend
 
 ## Version  [![PyPI version](https://badge.fury.io/py/fathon.svg)](https://badge.fury.io/py/fathon)
 
-fathon v1.1
+fathon v1.2
 
 ## Changelog
 
+#### v1.2
+
+- few adjustments to C extensions for Windows' C compiler compatibility
+
 #### v1.1
 
 - save object state to binary file and reload it later

diff --git a/docs/Makefile b/docs/Makefile
@@ -4,7 +4,7 @@
 # You can set these variables from the command line, and also
 # from the environment for the first two.
 SPHINXOPTS    ?=
-SPHINXBUILD   ?= "$(HOME)/.local/bin/sphinx-build"
+SPHINXBUILD   ?= "/anaconda3/bin/sphinx-build"
 SOURCEDIR     = .
 BUILDDIR      = _build
 

diff --git a/docs/_build/doctrees/environment.pickle b/docs/_build/doctrees/environment.pickle
diff --git a/docs/_build/doctrees/fun_class/fathon.DCCA.doctree b/docs/_build/doctrees/fun_class/fathon.DCCA.doctree
diff --git a/docs/_build/doctrees/fun_class/fathon.DFA.doctree b/docs/_build/doctrees/fun_class/fathon.DFA.doctree
diff --git a/docs/_build/doctrees/fun_class/fathon.HT.doctree b/docs/_build/doctrees/fun_class/fathon.HT.doctree
diff --git a/docs/_build/doctrees/fun_class/fathon.MFDFA.doctree b/docs/_build/doctrees/fun_class/fathon.MFDFA.doctree
diff --git a/docs/_build/doctrees/fun_class/fathon.fathonUtils.doctree b/docs/_build/doctrees/fun_class/fathon.fathonUtils.doctree
diff --git a/docs/_build/doctrees/fun_class/fu/fathonUtils.getObjectMember.doctree b/docs/_build/doctrees/fun_class/fu/fathonUtils.getObjectMember.doctree
diff --git a/docs/_build/doctrees/fun_class/fu/fathonUtils.linRangeByCount.doctree b/docs/_build/doctrees/fun_class/fu/fathonUtils.linRangeByCount.doctree
diff --git a/docs/_build/doctrees/fun_class/fu/fathonUtils.linRangeByStep.doctree b/docs/_build/doctrees/fun_class/fu/fathonUtils.linRangeByStep.doctree
diff --git a/docs/_build/doctrees/fun_class/fu/fathonUtils.powRangeByCount.doctree b/docs/_build/doctrees/fun_class/fu/fathonUtils.powRangeByCount.doctree
diff --git a/docs/_build/doctrees/fun_class/fu/fathonUtils.powRangeByStep.doctree b/docs/_build/doctrees/fun_class/fu/fathonUtils.powRangeByStep.doctree
diff --git a/docs/_build/doctrees/fun_class/fu/fathonUtils.subtractMean.doctree b/docs/_build/doctrees/fun_class/fu/fathonUtils.subtractMean.doctree
diff --git a/docs/_build/doctrees/fun_class/fu/fathonUtils.toAggregated.doctree b/docs/_build/doctrees/fun_class/fu/fathonUtils.toAggregated.doctree
diff --git a/docs/_build/doctrees/index.doctree b/docs/_build/doctrees/index.doctree
diff --git a/docs/_build/html/.buildinfo b/docs/_build/html/.buildinfo
@@ -1,4 +1,4 @@
 # Sphinx build info version 1
 # This file hashes the configuration used when building these files. When it is not found, a full rebuild will be done.
-config: bf8bc797bceb48fe5abc3d1b252c1993
+config: 3f3a3a407d4e9d370d01da6a59f49d6a
 tags: 645f666f9bcd5a90fca523b33c5a78b7
diff --git a/docs/_build/html/_sources/fun_class/fathon.DCCA.rst.txt b/docs/_build/html/_sources/fun_class/fathon.DCCA.rst.txt
@@ -33,7 +33,7 @@ Usage examples
    #initialize non-empty dcca object
    pydcca = fathon.DCCA(a, b)
    #compute fluctuation function and Hurst exponent
-   wins = fu.linRangeByStep(20, 100, step=50)
+   wins = fu.linRangeByStep(20, 1000, step=50)
    n, F = pydcca.computeFlucVec(wins, polOrd=1)
    H, H_intercept = pydcca.fitFlucVec()
 

diff --git a/docs/_build/html/_sources/index.rst.txt b/docs/_build/html/_sources/index.rst.txt
@@ -3,10 +3,10 @@
    You can adapt this file completely to your liking, but it should at least
    contain the root `toctree` directive.
 
-fathon (v1.1)
+fathon (v1.2)
 ***************
 
-Current version is available for Linux (64 bit) and macOS only.
+Current version is available for Linux (x86_64 and ARM64), macOS, and Windows (64bit).
 
 Python package for detrended fluctuation analysis (DFA) and related algorithms.
 `fathon` provides four main algorithms, namely