Migrate to python 3.7 (#52) and prepare for release v2.0.0

* Apply 2to3 to get initial version and fix remaining incompatibilities

* Update portals and refactor HDF5 (including pytables) and mzML portals

* Update dependencies and test environment - Travis and AppVeyor

* Add mybinder and initial python notebook (#47)

* Add RTD and clean up docs folder (#51)

.gitignore

@@ -45,6 +45,7 @@ nosetests.xml
 coverage.xml
 *,cover
 .hypothesis/
+debug.py
 
 # Translations
 *.mo
@@ -63,6 +64,7 @@ instance/
 
 # Sphinx documentation
 docs/_build/
+docs/source/images/alignment.graffle
 
 # PyBuilder
 target/
@@ -82,12 +84,16 @@ celerybeat-schedule
 # virtualenv
 .venv
 venv/
+venv-py3/
 ENV/
 
 # PyCharm
 # User-specific stuff:
 .idea/
 
+# vscode
+.vscode
+
 # R-lanaguage
 # History files
 .Rhistory

.readthedocs.yml

@@ -0,0 +1,22 @@
+# .readthedocs.yml
+# Read the Docs configuration file
+# See https://docs.readthedocs.io/en/stable/config-file/v2.html for details
+
+# Required
+version: 2
+
+# Build documentation in the docs/ directory with Sphinx
+sphinx:
+  configuration: docs/source/conf.py
+
+# Optionally build your docs in additional formats such as PDF and ePub
+formats: all
+
+conda:
+  environment: environment.yml
+
+python:
+  version: 3.7
+  install:
+    - method: pip
+      path: .

.travis.yml

@@ -1,23 +1,20 @@
+dist: xenial
 language: python
 python:
-  - "2.7"
+  - "3.7"
 
 install:
   - sudo apt-get update
-  - if [[ "$TRAVIS_PYTHON_VERSION" == "2.7" ]]; then
-      wget https://repo.continuum.io/miniconda/Miniconda2-latest-Linux-x86_64.sh -O miniconda.sh;
-    else
-      wget https://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh -O miniconda.sh;
-    fi
+  - wget https://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh -O miniconda.sh;
   - bash miniconda.sh -b -p $HOME/miniconda
   - export PATH="$HOME/miniconda/bin:$PATH"
   - hash -r
   - conda config --set always_yes yes --set changeps1 no
   - conda update -q conda
   - conda info -a
-
-  - conda create -q -n test-environment python=$TRAVIS_PYTHON_VERSION coverage green codecov --file conda-requirements.txt -c conda-forge -c bioconda
+  - conda env create -n test-environment -f environment.yml
   - source activate test-environment
+  - conda install coverage green codecov -c conda-forge
   - python setup.py install
 
 script:

README.rst

@@ -1,6 +1,6 @@
 DIMSpy
 ======
-|Version| |Py versions| |Git| |Bioconda| |Build Status (Travis)| |Build Status (AppVeyor)| |License| |RTD doc| |codecov|
+|Version| |Py versions| |Git| |Bioconda| |Build Status (Travis)| |Build Status (AppVeyor)| |License| |RTD doc| |codecov| |binder|
 
 Python package to process direct-infusion mass spectrometry-based metabolomics and lipidomics data
 
@@ -67,3 +67,7 @@ Released under the GNU General Public License v3.0 (see `LICENSE file <https://g
 
 .. |codecov| image:: https://codecov.io/gh/computational-metabolomics/dimspy/branch/master/graph/badge.svg
    :target: https://codecov.io/gh/computational-metabolomics/dimspy
+
+.. |binder| image:: https://mybinder.org/badge_logo.svg
+   :target: https://mybinder.org/v2/gh/computational-metabolomics/dimspy/master?filepath=notebooks%2Fworkflow.ipynb
+

appveyor.yml

@@ -2,7 +2,7 @@ build: false
 
 environment:
   matrix:
-    - PYTHON_VERSION: 2.7
+    - PYTHON_VERSION: 3.7
       MINICONDA: C:\Miniconda-x64
 
 init:
@@ -13,7 +13,7 @@ install:
   - conda config --set always_yes yes --set changeps1 no
   - conda update -q conda
   - conda info -a
-  - "conda create -q -n test-environment python=%PYTHON_VERSION% --file conda-requirements.txt -c conda-forge -c bioconda -c pythonnet"
+  - conda env create -n test-environment -f environment_win.yml
   - activate test-environment
   - python setup.py install
 

binder/environment.yml

@@ -0,0 +1,9 @@
+name: dimspy
+channels:
+  - conda-forge
+  - bioconda
+  - computational-metabolomics
+dependencies:
+ - python=3.7
+ - dimspy
+