Merge branch 'feature/TravisCI' into develop

.travis.yml

@@ -1,15 +1,15 @@
 language: python
 
 python:
-- 3.6
+- 3.7
 
 matrix:
   include:
   - os: linux
     dist: bionic
     sudo: required
     language: python
-    python: 3.6
+    python: 3.7
     install:
       - wget https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh -O miniconda.sh
       - bash miniconda.sh -b -p $HOME/miniconda
@@ -18,10 +18,9 @@ matrix:
       - conda config --set always_yes yes --set changeps1 no
       - conda update -q conda
       - conda info -a
-      - conda config --add channels conda-forge
-      - conda config --set channel_priority strict
-      - conda create -c conda-forge -n envlipidhunter python=3.7.6
+      - conda create -n envlipidhunter python=3.7.6
       - source activate envlipidhunter
+      - pip install numpy
       - pip install -r requirements.txt
       - conda env export > env.yml
       - ls
@@ -30,15 +29,14 @@ matrix:
     - travis_wait pytest --cov=./
     after_success:
     - travis_wait codecov
-    - conda install -c conda-forge pyside2
     - conda env export > env.yml
     - ls
     - cat env.yml
 
   - os: osx
     sudo: required
     language: sh
-    python: 3.6
+    python: 3.7
     install:
       - wget https://repo.anaconda.com/miniconda/Miniconda3-latest-MacOSX-x86_64.sh -O miniconda.sh
       - bash miniconda.sh -b -p $HOME/miniconda
@@ -47,11 +45,10 @@ matrix:
       - conda config --set always_yes yes --set changeps1 no
       - conda update -q conda
       - conda info -a
-      - conda config --add channels conda-forge
-      - conda config --set channel_priority strict
-      - conda create -c conda-forge -n envlipidhunter python=3.7.6
+      - conda create -n envlipidhunter python=3.7.6
       - source activate envlipidhunter
       - ls
+      - pip install numpy
       - pip install -r requirements.txt
       - conda env export > env.yml
       - ls
@@ -60,14 +57,13 @@ matrix:
       - travis_wait pytest --cov=./
     after_success:
       - travis_wait codecov
-      - conda install -c conda-forge pyside2
       - conda env export > env.yml
       - ls
       - cat env.yml
 
   - os: windows
     language: sh
-    python: 3.6
+    python: 3.7
     env: PATH="/c/tools/miniconda3/:/c/tools/miniconda3/Scripts:/c/tools/miniconda3/bin:$PATH"
     before_install:
     - choco install openssl.light
@@ -76,11 +72,10 @@ matrix:
       - hash -r
       - conda config --set always_yes yes --set changeps1 no
       - conda update -q conda
-      - conda config --add channels conda-forge
-      - conda config --set channel_priority strict
       - source activate base
-      - conda create -c conda-forge -n envlipidhunter python=3.7.6
+      - conda create -n envlipidhunter python=3.7.6
       - source activate envlipidhunter
+      - pip install numpy
       - pip install -r requirements.txt
       - conda env export > env.yml
       - conda list
@@ -89,5 +84,4 @@ matrix:
       - travis_wait pytest --cov=./
     after_success:
       - travis_wait codecov
-      - conda install -c conda-forge pyside2
       - conda list

LibLipidHunter/SpectraReader.py

@@ -22,7 +22,7 @@
 
 import pandas as pd
 import pymzml
-import ms_deisotope
+# import ms_deisotope
 
 from LibLipidHunter.ParallelFunc import ppm_window_para
 

README.md

@@ -84,7 +84,7 @@ https://github.com/SysMedOs/lipidhunter/releases
 
 * Python environment
 
-    + LipidHunter 2 is developed under python 3.6, the current version can still run on python 2.7 (not recommended).
+    + LipidHunter 2 is developed under python 3.7, the current version can still run on python 2.7 (not recommended).
     + The best way is to use virtual environment such as `conda`
     + The requirements is listed in conda_env_{OS}.yml for `conda` users and [requirements.txt](requirements.txt) for `pip` users.
         - conda: run `conda env create -f conda_env.yml` you will get an environment named `envlipidhunter` 

requirements.txt

@@ -1,17 +1,19 @@
-PySide2
 codecov>=2.0.15
-coverage>=4.5.3
+coverage>=4.5.4
 cython>=0.29.14
 matplotlib>=3.1.1
+ms_deisotope>=0.0.9
 natsort>=6.0.0
-numba==0.47.0
-numpy==1.18.1
+numba>=0.47.0
+numpy>=1.18.1
 openpyxl>=2.6.2
-pandas==0.25.3
+regex>=2020.1.8
+pandas>=0.25.3
 plotly>=4.0.0
 pymzml>=2.4.5
+pyside2==5.14.0
 pytest>=5.0.1
 pytest-cov>=2.7.1
 scipy>=1.3.0
 xlrd>=1.2.0
-xlwt>=1.3.0
+xlwt>=1.3.0