Merge pull request #1 from DeepanshS/latest

Code cleanup and documentation

Author: deepanshs

.flake8

@@ -1,10 +1,9 @@
 [flake8]
-ignore = E741 W503, E203 E265 C901
-exclude = .eggs,*.egg,build, mrinversion/kernel/__init__.py examples/**
-filename = *.pyx,*.px*, *py
+ignore = E203
+exclude = .eggs,*.egg,build, mrinversion/kernel/__init__.py, mrinversion/utils.py
+filename = *.pyx, *.px*, *py
 max-line-length = 88
-max-complexity = 18
-select = B,C,E,F,W,T4,B9
-
-
-## E203, E266, E501, F403, F811, F841, F401, C901
+max-complexity = 10
+select = C,E,F,W,N8
+count = True
+statistics = True

.github/workflows/continuous-integration-pip.yml

@@ -1,46 +1,40 @@
 # This workflow will install Python dependencies, run tests and lint with a variety of Python versions
 # For more information see: https://help.github.com/actions/language-and-framework-guides/using-python-with-github-actions
 
-name: Python package
+name: CI (pip)
 
 on:
   push:
-    branches: [ master ]
+    branches: [master]
   pull_request:
-    branches: [ master ]
+    branches: [master]
 
 jobs:
   build:
-
     runs-on: ubuntu-latest
     strategy:
       matrix:
         python-version: [3.6, 3.7, 3.8]
 
     steps:
-    - uses: actions/checkout@v2
-    - name: Set up Python ${{ matrix.python-version }}
-      uses: actions/setup-python@v2
-      with:
-        python-version: ${{ matrix.python-version }}
-    - name: Install mrsimulator dependencies
-      run: |
-        sudo apt-get install libopenblas-dev libfftw3-dev -y
-        pip install "numpy>=1.17" cython
-        pip install git+https://github.com/DeepanshS/mrsimulator.git
-    - name: Install mrinversion
-      run: |
-        python -m pip install --upgrade pip
-        pip install flake8 pytest
-        pip install -r requirements.txt
-        pip install -r requirements-dev.txt
-        python setup.py develop
-    - name: Lint with flake8
-      run: |
-        # stop the build if there are Python syntax errors or undefined names
-        flake8 . --count --select=E9,F63,F7,F82 --show-source --statistics --exclude="docs/*"
-        # exit-zero treats all errors as warnings. The GitHub editor is 127 chars wide
-        flake8 . --count --exit-zero --max-complexity=10 --max-line-length=127 --statistics --exclude="docs/* mrinversion/plot.py"
-    - name: Test with pytest
-      run: |
-        pytest --cov=./ --cov-report=xml
+      - uses: actions/checkout@v2
+      - name: Set up Python ${{ matrix.python-version }}
+        uses: actions/setup-python@v2
+        with:
+          python-version: ${{ matrix.python-version }}
+      - name: Install mrinversion
+        run: |
+          python -m pip install --upgrade pip
+          pip install flake8 pytest
+          pip install -r requirements.txt
+          pip install -r requirements-dev.txt
+          python setup.py develop
+      - name: Lint with flake8
+        run: |
+          # stop the build if there are Python syntax errors or undefined names
+          flake8 . --count --select=E9,F63,F7,F82 --show-source --statistics --exclude="docs/*"
+          # exit-zero treats all errors as warnings. The GitHub editor is 127 chars wide
+          flake8 . --count --exit-zero --max-complexity=10 --max-line-length=127 --statistics --exclude="docs/* mrinversion/plot.py"
+      - name: Test with pytest
+        run: |
+          pytest --cov=./ --cov-report=xml

.gitignore

@@ -3,9 +3,6 @@ __pycache__/
 *.py[cod]
 *$py.class
 
-# files
-*.html
-
 #folders
 cython_debug/
 .vscode/**

.pre-commit-config.yaml

@@ -2,47 +2,56 @@ default_language_version:
   python: python3.7
 default_stages: [commit, push, manual]
 repos:
--   repo: https://github.com/ambv/black
+  - repo: https://github.com/ambv/black
     rev: stable
     hooks:
-    - id: black
-      name: black
-      entry: black
-      language_version: python3.7
-      require_serial: true
-      types: [python]
-      files: \.pyi?$
+      - id: black
+        name: black
+        entry: black
+        language_version: python3.7
+        require_serial: true
+        types: [python]
+        files: \.pyi?$
 
--   repo: https://github.com/asottile/blacken-docs
+  - repo: https://github.com/asottile/blacken-docs
     rev: v1.0.0
     hooks:
-    -   id: blacken-docs
+      - id: blacken-docs
         additional_dependencies: [black==19.3b0]
         language: python
         language_version: python3.7
 
--   repo: https://github.com/pre-commit/pre-commit-hooks
+  - repo: https://github.com/pre-commit/pre-commit-hooks
     rev: v1.2.3
     hooks:
-    - id: flake8
-    - id: trailing-whitespace
-      language: python
-      types: [text]
-    - id: debug-statements
-      name: Debug Statements (Python)
-      description: Check for debugger imports and py37+ `breakpoint()` calls in python source.
-      entry: debug-statement-hook
-      language: python
-      types: [python]
-
--   repo: https://github.com/asottile/reorder_python_imports
+      - id: check-yaml
+        language: python
+      - id: check-added-large-files
+        language: python
+      - id: fix-encoding-pragma
+        language: python
+      - id: check-docstring-first
+        language: python
+      - id: flake8
+        language: python
+      - id: end-of-file-fixer
+        language: python
+      - id: trailing-whitespace
+        language: python
+        types: [text]
+      - id: debug-statements
+        name: Debug Statements (Python)
+        description: Check for debugger imports and py37+ `breakpoint()` calls in python source.
+        entry: debug-statement-hook
+        language: python
+        types: [python]
+  - repo: https://github.com/asottile/reorder_python_imports
     rev: v1.4.0
     hooks:
-    - id: reorder-python-imports
-      name: Reorder python imports
-      description: This hook reorders imports in python files.
-      entry: reorder-python-imports
-      language: python
-      types: [python]
-      minimum_pre_commit_version: "0.15.0"
-
+      - id: reorder-python-imports
+        name: Reorder python imports
+        description: This hook reorders imports in python files.
+        entry: reorder-python-imports
+        language: python
+        types: [python]
+        minimum_pre_commit_version: "0.15.0"

.travis.yml

@@ -0,0 +1,27 @@
+os: linux
+dist: xenial
+language: python
+python:
+  - "3.6"
+  - "3.7"
+
+cache: pip
+
+# safelist
+branches:
+  only:
+    - master
+
+before_install:
+  - pip install --upgrade pip
+  - pip install -r requirements-dev.txt
+
+install:
+  - python setup.py develop
+
+# command to run tests
+script:
+  - pytest --cov=./
+
+after_success:
+  - codecov

docs/Makefile

@@ -22,4 +22,4 @@ help:
 
 clean:
 	rm -rf $(BUILDDIR)/*
-	rm -rf auto_examples/
+	rm -rf auto_examples/