ci: add flake8 and fix warnings

.github/workflows/lint.yml

@@ -0,0 +1,21 @@
+name: Lint
+
+on: push
+
+jobs:
+  formatting:
+    if: "!contains(github.event.head_commit.message, 'skip_ci')"
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v2
+      - uses: actions/setup-python@v2
+      - run: python -m pip install --upgrade tox
+      - run: tox -e checkformatting
+  flake8:
+    if: "!contains(github.event.head_commit.message, 'skip_ci')"
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v2
+      - uses: actions/setup-python@v2
+      - run: python -m pip install --upgrade tox
+      - run: tox -e flake8

.github/workflows/test.yml

@@ -0,0 +1,24 @@
+name: Pytest
+
+on: push
+
+jobs:
+  test:
+    if: "!contains(github.event.head_commit.message, 'skip_ci')"
+    runs-on: ubuntu-latest
+    strategy:
+        fail-fast: false
+        matrix:
+          python-version: [3.6, 3.7, 3.8]
+
+    name: Python ${{ matrix.python-version }}
+    steps:
+      - uses: actions/checkout@v2
+
+      - name: Set up Python ${{ matrix.python-version }}
+        uses: actions/setup-python@v2
+        with:
+          python-version: ${{ matrix.python-version }}
+
+      - run: python -m pip install --upgrade pip tox
+      - run: tox -e pytest

pyreisejl/utility/call.py

@@ -1,9 +1,7 @@
 import argparse
 import os
-from collections import OrderedDict
 from time import time
 
-import numpy as np
 import pandas as pd
 
 from pyreisejl.utility import const
@@ -87,7 +85,7 @@ def launch_scenario(
     # Import these within function because there is a lengthy compilation step
     from julia.api import Julia
 
-    jl = Julia(compiled_modules=False)
+    Julia(compiled_modules=False)
     from julia import REISE
 
     start = time()

pyreisejl/utility/extract_data.py

@@ -1,11 +1,8 @@
 import argparse
-import datetime as dt
 import glob
 import os
 import re
-import subprocess
 import time
-from collections import OrderedDict
 
 import numpy as np
 import pandas as pd
@@ -74,7 +71,7 @@ def extract_data(results):
     outputs = {}
 
     tic = time.process_time()
-    for filename in tqdm(results):
+    for i, filename in tqdm(enumerate(results)):
         # For each result_#.mat file
         output = load_mat73(filename)
 

pyreisejl/utility/helpers.py

@@ -1,6 +1,6 @@
-from collections import OrderedDict
 import os
 import re
+from collections import OrderedDict
 
 import h5py
 import numpy as np

pyreisejl/utility/tests/test_extract_data.py

@@ -5,7 +5,6 @@
 from pyreisejl.utility.extract_data import (
     _cast_keys_as_lists,
     _get_pkl_path,
-    _update_outputs_labels,
     calculate_averaged_congestion,
     result_num,
 )

pyreisejl/utility/tests/test_helpers.py

@@ -1,6 +1,5 @@
 from io import StringIO
 
-import numpy as np
 import pandas as pd
 import pytest
 

requirements.txt

@@ -1,7 +1,8 @@
-h5py>=2.9.0
-ipython>=7.0
-julia>=0.5.1
-numpy>=1.16.0
-pandas>=0.25.3
-scipy>=1.2
-tqdm>=4.29.1
+h5py~=2.10.0
+ipython~=7.0
+julia~=0.5.1
+numpy~=1.18.5
+pandas~=1.1.3
+scipy~=1.2
+tqdm~=4.29.1
+pytest~=6.1.1

tox.ini

@@ -0,0 +1,21 @@
+[tox]
+envlist = pytest, format, flake8
+skipsdist = true
+
+[testenv]
+deps = 
+    pytest: -rrequirements.txt
+    {format,checkformatting}: black
+    {format,checkformatting}: isort
+    flake8: flake8
+changedir = pyreisejl
+commands =
+    pytest: pytest 
+    format: black .
+    format: isort -m 3 --tc .
+    checkformatting: black . --check --diff
+    checkformatting: isort -m 3 --tc --check --diff .
+    flake8: flake8
+
+[flake8]
+ignore = E501,E731