Enable Flake8 on CI and fix issues

.github/workflows/linting.yml

@@ -0,0 +1,20 @@
+name: Static Analysis
+on: [push, pull_request]
+jobs:
+  python-linting:
+    runs-on: ubuntu-18.04
+    steps:
+    - uses: actions/checkout@v2
+
+    - name: set up Python
+      uses: actions/setup-python@v1
+      with:
+        python-version: 3.8
+
+    - name: install Python packages
+      run: |
+        pip install --upgrade pip
+        pip install --upgrade flake8
+
+    - name: Run flake8 to verify PEP8-compliance of Python code
+      run: flake8 -j3

easybuild/easyconfigs/l/LAMMPS/LAMMPS-3Mar2020-foss-2019b-Python-3.7.4-kokkos.eb

@@ -27,7 +27,7 @@ sources = [
 ]
 checksums = [
     'a1a2e3e763ef5baecea258732518d75775639db26e60af1634ab385ed89224d1',  # stable_3Mar2020.tar.gz
-    '5e5211f64113e8a38c102f8542fd59169b689fdb92afbff29c3b88f802f1a96c',  # lammps_vs_yaff_test_single_point_energy.py
+    'c28fa5a1ea9608e4fd8686937be501c3bed8cc03ce1956f1cf0a1efce2c75349',  # lammps_vs_yaff_test_single_point_energy.py
 ]
 
 local_source_dir_name = '%(namelower)s-%(version)s'

easybuild/easyconfigs/l/LAMMPS/LAMMPS-3Mar2020-foss-2020a-Python-3.8.2-kokkos.eb

@@ -29,7 +29,7 @@ sources = [
 patches = ['lammps-stable_3Mar2020_hack_openmp_gcc9.patch']
 checksums = [
     'a1a2e3e763ef5baecea258732518d75775639db26e60af1634ab385ed89224d1',  # stable_3Mar2020.tar.gz
-    '5e5211f64113e8a38c102f8542fd59169b689fdb92afbff29c3b88f802f1a96c',  # lammps_vs_yaff_test_single_point_energy.py
+    'c28fa5a1ea9608e4fd8686937be501c3bed8cc03ce1956f1cf0a1efce2c75349',  # lammps_vs_yaff_test_single_point_energy.py
     '41a0bcb828be22d38bb489bbd4b1fd7803d7771a2308371f01e961c52b8c869f',  # lammps-stable_3Mar2020_hack_openmp_gcc9.patch
 ]
 

easybuild/easyconfigs/l/LAMMPS/LAMMPS-3Mar2020-intel-2019b-Python-3.7.4-kokkos.eb

@@ -27,7 +27,7 @@ sources = [
 ]
 checksums = [
     'a1a2e3e763ef5baecea258732518d75775639db26e60af1634ab385ed89224d1',  # stable_3Mar2020.tar.gz
-    '5e5211f64113e8a38c102f8542fd59169b689fdb92afbff29c3b88f802f1a96c',  # lammps_vs_yaff_test_single_point_energy.py
+    'c28fa5a1ea9608e4fd8686937be501c3bed8cc03ce1956f1cf0a1efce2c75349',  # lammps_vs_yaff_test_single_point_energy.py
 ]
 
 local_source_dir_name = '%(namelower)s-%(version)s'

easybuild/easyconfigs/l/LAMMPS/LAMMPS-3Mar2020-intel-2020a-Python-3.8.2-kokkos.eb

@@ -28,7 +28,7 @@ sources = [
 patches = ['LAMMPS-3Mar2020_fix-docs-build.patch']
 checksums = [
     'a1a2e3e763ef5baecea258732518d75775639db26e60af1634ab385ed89224d1',  # stable_3Mar2020.tar.gz
-    '5e5211f64113e8a38c102f8542fd59169b689fdb92afbff29c3b88f802f1a96c',  # lammps_vs_yaff_test_single_point_energy.py
+    'c28fa5a1ea9608e4fd8686937be501c3bed8cc03ce1956f1cf0a1efce2c75349',  # lammps_vs_yaff_test_single_point_energy.py
     '7f010853d81022f286cf32e3babe252d5cc7c0bfb274bee5a2c64e810e170239',  # LAMMPS-3Mar2020_fix-docs-build.patch
 ]
 

easybuild/easyconfigs/l/LAMMPS/LAMMPS-7Aug2019-foss-2019b-Python-3.7.4-kokkos.eb

@@ -27,7 +27,7 @@ sources = [
 ]
 checksums = [
     '5380c1689a93d7922e3d65d9c186401d429878bb3cbe9a692580d3470d6a253f',  # stable_7Aug2019.tar.gz
-    '5e5211f64113e8a38c102f8542fd59169b689fdb92afbff29c3b88f802f1a96c',  # lammps_vs_yaff_test_single_point_energy.py
+    'c28fa5a1ea9608e4fd8686937be501c3bed8cc03ce1956f1cf0a1efce2c75349',  # lammps_vs_yaff_test_single_point_energy.py
 ]
 
 local_source_dir_name = '%(namelower)s-%(version)s'

easybuild/easyconfigs/l/LAMMPS/LAMMPS-7Aug2019-intel-2019b-Python-3.7.4-kokkos.eb

@@ -27,7 +27,7 @@ sources = [
 ]
 checksums = [
     '5380c1689a93d7922e3d65d9c186401d429878bb3cbe9a692580d3470d6a253f',  # stable_7Aug2019.tar.gz
-    '5e5211f64113e8a38c102f8542fd59169b689fdb92afbff29c3b88f802f1a96c',  # lammps_vs_yaff_test_single_point_energy.py
+    'c28fa5a1ea9608e4fd8686937be501c3bed8cc03ce1956f1cf0a1efce2c75349',  # lammps_vs_yaff_test_single_point_energy.py
 ]
 
 local_source_dir_name = '%(namelower)s-%(version)s'

easybuild/easyconfigs/l/LAMMPS/lammps_vs_yaff_test_single_point_energy.py

@@ -12,12 +12,9 @@
 
 import numpy as np
 import os
-import h5py
 from mpi4py import MPI
-from glob import glob
-from yaff import *
+from yaff import log, System, angstrom, ForceField, swap_noncovalent_lammps
 from molmod import kjmol
-from io import StringIO
 import tempfile
 
 
@@ -42,31 +39,34 @@ def main():
     np.random.seed(5)
     # Turn off logging for all processes, it can be turned on for one selected process later on
     log.set_level(log.silent)
-    if rank==0: log.set_level(log.medium)
+    if rank == 0:
+        log.set_level(log.medium)
 
     # Load in the structure and the force field
     system = System.from_file(init_chk)
 
     # Initialize the Yaff and LAMMPS force fields
-    rcut = 12*angstrom
-    ff_yaff = ForceField.generate(system, pars_txt, rcut=rcut, smooth_ei=False, gcut_scale=1.5, alpha_scale=3.2)#, tailcorrections=True)
-    ff = swap_noncovalent_lammps(ff_yaff, fn_system='lammps.dat', fn_log="log.lammps", suffix='', fn_table='lammps_smoothei2.table', comm=comm)
+    rcut = 12 * angstrom
+    ff_yaff = ForceField.generate(system, pars_txt, rcut=rcut, smooth_ei=False,
+                                  gcut_scale=1.5, alpha_scale=3.2)  # , tailcorrections=True)
+    ff = swap_noncovalent_lammps(ff_yaff, fn_system='lammps.dat', fn_log="log.lammps",
+                                 suffix='', fn_table='lammps_smoothei2.table', comm=comm)
 
     # Print out the Yaff single-point energy
     print('Yaff energy')
     energy_yaff = ff_yaff.compute()
-    print(energy_yaff/kjmol)
+    print(energy_yaff / kjmol)
     for part in ff_yaff.parts:
-        print('%s: %.3f kJ/mol' %(part.name,part.energy/kjmol))
+        print('%s: %.3f kJ/mol' % (part.name, part.energy / kjmol))
 
     # Print out the LAMMPS single-point energy
     print('LAMMPS energy')
     energy_lammps = ff.compute()
-    print(energy_lammps/kjmol)
+    print(energy_lammps / kjmol)
     for part in ff.parts:
-        print('%s: %.3f kJ/mol' %(part.name,part.energy/kjmol))
+        print('%s: %.3f kJ/mol' % (part.name, part.energy / kjmol))
 
-    assert np.abs(energy_yaff- energy_lammps) < 1*kjmol, "The two energies are not the same"
+    assert np.abs(energy_yaff - energy_lammps) < 1 * kjmol, "The two energies are not the same"
 
 
 INIT_CHK = """bonds                                     kind=intar 592,2
@@ -1274,7 +1274,7 @@ def main():
 
 # Bond parameters
 # ----------------------------------------------------
-# KEY         label0   label1           P_AB          
+# KEY         label0   label1           P_AB
 # ----------------------------------------------------
 FIXQ:BOND      C_PH      C_PH   0.0000928607
 FIXQ:BOND      C_CA      C_PC   0.0432515406

easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.x_mnist-test.py

@@ -19,4 +19,4 @@
 
 model.fit(x_train, y_train, epochs=5)
 
-model.evaluate(x_test,  y_test, verbose=2)
+model.evaluate(x_test, y_test, verbose=2)