Merge pull request #33 from rdemaria/master

From Riccardo (looks heavy)

.flake8

@@ -0,0 +1,5 @@
+[flake8]
+extend-ignore =
+    # See https://github.com/PyCQA/pycodestyle/issues/373
+    E203,
+

.github/workflows/pythonpackage.yml

@@ -0,0 +1,34 @@
+name: Python package
+
+on: [push]
+
+jobs:
+  build:
+
+    runs-on: ubuntu-latest
+    strategy:
+      max-parallel: 4
+      matrix:
+        python-version: [3.6, 3.7]
+
+    steps:
+    - uses: actions/checkout@v1
+    - name: Set up Python ${{ matrix.python-version }}
+      uses: actions/setup-python@v1
+      with:
+        python-version: ${{ matrix.python-version }}
+    - name: Install dependencies
+      run: |
+        python -m pip install --upgrade pip
+        pip install -r requirements.txt
+    - name: Lint with flake8
+      run: |
+        pip install flake8
+        # stop the build if there are Python syntax errors or undefined names
+        flake8 . --count --select=E9,F63,F7,F82 --show-source --statistics
+        # 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
+    - name: Test with pytest
+      run: |
+        pip install pytest
+        pytest

.github/workflows/pythonpublish.yml

@@ -0,0 +1,26 @@
+name: Upload Python Package
+
+on:
+  release:
+    types: [created]
+
+jobs:
+  deploy:
+    runs-on: ubuntu-latest
+    steps:
+    - uses: actions/checkout@v1
+    - name: Set up Python
+      uses: actions/setup-python@v1
+      with:
+        python-version: '3.x'
+    - name: Install dependencies
+      run: |
+        python -m pip install --upgrade pip
+        pip install setuptools wheel twine
+    - name: Build and publish
+      env:
+        TWINE_USERNAME: ${{ secrets.PYPI_USERNAME }}
+        TWINE_PASSWORD: ${{ secrets.PYPI_PASSWORD }}
+      run: |
+        python setup.py sdist bdist_wheel
+        twine upload dist/*

examples/aperture/000_test_aperture.py

@@ -1,23 +1,26 @@
 import numpy as np
+from numpy.random import uniform
+import matplotlib.pyplot as plt
+
 import pysixtrack
 
 p = pysixtrack.Particles()
 
-rect_aperture = pysixtrack.elements.LimitRect( min_x=-1e-2, max_x=2e-2,
-        min_y=-0.5e-2, max_y=2.5e-2)
+rect_aperture = pysixtrack.elements.LimitRect(
+    min_x=-1e-2, max_x=2e-2, min_y=-0.5e-2, max_y=2.5e-2
+)
 
-ellip_aperture = pysixtrack.elements.LimitEllipse(a=1.5e-2, b=.3e-2)
+ellip_aperture = pysixtrack.elements.LimitEllipse(a=1.5e-2, b=0.3e-2)
 
 # Test scalar
-assert(rect_aperture.track(p) is None)
-assert(ellip_aperture.track(p) is None)
+assert rect_aperture.track(p) is None
+assert ellip_aperture.track(p) is None
 
-p.x= 100.
-assert(rect_aperture.track(p)==0)
-assert(ellip_aperture.track(p)==0)
+p.x = 100.0
+assert rect_aperture.track(p) == 0
+assert ellip_aperture.track(p) == 0
 
 # Test vector
-from numpy.random import uniform
 
 N_part = 10000
 
@@ -29,14 +32,10 @@
 rect_aperture.track(p)
 ellip_aperture.track(p)
 
-import matplotlib.pyplot as plt
-
-plt.close('all')
+plt.close("all")
 fig1 = plt.figure(1)
 ax = fig1.add_subplot(111)
 
-ax.plot(p.x, p.y, '.b')
-ax.plot(p.lost_particles[0].x, p.lost_particles[0].y, 'r.')
-ax.plot(p.lost_particles[1].x, p.lost_particles[1].y, 'g.')
-
-plt.show()
+ax.plot(p.x, p.y, ".b")
+ax.plot(p.lost_particles[0].x, p.lost_particles[0].y, "r.")
+ax.plot(p.lost_particles[1].x, p.lost_particles[1].y, "g.")

examples/bbsimple/testbb6d.py

@@ -17,7 +17,7 @@
 line, other_data = pysixtrack.Line.from_sixinput(sixinput)
 
 # Info on sixtrack->pyblep conversion
-iconv = other_data["iconv"]
+iconv = line.other_data["iconv"]
 
 ########################################################
 #                  Search closed orbit                 #
@@ -125,10 +125,15 @@ def compare(prun, pbench, pbench_prev):
         vbench = getattr(pbench, att)
         vbench_prev = getattr(pbench_prev, att)
         diff = vrun - vbench
-        diffrel = abs(1.0 - abs(vrun - vbench_prev) / abs(vbench - vbench_prev))
+        diffrel = abs(
+            1.0 - abs(vrun - vbench_prev) / abs(vbench - vbench_prev)
+        )
         out.append(abs(diff))
         out_rel.append(diffrel)
-        print(f"{att:<5} {vrun:22.13e} {vbench:22.13e} {diff:22.13g} {diffrel:22.13g}")
+        print(
+            f"{att:<5} {vrun:22.13e} {vbench:22.13e}"
+            "{diff:22.13g} {diffrel:22.13g}"
+        )
         if diffrel > 1e-5 or np.isnan(diffrel):
             if np.abs(diff) > 9e-10:
                 print("Too large discrepancy!")

examples/beambeam/testbb6d.py

@@ -14,10 +14,10 @@
 p0c_eV = sixinput.initialconditions[-3] * 1e6
 
 # Build pysixtrack line from sixtrack input
-line, other_data = pysixtrack.Line.from_sixinput(sixinput)
+line = pysixtrack.Line.from_sixinput(sixinput)
 
 # Info on sixtrack->pyblep conversion
-iconv = other_data["iconv"]
+iconv = line.other_data["iconv"]
 
 ########################################################
 #                  Search closed orbit                 #
@@ -125,10 +125,15 @@ def compare(prun, pbench, pbench_prev):
         vbench = getattr(pbench, att)
         vbench_prev = getattr(pbench_prev, att)
         diff = vrun - vbench
-        diffrel = abs(1.0 - abs(vrun - vbench_prev) / abs(vbench - vbench_prev))
+        diffrel = abs(
+            1.0 - abs(vrun - vbench_prev) / abs(vbench - vbench_prev)
+        )
         out.append(abs(diff))
         out_rel.append(diffrel)
-        print(f"{att:<5} {vrun:22.13e} {vbench:22.13e} {diff:22.13g} {diffrel:22.13g}")
+        print(
+            f"{att:<5} {vrun:22.13e} {vbench:22.13e}"
+            "{diff:22.13g} {diffrel:22.13g}"
+        )
         if diffrel > 1e-8 or np.isnan(diffrel):
             if np.abs(diff) > 1e-11:
                 print("Too large discrepancy!")

examples/fodo/benchmark.py

@@ -2,8 +2,8 @@
 import pysixtrack
 
 six = sixtracktools.SixInput(".")
-line, other = pysixtrack.Line.from_sixinput(six)
-iconv = other["iconv"]
+line = pysixtrack.Line.from_sixinput(six)
+iconv = line.other_data["iconv"]
 
 sixdump = sixtracktools.SixDump101("res/dump.dat")[1::2]
 

examples/lhc/benchmark.py

@@ -2,8 +2,8 @@
 import pysixtrack
 
 six = sixtracktools.SixInput(".")
-line, other = pysixtrack.Line.from_sixinput(six)
-iconv = other["iconv"]
+line = pysixtrack.Line.from_sixinput(six)
+iconv = line.other_info["iconv"]
 
 sixdump = sixtracktools.SixDump101("res/dump3.dat")[1::2]
 

examples/load_from_mad/000_from_madx_disabled_bb.py

@@ -8,6 +8,6 @@
 
 mad.call("mad/lhcwbb.seq")
 
-line, other = pysixtrack.Line.from_madx_sequence(mad.sequence.lhcb1)
+line = pysixtrack.Line.from_madx_sequence(mad.sequence.lhcb1)
 
 print(line)

examples/load_from_mad/001_line_with_bb_from_madx.py

@@ -5,7 +5,6 @@
 from cpymad.madx import Madx
 import pysixtrack
 
-from pysixtrack.be_beamfields.tools import norm, find_alpha_and_phi
 from pysixtrack.be_beamfields.tools import get_bb_names_madpoints_sigmas
 from pysixtrack.be_beamfields.tools import shift_strong_beam_based_on_close_ip
 from pysixtrack.be_beamfields.tools import setup_beam_beam_in_line
@@ -64,7 +63,8 @@
 
 # Check number of slices
 assert (
-    len([nn for nn in bb_names_b1 if nn.startswith("bb_ho.l1")]) == (n_slices - 1) / 2
+    len([nn for nn in bb_names_b1 if nn.startswith("bb_ho.l1")])
+    == (n_slices - 1) / 2
 )
 
 # Correct for small shifts between surveys of the two beams
@@ -85,7 +85,9 @@
 mad_ft.use("lhcb1")  # without this the sequence does not work properly
 
 # Build pysixtrack line
-line_for_tracking, _ = pysixtrack.Line.from_madx_sequence(mad_ft.sequence["lhcb1"])
+line_for_tracking = pysixtrack.Line.from_madx_sequence(
+    mad_ft.sequence["lhcb1"]
+)
 
 # Setup 4D and 6D beam beam lenses
 setup_beam_beam_in_line(
@@ -101,18 +103,23 @@
 )
 
 # A check
-assert np.abs(line_for_tracking.get_length() - mad.sequence.lhcb1.beam.circ) < 1e-6
+assert (
+    np.abs(line_for_tracking.get_length() - mad.sequence.lhcb1.beam.circ)
+    < 1e-6
+)
 
 # There is a problem in the mask
 # (the RF frequancy is wrong in the machine for tracking
 # I patch it here -> to be fixed properly!!!!
-line_temp, _ = pysixtrack.Line.from_madx_sequence(mad.sequence.lhcb1)
+line_temp = pysixtrack.Line.from_madx_sequence(mad.sequence.lhcb1)
 dct_correct_cavities = dict(
     zip(*line_temp.get_elements_of_type(pysixtrack.elements.Cavity)[::-1])
 )
 for ii, nn in enumerate(line_for_tracking.element_names):
     if nn in dct_correct_cavities.keys():
-        line_for_tracking.elements[ii].frequency = dct_correct_cavities[nn].frequency
+        line_for_tracking.elements[ii].frequency = dct_correct_cavities[
+            nn
+        ].frequency
 
 # Save line
 with open("line_from_mad.pkl", "wb") as fid:

examples/load_from_mad/002_compare_against_sixinput.py

@@ -47,7 +47,9 @@ def norm(x):
 
         # Check if the relative error is small
         try:
-            diff_rel = norm(np.array(dmad[kk]) - np.array(dsix[kk])) / norm(dmad[kk])
+            diff_rel = norm(np.array(dmad[kk]) - np.array(dsix[kk])) / norm(
+                dmad[kk]
+            )
         except ZeroDivisionError:
             diff_rel = 100.0
         if diff_rel < 3e-5:

examples/load_from_sixtrack_input/000_basics.py

@@ -1,15 +1,16 @@
-# Read sixtrack input using sixtracktools
 import sixtracktools
+import pysixtrack
+import pysixtracklib
+
+# Read sixtrack input using sixtracktools
 
 sixinput = sixtracktools.SixInput("sixtrack_input")
 
 # Build a pysixtrack line from pyblep line
-import pysixtrack
 
-ps_line, other = pysixtrack.Line.from_sixinput(sixinput)
+ps_line = pysixtrack.Line.from_sixinput(sixinput)
 
 # Build a pysixtracklib line from pyblep line
-import pysixtracklib
 
 pslib_line = pysixtracklib.Elements()
 pslib_line.append_line(ps_line)