25 files changed, 88 insertions, 36 deletions

diff --git a/.travis.yml b/.travis.yml
index 0bac320..3056665 100644
--- a/.travis.yml
+++ b/.travis.yml
@@ -26,10 +26,11 @@ before_install:
 
 install:
   - pip install codecov
-  - pip install -e ".[picoscope_sdk, picoscope_alt, chipwhisperer, test, typecheck]"
+  - pip install -e ".[picoscope_sdk, picoscope_alt, chipwhisperer, test, dev]"
 
 script:
   - make -i typecheck
+  - make -i codestyle
   - make test
 
 after_success:
diff --git a/LICENSE b/LICENSE
index 4b575c2..2df33a6 100644
--- a/LICENSE
+++ b/LICENSE
@@ -1,6 +1,6 @@
 MIT License
 
-Copyright (c) 2018-2019
+Copyright (c) 2018-2020 Jan Jancar
 
 Permission is hereby granted, free of charge, to any person obtaining a copy
 of this software and associated documentation files (the "Software"), to deal
diff --git a/Makefile b/Makefile
index ca481bd..e8609e3 100644
--- a/Makefile
+++ b/Makefile
@@ -18,4 +18,11 @@ test-all:
 typecheck:
 	mypy pyecsca --ignore-missing-imports
 
-.PHONY: test test-plots test-all typecheck
\ No newline at end of file
+codestyle:
+	flake8 --ignore=E501,F405,F403,F401,E126 pyecsca
+
+docs:
+	$(MAKE) -C docs apidoc
+	$(MAKE) -C docs html
+
+.PHONY: test test-plots test-all typecheck codestyle docs
\ No newline at end of file
diff --git a/Pipfile b/Pipfile
index c545fd7..a8bc468 100644
--- a/Pipfile
+++ b/Pipfile
@@ -7,6 +7,7 @@ verify_ssl = true
 nose2 = "*"
 green = "*"
 mypy = "*"
+flake8 = "*"
 sphinx = "*"
 sphinx-autodoc-typehints = "*"
 coverage = "*"
diff --git a/README.md b/README.md
index 42b07ae..20abe8d 100644
--- a/README.md
+++ b/README.md
@@ -20,6 +20,10 @@ and ECC simulation in the [*pyecsca.ec*](pyecsca/ec) package.
  - [atpublic](https://public.readthedocs.io/)
  - [fastdtw](https://github.com/slaypni/fastdtw)
  - [asn1crypto](https://github.com/wbond/asn1crypto)
+ - **Optionally**:
+   - [picosdk](https://github.com/picotech/picosdk-python-wrappers/)
+   - [picoscope](https://github.com/colinoflynn/pico-python)
+   - [chipwhisperer](https://github.com/newaetech/chipwhisperer)
 
 *pyecsca* contains data from the [Explicit-Formulas Database](https://www.hyperelliptic.org/EFD/index.html) by Daniel J. Bernstein and Tanja Lange.
 The data was partially changed, to make working with it easier.
@@ -31,6 +35,7 @@ It also supports working with [Riscure](https://www.riscure.com) Inspector trace
  - [nose2](https://nose2.readthedocs.io)
  - [green](https://github.com/CleanCut/green)
  - [mypy](http://mypy-lang.org/)
+ - [flake8](https://flake8.pycqa.org/)
  - [coverage](https://coverage.readthedocs.io/)
 
 ### Docs
@@ -43,7 +48,7 @@ It also supports working with [Riscure](https://www.riscure.com) Inspector trace
 
     MIT License
 
-    Copyright (c) 2018-2019
+    Copyright (c) 2018-2020 Jan Jancar
     
     Permission is hereby granted, free of charge, to any person obtaining a copy
     of this software and associated documentation files (the "Software"), to deal
diff --git a/docs/Makefile b/docs/Makefile
index 689e069..4f2a169 100644
--- a/docs/Makefile
+++ b/docs/Makefile
@@ -14,8 +14,8 @@ help:
 
 apidoc:
 	mkdir -p api/codegen/
-	sphinx-apidoc ../pyecsca/ --implicit-namespaces --ext-autodoc -f -e -o api/
-	sphinx-apidoc ../../pyecsca-codegen/pyecsca/ --implicit-namespaces --ext-autodoc --no-toc -f -e -o api/codegen/
+	sphinx-apidoc  ../pyecsca/ --implicit-namespaces --ext-autodoc -M -f -e -o api/
+	sphinx-apidoc ../../pyecsca-codegen/pyecsca/ --implicit-namespaces --ext-autodoc -M -no-toc -f -e -o api/codegen/
 	echo "   codegen/pyecsca.codegen" >> api/modules.rst
 
 .PHONY: help apidoc Makefile
diff --git a/docs/index.rst b/docs/index.rst
index 795713b..49bab42 100644
--- a/docs/index.rst
+++ b/docs/index.rst
@@ -39,6 +39,11 @@ Requirements
  - atpublic_
  - fastdtw_
  - asn1crypto_
+ - **Optionally**:
+
+   - picosdk_
+   - picoscope_
+   - chipwhisperer_
 
 *pyecsca* contains data from the `Explicit-Formulas Database`_ by Daniel J. Bernstein and Tanja Lange.
 
@@ -51,6 +56,7 @@ Testing
  - nose2_
  - green_
  - mypy_
+ - flake8
  - coverage_
 
 Docs
@@ -64,7 +70,7 @@ License
 
     MIT License
 
-    Copyright (c) 2018-2019
+    Copyright (c) 2018-2020 Jan Jancar
 
     Permission is hereby granted, free of charge, to any person obtaining a copy
     of this software and associated documentation files (the "Software"), to deal
@@ -93,9 +99,13 @@ this support is very appreciated.
 .. _atpublic: https://public.readthedocs.io/
 .. _fastdtw: https://github.com/slaypni/fastdtw
 .. _asn1crypto: https://github.com/wbond/asn1crypto
+.. _picosdk: https://github.com/picotech/picosdk-python-wrappers/
+.. _picoscope: https://github.com/colinoflynn/pico-python
+.. _chipwhisperer: https://github.com/newaetech/chipwhisperer
 .. _nose2: https://nose2.readthedocs.io
 .. _green: https://github.com/CleanCut/green
 .. _mypy: http://mypy-lang.org/
+.. _flake8: https://flake8.pycqa.org/
 .. _coverage: https://coverage.readthedocs.io/
 .. _sphinx: https://www.sphinx-doc.org/
 .. _sphinx-autodoc-typehints: https://pypi.org/project/sphinx-autodoc-typehints/
diff --git a/pyecsca/ec/__init__.py b/pyecsca/ec/__init__.py
index e69de29..a1fa2ce 100644
--- a/pyecsca/ec/__init__.py
+++ b/pyecsca/ec/__init__.py
@@ -0,0 +1 @@
+"""Package for handling Elliptic Curves."""
diff --git a/pyecsca/ec/coordinates.py b/pyecsca/ec/coordinates.py
index e082a41..89452c9 100644
--- a/pyecsca/ec/coordinates.py
+++ b/pyecsca/ec/coordinates.py
@@ -88,7 +88,7 @@ class EFDCoordinateModel(CoordinateModel):
                         code = parse(line[11:].replace("^", "**"), mode="exec")
                         self.satisfying.append(code)
                     except SyntaxError:
-                        #code = parse(line[11:].replace("=", "==").replace("^", "**"), mode="eval")
+                        # code = parse(line[11:].replace("=", "==").replace("^", "**"), mode="eval")
                         pass
                 elif line.startswith("parameter"):
                     self.parameters.append(line[10:])
diff --git a/pyecsca/ec/curves.py b/pyecsca/ec/curves.py
index de919b8..7fcfcbd 100644
--- a/pyecsca/ec/curves.py
+++ b/pyecsca/ec/curves.py
@@ -85,7 +85,7 @@ SHORT_WEIERSTRASS: Mapping[str, Mapping[str, Any]] = {
         "g": (0x7b6aa5d85e572983e6fb32a7cdebc140,
               0x27b6916a894d3aee7106fe805fc34b44),
         "n": 0x3fffffff7fffffffbe0024720613b5a3,
-        "h":0x4},
+        "h": 0x4},
     "secp160k1": {
         "p": 0xfffffffffffffffffffffffffffffffeffffac73,
         "a": 0x0000000000000000000000000000000000000000,
diff --git a/pyecsca/ec/formula.py b/pyecsca/ec/formula.py
index 2da6ad5..aeed4a6 100644
--- a/pyecsca/ec/formula.py
+++ b/pyecsca/ec/formula.py
@@ -1,6 +1,6 @@
 from ast import parse, Expression, Mult, Add, Sub, Pow, Div
-from typing import List, Set, Any, ClassVar, MutableMapping
 from itertools import product
+from typing import List, Set, Any, ClassVar, MutableMapping
 
 from pkg_resources import resource_stream
 from public import public
@@ -68,6 +68,7 @@ class Formula(object):
         """Number of additions and subtractions."""
         return len(list(filter(lambda op: isinstance(op.operator, (Add, Sub)), self.code)))
 
+
 class EFDFormula(Formula):
 
     def __init__(self, path: str, name: str, coordinate_model: Any):
@@ -116,7 +117,8 @@ class EFDFormula(Formula):
     @property
     def outputs(self):
         return set(var + str(i) for var, i in product(self.coordinate_model.variables,
-                                                      range(self.output_index, self.output_index + self.num_outputs)))
+                                                      range(self.output_index,
+                                                            self.output_index + self.num_outputs)))
 
     def __eq__(self, other):
         if not isinstance(other, EFDFormula):
@@ -126,6 +128,7 @@ class EFDFormula(Formula):
     def __hash__(self):
         return hash(self.name) + hash(self.coordinate_model)
 
+
 @public
 class AdditionFormula(Formula):
     shortname = "add"
diff --git a/pyecsca/ec/model.py b/pyecsca/ec/model.py
index c8a9b46..a313a00 100644
--- a/pyecsca/ec/model.py
+++ b/pyecsca/ec/model.py
@@ -20,8 +20,8 @@ class CurveModel(object):
     to_weierstrass: List[Module]
     from_weierstrass: List[Module]
 
-    #TODO: move the base_formulas into methods, operatin on affine points?
-    #      Also to_weierstrass anf from_weierstrass.
+    # TODO: move the base_formulas into methods, operatin on affine points?
+    #       Also to_weierstrass anf from_weierstrass.
 
     # TODO: __eq__
 
diff --git a/pyecsca/ec/mult.py b/pyecsca/ec/mult.py
index ef74bc8..5a76a18 100644
--- a/pyecsca/ec/mult.py
+++ b/pyecsca/ec/mult.py
@@ -32,7 +32,7 @@ class ScalarMultiplier(object):
                    formula is not None)) != 1:
             raise ValueError
         self.short_circuit = short_circuit
-        self.formulas = {k:v for k, v in formulas.items() if v is not None}
+        self.formulas = {k: v for k, v in formulas.items() if v is not None}
 
     def _add(self, one: Point, other: Point) -> Point:
         if "add" not in self.formulas:
diff --git a/pyecsca/ec/point.py b/pyecsca/ec/point.py
index 368dd0d..b5ba10b 100644
--- a/pyecsca/ec/point.py
+++ b/pyecsca/ec/point.py
@@ -35,7 +35,7 @@ class Point(object):
         for s in self.coordinate_model.satisfying:
             try:
                 ops.add(CodeOp(s))
-            except:
+            except Exception:
                 pass
         affine_model = AffineCoordinateModel(self.coordinate_model.curve_model)
         result_variables = set(map(lambda x: x.result, ops))
diff --git a/pyecsca/sca/__init__.py b/pyecsca/sca/__init__.py
index 4e5c985..3117331 100644
--- a/pyecsca/sca/__init__.py
+++ b/pyecsca/sca/__init__.py
@@ -1,3 +1,5 @@
+"""Package for Side-Channel Analysis."""
+
 from .scope import *
 from .target import *
 from .trace import *
diff --git a/pyecsca/sca/scope/__init__.py b/pyecsca/sca/scope/__init__.py
index d11ed82..b609e94 100644
--- a/pyecsca/sca/scope/__init__.py
+++ b/pyecsca/sca/scope/__init__.py
@@ -1,3 +1,5 @@
+"""Package for handling oscilloscopes for measurement of power/EM traces."""
+
 from typing import Type
 
 from .base import *
@@ -30,9 +32,11 @@ except ImportError:
 PicoScope: Type[Scope]
 if has_picoscope:
     from .picoscope_alt import *
+
     PicoScope = PicoScopeAlt
 elif has_picosdk:
     from .picoscope_sdk import *
+
     PicoScope = PicoScopeSdk
 
 if has_chipwhisperer:
diff --git a/pyecsca/sca/scope/chipwhisperer.py b/pyecsca/sca/scope/chipwhisperer.py
index 60fe7cf..8f5590d 100644
--- a/pyecsca/sca/scope/chipwhisperer.py
+++ b/pyecsca/sca/scope/chipwhisperer.py
@@ -1,47 +1,56 @@
-from typing import Optional, Tuple, Sequence
+from typing import Optional, Tuple, Sequence, Set
 
 import numpy as np
-from chipwhisperer.capture.scopes.base import ScopeTemplate
+from chipwhisperer.capture.scopes.OpenADC import OpenADC
 from public import public
 
 from .base import Scope
 
+
 @public
-class ChipWhispererScope(Scope):
+class ChipWhispererScope(Scope):  # pragma: no cover
     """A ChipWhisperer based scope."""
 
-    def __init__(self, scope: ScopeTemplate):
+    def __init__(self, scope: OpenADC):
         self.scope = scope
+        self.triggers: Set[str] = set()
 
     def open(self) -> None:
         self.scope.con()
 
     @property
     def channels(self) -> Sequence[str]:
-        return ["tio1", "tio2", "tio3", "tio4"]
+        return []
 
     def setup_frequency(self, frequency: int, samples: int) -> Tuple[int, int]:
-        pass
+        self.scope.clock.clkgen_freq = frequency
+        self.scope.samples = samples
+        return self.scope.clock.freq_ctr, self.scope.samples
 
     def setup_channel(self, channel: str, coupling: str, range: float, enable: bool) -> None:
         pass
 
     def setup_trigger(self, channel: str, threshold: float, direction: str, delay: int,
                       timeout: int, enable: bool) -> None:
-        pass
+        if enable:
+            self.triggers.add(channel)
+        elif channel in self.triggers:
+            self.triggers.remove(channel)
+        self.scope.adc.basic_mode = direction
+        self.scope.trigger.triggers = " OR ".join(self.triggers)
 
     def setup_capture(self, channel: str, enable: bool) -> None:
         pass
 
     def arm(self) -> None:
-        pass
+        self.scope.arm()
 
     def capture(self, channel: str, timeout: Optional[int] = None) -> Optional[np.ndarray]:
-        pass
+        self.scope.capture()
+        return self.scope.get_last_trace()
 
     def stop(self) -> None:
         pass
 
     def close(self) -> None:
-        pass
-
+        self.scope.dis()
diff --git a/pyecsca/sca/scope/picoscope_sdk.py b/pyecsca/sca/scope/picoscope_sdk.py
index d44d8c8..e552188 100644
--- a/pyecsca/sca/scope/picoscope_sdk.py
+++ b/pyecsca/sca/scope/picoscope_sdk.py
@@ -1,6 +1,6 @@
 import ctypes
-from time import time_ns, sleep
 from math import log2, floor
+from time import time_ns, sleep
 from typing import Mapping, Optional, MutableMapping, Union, Tuple
 
 import numpy as np
@@ -22,7 +22,7 @@ def adc2volt(adc: Union[np.ndarray, ctypes.c_int16],
 
 def volt2adc(volt: Union[np.ndarray, float],
              volt_range: float, adc_minmax: int) -> Union[
-    np.ndarray, ctypes.c_int16]:  # pragma: no cover
+             np.ndarray, ctypes.c_int16]:  # pragma: no cover
     if isinstance(volt, float):
         return ctypes.c_int16(int((volt / volt_range) * adc_minmax))
     return (volt / volt_range) * adc_minmax
@@ -130,12 +130,14 @@ class PicoScopeSdk(Scope):  # pragma: no cover
             if channel in self.buffers:
                 del self.buffers[channel]
             buffer = (ctypes.c_int16 * self.samples)()
-            assert_pico_ok(self.__dispatch_call("SetDataBuffer", self.handle, self.CHANNELS[channel],
-                                                ctypes.byref(buffer), self.samples))
+            assert_pico_ok(
+                self.__dispatch_call("SetDataBuffer", self.handle, self.CHANNELS[channel],
+                                     ctypes.byref(buffer), self.samples))
             self.buffers[channel] = buffer
         else:
-            assert_pico_ok(self.__dispatch_call("SetDataBuffer", self.handle, self.CHANNELS[channel],
-                                                None, self.samples))
+            assert_pico_ok(
+                self.__dispatch_call("SetDataBuffer", self.handle, self.CHANNELS[channel],
+                                     None, self.samples))
             del self.buffers[channel]
 
     def arm(self):
diff --git a/pyecsca/sca/target/__init__.py b/pyecsca/sca/target/__init__.py
index e69de29..750f885 100644
--- a/pyecsca/sca/target/__init__.py
+++ b/pyecsca/sca/target/__init__.py
@@ -0,0 +1 @@
+"""Package for communicating with targets of measurement."""
diff --git a/pyecsca/sca/trace/__init__.py b/pyecsca/sca/trace/__init__.py
index 62f2864..696e387 100644
--- a/pyecsca/sca/trace/__init__.py
+++ b/pyecsca/sca/trace/__init__.py
@@ -1,3 +1,5 @@
+"""Package for manipulating traces."""
+
 from .align import *
 from .combine import *
 from .edit import *
@@ -6,4 +8,4 @@ from .match import *
 from .process import *
 from .sampling import *
 from .test import *
-from .trace import *
\ No newline at end of file
+from .trace import *
diff --git a/pyecsca/sca/trace/align.py b/pyecsca/sca/trace/align.py
index ff586ab..643efcf 100644
--- a/pyecsca/sca/trace/align.py
+++ b/pyecsca/sca/trace/align.py
@@ -121,6 +121,7 @@ def align_offset(reference: Trace, *traces: Trace,
     :return:
     """
     reference_part = reference.samples[reference_offset: reference_offset + reference_length]
+
     def align_func(trace):
         length = len(trace.samples)
         best_distance = 0
diff --git a/pyecsca/sca/trace/match.py b/pyecsca/sca/trace/match.py
index ba69026..3b4daed 100644
--- a/pyecsca/sca/trace/match.py
+++ b/pyecsca/sca/trace/match.py
@@ -32,6 +32,7 @@ def match_pattern(trace: Trace, pattern: Trace, threshold: float = 0.8) -> List[
                 filtered_peaks.append(peak - half)
     return filtered_peaks
 
+
 @public
 def match_part(trace: Trace, offset: int, length: int) -> List[int]:
     return match_pattern(trace, trim(trace, offset, offset + length))
diff --git a/pyecsca/sca/trace/test.py b/pyecsca/sca/trace/test.py
index 92cda68..f2cfb33 100644
--- a/pyecsca/sca/trace/test.py
+++ b/pyecsca/sca/trace/test.py
@@ -32,7 +32,7 @@ def welch_ttest(first_set: Sequence[Trace], second_set: Sequence[Trace]) -> Opti
 
 @public
 def student_ttest(first_set: Sequence[Trace], second_set: Sequence[Trace]) -> Optional[
-    CombinedTrace]:
+        CombinedTrace]:
     """
     Perform the Students's t-test sample wise on two sets of traces `first_set` and `second_set`.
     Useful for Test Vector Leakage Analysis (TVLA).
diff --git a/pyecsca/sca/trace_set/__init__.py b/pyecsca/sca/trace_set/__init__.py
index 517b3b7..cdede67 100644
--- a/pyecsca/sca/trace_set/__init__.py
+++ b/pyecsca/sca/trace_set/__init__.py
@@ -1,3 +1,5 @@
+"""Package for manipulating, reading and writing trace sets."""
+
 from .base import *
 from .inspector import *
-from .chipwhisperer import *
\ No newline at end of file
+from .chipwhisperer import *
diff --git a/setup.py b/setup.py
index 60941fc..d42b997 100644
--- a/setup.py
+++ b/setup.py
@@ -37,7 +37,7 @@ setup(
             "picoscope_sdk": ["picosdk"],
             "picoscope_alt": ["picoscope"],
             "chipwhisperer": ["chipwhisperer"],
-            "typecheck": ["mypy"],
+            "dev": ["mypy", "flake8"],
             "test": ["nose2", "parameterized", "green", "coverage"]
         }
 )