Merge pull request #42 from sfarrens/new_release

Added pycodestyle tests and updated release

README.rst

@@ -23,9 +23,9 @@ ModOpt
 
 :Author: Samuel Farrens `(samuel.farrens@cea.fr) <samuel.farrens@cea.fr>`_
 
-:Version: 1.2.0
+:Version: 1.3.0
 
-:Date: 21/11/2018
+:Date: 27/03/2019
 
 :Documentation: |link-to-docs|
 

docs/source/index.rst

@@ -8,9 +8,9 @@ ModOpt Documentation
 
 :Author: Samuel Farrens <samuel.farrens@cea.fr>
 
-:Version: 1.2.0
+:Version: 1.3.0
 
-:Date: 21/11/2018
+:Date: 27/03/2019
 
 ModOpt is a series of Modular Optimisation tools for solving inverse problems.
 

modopt/info.py

@@ -6,12 +6,12 @@
 
 :Author: Samuel Farrens <samuel.farrens@cea.fr>
 
-:Version: 1.2.0
+:Version: 1.3.0
 
 """
 
 # Package Version
-version_info = (1, 2, 0)
+version_info = (1, 3, 0)
 __version__ = '.'.join(str(c) for c in version_info)
 
 __about__ = ('ModOpt \n\n '

modopt/opt/algorithms.py

@@ -4,7 +4,8 @@
 
 This module contains class implementations of various optimisation algoritms.
 
-:Author: Samuel Farrens <samuel.farrens@cea.fr>, Zaccharie Ramzi <zaccharie.ramzi@cea.fr>
+:Author: Samuel Farrens <samuel.farrens@cea.fr>,
+         Zaccharie Ramzi <zaccharie.ramzi@cea.fr>
 
 NOTES
 -----
@@ -260,58 +261,43 @@ class FISTA(object):
         None,  # no restarting
     ]
 
-    def __init__(
-            self,
-            restart_strategy=None,
-            min_beta=None,
-            s_greedy=None,
-            xi_restart=None,
-            a_cd=None,
-            p_lazy=1,
-            q_lazy=1,
-            r_lazy=4,
-        ):
+    def __init__(self, restart_strategy=None, min_beta=None, s_greedy=None,
+                 xi_restart=None, a_cd=None, p_lazy=1, q_lazy=1, r_lazy=4):
+
         if isinstance(a_cd, type(None)):
             self.mode = 'regular'
             self.p_lazy = p_lazy
             self.q_lazy = q_lazy
             self.r_lazy = r_lazy
+
         elif a_cd > 2:
             self.mode = 'CD'
             self.a_cd = a_cd
             self._n = 0
+
         else:
-            raise ValueError(
-                "a_cd must either be None (for regular mode) or a number > 2",
-            )
+            raise ValueError('a_cd must either be None (for regular mode) or '
+                             'a number > 2')
+
         if restart_strategy in self.__class__.__restarting_strategies__:
-            self._check_restart_params(
-                restart_strategy,
-                min_beta,
-                s_greedy,
-                xi_restart,
-            )
+            self._check_restart_params(restart_strategy, min_beta, s_greedy,
+                                       xi_restart)
             self.restart_strategy = restart_strategy
             self.min_beta = min_beta
             self.s_greedy = s_greedy
             self.xi_restart = xi_restart
+
         else:
-            raise ValueError(
-                "Restarting strategy must be one of %s." %
-                ", ".join(self.__class__.__restarting_strategies__)
-            )
+            raise ValueError('Restarting strategy must be one of {}.'.format(
+                             ', '.join(
+                                self.__class__.__restarting_strategies__)))
         self._t_now = 1.0
         self._t_prev = 1.0
         self._delta_0 = None
         self._safeguard = False
 
-    def _check_restart_params(
-            self,
-            restart_strategy,
-            min_beta,
-            s_greedy,
-            xi_restart,
-        ):
+    def _check_restart_params(self, restart_strategy, min_beta, s_greedy,
+                              xi_restart):
         r""" Check restarting parameters
 
         This method checks that the restarting parameters are set and satisfy
@@ -346,23 +332,24 @@ def _check_restart_params(
             When a parameter that should be set isn't or doesn't verify the
             correct assumptions.
         """
+
         if restart_strategy is None:
             return True
+
         if self.mode != 'regular':
-            raise ValueError(
-                "Restarting strategies can only be used with regular mode."
-            )
-        greedy_params_check = (
-            min_beta is None or s_greedy is None or s_greedy <= 1
-        )
+            raise ValueError('Restarting strategies can only be used with '
+                             'regular mode.')
+
+        greedy_params_check = (min_beta is None or s_greedy is None or
+                               s_greedy <= 1)
+
         if restart_strategy == 'greedy' and greedy_params_check:
-            raise ValueError(
-                "You need a min_beta and an s_greedy > 1 for greedy restart."
-            )
+            raise ValueError('You need a min_beta and an s_greedy > 1 for '
+                             'greedy restart.')
+
         if xi_restart is None or xi_restart >= 1:
-            raise ValueError(
-                "You need a xi_restart < 1 for restart."
-            )
+            raise ValueError('You need a xi_restart < 1 for restart.')
+
         return True
 
     def is_restart(self, z_old, x_new, x_old):
@@ -393,18 +380,22 @@ def is_restart(self, z_old, x_new, x_old):
         """
         if self.restart_strategy is None:
             return False
+
         criterion = np.vdot(z_old - x_new, x_new - x_old) >= 0
+
         if criterion:
             if 'adaptive' in self.restart_strategy:
                 self.r_lazy *= self.xi_restart
             if self.restart_strategy in ['adaptive-ii', 'adaptive-2']:
                 self._t_now = 1
+
         if self.restart_strategy == 'greedy':
             cur_delta = np.linalg.norm(x_new - x_old)
             if self._delta_0 is None:
                 self._delta_0 = self.s_greedy * cur_delta
             else:
                 self._safeguard = cur_delta >= self._delta_0
+
         return criterion
 
     def update_beta(self, beta):
@@ -422,9 +413,11 @@ def update_beta(self, beta):
         -------
         float: the new value for the beta parameter
         """
+
         if self._safeguard:
             beta *= self.xi_restart
             beta = max(beta, self.min_beta)
+
         return beta
 
     def update_lambda(self, *args, **kwargs):
@@ -441,12 +434,17 @@ def update_lambda(self, *args, **kwargs):
         Implements steps 3 and 4 from algoritm 10.7 in [B2011]_
 
         """
+
         if self.restart_strategy == 'greedy':
             return 2
+
         # Steps 3 and 4 from alg.10.7.
         self._t_prev = self._t_now
+
         if self.mode == 'regular':
-            self._t_now = (self.p_lazy + np.sqrt(self.r_lazy * self._t_prev ** 2 + self.q_lazy)) * 0.5
+            self._t_now = (self.p_lazy + np.sqrt(self.r_lazy *
+                           self._t_prev ** 2 + self.q_lazy)) * 0.5
+
         elif self.mode == 'CD':
             self._t_now = (self._n + self.a_cd - 1) / self.a_cd
             self._n += 1
@@ -538,7 +536,7 @@ def __init__(self, x, grad, prox, cost='auto', beta_param=1.0,
         else:
             self._check_param_update(lambda_update)
             self._lambda_update = lambda_update
-            self._is_restart = lambda *args, **kwargs:False
+            self._is_restart = lambda *args, **kwargs: False
 
         # Automatically run the algorithm
         if auto_iterate:
@@ -688,8 +686,8 @@ def __init__(self, x, grad, prox_list, cost='auto', gamma_param=1.0,
         self._x_old = np.copy(x)
 
         # Set the algorithm operators
-        (self._check_operator(operator) for operator in [grad, cost]
-         + prox_list)
+        (self._check_operator(operator) for operator in [grad, cost] +
+         prox_list)
         self._grad = grad
         self._prox_list = np.array(prox_list)
         self._linear = linear
@@ -910,7 +908,7 @@ class Condat(SetUp):
     """
 
     def __init__(self, x, y, grad, prox, prox_dual, linear=None, cost='auto',
-                 reweight=None, rho=0.5,  sigma=1.0, tau=1.0, rho_update=None,
+                 reweight=None, rho=0.5, sigma=1.0, tau=1.0, rho_update=None,
                  sigma_update=None, tau_update=None, auto_iterate=True,
                  max_iter=150, n_rewightings=1, metric_call_period=5,
                  metrics={}):
@@ -1070,6 +1068,7 @@ def retrieve_outputs(self):
             metrics[obs.name] = obs.retrieve_metrics()
         self.metrics = metrics
 
+
 class POGM(SetUp):
     r"""Proximal Optimised Gradient Method
 
@@ -1103,28 +1102,13 @@ class POGM(SetUp):
         Option to automatically begin iterations upon initialisation (default
         is 'True')
     """
-    def __init__(
-            self,
-            u,
-            x,
-            y,
-            z,
-            grad,
-            prox,
-            cost='auto',
-            linear=None,
-            beta_param=1.0,
-            sigma_bar=1.0,
-            auto_iterate=True,
-            metric_call_period=5,
-            metrics={},
-        ):
+    def __init__(self, u, x, y, z, grad, prox, cost='auto', linear=None,
+                 beta_param=1.0, sigma_bar=1.0, auto_iterate=True,
+                 metric_call_period=5, metrics={}):
+
         # Set default algorithm properties
-        super(POGM, self).__init__(
-            metric_call_period=metric_call_period,
-            metrics=metrics,
-            linear=linear,
-        )
+        super(POGM, self).__init__(metric_call_period=metric_call_period,
+                                   metrics=metrics, linear=linear)
 
         # set the initial variable values
         (self._check_input_data(data) for data in (u, x, y, z))
@@ -1145,7 +1129,7 @@ def __init__(
 
         # Set the algorithm parameters
         (self._check_param(param) for param in (beta_param, sigma_bar))
-        if not (0 <= sigma_bar <=1):
+        if not (0 <= sigma_bar <= 1):
             raise ValueError('The sigma bar parameter needs to be in [0, 1]')
         self._beta = beta_param
         self._sigma_bar = sigma_bar
@@ -1169,7 +1153,7 @@ def _update(self):
         """
         # Step 4 from alg. 3
         self._grad.get_grad(self._x_old)
-        self._u_new = self._x_old - self._beta *  self._grad.grad
+        self._u_new = self._x_old - self._beta * self._grad.grad
 
         # Step 5 from alg. 3
         self._t_new = 0.5 * (1 + np.sqrt(1 + 4 * self._t_old**2))
@@ -1218,7 +1202,6 @@ def _update(self):
             self.converge = self.any_convergence_flag() or \
                             self._cost_func.get_cost(self._x_new)
 
-
     def iterate(self, max_iter=150):
         r"""Iterate
 

modopt/opt/gradient.py

@@ -168,7 +168,7 @@ def cost(self, method):
         self._cost = check_callable(method)
 
     def trans_op_op(self, data):
-        """Transpose Operation of the Operator
+        r"""Transpose Operation of the Operator
 
         This method calculates the action of the transpose operator on
         the action of the operator on the data

modopt/opt/proximity.py

@@ -292,7 +292,6 @@ def __init__(self, linear_op, prox_op):
         self.op = self._op_method
         self.cost = self._cost_method
 
-
     def _op_method(self, data, extra_factor=1.0):
         r"""Operator method
 

modopt/tests/test_base.py

@@ -42,7 +42,7 @@ def test_rotate_stack(self):
         npt.assert_array_equal(np_adjust.rotate_stack(self.data2),
                                np.array([[[8, 7, 6], [5, 4, 3], [2, 1, 0]],
                                          [[17, 16, 15], [14, 13, 12],
-                                         [11, 10,  9]]]),
+                                         [11, 10, 9]]]),
                                err_msg='Incorrect stack rotation')
 
     def test_pad2d(self):

modopt/tests/test_opt.py

@@ -187,6 +187,7 @@ def test_pogm(self):
             err_msg='Incorrect POGM result.',
         )
 
+
 class CostTestCase(TestCase):
 
     def setUp(self):