Merge pull request #222 from ImperialCollegeLondon/dev_env

updating from python 3.7 to 3.10

.github/workflows/sharpy_tests.yaml

@@ -18,7 +18,7 @@ jobs:
     runs-on: ubuntu-latest
     strategy:
       matrix:
-        python-version: [3.7]
+        python-version: [3.10.8]
 
     steps:
       - uses: actions/checkout@v2
@@ -34,24 +34,26 @@ jobs:
       - name: Setup conda
         uses: s-weigand/setup-conda@v1
         with:
-          python-version: 3.7
+          python-version: 3.9
       - name: Pre-Install dependencies
         run: |
           gfortran --version
           wget https://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh -O miniconda.sh;
+          # wget https://repo.anaconda.com/archive/Anaconda3-2022.10-Linux-x86_64.sh -O miniconda.sh;
           bash miniconda.sh -b -p $HOME/miniconda
           export PATH="$HOME/miniconda/bin:$PATH"
           hash -r
           conda config --set always_yes yes --set changeps1 no
+          # conda config --append channels conda-forge
           conda update --name base conda
           conda list --name base conda
           conda init bash
           hash -r
           export QT_QPA_PLATFORM='offscreen'
           sudo apt install libeigen3-dev
-          conda env create -f utils/environment_minimal.yml
+          conda env create -f utils/environment_new.yml
           conda init bash
-          source activate sharpy_minimal
+          source activate sharpy
           git submodule init
           git submodule update
           git fetch --tags -f
@@ -60,7 +62,8 @@ jobs:
           pip install .
           pip install coverage
           coverage run -m unittest discover
+          coverage json
       - name: Upload Coverage to Codecov
-        uses: codecov/codecov-action@v2
+        uses: codecov/codecov-action@v3
         with:
           verbose: true

sharpy/generators/turbvelocityfield.py

@@ -113,9 +113,9 @@ def initialise(self, in_dict, restart=False):
 
         _, self.extension = os.path.splitext(self.settings['turbulent_field'])
 
-        if self.extension is '.h5':
+        if self.extension == '.h5':
             self.read_btl(self.settings['turbulent_field'])
-        if self.extension in '.xdmf':
+        if self.extension == '.xdmf':
             self.read_xdmf(self.settings['turbulent_field'])
 
         if 'z' in self.settings['periodicity']:

sharpy/linear/assembler/lineargustassembler.py

@@ -5,7 +5,7 @@
 import sharpy.utils.settings as settings
 import sharpy.utils.cout_utils as cout
 from abc import ABCMeta, abstractmethod
-
+from scipy import signal
 dict_of_linear_gusts = {}
 
 
@@ -504,9 +504,9 @@ def campbell(sigma_w, length_scale, velocity, dt=None):
     den_tf = np.array([935/216, 561/12, 102, 60])
     if dt is not None:
         num_tf, den_tf, dt = scsig.cont2discrete((num_tf, den_tf), dt, method='bilinear')
-        camp_tf = scsig.ltisys.TransferFunctionDiscrete(num_tf, den_tf, dt=dt)
+        camp_tf = signal.TransferFunction(num_tf, den_tf, dt=dt)
     else:
-        camp_tf = scsig.ltisys.TransferFunction(num_tf, den_tf)
+        camp_tf = signal.TransferFunction(num_tf, den_tf)
     ss_turb = libss.StateSpace.from_scipy(camp_tf.to_ss())
 
     ss_turb.initialise_variables(({'name': 'noise_in', 'size': 1}), var_type='in')

sharpy/linear/src/libsparse.py

@@ -35,8 +35,8 @@
 import warnings
 import numpy as np
 import scipy.sparse as sparse
+from scipy.sparse._sputils import upcast_char
 import scipy.sparse.linalg as spalg
-import scipy.sparse.sputils as sputils
 
 # --------------------------------------------------------------------- Classes
 
@@ -65,7 +65,7 @@ def todense(self):
 	def _add_dense(self, other):
 		if other.shape != self.shape:
 		    raise ValueError('Incompatible shapes.')
-		dtype = sputils.upcast_char(self.dtype.char, other.dtype.char)
+		dtype = upcast_char(self.dtype.char, other.dtype.char)
 		order = self._swap('CF')[0]
 		result = np.array(other, dtype=dtype, order=order, copy=True)
 		M, N = self._swap(self.shape)

sharpy/linear/src/libss.py

@@ -1841,12 +1841,12 @@ def Hnorm_from_freq_resp(gv, method):
     Warning: only use for SISO systems! For MIMO definitions are different
     """
 
-    if method is 'H2':
+    if method == 'H2':
         Nk = len(gv)
         gvsq = gv * gv.conj()
         Gnorm = np.sqrt(np.trapz(gvsq / (Nk - 1.)))
 
-    elif method is 'Hinf':
+    elif method == 'Hinf':
         Gnorm = np.linalg.norm(gv, np.inf)
 
     if np.abs(Gnorm.imag / Gnorm.real) > 1e-16:

sharpy/linear/src/lingebm.py

@@ -1337,7 +1337,7 @@ def update_matrices_time_scale(self, time_ref):
     def cont2disc(self, dt=None):
         """Convert continuous-time SS model into """
 
-        assert self.discr_method is not 'newmark', \
+        assert self.discr_method != 'newmark', \
             'For Newmark-beta discretisation, use assemble method directly.'
 
         if dt is not None:

sharpy/linear/utils/ss_interface.py

@@ -475,7 +475,8 @@ def load_from_h5_file(cls, variable_type, variables_data):
             raise KeyError(f'Unknown variable type {variable_type}. Must be either InputVariable, OutputVariable '
                            f'or StateVariable')
         for ith_variable in range(n_variables):
-            name = variables_data['names'][ith_variable].astype('U13')  # decode to unicode
+            # name = variables_data['names'][ith_variable].astype('U13')  # decode to unicode
+            name = str(variables_data['names'][ith_variable], 'utf8')  # decode to unicode
             list_of_variables.append(var_class(name,
                                                size=variables_data['sizes'][ith_variable],
                                                index=variables_data['indices'][ith_variable]),

sharpy/rom/utils/librom.py

@@ -1024,7 +1024,7 @@ def modred(SSb, N, method='residualisation'):
     C11 = SSb.C[:, :N]
     D = SSb.D
 
-    if method is 'truncation':
+    if method == 'truncation':
         SSrom = libss.StateSpace(A11, B11, C11, D, dt=SSb.dt)
     else:
         Nb = SSb.A.shape[0]

sharpy/solvers/beamloader.py

@@ -122,8 +122,8 @@ def read_files(self):
             # Need to redefine strings to remove the "b" at the beginning
             for iconstraint in range(self.mb_data_dict['num_constraints']):
                 self.mb_data_dict["constraint_%02d" % iconstraint]['behaviour'] = self.mb_data_dict["constraint_%02d" % iconstraint]['behaviour'].decode()
-            #for ibody in range(self.mb_data_dict['num_bodies']):
-            #    self.mb_data_dict["body_%02d" % ibody]['FoR_movement'] = self.mb_data_dict["body_%02d" % ibody]['FoR_movement'].decode()
+            for ibody in range(self.mb_data_dict['num_bodies']):
+                self.mb_data_dict["body_%02d" % ibody]['FoR_movement'] = self.mb_data_dict["body_%02d" % ibody]['FoR_movement'].decode()
 
     def validate_fem_file(self):
         raise NotImplementedError('validation of the fem file in beamloader is not yet implemented!')

sharpy/solvers/dynamiccoupled.py

@@ -334,7 +334,7 @@ def initialise(self, data, custom_settings=None, restart=False):
                                               'FoR_vel(x)', 'FoR_vel(z)'])
 
         # Define the function to correct aerodynamic forces
-        if self.settings['correct_forces_method'] is not '':
+        if self.settings['correct_forces_method'] != '':
             self.correct_forces = True
             self.correct_forces_generator = gen_interface.generator_from_string(self.settings['correct_forces_method'])()
             self.correct_forces_generator.initialise(in_dict=self.settings['correct_forces_settings'],

sharpy/solvers/staticcoupled.py

@@ -124,7 +124,7 @@ def initialise(self, data, input_dict=None, restart=False):
             self.residual_table.print_header(['iter', 'step', 'log10(res)', 'Fx', 'Fy', 'Fz', 'Mx', 'My', 'Mz'])
 
         # Define the function to correct aerodynamic forces
-        if self.settings['correct_forces_method'] is not '':
+        if self.settings['correct_forces_method'] != '':
             self.correct_forces = True
             self.correct_forces_generator = gen_interface.generator_from_string(self.settings['correct_forces_method'])()
             self.correct_forces_generator.initialise(in_dict=self.settings['correct_forces_settings'],

tests/coupled/multibody/double_pendulum/test_double_pendulum_geradin.py

@@ -417,3 +417,6 @@ def tearDown(self):
                 os.remove(solver_path + f)
 
         shutil.rmtree(solver_path + 'output/')
+
+if __name__ == '__main__':
+    unittest.main()

tests/linear/rom/test_krylov.py

@@ -64,6 +64,8 @@ def run_test(self, test_settings):
         assert np.log10(max_error) < -2, 'Significant mismatch in ROM frequency Response'
 
         # check saving function
+        if os.path.isfile(self.test_dir + '/rom_data.h5'):
+            os.remove(self.test_dir + '/rom_data.h5')
         self.rom.save(self.test_dir + '/rom_data.h5')
 
     def test_krylov(self):

tests/uvlm/static/big_wake_planarwing/generate_big_wake_planarwing.py

@@ -336,7 +336,7 @@ def generate_solver_file(horseshoe=False):
                                 }
 
     minus_m_star = 0
-    if config['StaticUvlm']['horseshoe'] is 'on':
+    if config['StaticUvlm']['horseshoe'] == 'on':
         minus_m_star = max(m_main - 1, 1)
     config['AerogridPlot'] = {'include_rbm': 'off',
                               'include_applied_forces': 'on',

tests/uvlm/static/planarwing/generate_planarwing.py

@@ -335,7 +335,7 @@ def generate_solver_file(horseshoe=False):
                                 }
 
     minus_m_star = 0
-    if config['StaticUvlm']['horseshoe'] is 'on':
+    if config['StaticUvlm']['horseshoe'] == 'on':
         minus_m_star = max(m_main - 1, 1)
     config['AerogridPlot'] = {'include_rbm': 'off',
                               'include_applied_forces': 'on',

utils/environment_new.yml

@@ -0,0 +1,26 @@
+name: sharpy
+channels:
+  - conda-forge
+  - defaults
+dependencies:
+  - asn1crypto>=1.2.0      
+  - colorama>=0.4.1        
+  - control>=0.8.4         
+  - dill>=0.3.1.1          
+  - h5py>=2.9.0            
+  - jupyterlab>=1.2.3      
+  - lxml>=4.4.1            
+  - mayavi>=4.7.1          
+  - nbsphinx>=0.4.3        
+  - pandas>=0.25.3         
+  - pyOpenSSL>=19.0.0      
+  - PySocks>=1.7.1         
+  - PyYAML>=5.1.2          
+  - recommonmark>=0.6.0    
+  - slycot>=0.4.0
+  - sphinx_rtd_theme>=0.4.3
+  - wheel>=0.33.6          
+  - xlrd>=1.2.0            
+  - python=3.10
+  - openpyxl>=3.0.10
+  - cmake=3.14.0