Merge branch 'hotfix/1.7.post13'

Numpy does not allow anylonger types np.int or np.float.
These are replaced simply by int and float python native types.

Makefile

@@ -32,10 +32,17 @@ devel: venv pybinding wx
 	@$(INSIDE_VENV) pip install -e src/
 
 
+light: VENV_PATH = ./_venv
+light: venv
+	@$(INSIDE_VENV) pip install src/
+
+
 _build_wx/wxPython.target:
 	@$(INSIDE_VENV) echo "Building wxPython for your `python --version 2>&1` under Linux $(DISTRO_RELEASE)..."
 	# Create a folder to build wx into
 	@mkdir -p _build_wx
+	@$(INSIDE_VENV) pip install attrdict sip
+	# TODO: attrdict is no longer compatible with collections package. The build will fail
 	# download the wheel or the source if it cannot find a wheel
 	@$(INSIDE_VENV) cd _build_wx && pip download -f https://extras.wxpython.org/wxPython4/extras/linux/gtk3/$(DISTRO_RELEASE) wxPython
 	# Build the source if a tar.gz was downloaded

src/msspec/calcio.py

@@ -727,15 +727,15 @@ class SpecIO(object):
         content += line
 
         nat = p.extra_nat
-        nra_arr = np.ones((nat), dtype=np.int)
+        nra_arr = np.ones((nat), dtype=int)
         thfwd_arr = np.ones((nat))
         path_filtering = p.extra_parameters['calculation'].get_parameter(
             'path_filtering').value
         if (path_filtering is not None and
                 'backward_scattering' in path_filtering):
-            ibwd_arr = np.ones((nat), dtype=np.int)
+            ibwd_arr = np.ones((nat), dtype=int)
         else:
-            ibwd_arr = np.zeros((nat), dtype=np.int)
+            ibwd_arr = np.zeros((nat), dtype=int)
         thbwd_arr = np.ones((nat))
         for at in p.extra_atoms:
             i = at.get('proto_index') - 1

src/msspec/calculator.py

@@ -301,7 +301,7 @@ class _MSCALCULATOR(Calculator):
         wf = 4.5
         source_energy = self.source_parameters.get_parameter('energy').value
         ke = source_energy - binding_energy - wf
-        #return np.array(ke, dtype=np.float).flatten()
+        #return np.array(ke, dtype=float).flatten()
         return ke
 
 
@@ -383,7 +383,7 @@ class _MSCALCULATOR(Calculator):
                'NODES_EX_M' : 3,
                'NSPIN_M'    : 1, # to change for spin dependent
                'NTH_M'      : 2000,
-               'NPH_M'      : 2000,
+               'NPH_M'      : 8000,
                'NDIM_M'     : 100000,
                'N_TILT_M'   : 11, # to change see extdir.f
                'N_ORD_M'    : 250,
@@ -615,7 +615,7 @@ class _PED(_MSCALCULATOR):
     def _get_scan(self, scan_type='theta', phi=0,
                   theta=np.linspace(-70, 70, 141), level=None,
                   kinetic_energy=None, data=None,
-                  malloc={}):
+                  malloc={}, other_parameters={}):
         LOGGER.info("Computting the %s scan...", scan_type)
         if data:
             self.iodata = data
@@ -650,6 +650,13 @@ class _PED(_MSCALCULATOR):
 
         self.spectroscopy_parameters.set_parameter('level', level)
 
+        # It is still possible to modify any option right before runing phagen
+        # and spec
+        for k, v in other_parameters.items():
+            grp_str, param_str = k.split('.')
+            grp = getattr(self, grp_str)
+            grp.set_parameter(param_str, v, force=True)
+
         self.get_tmatrix()
         self.run_spec(malloc)
 
@@ -851,7 +858,7 @@ class _PED(_MSCALCULATOR):
         return self.iodata
 
     def get_scattering_factors(self, level='1s', kinetic_energy=None,
-                               data=None):
+                               data=None, **kwargs):
         """Computes the scattering factors of all prototypical atoms in the
         cluster.
 
@@ -870,11 +877,11 @@ class _PED(_MSCALCULATOR):
 
         """
         data = self._get_scan(scan_type='scatf', level=level, data=data,
-                              kinetic_energy=kinetic_energy)
+                              kinetic_energy=kinetic_energy, **kwargs)
         return data
 
     def get_theta_scan(self, phi=0, theta=np.linspace(-70, 70, 141),
-                       level=None, kinetic_energy=None, data=None):
+                       level=None, kinetic_energy=None, data=None, **kwargs):
         """Computes a polar scan of the emitted photoelectrons.
 
         :param phi: The azimuthal angle in degrees. See
@@ -891,11 +898,12 @@ class _PED(_MSCALCULATOR):
 
         """
         data = self._get_scan(scan_type='theta', level=level, theta=theta,
-                              phi=phi, kinetic_energy=kinetic_energy, data=data)
+                              phi=phi, kinetic_energy=kinetic_energy,
+                              data=data, **kwargs)
         return data
 
     def get_phi_scan(self, phi=np.linspace(0, 359, 359), theta=0,
-                     level=None, kinetic_energy=None, data=None):
+                     level=None, kinetic_energy=None, data=None, **kwargs):
         """Computes an azimuthal scan of the emitted photoelectrons.
 
         :param phi: All the values of the azimuthal angle to be computed. See
@@ -912,12 +920,13 @@ class _PED(_MSCALCULATOR):
 
         """
         data = self._get_scan(scan_type='phi', level=level, theta=theta,
-                              phi=phi, kinetic_energy=kinetic_energy, data=data)
+                              phi=phi, kinetic_energy=kinetic_energy,
+                              data=data, **kwargs)
         return data
 
     def get_theta_phi_scan(self, phi=np.linspace(0, 360),
                            theta=np.linspace(0, 90, 45), level=None,
-                           kinetic_energy=None, data=None):
+                           kinetic_energy=None, data=None, **kwargs):
         """Computes a stereographic scan of the emitted photoelectrons.
 
         The azimuth ranges from 0 to 360° and the polar angle ranges from 0 to
@@ -934,11 +943,11 @@ class _PED(_MSCALCULATOR):
         """
         data = self._get_scan(scan_type='theta_phi', level=level, theta=theta,
                               phi=phi, kinetic_energy=kinetic_energy, data=data,
-                              malloc={'NPH_M': 8000})
+                              **kwargs)
         return data
 
     def get_energy_scan(self, phi=0, theta=0,
-                        level=None, kinetic_energy=None, data=None):
+                        level=None, kinetic_energy=None, data=None, **kwargs):
         """Computes an energy scan of the emitted photoelectrons.
 
         :param phi: All the values of the azimuthal angle to be computed. See
@@ -955,7 +964,8 @@ class _PED(_MSCALCULATOR):
 
         """
         data = self._get_scan(scan_type='energy', level=level, theta=theta,
-                              phi=phi, kinetic_energy=kinetic_energy, data=data)
+                              phi=phi, kinetic_energy=kinetic_energy,
+                              data=data, **kwargs)
         return data
 
 

src/msspec/parameters.py

@@ -1310,8 +1310,8 @@ class ScanParameters(BaseParameters):
         #    LOGGER.error('Incompatible options!')
         #    raise ValueError(msg)
 
-        # p._value = np.array(p.value, dtype=np.float).flatten()
-        arr = np.array(p.value, dtype=np.float).flatten()
+        # p._value = np.array(p.value, dtype=float).flatten()
+        arr = np.array(p.value, dtype=float).flatten()
 
         theta0 = arr[0]
         theta1 = arr[-1]
@@ -1345,7 +1345,7 @@ class ScanParameters(BaseParameters):
        #    LOGGER.error('Incompatible options')
        #    raise ValueError(msg)
 
-        arr = np.array(p.value, dtype=np.float).flatten()
+        arr = np.array(p.value, dtype=float).flatten()
 
         phi0 = arr[0]
         phi1 = arr[-1]
@@ -1539,7 +1539,7 @@ class CalculationParameters(BaseParameters):
             Parameter('cutoff_factor', types=(int, float),
                       limits=(1e-4, 999.9999), default=0.01, private=False),
             Parameter('mean_free_path', types=(int, float, str),
-                      default='SeahDench', allowed_values=('mono', 'SeahDench'),
+                      default='SeahDench', #allowed_values=('mono', 'SeahDench'),
                       doc="""
             The electron mean free path value. You can either:
             - Enter a value (in Angströms), in this case any value <=0 will disable the damping

src/msspec/utils.py

@@ -18,8 +18,8 @@
 # along with this msspec.  If not, see <http://www.gnu.org/licenses/>.
 #
 # Source file  : src/msspec/utils.py
-# Last modified: ven. 10 avril 2020 15:49:35
-# Committed by : "Sylvain Tricot <sylvain.tricot@univ-rennes1.fr>"
+# Last modified: Thu, 06 Oct 2022 18:19:16 +0200
+# Committed by : Sylvain Tricot <sylvain.tricot@univ-rennes1.fr> 1665073156 +0200
 
 
 """
@@ -38,7 +38,11 @@ import ase.atom
 from ase import Atom
 from ase import Atoms
 
+try:
     from msspec.iodata import Data
+except ImportError as err:
+    print(err)
+
 from msspec.misc import LOGGER
 
 
@@ -476,7 +480,7 @@ def hemispherical_cluster(cluster, emitter_tag=0, emitter_plane=0, diameter=0,
     a = cell[:, 0].max()    # a lattice parameter
 
     # the number of planes in the cluster
-    p = np.alen(np.unique(np.round(cluster.get_positions()[:, 2], 4)))
+    p = len(np.unique(np.round(cluster.get_positions()[:, 2], 4)))
     # the symbol of your emitter
     symbol = cluster[np.where(cluster.get_tags() == emitter_tag)[0][0]].symbol
 
@@ -581,7 +585,7 @@ def hemispherical_cluster(cluster, emitter_tag=0, emitter_plane=0, diameter=0,
     # an array of all unique remaining z
     all_z = np.sort(np.unique(np.round(cluster.get_positions()[:, 2], 4)))
 
-    assert emitter_plane < np.alen(all_z), ("There are not enough existing "
+    assert emitter_plane < len(all_z), ("There are not enough existing "
                                             "plans.")
     ze = all_z[- emitter_plane - 1]         # the z-coordinate of the emitter
     Atoms.translate(cluster, [0, 0, -ze])   # put the emitter in (0,0,0)

src/msspec/version.py

@@ -16,39 +16,38 @@
 # along with this msspec.  If not, see <http://www.gnu.org/licenses/>.
 #
 # Source file  : src/msspec/version.py
-# Last modified: ven. 10 avril 2020 17:34:38
-# Committed by : "Sylvain Tricot <sylvain.tricot@univ-rennes1.fr>"
+# Last modified: Thu, 06 Oct 2022 18:19:16 +0200
+# Committed by : Sylvain Tricot <sylvain.tricot@univ-rennes1.fr> 1665073156 +0200
 
 
 import os
 
-from pkg_resources import DistributionNotFound
-from pkg_resources import get_distribution
-from pkg_resources import parse_version
+from importlib.metadata import version
+import subprocess
 
 # find the version number
-# 1- Try to read it from the git info
-# 2- If it fails, try to read it from the distribution file
+# 1- If it fails, try to read it from the distribution file
+# 2- Try to read it from the git info
 # 3- If it fails, try to read it from the VERSION file
 
+PKGNAME = 'msspec'
+
 try:
-    from setuptools_scm import get_version
-    v = get_version(root='../../', relative_to=__file__, version_scheme="post-release")
-    v = parse_version(v)
-    if v._version.post[-1] == 0:
-        __version__ = v.base_version
-    else:
-        __version__ = v.public
+    __version__ = version(PKGNAME)
 except Exception as err:
     try:
-        __version__ = get_distribution(__name__.strip('.version')).version
+        p = subprocess.run(["git", "describe"], capture_output=True, text=True)
+        if p.stdout not in ("", None):
+            __version__ = p.stdout.strip()
+        else:
+            raise NameError("git describe failed!")
     except Exception as err:
         try:
             thisfile_path = os.path.abspath(__file__)
             thisfile_dir = os.path.dirname(thisfile_path)
             versionfile = os.path.join(thisfile_dir, "../VERSION")
             with open(versionfile, "r") as fd:
-                __version__ = fd.readline()
+                __version__ = fd.readline().strip()
         except Exception as err:
             print("Unable to get the version number!")
             __version__ = "9.9.9"

src/options.mk

@@ -41,8 +41,7 @@ F2PYFLAGS_DBG = --debug-capi --debug
 # /!\ DO NOT EDIT BELOW THAT LINE (unlesss you know what you're doing...)      #
 # CORE CONFIGURATION                                                           #
 ################################################################################
-#VERSION:=$(shell python -c "import msspec; print(msspec.__version__)")
-VERSION:=$(shell git describe|sed 's/-\([[:digit:]]\+\)-.*/\.post\1/')
+VERSION:=$(shell git describe)
 VENV_PATH := $(INSTALL_PREFIX)/src/msspec_venv_$(VERSION)
 
 

src/pip.freeze

@@ -2,7 +2,7 @@ ase
 h5py
 ipython
 lxml
-matplotlib
+matplotlib==3.4.3
 numpy
 Pint
 pandas