Fix deprecation warnings

abipy/abio/inputs.py

@@ -1531,7 +1531,7 @@ def new_with_structure(self, new_structure, scdims=None, verbose=1) -> AbinitInp
             if scdims.shape != (3,):
                 raise ValueError("Expecting 3 int in scdims but got %s" % str(scdims))
 
-            numcells = np.product(scdims)
+            numcells = np.prod(scdims)
             if len(new_structure) != numcells * len(self.structure):
                 errmsg = "Number of atoms in the input structure should be %d * %d but found %d" % (
                     numcells, len(self.structure), len(new_structure))

abipy/examples/_runflows.py

@@ -9,17 +9,19 @@
 import argparse
 import shutil
 import tempfile
+import abipy.tools.cli_parsers as cli
 
 from subprocess import call
 from abipy import __version__
 from abipy import flowtk
 
 
+
 def main():
     def str_examples():
         examples = """
           Usage example:\n\n
-          runall.py => Run all scripts.
+          _runflows.py => Run all scripts.
         """
         return examples
 
@@ -37,27 +39,14 @@ def show_examples_and_exit(err_msg=None, error_code=1):
                         help="set the loglevel. Possible values: CRITICAL, ERROR (default), WARNING, INFO, DEBUG")
 
     parser.add_argument('-m', '--mode', type=str, default="sequential", help="execution mode. Default is sequential.")
-
     parser.add_argument('-e', '--exclude', type=str, default="", help="Exclude scripts. Comma-separated names")
-
     parser.add_argument('-x', '--execute', default=False, action="store_true", help="Execute flows.")
-
-    parser.add_argument('--keep-dirs', action="store_true", default=False,
-                        help="Do not remove flowdirectories.")
-
+    parser.add_argument('--keep-dirs', action="store_true", default=False, help="Do not remove flow directories.")
     parser.add_argument('-b', '--bail-on-failure', default=False, help="Exit at the first error.")
 
-    #parser.add_argument("scripts", nargs="+",help="List of scripts to be executed")
-
     options = parser.parse_args()
 
-    # loglevel is bound to the string value obtained from the command line argument.
-    # Convert to upper case to allow the user to specify --loglevel=DEBUG or --loglevel=debug
-    import logging
-    numeric_level = getattr(logging, options.loglevel.upper(), None)
-    if not isinstance(numeric_level, int):
-        raise ValueError('Invalid log level: %s' % options.loglevel)
-    logging.basicConfig(level=numeric_level)
+    cli.set_loglevel(options.loglevel)
 
     # Find scripts.
     if options.exclude:
@@ -85,7 +74,7 @@ def show_examples_and_exit(err_msg=None, error_code=1):
             retcode += ret
 
             if ret != 0:
-                e = "python %s returned retcode !=0" % script
+                e = "python %s returned retcode != 0" % script
                 print(e)
                 errors.append(e)
                 if options.bail_on_failure:

abipy/flowtk/abiphonopy.py

@@ -99,7 +99,7 @@ def from_gs_input(cls, gsinp, scdims, phonopy_kwargs=None, displ_kwargs=None) ->
         phonon.generate_displacements(**displ_kwargs)  # distance=0.01,
 
         # Obtain supercells containing respective displacements (list of Atoms objects).
-        for atoms in phonon.get_supercells_with_displacements():
+        for atoms in phonon.supercells_with_displacements:
             sc_struct = structure_from_atoms(atoms)
             sc_gsinp = gsinp.new_with_structure(sc_struct, scdims=new.scdims)
             sc_gsinp.pop_tolerances()

abipy/iotools/xsf.py

@@ -201,7 +201,7 @@ def bxsf_write(file, structure, nsppol, nband, ndivs, ucdata_sbk, fermie, unit="
     ucdata_sbk = EnergyArray(ucdata_sbk, unit).to("Ha")
     fermie = Energy(fermie, unit).to("Ha")
 
-    ucdata_sbk = np.reshape(ucdata_sbk, (nsppol, nband, np.product(ndivs)))
+    ucdata_sbk = np.reshape(ucdata_sbk, (nsppol, nband, np.prod(ndivs)))
 
     close_it = False
     if not hasattr(file, "write"):

abipy/ml/ml_relax.py

@@ -302,6 +302,7 @@ def run(self, workdir=None, prefix=None):
 
 
 if __name__ == "__main__":
+    # Get pseudos
     from abipy.flowtk.psrepos import get_oncvpsp_pseudos
     xc_name = "PBE"
     pseudos = get_oncvpsp_pseudos(xc_name=xc_name, version="0.4")

abipy/panels/viewers.py

@@ -19,8 +19,8 @@ def __init__(self, filepath: str, theme="terminal", height=1200, **params):
         self.open_btn = pnw.Button(name=f"Open {basename}", button_type='primary')
         self.open_btn.on_click(self.open_ace_editor)
 
-        self.ace = pnw.Ace(language='text', readonly=True, theme=theme,
-                           sizing_mode='stretch_width', height=height, visible=False)
+        self.ace = pnw.CodeEditor(language='text', readonly=True, theme=theme,
+                                  sizing_mode='stretch_width', height=height, visible=False)
 
         self.controls = pn.Card(self.ace.param.height, self.ace.param.theme, self.ace.param.visible,
                                 title="ACE controls", collapsed=True)

dev_scripts/mlrun.py

@@ -4,7 +4,6 @@
 """
 from __future__ import annotations
 
-
 import sys
 import os
 import click
@@ -13,7 +12,6 @@
 from ase.atoms import Atoms
 from ase.build import bulk
 from abipy.core.structure import Structure
-from abipy.flowtk.psrepos import get_repo_from_name
 from abipy.ml.aseml import get_atoms, ase_optimizer_cls, CORRALGO
 from abipy.ml.ml_relax import RelaxationProfiler
 
@@ -70,28 +68,23 @@ def main(filepath, nn_name, corr_algo_str,
     warnings.simplefilter("ignore")
 
     # Get pseudos
-    repo_name = {
-        "PBE": "ONCVPSP-PBE-SR-PDv0.4",
-        "PBEsol": "ONCVPSP-PBEsol-SR-PDv0.4",
-        "LDA": "ONCVPSP-LDA-SR-PDv0.4",
-    }[xc_nane]
-    print(f"Using {repo_name=}")
-    pseudos = get_repo_from_name(repo_name).get_pseudos("standard")
-    #from abipy.flowtk.psrepos import get_repo_from_name get_oncvpsp_pseudos
-    #pseudos = get_oncvpsp_pseudos(xc_name=xc_name, version="0.4")
-
-    # Get atoms
+    from abipy.flowtk.psrepos import get_oncvpsp_pseudos
+    pseudos = get_oncvpsp_pseudos(xc_name=xc_name, version="0.4")
+
     if os.path.exists(filepath):
+        # Read structure from file.
         structure = Structure.from_file(filepath)
-        if abs(scale_volume - 1.0) > 0.0:
-            print(f"Scaling input volume by {scale_volume=}")
-            #print("before structure:\n", structure)
-            structure = structure.scale_lattice(scale_volume * structure.lattice.volume)
-            #print("after structure:\n", structure)
-        atoms = get_atoms(structure)
-    else:
-        raise ValueError(f"Cannot init Atoms from {filepath=}")
-        #atoms = bulk(filepath)
+
+    elif filepath.startswith("__mp-"):
+        print(f"Fetching structure for mp-id {filepath[2:]} from the materials project database.")
+        structure = Structure.from_mpid(filepath[2:])
+
+    if abs(scale_volume - 1.0) > 0.0:
+        print(f"Scaling input volume by {scale_volume=}")
+        structure = structure.scale_lattice(scale_volume * structure.lattice.volume)
+
+    # Convert to ASE atoms
+    atoms = get_atoms(structure)
 
     if rattle:
         print("Displacing atoms randomly with stdev=", rattle)