Don't invoke open in Makefile

abipy/ml/extxyz_generator.py

@@ -1,4 +1,6 @@
 """
+Tools to read data from output files generated by ab-initio codes 
+and generate extended XYZ files.
 """
 from __future__ import annotations
 
@@ -25,7 +27,7 @@ class ExtxyzIOWriter:
     """
     Example:
 
-        # To find all the vasprun.xml files starting from the a top-level directory, use:
+        # To find all the vasprun.xml files starting from a top-level directory, use:
 
             xyz_writer = ExtxyzIOWriter.from_top(".", "vasprun.xml")
             print(xyz_writer)
@@ -46,6 +48,20 @@ class ExtxyzIOWriter:
         "GSR.nc",
     ]
 
+    @classmethod
+    def from_top_vasprun(cls, top: PathLike):
+        """
+        Find all the vasprun.xml files starting from the top-level directory top.
+        """
+        return cls(top, "vasprun.xml")
+
+    @classmethod
+    def from_top_gsr(cls, top: PathLike):
+        """
+        Find all the GSR.nc files starting from the top-level directory top.
+        """
+        return cls(top, "GSR.nc")
+
     @classmethod
     def from_top(cls, top: PathLike, ext: str):
         """
@@ -79,6 +95,11 @@ def __str__(self) -> str:
 
     def write(self, xyz_filepath: PathLike, overwrite: bool = False):
         """
+        Write data to xyz_filepath.
+
+        Args:
+            xyz_filepath: Filename
+            overwrite: True to allow overwriting.
         """
         if not overwrite and os.path.isfile(xyz_filepath):
             raise RuntimeError(f"Cannot overwrite pre-existent file: {xyz_filepath=}, use overwrite=True to allow overwriting.")
@@ -89,6 +110,7 @@ def write(self, xyz_filepath: PathLike, overwrite: bool = False):
 
     def yield_atoms(self):
         """
+        Generate ASE atoms.
         """
         for filepath in self.filepaths:
             if self.ext == "vasprun.xml":

abipy/ml/tools.py

@@ -1,4 +1,5 @@
 """
+Low-level tools used in abipy.ml
 """
 from __future__ import annotations
 
@@ -95,5 +96,4 @@ def get_structures_labels_from_files(filepaths) -> tuple[list[Structure], dict]:
     #for s in structures: print(s)
     #for k, v in labels.items(): print(k, v)
 
-    return structures, labels
-
+    return structures, labels

abipy/ppcodes/ppgen.py

@@ -296,7 +296,6 @@ def check_status(self):
 #    fr = "fully-relativistic"
 
 
-
 class OncvGenerator(_PseudoGenerator):
     """
     This object receives an input file for oncvpsp, a string
@@ -394,4 +393,4 @@ def check_status(self):
             logger.warning("setting status to S_ERROR")
             self._status = self.S_ERROR
 
-        return self._status
+        return self._status

abipy/scripts/abiml.py

@@ -15,7 +15,7 @@
 from functools import wraps
 from time import time
 from abipy.core.structure import Structure
-from abipy.tools.printing import print_dataframe
+#from abipy.tools.printing import print_dataframe
 
 
 ASE_OPTIMIZERS = aseml.ase_optimizer_cls("__all__")
@@ -319,8 +319,7 @@ def md(ctx, filepath, nn_name,
 def neb(ctx, filepaths, nn_name,
         nimages, relax_mode, fmax, pressure, optimizer, neb_method, climb,
         fix_inds, fix_symbols,
-        workdir, verbose
-    ):
+        workdir, verbose):
     """
     NEB calculation with ASE and ML potential.
 
@@ -789,4 +788,4 @@ def cwf_eos(ctx, elements, nn_names,
 
 
 if __name__ == "__main__":
-    sys.exit(main())
+    sys.exit(main())

abipy/scripts/abislurm.py

@@ -12,7 +12,7 @@
 
 
 def get_epilog() -> str:
-   return """\
+    return """\
 Usage example:\n
 
     abislurm.py running                => Get info on all the running jobs

abipy/scripts/oncv.py

@@ -158,7 +158,7 @@ def oncv_run(options):
             cprint("FR calculation with input file without `_r` suffix. Will add `_r` to output files", color="yellow")
 
     elif options.rel == "from_file":
-        calc_type  = "scalar-relativistic"
+        calc_type = "scalar-relativistic"
         if root.endswith("_r"): calc_type = "fully-relativistic"
         if root.endswith("_nor"): calc_type = "non-relativistic"
 
@@ -326,7 +326,7 @@ def build():
 
 
 def get_epilog() -> str:
-        return """\
+    return """\
 Usage example:
 
     oncv.py run H.in                   ==> Run oncvpsp input file (scalar relativistic mode).
@@ -458,4 +458,4 @@ def show_examples_and_exit(err_msg=None, error_code=1):
 
 
 if __name__ == "__main__":
-    sys.exit(main())
+    sys.exit(main())

docs/Makefile

@@ -66,7 +66,7 @@ html: check_dot
 	$(SPHINXBUILD) -b html $(ALLSPHINXOPTS) $(BUILDDIR)/html || { echo "Error: Sphinx build failed"; exit 1; }
 	@echo
 	@echo "Build finished. The HTML pages are in $(BUILDDIR)/html."
-	open $(BUILDDIR)/html/index.html || { echo "Error: Failed to open index.html"; exit 1; }
+	#open $(BUILDDIR)/html/index.html || { echo "Error: Failed to open index.html"; exit 1; }
 
 dirhtml:
 	$(SPHINXBUILD) -b dirhtml $(ALLSPHINXOPTS) $(BUILDDIR)/dirhtml