Merge pull request #26 from aiida-phonopy/pre-commit-ci-update-config

[pre-commit.ci] pre-commit autoupdate
aiida-phonopy · Apr 4, 2022 · f1a3e3d · f1a3e3d
2 parents 8aff176 + cf5057c
commit f1a3e3d
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Showing 4 changed files with 28 additions and 19 deletions.
diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
@@ -1,6 +1,6 @@
 repos:
 - repo: https://github.com/pre-commit/pre-commit-hooks
-  rev: v4.0.1
+  rev: v4.1.0
   hooks:
   - id: trailing-whitespace
   - id: end-of-file-fixer
@@ -17,7 +17,7 @@ repos:
     - "--ignore=E203,W503"
 
 - repo: https://github.com/psf/black
-  rev: 21.12b0
+  rev: 22.3.0
   hooks:
   - id: black
     args:

diff --git a/aiida_phonopy/calculations/functions/preprocess.py b/aiida_phonopy/calculations/functions/preprocess.py
@@ -114,7 +114,7 @@ def phonopy_atoms_from_structure(structure, to_map=False):
 
         kind_names = structure.get_kind_names()
         # The numbers start from 1, otherwise phonopy will complain in the post processing.
-        kinds_to_numbers = {kind_names[i]: i+1 for i in range(len(kind_names))} 
+        kinds_to_numbers = {kind_names[i]: i + 1 for i in range(len(kind_names))}
 
         for site in sites:
             kind = structure.get_kind(site.kind_name)
@@ -136,10 +136,10 @@ def phonopy_atoms_from_structure(structure, to_map=False):
             masses=masses,
             cell=structure.cell,
         )
-        
+
         # Also here we start from 1.
-        numbers_to_kinds = {i+1: kind_names[i] for i in range(len(kind_names))}
-        
+        numbers_to_kinds = {i + 1: kind_names[i] for i in range(len(kind_names))}
+
         return (cell, [numbers_to_kinds, numbers_to_symbols])
 
 

diff --git a/aiida_phonopy/calculations/phonopy.py b/aiida_phonopy/calculations/phonopy.py
@@ -89,7 +89,7 @@ class PhonopyCalculation(BasePhonopyCalculation):
         "GROUP_VELOCITY": [bool],
         "GV_DELTA_Q": [int, float],
         # Symmetry
-        "SYMMETRY_TOLERANCE": [int, float], # !!!! ATTENTION TO INPUTS !!!!
+        "SYMMETRY_TOLERANCE": [int, float],  # !!!! ATTENTION TO INPUTS !!!!
         "SYMMETRY": [bool],
         "MESH_SYMMETRY": [bool],
         "FC_SYMMETRY": [bool],
@@ -110,7 +110,7 @@ class PhonopyCalculation(BasePhonopyCalculation):
     _BLOCKED_TAGS = [
         "DIM",
         "ATOM_NAME",
-        "MASS", #??? from structure or also from here??
+        "MASS",  # ??? from structure or also from here??
         "MAGMOM",
         "CREATE_DISPLACEMENTS",
         "DISPLACEMENT_DISTANCE",
@@ -182,7 +182,12 @@ def prepare_for_submission(self, folder):
 
         # =============== prepare the submit and conf file ====================
 
-        cmd_readcell = ["-c", self._DEFAULT_CELL_FILE, "--tolerance", str(self.inputs.symmetry_tolerance.value)]  # in front any phonopy cmd line
+        cmd_readcell = [
+            "-c",
+            self._DEFAULT_CELL_FILE,
+            "--tolerance",
+            str(self.inputs.symmetry_tolerance.value),
+        ]  # in front any phonopy cmd line
         cmd_writefc = ["--writefc", "--writefc-format=hdf5"]  # first cmd if `parent_folder` is not specified
         cmd_readfc = ["--readfc", "--readfc-format=hdf5"]  # in front any phonopy post-process cmd line
 
@@ -283,7 +288,11 @@ def _write_born(self, folder):
 
     def _write_cells_info(self, folder):
         """Write in `folder` the `phonopy_cells.yaml` file."""
-        phpy_yaml_txt = get_phonopy_yaml_txt(self.inputs.structure, symprec=self.inputs.symmetry_tolerance.value, supercell_matrix=self.inputs["supercell_matrix"])
+        phpy_yaml_txt = get_phonopy_yaml_txt(
+            self.inputs.structure,
+            symprec=self.inputs.symmetry_tolerance.value,
+            supercell_matrix=self.inputs["supercell_matrix"],
+        )
         with folder.open(self._DEFAULT_CELL_FILE, "w", encoding="utf8") as handle:
             handle.write(phpy_yaml_txt)
 

diff --git a/docs/conf.py b/docs/conf.py
@@ -46,18 +46,18 @@
 master_doc = "index"
 
 # General information about the project.
-project = u"aiida-phonopy"
-copyright = u"2017, Atsushi Togo, Abel Carreras"
-author = u"Atsushi Togo, Abel Carreras"
+project = "aiida-phonopy"
+copyright = "2017, Atsushi Togo, Abel Carreras"
+author = "Atsushi Togo, Abel Carreras"
 
 # The version info for the project you're documenting, acts as replacement for
 # |version| and |release|, also used in various other places throughout the
 # built documents.
 #
 # The short X.Y version.
-version = u"0.3"
+version = "0.3"
 # The full version, including alpha/beta/rc tags.
-release = u"0.3"
+release = "0.3"
 
 # The language for content autogenerated by Sphinx. Refer to documentation
 # for a list of supported languages.
@@ -126,8 +126,8 @@
     (
         master_doc,
         "aiida-phonopy.tex",
-        u"aiida-phonopy Documentation",
-        u"Abel Carreras",
+        "aiida-phonopy Documentation",
+        "Abel Carreras",
         "manual",
     ),
 ]
@@ -136,7 +136,7 @@
 
 # One entry per manual page. List of tuples
 # (source start file, name, description, authors, manual section).
-man_pages = [(master_doc, "aiida-phonopy", u"aiida-phonopy Documentation", [author], 1)]
+man_pages = [(master_doc, "aiida-phonopy", "aiida-phonopy Documentation", [author], 1)]
 
 # -- Options for Texinfo output -------------------------------------------
 
@@ -147,7 +147,7 @@
     (
         master_doc,
         "aiida-phonopy",
-        u"aiida-phonopy Documentation",
+        "aiida-phonopy Documentation",
         author,
         "aiida-phonopy",
         "Running phonopy using AiiDA",