Update dependencies and pre-commit

.pre-commit-config.yaml

@@ -3,13 +3,13 @@ default_language_version:
 
 repos:
   - repo: https://github.com/ambv/black
-    rev: 19.10b0
+    rev: 20.8b1
     hooks:
     - id: black
       name: Blacken
 
   - repo: https://github.com/pre-commit/pre-commit-hooks
-    rev: v3.1.0
+    rev: v3.2.0
     hooks:
     - id: trailing-whitespace
       exclude: README.md

openapi/openapi.json

@@ -995,7 +995,7 @@
             "description": "Statistical probability of each group. It MUST have the same length as `sites_in_groups`.\nIt SHOULD sum to one.\nSee below for examples of how to specify the probability of the occurrence of a vacancy.\nThe possible reasons for the values not to sum to one are the same as already specified above for the `concentration` of each `species`."
           }
         },
-        "description": "A description of groups of sites that are statistically correlated.\n\n- **Examples** (for each entry of the assemblies list):\n    - `{\"sites_in_groups\": [[0], [1]], \"group_probabilities: [0.3, 0.7]}`: the first site and the second site never occur at the same time in the unit cell.\n      Statistically, 30 % of the times the first site is present, while 70 % of the times the second site is present.\n    - `{\"sites_in_groups\": [[1,2], [3]], \"group_probabilities: [0.3, 0.7]}`: the second and third site are either present together or not present; they form the first group of atoms for this assembly.\n      The second group is formed by the fourth site. Sites of the first group (the second and the third) are never present at the same time as the fourth site.\n      30 % of times sites 1 and 2 are present (and site 3 is absent); 70 % of times site 3 is present (and sites 1 and 2 are absent).\n\n    "
+        "description": "A description of groups of sites that are statistically correlated.\n\n- **Examples** (for each entry of the assemblies list):\n    - `{\"sites_in_groups\": [[0], [1]], \"group_probabilities: [0.3, 0.7]}`: the first site and the second site never occur at the same time in the unit cell.\n      Statistically, 30 % of the times the first site is present, while 70 % of the times the second site is present.\n    - `{\"sites_in_groups\": [[1,2], [3]], \"group_probabilities: [0.3, 0.7]}`: the second and third site are either present together or not present; they form the first group of atoms for this assembly.\n      The second group is formed by the fourth site. Sites of the first group (the second and the third) are never present at the same time as the fourth site.\n      30 % of times sites 1 and 2 are present (and site 3 is absent); 70 % of times site 3 is present (and sites 1 and 2 are absent)."
       },
       "Attributes": {
         "title": "Attributes",
@@ -1197,7 +1197,7 @@
           "dictionary",
           "unknown"
         ],
-        "description": "Optimade Data Types\n\nSee the section \"Data types\" in the OPTIMADE API specification for more information.\n    "
+        "description": "Optimade Data Types\n\nSee the section \"Data types\" in the OPTIMADE API specification for more information."
       },
       "EntryInfoProperty": {
         "title": "EntryInfoProperty",
@@ -2256,7 +2256,7 @@
             "description": "A dictionary containing references to other entries according to the description in section Relationships encoded as [JSON API Relationships](https://jsonapi.org/format/1.0/#document-resource-object-relationships).\nThe OPTIONAL human-readable description of the relationship MAY be provided in the `description` field inside the `meta` dictionary of the JSON API resource identifier object."
           }
         },
-        "description": "The `references` entries describe bibliographic references.\nThe following properties are used to provide the bibliographic details:\n\n- **address**, **annote**, **booktitle**, **chapter**, **crossref**, **edition**, **howpublished**, **institution**, **journal**, **key**, **month**, **note**, **number**, **organization**, **pages**, **publisher**, **school**, **series**, **title**, **volume**, **year**: meanings of these properties match the [BibTeX specification](http://bibtexml.sourceforge.net/btxdoc.pdf), values are strings;\n- **bib_type**: type of the reference, corresponding to **type** property in the BibTeX specification, value is string;\n- **authors** and **editors**: lists of *person objects* which are dictionaries with the following keys:\n    - **name**: Full name of the person, REQUIRED.\n    - **firstname**, **lastname**: Parts of the person's name, OPTIONAL.\n- **doi** and **url**: values are strings.\n- **Requirements/Conventions**:\n    - **Support**: OPTIONAL support in implementations, i.e., any of the properties MAY be `null`.\n    - **Query**: Support for queries on any of these properties is OPTIONAL.\n        If supported, filters MAY support only a subset of comparison operators.\n    - Every references entry MUST contain at least one of the properties.\n\n    "
+        "description": "The `references` entries describe bibliographic references.\n\nThe following properties are used to provide the bibliographic details:\n\n- **address**, **annote**, **booktitle**, **chapter**, **crossref**, **edition**, **howpublished**, **institution**, **journal**, **key**, **month**, **note**, **number**, **organization**, **pages**, **publisher**, **school**, **series**, **title**, **volume**, **year**: meanings of these properties match the [BibTeX specification](http://bibtexml.sourceforge.net/btxdoc.pdf), values are strings;\n- **bib_type**: type of the reference, corresponding to **type** property in the BibTeX specification, value is string;\n- **authors** and **editors**: lists of *person objects* which are dictionaries with the following keys:\n    - **name**: Full name of the person, REQUIRED.\n    - **firstname**, **lastname**: Parts of the person's name, OPTIONAL.\n- **doi** and **url**: values are strings.\n- **Requirements/Conventions**:\n    - **Support**: OPTIONAL support in implementations, i.e., any of the properties MAY be `null`.\n    - **Query**: Support for queries on any of these properties is OPTIONAL.\n        If supported, filters MAY support only a subset of comparison operators.\n    - Every references entry MUST contain at least one of the properties."
       },
       "ReferenceResourceAttributes": {
         "title": "ReferenceResourceAttributes",
@@ -2416,7 +2416,7 @@
             "description": "Meaning of property matches the BiBTeX specification."
           }
         },
-        "description": "Model that stores the attributes of a reference. Many properties match the\nmeaning described in the\n[BibTeX specification](http://bibtexml.sourceforge.net/btxdoc.pdf)."
+        "description": "Model that stores the attributes of a reference.\n\nMany properties match the meaning described in the\n[BibTeX specification](http://bibtexml.sourceforge.net/btxdoc.pdf)."
       },
       "ReferenceResponseMany": {
         "title": "ReferenceResponseMany",
@@ -2873,7 +2873,7 @@
             "description": "If provided MUST be a list of length 1 or more of integers indicating the number of attached atoms of the kind specified in the value of the :field:`attached` key."
           }
         },
-        "description": "A list describing the species of the sites of this structure.\nSpecies can represent pure chemical elements, virtual-crystal atoms representing a\nstatistical occupation of a given site by multiple chemical elements, and/or a\nlocation to which there are attached atoms, i.e., atoms whose precise location are\nunknown beyond that they are attached to that position (frequently used to indicate\nhydrogen atoms attached to another element, e.g., a carbon with three attached\nhydrogens might represent a methyl group, -CH3).\n\n- **Examples**:\n    - `[ {\"name\": \"Ti\", \"chemical_symbols\": [\"Ti\"], \"concentration\": [1.0]} ]`: any site with this species is occupied by a Ti atom.\n    - `[ {\"name\": \"Ti\", \"chemical_symbols\": [\"Ti\", \"vacancy\"], \"concentration\": [0.9, 0.1]} ]`: any site with this species is occupied by a Ti atom with 90 % probability, and has a vacancy with 10 % probability.\n    - `[ {\"name\": \"BaCa\", \"chemical_symbols\": [\"vacancy\", \"Ba\", \"Ca\"], \"concentration\": [0.05, 0.45, 0.5], \"mass\": 88.5} ]`: any site with this species is occupied by a Ba atom with 45 % probability, a Ca atom with 50 % probability, and by a vacancy with 5 % probability. The mass of this site is (on average) 88.5 a.m.u.\n    - `[ {\"name\": \"C12\", \"chemical_symbols\": [\"C\"], \"concentration\": [1.0], \"mass\": 12.0} ]`: any site with this species is occupied by a carbon isotope with mass 12.\n    - `[ {\"name\": \"C13\", \"chemical_symbols\": [\"C\"], \"concentration\": [1.0], \"mass\": 13.0} ]`: any site with this species is occupied by a carbon isotope with mass 13.\n    - `[ {\"name\": \"CH3\", \"chemical_symbols\": [\"C\"], \"concentration\": [1.0], \"attached\": [\"H\"], \"nattached\": [3]} ]`: any site with this species is occupied by a methyl group, -CH3, which is represented without specifying precise positions of the hydrogen atoms.\n\n    "
+        "description": "A list describing the species of the sites of this structure.\n\nSpecies can represent pure chemical elements, virtual-crystal atoms representing a\nstatistical occupation of a given site by multiple chemical elements, and/or a\nlocation to which there are attached atoms, i.e., atoms whose precise location are\nunknown beyond that they are attached to that position (frequently used to indicate\nhydrogen atoms attached to another element, e.g., a carbon with three attached\nhydrogens might represent a methyl group, -CH3).\n\n- **Examples**:\n    - `[ {\"name\": \"Ti\", \"chemical_symbols\": [\"Ti\"], \"concentration\": [1.0]} ]`: any site with this species is occupied by a Ti atom.\n    - `[ {\"name\": \"Ti\", \"chemical_symbols\": [\"Ti\", \"vacancy\"], \"concentration\": [0.9, 0.1]} ]`: any site with this species is occupied by a Ti atom with 90 % probability, and has a vacancy with 10 % probability.\n    - `[ {\"name\": \"BaCa\", \"chemical_symbols\": [\"vacancy\", \"Ba\", \"Ca\"], \"concentration\": [0.05, 0.45, 0.5], \"mass\": 88.5} ]`: any site with this species is occupied by a Ba atom with 45 % probability, a Ca atom with 50 % probability, and by a vacancy with 5 % probability. The mass of this site is (on average) 88.5 a.m.u.\n    - `[ {\"name\": \"C12\", \"chemical_symbols\": [\"C\"], \"concentration\": [1.0], \"mass\": 12.0} ]`: any site with this species is occupied by a carbon isotope with mass 12.\n    - `[ {\"name\": \"C13\", \"chemical_symbols\": [\"C\"], \"concentration\": [1.0], \"mass\": 13.0} ]`: any site with this species is occupied by a carbon isotope with mass 13.\n    - `[ {\"name\": \"CH3\", \"chemical_symbols\": [\"C\"], \"concentration\": [1.0], \"attached\": [\"H\"], \"nattached\": [3]} ]`: any site with this species is occupied by a methyl group, -CH3, which is represented without specifying precise positions of the hydrogen atoms."
       },
       "StructureFeatures": {
         "title": "StructureFeatures",

optimade/adapters/structures/aiida.py

@@ -26,7 +26,7 @@
 
 
 def get_aiida_structure_data(optimade_structure: OptimadeStructure) -> StructureData:
-    """ Get AiiDA `StructureData` from OPTIMADE structure.
+    """Get AiiDA `StructureData` from OPTIMADE structure.
 
     Parameters:
         optimade_structure: OPTIMADE structure.

optimade/adapters/structures/ase.py

@@ -27,7 +27,7 @@
 
 
 def get_ase_atoms(optimade_structure: OptimadeStructure) -> Atoms:
-    """ Get ASE `Atoms` from OPTIMADE structure.
+    """Get ASE `Atoms` from OPTIMADE structure.
 
     Caution:
         Cannot handle partial occupancies (this includes vacancies).

optimade/adapters/structures/cif.py

@@ -41,7 +41,7 @@
 def get_cif(  # pylint: disable=too-many-locals,too-many-branches
     optimade_structure: OptimadeStructure,
 ) -> str:
-    """ Get CIF file as string from OPTIMADE structure.
+    """Get CIF file as string from OPTIMADE structure.
 
     Parameters:
         optimade_structure: OPTIMADE structure.

optimade/adapters/structures/jarvis.py

@@ -26,7 +26,7 @@
 
 
 def get_jarvis_atoms(optimade_structure: OptimadeStructure) -> Atoms:
-    """ Get jarvis `Atoms` from OPTIMADE structure.
+    """Get jarvis `Atoms` from OPTIMADE structure.
 
     Caution:
         Cannot handle partial occupancies.

optimade/adapters/structures/proteindatabank.py

@@ -48,7 +48,7 @@
 def get_pdbx_mmcif(  # pylint: disable=too-many-locals
     optimade_structure: OptimadeStructure,
 ) -> str:
-    """ Write Protein Data Bank (PDB) structure in the PDBx/mmCIF format from OPTIMADE structure.
+    """Write Protein Data Bank (PDB) structure in the PDBx/mmCIF format from OPTIMADE structure.
 
     Warning:
         The result of this function can currently not be parsed as a complete PDBx/mmCIF file.
@@ -199,7 +199,7 @@ def get_pdbx_mmcif(  # pylint: disable=too-many-locals
 def get_pdb(  # pylint: disable=too-many-locals
     optimade_structure: OptimadeStructure,
 ) -> str:
-    """ Write Protein Data Bank (PDB) structure in the old PDB format from OPTIMADE structure.
+    """Write Protein Data Bank (PDB) structure in the old PDB format from OPTIMADE structure.
 
     Parameters:
         optimade_structure: OPTIMADE structure.

optimade/adapters/structures/pymatgen.py

@@ -27,7 +27,7 @@
 
 
 def get_pymatgen(optimade_structure: OptimadeStructure) -> Union[Structure, Molecule]:
-    """ Get pymatgen Structure or Molecule from OPTIMADE structure.
+    """Get pymatgen `Structure` or `Molecule` from OPTIMADE structure.
 
     This function will return either a pymatgen `Structure` or `Molecule` based
     on the periodicity or periodic dimensionality of OPTIMADE structure.

optimade/adapters/structures/utils.py

@@ -309,5 +309,8 @@ def pad_cell(
 
     """
     return _pad_iter_of_iters(
-        iterable=lattice_vectors, padding=padding, outer=tuple, inner=tuple,
+        iterable=lattice_vectors,
+        padding=padding,
+        outer=tuple,
+        inner=tuple,
     )

optimade/filtertransformers/elasticsearch.py

@@ -16,9 +16,9 @@
 
 
 class Quantity:
-    """ Class to provide information about available quantities to the transformer.
+    """Class to provide information about available quantities to the transformer.
 
-    The elasticsearch transformer will :class:`Quantity`s to (a) do some semantic checks,
+    The elasticsearch transformer will use `Quantity`s to (a) do some semantic checks,
     (b) map quantities to the underlying elastic index.
 
     Attributes:
@@ -66,9 +66,9 @@ def __repr__(self):
 
 
 class Transformer(lark.Transformer):
-    """ Transformer that transforms ``v0.10.0`` grammer parse trees into queries.
+    """Transformer that transforms ``v0.10.0`` grammer parse trees into queries.
 
-    Uses elasticsearch_dsl and will produce a :class:`Q` instance.
+    Uses elasticsearch_dsl and will produce a `Q` instance.
     """
 
     def __init__(self, quantities: List[Quantity]):

optimade/filtertransformers/mongo.py

@@ -24,7 +24,7 @@ class MongoTransformer(Transformer):
     }
 
     def __init__(self, mapper: BaseResourceMapper = None):
-        """ Initialise the object, optionally loading in a
+        """Initialise the object, optionally loading in a
         resource mapper for use when post-processing.
 
         """
@@ -71,7 +71,7 @@ def non_string_value(self, value):
 
     @v_args(inline=True)
     def not_implemented_string(self, value):
-        """ not_implemented_string: value
+        """not_implemented_string: value
 
         Raise NotImplementedError.
         For further information, see Materials-Consortia/OPTIMADE issue 157:
@@ -231,8 +231,8 @@ def __default__(self, data, children, meta):
         )
 
     def _recursive_expression_phrase(self, arg):
-        """ Helper function for parsing `expression_phrase`. Recursively sorts out
-        the correct precedence for $and, $or and $nor.
+        """Helper function for parsing `expression_phrase`. Recursively sorts out
+        the correct precedence for `$and`, `$or` and `$nor`.
 
         """
         if len(arg) == 1:
@@ -258,7 +258,7 @@ def _recursive_expression_phrase(self, arg):
         return {prop: {"$not": expr} for prop, expr in arg[1].items()}
 
     def _apply_length_aliases(self, filter_: dict) -> dict:
-        """ Recursively search query for any $size calls, and check
+        """Recursively search query for any `$size` operations, and check
         if the property can be replaced with its corresponding length
         alias.
 
@@ -283,7 +283,7 @@ def replace_with_length_alias(subdict, prop, expr):
         )
 
     def _apply_aliases(self, filter_: dict) -> dict:
-        """ Check whether any fields in the filter have aliases so
+        """Check whether any fields in the filter have aliases so
         that they can be renamed for the Mongo query.
 
         """
@@ -307,7 +307,7 @@ def apply_alias(subdict, prop, expr):
         return recursive_postprocessing(filter_, check_for_alias, apply_alias)
 
     def _apply_length_operators(self, filter_: dict) -> dict:
-        """ Check for any invalid pymongo queries that involve
+        """Check for any invalid pymongo queries that involve
         applying an operator to the length of a field, and transform
         them into a test for existence of the relevant entry, e.g.
         "list LENGTH > 3" becomes "does the 4th list entry exist?".
@@ -348,11 +348,13 @@ def apply_length_op(subdict, prop, expr):
             return subdict
 
         return recursive_postprocessing(
-            filter_, check_for_length_op_filter, apply_length_op,
+            filter_,
+            check_for_length_op_filter,
+            apply_length_op,
         )
 
     def _apply_relationship_filtering(self, filter_: dict) -> dict:
-        """ Check query for property names that match the entry
+        """Check query for property names that match the entry
         types, and transform them as relationship filters rather than
         property filters.
 
@@ -394,14 +396,14 @@ def replace_with_relationship(subdict, prop, expr):
         )
 
     def _apply_unknown_or_null_filter(self, filter_: dict) -> dict:
-        """ This method loops through the query and replaces the check for
+        """This method loops through the query and replaces the check for
         KNOWN with a check for existence and a check for not null, and the
         inverse for UNKNOWN.
 
         """
 
         def check_for_known_filter(_, expr):
-            """ Find cases where the query dict looks like
+            """Find cases where the query dict looks like
             `{"field": {"#known": T/F}}` or
             `{"field": "$not": {"#known": T/F}}`, which is a magic word
             for KNOWN/UNKNOWN filters in this transformer.
@@ -412,7 +414,7 @@ def check_for_known_filter(_, expr):
             )
 
         def replace_known_filter_with_or(subdict, prop, expr):
-            """ Replace #known and $not->#known parsed filters with the appropriate
+            """Replace #known and $not->#known parsed filters with the appropriate
             combination of $exists and/or $eq/$ne null.
 
             """
@@ -444,7 +446,7 @@ def replace_known_filter_with_or(subdict, prop, expr):
 
 
 def recursive_postprocessing(filter_, condition, replacement):
-    """ Recursively descend into the query, checking each dictionary
+    """Recursively descend into the query, checking each dictionary
     (contained in a list, or as an entry in another dictionary) for
     the condition passed. If the condition is true, apply the
     replacement to the dictionary.