Fix docs

aiida_lammps/data/lammps_potential.py

@@ -578,7 +578,7 @@ def source_citations(self) -> typing.Union[str, list]:
         corresponding to primary published work(s) describing the KIM Item.
 
         :return: the citation where the potential was originally published.
-        :rtype: typing.Union[str, list].
+        :rtype: typing.Union[str, list]
         """
         return self.get_attribute("source_citations")
 

docs/source/conf.py

@@ -47,6 +47,8 @@
     "pymatgen": ("https://pymatgen.org/", None),
 }
 
+suppress_warnings = ["etoc.toctree"]
+
 html_theme = "furo"  # pylint: disable=invalid-name
 html_title = f"v{__version__}"  # pylint: disable=invalid-name
 html_logo = "static/logo.png"  # pylint: disable=invalid-name

docs/source/nitpick-exceptions

@@ -1,163 +1,17 @@
-### python builtins
-
-# note: there doesn't seem to be a standard way of indicating a callable in python3
-# https://stackoverflow.com/questions/23571253/how-to-define-a-callable-parameter-in-a-python-docstring
-py:class callable
-
-# For some reason, "filter" does not seem to be found
-py:class filter
-
+py:class collections.namedtuple
+py:class list of str
 py:class optional
-
-py:class unittest.case.TestCase
-py:class unittest.runner.TextTestRunner
-
-# required for metaclasses(?)
-py:class builtins.bool
-py:class builtins.float
-py:class builtins.int
-py:class builtins.object
-py:class builtins.str
-py:class builtins.dict
-
-# typing
-py:class asyncio.events.AbstractEventLoop
-py:class EntityType
-py:class function
-py:class IO
-py:class traceback
-
-### AiiDA
-
-# issues with order of object processing and type hinting
-py:class aiida.engine.runners.ResultAndNode
-py:class aiida.engine.runners.ResultAndPk
-py:class aiida.engine.processes.workchains.workchain.WorkChainSpec
-py:class aiida.manage.manager.Manager
-py:class aiida.orm.nodes.node.WarnWhenNotEntered
-py:class aiida.orm.utils.links.LinkQuadruple
-py:class aiida.tools.importexport.dbexport.ExportReport
-py:class aiida.tools.importexport.dbexport.ArchiveData
-py:class aiida.tools.groups.paths.WalkNodeResult
-py:class aiida.orm.Float
-py:class aiida.orm.Dict
-py:class aiida.orm.StructureData
-
-py:class Backend
-py:class BackendEntity
-py:class BackendNode
-py:class AuthInfo
-py:class CalcJob
-py:class CalcJobNode
-py:class Data
-py:class ExitCode
-py:class File
-py:class FolderData
-py:class JobInfo
-py:class JobState
-py:class Node
-py:class Parser
-py:class PersistenceError
-py:class Process
-py:class ProcessBuilder
-py:class ProcessNode
-py:class ProcessSpec
-py:class Port
-py:class PortNamespace
-py:class Runner
-py:class Transport
-py:class TransportQueue
-py:class WorkChainSpec
-
-py:class kiwipy.communications.Communicator
-py:class plumpy.process_states.State
-py:class plumpy.workchains._If
-py:class plumpy.workchains._While
-
-### python packages
-# Note: These exceptions are needed if
-# * the objects are referenced e.g. as param/return types types in method docstrings (without intersphinx mapping)
-# * the documentation linked via intersphinx lists the objects at a different (usually lower) import hierarchy
-py:class click.core.Group
-py:class click.core.Option
-py:class click.types.ParamType
-py:class click.types.Choice
-py:class click.types.IntParamType
-py:class click.types.StringParamType
-py:class click.types.Path
-py:class click.types.File
-py:meth  click.Option.get_default
-
-py:class concurrent.futures._base.TimeoutError
-
-py:class sphinx.util.docutils.SphinxDirective
-
-py:class frozenset
-
-py:class numpy.bool_
-
-py:class paramiko.proxy.ProxyCommand
-
-# These can be removed once they are properly included in the `__all__` in `plumpy`
-py:class plumpy.ports.PortNamespace
-py:class plumpy.utils.AttributesDict
-
-py:class _asyncio.Future
-
-py:class tqdm.std.tqdm
-
-py:class IPython.core.magic.Magics
-
-py:class HTMLParser.HTMLParser
-py:class html.parser.HTMLParser
-
-py:class django.contrib.auth.base_user.AbstractBaseUser
-py:class django.contrib.auth.base_user.BaseUserManager
-py:class django.contrib.auth.models.AbstractBaseUser
-py:class django.contrib.auth.models.BaseUserManager
-py:class django.contrib.auth.models.PermissionsMixin
-py:class django.core.exceptions.MultipleObjectsReturned
-py:class django.core.exceptions.ObjectDoesNotExist
-py:class django.db.models.base.Model
-py:class django.db.models.manager.Manager
-py:class django.db.models.query.QuerySet
-py:class django.db.migrations.migration.Migration
-
-py:class flask.app.Flask
-
-py:class sqlalchemy.ext.declarative.api.Base
-py:class sqlalchemy.ext.declarative.api.Model
-py:class sqlalchemy.sql.functions.FunctionElement
-py:class sqlalchemy.orm.query.Query
-py:class sqlalchemy.orm.util.AliasedClass
-py:class sqlalchemy.orm.session.Session
-py:exc sqlalchemy.orm.exc.MultipleResultsFound
-
-py:class sphinx.ext.autodoc.ClassDocumenter
-
-py:class yaml.Dumper
-py:class yaml.Loader
-py:class yaml.dumper.Dumper
-py:class yaml.loader.Loader
-py:class yaml.FullLoader
-py:class yaml.loader.FullLoader
-py:class uuid.UUID
-
-py:class psycopg2.extensions.cursor
-
-py:class aldjemy.orm.DbNode
-py:class aldjemy.orm.DbLink
-py:class aldjemy.orm.DbComputer
-py:class aldjemy.orm.DbUser
-py:class aldjemy.orm.DbGroup
-py:class aldjemy.orm.DbAuthInfo
-py:class aldjemy.orm.DbComment
-py:class aldjemy.orm.DbLog
-py:class aldjemy.orm.DbSetting
-
-py:class alembic.config.Config
-
-py:class pgsu.PGSU
-py:meth  pgsu.PGSU.__init__
-
-py:class jsonschema.exceptions._Error
+py:class namedtuple
+py:class numpy.array
+py:class np.array
+py:class State
+py:class EVENT_CALLBACK_TYPE
+py:class orm.ArrayData
+py:class orm.Dict
+py:class orm.ProcessNode
+py:class orm.StructureData
+py:class utils.AttributesFrozendict
+py:exc jsonschema.exceptions.ValidationError
+py:exc jsonschema.exceptions.SchemaError
+py:exc InputValidationError
+py:class aiida_lammps.common.parse_trajectory.TRAJ_BLOCK

pyproject.toml

@@ -10,7 +10,7 @@ force_sort_within_sections = true
 no_lines_before = ["LOCALFOLDER"]
 
 # Configure isort to work without access to site-packages
-known_first_party = ["aiida_lammos"]
+known_first_party = ["aiida_lammps"]
 
 # Settings for Black compatibility
 profile = "black"

tox.ini

@@ -11,7 +11,7 @@
 envlist = py37
 
 [testenv]
-use_develop = true
+usedevelop = true
 
 [testenv:py{37,38,39}]
 extras = testing
@@ -29,6 +29,7 @@ allowlist_externals =
     echo
 commands =
     clean: rm -rf docs/_build
+    clean: rm -rf docs/source/reference/apidoc
     sphinx-build -n -W --keep-going -c docs/source docs/source docs/_build
 commands_post = echo "open docs/_build/index.html"