From d89f44190091cbe31ce279ec7c438de7bfd63f0c Mon Sep 17 00:00:00 2001
From: Graham Gower <graham.gower@gmail.com>
Date: Sat, 4 Dec 2021 11:51:31 +0100
Subject: [PATCH] Add toplevel metadata.

Closes #275.
---
 demes/demes.py      | 18 ++++++++++++++++--
 setup.cfg           |  1 +
 tests/test_demes.py | 34 ++++++++++++++++++++++++++++++++++
 3 files changed, 51 insertions(+), 2 deletions(-)

diff --git a/demes/demes.py b/demes/demes.py
index c5259f21..e1e429be 100644
--- a/demes/demes.py
+++ b/demes/demes.py
@@ -1,9 +1,10 @@
-from typing import List, Union, Optional, Dict, MutableMapping, Any, Set, Tuple
+import copy
+import collections
 import itertools
 import math
 import numbers
-import copy
 import operator
+from typing import List, Union, Optional, Dict, MutableMapping, Any, Set, Tuple
 import warnings
 
 import attr
@@ -1231,6 +1232,7 @@ class Graph:
         See also: :meth:`.in_generations`.
     :ivar list[str] doi: If the graph describes a published demography,
         the DOI(s) should be be given here as a list.
+    :ivar dict metadata: A dictionary of arbitrary additional data.
     :ivar list[Deme] demes: The demes in the demography.
     :ivar list[AsymmetricMigration] migrations: The continuous migrations for
         the demographic model.
@@ -1257,6 +1259,12 @@ class Graph:
             iterable_validator=attr.validators.instance_of(list),
         ),
     )
+    metadata: collections.abc.Mapping = attr.ib(
+        factory=dict,
+        validator=attr.validators.instance_of(
+            collections.abc.Mapping  # type: ignore[misc]
+        ),
+    )
     demes: List[Deme] = attr.ib(factory=list, init=False)
     migrations: List[AsymmetricMigration] = attr.ib(factory=list, init=False)
     pulses: List[Pulse] = attr.ib(factory=list, init=False)
@@ -1919,6 +1927,7 @@ def fromdict(cls, data: MutableMapping[str, Any]) -> "Graph":
                 "generation_time",
                 "defaults",
                 "doi",
+                "metadata",
                 "demes",
                 "migrations",
                 "pulses",
@@ -1980,6 +1989,7 @@ def fromdict(cls, data: MutableMapping[str, Any]) -> "Graph":
             time_units=data.pop("time_units"),
             doi=data.pop("doi", []),
             generation_time=data.pop("generation_time", None),
+            metadata=data.pop("metadata", {}),
         )
 
         for i, deme_data in enumerate(
@@ -2315,6 +2325,7 @@ def __init__(
         generation_time: float = None,
         doi: list = None,
         defaults: dict = None,
+        metadata: dict = None,
     ):
         """
         :param str description: A human readable description of the demography.
@@ -2329,6 +2340,7 @@ def __init__(
         :param doi: If the graph describes a published demography, the DOI(s)
             should be be given here as a list.
         :type doi: list[str]
+        :param dict metadata: A dictionary of arbitrary additional data.
         """
         self.data: MutableMapping[str, Any] = dict(time_units=time_units)
         if description is not None:
@@ -2339,6 +2351,8 @@ def __init__(
             self.data["doi"] = doi
         if defaults is not None:
             self.data["defaults"] = defaults
+        if metadata is not None:
+            self.data["metadata"] = metadata
 
     def add_deme(
         self,
diff --git a/setup.cfg b/setup.cfg
index bec2e0c0..3303ced5 100644
--- a/setup.cfg
+++ b/setup.cfg
@@ -51,6 +51,7 @@ per-file-ignores =
 
 [mypy]
 files = demes, tests
+warn_unused_ignores = True
 
 [mypy-numpy.*]
 ignore_missing_imports = True
diff --git a/tests/test_demes.py b/tests/test_demes.py
index 035ae7d6..6d2400f9 100644
--- a/tests/test_demes.py
+++ b/tests/test_demes.py
@@ -1824,6 +1824,20 @@ def test_bad_doi(self):
                 doi=[""],
             )
 
+    def test_metadata_empty(self):
+        graph = Graph(time_units="generations")
+        assert graph.metadata == {}
+
+    def test_metadata_simple(self):
+        metadata = dict(one=1, two="string", three=dict(four=[4, 4, 4, 4]))
+        graph = Graph(time_units="generations", metadata=metadata)
+        assert graph.metadata == metadata
+
+    @pytest.mark.parametrize("metadata", [None, 1, "string", [1, 2, 3]])
+    def test_bad_metadata(self, metadata):
+        with pytest.raises(TypeError):
+            Graph(time_units="generations", metadata=metadata)
+
     @pytest.mark.parametrize("graph", tests.example_graphs())
     def test_in_generations(self, graph):
         dg1 = copy.deepcopy(graph)
@@ -4233,3 +4247,23 @@ def test_infinities_in_defaults(self):
         assert g.demes[0].start_time == math.inf
         assert g.demes[1].start_time == math.inf
         assert g.migrations[0].start_time == math.inf
+
+    def test_metadata_empty(self):
+        b = Builder()
+        b.add_deme("a", epochs=[dict(start_size=1)])
+        graph = b.resolve()
+        assert graph.metadata == {}
+
+    def test_metadata_simple(self):
+        metadata = dict(one=1, two="string", three=dict(four=[4, 4, 4, 4]))
+        b = Builder(metadata=metadata)
+        b.add_deme("a", epochs=[dict(start_size=1)])
+        graph = b.resolve()
+        assert graph.metadata == metadata
+
+    @pytest.mark.parametrize("metadata", [1, "string", [1, 2, 3]])
+    def test_bad_metadata(self, metadata):
+        b = Builder(metadata=metadata)
+        b.add_deme("a", epochs=[dict(start_size=1)])
+        with pytest.raises(TypeError):
+            b.resolve()