From e974cb28f97736070b85ca2009b95a22e945ce86 Mon Sep 17 00:00:00 2001
From: cortadocodes <cortado.codes@protonmail.com>
Date: Thu, 12 Dec 2024 10:20:40 +0000
Subject: [PATCH 01/12] DEP: Remove `flake8` and `black` dependencies

---
 poetry.lock    | 501 +++++++++++--------------------------------------
 pyproject.toml |   4 +-
 2 files changed, 110 insertions(+), 395 deletions(-)

diff --git a/poetry.lock b/poetry.lock
index 285b13f..aa375c5 100644
--- a/poetry.lock
+++ b/poetry.lock
@@ -1,16 +1,5 @@
 # This file is automatically @generated by Poetry 1.8.3 and should not be changed by hand.
 
-[[package]]
-name = "appdirs"
-version = "1.4.4"
-description = "A small Python module for determining appropriate platform-specific dirs, e.g. a \"user data dir\"."
-optional = false
-python-versions = "*"
-files = [
-    {file = "appdirs-1.4.4-py2.py3-none-any.whl", hash = "sha256:a841dacd6b99318a741b166adb07e19ee71a274450e68237b4650ca1055ab128"},
-    {file = "appdirs-1.4.4.tar.gz", hash = "sha256:7d5d0167b2b1ba821647616af46a749d1c653740dd0d2415100fe26e27afdf41"},
-]
-
 [[package]]
 name = "attrs"
 version = "24.2.0"
@@ -30,29 +19,6 @@ docs = ["cogapp", "furo", "myst-parser", "sphinx", "sphinx-notfound-page", "sphi
 tests = ["cloudpickle", "hypothesis", "mypy (>=1.11.1)", "pympler", "pytest (>=4.3.0)", "pytest-mypy-plugins", "pytest-xdist[psutil]"]
 tests-mypy = ["mypy (>=1.11.1)", "pytest-mypy-plugins"]
 
-[[package]]
-name = "black"
-version = "19.10b0"
-description = "The uncompromising code formatter."
-optional = false
-python-versions = ">=3.6"
-files = [
-    {file = "black-19.10b0-py36-none-any.whl", hash = "sha256:1b30e59be925fafc1ee4565e5e08abef6b03fe455102883820fe5ee2e4734e0b"},
-    {file = "black-19.10b0.tar.gz", hash = "sha256:c2edb73a08e9e0e6f65a0e6af18b059b8b1cdd5bef997d7a0b181df93dc81539"},
-]
-
-[package.dependencies]
-appdirs = "*"
-attrs = ">=18.1.0"
-click = ">=6.5"
-pathspec = ">=0.6,<1"
-regex = "*"
-toml = ">=0.9.4"
-typed-ast = ">=1.4.0"
-
-[package.extras]
-d = ["aiohttp (>=3.3.2)", "aiohttp-cors"]
-
 [[package]]
 name = "cfgv"
 version = "3.4.0"
@@ -64,31 +30,6 @@ files = [
     {file = "cfgv-3.4.0.tar.gz", hash = "sha256:e52591d4c5f5dead8e0f673fb16db7949d2cfb3f7da4582893288f0ded8fe560"},
 ]
 
-[[package]]
-name = "click"
-version = "8.1.7"
-description = "Composable command line interface toolkit"
-optional = false
-python-versions = ">=3.7"
-files = [
-    {file = "click-8.1.7-py3-none-any.whl", hash = "sha256:ae74fb96c20a0277a1d615f1e4d73c8414f5a98db8b799a7931d1582f3390c28"},
-    {file = "click-8.1.7.tar.gz", hash = "sha256:ca9853ad459e787e2192211578cc907e7594e294c7ccc834310722b41b9ca6de"},
-]
-
-[package.dependencies]
-colorama = {version = "*", markers = "platform_system == \"Windows\""}
-
-[[package]]
-name = "colorama"
-version = "0.4.6"
-description = "Cross-platform colored terminal text."
-optional = false
-python-versions = "!=3.0.*,!=3.1.*,!=3.2.*,!=3.3.*,!=3.4.*,!=3.5.*,!=3.6.*,>=2.7"
-files = [
-    {file = "colorama-0.4.6-py2.py3-none-any.whl", hash = "sha256:4f1d9991f5acc0ca119f9d443620b77f9d6b33703e51011c16baf57afb285fc6"},
-    {file = "colorama-0.4.6.tar.gz", hash = "sha256:08695f5cb7ed6e0531a20572697297273c47b8cae5a63ffc6d6ed5c201be6e44"},
-]
-
 [[package]]
 name = "coverage"
 version = "7.6.1"
@@ -200,22 +141,6 @@ docs = ["furo (>=2024.8.6)", "sphinx (>=8.0.2)", "sphinx-autodoc-typehints (>=2.
 testing = ["covdefaults (>=2.3)", "coverage (>=7.6.1)", "diff-cover (>=9.2)", "pytest (>=8.3.3)", "pytest-asyncio (>=0.24)", "pytest-cov (>=5)", "pytest-mock (>=3.14)", "pytest-timeout (>=2.3.1)", "virtualenv (>=20.26.4)"]
 typing = ["typing-extensions (>=4.12.2)"]
 
-[[package]]
-name = "flake8"
-version = "3.8.3"
-description = "the modular source code checker: pep8 pyflakes and co"
-optional = false
-python-versions = "!=3.0.*,!=3.1.*,!=3.2.*,!=3.3.*,>=2.7"
-files = [
-    {file = "flake8-3.8.3-py2.py3-none-any.whl", hash = "sha256:15e351d19611c887e482fb960eae4d44845013cc142d42896e9862f775d8cf5c"},
-    {file = "flake8-3.8.3.tar.gz", hash = "sha256:f04b9fcbac03b0a3e58c0ab3a0ecc462e023a9faf046d57794184028123aa208"},
-]
-
-[package.dependencies]
-mccabe = ">=0.6.0,<0.7.0"
-pycodestyle = ">=2.6.0a1,<2.7.0"
-pyflakes = ">=2.2.0,<2.3.0"
-
 [[package]]
 name = "identify"
 version = "2.6.1"
@@ -290,17 +215,6 @@ files = [
 importlib-resources = {version = ">=1.4.0", markers = "python_version < \"3.9\""}
 referencing = ">=0.31.0"
 
-[[package]]
-name = "mccabe"
-version = "0.6.1"
-description = "McCabe checker, plugin for flake8"
-optional = false
-python-versions = "*"
-files = [
-    {file = "mccabe-0.6.1-py2.py3-none-any.whl", hash = "sha256:ab8a6258860da4b6677da4bd2fe5dc2c659cff31b3ee4f7f5d64e79735b80d42"},
-    {file = "mccabe-0.6.1.tar.gz", hash = "sha256:dd8d182285a0fe56bace7f45b5e7d1a6ebcbf524e8f3bd87eb0f125271b8831f"},
-]
-
 [[package]]
 name = "nodeenv"
 version = "1.9.1"
@@ -349,17 +263,6 @@ files = [
     {file = "numpy-1.24.4.tar.gz", hash = "sha256:80f5e3a4e498641401868df4208b74581206afbee7cf7b8329daae82676d9463"},
 ]
 
-[[package]]
-name = "pathspec"
-version = "0.12.1"
-description = "Utility library for gitignore style pattern matching of file paths."
-optional = false
-python-versions = ">=3.8"
-files = [
-    {file = "pathspec-0.12.1-py3-none-any.whl", hash = "sha256:a0d503e138a4c123b27490a4f7beda6a01c6f288df0e4a8b79c7eb0dc7b4cc08"},
-    {file = "pathspec-0.12.1.tar.gz", hash = "sha256:a482d51503a1ab33b1c67a6c3813a26953dbdc71c31dacaef9a838c4e29f5712"},
-]
-
 [[package]]
 name = "pkgutil-resolve-name"
 version = "1.3.10"
@@ -405,28 +308,6 @@ nodeenv = ">=0.11.1"
 pyyaml = ">=5.1"
 virtualenv = ">=20.10.0"
 
-[[package]]
-name = "pycodestyle"
-version = "2.6.0"
-description = "Python style guide checker"
-optional = false
-python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*"
-files = [
-    {file = "pycodestyle-2.6.0-py2.py3-none-any.whl", hash = "sha256:2295e7b2f6b5bd100585ebcb1f616591b652db8a741695b3d8f5d28bdc934367"},
-    {file = "pycodestyle-2.6.0.tar.gz", hash = "sha256:c58a7d2815e0e8d7972bf1803331fb0152f867bd89adf8a01dfd55085434192e"},
-]
-
-[[package]]
-name = "pyflakes"
-version = "2.2.0"
-description = "passive checker of Python programs"
-optional = false
-python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*"
-files = [
-    {file = "pyflakes-2.2.0-py2.py3-none-any.whl", hash = "sha256:0d94e0e05a19e57a99444b6ddcf9a6eb2e5c68d3ca1e98e90707af8152c90a92"},
-    {file = "pyflakes-2.2.0.tar.gz", hash = "sha256:35b2d75ee967ea93b55750aa9edbbf72813e06a66ba54438df2cfac9e3c27fc8"},
-]
-
 [[package]]
 name = "python-dotenv"
 version = "1.0.1"
@@ -518,219 +399,116 @@ files = [
 attrs = ">=22.2.0"
 rpds-py = ">=0.7.0"
 
-[[package]]
-name = "regex"
-version = "2024.9.11"
-description = "Alternative regular expression module, to replace re."
-optional = false
-python-versions = ">=3.8"
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-    {file = "typed_ast-1.5.5-cp36-cp36m-musllinux_1_1_x86_64.whl", hash = "sha256:16f7313e0a08c7de57f2998c85e2a69a642e97cb32f87eb65fbfe88381a5e44d"},
-    {file = "typed_ast-1.5.5-cp36-cp36m-win_amd64.whl", hash = "sha256:2b946ef8c04f77230489f75b4b5a4a6f24c078be4aed241cfabe9cbf4156e7e5"},
-    {file = "typed_ast-1.5.5-cp37-cp37m-macosx_10_9_x86_64.whl", hash = "sha256:2188bc33d85951ea4ddad55d2b35598b2709d122c11c75cffd529fbc9965508e"},
-    {file = "typed_ast-1.5.5-cp37-cp37m-manylinux_2_17_aarch64.manylinux2014_aarch64.whl", hash = "sha256:0635900d16ae133cab3b26c607586131269f88266954eb04ec31535c9a12ef1e"},
-    {file = "typed_ast-1.5.5-cp37-cp37m-manylinux_2_17_x86_64.manylinux2014_x86_64.whl", hash = "sha256:57bfc3cf35a0f2fdf0a88a3044aafaec1d2f24d8ae8cd87c4f58d615fb5b6311"},
-    {file = "typed_ast-1.5.5-cp37-cp37m-musllinux_1_1_aarch64.whl", hash = "sha256:fe58ef6a764de7b4b36edfc8592641f56e69b7163bba9f9c8089838ee596bfb2"},
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-    {file = "typed_ast-1.5.5-cp37-cp37m-win_amd64.whl", hash = "sha256:d40c10326893ecab8a80a53039164a224984339b2c32a6baf55ecbd5b1df6431"},
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-    {file = "typed_ast-1.5.5-cp39-cp39-musllinux_1_1_x86_64.whl", hash = "sha256:429ae404f69dc94b9361bb62291885894b7c6fb4640d561179548c849f8492ba"},
-    {file = "typed_ast-1.5.5-cp39-cp39-win_amd64.whl", hash = "sha256:335f22ccb244da2b5c296e6f96b06ee9bed46526db0de38d2f0e5a6597b81155"},
-    {file = "typed_ast-1.5.5.tar.gz", hash = "sha256:94282f7a354f36ef5dbce0ef3467ebf6a258e370ab33d5b40c249fa996e590dd"},
-]
-
 [[package]]
 name = "virtualenv"
-version = "20.26.6"
+version = "20.28.0"
 description = "Virtual Python Environment builder"
 optional = false
-python-versions = ">=3.7"
+python-versions = ">=3.8"
 files = [
-    {file = "virtualenv-20.26.6-py3-none-any.whl", hash = "sha256:7345cc5b25405607a624d8418154577459c3e0277f5466dd79c49d5e492995f2"},
-    {file = "virtualenv-20.26.6.tar.gz", hash = "sha256:280aede09a2a5c317e409a00102e7077c6432c5a38f0ef938e643805a7ad2c48"},
+    {file = "virtualenv-20.28.0-py3-none-any.whl", hash = "sha256:23eae1b4516ecd610481eda647f3a7c09aea295055337331bb4e6892ecce47b0"},
+    {file = "virtualenv-20.28.0.tar.gz", hash = "sha256:2c9c3262bb8e7b87ea801d715fae4495e6032450c71d2309be9550e7364049aa"},
 ]
 
 [package.dependencies]
@@ -863,4 +580,4 @@ type = ["pytest-mypy"]
 [metadata]
 lock-version = "2.0"
 python-versions = "^3.8"
-content-hash = "63a41dc4b5ba505280fc7535047f493179bec549b6b4998fc2f5421acf5457bb"
+content-hash = "7ab2b6a1889db14af69548dee8b8d0091615ec54901e5412ddcf7e05a1d170ae"
diff --git a/pyproject.toml b/pyproject.toml
index 83259e6..0d6a331 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -1,6 +1,6 @@
 [tool.poetry]
 name = "twined"
-version = "0.5.6"
+version = "0.6.0"
 repository = "https://www.github.com/octue/twined"
 description = "A library to help digital twins and data services talk to one another."
 authors = [
@@ -27,8 +27,6 @@ jsonschema = "^4"
 python-dotenv = ">=0,<=2"
 
 [tool.poetry.group.dev.dependencies]
-flake8 = "3.8.3"
-black = "19.10.b0"
 pre-commit = ">=2.6.0"
 coverage = ">=5.2.1"
 numpy = "^1"

From 93bea38c62109cae5e00d64f884a8e5db2aea524 Mon Sep 17 00:00:00 2001
From: cortadocodes <cortado.codes@protonmail.com>
Date: Thu, 12 Dec 2024 10:22:08 +0000
Subject: [PATCH 02/12] FEA: Allow strands to be optional

---
 twined/schema/twine_schema.json |  4 ++++
 twined/twine.py                 | 17 +++++++++++++----
 2 files changed, 17 insertions(+), 4 deletions(-)

diff --git a/twined/schema/twine_schema.json b/twined/schema/twine_schema.json
index 0974502..f7fb6d9 100644
--- a/twined/schema/twine_schema.json
+++ b/twined/schema/twine_schema.json
@@ -37,6 +37,10 @@
     "manifest": {
       "type": "object",
       "properties": {
+        "optional": {
+          "type": "boolean",
+          "description": "This should be `true` if the manifest is optional."
+        },
         "datasets": {
           "type": "object",
           "description": "A list of entries, each describing a dataset that should be attached to / made available to the digital twin",
diff --git a/twined/twine.py b/twined/twine.py
index 0b44188..de16742 100644
--- a/twined/twine.py
+++ b/twined/twine.py
@@ -58,8 +58,9 @@ def __init__(self, **kwargs):
         for name, strand in self._load_twine(**kwargs).items():
             setattr(self, name, strand)
 
-        self._available_strands = set(trim_suffix(name, "_schema") for name in vars(self))
+        self._available_strands = {trim_suffix(name, "_schema") for name in vars(self)}
         self._available_manifest_strands = self._available_strands & set(MANIFEST_STRANDS)
+        self._required_strands = {strand for strand in self._available_strands if not strand.get("optional", False)}
 
     def _load_twine(self, source=None):
         """Load twine from a *.json filename, file-like or a json string and validates twine contents."""
@@ -216,7 +217,7 @@ def _validate_all_expected_datasets_are_present_in_manifest(self, manifest_kind,
     def available_strands(self):
         """Get the names of strands that are found in this twine.
 
-        :return set:
+        :return set(str):
         """
         return self._available_strands
 
@@ -224,10 +225,18 @@ def available_strands(self):
     def available_manifest_strands(self):
         """Get the names of the manifest strands that are found in this twine.
 
-        :return set:
+        :return set(str):
         """
         return self._available_manifest_strands
 
+    @property
+    def required_strands(self):
+        """Get the names of strands that are required in this twine.
+
+        :return set(str):
+        """
+        return self._required_strands
+
     def validate_children(self, source, **kwargs):
         """Validate that the children values, passed as either a file or a json string, are correct."""
         # TODO cache this loaded data keyed on a hashed version of kwargs
@@ -371,7 +380,7 @@ def validate(self, allow_missing=False, allow_extra=False, cls=None, **kwargs):
                     )
 
             if not allow_missing:
-                if (strand_name in self.available_strands) and (strand_data is None):
+                if (strand_name in self.required_strands) and (strand_data is None):
                     raise exceptions.TwineValueException(
                         f"The '{strand_name}' strand is defined in the twine, but no data is provided in sources"
                     )

From 17f6fb664101e509e2194dc72f0dfc0cc2448144 Mon Sep 17 00:00:00 2001
From: cortadocodes <cortado.codes@protonmail.com>
Date: Thu, 12 Dec 2024 10:22:56 +0000
Subject: [PATCH 03/12] REF: Remove unused `allow_missing` argument of
 `Twine.validate`

BREAKING CHANGE: Remove use of the `allow_missing` argument in `Twine.validate` and set the `optional` field to `true` in the individual strands of the twine if required.
---
 twined/twine.py | 14 ++++++--------
 1 file changed, 6 insertions(+), 8 deletions(-)

diff --git a/twined/twine.py b/twined/twine.py
index de16742..1c8073f 100644
--- a/twined/twine.py
+++ b/twined/twine.py
@@ -348,7 +348,7 @@ def _get_cls(name, cls):
         """Getter that will return cls[name] if cls is a dict or cls otherwise"""
         return cls.get(name, None) if isinstance(cls, dict) else cls
 
-    def validate(self, allow_missing=False, allow_extra=False, cls=None, **kwargs):
+    def validate(self, allow_extra=False, cls=None, **kwargs):
         """Validate strands from sources provided as keyword arguments
 
         Usage:
@@ -359,12 +359,10 @@ def validate(self, allow_missing=False, allow_extra=False, cls=None, **kwargs):
                 credentials=credentials,
                 children=children,
                 cls=CLASS_MAP,
-                allow_missing=False,
                 allow_extra=False,
             )
         ```
 
-        :param bool allow_missing: If strand is present in the twine, but the source is equal to None, allow validation to continue.
         :param bool allow_extra: If strand is present in the sources, but not in the twine, allow validation to continue (only strands in the twine will be validated and converted, others will be returned as-is)
         :param any cls: optional dict of classes keyed on strand name (alternatively, one single class which will be applied to strands) which will be instantiated with the validated source data.
         :return dict: dict of validated and initialised sources
@@ -372,6 +370,7 @@ def validate(self, allow_missing=False, allow_extra=False, cls=None, **kwargs):
         # pop any strand name:data pairs out of kwargs and into their own dict
         source_kwargs = tuple(name for name in kwargs.keys() if name in ALL_STRANDS)
         sources = dict((name, kwargs.pop(name)) for name in source_kwargs)
+
         for strand_name, strand_data in sources.items():
             if not allow_extra:
                 if (strand_data is not None) and (strand_name not in self.available_strands):
@@ -379,11 +378,10 @@ def validate(self, allow_missing=False, allow_extra=False, cls=None, **kwargs):
                         f"Source data is provided for '{strand_name}' but no such strand is defined in the twine"
                     )
 
-            if not allow_missing:
-                if (strand_name in self.required_strands) and (strand_data is None):
-                    raise exceptions.TwineValueException(
-                        f"The '{strand_name}' strand is defined in the twine, but no data is provided in sources"
-                    )
+            if (strand_name in self.required_strands) and (strand_data is None):
+                raise exceptions.TwineValueException(
+                    f"The '{strand_name}' strand is defined in the twine, but no data is provided in sources"
+                )
 
             if strand_data is not None:
                 # TODO Consider reintroducing a skip based on whether cls is already instantiated. For now, leave it the

From 9a3399eca7a19128cdb915aee367591d2a939e58 Mon Sep 17 00:00:00 2001
From: cortadocodes <cortado.codes@protonmail.com>
Date: Thu, 12 Dec 2024 10:32:50 +0000
Subject: [PATCH 04/12] FIX: Fix populating `Twine.required_strands`

---
 twined/twine.py | 9 +++++++--
 1 file changed, 7 insertions(+), 2 deletions(-)

diff --git a/twined/twine.py b/twined/twine.py
index 1c8073f..2fc87ba 100644
--- a/twined/twine.py
+++ b/twined/twine.py
@@ -55,12 +55,17 @@ class Twine:
     """
 
     def __init__(self, **kwargs):
+        self._available_strands = set()
+        self._required_strands = set()
+
         for name, strand in self._load_twine(**kwargs).items():
             setattr(self, name, strand)
+            self._available_strands.add(trim_suffix(name, "_schema"))
+
+            if isinstance(strand, dict) and not strand.get("optional", False):
+                self._required_strands.add(name)
 
-        self._available_strands = {trim_suffix(name, "_schema") for name in vars(self)}
         self._available_manifest_strands = self._available_strands & set(MANIFEST_STRANDS)
-        self._required_strands = {strand for strand in self._available_strands if not strand.get("optional", False)}
 
     def _load_twine(self, source=None):
         """Load twine from a *.json filename, file-like or a json string and validates twine contents."""

From 79771c8774c7873ecd757697c3b7302497de9a32 Mon Sep 17 00:00:00 2001
From: cortadocodes <cortado.codes@protonmail.com>
Date: Thu, 12 Dec 2024 10:33:50 +0000
Subject: [PATCH 05/12] ENH: Allow all value strands to be optional

---
 twined/schema/twine_schema.json | 53 +++++++++++++++++++++++++++++----
 1 file changed, 47 insertions(+), 6 deletions(-)

diff --git a/twined/schema/twine_schema.json b/twined/schema/twine_schema.json
index f7fb6d9..b19f0d9 100644
--- a/twined/schema/twine_schema.json
+++ b/twined/schema/twine_schema.json
@@ -96,10 +96,23 @@
         ]
       }
     },
-    "configuration_manifest": {"$ref": "#/$defs/manifest"},
+    "configuration_manifest": {
+      "$ref": "#/$defs/manifest"
+    },
     "configuration_values_schema": {
       "type": "object",
-      "required": ["properties"]
+      "properties": {
+        "properties": {
+          "type": "object"
+        },
+        "optional": {
+          "type": "boolean",
+          "description": "This should be `true` if the configuration values are optional."
+        }
+      },
+      "required": [
+        "properties"
+      ]
     },
     "credentials": {
       "type": "array",
@@ -122,13 +135,41 @@
         "additionalProperties": false
       }
     },
-    "input_manifest": {"$ref": "#/$defs/manifest"},
+    "input_manifest": {
+      "$ref": "#/$defs/manifest"
+    },
     "input_values_schema": {
-      "type": "object"
+      "type": "object",
+      "properties": {
+        "properties": {
+          "type": "object"
+        },
+        "optional": {
+          "type": "boolean",
+          "description": "This should be `true` if the input values are optional."
+        }
+      },
+      "required": [
+        "properties"
+      ]
+    },
+    "output_manifest": {
+      "$ref": "#/$defs/manifest"
     },
-    "output_manifest": {"$ref": "#/$defs/manifest"},
     "output_values_schema": {
-      "type": "object"
+      "type": "object",
+      "properties": {
+        "properties": {
+          "type": "object"
+        },
+        "optional": {
+          "type": "boolean",
+          "description": "This should be `true` if the output values are optional."
+        }
+      },
+      "required": [
+        "properties"
+      ]
     }
   }
 }

From 421926a530b07caf8128d6b3885790dfddfe355b Mon Sep 17 00:00:00 2001
From: cortadocodes <cortado.codes@protonmail.com>
Date: Thu, 12 Dec 2024 10:35:55 +0000
Subject: [PATCH 06/12] OPS: Extend test matrix to python versions up to 3.12

---
 .github/workflows/codeql.yml    | 2 +-
 .github/workflows/python-ci.yml | 6 +++---
 .github/workflows/release.yml   | 4 ++--
 3 files changed, 6 insertions(+), 6 deletions(-)

diff --git a/.github/workflows/codeql.yml b/.github/workflows/codeql.yml
index 544498d..ccf786d 100644
--- a/.github/workflows/codeql.yml
+++ b/.github/workflows/codeql.yml
@@ -35,7 +35,7 @@ jobs:
 
     steps:
     - name: Checkout repository
-      uses: actions/checkout@v3
+      uses: actions/checkout@v4
 
     # Initializes the CodeQL tools for scanning.
     - name: Initialize CodeQL
diff --git a/.github/workflows/python-ci.yml b/.github/workflows/python-ci.yml
index 721e0c6..86dbfea 100644
--- a/.github/workflows/python-ci.yml
+++ b/.github/workflows/python-ci.yml
@@ -23,10 +23,10 @@ jobs:
       USING_COVERAGE: '3.9'
     strategy:
       matrix:
-        python: ['3.8', '3.9']
+        python: ['3.8', '3.9', '3.10', '3.11', '3.12']
     steps:
       - name: Checkout Repository
-        uses: actions/checkout@v3
+        uses: actions/checkout@v4
 
       - name: Setup Python
         uses: actions/setup-python@v5
@@ -60,7 +60,7 @@ jobs:
       contents: read
     steps:
       - name: Checkout Repository
-        uses: actions/checkout@v3
+        uses: actions/checkout@v4
 
       - name: Install Poetry
         uses: snok/install-poetry@v1.4.1
diff --git a/.github/workflows/release.yml b/.github/workflows/release.yml
index b69d6f8..7e6c2d8 100644
--- a/.github/workflows/release.yml
+++ b/.github/workflows/release.yml
@@ -18,7 +18,7 @@ jobs:
         python: ['3.8', '3.9']
     steps:
       - name: Checkout Repository
-        uses: actions/checkout@v3
+        uses: actions/checkout@v4
 
       - name: Setup Python
         uses: actions/setup-python@v5
@@ -48,7 +48,7 @@ jobs:
     needs: run-tests
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
 
       - name: Install Poetry
         uses: snok/install-poetry@v1.4.1

From fa4e7474962711d83cf367453edd73d015ce5155 Mon Sep 17 00:00:00 2001
From: cortadocodes <cortado.codes@protonmail.com>
Date: Thu, 12 Dec 2024 10:43:20 +0000
Subject: [PATCH 07/12] OPS: Only run tests up to python3.11

---
 .github/workflows/python-ci.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/python-ci.yml b/.github/workflows/python-ci.yml
index 86dbfea..dbc9390 100644
--- a/.github/workflows/python-ci.yml
+++ b/.github/workflows/python-ci.yml
@@ -23,7 +23,7 @@ jobs:
       USING_COVERAGE: '3.9'
     strategy:
       matrix:
-        python: ['3.8', '3.9', '3.10', '3.11', '3.12']
+        python: ['3.8', '3.9', '3.10', '3.11']
     steps:
       - name: Checkout Repository
         uses: actions/checkout@v4

From 14b0c5ef58c84a01f9561814470b67274cb30828 Mon Sep 17 00:00:00 2001
From: cortadocodes <cortado.codes@protonmail.com>
Date: Thu, 12 Dec 2024 10:52:42 +0000
Subject: [PATCH 08/12] FIX: Trim strand name suffixes in
 `Twine._required_strands`

---
 twined/twine.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/twined/twine.py b/twined/twine.py
index 2fc87ba..ce8725e 100644
--- a/twined/twine.py
+++ b/twined/twine.py
@@ -63,7 +63,7 @@ def __init__(self, **kwargs):
             self._available_strands.add(trim_suffix(name, "_schema"))
 
             if isinstance(strand, dict) and not strand.get("optional", False):
-                self._required_strands.add(name)
+                self._required_strands.add(trim_suffix(name, "_schema"))
 
         self._available_manifest_strands = self._available_strands & set(MANIFEST_STRANDS)
 

From f5db9840c53201092a3b9e287f791e3d8d313c5a Mon Sep 17 00:00:00 2001
From: cortadocodes <cortado.codes@protonmail.com>
Date: Thu, 12 Dec 2024 10:53:10 +0000
Subject: [PATCH 09/12] FIX: Avoid making "properties" key required in values
 schemas

---
 twined/schema/twine_schema.json | 15 +++------------
 1 file changed, 3 insertions(+), 12 deletions(-)

diff --git a/twined/schema/twine_schema.json b/twined/schema/twine_schema.json
index b19f0d9..aaab048 100644
--- a/twined/schema/twine_schema.json
+++ b/twined/schema/twine_schema.json
@@ -109,10 +109,7 @@
           "type": "boolean",
           "description": "This should be `true` if the configuration values are optional."
         }
-      },
-      "required": [
-        "properties"
-      ]
+      }
     },
     "credentials": {
       "type": "array",
@@ -148,10 +145,7 @@
           "type": "boolean",
           "description": "This should be `true` if the input values are optional."
         }
-      },
-      "required": [
-        "properties"
-      ]
+      }
     },
     "output_manifest": {
       "$ref": "#/$defs/manifest"
@@ -166,10 +160,7 @@
           "type": "boolean",
           "description": "This should be `true` if the output values are optional."
         }
-      },
-      "required": [
-        "properties"
-      ]
+      }
     }
   }
 }

From 1515ebf9a4a5a894804120153a6a832fe2432a71 Mon Sep 17 00:00:00 2001
From: cortadocodes <cortado.codes@protonmail.com>
Date: Thu, 12 Dec 2024 10:57:50 +0000
Subject: [PATCH 10/12] TST: Test `Twine.required_strands`

skipci
---
 tests/test_twine.py | 34 ++++++++++++++++++++++++++++++++++
 1 file changed, 34 insertions(+)

diff --git a/tests/test_twine.py b/tests/test_twine.py
index f59cddf..ad5fbf2 100644
--- a/tests/test_twine.py
+++ b/tests/test_twine.py
@@ -124,3 +124,37 @@ def test_available_strands_properties(self):
         )
 
         self.assertEqual(twine.available_manifest_strands, {"output_manifest"})
+
+    def test_required_strands_property(self):
+        """Test that the required strands property is correct."""
+        twines = [
+            {
+                "configuration_values_schema": {},
+                "input_values_schema": {},
+                "output_values_schema": {},
+                "output_manifest": {"datasets": {}},
+            },
+            {
+                "configuration_values_schema": {"optional": True},
+                "input_values_schema": {},
+                "output_values_schema": {},
+                "output_manifest": {"datasets": {}, "optional": True},
+            },
+            {
+                "configuration_values_schema": {"optional": False},
+                "input_values_schema": {},
+                "output_values_schema": {},
+                "output_manifest": {"datasets": {}, "optional": False},
+            },
+        ]
+
+        expected_required_strands = [
+            {"configuration_values", "input_values", "output_values", "output_manifest"},
+            {"input_values", "output_values"},
+            {"configuration_values", "input_values", "output_values", "output_manifest"},
+        ]
+
+        for twine, expected in zip(twines, expected_required_strands):
+            with self.subTest(twine=twine):
+                twine = Twine(source=twine)
+                self.assertEqual(twine.required_strands, expected)

From ca873564bd0d5c05ff9701fdea8a4cf09079ac27 Mon Sep 17 00:00:00 2001
From: cortadocodes <cortado.codes@protonmail.com>
Date: Thu, 12 Dec 2024 11:24:23 +0000
Subject: [PATCH 11/12] TST: Test missing optional strands don't raise errors

---
 tests/test_manifest_strands.py | 5 +++++
 tests/test_schema_strands.py   | 5 +++++
 2 files changed, 10 insertions(+)

diff --git a/tests/test_manifest_strands.py b/tests/test_manifest_strands.py
index ac0fd3d..3ee6f54 100644
--- a/tests/test_manifest_strands.py
+++ b/tests/test_manifest_strands.py
@@ -308,3 +308,8 @@ def test_error_raised_if_multiple_datasets_have_same_name(self):
 
         with self.assertRaises(KeyError):
             twine.validate_input_manifest(source=input_manifest)
+
+    def test_missing_optional_manifest_does_not_raise_error(self):
+        """Test that not providing an optional strand doesn't result in a validation error."""
+        twine = Twine(source={"output_manifest": {"datasets": {}, "optional": True}})
+        twine.validate(output_manifest=None)
diff --git a/tests/test_schema_strands.py b/tests/test_schema_strands.py
index d60dece..44c8d40 100644
--- a/tests/test_schema_strands.py
+++ b/tests/test_schema_strands.py
@@ -111,6 +111,11 @@ def test_valid_with_extra_values(self):
 
         Twine(source=VALID_SCHEMA_TWINE).validate_configuration_values(source=configuration_valid_with_extra_field)
 
+    def test_missing_optional_values_do_not_raise_error(self):
+        """Test that not providing an optional strand doesn't result in a validation error."""
+        twine = Twine(source={"configuration_values_schema": {"optional": True}})
+        twine.validate(configuration_values=None)
+
 
 if __name__ == "__main__":
     unittest.main()

From eb3c74f5a5219345dd126ecb74153075d5e5b318 Mon Sep 17 00:00:00 2001
From: cortadocodes <cortado.codes@protonmail.com>
Date: Thu, 12 Dec 2024 11:26:03 +0000
Subject: [PATCH 12/12] OPS: Run tests over more python versions on release too

skipci
---
 .github/workflows/python-ci.yml | 2 +-
 .github/workflows/release.yml   | 4 ++--
 2 files changed, 3 insertions(+), 3 deletions(-)

diff --git a/.github/workflows/python-ci.yml b/.github/workflows/python-ci.yml
index dbc9390..0a4816f 100644
--- a/.github/workflows/python-ci.yml
+++ b/.github/workflows/python-ci.yml
@@ -20,7 +20,7 @@ jobs:
     if: "!contains(github.event.head_commit.message, 'skipci')"
     runs-on: ubuntu-latest
     env:
-      USING_COVERAGE: '3.9'
+      USING_COVERAGE: '3.11'
     strategy:
       matrix:
         python: ['3.8', '3.9', '3.10', '3.11']
diff --git a/.github/workflows/release.yml b/.github/workflows/release.yml
index 7e6c2d8..262a893 100644
--- a/.github/workflows/release.yml
+++ b/.github/workflows/release.yml
@@ -12,10 +12,10 @@ jobs:
     if: "github.event.pull_request.merged == true"
     runs-on: ubuntu-latest
     env:
-      USING_COVERAGE: '3.9'
+      USING_COVERAGE: '3.11'
     strategy:
       matrix:
-        python: ['3.8', '3.9']
+        python: ['3.8', '3.9', '3.10', '3.11']
     steps:
       - name: Checkout Repository
         uses: actions/checkout@v4