From a21ea7a5e3bd05e635220472b6a81f9cb8f98f67 Mon Sep 17 00:00:00 2001
From: Kieron Taylor <kt19@sanger.ac.uk>
Date: Wed, 4 Oct 2023 15:27:20 +0100
Subject: [PATCH 1/7] Update pydantic dependency to 2.0 and up. No backward
 compatibility

---
 npg_id_generation/pac_bio.py | 26 +++++++++++---------
 pyproject.toml               |  2 +-
 tests/test_hashing.py        | 46 +++++++++++++++++-------------------
 3 files changed, 38 insertions(+), 36 deletions(-)

diff --git a/npg_id_generation/pac_bio.py b/npg_id_generation/pac_bio.py
index 104d4d6..67b1a50 100644
--- a/npg_id_generation/pac_bio.py
+++ b/npg_id_generation/pac_bio.py
@@ -21,8 +21,9 @@
 # this program. If not, see <http://www.gnu.org/licenses/>.
 
 from hashlib import sha256
+from typing import Optional
 
-from pydantic import BaseModel, Extra, Field, validator
+from pydantic import BaseModel, Field, field_validator, ConfigDict
 import re
 
 
@@ -42,7 +43,7 @@ def concatenate_tags(tags: list[str]):
         return ",".join(tags)
 
 
-class PacBioEntity(BaseModel, extra=Extra.forbid):
+class PacBioEntity(BaseModel):
     """A PacBio class for product ID generation."""
 
     """
@@ -56,10 +57,11 @@ class PacBioEntity(BaseModel, extra=Extra.forbid):
 
       Order the attributes alphabetically!
     """
+    model_config = ConfigDict(extra="forbid")
 
     run_name: str = Field(title="Pac Bio run name as in LIMS")
     well_label: str = Field(title="Pac Bio well label")
-    plate_number: int = Field(
+    plate_number: Optional[int] = Field(
         default=None,
         ge=1,
         title="Pac Bio plate number",
@@ -70,7 +72,7 @@ class PacBioEntity(BaseModel, extra=Extra.forbid):
         when the value of this attribute is 1, we reset it to undefined.
         """,
     )
-    tags: str = Field(
+    tags: Optional[str] = Field(
         default=None,
         title="A string representing tag or tags",
         description="""
@@ -81,13 +83,15 @@ class PacBioEntity(BaseModel, extra=Extra.forbid):
         """,
     )
 
-    @validator("run_name", "well_label", "tags")
+    @field_validator("run_name", "well_label", "tags")
+    @classmethod
     def attributes_are_non_empty_strings(cls, v):
         if (v is not None) and (v == ""):
             raise ValueError("Cannot be an empty string")
         return v
 
-    @validator("well_label")
+    @field_validator("well_label")
+    @classmethod
     def well_label_conforms_to_pattern(cls, v):
         if not re.match("^[A-Z][1-9][0-9]?$", v):
             raise ValueError(
@@ -95,11 +99,13 @@ def well_label_conforms_to_pattern(cls, v):
             )
         return v
 
-    @validator("plate_number")
+    @field_validator("plate_number")
+    @classmethod
     def plate_number_default(cls, v):
         return None if (v is None) or (v == 1) else v
 
-    @validator("tags")
+    @field_validator("tags")
+    @classmethod
     def tags_have_correct_characters(cls, v):
         if (v is not None) and (not re.match("^[ACGT]+(,[ACGT]+)*$", v)):
             raise ValueError(
@@ -110,6 +116,4 @@ def tags_have_correct_characters(cls, v):
     def hash_product_id(self):
         """Generate a sha256sum for the PacBio Entity"""
 
-        return sha256(
-            self.json(exclude_none=True, separators=(",", ":")).encode()
-        ).hexdigest()
+        return sha256(self.model_dump_json(exclude_none=True).encode()).hexdigest()
diff --git a/pyproject.toml b/pyproject.toml
index 3a2c644..8a47860 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -7,7 +7,7 @@ license = "GPL3-or-later"
 
 [tool.poetry.dependencies]
 python = "^3.10"
-pydantic = "^1.9.1"
+pydantic = "^2"
 
 [tool.poetry.dev-dependencies]
 pytest = "^7.1.2"
diff --git a/tests/test_hashing.py b/tests/test_hashing.py
index 835c3d0..1ba69b5 100644
--- a/tests/test_hashing.py
+++ b/tests/test_hashing.py
@@ -15,7 +15,7 @@ def test_different_orderings():
     ]
 
     results = [
-        PacBioEntity.parse_raw(test_case, content_type="json").hash_product_id()
+        PacBioEntity.model_validate_json(test_case).hash_product_id()
         for test_case in test_cases
     ]
 
@@ -33,7 +33,7 @@ def test_whitespace():
     ]
 
     results = [
-        PacBioEntity.parse_raw(test_case, content_type="json").hash_product_id()
+        PacBioEntity.model_validate_json(test_case).hash_product_id()
         for test_case in test_cases
     ]
 
@@ -48,15 +48,15 @@ def test_different_ways_to_create_object():
         PacBioEntity(run_name="MARATHON", well_label="A1", tags=None).hash_product_id()
     )
     results.append(
-        PacBioEntity.parse_raw(
-            '{"run_name": "MARATHON", "well_label": "A1"}', content_type="json"
+        PacBioEntity.model_validate_json(
+            '{"run_name": "MARATHON", "well_label": "A1"}'
         ).hash_product_id()
     )
     assert len(set(results)) == 1
 
     with pytest.raises(ValidationError) as excinfo:
         PacBioEntity(run_name="MARATHON", well_label="A1", some_arg=3)
-    assert "extra fields not permitted" in str(excinfo.value)
+    assert "Extra inputs are not permitted" in str(excinfo.value)
 
 
 def test_tags_make_difference():
@@ -82,9 +82,7 @@ def test_attributes_cannot_be_empty():
         PacBioEntity(run_name="MARATHON", well_label="")
     assert "Cannot be an empty string" in str(excinfo.value)
     with pytest.raises(ValidationError) as excinfo:
-        PacBioEntity.parse_raw(
-            '{"run_name": "MARATHON", "well_label": ""}', content_type="json"
-        )
+        PacBioEntity.model_validate_json('{"run_name": "MARATHON", "well_label": ""}')
     assert "Cannot be an empty string" in str(excinfo.value)
 
 
@@ -98,9 +96,7 @@ def test_well_label_conforms_to_pattern():
             in str(excinfo.value)
         )
     with pytest.raises(ValidationError) as excinfo:
-        PacBioEntity.parse_raw(
-            '{"run_name": "MARATHON", "well_label":"1A"}', content_type="json"
-        )
+        PacBioEntity.model_validate_json('{"run_name": "MARATHON", "well_label":"1A"}')
     assert (
         "Well label must be an alphabetic character followed by a number between 1 and 99"
         in str(excinfo.value)
@@ -130,11 +126,10 @@ def test_tags_have_correct_characters():
 
 
 def test_plate_number_validation():
-
     for n in [-1, 0]:
         with pytest.raises(ValidationError) as excinfo:
             PacBioEntity(run_name="MARATHON", well_label="A1", plate_number=n)
-        assert "ensure this value is greater than or equal to 1" in str(excinfo.value)
+        assert "Input should be greater than or equal to 1" in str(excinfo.value)
 
 
 def test_plate_number_defaults():
@@ -148,8 +143,12 @@ def test_plate_number_defaults():
     assert e1.plate_number is None
     assert e2.plate_number is None
     assert e3.plate_number is None
-    assert e1.json(exclude_none=True) == e2.json(exclude_none=True)
-    assert e1.json(exclude_none=True) == e3.json(exclude_none=True)
+    assert e1.model_dump_json(exclude_none=True) == e2.model_dump_json(
+        exclude_none=True
+    )
+    assert e1.model_dump_json(exclude_none=True) == e3.model_dump_json(
+        exclude_none=True
+    )
     assert e1.hash_product_id() == e2.hash_product_id()
     assert e1.hash_product_id() == e3.hash_product_id()
 
@@ -157,12 +156,11 @@ def test_plate_number_defaults():
     e2 = PacBioEntity(run_name="MARATHON", well_label="A1")
     assert e1.plate_number is None
     assert e2.plate_number is None
-    assert e1.json() == e2.json()
+    assert e1.model_dump_json() == e2.model_dump_json()
     assert e1.hash_product_id() == e2.hash_product_id()
 
 
 def test_multiple_plates_make_difference():
-
     id_1 = PacBioEntity(
         run_name="MARATHON", well_label="A1", tags="ACGT"
     ).hash_product_id()
@@ -185,16 +183,16 @@ def test_multiple_plates_make_difference():
     assert id_1 != id_2
     assert id_3 != id_2
 
-    json = PacBioEntity(run_name="MARATHON", well_label="A1", plate_number=2).json(
-        exclude_none=True
-    )
-    assert json == '{"run_name": "MARATHON", "well_label": "A1", "plate_number": 2}'
+    json = PacBioEntity(
+        run_name="MARATHON", well_label="A1", plate_number=2
+    ).model_dump_json(exclude_none=True)
+    assert json == '{"run_name":"MARATHON","well_label":"A1","plate_number":2}'
     json = PacBioEntity(
         run_name="MARATHON", well_label="A1", tags="ACTGG", plate_number=2
-    ).json(exclude_none=True)
+    ).model_dump_json(exclude_none=True)
     assert (
         json
-        == '{"run_name": "MARATHON", "well_label": "A1", "plate_number": 2, "tags": "ACTGG"}'
+        == '{"run_name":"MARATHON","well_label":"A1","plate_number":2,"tags":"ACTGG"}'
     )
 
 
@@ -222,7 +220,7 @@ def test_expected_hashes():
 
     for json_str, expected_hash in test_cases:
         assert (
-            PacBioEntity.parse_raw(json_str, content_type="json").hash_product_id()
+            PacBioEntity.model_validate_json(json_str).hash_product_id()
             == expected_hash
         )
 

From c0bf4aad4d269a79f7e3d6ea6093f7c60aa777e5 Mon Sep 17 00:00:00 2001
From: Kieron Taylor <kt19@sanger.ac.uk>
Date: Wed, 4 Oct 2023 15:27:38 +0100
Subject: [PATCH 2/7] Correct some readme text

---
 README.md | 14 +++++++-------
 1 file changed, 7 insertions(+), 7 deletions(-)

diff --git a/README.md b/README.md
index 4bc4462..f26507f 100644
--- a/README.md
+++ b/README.md
@@ -20,9 +20,9 @@ package implements a Python API. The attributes of objects are sequencing
 platform specific. The generator for the PacBio platform is implemented by the
 `PacBioEntity` class.
 
-Examles of generating IDs for PacBio data from Python code:
+Examples of generating IDs for PacBio data from Python code:
 
-```
+```python
 from npg_id_generation.pac_bio import PacBioEntity
 
 # from a JSON string via a class method
@@ -47,7 +47,7 @@ The npg_id_generation package also contains a script, `generate_pac_bio_id`,
 which can be called from the command line. The script outputs the generated
 ID to the STDOUT stream. Use the `--help` option to find out details.
 
-```
+```perl
 # Using the script in the Perl code:
 my $id = `npg_id_generation --run_name 'MARATHON' --well_label 'D1'`;
 ```
@@ -55,7 +55,7 @@ my $id = `npg_id_generation --run_name 'MARATHON' --well_label 'D1'`;
 All generators should conform to a few simple rules:
 
 1. Uniqueness of the ID should be guaranteed.
-2. The ID should be a 64 characher string.
+2. The ID should be a 64 character string.
 3. It should be possible to generate an ID from a JSON string.
 4. The value of the ID should **not** depend on the order of attributes given
    to the constructor or the order of keys used in JSON.
@@ -64,9 +64,9 @@ All generators should conform to a few simple rules:
 6. The value of the ID should **not** depend on whether the undefined values
    of attributes are explicitly set.
 
-The examples below clarity the rules. Objects `o1` - `o6` should generate the same ID.
+The examples below clarify the rules. Objects `o1` - `o6` should generate the same ID.
 
-```
+```python
 o1 = PacBioEntity(run_name="r1", well_label="l1")
 o2 = PacBioEntity(run_name="r1", well_label="l1", tags = None)
 o3 = PacBioEntity(well_label="l1", run_name="r1", )
@@ -79,7 +79,7 @@ In addition, to maintain backwards compatibility for PacBio Revio products,
 the following two objects should generate the same ID, meaning that the
 value of 1 for the plate number attribute is disregarded.
 
-```
+```python
 o1 = PacBioEntity(run_name="r1", well_label="l1")
 o2 = PacBioEntity(run_name="r1", well_label="l1", plate_number=1)
 ```

From dfd02f084b379cf470758e087afa3cd89adac54d Mon Sep 17 00:00:00 2001
From: Kieron Taylor <kt19@sanger.ac.uk>
Date: Wed, 4 Oct 2023 16:04:28 +0100
Subject: [PATCH 3/7] Update poetry lockfile...

---
 poetry.lock | 450 ++++++++++++++++++++++++++++------------------------
 1 file changed, 241 insertions(+), 209 deletions(-)

diff --git a/poetry.lock b/poetry.lock
index 5bcf1b5..ce9ff7a 100644
--- a/poetry.lock
+++ b/poetry.lock
@@ -1,24 +1,36 @@
+# This file is automatically @generated by Poetry 1.6.1 and should not be changed by hand.
+
 [[package]]
-name = "attrs"
-version = "22.1.0"
-description = "Classes Without Boilerplate"
-category = "dev"
+name = "annotated-types"
+version = "0.5.0"
+description = "Reusable constraint types to use with typing.Annotated"
 optional = false
-python-versions = ">=3.5"
-
-[package.extras]
-dev = ["cloudpickle", "coverage[toml] (>=5.0.2)", "furo", "hypothesis", "mypy (>=0.900,!=0.940)", "pre-commit", "pympler", "pytest (>=4.3.0)", "pytest-mypy-plugins", "sphinx", "sphinx-notfound-page", "zope.interface"]
-docs = ["furo", "sphinx", "sphinx-notfound-page", "zope.interface"]
-tests = ["cloudpickle", "coverage[toml] (>=5.0.2)", "hypothesis", "mypy (>=0.900,!=0.940)", "pympler", "pytest (>=4.3.0)", "pytest-mypy-plugins", "zope.interface"]
-tests-no-zope = ["cloudpickle", "coverage[toml] (>=5.0.2)", "hypothesis", "mypy (>=0.900,!=0.940)", "pympler", "pytest (>=4.3.0)", "pytest-mypy-plugins"]
+python-versions = ">=3.7"
+files = [
+    {file = "annotated_types-0.5.0-py3-none-any.whl", hash = "sha256:58da39888f92c276ad970249761ebea80ba544b77acddaa1a4d6cf78287d45fd"},
+    {file = "annotated_types-0.5.0.tar.gz", hash = "sha256:47cdc3490d9ac1506ce92c7aaa76c579dc3509ff11e098fc867e5130ab7be802"},
+]
 
 [[package]]
 name = "black"
-version = "22.10.0"
+version = "22.12.0"
 description = "The uncompromising code formatter."
-category = "dev"
 optional = false
 python-versions = ">=3.7"
+files = [
+    {file = "black-22.12.0-cp310-cp310-manylinux_2_17_x86_64.manylinux2014_x86_64.whl", hash = "sha256:9eedd20838bd5d75b80c9f5487dbcb06836a43833a37846cf1d8c1cc01cef59d"},
+    {file = "black-22.12.0-cp310-cp310-win_amd64.whl", hash = "sha256:159a46a4947f73387b4d83e87ea006dbb2337eab6c879620a3ba52699b1f4351"},
+    {file = "black-22.12.0-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl", hash = "sha256:d30b212bffeb1e252b31dd269dfae69dd17e06d92b87ad26e23890f3efea366f"},
+    {file = "black-22.12.0-cp311-cp311-win_amd64.whl", hash = "sha256:7412e75863aa5c5411886804678b7d083c7c28421210180d67dfd8cf1221e1f4"},
+    {file = "black-22.12.0-cp37-cp37m-manylinux_2_17_x86_64.manylinux2014_x86_64.whl", hash = "sha256:c116eed0efb9ff870ded8b62fe9f28dd61ef6e9ddd28d83d7d264a38417dcee2"},
+    {file = "black-22.12.0-cp37-cp37m-win_amd64.whl", hash = "sha256:1f58cbe16dfe8c12b7434e50ff889fa479072096d79f0a7f25e4ab8e94cd8350"},
+    {file = "black-22.12.0-cp38-cp38-manylinux_2_17_x86_64.manylinux2014_x86_64.whl", hash = "sha256:77d86c9f3db9b1bf6761244bc0b3572a546f5fe37917a044e02f3166d5aafa7d"},
+    {file = "black-22.12.0-cp38-cp38-win_amd64.whl", hash = "sha256:82d9fe8fee3401e02e79767016b4907820a7dc28d70d137eb397b92ef3cc5bfc"},
+    {file = "black-22.12.0-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl", hash = "sha256:101c69b23df9b44247bd88e1d7e90154336ac4992502d4197bdac35dd7ee3320"},
+    {file = "black-22.12.0-cp39-cp39-win_amd64.whl", hash = "sha256:559c7a1ba9a006226f09e4916060982fd27334ae1998e7a38b3f33a37f7a2148"},
+    {file = "black-22.12.0-py3-none-any.whl", hash = "sha256:436cc9167dd28040ad90d3b404aec22cedf24a6e4d7de221bec2730ec0c97bcf"},
+    {file = "black-22.12.0.tar.gz", hash = "sha256:229351e5a18ca30f447bf724d007f890f97e13af070bb6ad4c0a441cd7596a2f"},
+]
 
 [package.dependencies]
 click = ">=8.0.0"
@@ -35,11 +47,14 @@ uvloop = ["uvloop (>=0.15.2)"]
 
 [[package]]
 name = "click"
-version = "8.1.3"
+version = "8.1.7"
 description = "Composable command line interface toolkit"
-category = "dev"
 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\""}
@@ -48,17 +63,23 @@ colorama = {version = "*", markers = "platform_system == \"Windows\""}
 name = "colorama"
 version = "0.4.6"
 description = "Cross-platform colored terminal text."
-category = "dev"
 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 = "exceptiongroup"
-version = "1.0.0rc9"
+version = "1.1.3"
 description = "Backport of PEP 654 (exception groups)"
-category = "dev"
 optional = false
 python-versions = ">=3.7"
+files = [
+    {file = "exceptiongroup-1.1.3-py3-none-any.whl", hash = "sha256:343280667a4585d195ca1cf9cef84a4e178c4b6cf2274caef9859782b567d5e3"},
+    {file = "exceptiongroup-1.1.3.tar.gz", hash = "sha256:097acd85d473d75af5bb98e41b61ff7fe35efe6675e4f9370ec6ec5126d160e9"},
+]
 
 [package.extras]
 test = ["pytest (>=6)"]
@@ -67,9 +88,12 @@ test = ["pytest (>=6)"]
 name = "flake8"
 version = "4.0.1"
 description = "the modular source code checker: pep8 pyflakes and co"
-category = "dev"
 optional = false
 python-versions = ">=3.6"
+files = [
+    {file = "flake8-4.0.1-py2.py3-none-any.whl", hash = "sha256:479b1304f72536a55948cb40a32dce8bb0ffe3501e26eaf292c7e60eb5e0428d"},
+    {file = "flake8-4.0.1.tar.gz", hash = "sha256:806e034dda44114815e23c16ef92f95c91e4c71100ff52813adf7132a6ad870d"},
+]
 
 [package.dependencies]
 mccabe = ">=0.6.0,<0.7.0"
@@ -78,66 +102,84 @@ pyflakes = ">=2.4.0,<2.5.0"
 
 [[package]]
 name = "iniconfig"
-version = "1.1.1"
-description = "iniconfig: brain-dead simple config-ini parsing"
-category = "dev"
+version = "2.0.0"
+description = "brain-dead simple config-ini parsing"
 optional = false
-python-versions = "*"
+python-versions = ">=3.7"
+files = [
+    {file = "iniconfig-2.0.0-py3-none-any.whl", hash = "sha256:b6a85871a79d2e3b22d2d1b94ac2824226a63c6b741c88f7ae975f18b6778374"},
+    {file = "iniconfig-2.0.0.tar.gz", hash = "sha256:2d91e135bf72d31a410b17c16da610a82cb55f6b0477d1a902134b24a455b8b3"},
+]
 
 [[package]]
 name = "mccabe"
 version = "0.6.1"
 description = "McCabe checker, plugin for flake8"
-category = "dev"
 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 = "mypy-extensions"
-version = "0.4.3"
-description = "Experimental type system extensions for programs checked with the mypy typechecker."
-category = "dev"
+version = "1.0.0"
+description = "Type system extensions for programs checked with the mypy type checker."
 optional = false
-python-versions = "*"
+python-versions = ">=3.5"
+files = [
+    {file = "mypy_extensions-1.0.0-py3-none-any.whl", hash = "sha256:4392f6c0eb8a5668a69e23d168ffa70f0be9ccfd32b5cc2d26a34ae5b844552d"},
+    {file = "mypy_extensions-1.0.0.tar.gz", hash = "sha256:75dbf8955dc00442a438fc4d0666508a9a97b6bd41aa2f0ffe9d2f2725af0782"},
+]
 
 [[package]]
 name = "packaging"
-version = "21.3"
+version = "23.2"
 description = "Core utilities for Python packages"
-category = "dev"
 optional = false
-python-versions = ">=3.6"
-
-[package.dependencies]
-pyparsing = ">=2.0.2,<3.0.5 || >3.0.5"
+python-versions = ">=3.7"
+files = [
+    {file = "packaging-23.2-py3-none-any.whl", hash = "sha256:8c491190033a9af7e1d931d0b5dacc2ef47509b34dd0de67ed209b5203fc88c7"},
+    {file = "packaging-23.2.tar.gz", hash = "sha256:048fb0e9405036518eaaf48a55953c750c11e1a1b68e0dd1a9d62ed0c092cfc5"},
+]
 
 [[package]]
 name = "pathspec"
-version = "0.10.1"
+version = "0.11.2"
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-category = "dev"
 optional = false
 python-versions = ">=3.7"
+files = [
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+]
 
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 name = "platformdirs"
-version = "2.5.2"
-description = "A small Python module for determining appropriate platform-specific dirs, e.g. a \"user data dir\"."
-category = "dev"
+version = "3.11.0"
+description = "A small Python package for determining appropriate platform-specific dirs, e.g. a \"user data dir\"."
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 python-versions = ">=3.7"
+files = [
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-test = ["appdirs (==1.4.4)", "pytest (>=6)", "pytest-cov (>=2.7)", "pytest-mock (>=3.6)"]
+docs = ["furo (>=2023.7.26)", "proselint (>=0.13)", "sphinx (>=7.1.1)", "sphinx-autodoc-typehints (>=1.24)"]
+test = ["appdirs (==1.4.4)", "covdefaults (>=2.3)", "pytest (>=7.4)", "pytest-cov (>=4.1)", "pytest-mock (>=3.11.1)"]
 
 [[package]]
 name = "pluggy"
-version = "1.0.0"
+version = "1.3.0"
 description = "plugin and hook calling mechanisms for python"
-category = "dev"
 optional = false
-python-versions = ">=3.6"
+python-versions = ">=3.8"
+files = [
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+]
 
 [package.extras]
 dev = ["pre-commit", "tox"]
@@ -147,54 +189,173 @@ testing = ["pytest", "pytest-benchmark"]
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 description = "Python style guide checker"
-category = "dev"
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+]
 
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-description = "Data validation and settings management using python type hints"
-category = "main"
+version = "2.4.2"
+description = "Data validation using Python type hints"
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 python-versions = ">=3.7"
+files = [
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+annotated-types = ">=0.4.0"
+pydantic-core = "2.10.1"
+typing-extensions = ">=4.6.1"
 
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-email = ["email-validator (>=1.0.3)"]
+email = ["email-validator (>=2.0.0)"]
+
+[[package]]
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From 9e68efd21f8273a224d2afbce55c481e906c82d3 Mon Sep 17 00:00:00 2001
From: Kieron Taylor <kt19@sanger.ac.uk>
Date: Wed, 4 Oct 2023 16:11:49 +0100
Subject: [PATCH 4/7] Update changelog

---
 CHANGELOG.md | 4 ++++
 1 file changed, 4 insertions(+)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index b7f9d0c..2b3bcf7 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -6,6 +6,10 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 ## [Unreleased]
 
+### [Changed]
+
+ - Upgrade python pydantic dependency to v2
+
 ## [4.0.0]
 
 ### Added

From 0a39753f6c2eb87b1f9834f9f74e927f6c89eb93 Mon Sep 17 00:00:00 2001
From: Kieron Taylor <kt19@sanger.ac.uk>
Date: Thu, 12 Oct 2023 16:25:54 +0100
Subject: [PATCH 5/7] Changelog for release

---
 CHANGELOG.md | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index 2b3bcf7..bd3f2d6 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -4,7 +4,7 @@ All notable changes to this project will be documented in this file.
 The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/),
 and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
 
-## [Unreleased]
+## [4.0.1]
 
 ### [Changed]
 

From d764378608a9f38bc790ac7c3feb2f6b4a55b176 Mon Sep 17 00:00:00 2001
From: Kieron Taylor <kt19@sanger.ac.uk>
Date: Thu, 12 Oct 2023 17:06:09 +0100
Subject: [PATCH 6/7] Automate release python builds?

---
 .github/workflows/release.yml | 49 +++++++++++++++++++++++++++++++++++
 1 file changed, 49 insertions(+)
 create mode 100644 .github/workflows/release.yml

diff --git a/.github/workflows/release.yml b/.github/workflows/release.yml
new file mode 100644
index 0000000..d0a258b
--- /dev/null
+++ b/.github/workflows/release.yml
@@ -0,0 +1,49 @@
+
+name: "Create release"
+on:
+  push:
+    tags:
+      - "*"
+
+jobs:
+  build:
+    runs-on: ubuntu-latest
+    defaults:
+      run:
+        shell: bash -l -e -o pipefail {0}
+
+    steps:
+      - uses: actions/checkout@v4
+
+      - name: "Fetch Tags"
+        run: git fetch --tags --force
+
+      - name: "Set up Python"
+        uses: actions/setup-python@v4
+        with:
+          python-version: "3.10"
+          architecture: "x64"
+
+      - name: Install Poetry
+        run: |
+          pipx install poetry
+
+      - name: Run poetry install
+        run: |
+          poetry env use '3.10'
+          poetry build
+
+      - name: "Get release variables"
+        run: |
+          echo RELEASE_VERSION=$(git describe --always --tags --dirty) >> $GITHUB_ENV
+          echo MASTER_SHA=$(git rev-parse origin/master) >> $GITHUB_ENV
+
+      - name: "Create Release"
+        uses: ncipollo/release-action@v1.13.0
+        with:
+          name: ${{ env.RELEASE_VERSION }}
+          prerelease: ${{ !(github.sha == env.MASTER_SHA) }}
+          artifacts: "dist/*.tar.gz"
+          removeArtifacts: true
+          artifactErrorsFailBuild: true
+          generateReleaseNotes: true
\ No newline at end of file

From e18c0c807f4e446bb9bc758e96588533d9185fae Mon Sep 17 00:00:00 2001
From: Kieron Taylor <kt19@sanger.ac.uk>
Date: Thu, 12 Oct 2023 17:14:53 +0100
Subject: [PATCH 7/7] Include dynamic versioning

---
 .github/workflows/release.yml | 1 +
 1 file changed, 1 insertion(+)

diff --git a/.github/workflows/release.yml b/.github/workflows/release.yml
index d0a258b..a3ed039 100644
--- a/.github/workflows/release.yml
+++ b/.github/workflows/release.yml
@@ -31,6 +31,7 @@ jobs:
       - name: Run poetry install
         run: |
           poetry env use '3.10'
+          poetry self add "poetry-dynamic-versioning[plugin]"
           poetry build
 
       - name: "Get release variables"