feat: add support for Pydantic V2 (#505)

* feat(api): add Pydantic V2 support

* chore: update dependencies pyproject.toml

* chore(api): improved version management

* feat: improve Pydantic V2 compat checks

.pre-commit-config.yaml

@@ -1,7 +1,6 @@
 fail_fast: true
 
 repos:
-
   - repo: https://github.com/pre-commit/pre-commit-hooks
     rev: v4.4.0
     hooks:
@@ -27,27 +26,41 @@ repos:
         args: ["--fix=lf"]
         description: Forces to replace line ending by the UNIX 'lf' character.
       - id: trailing-whitespace
-        exclude: '.bumpversion.cfg'
+        exclude: ".bumpversion.cfg"
       - id: check-merge-conflict
 
   - repo: https://github.com/psf/black
-    rev: '23.3.0'
+    rev: "23.3.0"
     hooks:
       - id: black
         language_version: python3.9
-        exclude: ^src\/polus\/plugins\/_plugins\/models\/\w*Schema.py$
+        exclude: |
+          (?x)(
+            ^src\/polus\/plugins\/_plugins\/models\/pydanticv1\/\w*Schema.py$|
+            ^src\/polus\/plugins\/_plugins\/models\/pydanticv2\/\w*Schema.py$
+          )
 
   - repo: https://github.com/charliermarsh/ruff-pre-commit
     # Ruff version.
-    rev: 'v0.0.274'
+    rev: "v0.0.274"
     hooks:
       - id: ruff
-        exclude: ^src\/polus\/plugins\/_plugins\/models\/\w*Schema.py$
+        exclude: |
+          (?x)(
+            test_[a-zA-Z0-9]+.py$|
+            ^src\/polus\/plugins\/_plugins\/models\/pydanticv1\/\w*Schema.py$|
+            ^src\/polus\/plugins\/_plugins\/models\/pydanticv2\/\w*Schema.py$
+          )
         args: [--fix]
 
   - repo: https://github.com/pre-commit/mirrors-mypy
-    rev: 'v1.4.0'
+    rev: "v1.4.0"
     hooks:
       - id: mypy
-        exclude: ^src\/polus\/plugins\/_plugins\/models\/\w*Schema.py$
+        exclude: |
+          (?x)(
+            test_[a-zA-Z0-9]+.py$|
+            ^src\/polus\/plugins\/_plugins\/models\/pydanticv1\/\w*Schema.py$|
+            ^src\/polus\/plugins\/_plugins\/models\/pydanticv2\/\w*Schema.py$
+          )
         additional_dependencies: [types-requests==2.31.0.1]

pyproject.toml

@@ -15,33 +15,33 @@ python = ">=3.9, <3.12"
 click = "^8.1.3"
 cwltool = "^3.1.20230513155734"
 fsspec = "^2023.6.0"
-pydantic = ">=1.10.9, <2.0"
+pydantic = ">=1.10.0"
 pygithub = "^1.58.2"
-python-on-whales = "^0.57.0"
+python-on-whales = "^0.68.0"
 pyyaml = "^6.0"
 tqdm = "^4.65.0"
+validators = "^0.22.0"
 xmltodict = "^0.13.0"
 
 [tool.poetry.group.dev.dependencies]
 python = ">=3.9, <3.12"
 
 black = "^23.3.0"
 bump2version = "^1.0.1"
-datamodel-code-generator = "^0.17.1"
+datamodel-code-generator = "^0.23.0"
 flake8 = "^6.0.0"
 fsspec = "^2023.1.0"
 mypy = "^1.4.0"
 nox = "^2022.11.21"
 poetry = "^1.3.2"
 pre-commit = "^3.3.3"
-pydantic = "^1.10.4"
-pydantic-to-typescript = "^1.0.10"
+pydantic = ">=1.10"
 pytest = "^7.3.2"
 pytest-benchmark = "^4.0.0"
 pytest-cov = "^4.1.0"
 pytest-sugar = "^0.9.7"
 pytest-xdist = "^3.3.1"
-python-on-whales = "^0.57.0"
+python-on-whales = "^0.68.0"
 pyyaml = "^6.0"
 ruff = "^0.0.274"
 tqdm = "^4.64.1"

src/polus/plugins/__init__.py

@@ -1,6 +1,7 @@
 """Initialize polus-plugins module."""
 
 import logging
+from pathlib import Path
 from typing import Union
 
 from polus.plugins._plugins.classes import (
@@ -30,6 +31,12 @@
 """
 logger = logging.getLogger("polus.plugins")
 
+with Path(__file__).parent.joinpath("_plugins/VERSION").open(
+    "r",
+    encoding="utf-8",
+) as version_file:
+    VERSION = version_file.read().strip()
+
 
 refresh()  # calls the refresh method when library is imported
 
@@ -39,6 +46,8 @@ def __getattr__(name: str) -> Union[Plugin, ComputePlugin, list]:
         return list_plugins()
     if name in list_plugins():
         return get_plugin(name)
+    if name in ["__version__", "VERSION"]:
+        return VERSION
     msg = f"module '{__name__}' has no attribute '{name}'"
     raise AttributeError(msg)
 

src/polus/plugins/_plugins/VERSION

@@ -1 +1 @@
-0.1.0
+0.1.1

src/polus/plugins/_plugins/_compat.py

@@ -0,0 +1,4 @@
+"""Compat of Pydantic."""
+import pydantic
+
+PYDANTIC_V2 = pydantic.VERSION.startswith("2.")

src/polus/plugins/_plugins/classes/__init__.py

@@ -1,6 +1,9 @@
 """Plugin classes and functions."""
+
+from polus.plugins._plugins.classes.plugin_classes import PLUGINS
 from polus.plugins._plugins.classes.plugin_classes import ComputePlugin
 from polus.plugins._plugins.classes.plugin_classes import Plugin
+from polus.plugins._plugins.classes.plugin_classes import _load_plugin
 from polus.plugins._plugins.classes.plugin_classes import get_plugin
 from polus.plugins._plugins.classes.plugin_classes import list_plugins
 from polus.plugins._plugins.classes.plugin_classes import load_config
@@ -19,4 +22,6 @@
     "remove_plugin",
     "remove_all",
     "load_config",
+    "_load_plugin",
+    "PLUGINS",
 ]