feat(api): add Pydantic V2 support

.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:
@@ -26,35 +25,41 @@ 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: |
           (?x)(
             test_[a-zA-Z0-9]+.py$|
-            ^src\/polus\/plugins\/_plugins\/models\/\w*Schema.py$
+            ^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: |
           (?x)(
             test_[a-zA-Z0-9]+.py$|
-            ^src\/polus\/plugins\/_plugins\/models\/\w*Schema.py$
+            ^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

@@ -15,27 +15,26 @@ 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"
 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"
 pytest = "^7.3.2"
 pytest-benchmark = "^4.0.0"
 pytest-cov = "^4.1.0"

src/polus/plugins/__init__.py

@@ -30,6 +30,8 @@
 """
 logger = logging.getLogger("polus.plugins")
 
+VERSION = "0.1.1"
+
 
 refresh()  # calls the refresh method when library is imported
 
@@ -39,6 +41,8 @@ def __getattr__(name: str) -> Union[Plugin, ComputePlugin, list]:
         return list_plugins()
     if name in list_plugins():
         return get_plugin(name)
+    if name == "__version__":
+        return VERSION
     msg = f"module '{__name__}' has no attribute '{name}'"
     raise AttributeError(msg)
 

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

@@ -1,13 +1,32 @@
 """Plugin classes and functions."""
-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 get_plugin
-from polus.plugins._plugins.classes.plugin_classes import list_plugins
-from polus.plugins._plugins.classes.plugin_classes import load_config
-from polus.plugins._plugins.classes.plugin_classes import refresh
-from polus.plugins._plugins.classes.plugin_classes import remove_all
-from polus.plugins._plugins.classes.plugin_classes import remove_plugin
-from polus.plugins._plugins.classes.plugin_classes import submit_plugin
+import pydantic
+
+PYDANTIC_VERSION = pydantic.__version__
+
+if PYDANTIC_VERSION.split(".")[0] == "1":
+    from polus.plugins._plugins.classes.plugin_classes_v1 import PLUGINS
+    from polus.plugins._plugins.classes.plugin_classes_v1 import ComputePlugin
+    from polus.plugins._plugins.classes.plugin_classes_v1 import Plugin
+    from polus.plugins._plugins.classes.plugin_classes_v1 import _load_plugin
+    from polus.plugins._plugins.classes.plugin_classes_v1 import get_plugin
+    from polus.plugins._plugins.classes.plugin_classes_v1 import list_plugins
+    from polus.plugins._plugins.classes.plugin_classes_v1 import load_config
+    from polus.plugins._plugins.classes.plugin_classes_v1 import refresh
+    from polus.plugins._plugins.classes.plugin_classes_v1 import remove_all
+    from polus.plugins._plugins.classes.plugin_classes_v1 import remove_plugin
+    from polus.plugins._plugins.classes.plugin_classes_v1 import submit_plugin
+elif PYDANTIC_VERSION.split(".")[0] == "2":
+    from polus.plugins._plugins.classes.plugin_classes_v2 import PLUGINS
+    from polus.plugins._plugins.classes.plugin_classes_v2 import ComputePlugin
+    from polus.plugins._plugins.classes.plugin_classes_v2 import Plugin
+    from polus.plugins._plugins.classes.plugin_classes_v2 import _load_plugin
+    from polus.plugins._plugins.classes.plugin_classes_v2 import get_plugin
+    from polus.plugins._plugins.classes.plugin_classes_v2 import list_plugins
+    from polus.plugins._plugins.classes.plugin_classes_v2 import load_config
+    from polus.plugins._plugins.classes.plugin_classes_v2 import refresh
+    from polus.plugins._plugins.classes.plugin_classes_v2 import remove_all
+    from polus.plugins._plugins.classes.plugin_classes_v2 import remove_plugin
+    from polus.plugins._plugins.classes.plugin_classes_v2 import submit_plugin
 
 __all__ = [
     "Plugin",
@@ -19,4 +38,6 @@
     "remove_plugin",
     "remove_all",
     "load_config",
+    "_load_plugin",
+    "PLUGINS",
 ]