From e1f97a266d4fb85217a9a6c738321b6eddc180d8 Mon Sep 17 00:00:00 2001
From: Dougie Squire <42455466+dougiesquire@users.noreply.github.com>
Date: Fri, 7 Jul 2023 12:15:24 +1000
Subject: [PATCH] Updates for pydantic v2 (#164)

---
 ci/environment-docs.yml         |  5 ++---
 ci/environment-upstream-dev.yml |  2 +-
 ci/environment.yml              |  2 +-
 docs/source/conf.py             |  5 -----
 ecgtools/builder.py             | 32 +++++++++++++++++---------------
 requirements.txt                |  2 +-
 6 files changed, 22 insertions(+), 26 deletions(-)

diff --git a/ci/environment-docs.yml b/ci/environment-docs.yml
index 21e7238..bf9d561 100644
--- a/ci/environment-docs.yml
+++ b/ci/environment-docs.yml
@@ -1,4 +1,4 @@
-name: ecgtools-dev
+name: ecgtools-doc
 channels:
   - conda-forge
   - nodefaults
@@ -12,14 +12,13 @@ dependencies:
   - myst-nb
   - netcdf4
   - pip
-  - pydantic<2.0 # Will remove in upcoming PR
+  - pydantic>=2.0
   - s3fs
   - sphinx-copybutton
   - sphinx-inline-tabs
   - xarray
   - pip:
       - sphinxext-opengraph
-      - autodoc_pydantic
       - -r ../requirements.txt
       - git+https://github.com/intake/intake-esm
       - -e ..
diff --git a/ci/environment-upstream-dev.yml b/ci/environment-upstream-dev.yml
index fb4cd81..302c462 100644
--- a/ci/environment-upstream-dev.yml
+++ b/ci/environment-upstream-dev.yml
@@ -14,7 +14,7 @@ dependencies:
   - numpydoc
   - pip
   - pre-commit
-  - pydantic<2.0 # Will remove in upcoming PR
+  - pydantic>=2.0
   - pytest
   - pytest-cov
   - pytest-sugar
diff --git a/ci/environment.yml b/ci/environment.yml
index da75638..2c1923b 100644
--- a/ci/environment.yml
+++ b/ci/environment.yml
@@ -11,7 +11,7 @@ dependencies:
   - netcdf4
   - pip
   - pre-commit
-  - pydantic<2.0 # Will remove in upcoming PR
+  - pydantic>=2.0
   - pytest
   - pytest-cov
   - pytest-sugar
diff --git a/docs/source/conf.py b/docs/source/conf.py
index 8450dda..b36a3cc 100644
--- a/docs/source/conf.py
+++ b/docs/source/conf.py
@@ -16,7 +16,6 @@
     'myst_nb',
     'sphinxext.opengraph',
     'sphinx_copybutton',
-    'sphinxcontrib.autodoc_pydantic',
     'sphinx_inline_tabs',
 ]
 
@@ -31,10 +30,6 @@
 copybutton_prompt_text = r'>>> |\.\.\. |\$ |In \[\d*\]: | {2,5}\.\.\.: | {5,8}: '
 copybutton_prompt_is_regexp = True
 
-
-autodoc_pydantic_model_show_json = True
-autodoc_pydantic_settings_show_json = False
-
 jupyter_execute_notebooks = 'off'
 execution_timeout = 600
 execution_allow_errors = True
diff --git a/ecgtools/builder.py b/ecgtools/builder.py
index 19e3594..1cc1205 100644
--- a/ecgtools/builder.py
+++ b/ecgtools/builder.py
@@ -109,13 +109,13 @@ class Builder:
     """
 
     paths: typing.List[str]
-    storage_options: typing.Dict[typing.Any, typing.Any] = None
+    storage_options: typing.Optional[typing.Dict[typing.Any, typing.Any]] = None
     depth: int = 0
-    exclude_patterns: typing.List[str] = None
-    include_patterns: typing.List[str] = None
-    joblib_parallel_kwargs: typing.Dict[str, typing.Any] = None
+    exclude_patterns: typing.Optional[typing.List[str]] = None
+    include_patterns: typing.Optional[typing.List[str]] = None
+    joblib_parallel_kwargs: typing.Optional[typing.Dict[str, typing.Any]] = None
 
-    def __post_init_post_parse__(self):
+    def __post_init__(self):
         self.storage_options = self.storage_options or {}
         self.joblib_parallel_kwargs = self.joblib_parallel_kwargs or {}
         self.exclude_patterns = self.exclude_patterns or []
@@ -146,7 +146,9 @@ def get_assets(self):
         return self
 
     @pydantic.validate_arguments
-    def parse(self, *, parsing_func: typing.Callable, parsing_func_kwargs: dict = None):
+    def parse(
+        self, *, parsing_func: typing.Callable, parsing_func_kwargs: typing.Optional[dict] = None
+    ):
         if not self.assets:
             raise ValueError('asset list provided is None. Please run `.get_assets()` first')
 
@@ -177,9 +179,9 @@ def build(
         self,
         *,
         parsing_func: typing.Callable,
-        parsing_func_kwargs: dict = None,
-        postprocess_func: typing.Callable = None,
-        postprocess_func_kwargs: dict = None,
+        parsing_func_kwargs: typing.Optional[dict] = None,
+        postprocess_func: typing.Optional[typing.Callable] = None,
+        postprocess_func_kwargs: typing.Optional[dict] = None,
     ):
         """Builds a catalog from a list of netCDF files or zarr stores.
 
@@ -218,14 +220,14 @@ def save(
         path_column_name: str,
         variable_column_name: str,
         data_format: DataFormat,
-        groupby_attrs: typing.List[str] = None,
-        aggregations: typing.List[Aggregation] = None,
+        groupby_attrs: typing.Optional[typing.List[str]] = None,
+        aggregations: typing.Optional[typing.List[Aggregation]] = None,
         esmcat_version: str = '0.0.1',
-        description: str = None,
-        directory: str = None,
+        description: typing.Optional[str] = None,
+        directory: typing.Optional[str] = None,
         catalog_type: str = 'file',
-        to_csv_kwargs: dict = None,
-        json_dump_kwargs: dict = None,
+        to_csv_kwargs: typing.Optional[dict] = None,
+        json_dump_kwargs: typing.Optional[dict] = None,
     ):
         """Persist catalog contents to files.
 
diff --git a/requirements.txt b/requirements.txt
index 7f203b8..3accc80 100644
--- a/requirements.txt
+++ b/requirements.txt
@@ -3,7 +3,7 @@ joblib
 netCDF4
 xarray
 pyyaml
-pydantic
+pydantic>=2.0
 pandas
 fsspec
 intake-esm