Merge pull request #31 from pepkit/dev

v0.3.0  release

Author: khoroshevskyi

.github/workflows/python-publish.yml

@@ -1,6 +1,3 @@
-# This workflows will upload a Python Package using Twine when a release is created
-# For more information see: https://help.github.com/en/actions/language-and-framework-guides/using-python-with-github-actions#publishing-to-package-registries
-
 name: Upload Python Package
 
 on:
@@ -9,9 +6,10 @@ on:
 
 jobs:
   deploy:
-
+    name: upload release to PyPI
     runs-on: ubuntu-latest
-
+    permissions:
+      id-token: write
     steps:
     - uses: actions/checkout@v2
     - name: Set up Python
@@ -23,9 +21,7 @@ jobs:
         python -m pip install --upgrade pip
         pip install setuptools wheel twine
     - name: Build and publish
-      env:
-        TWINE_USERNAME: ${{ secrets.PYPI_USERNAME }}
-        TWINE_PASSWORD: ${{ secrets.PYPI_PASSWORD }}
       run: |
         python setup.py sdist bdist_wheel
-        twine upload dist/*
+    - name: Publish package distributions to PyPI
+      uses: pypa/gh-action-pypi-publish@release/v1

docs/changelog.md

@@ -2,10 +2,14 @@
 
 This project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html) and [Keep a Changelog](https://keepachangelog.com/en/1.0.0/) format.
 
-## [0.2.2] - 2024-01-06
+## [0.3.0] - 2024-01-17
 ### Added
 - customization of the base pephub URL. [#22](https://github.com/pepkit/pephubclient/issues/22)
 
+### Updated 
+- PEPhub API URL
+- Increased the required pydantic version to >2.5.0
+
 ## [0.2.1] - 2023-11-01
 ### Added
 - is_registry_path checker function

pephubclient/constants.py

@@ -2,10 +2,11 @@
 from typing import Optional
 import os
 
-import pydantic
-from pydantic import BaseModel
+from pydantic import BaseModel, field_validator
 
-PEPHUB_BASE_URL = os.getenv("PEPHUB_BASE_URL", default="https://pephub.databio.org/")
+PEPHUB_BASE_URL = os.getenv(
+    "PEPHUB_BASE_URL", default="https://pephub-api.databio.org/"
+)
 # PEPHUB_BASE_URL = "http://0.0.0.0:8000/"
 PEPHUB_PEP_API_BASE_URL = f"{PEPHUB_BASE_URL}api/v1/projects/"
 PEPHUB_PEP_SEARCH_URL = f"{PEPHUB_BASE_URL}api/v1/namespaces/{{namespace}}/projects"
@@ -19,7 +20,7 @@ class RegistryPath(BaseModel):
     subitem: Optional[str]
     tag: Optional[str] = "default"
 
-    @pydantic.validator("tag")
+    @field_validator("tag")
     def tag_should_not_be_none(cls, v):
         return v or "default"
 

pephubclient/helpers.py

@@ -1,11 +1,11 @@
 import json
-from typing import Any, Callable, NoReturn, Optional
+from typing import Any, Callable, Optional
 
 import requests
 from requests.exceptions import ConnectionError
 
 from ubiquerg import parse_registry_path
-from pydantic.error_wrappers import ValidationError
+from pydantic import ValidationError
 
 from pephubclient.exceptions import PEPExistsError, ResponseError
 from pephubclient.constants import RegistryPath
@@ -57,15 +57,15 @@ class MessageHandler:
     GREEN = 40
 
     @staticmethod
-    def print_error(text: str) -> NoReturn:
+    def print_error(text: str) -> None:
         print(f"\033[38;5;9m{text}\033[0m")
 
     @staticmethod
-    def print_success(text: str) -> NoReturn:
+    def print_success(text: str) -> None:
         print(f"\033[38;5;40m{text}\033[0m")
 
     @staticmethod
-    def print_warning(text: str) -> NoReturn:
+    def print_warning(text: str) -> None:
         print(f"\033[38;5;11m{text}\033[0m")
 
 

pephubclient/models.py

@@ -1,8 +1,7 @@
 import datetime
 from typing import Optional, List
 
-import pydantic
-from pydantic import BaseModel, Extra, Field
+from pydantic import BaseModel, Field, field_validator, ConfigDict
 from peppy.const import CONFIG_KEY, SUBSAMPLE_RAW_LIST_KEY, SAMPLE_RAW_DICT_KEY
 
 
@@ -15,9 +14,7 @@ class ProjectDict(BaseModel):
     subsample_list: Optional[list] = Field(alias=SUBSAMPLE_RAW_LIST_KEY)
     sample_list: list = Field(alias=SAMPLE_RAW_DICT_KEY)
 
-    class Config:
-        allow_population_by_field_name = True
-        extra = Extra.allow
+    model_config = ConfigDict(populate_by_name=True, extra="allow")
 
 
 class ProjectUploadData(BaseModel):
@@ -30,7 +27,7 @@ class ProjectUploadData(BaseModel):
     is_private: Optional[bool] = False
     overwrite: Optional[bool] = False
 
-    @pydantic.validator("tag")
+    @field_validator("tag")
     def tag_should_not_be_none(cls, v):
         return v or "default"
 

pephubclient/pephubclient.py

@@ -13,7 +13,7 @@
 )
 import requests
 import urllib3
-from pydantic.error_wrappers import ValidationError
+from pydantic import ValidationError
 from ubiquerg import parse_registry_path
 
 from pephubclient.constants import (
@@ -170,7 +170,7 @@ def upload(
             method="POST",
             url=self._build_push_request_url(namespace=namespace),
             headers=self._get_header(jwt_data),
-            json=upload_data.dict(),
+            json=upload_data.model_dump(),
             cookies=None,
         )
         if pephub_response.status_code == ResponseStatusCodes.ACCEPTED:
@@ -345,7 +345,7 @@ def _load_raw_pep(
             correct_proj_dict = ProjectDict(**json.loads(decoded_response))
 
             # This step is necessary because of this issue: https://github.com/pepkit/pephub/issues/124
-            return correct_proj_dict.dict(by_alias=True)
+            return correct_proj_dict.model_dump(by_alias=True)
 
         if pephub_response.status_code == ResponseStatusCodes.NOT_EXIST:
             raise ResponseError("File does not exist, or you are unauthorized.")

requirements/requirements-all.txt

@@ -1,6 +1,6 @@
 typer>=0.7.0
-peppy>=0.35.7
+peppy>=0.40.0
 requests>=2.28.2
-pydantic<2.0
+pydantic>2.5.0
 pandas>=2.0.0
 ubiquerg>=0.6.3