Merge pull request #23 from pepkit/dev

Release 0.1.2

Author: khoroshevskyi

codecov.yml

@@ -2,4 +2,20 @@ ignore:
   - "*/cli.py"
   - "*/__main__.py"
   - "*/__init__.py"
-  - "setup.py"
+  - "setup.py"
+
+coverage:
+  status:
+    project:
+      default: false  # disable the default status that measures entire project
+      tests:
+        paths:
+          - "tests/"
+        target: 100%
+      source:
+        paths:
+          - "jupytext/"
+        target: 70%
+    patch:
+      default:
+        target: 70%

docs/changelog.md

@@ -2,6 +2,10 @@
 
 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.
 
+## [0.1.1] - 2023-07-29
+### Fixed
+- Incorrect base url
+
 ## [0.1.1] - 2023-07-29
 ### Fixed
 - New raw PEP structure was broken. ([#20](https://github.com/pepkit/pephubclient/issues/20))

pephubclient/__init__.py

@@ -1,7 +1,7 @@
 from pephubclient.pephubclient import PEPHubClient
 
 __app_name__ = "pephubclient"
-__version__ = "0.1.1"
+__version__ = "0.1.2"
 __author__ = "Oleksandr Khoroshevskyi, Rafal Stepien"
 
 

pephubclient/constants.py

@@ -4,8 +4,8 @@
 import pydantic
 from pydantic import BaseModel
 
-# PEPHUB_BASE_URL = "https://pephub.databio.org/"
-PEPHUB_BASE_URL = "http://0.0.0.0:8000/"
+PEPHUB_BASE_URL = "https://pephub.databio.org/"
+# PEPHUB_BASE_URL = "http://0.0.0.0:8000/"
 PEPHUB_PEP_API_BASE_URL = f"{PEPHUB_BASE_URL}api/v1/projects/"
 PEPHUB_PUSH_URL = f"{PEPHUB_BASE_URL}api/v1/namespaces/{{namespace}}/projects/json"
 

pephubclient/pephubclient.py

@@ -4,7 +4,13 @@
 
 import pandas as pd
 import peppy
-from peppy.const import NAME_KEY, DESC_KEY, CONFIG_KEY
+from peppy.const import (
+    NAME_KEY,
+    DESC_KEY,
+    CONFIG_KEY,
+    SUBSAMPLE_RAW_LIST_KEY,
+    SAMPLE_RAW_DICT_KEY,
+)
 import requests
 import urllib3
 from pydantic.error_wrappers import ValidationError
@@ -143,7 +149,7 @@ def upload(
         """
         jwt_data = FilesManager.load_jwt_data_from_file(self.PATH_TO_FILE_WITH_JWT)
         if name:
-            project["name"] = name
+            project[NAME_KEY] = name
 
         upload_data = ProjectUploadData(
             pep_dict=project.to_dict(
@@ -216,10 +222,11 @@ def full_path(fn: str) -> str:
         config_dict[DESC_KEY] = project_dict[CONFIG_KEY][DESC_KEY]
         config_dict["sample_table"] = sample_table_filename
 
-        sample_pandas = pd.DataFrame(project_dict.get("_sample_dict", {}))
+        sample_pandas = pd.DataFrame(project_dict.get(SAMPLE_RAW_DICT_KEY, {}))
 
         subsample_list = [
-            pd.DataFrame(sub_a) for sub_a in project_dict.get("_subsample_dict") or []
+            pd.DataFrame(sub_a)
+            for sub_a in project_dict.get(SUBSAMPLE_RAW_LIST_KEY) or []
         ]
 
         filenames = []