polly-python 2.1.0__tar.gz → 3.0.0__tar.gz

{polly_python-2.1.0/polly_python.egg-info → polly_python-3.0.0}/PKG-INFO

@@ -1,14 +1,14 @@
 Metadata-Version: 2.1
 Name: polly_python
-Version: 2.1.0
+Version: 3.0.0
 Summary: Polly SDK
 Home-page: https://github.com/ElucidataInc/polly-python
 Project-URL: Documentation, https://docs.elucidata.io
 Project-URL: Tutorial Notebooks, https://github.com/ElucidataInc/polly-python
-Requires-Python: >3.6
+Requires-Python: <=3.11,>=3.9
 Description-Content-Type: text/markdown
 License-File: LICENSE.md
-Requires-Dist: elucidatacmapPy==3.3.4
+Requires-Dist: cmapPy<=4.0.1
 Requires-Dist: cloudpathlib>=0.15.0
 Requires-Dist: retrying==1.3.4
 Requires-Dist: rst2txt==1.1.0
@@ -17,22 +17,15 @@ Requires-Dist: mixpanel==4.10.0
 Requires-Dist: Deprecated>=1.2.12
 Requires-Dist: pytest>=6.2.5
 Requires-Dist: cryptography<=38.0.0,>=37.0.1
-Requires-Dist: plotly<5.0.0,>=4.8.1; python_version > "3.6" and python_version < "3.7"
 Requires-Dist: plotly>=5.0.0; python_version >= "3.7"
-Requires-Dist: pandas<1.2.0,>=1.1.0; python_version > "3.6" and python_version < "3.7"
-Requires-Dist: pandas>=1.3.5; python_version >= "3.7"
-Requires-Dist: pydantic<1.10.0a1,>=1.8.2; python_version > "3.6" and python_version < "3.7"
+Requires-Dist: pandas<=2.2.2,>=1.3.5; python_version >= "3.7"
+Requires-Dist: numpy<=1.26.4
 Requires-Dist: pydantic==1.10.12; python_version >= "3.7"
 Requires-Dist: requests==2.28.1
-Requires-Dist: numpy==1.26.4
-Requires-Dist: boto3<1.24.0,>=1.17.73; python_version > "3.6" and python_version < "3.7"
-Requires-Dist: boto3>=1.24.0; python_version >= "3.7"
-Requires-Dist: botocore<1.27.0,>=1.20.73; python_version > "3.6" and python_version < "3.7"
-Requires-Dist: botocore>=1.27.0; python_version >= "3.7"
-Requires-Dist: joblib<=1.1.0,>0.11.0; python_version > "3.6" and python_version < "3.7"
+Requires-Dist: boto3<2.0,>=1.24.0; python_version >= "3.7"
+Requires-Dist: botocore<2.0,>=1.27.0; python_version >= "3.7"
 Requires-Dist: joblib>=1.2.0; python_version >= "3.7"
 Requires-Dist: tabulate==0.9.0
-Requires-Dist: tqdm<4.65.0,>=4.61.0; python_version > "3.6" and python_version < "3.7"
 Requires-Dist: tqdm==4.65.0; python_version >= "3.7"
 Provides-Extra: testing
 Requires-Dist: black; extra == "testing"

polly_python-3.0.0/polly/__init__.py

@@ -0,0 +1 @@
+__version__ = "3.0.0"

{polly_python-2.1.0 → polly_python-3.0.0}/polly/analyze.py

@@ -23,9 +23,11 @@ import numpy as np
 class Analyze:
     """
     The Analyze class contains functions which can be used to identify cohorts in datasets, \
-    perform differential expression and pathway analysis, and execute meta-analysis workflows.\
+    perform differential expression and pathway analysis, and execute meta-analysis workflows.
+
     Args:
         token (str): Authentication token from polly
+
     Usage:
         from polly.analyze import Analyze
 
@@ -58,6 +60,7 @@ class Analyze:
         Args:
             repo_key (int/str): repo_id or repo_name in str or int format
             dataset_id (str): dataset_id of the GEO dataset. eg. "GSE132270_GPL11154_raw"
+
         Returns:
             Dataframe showing values of samples across factors/cohorts.
         """
@@ -290,6 +293,7 @@ class Analyze:
         """
         Use this function to execute the Polly DIY Meta-Analysis Pipeline.
         Only the 'geo_transcriptomics_omixatlas' omixatlas is supported currently.
+
         Args:
             repo_key (int/str): repo_id or repo_name in str or int format
             workspace_id (int): the workspace in which the datasets and results should be stored

{polly_python-2.1.0 → polly_python-3.0.0}/polly/constants.py

@@ -92,22 +92,22 @@ IO_CHUNKSIZE_LARGE_FILE_SIZE = 100 * MB
 EXPIRED_TOKEN = "ExpiredToken"
 
 # cohort constants
-COHORT_VERSION = "0.2"
-COHORT_CONSTANTS_URL = (
-    "https://elucidatainc.github.io/PublicAssets/cohort_constants.txt"
-)
+# COHORT_VERSION = "0.2"
+# COHORT_CONSTANTS_URL = (
+#     "https://elucidatainc.github.io/PublicAssets/cohort_constants.txt"
+# )
 
-OBSOLETE_METADATA_FIELDS = [
-    "package",
-    "region",
-    "bucket",
-    "key",
-    "file_type",
-    "file_location",
-    "src_uri",
-    "timestamp_",
-]
-dot = "."
+# OBSOLETE_METADATA_FIELDS = [
+#     "package",
+#     "region",
+#     "bucket",
+#     "key",
+#     "file_type",
+#     "file_location",
+#     "src_uri",
+#     "timestamp_",
+# ]
+# dot = "."
 
 GETTING_UPLOAD_URLS_PAYLOAD = {"data": {"type": "files", "attributes": {"folder": ""}}}