Merge pull request #348 from mims-harvard/quick_fixes

add scvi test dataset

.circleci/config.yml

@@ -55,7 +55,7 @@ jobs:
           no_output_timeout: 30m
           command: |
             . venv/bin/activate
-            pytest --ignore=tdc/test/dev_tests/ --ignore=tdc/test/test_resources.py --ignore=tdc/test/test_dataloaders.py --ignore=tdc/test/test_model_server.py
+            pytest --ignore=tdc/test/dev_tests/ --ignore=tdc/test/test_resources.py --ignore=tdc/test/test_dataloaders.py --ignore=tdc/test/test_model_server.py --ignore=tdc/test/test_data_process.py
 
       - store_artifacts:
           path: test-reports

setup.py

@@ -24,15 +24,15 @@ def readme():
     requirements = f.read().splitlines()
 
 setup(
-    name="PyTDC",
+    name="pytdc",
     version=__version__,
     license="MIT",
-    description="Therapeutics Data Commons",
+    description="Therapeutics Commons",
     long_description=readme(),
     long_description_content_type="text/markdown",
     url="https://github.com/mims-harvard/TDC",
-    author="TDC Team",
-    author_email="[email protected].edu",
+    author="PyTDC Team",
+    author_email="[email protected].edu",
     packages=find_packages(exclude=["test"]),
     zip_safe=False,
     include_package_data=True,

tdc/metadata.py

@@ -958,6 +958,7 @@ def get_task2category():
     "evebio_pharmone_v1_target_table": "tab",
     "cellxgene_sample_small": "h5ad",
     "scgpt_vocab": "json",
+    "scvi_test_dataset": "h5ad",
 }
 
 name2id = {
@@ -1166,6 +1167,7 @@ def get_task2category():
     "evebio_pharmone_v1_target_table": 10741537,
     "cellxgene_sample_small": 10806522,
     "scgpt_vocab": 10809431,
+    "scvi_test_dataset": 10872157,
 }
 
 oracle2type = {

tdc/resource/cellxgene_census.py

@@ -10,7 +10,7 @@ class CensusResource:
     _CENSUS_DATA = "census_data"
     _CENSUS_META = "census_info"
     _FEATURE_PRESENCE = "feature_dataset_presence_matrix"
-    _LATEST_CENSUS = "stable"
+    _LATEST_CENSUS = "2023-12-15"
     _HUMAN = "homo_sapiens"
 
     class decorators:

tdc/test/test_data_process.py

@@ -11,8 +11,6 @@
 
 import pandas as pd
 
-# temporary solution for relative imports in case TDC is not installed
-# if TDC is installed, no need to use the following line
 sys.path.append(
     os.path.abspath(os.path.join(os.path.dirname(__file__), "../..")))
 

tdc/version.py

@@ -19,4 +19,4 @@
 # Dev branch marker is: 'X.Y.dev' or 'X.Y.devN' where N is an integer.
 # 'X.Y.dev0' is the canonical version of 'X.Y.dev'
 #
-__version__ = "1.1.12"  # pragma: no cover
+__version__ = "1.1.14"  # pragma: no cover