diff --git a/.circleci/config.yml b/.circleci/config.yml index abb6a1de..e4fe5322 100644 --- a/.circleci/config.yml +++ b/.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 diff --git a/setup.py b/setup.py index 68809ac4..865982bf 100644 --- a/setup.py +++ b/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="alejandro_velez-arce@hms.harvard.edu", + author="PyTDC Team", + author_email="amva13@alum.mit.edu", packages=find_packages(exclude=["test"]), zip_safe=False, include_package_data=True, diff --git a/tdc/metadata.py b/tdc/metadata.py index f4779c40..b805138e 100644 --- a/tdc/metadata.py +++ b/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 = { diff --git a/tdc/resource/cellxgene_census.py b/tdc/resource/cellxgene_census.py index bf5ec5f5..9a03c2f4 100644 --- a/tdc/resource/cellxgene_census.py +++ b/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: diff --git a/tdc/test/test_data_process.py b/tdc/test/test_data_process.py index 735c9186..0e509a03 100644 --- a/tdc/test/test_data_process.py +++ b/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__), "../.."))) diff --git a/tdc/version.py b/tdc/version.py index b11adef6..21b7a498 100644 --- a/tdc/version.py +++ b/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