cellxlineage 0.1.0__tar.gz

cellxlineage-0.1.0/MANIFEST.in

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+recursive-include server/common/web/templates *
+recursive-include server/common/web/static *
+
+include server/requirements.txt
+include server/requirements-prepare.txt
+include server/requirements-annotate.txt
+include server/converters/schema/hgnc_complete_set.txt.gz
+include server/converters/schema/schema_definitions/*

cellxlineage-0.1.0/PKG-INFO

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+Metadata-Version: 2.4
+Name: cellxlineage
+Version: 0.1.0
+Summary: Web application for exploration of single-cell datasets with lineage tree visualization
+Home-page: https://github.com/colganwi/cellxlineage
+Author: William Colgan
+Author-email: wcolgan@wi.mit.edu
+License: MIT
+Classifier: Framework :: Flask
+Classifier: Intended Audience :: Science/Research
+Classifier: License :: OSI Approved :: MIT License
+Classifier: Natural Language :: English
+Classifier: Operating System :: POSIX
+Classifier: Operating System :: Unix
+Classifier: Operating System :: MacOS :: MacOS X
+Classifier: Programming Language :: JavaScript
+Classifier: Programming Language :: Python :: 3
+Classifier: Programming Language :: Python :: 3.10
+Classifier: Programming Language :: Python :: 3.11
+Classifier: Programming Language :: Python :: 3.12
+Classifier: Programming Language :: Python :: 3 :: Only
+Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
+Requires-Python: >=3.10
+Description-Content-Type: text/markdown
+Requires-Dist: anndata>=0.8.0
+Requires-Dist: treedata>=0.2.5
+Requires-Dist: boto3>=1.12.18
+Requires-Dist: click>=7.1.2
+Requires-Dist: Flask>=3.0.0
+Requires-Dist: Flask-Compress>=1.4.0
+Requires-Dist: Flask-Cors>=3.0.9
+Requires-Dist: Flask-RESTful>=0.3.6
+Requires-Dist: flask-server-timing>=0.1.2
+Requires-Dist: flask-talisman>=0.7.0
+Requires-Dist: flatbuffers==2.0.7
+Requires-Dist: flatten-dict>=0.2.0
+Requires-Dist: fsspec>0.8.0
+Requires-Dist: gunicorn>=20.0.4
+Requires-Dist: h5py>=3.0.0
+Requires-Dist: numba>=0.60.0
+Requires-Dist: numpy==2.0.1
+Requires-Dist: packaging>=20.0
+Requires-Dist: pandas>=2.2.2
+Requires-Dist: PyYAML>=5.4
+Requires-Dist: requests>=2.22.0
+Requires-Dist: s3fs==0.4.2
+Requires-Dist: scipy>=1.4
+Requires-Dist: setuptools
+Provides-Extra: prepare
+Requires-Dist: python-igraph>=0.8; extra == "prepare"
+Requires-Dist: louvain>=0.6; extra == "prepare"
+Requires-Dist: scanpy; extra == "prepare"
+Requires-Dist: umap-learn<0.5.0; extra == "prepare"
+Provides-Extra: annotate
+Requires-Dist: mlflow==2.16.0; extra == "annotate"
+Requires-Dist: scanpy; extra == "annotate"
+Dynamic: author
+Dynamic: author-email
+Dynamic: classifier
+Dynamic: description
+Dynamic: description-content-type
+Dynamic: home-page
+Dynamic: license
+Dynamic: provides-extra
+Dynamic: requires-dist
+Dynamic: requires-python
+Dynamic: summary
+
+<img src="./docs/cellxlineage-logo.png" width="300">
+
+_An interactive explorer for single-cell lineage tracing._
+
+CELLxLINEAGE is a fork of [CELLxGENE](https://cellxgene.cziscience.com/docs/01__CellxGene) extended to support [TreeData](https://github.com/YosefLab/treedata) objects and lineage tree visualization alongside the standard UMAP embedding.
+
+<img src="./docs/images/cellxlineage-opening.png" width="500">
+
+## Installation
+
+You need to have Python 3.10 or newer installed on your system. If you don't have
+Python installed, we recommend installing [Mambaforge](https://github.com/conda-forge/miniforge#mambaforge).
+
+Install the latest release of `cellxlineage` from [PyPI](https://pypi.org/project/cellxlineage):
+
+```bash
+pip install cellxlineage
+```
+
+## Usage
+
+```bash
+# Launch with a TreeData file
+cellxlineage launch data.h5td
+```
+
+## CELLxGENE documentation
+
+CELLxLINEAGE inherits all standard CELLxGENE Annotate features. For documentation on exploration, filtering, differential expression, and annotations, see the [CELLxGENE Annotate documentation](https://cellxgene.cziscience.com/docs/01__CellxGene).
+
+## Contact
+
+For questions and bug reports please use the [issue tracker](https://github.com/colganwi/cellxlineage/issues).
+
+## License
+
+MIT — see [LICENSE](LICENSE). Portions copyright Chan Zuckerberg Initiative; lineage extensions copyright William Colgan.
+

cellxlineage-0.1.0/README.md

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+<img src="./docs/cellxlineage-logo.png" width="300">
+
+_An interactive explorer for single-cell lineage tracing._
+
+CELLxLINEAGE is a fork of [CELLxGENE](https://cellxgene.cziscience.com/docs/01__CellxGene) extended to support [TreeData](https://github.com/YosefLab/treedata) objects and lineage tree visualization alongside the standard UMAP embedding.
+
+<img src="./docs/images/cellxlineage-opening.png" width="500">
+
+## Installation
+
+You need to have Python 3.10 or newer installed on your system. If you don't have
+Python installed, we recommend installing [Mambaforge](https://github.com/conda-forge/miniforge#mambaforge).
+
+Install the latest release of `cellxlineage` from [PyPI](https://pypi.org/project/cellxlineage):
+
+```bash
+pip install cellxlineage
+```
+
+## Usage
+
+```bash
+# Launch with a TreeData file
+cellxlineage launch data.h5td
+```
+
+## CELLxGENE documentation
+
+CELLxLINEAGE inherits all standard CELLxGENE Annotate features. For documentation on exploration, filtering, differential expression, and annotations, see the [CELLxGENE Annotate documentation](https://cellxgene.cziscience.com/docs/01__CellxGene).
+
+## Contact
+
+For questions and bug reports please use the [issue tracker](https://github.com/colganwi/cellxlineage/issues).
+
+## License
+
+MIT — see [LICENSE](LICENSE). Portions copyright Chan Zuckerberg Initiative; lineage extensions copyright William Colgan.
+

cellxlineage-0.1.0/cellxlineage.egg-info/PKG-INFO

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+Metadata-Version: 2.4
+Name: cellxlineage
+Version: 0.1.0
+Summary: Web application for exploration of single-cell datasets with lineage tree visualization
+Home-page: https://github.com/colganwi/cellxlineage
+Author: William Colgan
+Author-email: wcolgan@wi.mit.edu
+License: MIT
+Classifier: Framework :: Flask
+Classifier: Intended Audience :: Science/Research
+Classifier: License :: OSI Approved :: MIT License
+Classifier: Natural Language :: English
+Classifier: Operating System :: POSIX
+Classifier: Operating System :: Unix
+Classifier: Operating System :: MacOS :: MacOS X
+Classifier: Programming Language :: JavaScript
+Classifier: Programming Language :: Python :: 3
+Classifier: Programming Language :: Python :: 3.10
+Classifier: Programming Language :: Python :: 3.11
+Classifier: Programming Language :: Python :: 3.12
+Classifier: Programming Language :: Python :: 3 :: Only
+Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
+Requires-Python: >=3.10
+Description-Content-Type: text/markdown
+Requires-Dist: anndata>=0.8.0
+Requires-Dist: treedata>=0.2.5
+Requires-Dist: boto3>=1.12.18
+Requires-Dist: click>=7.1.2
+Requires-Dist: Flask>=3.0.0
+Requires-Dist: Flask-Compress>=1.4.0
+Requires-Dist: Flask-Cors>=3.0.9
+Requires-Dist: Flask-RESTful>=0.3.6
+Requires-Dist: flask-server-timing>=0.1.2
+Requires-Dist: flask-talisman>=0.7.0
+Requires-Dist: flatbuffers==2.0.7
+Requires-Dist: flatten-dict>=0.2.0
+Requires-Dist: fsspec>0.8.0
+Requires-Dist: gunicorn>=20.0.4
+Requires-Dist: h5py>=3.0.0
+Requires-Dist: numba>=0.60.0
+Requires-Dist: numpy==2.0.1
+Requires-Dist: packaging>=20.0
+Requires-Dist: pandas>=2.2.2
+Requires-Dist: PyYAML>=5.4
+Requires-Dist: requests>=2.22.0
+Requires-Dist: s3fs==0.4.2
+Requires-Dist: scipy>=1.4
+Requires-Dist: setuptools
+Provides-Extra: prepare
+Requires-Dist: python-igraph>=0.8; extra == "prepare"
+Requires-Dist: louvain>=0.6; extra == "prepare"
+Requires-Dist: scanpy; extra == "prepare"
+Requires-Dist: umap-learn<0.5.0; extra == "prepare"
+Provides-Extra: annotate
+Requires-Dist: mlflow==2.16.0; extra == "annotate"
+Requires-Dist: scanpy; extra == "annotate"
+Dynamic: author
+Dynamic: author-email
+Dynamic: classifier
+Dynamic: description
+Dynamic: description-content-type
+Dynamic: home-page
+Dynamic: license
+Dynamic: provides-extra
+Dynamic: requires-dist
+Dynamic: requires-python
+Dynamic: summary
+
+<img src="./docs/cellxlineage-logo.png" width="300">
+
+_An interactive explorer for single-cell lineage tracing._
+
+CELLxLINEAGE is a fork of [CELLxGENE](https://cellxgene.cziscience.com/docs/01__CellxGene) extended to support [TreeData](https://github.com/YosefLab/treedata) objects and lineage tree visualization alongside the standard UMAP embedding.
+
+<img src="./docs/images/cellxlineage-opening.png" width="500">
+
+## Installation
+
+You need to have Python 3.10 or newer installed on your system. If you don't have
+Python installed, we recommend installing [Mambaforge](https://github.com/conda-forge/miniforge#mambaforge).
+
+Install the latest release of `cellxlineage` from [PyPI](https://pypi.org/project/cellxlineage):
+
+```bash
+pip install cellxlineage
+```
+
+## Usage
+
+```bash
+# Launch with a TreeData file
+cellxlineage launch data.h5td
+```
+
+## CELLxGENE documentation
+
+CELLxLINEAGE inherits all standard CELLxGENE Annotate features. For documentation on exploration, filtering, differential expression, and annotations, see the [CELLxGENE Annotate documentation](https://cellxgene.cziscience.com/docs/01__CellxGene).
+
+## Contact
+
+For questions and bug reports please use the [issue tracker](https://github.com/colganwi/cellxlineage/issues).
+
+## License
+
+MIT — see [LICENSE](LICENSE). Portions copyright Chan Zuckerberg Initiative; lineage extensions copyright William Colgan.
+

cellxlineage-0.1.0/cellxlineage.egg-info/SOURCES.txt

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+MANIFEST.in
+README.md
+pyproject.toml
+setup.cfg
+setup.py
+cellxlineage.egg-info/PKG-INFO
+cellxlineage.egg-info/SOURCES.txt
+cellxlineage.egg-info/dependency_links.txt
+cellxlineage.egg-info/entry_points.txt
+cellxlineage.egg-info/not-zip-safe
+cellxlineage.egg-info/requires.txt
+cellxlineage.egg-info/top_level.txt
+server/__init__.py
+server/__main__.py
+server/default_config.py
+server/requirements-annotate.txt
+server/requirements-prepare.txt
+server/requirements.txt
+server/annotate/__init__.py
+server/annotate/annotation_types.py
+server/app/__init__.py
+server/app/app.py
+server/app/session.py
+server/cli/__init__.py
+server/cli/annotate.py
+server/cli/cli.py
+server/cli/launch.py
+server/cli/prepare.py
+server/cli/upgrade.py
+server/common/__init__.py
+server/common/colors.py
+server/common/constants.py
+server/common/corpora.py
+server/common/errors.py
+server/common/genesets.py
+server/common/health.py
+server/common/rest.py
+server/common/annotations/__init__.py
+server/common/annotations/annotations.py
+server/common/annotations/local_file_csv.py
+server/common/compute/__init__.py
+server/common/compute/diffexp_generic.py
+server/common/compute/estimate_distribution.py
+server/common/config/__init__.py
+server/common/config/app_config.py
+server/common/config/base_config.py
+server/common/config/client_config.py
+server/common/config/dataset_config.py
+server/common/config/external_config.py
+server/common/config/server_config.py
+server/common/fbs/__init__.py
+server/common/fbs/matrix.py
+server/common/fbs/NetEncoding/Column.py
+server/common/fbs/NetEncoding/Float32Array.py
+server/common/fbs/NetEncoding/Float64Array.py
+server/common/fbs/NetEncoding/Int32Array.py
+server/common/fbs/NetEncoding/JSONEncodedArray.py
+server/common/fbs/NetEncoding/Matrix.py
+server/common/fbs/NetEncoding/TypedArray.py
+server/common/fbs/NetEncoding/Uint32Array.py
+server/common/fbs/NetEncoding/__init__.py
+server/common/utils/__init__.py
+server/common/utils/corpora_constants.py
+server/common/utils/data_locator.py
+server/common/utils/type_conversion_utils.py
+server/common/utils/utils.py
+server/common/web/__init__.py
+server/common/web/static/main-6835a9ad4754cf2ffc45.css
+server/common/web/static/main-6835a9ad4754cf2ffc45.css.map
+server/common/web/static/main-9a36e52e0714b93a3def.js
+server/common/web/static/main-9a36e52e0714b93a3def.js.LICENSE.txt
+server/common/web/static/main-9a36e52e0714b93a3def.js.map
+server/common/web/static/assets/RobotoCondensed-Bold-89a396525c0de98da36505cb04eb9373.ttf
+server/common/web/static/assets/RobotoCondensed-Italic-aca8cfe6a0fd2abecaa6e21a19f66eba.ttf
+server/common/web/static/assets/RobotoCondensed-Regular-db6d916952fb988edac1e531d47ff83a.ttf
+server/common/web/static/assets/icons-16-13933033991f62d6bb641c7a19c8c431.ttf
+server/common/web/static/assets/icons-16-1645f50fb7f7c109f64eedae92080228.woff
+server/common/web/static/assets/icons-16-2368f88a078780d80145531133100823.eot
+server/common/web/static/assets/icons-20-1ef633d3a28d0986f63e78a70178d06d.woff
+server/common/web/static/assets/icons-20-57b3e708b232fdcb64f9cb115cdda7bb.ttf
+server/common/web/static/assets/icons-20-cde033c5d3f24283f7578120bb9dc288.eot
+server/common/web/static/assets/logo-f85fdd6972a827124b5ed7f6499e68f6.png
+server/common/web/templates/index.html
+server/data_anndata/__init__.py
+server/data_anndata/anndata_adaptor.py
+server/data_common/__init__.py
+server/data_common/data_adaptor.py
+server/data_common/matrix_loader.py
+server/data_treedata/__init__.py
+server/data_treedata/treedata_adaptor.py

cellxlineage-0.1.0/cellxlineage.egg-info/dependency_links.txt

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+

cellxlineage-0.1.0/cellxlineage.egg-info/entry_points.txt

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+[console_scripts]
+cellxlineage = server.cli.cli:cli

cellxlineage-0.1.0/cellxlineage.egg-info/not-zip-safe

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+

cellxlineage-0.1.0/cellxlineage.egg-info/requires.txt

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+anndata>=0.8.0
+treedata>=0.2.5
+boto3>=1.12.18
+click>=7.1.2
+Flask>=3.0.0
+Flask-Compress>=1.4.0
+Flask-Cors>=3.0.9
+Flask-RESTful>=0.3.6
+flask-server-timing>=0.1.2
+flask-talisman>=0.7.0
+flatbuffers==2.0.7
+flatten-dict>=0.2.0
+fsspec>0.8.0
+gunicorn>=20.0.4
+h5py>=3.0.0
+numba>=0.60.0
+numpy==2.0.1
+packaging>=20.0
+pandas>=2.2.2
+PyYAML>=5.4
+requests>=2.22.0
+s3fs==0.4.2
+scipy>=1.4
+setuptools
+
+[annotate]
+mlflow==2.16.0
+scanpy
+
+[prepare]
+python-igraph>=0.8
+louvain>=0.6
+scanpy
+umap-learn<0.5.0

cellxlineage-0.1.0/cellxlineage.egg-info/top_level.txt

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+server

cellxlineage-0.1.0/pyproject.toml

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+[build-system]
+requires = ["setuptools>=61.0", "wheel"]
+build-backend = "setuptools.build_meta"
+
+[tool.black]
+line-length = 120
+target_version = ['py37']
+include = '\.pyi?$'
+exclude = '''
+
+(
+  /(
+      \.eggs         # exclude a few common directories in the
+    | \.git          # root of the project
+    | \.hg
+    | \.mypy_cache
+    | \.tox
+    | \.venv
+    | venv
+    | _build
+    | buck-out
+    | build
+    | dist
+    | server/common/fbs/NetEncoding
+  )/
+
+)
+'''

cellxlineage-0.1.0/server/__init__.py

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+import logging
+import sys
+from server.common.utils.utils import import_plugins
+
+__version__ = "0.1.0"
+display_version = "cellxlineage v" + __version__
+
+try:
+    import_plugins("server.plugins")
+except Exception as e:
+    # Make sure to exit in this case, as the server may not be configured as expected.
+    logging.critical(f"Error in import_plugins: {str(e)}")
+    sys.exit(1)

cellxlineage-0.1.0/server/__main__.py

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+# Work around bug https://github.com/pallets/werkzeug/issues/461
+if __package__ is None:
+    import sys
+    from pathlib import Path
+
+    PKG_PATH = Path(__file__).parent
+    sys.path.insert(0, str(PKG_PATH.parent))
+    import server  # noqa F401
+
+    __package__ = PKG_PATH.name
+
+# Main thing
+from .cli.cli import cli  # noqa F402
+
+cli()

cellxlineage-0.1.0/server/annotate/annotation_types.py

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+from enum import Enum
+
+
+class AnnotationType(Enum):
+    CELL_TYPE = "cell_type"