torchcell 0.2.7__tar.gz → 0.2.8__tar.gz

{torchcell-0.2.7 → torchcell-0.2.8}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: torchcell
-Version: 0.2.7
+Version: 0.2.8
 Summary: An example package
 Author-email: Michael Volk <michaeljvolk7@gmail.com>
 Project-URL: Homepage, https://github.com/Mjvolk3/Dendron-Template
@@ -20,11 +20,12 @@ Requires-Dist: scipy>=1.11.4
 Requires-Dist: networkx>=3.2.1
 Requires-Dist: umap-learn>=0.5.3
 Requires-Dist: hydra-core>=1.3.2
-Requires-Dist: torch>=2.1.0
+Requires-Dist: deepdiff>=7.0.1
+Requires-Dist: torch>=2.4.0
 Requires-Dist: torch_geometric>=2.4.0
 Requires-Dist: torchmetrics>=1.2.1
 Requires-Dist: lightning>=2.1.2
-Requires-Dist: wandb>=0.16.6
+Requires-Dist: wandb>=0.17.5
 Requires-Dist: wandb_osh>=1.2.2
 Requires-Dist: matplotlib>=3.7.2
 Requires-Dist: adjustText>=0.8
@@ -38,12 +39,13 @@ Requires-Dist: biopython>=1.81
 Requires-Dist: goatools>=1.3.1
 Requires-Dist: intermine>=1.13.0
 Requires-Dist: gffutils>=0.12
+Requires-Dist: GEOparse>=2.0.4
 Requires-Dist: pandas-stubs>=2.0.3.230814
 Requires-Dist: types-tqdm>=4.65.0.2
 Requires-Dist: types-requests>=2.31.0.2
 Requires-Dist: sortedcontainers>=2.4.0
 Requires-Dist: attrs>=23.1.0
-Requires-Dist: pydantic>=2.5.2
+Requires-Dist: pydantic>=2.8.2
 Requires-Dist: h5py>=3.9.0
 Requires-Dist: lmdb>=1.4.1
 Requires-Dist: aiohttp>=3.8.5
@@ -57,7 +59,7 @@ Requires-Dist: pip-tools>=7.1.0
 Requires-Dist: snakeviz>=2.2.0
 Requires-Dist: twine>=4.0.2
 Requires-Dist: memory-profiler>=0.61.0
-Requires-Dist: neo4j>=4.4.11
+Requires-Dist: neo4j<5.0,>=4.4.11
 Requires-Dist: cliff>=4.5.0
 Provides-Extra: dev
 Requires-Dist: black; extra == "dev"
@@ -75,4 +77,4 @@ Packaging: Add packing <!-- ![Python application](https://github.com/mjvolk3/tor
 
 Testing: ![Code Styling](https://github.com/mjvolk3/torchcell/workflows/Code%20Styling/badge.svg) [![codecov](https://codecov.io/gh/mjvolk3/torchcell/branch/main/graph/badge.svg)](https://codecov.io/gh/mjvolk3/torchcell)
 
-Docs to come soon!!
+Docs to come soon!!!

{torchcell-0.2.7 → torchcell-0.2.8}/README.md

@@ -8,4 +8,4 @@ Packaging: Add packing <!-- ![Python application](https://github.com/mjvolk3/tor
 
 Testing: ![Code Styling](https://github.com/mjvolk3/torchcell/workflows/Code%20Styling/badge.svg) [![codecov](https://codecov.io/gh/mjvolk3/torchcell/branch/main/graph/badge.svg)](https://codecov.io/gh/mjvolk3/torchcell)
 
-Docs to come soon!!
+Docs to come soon!!!

torchcell-0.2.8/env/requirements.txt

@@ -0,0 +1,112 @@
+    # env/requirements.txt
+    # scientific computing stack
+    # We pin numpy because transformers lib cannot yet use 2.0
+    numpy==1.26.0
+    pandas>=2.1.1
+    pyarrow>=15.0.0
+
+    #polars
+    openpyxl>=3.1.2
+    # xlrd with pandas
+    xlrd>= 2.0.1
+    # pyreader use with RDS
+    pyreadr>=0.4.9
+    scipy>=1.11.4
+    networkx>=3.2.1
+    #dask
+    umap-learn>=0.5.3
+
+    # configuration
+    hydra-core>=1.3.2
+    deepdiff>=7.0.1
+
+    # torch stack
+    torch>=2.4.0
+    torch_geometric>=2.4.0
+    torchmetrics>=1.2.1
+    lightning>=2.1.2
+    # torch-scatter>=2.1.2
+
+    # visualization stack and logging
+    wandb>=0.17.5
+    wandb_osh>=1.2.2
+    matplotlib>=3.7.2
+    # adjustTest used with with matplotlib
+    adjustText>=0.8
+    #pydot Don't think I am using this... outdate
+    pydot>=1.4.2
+    # pygraphviz don't think I am using this
+    # graphviz don't think I am using this.
+    # graphviz
+    plotly>=5.18.0
+    seaborn>=0.12.2
+
+    # ML stack
+    scikit-learn>=1.2.2
+
+    # Transformer / Huggingface Stack
+    transformers>=4.31.0
+    ## used with protT5 model
+    sentencepiece>=0.1.99
+
+    # Bio stack
+    biopython>=1.81
+    goatools>=1.3.1
+    intermine>=1.13.0
+    gffutils>=0.12
+    GEOparse>=2.0.4
+
+    # stubs and types
+    pandas-stubs>=2.0.3.230814
+    types-tqdm>=4.65.0.2
+    types-requests>= 2.31.0.2
+
+    # data stack
+    sortedcontainers>=2.4.0
+    attrs>=23.1.0
+    pydantic>=2.8.2
+    h5py>=3.9.0
+    # R is needed for installation. This creates issues.
+    #rpy2>=3.5.16 # needed for mechanistic aware. can probably get rid of.
+
+
+    # database stack
+    lmdb>=1.4.1
+
+
+    # web stack
+    aiohttp>=3.8.5
+
+    # ontology stack
+    pronto>=2.5.4
+    nxontology>=0.5.0
+    owlready2>=0.45
+
+
+    # Workspace
+    python-dotenv>=1.0.0
+
+    # dev-tools
+    python-semantic-release>=9.0.3
+    pre-commit>=3.3.3
+    # ptpython>=3.0.23
+    pip-tools>=7.1.0
+    snakeviz>=2.2.0
+    twine>=4.0.2
+    memory-profiler>=0.61.0
+
+    # biocypher
+    # Swith to biocypher after path change is implemented
+    # biocypher>=0.5.35
+    # Not allowed in Pypi
+    # biocypher@git+https://github.com/Mjvolk3/biocypher@main
+
+    # neo4j
+    neo4j>=4.4.11,<5.0
+
+    # command line
+    cliff>=4.5.0
+
+    # twine cannot handle these
+    # Not allowed in Pypi
+    # CaLM@git+https://github.com/oxpig/CaLM@main

{torchcell-0.2.7 → torchcell-0.2.8}/pyproject.toml

@@ -6,7 +6,7 @@ build-backend = "setuptools.build_meta"
 
 [project]
 name = "torchcell"
-version = "0.2.7"
+version = "0.2.8"
 description = "An example package"
 readme = "README.md"
 authors = [{ name = "Michael Volk", email = "michaeljvolk7@gmail.com" }]
@@ -87,7 +87,7 @@ dependencies = { file = ["env/requirements.txt"] }
 version = { attr = "torchcell.__version__" }
 
 [tool.setuptools.package-data]
-torchcell = ["py.typed", "knowledge_graphs/conf/*.yaml"]
+torchcell = ["py.typed", "knowledge_graphs/conf/*.yaml", "adapters/conf/*.yaml"]
 
 [tool.setuptools.packages.find]
 include = ["torchcell*"]

{torchcell-0.2.7 → torchcell-0.2.8}/torchcell/__version__.py

@@ -3,4 +3,4 @@
 # https://github.com/Mjvolk3/torchcell/tree/main/torchcell/__version__.py
 # Test file: tests/torchcell/test___version__.py
 
-__version__ = "0.2.7"  # Linked to semantic-release in toml
+__version__ = "0.2.8"  # Linked to semantic-release in toml

torchcell-0.2.8/torchcell/adapters/__init__.py

@@ -0,0 +1,68 @@
+from .cell_adapter import CellAdapter
+from .costanzo2016_adapter import (
+    SmfCostanzo2016Adapter,
+    DmfCostanzo2016Adapter,
+    DmiCostanzo2016Adapter,
+)
+from .kuzmin2018_adapter import (
+    SmfKuzmin2018Adapter,
+    DmfKuzmin2018Adapter,
+    TmfKuzmin2018Adapter,
+    DmiKuzmin2018Adapter,
+    TmiKuzmin2018Adapter,
+)
+from .kuzmin2020_adapter import (
+    SmfKuzmin2020Adapter,
+    DmfKuzmin2020Adapter,
+    TmfKuzmin2020Adapter,
+    DmiKuzmin2020Adapter,
+    TmiKuzmin2020Adapter,
+)
+
+from .sgd_adapter import GeneEssentialitySgdAdapter
+
+from .synth_leth_db_adapter import (
+    SynthLethalityYeastSynthLethDbAdapter,
+    SynthRescueYeastSynthLethDbAdapter,
+)
+
+cell_adapters = ["CellAdapter"]
+
+costanzo2016_adapters = [
+    "SmfCostanzo2016Adapter",
+    "DmfCostanzo2016Adapter",
+    "DmiCostanzo2016Adapter",
+]
+
+kuzmin2018_adapters = [
+    "SmfKuzmin2018Adapter",
+    "DmfKuzmin2018Adapter",
+    "TmfKuzmin2018Adapter",
+    "DmiKuzmin2018Adapter",
+    "TmiKuzmin2018Adapter",
+]
+
+kuzmin2020_adapters = [
+    "SmfKuzmin2020Adapter",
+    "DmfKuzmin2020Adapter",
+    "TmfKuzmin2020Adapter",
+    "DmiKuzmin2020Adapter",
+    "TmiKuzmin2020Adapter",
+]
+
+gene_essentiality_adapters = ["GeneEssentialitySgdAdapter"]
+
+synth_leth_db_adapters = [
+    "SynthLethalityYeastSynthLethDbAdapter",
+    "SynthRescueYeastSynthLethDbAdapter",
+]
+
+
+__all__ = (
+    cell_adapters
+    + costanzo2016_adapters
+    + kuzmin2018_adapters
+    + kuzmin2020_adapters
+    + gene_essentiality_adapters
+    + synth_leth_db_adapters
+)