salmopredict 0.1.0__tar.gz

salmopredict-0.1.0/LICENSE

@@ -0,0 +1,202 @@
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salmopredict-0.1.0/MANIFEST.in

@@ -0,0 +1,8 @@
+# The wheel gets the model + assets via [tool.setuptools.package-data]; the
+# source distribution (sdist) needs them listed here too, otherwise `python -m
+# build` produces a modelless tarball.
+recursive-include salmopredict/models *
+recursive-include salmopredict/gui/assets *.png
+include LICENSE
+include environment.yml
+include examples/*.csv

salmopredict-0.1.0/PKG-INFO

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+Metadata-Version: 2.4
+Name: salmopredict
+Version: 0.1.0
+Summary: AutoGluon-based Incidence predictor for Salmonella virulence-factor gene-frequency features
+Author-email: Dongyan Shao <563608176@qq.com>
+License: Apache-2.0
+Project-URL: Homepage, https://github.com/shaodongyan/SalmoPredict
+Project-URL: Repository, https://github.com/shaodongyan/SalmoPredict
+Project-URL: Issues, https://github.com/shaodongyan/SalmoPredict/issues
+Keywords: salmonella,incidence,autogluon,prediction,bioinformatics
+Classifier: License :: OSI Approved :: Apache Software License
+Classifier: Programming Language :: Python :: 3
+Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
+Requires-Python: <3.11,>=3.10
+Description-Content-Type: text/markdown
+License-File: LICENSE
+Requires-Dist: autogluon.tabular==1.1.1
+Requires-Dist: pandas>=2.0
+Requires-Dist: openpyxl>=3.0
+Requires-Dist: rich-argparse>=1.4
+Provides-Extra: gui
+Requires-Dist: streamlit>=1.30; extra == "gui"
+Dynamic: license-file
+
+<p align="center">
+  <img src="https://raw.githubusercontent.com/shaodongyan/SalmoPredict/main/salmopredict/gui/assets/salmopredict_icon.png" alt="salmopredict" width="200">
+</p>
+
+# salmopredict
+
+AutoGluon-based **Incidence** predictor for *Salmonella* virulence-factor
+gene-frequency features, with a command-line interface and a Streamlit GUI.
+
+Given a feature table (rows = samples, columns = virulence-factor genes),
+salmopredict aligns the columns to the features a pre-trained AutoGluon
+`TabularPredictor` expects, runs the `WeightedEnsemble_L2` model, and writes a
+single prediction file. It reproduces the alignment used by the original
+`predict_autogluon.py`: column names are normalised R-`make.names`-style
+(`/` and `-` become `.`), genes the model expects but the input lacks are filled
+with `0` (a missing gene means frequency 0), and extra input columns are ignored.
+
+**Input/output contract** — one input CSV in, one output CSV out. The output
+columns depend on whether the input has a `Sample` column:
+
+| Input | Output columns |
+|-------|----------------|
+| No `Sample` column (features only) | `Incidence(%)` |
+| Has a `Sample` column | `Sample`, `Incidence(%)` |
+| Has a `Sample` column **and** `--attach meta.csv` | `Sample`, `Incidence(%)`, + the metadata's other columns |
+
+Metadata is joined on the `Sample` key (the metadata CSV must also have a
+`Sample` column), so attaching metadata requires a `Sample` column in the input.
+
+## Install
+
+The model must be loaded with **AutoGluon 1.1.1**. Reproduce the environment
+with conda (AutoGluon is installed via pip inside the env — conda-installed
+AutoGluon does not resolve cleanly for this project):
+
+```bash
+conda env create -f environment.yml
+conda activate salmopredict
+```
+
+Or install into an existing env that already has a working AutoGluon 1.1.1:
+
+```bash
+pip install -e .          # add [gui] for the Streamlit interface: pip install -e ".[gui]"
+```
+
+## The model
+
+The prediction model is **already bundled** in this repository at
+`salmopredict/models/model_default` — a 30 MB deployment. salmopredict uses it
+automatically, so the tool works out of the box with no extra download or build
+step.
+
+Model resolution order is `--model`, then `$SALMOPREDICT_MODEL`, then the single
+directory under the package `models/` folder; with nothing specified it uses the
+bundled `model_default`. Pass `--model /path/to/other` to run a different
+AutoGluon model.
+
+## Usage
+
+Ready-to-run inputs live in [`examples/`](examples/) (see its README):
+`example_features.csv` (Type 1, no `Sample`), `example_with_sample.csv`
+(Type 2, with `Sample`), and `example_meta.csv` (metadata to attach). Features
+are `gene_frequency × log10(CFU dose)`, matching how the model was trained. Try
+one immediately:
+
+```bash
+salmopredict run -i examples/example_features.csv -o results/
+```
+
+```bash
+# Features only  -> output has just Incidence(%)
+salmopredict run -i features.csv -o results/ --model /path/to/model
+
+# With a Sample column  -> output has Sample, Incidence(%)
+salmopredict run -i examples/example_with_sample.csv -o results/
+
+# Attach metadata joined on the Sample key -> Sample, Incidence(%), + meta columns
+salmopredict run -i examples/example_with_sample.csv -o results/ \
+  --attach examples/example_meta.csv
+
+# Launch the GUI, or check the environment/model
+salmopredict gui
+salmopredict check --model /path/to/model
+```
+
+Each run writes one `pred_<input-stem>.csv` to the output directory; the
+prediction column is `Incidence(%)`. Features filled with `0` (genes the model
+expects but the input lacks) are always reported, and a prominent warning
+appears when more than `--missing-warn-frac` (default 0.3) of the model's
+features are missing.
+
+## License
+
+Licensed under the [Apache License, Version 2.0](LICENSE). Developed at the State
+Key Laboratory of Veterinary Public Health and Safety, China Agricultural
+University, in collaboration with the China National Center for Food Safety Risk
+Assessment (CFSA).
+
+<p align="center">
+  <img src="https://raw.githubusercontent.com/shaodongyan/SalmoPredict/main/salmopredict/gui/assets/vphs_logo.png" alt="State Key Laboratory of Veterinary Public Health and Safety" width="360">
+</p>

salmopredict-0.1.0/README.md

@@ -0,0 +1,102 @@
+<p align="center">
+  <img src="https://raw.githubusercontent.com/shaodongyan/SalmoPredict/main/salmopredict/gui/assets/salmopredict_icon.png" alt="salmopredict" width="200">
+</p>
+
+# salmopredict
+
+AutoGluon-based **Incidence** predictor for *Salmonella* virulence-factor
+gene-frequency features, with a command-line interface and a Streamlit GUI.
+
+Given a feature table (rows = samples, columns = virulence-factor genes),
+salmopredict aligns the columns to the features a pre-trained AutoGluon
+`TabularPredictor` expects, runs the `WeightedEnsemble_L2` model, and writes a
+single prediction file. It reproduces the alignment used by the original
+`predict_autogluon.py`: column names are normalised R-`make.names`-style
+(`/` and `-` become `.`), genes the model expects but the input lacks are filled
+with `0` (a missing gene means frequency 0), and extra input columns are ignored.
+
+**Input/output contract** — one input CSV in, one output CSV out. The output
+columns depend on whether the input has a `Sample` column:
+
+| Input | Output columns |
+|-------|----------------|
+| No `Sample` column (features only) | `Incidence(%)` |
+| Has a `Sample` column | `Sample`, `Incidence(%)` |
+| Has a `Sample` column **and** `--attach meta.csv` | `Sample`, `Incidence(%)`, + the metadata's other columns |
+
+Metadata is joined on the `Sample` key (the metadata CSV must also have a
+`Sample` column), so attaching metadata requires a `Sample` column in the input.
+
+## Install
+
+The model must be loaded with **AutoGluon 1.1.1**. Reproduce the environment
+with conda (AutoGluon is installed via pip inside the env — conda-installed
+AutoGluon does not resolve cleanly for this project):
+
+```bash
+conda env create -f environment.yml
+conda activate salmopredict
+```
+
+Or install into an existing env that already has a working AutoGluon 1.1.1:
+
+```bash
+pip install -e .          # add [gui] for the Streamlit interface: pip install -e ".[gui]"
+```
+
+## The model
+
+The prediction model is **already bundled** in this repository at
+`salmopredict/models/model_default` — a 30 MB deployment. salmopredict uses it
+automatically, so the tool works out of the box with no extra download or build
+step.
+
+Model resolution order is `--model`, then `$SALMOPREDICT_MODEL`, then the single
+directory under the package `models/` folder; with nothing specified it uses the
+bundled `model_default`. Pass `--model /path/to/other` to run a different
+AutoGluon model.
+
+## Usage
+
+Ready-to-run inputs live in [`examples/`](examples/) (see its README):
+`example_features.csv` (Type 1, no `Sample`), `example_with_sample.csv`
+(Type 2, with `Sample`), and `example_meta.csv` (metadata to attach). Features
+are `gene_frequency × log10(CFU dose)`, matching how the model was trained. Try
+one immediately:
+
+```bash
+salmopredict run -i examples/example_features.csv -o results/
+```
+
+```bash
+# Features only  -> output has just Incidence(%)
+salmopredict run -i features.csv -o results/ --model /path/to/model
+
+# With a Sample column  -> output has Sample, Incidence(%)
+salmopredict run -i examples/example_with_sample.csv -o results/
+
+# Attach metadata joined on the Sample key -> Sample, Incidence(%), + meta columns
+salmopredict run -i examples/example_with_sample.csv -o results/ \
+  --attach examples/example_meta.csv
+
+# Launch the GUI, or check the environment/model
+salmopredict gui
+salmopredict check --model /path/to/model
+```
+
+Each run writes one `pred_<input-stem>.csv` to the output directory; the
+prediction column is `Incidence(%)`. Features filled with `0` (genes the model
+expects but the input lacks) are always reported, and a prominent warning
+appears when more than `--missing-warn-frac` (default 0.3) of the model's
+features are missing.
+
+## License
+
+Licensed under the [Apache License, Version 2.0](LICENSE). Developed at the State
+Key Laboratory of Veterinary Public Health and Safety, China Agricultural
+University, in collaboration with the China National Center for Food Safety Risk
+Assessment (CFSA).
+
+<p align="center">
+  <img src="https://raw.githubusercontent.com/shaodongyan/SalmoPredict/main/salmopredict/gui/assets/vphs_logo.png" alt="State Key Laboratory of Veterinary Public Health and Safety" width="360">
+</p>

salmopredict-0.1.0/environment.yml

@@ -0,0 +1,16 @@
+name: salmopredict
+channels:
+  - conda-forge
+dependencies:
+  # Conda provides only Python (matched to the model's pickle version); the
+  # AutoGluon stack is installed via pip below, because conda-installed
+  # autogluon does not resolve cleanly for this project.
+  - python=3.10
+  - pip
+  - pip:
+      - autogluon.tabular==1.1.1
+      - pandas>=2.0
+      - openpyxl>=3.0
+      - rich-argparse>=1.4
+      - streamlit>=1.30
+      - -e .

salmopredict-0.1.0/examples/example_features.csv

@@ -0,0 +1,11 @@
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salmopredict-0.1.0/examples/example_meta.csv

@@ -0,0 +1,11 @@
+Sample,serotype,dose_cfu,source,region
+S001,Enteritidis,500,retail chicken,North
+S002,Enteritidis,1000,retail pork,East
+S003,Enteritidis,2000,retail beef,South
+S004,Enteritidis,10000,retail chicken,Central
+S005,Enteritidis,100000,retail pork,West
+S006,Typhimurium,500,retail chicken,North
+S007,Typhimurium,1000,retail pork,East
+S008,Typhimurium,2000,retail beef,South
+S009,Typhimurium,10000,retail chicken,Central
+S010,Typhimurium,100000,retail pork,West

salmopredict-0.1.0/examples/example_with_sample.csv

@@ -0,0 +1,11 @@
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salmopredict-0.1.0/pyproject.toml

@@ -0,0 +1,45 @@
+[build-system]
+requires = ["setuptools>=64", "wheel"]
+build-backend = "setuptools.build_meta"
+
+[project]
+name = "salmopredict"
+version = "0.1.0"
+description = "AutoGluon-based Incidence predictor for Salmonella virulence-factor gene-frequency features"
+readme = "README.md"
+# Pinned to 3.10 to match the Python version the bundled model was pickled with.
+requires-python = ">=3.10,<3.11"
+license = { text = "Apache-2.0" }
+authors = [{ name = "Dongyan Shao", email = "563608176@qq.com" }]
+keywords = ["salmonella", "incidence", "autogluon", "prediction", "bioinformatics"]
+classifiers = [
+    "License :: OSI Approved :: Apache Software License",
+    "Programming Language :: Python :: 3",
+    "Topic :: Scientific/Engineering :: Bio-Informatics",
+]
+dependencies = [
+    "autogluon.tabular==1.1.1",
+    "pandas>=2.0",
+    "openpyxl>=3.0",
+    "rich-argparse>=1.4",
+]
+
+[project.optional-dependencies]
+gui = ["streamlit>=1.30"]
+
+[project.urls]
+Homepage = "https://github.com/shaodongyan/SalmoPredict"
+Repository = "https://github.com/shaodongyan/SalmoPredict"
+Issues = "https://github.com/shaodongyan/SalmoPredict/issues"
+
+[project.scripts]
+salmopredict = "salmopredict.cli:main"
+
+[tool.setuptools]
+packages = ["salmopredict", "salmopredict.core", "salmopredict.gui"]
+
+[tool.setuptools.package-data]
+"salmopredict.gui" = ["assets/*.png"]
+# Ship the ~30 MB slim deployment model inside the wheel so `pip install
+# salmopredict` works out of the box -- no extra download and no --model flag.
+"salmopredict" = ["models/**"]

salmopredict-0.1.0/salmopredict/__init__.py

@@ -0,0 +1,30 @@
+"""salmopredict: predict Salmonella Incidence from virulence-factor gene features.
+
+Given a feature table of Salmonella virulence-factor gene presence/frequency,
+salmopredict:
+
+1. Aligns the input columns to the features expected by a pre-trained AutoGluon
+   TabularPredictor (normalising R-``make.names``-style column names and filling
+   genes the model expects but the input lacks with zero).
+2. Runs the ``WeightedEnsemble_L2`` model to predict the ``Incidence`` target.
+3. Writes one prediction file (``Incidence(%)``, plus a ``Sample`` column and any
+   attached metadata when the input carries a ``Sample`` column).
+
+The same core is shared by a command-line interface and a Streamlit GUI.
+"""
+
+__version__ = "0.1.0"
+
+# One-paragraph summary shown in both the CLI help and the GUI, so the two
+# interfaces describe the tool with identical wording.
+DESCRIPTION = (
+    "salmopredict predicts Salmonella incidence from virulence-factor "
+    "gene-frequency features and provides both command-line and graphical "
+    "interfaces. It standardizes the input feature table and outputs per-row "
+    "incidence predictions. salmopredict was developed at the State Key "
+    "Laboratory of Veterinary Public Health and Safety, China Agricultural "
+    "University, in collaboration with the China National Center for Food Safety "
+    "Risk Assessment (CFSA)."
+)
+
+__all__ = ["__version__", "DESCRIPTION"]