foodnet 0.1.0__tar.gz

foodnet-0.1.0/LICENSE

@@ -0,0 +1,201 @@
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foodnet-0.1.0/NOTICE

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+foodnet
+Copyright 2026 The foodnet authors (KU Leuven, Lab of Molecular Bacteriology).
+
+foodnet is derived in part from grownet (https://github.com/crossfeed-bio/crossfeed),
+Copyright 2026 The crossfeed authors, licensed under the Apache License, Version 2.0.
+
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foodnet-0.1.0/PKG-INFO

@@ -0,0 +1,182 @@
+Metadata-Version: 2.4
+Name: foodnet
+Version: 0.1.0
+Summary: Build taxon and metabolite networks (who produces and who consumes what) from mGrowthDB batch monocultures, with the parameters of a consumer-resource model.
+Author: KU Leuven, Lab of Molecular Bacteriology
+License-Expression: Apache-2.0
+Project-URL: Homepage, https://github.com/hallucigenia-sparsa/foodnet
+Project-URL: Repository, https://github.com/hallucigenia-sparsa/foodnet
+Keywords: metabolites,cross-feeding,consumer-resource-model,mGrowthDB,microbial-ecology,open-science
+Requires-Python: >=3.10
+Description-Content-Type: text/markdown
+License-File: LICENSE
+License-File: NOTICE
+Provides-Extra: dev
+Requires-Dist: pytest>=8; extra == "dev"
+Requires-Dist: ruff>=0.6; extra == "dev"
+Dynamic: license-file
+
+# foodnet: who produces and who consumes which metabolite
+
+[![ci](https://github.com/hallucigenia-sparsa/foodnet/actions/workflows/ci.yml/badge.svg)](https://github.com/hallucigenia-sparsa/foodnet/actions/workflows/ci.yml)
+[![license: Apache-2.0](https://img.shields.io/badge/license-Apache--2.0-blue.svg)](LICENSE)
+[![python: 3.10+](https://img.shields.io/badge/python-3.10%2B-blue.svg)](pyproject.toml)
+
+food**net** builds bipartite taxon and metabolite networks from the batch monocultures in
+[mGrowthDB](https://mgrowthdb.gbiomed.kuleuven.be/): which taxon produces which compound, and which consumes
+it, with the amount moved in each growth phase. It hands the result to Cytoscape, to graph formats, to two
+matrix formats, and to R as the parameters of a consumer-resource model (CRM), with
+[miaSim](https://bioconductor.org/packages/release/bioc/html/miaSim.html) as the example simulator.
+
+It is the sister tool of [grow**net**](https://github.com/crossfeed-bio/crossfeed), which builds
+interaction networks from co-cultures, and is built the same way: a thin client with no runtime
+dependencies, a local page and a command line, nothing hosted and nothing uploaded.
+
+## Contents
+
+- [Install](#install)
+- [Quickstart](#quickstart)
+- [What it does](#what-it-does)
+- [The outputs](#the-outputs)
+- [Consumer-resource models in R](#consumer-resource-models-in-r)
+- [The command line](#the-command-line)
+- [Guardrails](#guardrails)
+- [License](#license)
+
+## Install
+
+With [uv](https://docs.astral.sh/uv/), which fetches a suitable Python by itself:
+
+```bash
+uv tool install foodnet
+```
+
+or with pipx (`pipx install foodnet`), or from a clone (`pip install -e .`). Each release also carries
+`foodnet-<version>-windows.zip`, the whole program in one folder with Python included: unzip it and
+double-click `foodnet.exe`. Windows warns about a program few people have run yet; click the small "More
+info" link, then "Run anyway".
+
+## Quickstart
+
+```bash
+foodnet gui
+```
+
+opens the page in your browser. Type taxa in the first box (a species, a strain, a genus or an NCBI taxon
+id, one per line), or press Example, and press Get taxon-metabolite network. The consumed and produced
+matrices appear first under the settings, then the taxa and the arcs with the downloads.
+
+![the legend](docs/legend.svg)
+
+## What it does
+
+1. **Taxa to monocultures.** Names resolve to the strains mGrowthDB holds (a species name to all its
+   strains). food**net** reads every batch monoculture of those strains that has metabolite measurements.
+   A culture-level growth curve counts in a monoculture, since it measures the one strain.
+2. **Growth phases.** Exponential growth ends at the first sample where the culture reaches 90% of its
+   maximal abundance; the stationary phase runs from there to the last metabolite sample. Below the boxes,
+   choose Exponential phase (the default), Stationary phase or Both. A time window in Advanced settings
+   replaces the phases, and a second window can be given to metabolites named there (trehalose over the whole
+   run, for example), so no compound needs a window of its own. Diauxic shifts are not detected.
+3. **A change per phase.** For each replicate and metabolite, the concentration at the end of the phase
+   minus the concentration at its start (interpolated between samples), averaged over replicates. A mean
+   change below the detection limit (0.2 mM, a setting) is no change. A metabolite series shorter than
+   24 h is used, and flagged.
+4. **Values from one medium, presence from the others.** With the second box empty, all data are
+   considered: the values come from the medium that holds data for the most taxa, and every other medium
+   only says whether a compound was produced or consumed (`presence_only` arcs, NA matrix cells). A filled
+   second box limits the data to what matches it: study or experiment ids, or a medium name, which gives the
+   values from the medium it matches for the most taxa; with ids and no medium, the majority rule runs within
+   the ids. "Include supporting evidence outside the
+   second box" adds the rest as presence. Because mGrowthDB does not report a medium's composition
+   systematically, an experiment whose description says something was added or taken away ("WC plus mucin
+   beads", "without glucose", "+Ac"), or whose recorded atmosphere differs, counts as another medium; this
+   can be switched off, and experiments can be excluded by id. "Ignore media differences" pools
+   every medium; "Report everything as booleans" drops the amounts.
+5. **Pooling, with what does not agree reported.** Studies in the value medium are pooled. Experiments
+   that disagree on what happened make a `conflict`, named in the report. The same experiment deposited
+   under two studies is counted once.
+6. **Arcs.** A produced arc runs from the taxon to the metabolite, a consumed arc from the metabolite to
+   the taxon, and its width is the amount in mM. One arc per study by default; "Merge arcs across studies"
+   and "Merge to genus" are advanced settings, as in grow**net**.
+
+**What a taxon produces and consumes alone is not necessarily what it does in a community.** Competition,
+cross-feeding, pH and regulation all change it, so the network is a map of capabilities and candidate links,
+and a consumer-resource model built from it is a hypothesis to check against the community itself.
+
+Acid and base forms of one compound are one metabolite (acetic acid and acetate), since mGrowthDB records
+both and an HPLC measures one pool. A compound that was never assayed for a taxon is never written as zero.
+Every decision and its reason is in [docs/METHOD_NOTES.md](docs/METHOD_NOTES.md).
+
+## The outputs
+
+- **The matrices as an image**, shown first under the settings: consumed and produced side by side (or one
+  above the other when they are wide): a number on a gray for a change, white for
+  measured without one, pale orange for not assayed, an open circle for a change seen only in another medium.
+  Downloadable as SVG, and in the matrices zip. Hovering over a cell shows its value, its replicates and the
+  studies, experiments and medium behind it (also in the downloaded SVG, opened in a browser).
+- **Network**: JSON (the canonical format, [schema](schema/metabolite_network.schema.json)) or GraphML.
+- **Taxa x metabolites matrix** (CSV): one cell per taxon and metabolite, the mean change in mM, positive
+  when produced and negative when consumed.
+- **Consumed and produced matrices** (zip): two matrices of non-negative amounts, an evidence matrix for
+  each (`measured`, `below_limit`, `presence_only`, `not_assayed`), and a README.
+- **Send to Cytoscape**: the network in a running Cytoscape, in the style of the legend. A downloaded
+  GraphML takes the same style from `foodnet style`.
+- **Report**: every setting, every arc, and every record left out with its reason.
+
+Every arc also says how long its cultures grew exponentially (`exponential_h`, in hours), in the result
+table and in every file.
+
+In every matrix a number is a change beyond the detection limit, 0 is measured without one, and NA is no
+value. A change seen only in another medium is NA by default; Advanced settings can write it as TRUE or as
+the amount measured there (drawn on a background of its own in the image), and the evidence matrices mark
+it `presence_only` either way. With Both, each metabolite has a column per phase.
+
+## Consumer-resource models in R
+
+CRM mode collects growth rates: from the replicates whose metabolites gave the values, else from another
+monoculture in the same medium. Get CRM parameters then downloads the matrices, the growth rates and the
+initial medium concentrations, or sends them to R. Install the companion package once:
+
+```r
+remotes::install_github("hallucigenia-sparsa/foodnet", subdir = "r")
+```
+
+then:
+
+```r
+library(foodnet)
+crm <- foodnet_listen()          # and press Send to R on the page
+E <- crm_efficiency(crm)         # positive for consumption, negative for production
+args <- as_miasim(crm)           # stops if a taxon has no growth rate
+tse <- do.call(miaSim::simulateConsumerResource, c(args, list(t_end = 48, t_store = 100)))
+```
+
+The matrices are measured amounts, not model parameters: `crm_efficiency()` turns them into an efficiency
+matrix, and how to scale it is a modeling choice. With the phase choice Both, the CRM parameters use the
+exponential phase, since a consumer-resource model describes growth. See [r/README.md](r/README.md).
+
+## The command line
+
+```bash
+foodnet derive --taxa "Escherichia coli LF82" "Bacteroides fragilis" --out network.json --report report.txt
+foodnet derive --taxa Roseburia --phase both --format matrices --out roseburia.zip
+foodnet derive --taxa Blautia Roseburia --conditions "Wilkins-Chalgren" --crm-mode --crm crm.zip
+foodnet validate network.json
+```
+
+`foodnet derive --help` lists every option, with examples.
+
+## Guardrails
+
+The same as grow**net**'s: no real data in git (only synthetic fixtures under `tests/fixtures/`), no
+runtime dependencies, the network format is a contract checked against its schema, and `make check` runs
+lint, the guardrail gate and the tests, in CI and before every commit. See [AGENTS.md](AGENTS.md) and
+[CONTRIBUTING.md](CONTRIBUTING.md).
+
+Every arc cites the studies behind it, so attribution resolves at the arc level; see
+[docs/DATA_GOVERNANCE.md](docs/DATA_GOVERNANCE.md).
+
+## License
+
+Apache License 2.0; see [LICENSE](LICENSE) and [NOTICE](NOTICE).

foodnet-0.1.0/README.md

@@ -0,0 +1,164 @@
+# foodnet: who produces and who consumes which metabolite
+
+[![ci](https://github.com/hallucigenia-sparsa/foodnet/actions/workflows/ci.yml/badge.svg)](https://github.com/hallucigenia-sparsa/foodnet/actions/workflows/ci.yml)
+[![license: Apache-2.0](https://img.shields.io/badge/license-Apache--2.0-blue.svg)](LICENSE)
+[![python: 3.10+](https://img.shields.io/badge/python-3.10%2B-blue.svg)](pyproject.toml)
+
+food**net** builds bipartite taxon and metabolite networks from the batch monocultures in
+[mGrowthDB](https://mgrowthdb.gbiomed.kuleuven.be/): which taxon produces which compound, and which consumes
+it, with the amount moved in each growth phase. It hands the result to Cytoscape, to graph formats, to two
+matrix formats, and to R as the parameters of a consumer-resource model (CRM), with
+[miaSim](https://bioconductor.org/packages/release/bioc/html/miaSim.html) as the example simulator.
+
+It is the sister tool of [grow**net**](https://github.com/crossfeed-bio/crossfeed), which builds
+interaction networks from co-cultures, and is built the same way: a thin client with no runtime
+dependencies, a local page and a command line, nothing hosted and nothing uploaded.
+
+## Contents
+
+- [Install](#install)
+- [Quickstart](#quickstart)
+- [What it does](#what-it-does)
+- [The outputs](#the-outputs)
+- [Consumer-resource models in R](#consumer-resource-models-in-r)
+- [The command line](#the-command-line)
+- [Guardrails](#guardrails)
+- [License](#license)
+
+## Install
+
+With [uv](https://docs.astral.sh/uv/), which fetches a suitable Python by itself:
+
+```bash
+uv tool install foodnet
+```
+
+or with pipx (`pipx install foodnet`), or from a clone (`pip install -e .`). Each release also carries
+`foodnet-<version>-windows.zip`, the whole program in one folder with Python included: unzip it and
+double-click `foodnet.exe`. Windows warns about a program few people have run yet; click the small "More
+info" link, then "Run anyway".
+
+## Quickstart
+
+```bash
+foodnet gui
+```
+
+opens the page in your browser. Type taxa in the first box (a species, a strain, a genus or an NCBI taxon
+id, one per line), or press Example, and press Get taxon-metabolite network. The consumed and produced
+matrices appear first under the settings, then the taxa and the arcs with the downloads.
+
+![the legend](docs/legend.svg)
+
+## What it does
+
+1. **Taxa to monocultures.** Names resolve to the strains mGrowthDB holds (a species name to all its
+   strains). food**net** reads every batch monoculture of those strains that has metabolite measurements.
+   A culture-level growth curve counts in a monoculture, since it measures the one strain.
+2. **Growth phases.** Exponential growth ends at the first sample where the culture reaches 90% of its
+   maximal abundance; the stationary phase runs from there to the last metabolite sample. Below the boxes,
+   choose Exponential phase (the default), Stationary phase or Both. A time window in Advanced settings
+   replaces the phases, and a second window can be given to metabolites named there (trehalose over the whole
+   run, for example), so no compound needs a window of its own. Diauxic shifts are not detected.
+3. **A change per phase.** For each replicate and metabolite, the concentration at the end of the phase
+   minus the concentration at its start (interpolated between samples), averaged over replicates. A mean
+   change below the detection limit (0.2 mM, a setting) is no change. A metabolite series shorter than
+   24 h is used, and flagged.
+4. **Values from one medium, presence from the others.** With the second box empty, all data are
+   considered: the values come from the medium that holds data for the most taxa, and every other medium
+   only says whether a compound was produced or consumed (`presence_only` arcs, NA matrix cells). A filled
+   second box limits the data to what matches it: study or experiment ids, or a medium name, which gives the
+   values from the medium it matches for the most taxa; with ids and no medium, the majority rule runs within
+   the ids. "Include supporting evidence outside the
+   second box" adds the rest as presence. Because mGrowthDB does not report a medium's composition
+   systematically, an experiment whose description says something was added or taken away ("WC plus mucin
+   beads", "without glucose", "+Ac"), or whose recorded atmosphere differs, counts as another medium; this
+   can be switched off, and experiments can be excluded by id. "Ignore media differences" pools
+   every medium; "Report everything as booleans" drops the amounts.
+5. **Pooling, with what does not agree reported.** Studies in the value medium are pooled. Experiments
+   that disagree on what happened make a `conflict`, named in the report. The same experiment deposited
+   under two studies is counted once.
+6. **Arcs.** A produced arc runs from the taxon to the metabolite, a consumed arc from the metabolite to
+   the taxon, and its width is the amount in mM. One arc per study by default; "Merge arcs across studies"
+   and "Merge to genus" are advanced settings, as in grow**net**.
+
+**What a taxon produces and consumes alone is not necessarily what it does in a community.** Competition,
+cross-feeding, pH and regulation all change it, so the network is a map of capabilities and candidate links,
+and a consumer-resource model built from it is a hypothesis to check against the community itself.
+
+Acid and base forms of one compound are one metabolite (acetic acid and acetate), since mGrowthDB records
+both and an HPLC measures one pool. A compound that was never assayed for a taxon is never written as zero.
+Every decision and its reason is in [docs/METHOD_NOTES.md](docs/METHOD_NOTES.md).
+
+## The outputs
+
+- **The matrices as an image**, shown first under the settings: consumed and produced side by side (or one
+  above the other when they are wide): a number on a gray for a change, white for
+  measured without one, pale orange for not assayed, an open circle for a change seen only in another medium.
+  Downloadable as SVG, and in the matrices zip. Hovering over a cell shows its value, its replicates and the
+  studies, experiments and medium behind it (also in the downloaded SVG, opened in a browser).
+- **Network**: JSON (the canonical format, [schema](schema/metabolite_network.schema.json)) or GraphML.
+- **Taxa x metabolites matrix** (CSV): one cell per taxon and metabolite, the mean change in mM, positive
+  when produced and negative when consumed.
+- **Consumed and produced matrices** (zip): two matrices of non-negative amounts, an evidence matrix for
+  each (`measured`, `below_limit`, `presence_only`, `not_assayed`), and a README.
+- **Send to Cytoscape**: the network in a running Cytoscape, in the style of the legend. A downloaded
+  GraphML takes the same style from `foodnet style`.
+- **Report**: every setting, every arc, and every record left out with its reason.
+
+Every arc also says how long its cultures grew exponentially (`exponential_h`, in hours), in the result
+table and in every file.
+
+In every matrix a number is a change beyond the detection limit, 0 is measured without one, and NA is no
+value. A change seen only in another medium is NA by default; Advanced settings can write it as TRUE or as
+the amount measured there (drawn on a background of its own in the image), and the evidence matrices mark
+it `presence_only` either way. With Both, each metabolite has a column per phase.
+
+## Consumer-resource models in R
+
+CRM mode collects growth rates: from the replicates whose metabolites gave the values, else from another
+monoculture in the same medium. Get CRM parameters then downloads the matrices, the growth rates and the
+initial medium concentrations, or sends them to R. Install the companion package once:
+
+```r
+remotes::install_github("hallucigenia-sparsa/foodnet", subdir = "r")
+```
+
+then:
+
+```r
+library(foodnet)
+crm <- foodnet_listen()          # and press Send to R on the page
+E <- crm_efficiency(crm)         # positive for consumption, negative for production
+args <- as_miasim(crm)           # stops if a taxon has no growth rate
+tse <- do.call(miaSim::simulateConsumerResource, c(args, list(t_end = 48, t_store = 100)))
+```
+
+The matrices are measured amounts, not model parameters: `crm_efficiency()` turns them into an efficiency
+matrix, and how to scale it is a modeling choice. With the phase choice Both, the CRM parameters use the
+exponential phase, since a consumer-resource model describes growth. See [r/README.md](r/README.md).
+
+## The command line
+
+```bash
+foodnet derive --taxa "Escherichia coli LF82" "Bacteroides fragilis" --out network.json --report report.txt
+foodnet derive --taxa Roseburia --phase both --format matrices --out roseburia.zip
+foodnet derive --taxa Blautia Roseburia --conditions "Wilkins-Chalgren" --crm-mode --crm crm.zip
+foodnet validate network.json
+```
+
+`foodnet derive --help` lists every option, with examples.
+
+## Guardrails
+
+The same as grow**net**'s: no real data in git (only synthetic fixtures under `tests/fixtures/`), no
+runtime dependencies, the network format is a contract checked against its schema, and `make check` runs
+lint, the guardrail gate and the tests, in CI and before every commit. See [AGENTS.md](AGENTS.md) and
+[CONTRIBUTING.md](CONTRIBUTING.md).
+
+Every arc cites the studies behind it, so attribution resolves at the arc level; see
+[docs/DATA_GOVERNANCE.md](docs/DATA_GOVERNANCE.md).
+
+## License
+
+Apache License 2.0; see [LICENSE](LICENSE) and [NOTICE](NOTICE).

foodnet-0.1.0/pyproject.toml

@@ -0,0 +1,41 @@
+[build-system]
+requires = ["setuptools>=77"]
+build-backend = "setuptools.build_meta"
+
+[project]
+name = "foodnet"
+version = "0.1.0"
+description = "Build taxon and metabolite networks (who produces and who consumes what) from mGrowthDB batch monocultures, with the parameters of a consumer-resource model."
+readme = "README.md"
+requires-python = ">=3.10"
+license = "Apache-2.0"
+license-files = ["LICENSE", "NOTICE"]
+authors = [
+    { name = "KU Leuven, Lab of Molecular Bacteriology" },
+]
+keywords = ["metabolites", "cross-feeding", "consumer-resource-model", "mGrowthDB", "microbial-ecology", "open-science"]
+dependencies = []
+
+[project.optional-dependencies]
+dev = ["pytest>=8", "ruff>=0.6"]
+
+[project.urls]
+Homepage = "https://github.com/hallucigenia-sparsa/foodnet"
+Repository = "https://github.com/hallucigenia-sparsa/foodnet"
+
+[project.scripts]
+foodnet = "foodnet.__main__:main"
+
+[tool.setuptools.packages.find]
+where = ["src"]
+
+[tool.pytest.ini_options]
+pythonpath = ["src", "."]
+testpaths = ["tests"]
+
+[tool.ruff]
+line-length = 120
+target-version = "py310"
+
+[tool.ruff.lint]
+select = ["E", "F", "I", "W", "B", "UP"]

foodnet-0.1.0/setup.cfg

@@ -0,0 +1,4 @@
+[egg_info]
+tag_build = 
+tag_date = 0
+

foodnet-0.1.0/src/foodnet/__init__.py

@@ -0,0 +1,3 @@
+"""foodnet: bipartite taxon and metabolite networks from mGrowthDB batch monocultures."""
+
+__version__ = "0.1.0"