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jaffgen

jaffgen is JAFF's command-line entry point for the full code-generation pipeline. It gathers a set of template files, loads a chemical reaction network, runs the template engine over each file, and writes the generated source into an output directory.

jaffgen --network <file> [options]

How it works

A jaffgen run is four phases:

  1. Resolve configuration — merge three sources by priority (see below): explicit CLI flags, a jaff.toml file, then Network constructor defaults.
  2. Gather template files — from --indir, --files, and --template. These combine — a single run can pull from all three.
  3. Load the network — exactly one Network, built from the resolved network/label/funcfile/radiation settings.
  4. Generate — run TemplateParser on every gathered file and write the result to --outdir, keeping the original filename.

The mental model: jaffgen is the template engine driven over a file set with one loaded network behind it.

Input sources

The three input flags are additive, not exclusive:

Flag Adds
--indir Every file in a directory (non-recursive)
--files Specific individual files
--template A built-in collection from jaff/templates/generator/<name>/

For --template, generator files are collected first; any preprocessor file (jaff/templates/preprocessor/<name>/) whose name does not clash is appended — so the generator always wins on a name collision.

Arguments

Network and network options

Argument Description
--network Network file path or a built-in network name; required (CLI or jaff.toml)
--label Override the network label (defaults to the file stem)
--funcfile Path to a .jfunc auxiliary file; auto-detected when omitted; "none" to skip
--replace-nH --replace-nH / --no-replace-nH — expand nh/nhe shorthands (default: on)
--errors --errors / --no-errors — exit on conservation violations instead of warning

When --network is a bare name (a sub-directory of networks/), jaffgen picks the first .jet file inside it.

Output

Argument Description
--outdir Output directory (created if absent; defaults to <repo>/generated/)

Input sources

Argument Description
--indir Directory of template files
--files One or more individual template files (space-separated)
--template Built-in template collection name

Code generation

Argument Description
--lang Fallback language for files with unrecognised extensions. Choices: c, cxx, fortran, python, rust, julia

Configuration file

Argument Description
--config Path to a jaff.toml; also auto-detected if a jaff.toml is among the gathered files

Configuration priority

Each setting is resolved highest-wins:

  1. Explicit CLI flag (e.g. --network)
  2. jaff.toml value (from --config, or auto-detected)
  3. Network constructor default

Paths taken from a jaff.toml are resolved relative to the config file's directory; paths given on the CLI are resolved relative to the current directory.

Examples

Generate from a template directory

jaffgen \
    --network networks/GOW/GOW.jet \
    --indir   templates/           \
    --outdir  output/

For predefined networks, the folder name can also be passed as the network

jaffgen \
    --network GOW                  \
    --indir   templates/           \
    --outdir  output/

Process specific files with a language hint

--lang supplies a language for files whose extension JAFF doesn't map (here, .txt):

jaffgen \
    --network networks/GOW/GOW.jet \
    --files   rates.txt odes.txt   \
    --lang    rust                 \
    --outdir  output/

Use a built-in template collection

jaffgen \
    --network  networks/GOW/GOW.jet \
    --template microphysics         \
    --lang     cxx                  \
    --outdir   output/

Templates that bundle build files need --lang

The microphysics collection ships non-source files (e.g. Make.package and an extension-less _parameters) alongside its .cpp/.H templates. TemplateParser infers the language from each file's extension and has no fallback for unknown ones, so pass --lang cxx to give it one. Without it the run aborts with "files are not yet supported".

Combine a template collection with custom files

jaffgen \
    --network  networks/GOW/GOW.jet \
    --template microphysics         \
    --files    custom_rhs.cpp       \
    --lang     cxx                  \
    --outdir   output/

Drive everything from a config file

A jaff.toml can carry the network, inputs, output, and radiation settings, so the command collapses to:

jaffgen --config jaff.toml

A bundled template can even supply its own config. The microphysics collection ships a jaff.toml with a [radiation] block, so --template microphysics auto-detects it and turns on photochemistry without any extra flags. See jaff.toml for the full schema.

Built-in templates

Collections live under src/jaff/templates/generator/. List them with:

ls src/jaff/templates/generator/