Command-line reference

NAME
       bigrapher-format - Automatically reformat a model.

SYNOPSIS
       bigrapher format [OPTION]… [FILE]

ARGUMENTS
       FILE
           Input model. Read from stdin if omitted.

OPTIONS
       -c ASSIGNMENT, --const=ASSIGNMENT
           Specify a comma-separated list of variable assignments. Example:
           x=4,t=.56.

       --debug
           Print extra diagnostic information (e.g. internal statistics).
           Disables coloured output.

       -N, --norm
           Enable model normalisation, i.e. rules, predicates, and actions
           are sorted in lexicographic order within the [aps]?brs block.

       -n, --no-colors (absent NO_COLOR env)
           Disable colored output.

       --no_comments, --no-comments
           Remove comments from the formatted model.

       -o FILE, --output=FILE
           Export the formatted model to FILE. Write to stdout if omitted.

       -q, --quiet (absent BIGQUIET env)
           Suppress diagnostic messages; the formatted model is still
           written. Flag --verbose is ignored if set.

       -v, --verbose (absent BIGVERBOSE env)
           Print file output status messages (exporting, saving) and
           operational detail (e.g. file sizes). By default only errors and
           results are printed.

       -W INT, --wrap=INT (absent=80)
           Set the line-wrap to INT.

       -w, --warnings
           Enable all warning families. Use --warn-family for fine-grained
           control over individual families.

       --warn-family=FAMILIES
           Enable specific warning families (comma-separated, e.g.
           W001,W003). Takes precedence over --warnings. Can be used in any
           command (including format). Use 'none' to disable all warnings
           (e.g. --warn-family=none).

COMMON OPTIONS
       --help[=FMT] (default=auto)
           Show this help in format FMT. The value FMT must be one of auto,
           pager, groff or plain. With auto, the format is pager or plain
           whenever the TERM env var is dumb or undefined.

       --version
           Show version information.

EXIT STATUS
       bigrapher format exits with:

       0   on success.

       1   on model errors (parse, validation, type, flag mismatch), export
           failures, or missing external dependencies (e.g. `dot').

       124 on command line parsing errors.

       125 on unexpected internal errors (bugs).

ENVIRONMENT
       These environment variables affect the execution of bigrapher format:

       BIGQUIET
           Suppress diagnostic messages; the formatted model is still
           written. Flag --verbose is ignored if set.

       BIGVERBOSE
           Print file output status messages (exporting, saving) and
           operational detail (e.g. file sizes). By default only errors and
           results are printed.

       NO_COLOR
           Disable colored output.

EXAMPLES
       Reformat a model to 100 columns:

         bigrapher format --wrap=100 model.big

       Reformat and normalise declaration order:

         bigrapher format --norm model.big

       Remove comments and write to a new file:

         bigrapher format --no-comments --output=model.clean.big model.big

WARNING FAMILIES
       BigraphER reports warnings about model issues. Warnings are grouped
       into families, each identified by a code (e.g. W001).

       By default, warnings are disabled in all commands except validate,
       where all families are enabled. --warnings (alias -w) enables all
       warning families. --warn-family enables only the specified families
       (comma-separated, e.g. --warn-family=W001,W003). If both flags are
       given, --warn-family takes precedence. --warn-family can be used in
       any command (including format). Use 'none' to disable all warnings.

       W001
           Unused declarations -- A reaction rule, control, or bigraph
           binding is defined but never used.

       W002
           Multiple declarations -- An identifier was declared more than
           once.

       W003
           No rules enabled from initial state -- The model will produce no
           transitions. Only reported during full and sim.

       W004
           Trivial instantiation map -- An instantiation map is the identity
           map, which is implicit and therefore unnecessary.

       W005
           CLI override -- A value provided via --const overrides a
           declaration in the model.

       W006
           Unused numeric declarations -- An integer, float, string, or
           parameter declaration is defined but never used.

       W007
           Large parameter domain -- A parameter domain (range or set)
           generates many values (>50), which may cause combinatorial
           explosion with parameterised declarations.

       W008
           Combinatorial explosion -- A parameterised declaration (fun react,
           fun big) is instantiated over BRS parameter domains whose product
           of sizes is large, materialising many rules.

       W009
           Large rule LHS -- A rule's left-hand side is large (size >=50),
           which is expensive to match.

       W012
           Identity rewrite step -- A reaction rule's LHS and RHS are
           isomorphic, so the rewrite step produces no structural change.

       W014
           Contradictory conditions -- The same predicate appears both
           positively and negatively in a rule's conditions, making the rule
           never fire.

       W015
           Unused parameters -- A functional rule (fun react or fun big)
           declares parameters that are not used in its body, rate, or
           conditions.

       W018
           Excessive condition count -- A rule has an unusually large number
           of conditions (>=5), which may indicate it is overly complex.

       W020
           Duplicate conditions -- The same condition appears multiple times
           in a rule's conditions, which is redundant.

       W022
           Degenerate bracket guard -- A bracket guard [$ = C] (or [v: $ = C]
           when the capture is labelled) is provably always true (the
           captured value always satisfies it, so the guard is redundant) or
           always false (no value satisfies it, so the rule can never fire).
           Feasibility is decided over the integers when the captured value
           is int-typed, over the reals otherwise; a guard that is linear
           apart from an absolute value of the captured value is also
           decided, by a split into the sign cases of each [abs]. A
           string-typed guard, which can only compare the captured value for
           equality, is decided over the string constants it contains plus
           the class of all other strings.

       W023
           Jointly unsatisfiable bracket guards -- A rule has multiple
           brackets capturing the same value, and their guards together can
           never all be satisfied by a single value, so the rule can never
           fire.

       W024
           Non-linear bracket guard -- A bracket guard [$ = C] (or [v: $ = C]
           when the capture is labelled) is not affine in the captured value
           (it contains products or divisions of terms that reference the
           value). The guard is still matched at run time, but the W022/W023
           degenerate-guard check cannot analyse it.

       Warning family W003 is only reported during transition system
       computation (full and sim), since it requires a computed transition
       system to determine whether any rules are enabled from the initial
       state.

SEE ALSO
       bigrapher(1)