Documentation/fix docstrings#260

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Maximilian-Stefan-Ernst merged 218 commits intomainfrom

documentation/fix_docstrings

Apr 15, 2025

Commits on Apr 23, 2024

Commits on Apr 24, 2024

Merge pull request #202 from alyst/spec_matrices
Maximilian-Stefan-Ernst
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Commits on May 27, 2024

SemSpecification base type
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SemSpecification: use in methods
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rename identifier -> param
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ParTable: columns[:identifier] => columns[:param]
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getindex(EnsParTable, i) instead of get_group()

Alexey Stukalov
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replace no-op ctors with convert(T, obj)

Alexey Stukalov
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ParamTable: convert vars from Dict to fields
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ParamTable: update StenGraph-based ctor

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rename Base.sort() to sort_vars()

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don't import ==

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don't import push!()

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don't import DataFrame
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remove no-op push!()

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ParTable ctor: simplify rows code
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ParTable: full support for Iterator iface
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RAMConstant: simplify

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RAMMatrices: optimize F_indices init

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RAMMatrices: declare types for all fields

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RAMMatrices: option to keep zero constants

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nonunique() helper function

Alexey Stukalov
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add check_vars() and check_params()
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RAMMatrices ctor: dims and vars checks
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RAMMatrices: cleanup params index
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include RAMMatrices before EnsParTable
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fix EnsParTable to Dict{RAMMatrices} convert

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DataFrame(EnsParTable)

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params() API method
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EnsParTable ctor: enforce same params in tables

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formatting fixes
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ParTable ctor: allow providing columns data
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update_partable!() cleanup + docstring
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update_partable!(): SemFit methods use basic one
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ParTable: add explicit params field
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n_par() -> nparams()

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param_values(ParTable)

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lavaan_param_values(lav_fit, partable)
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compare_estimates() -> test_estimates()
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update_partable!(): dict-based generic version

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ParTable: getindex() returns NamedTuple
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ParTable: graph-based ctor supports params= kw
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rename parameter_type to relation
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sem_summary(): cleanup filters
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fix sem_summary method for partable

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show(ParTable): suppress NaNs
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sort_vars!(ParTable): cleanup
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Project.toml: disable SymbolicUtils 1.6
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Project.toml: support StenoGraphs 0.3
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RAM ctor: better error for missing meanstruct

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add function param_indices

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start fixing docs

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fix regularization docs

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introduce formatting error

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update_start(): fix docstring typo

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push!(::ParTable, Tuple): check keys compat

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SemObsCov ctor: restrict n_obs to integer
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fixup param_indices()
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Commits on May 31, 2024

Merge pull request #203 from alyst/refactor_semspec
Maximilian-Stefan-Ernst
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Commits on Jul 30, 2024

common.jl: common vars API methods
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SemSpecification: vars API
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RAMMatrices: vars API

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ParamTable: vars API
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SemImply: vars and params API
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RAM imply: use vars API

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RAMSymbolic: use vars API

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start_simple(): use vars API

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starts_fabin3: use vars API

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remove get_colnames()

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remove get_n_nodes()

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get_data() -> samples()
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SemObsData: remove rowwise
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AbstractSemSingle: vars API
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rename n_obs() -> nsamples()
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rename n_man() -> nobserved_vars()
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move Sem methods out of types.jl
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rows(::SemObservedMissing) -> pattern_rows()
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fix formatting
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samples(SemObsCov) throws an exception
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SemObserved tests: refactor and add var API tests
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ParTable(graph): group is only valid for ensemble
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ParTable(graph): fix NaN modif detection
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export vars, params and observed APIs
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refactor SemSpec tests
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add Sem unit tests
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Commits on Jul 31, 2024

Commits on Aug 7, 2024

Commits on Aug 11, 2024

remove get_observed()
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fix ridge eval

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MeanStructure, HessianEvaluation traits

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obj/grad/hess: refactor evaluation API
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se_hessian(): rename hessian -> method
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se_hessian!(): optimize calc

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H_scaling(): cleanup
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SemOptOptim: remove redundant sem_fit()
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SemOptNLopt: remove redundant sem_fit()
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SemOptOptim: use evaluate!() directly
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SemOptNLopt: use evaluate!() directly
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SemWLS: dim checks

Alexey Stukalov
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fixup formatting
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WLS: use 5-arg mul!()

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ML: use 5-arg mul!()

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FIML: use 5-arg mul!

Alexey Stukalov
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Commits on Aug 14, 2024

fix the error message

alyst
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Maximilian-Stefan-Ernst
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Commits on Oct 8, 2024

Commits on Nov 22, 2024

Project.toml: update Symbolics deps

Alexey Stukalov
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tests/examples: import -> using
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add ParamsArray
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materialize!(Symm/LowTri/UpTri)

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ParamsArray: faster sparse materialize!

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ParamsArray: use Iterators.flatten() (faster)

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Base.hash(::ParamsArray)
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colnames -> vars
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update_partable!(): better params unique check

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start_fabin3: check obs_mean data & meanstructure
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params/vars API tweaks and tests
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generic imply: keep F sparse

Alexey Stukalov
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Commits on Nov 23, 2024

Merge pull request #219 from alyst/params_array
Maximilian-Stefan-Ernst
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Commits on Dec 20, 2024

tests helper: is_extended_tests()

Alexey Stukalov
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Optim sem_fit(): use provided optimizer

Alexey Stukalov
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prepare_start_params(): arg-dependent dispatch
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prepare_param_bounds() API for optim
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u/l_bounds support for Optim.jl
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SemOptimizer(engine = ...) ctor
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SEMNLOptExt for NLopt

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NLopt: sem_fit(): use provided optimizer
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SEMProximalOptExt for Proximal opt
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merge diff/*.jl optimizer code into optimizer/*.jl
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Optim: document u/l bounds
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remove unused options field from Proximal optimizer

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decouple optimizer from Sem model

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fix inequality constraints test
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add ProximalSEM tests

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optim/documentation.jl: rename to abstract.jl
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ext: change folder layout
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Commits on Dec 22, 2024

Merge pull request #228 from alyst/optim_extensions
Maximilian-Stefan-Ernst
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Commits on Dec 25, 2024

Commits on Jan 1, 2025

SemObservedCov: def as an alias of SemObservedData
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SemObserved: store observed_vars

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nsamples(observed::SemObserved): unify

Alexey Stukalov
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FIML: simplify index generation
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SemObservedMissing: refactor
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remove cov_and_mean(): not used anymore
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SemObserved: unify data preparation

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tests: update SemObserved tests
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prep_data: warn if obs_vars order don't match spec
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SemObsData: observed_var_prefix kwarg
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Commits on Jan 6, 2025

ParTable: add graph-based kw-only constructor

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Project.toml: fix ProximalAlgorithms to 0.5
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Commits on Jan 9, 2025

Commits on Feb 2, 2025

Commits on Feb 4, 2025

Commits on Mar 17, 2025

Rename params (#253)

aaronpeikert
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Maximilian-Stefan-Ernst
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Commits on Apr 14, 2025

merge main into devel
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