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Check for all functions that documentation and tests agree #215

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gustavdelius opened this issue Aug 21, 2021 · 0 comments
Open

Check for all functions that documentation and tests agree #215

gustavdelius opened this issue Aug 21, 2021 · 0 comments
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code improvement This issue relates to code quality rather than user-facing features documentation Issue relates to documentation help wanted We are looking for someone to help with this issue

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@gustavdelius
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gustavdelius commented Aug 21, 2021

Every aspect of a function that is documented should be tested. That way we will never break things unexpectedly that the user has a right to expect will work. I expect that we will need to add a lot more tests.

Conversely, if a behaviour is being tested, then that behaviour should be something the reader of the documentation will expect. I suspect that while looking over the tests we will get ideas of how to clarify the documentation.

Here is an alphabetical list of currently exported functions, so that we can check off any where we are happy with both documentation and tests.

  • addSpecies
  • animateSpectra
  • BevertonHoltRDD
  • box_pred_kernel
  • compareParams
  • constant_other
  • constantEggRDI
  • constantRDD
  • customFunction
  • default_pred_kernel_params
  • distanceMaxRelRDI
  • distanceSSLogN
  • double_sigmoid_length
  • dw
  • dw_full
  • emptyParams
  • finalN
  • finalNOther
  • finalNResource
  • gear_params
  • get_f0_default
  • get_gamma_default
  • get_h_default
  • get_initial_n
  • get_ks_default
  • get_phi
  • get_size_range_array
  • get_time_elements
  • getBiomass
  • getCatchability
  • getColours
  • getCommunitySlope
  • getComponent
  • getCriticalFeedingLevel
  • getDiet
  • getEffort
  • getEGrowth
  • getEncounter
  • getERepro
  • getEReproAndGrowth
  • getESpawning
  • getExtMort
  • getFeedingLevel
  • getFMort
  • getFMortGear
  • getGrowthCurves
  • getInitialEffort
  • getInteraction
  • getLinetypes
  • getM2
  • getM2Background
  • getMaturityProportion
  • getMaxIntakeRate
  • getMeanMaxWeight
  • getMeanWeight
  • getMetabolicRate
  • getMort
  • getN
  • getParams
  • getPhiPrey
  • getPredKernel
  • getPredMort
  • getPredRate
  • getProportionOfLargeFish
  • getRateFunction
  • getRates
  • getRDD
  • getRDI
  • getReproductionLevel
  • getReproductionProportion
  • getResourceCapacity
  • getResourceDynamics
  • getResourceMort
  • getResourceRate
  • getSearchVolume
  • getSelectivity
  • getSSB
  • getTimes
  • getYield
  • getYieldGear
  • getZ
  • idxFinalT
  • initialN
  • initialNOther
  • initialNResource
  • knife_edge
  • log_breaks
  • lognormal_pred_kernel
  • melt
  • mizerEGrowth
  • mizerEncounter
  • mizerERepro
  • mizerEReproAndGrowth
  • mizerFeedingLevel
  • mizerFMort
  • mizerFMortGear
  • mizerMort
  • MizerParams
  • mizerPredMort
  • mizerPredRate
  • mizerRates
  • mizerRDI
  • mizerResourceMort
  • MizerSim
  • N
  • newCommunityParams
  • newMultispeciesParams
  • newSingleSpeciesParams
  • newTraitParams
  • noRDD
  • NOther
  • NResource
  • other_params
  • plotBiomass
  • plotDataFrame
  • plotDiet
  • plotFeedingLevel
  • plotFMort
  • plotGrowthCurves
  • plotlyBiomass
  • plotlyFeedingLevel
  • plotlyFMort
  • plotlyGrowthCurves
  • plotlyPredMort
  • plotlySpectra
  • plotlyYield
  • plotlyYieldGear
  • plotM2
  • plotPredMort
  • plotSpectra
  • plotYield
  • plotYieldGear
  • power_law_pred_kernel
  • project
  • project_simple
  • projectToSteady
  • removeComponent
  • removeSpecies
  • renameSpecies
  • resource_constant
  • resource_params
  • resource_semichemostat
  • RickerRDD
  • set_community_model
  • set_multispecies_model
  • set_species_param_default
  • set_trait_model
  • setBevertonHolt
  • setColours
  • setComponent
  • setExtMort
  • setFishing
  • setInitialValues
  • setInteraction
  • setLinetypes
  • setMaxIntakeRate
  • setMetabolicRate
  • setParams
  • setPredKernel
  • setRateFunction
  • setReproduction
  • setResource
  • setRmax
  • setSearchVolume
  • SheperdRDD
  • sigmoid_length
  • sigmoid_weight
  • species_params
  • steady
  • truncated_lognormal_pred_kernel
  • upgradeParams
  • upgradeSim
  • valid_species_arg
  • validEffortVector
  • validGearParams
  • validParams
  • validSpeciesParams
  • w
  • w_full
@gustavdelius gustavdelius added code improvement This issue relates to code quality rather than user-facing features documentation Issue relates to documentation help wanted We are looking for someone to help with this issue labels Aug 21, 2021
gustavdelius added a commit that referenced this issue Aug 21, 2021
…roposed in #215 and promptly found a bug.

The test checking that the new species stays at its low abundance is failing.
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Labels
code improvement This issue relates to code quality rather than user-facing features documentation Issue relates to documentation help wanted We are looking for someone to help with this issue
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