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Support julia 0.5 #135

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merged 5 commits into from
Mar 6, 2016
Merged

Support julia 0.5 #135

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2cf4a48
changes to get unit tests passing on julia nightly
jeff-regier Mar 5, 2016
df09781
replaced Exception with AssertionError, and required Compat for backw…
jeff-regier Mar 5, 2016
072a82c
changes to PR suggested by kyle
jeff-regier Mar 5, 2016
1c04180
fixing .travis file
jeff-regier Mar 5, 2016
23f0068
fixing travis again
jeff-regier Mar 5, 2016
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1 change: 1 addition & 0 deletions .travis.yml
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Expand Up @@ -3,6 +3,7 @@ os:
- linux
julia:
- 0.4
- nightly
notifications:
email: false

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1 change: 1 addition & 0 deletions REQUIRE
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@@ -1,4 +1,5 @@
julia 0.4
Compat
DataFrames
Distributions
DocOpt
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2 changes: 1 addition & 1 deletion src/ModelInit.jl
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Expand Up @@ -464,7 +464,7 @@ function limit_to_object_data(
# Get the sources that overlap with this object.
relevant_sources = Int[]
for b = 1:length(blob), tile_sources in mp.tile_sources[b]
if s_original in tile_sources > 0
if s_original in tile_sources
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We probably didn't mean to compare a boolean to an int before, but for whatever reason 0.4 doesn't complain, while 0.5 stops.

relevant_sources = union(relevant_sources, tile_sources);
end
end
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1 change: 1 addition & 0 deletions src/Transform.jl
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Expand Up @@ -9,6 +9,7 @@ export DataTransform, ParamBounds, ParamBox, SimplexBox,
get_mp_transform, generate_valid_parameters, enforce_bounds!



################################
# Elementary functions.

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5 changes: 3 additions & 2 deletions src/elbo_kl.jl
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Expand Up @@ -72,9 +72,10 @@ function subtract_kl!{NumType <: Number}(
mp::ModelParams{NumType}, accum::SensitiveFloat{CanonicalParams, NumType};
calculate_derivs::Bool=true, calculate_hessian::Bool=true)


# The KL divergence as a function of the active source variational parameters.
function subtract_kl_value_wrapper{NumType <: Number}(vp_vec::Vector{NumType})
elbo_val = zero(NumType)
function subtract_kl_value_wrapper{NumType2 <: Number}(vp_vec::Vector{NumType2})
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This was causing a seg fault in 0.5, rather than an error

elbo_val = zero(NumType2)
vp_active = reshape(vp_vec, length(CanonicalParams), length(mp.active_sources))
for sa in 1:length(mp.active_sources)
vs = vp_active[:, sa]
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7 changes: 7 additions & 0 deletions test/runtests.jl
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@@ -1,5 +1,12 @@
#!/usr/bin/env julia

if VERSION > v"0.5.0-dev"
Pkg.checkout("Optim")
Pkg.checkout("DataFrames")
Pkg.rm("GaussianMixtures")
Pkg.clone("https://github.com/jeff-regier/GaussianMixtures.jl.git")
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These run-time changes to which packages are installed seem like a bad idea. Better to document in the README the requirements for running on v0.5.

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(and for travis, add these commands to .travis.yml)

end

using Celeste: Types, SampleData, Transform
import Celeste.Synthetic

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3 changes: 3 additions & 0 deletions test/test_derivatives.jl
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Expand Up @@ -16,6 +16,9 @@ else
end
end

const datadir = joinpath(Pkg.dir("Celeste"), "test", "data")
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I might be redefining a constant here, but it's nice to run just one file or tests without having to run all the tests. (Is there a better way?)

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Yes, just remove this. datadir is already defined in runtests.jl. All the test_*.jl files are included into that file, so they'll be in the same namespace/scope as datadir already: including just a subset of the test_*.jl files doesn't affect this.

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Oh I see, I can call runtests with ARGS now.



println("Running hessian tests.")


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8 changes: 5 additions & 3 deletions test/test_images.jl
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Expand Up @@ -4,12 +4,14 @@ using DataFrames
import SloanDigitalSkySurvey: SDSS, WCSUtils, PSF

using Celeste: Types, SampleData
import Celeste: ModelInit, SkyImages, ElboDeriv
import Celeste: ModelInit, SkyImages, ElboDeriv, Synthetic


println("Running SkyImages tests.")

field_dir = joinpath(dat_dir, "sample_field")
const datadir = joinpath(Pkg.dir("Celeste"), "test", "data")

field_dir = joinpath(datadir, "sample_field")
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There's no sample_field subdirectory in test/data anymore; the files are all in test/data.

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It's weird we have both dat_dir defined in SampleData.jl and datadir defined runtests.jl. SampleData.jl probably shouldn't know about the test data's location.

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It's weird we have both dat_dir defined in SampleData.jl and datadir
defined runtests.jl. SampleData.jl probably shouldn't know about the test
data's location.

I agree. Probably SampleData.jl should eventually be moved to tests, as its
not necessary for the core functionality in the app. This is something to
think about after SC though!

run_num = "003900"
camcol_num = "6"
field_num = "0269"
Expand Down Expand Up @@ -191,7 +193,7 @@ function test_set_patch_size()
end

srand(1)
blob0 = SkyImages.load_stamp_blob(dat_dir, "164.4311-39.0359");
blob0 = SkyImages.load_stamp_blob(datadir, "164.4311-39.0359");
img_size = 150
for b in 1:5
blob0[b].H, blob0[b].W = img_size, img_size
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2 changes: 1 addition & 1 deletion test/test_misc.jl
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Expand Up @@ -3,7 +3,7 @@ using Base.Test
import SloanDigitalSkySurvey: SDSS, WCSUtils

using Celeste: Types, SampleData
import Celeste: SkyImages, Util, ModelInit
import Celeste: SkyImages, Util, ModelInit, Synthetic


println("Running misc tests.")
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20 changes: 10 additions & 10 deletions test/test_transforms.jl
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Expand Up @@ -5,7 +5,7 @@ using Base.Test

using Celeste: Types, SampleData, Transform, SensitiveFloats
import Celeste: ModelInit, ElboDeriv

using Compat
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Sorry for removing all the using Compats in #134! I figured most were for 0.3->0.4 changes and thus no longer needed.

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Removing them before seemed like a good thing to do...I didn't realize how soon we'd need them again


function test_transform_sensitive_float()
blob, mp, body, tiled_blob = gen_two_body_dataset();
Expand Down Expand Up @@ -280,13 +280,13 @@ function test_transform_simplex_functions()
this_scale * Transform.unsimplexify_parameter(param, unscaled_simplex_box))

# Test the bound checking
@test_throws(Exception,
@test_throws(AssertionError,
Transform.unsimplexify_parameter([ lb - 1e-6, 1 - lb + 1e-6 ], simplex_box))
@test_throws(Exception,
@test_throws(AssertionError,
Transform.unsimplexify_parameter([ 0.3, 0.8 ], simplex_box))
@test_throws(Exception,
@test_throws(AssertionError,
Transform.unsimplexify_parameter([ 0.2, 0.3, 0.5 ], simplex_box))
@test_throws(Exception, Transform.simplexify_parameter([ 1., 2. ], simplex_box))
@test_throws(AssertionError, Transform.simplexify_parameter([ 1., 2. ], simplex_box))
end
end

Expand Down Expand Up @@ -315,9 +315,9 @@ function test_transform_box_functions()
this_scale * Transform.unbox_parameter(param, unscaled_param_box))

# Test the bound checking
@test_throws Exception Transform.unbox_parameter(lb - 1.0, param_box)
@test_throws AssertionError Transform.unbox_parameter(lb - 1.0, param_box)
ub < Inf &&
@test_throws Exception Transform.unbox_parameter(ub + 1.0, param_box)
@test_throws AssertionError Transform.unbox_parameter(ub + 1.0, param_box)
end
end

Expand Down Expand Up @@ -361,7 +361,7 @@ function test_enforce_bounds()
mp.vp[2][ids.r1[2]] = transform.bounds[2][:r1][1].upper_bound + 1.0
mp.vp[3][ids.k[1, 1]] = transform.bounds[3][:k][1, 1].lower_bound - 0.00001

@test_throws Exception transform.from_vp(mp.vp)
@test_throws AssertionError transform.from_vp(mp.vp)
Transform.enforce_bounds!(mp, transform)
transform.from_vp(mp.vp) # Check that it now works

Expand All @@ -375,15 +375,15 @@ function test_enforce_bounds()
mp.vp[sa][ids.r1[2]] = transform.bounds[1][:r1][1].upper_bound + 1.0
mp.vp[sa][ids.k[1, 1]] = transform.bounds[1][:k][1, 1].lower_bound - 0.00001

@test_throws Exception transform.from_vp(mp.vp)
@test_throws AssertionError transform.from_vp(mp.vp)
Transform.enforce_bounds!(mp, transform)
transform.from_vp(mp.vp) # Check that it now works

end


test_transform_sensitive_float()
test_transform_box_functions()
test_transform_sensitive_float()
test_box_derivatives()
test_box_simplex_derivatives()
test_simplex_derivatives()
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