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DilumAluthgeDilumAluthge
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Merge branch 'release/v0.27.0'
2 parents 62bccc3 + 4e72ea0 commit 039ee15

26 files changed

+1135
-953
lines changed

‎Project.toml

Lines changed: 1 addition & 5 deletions
Original file line numberDiff line numberDiff line change
@@ -1,12 +1,11 @@
11
name = "PredictMD"
22
uuid = "3e7d7328-36f8-4388-bd01-4613c92c7370"
33
authors = ["Dilum Aluthge <dilum@aluthge.com>", "Ishan Sinha <ishan_sinha@brown.edu>", "Paul Stey <paulstey@gmail.com>", "Isabel Restrepo <isabelrestre@gmail.com>", "Elizabeth Chen <liz_chen@brown.edu>", "Neil Sarkar <neil_sarkar@brown.edu>", "Brown Center for Biomedical Informatics <bcbi@brown.edu>"]
4-
version = "0.26.0"
4+
version = "0.27.0"
55

66
[deps]
77
Adapt = "79e6a3ab-5dfb-504d-930d-738a2a938a0e"
88
Atom = "c52e3926-4ff0-5f6e-af25-54175e0327b1"
9-
AutoGrad = "6710c13c-97f1-543f-91c5-74e8f7d95b35"
109
BSON = "fbb218c0-5317-5bc6-957e-2ee96dd4b1f0"
1110
CSV = "336ed68f-0bac-5ca0-87d4-7b16caf5d00b"
1211
CSVFiles = "5d742f6a-9f54-50ce-8119-2520741973ca"
@@ -36,12 +35,10 @@ Literate = "98b081ad-f1c9-55d3-8b20-4c87d4299306"
3635
MLBase = "f0e99cf1-93fa-52ec-9ecc-5026115318e0"
3736
MbedTLS = "739be429-bea8-5141-9913-cc70e7f3736d"
3837
Metalhead = "dbeba491-748d-5e0e-a39e-b530a07fa0cc"
39-
Mux = "a975b10e-0019-58db-a62f-e48ff68538c9"
4038
NNlib = "872c559c-99b0-510c-b3b7-b6c96a88d5cd"
4139
NumericalIntegration = "e7bfaba1-d571-5449-8927-abc22e82249b"
4240
OnlineStats = "a15396b6-48d5-5d58-9928-6d29437db91e"
4341
PGFPlotsX = "8314cec4-20b6-5062-9cdb-752b83310925"
44-
PackageCompiler = "9b87118b-4619-50d2-8e1e-99f35a4d4d9d"
4542
Pkg = "44cfe95a-1eb2-52ea-b672-e2afdf69b78f"
4643
ProgressMeter = "92933f4c-e287-5a05-a399-4b506db050ca"
4744
Query = "1a8c2f83-1ff3-5112-b086-8aa67b057ba1"
@@ -58,7 +55,6 @@ TikzPictures = "37f6aa50-8035-52d0-81c2-5a1d08754b2d"
5855
TimeSeries = "9e3dc215-6440-5c97-bce1-76c03772f85e"
5956
UnicodePlots = "b8865327-cd53-5732-bb35-84acbb429228"
6057
ValueHistories = "98cad3c8-aec3-5f06-8e41-884608649ab7"
61-
Zygote = "e88e6eb3-aa80-5325-afca-941959d7151f"
6258

6359
[compat]
6460
Documenter = "~0.19"

‎README.md

Lines changed: 4 additions & 2 deletions
Original file line numberDiff line numberDiff line change
@@ -62,7 +62,9 @@ If you use PredictMD in research, please cite the software using the following D
6262

6363
- [bcbi/PredictMDFull.jl](https://github.com/bcbi/PredictMDFull.jl) - Install PredictMD and all of its Julia dependencies
6464
- [bcbi/PredictMDExtra.jl](https://github.com/bcbi/PredictMDExtra.jl) - Install all of the Julia dependencies of PredictMD (but does not install PredictMD)
65-
- [bcbi/predictmd-conda-recipes](https://github.com/bcbi/predictmd-conda-recipes) - Conda recipes for building the binary dependencies that are required for plotting in PredictMD
65+
- [DilumAluthge/PredictMD-docker](https://github.com/DilumAluthge/PredictMD-docker) - Generate a custom Julia package registry, mirror, and depot for use on workstations without internet access
66+
- [bcbi/PredictMDRegistry](https://github.com/bcbi/PredictMDRegistry) - Julia package registry for PredictMD.jl and related packages
67+
- [DilumAluthge/OfflineRegistry](https://github.com/DilumAluthge/OfflineRegistry) - Generate a custom Julia package registry, mirror, and depot for use on workstations without internet access
6668

6769
## Contributing
6870

@@ -79,7 +81,7 @@ If you would like to contribute to the PredictMD source code, please read the in
7981
<tr>
8082
<th></th>
8183
<th>master (stable)</th>
82-
<th>develop (latest)</th>
84+
<th>develop (latest/unstable)</th>
8385
</tr>
8486
</thead>
8587
<tbody>

‎TEST_GROUPS.md

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Original file line numberDiff line numberDiff line change
@@ -7,6 +7,8 @@ For example, to run the `all` test group, you would run the following lines in J
77
ENV["PREDICTMD_TEST_GROUP"] = "all"
88
import Pkg
99
Pkg.test("PredictMD")
10+
Pkg.test("PredictMDExtra")
11+
Pkg.test("PredictMDFull")
1012
```
1113

1214
## Available test groups

‎bors.toml

Lines changed: 1 addition & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -6,4 +6,4 @@ status = [
66
"continuous-integration/travis-ci/push",
77
]
88

9-
timeout_sec = 57600
9+
timeout_sec = 576000

‎deps/build.jl

Lines changed: 0 additions & 135 deletions
Original file line numberDiff line numberDiff line change
@@ -1,136 +1 @@
1-
##### Beginning of file
21

3-
# Parts of this file are based on:
4-
# 1. https://github.com/KristofferC/PGFPlotsX.jl/blob/master/deps/build.jl
5-
6-
have_lualatex = try success(`lualatex -v`); catch; false; end
7-
if have_lualatex
8-
@info(string("SUCCESS: Found lualatex."))
9-
else
10-
@warn(string("FAILURE: Did not find lualatex."))
11-
end
12-
13-
have_pdflatex = try success(`pdflatex -v`); catch; false; end
14-
if have_pdflatex
15-
@info(string("SUCCESS: Found pdflatex."))
16-
else
17-
@warn(string("FAILURE: Did not find pdflatex."))
18-
end
19-
20-
default_latex_engine = ""
21-
if have_lualatex
22-
default_latex_engine = "LUALATEX"
23-
elseif have_pdflatex
24-
default_latex_engine = "PDFLATEX"
25-
else
26-
@warn(
27-
string(
28-
"No LaTeX installation found, ",
29-
"figures will not be generated. ",
30-
"Make sure either pdflatex or lualatex are installed ",
31-
"and that the correct paths are set ",
32-
"then run Pkg.build(\"PredictMD\")",
33-
)
34-
)
35-
end
36-
37-
have_pdftoppm = try success(`pdftoppm -v`); catch; false; end
38-
if have_pdftoppm
39-
@info(string("SUCCESS: Found pdftoppm."))
40-
else
41-
@warn(string("FAILURE: Did not find pdftoppm."))
42-
end
43-
44-
if !have_pdftoppm
45-
@warn(
46-
string(
47-
"Did not find `pdftoppm`, ",
48-
"png output will be disabled. ",
49-
"Install `pdftoppm` and run ",
50-
"Pkg.build(\"PredictMD\") ",
51-
"to enable.",
52-
)
53-
)
54-
end
55-
56-
pdf2svg_temp_directory = mktempdir()
57-
pdf_original = joinpath(
58-
@__DIR__,
59-
"pdf2svg-example-file.pdf",
60-
)
61-
pdfpath = joinpath(
62-
pdf2svg_temp_directory,
63-
"pdf2svg-example-file.pdf",
64-
)
65-
cp(
66-
pdf_original,
67-
pdfpath;
68-
force = true,
69-
)
70-
svgpath = joinpath(
71-
pdf2svg_temp_directory,
72-
"pdf2svg-example-file.svg",
73-
)
74-
have_pdf2svg = try success(`pdf2svg $(pdfpath) $(svgpath)`); catch; false; end
75-
if have_pdf2svg
76-
@info(string("SUCCESS: Found pdf2svg."))
77-
else
78-
@warn(string("FAILURE: Did not find pdf2svg."))
79-
end
80-
81-
if !have_pdf2svg
82-
@warn(
83-
string(
84-
"Did not find `pdf2svg`, ",
85-
"svg output will be disabled. ",
86-
"Install `pdf2svg` and run ",
87-
"Pkg.build(\"PredictMD\")",
88-
"to enable.",
89-
)
90-
)
91-
end
92-
93-
if !have_pdf2svg && !have_pdftoppm
94-
@warn(
95-
string(
96-
"Found neither pdf2svg or pdftoppm, ",
97-
"figures will not be viewable in ",
98-
"IJulia/Jupyter notebooks.",
99-
)
100-
)
101-
end
102-
103-
line_1_default_latex_engine = string(
104-
"PREDICTMD_DEFAULT_LATEX_ENGINE = \"",
105-
default_latex_engine,
106-
"\"",
107-
)
108-
line_2_have_pdftoppm = string(
109-
"PREDICTMD_HAVE_PDFTOPPM = ",
110-
have_pdftoppm,
111-
)
112-
line_3_have_pdftosvg = string(
113-
"PREDICTMD_HAVE_PDFTOSVG = ",
114-
have_pdf2svg,
115-
)
116-
@info(line_1_default_latex_engine)
117-
@info(line_2_have_pdftoppm)
118-
@info(line_3_have_pdftosvg)
119-
try
120-
open(joinpath(@__DIR__, "deps.jl"), "w") do f
121-
println(f, line_1_default_latex_engine)
122-
println(f, line_2_have_pdftoppm)
123-
println(f, line_3_have_pdftosvg)
124-
end
125-
catch
126-
end
127-
128-
const PREAMBLE_PATH = joinpath(@__DIR__, "custom_preamble.tex")
129-
if !isfile(PREAMBLE_PATH)
130-
try
131-
touch(PREAMBLE_PATH)
132-
catch
133-
end
134-
end
135-
136-
##### End of file

‎deps/pdf2svg-example-file.pdf

-17.7 KB
Binary file not shown.

‎src/submodules/Server/Server.jl

Lines changed: 7 additions & 7 deletions
Original file line numberDiff line numberDiff line change
@@ -9,16 +9,16 @@ module Server # begin submodule PredictMD.Server
99
############################################################################
1010

1111
# submodules/Server/cryptography/
12-
include(joinpath("cryptography", "mbedtls.jl",))
13-
include(joinpath("cryptography", "transportlayersecurity.jl",))
12+
# include(joinpath("cryptography", "mbedtls.jl",))
13+
# include(joinpath("cryptography", "transportlayersecurity.jl",))
1414

1515
# submodules/Server/web/
16-
include(joinpath("web", "genie.jl",))
16+
# include(joinpath("web", "genie.jl",))
1717
include(joinpath("web", "http.jl",))
18-
include(joinpath("web", "httpclient.jl",))
19-
include(joinpath("web", "httpserver.jl",))
20-
include(joinpath("web", "juliawebapi.jl",))
21-
include(joinpath("web", "mux.jl",))
18+
# include(joinpath("web", "httpclient.jl",))
19+
# include(joinpath("web", "httpserver.jl",))
20+
# include(joinpath("web", "juliawebapi.jl",))
21+
# include(joinpath("web", "mux.jl",))
2222
# include(joinpath("web", "websockets.jl",))
2323

2424
end # end submodule PredictMD.Server

‎src/submodules/Server/cryptography/mbedtls.jl

Lines changed: 1 addition & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -1,5 +1,5 @@
11
##### Beginning of file
22

3-
import MbedTLS
3+
# import MbedTLS
44

55
##### End of file

‎src/submodules/Server/web/mux.jl

Lines changed: 1 addition & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -1,5 +1,5 @@
11
##### Beginning of file
22

3-
import Mux
3+
# import Mux
44

55
##### End of file

‎src/toplevel/neuralnetwork/knet.jl

Lines changed: 0 additions & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -1,6 +1,5 @@
11
##### Beginning of file
22

3-
import AutoGrad
43
import CUDAapi
54
import GPUArrays
65
import Knet

‎src/toplevel/plotting/pgfplotsx.jl

Lines changed: 19 additions & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -35,12 +35,30 @@ function PGFPlotsX.save(
3535
underlying_object = get_underlying(p)
3636
try
3737
@info(string("Attempting to save plot..."))
38-
PGFPlotsX.save(filename,underlying_object;kwargs...)
38+
mkpath(dirname(filename))
39+
PGFPlotsX.save(
40+
filename,
41+
underlying_object;
42+
kwargs...,
43+
)
3944
@info(string("Saved plot to file: \"", filename, "\"",))
4045
catch e
4146
handle_plotting_error(e)
4247
end
4348
return nothing
4449
end
4550

51+
function save_plot(
52+
filename::String,
53+
p::PGFPlotsXPlot;
54+
kwargs...,
55+
)::Nothing
56+
PGFPlotsX.save(
57+
filename,
58+
p;
59+
kwargs...,
60+
)
61+
return nothing
62+
end
63+
4664
##### End of file

‎templates/examples/cpu/boston_housing/01_preprocess_data.jl

Lines changed: 0 additions & 11 deletions
Original file line numberDiff line numberDiff line change
@@ -34,21 +34,10 @@ end
3434

3535
# PREDICTMD IF INCLUDE TEST STATEMENTS
3636
import PredictMDExtra
37-
import Test
3837
# PREDICTMD ELSE
3938
import PredictMDFull
4039
# PREDICTMD ENDIF INCLUDE TEST STATEMENTS
4140

42-
import Pkg
43-
try Pkg.add("GZip") catch end
44-
import GZip
45-
46-
import Pkg
47-
try Pkg.add("StatsBase") catch end
48-
import StatsBase
49-
50-
import Statistics
51-
5241
Random.seed!(999)
5342

5443
df = DataFrames.DataFrame(

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