Switch to TF-based programs.

tanaylab · Aug 5, 2024 · b3acb34 · b3acb34
1 parent 7af523a
commit b3acb34
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Showing 35 changed files with 6,316 additions and 1,379 deletions.
diff --git a/Project.toml b/Project.toml
@@ -7,18 +7,19 @@ version = "0.1.0"
 CSV = "336ed68f-0bac-5ca0-87d4-7b16caf5d00b"
 Clustering = "aaaa29a8-35af-508c-8bc3-b662a17a0fe5"
 ConcurrentUtils = "3df5f688-6c4c-4767-8685-17f5ad261477"
-Convex = "f65535da-76fb-5f13-bab9-19810c17039a"
 Daf = "1375bf9c-a47d-45a1-aad5-626dd8629d98"
 DataFrames = "a93c6f00-e57d-5684-b7b6-d8193f3e46c0"
 DataStructures = "864edb3b-99cc-5e75-8d2d-829cb0a9cfe8"
+Distances = "b4f34e82-e78d-54a5-968a-f98e89d6e8f7"
 Distributions = "31c24e10-a181-5473-b8eb-7969acd0382f"
 GZip = "92fee26a-97fe-5a0c-ad85-20a5f3185b63"
 HTTP = "cd3eb016-35fb-5094-929b-558a96fad6f3"
 LinearAlgebra = "37e2e46d-f89d-539d-b4ee-838fcccc9c8e"
-LinearSolve = "7ed4a6bd-45f5-4d41-b270-4a48e9bafcae"
+MultivariateStats = "6f286f6a-111f-5878-ab1e-185364afe411"
+NonNegLeastSquares = "b7351bd1-99d9-5c5d-8786-f205a815c4d7"
+Printf = "de0858da-6303-5e67-8744-51eddeeeb8d7"
 Random = "9a3f8284-a2c9-5f02-9a11-845980a1fd5c"
 Reexport = "189a3867-3050-52da-a836-e630ba90ab69"
-SCS = "c946c3f1-0d1f-5ce8-9dea-7daa1f7e2d13"
 Serialization = "9e88b42a-f829-5b0c-bbe9-9e923198166b"
 SparseArrays = "2f01184e-e22b-5df5-ae63-d93ebab69eaf"
 Statistics = "10745b16-79ce-11e8-11f9-7d13ad32a3b2"

diff --git a/deps/add_pkgs.jl b/deps/add_pkgs.jl
@@ -9,7 +9,6 @@ for pkg in (
     "LanguageServer",
     "Logging",
     "LoggingExtras",
-    "SnoopCompile",
     "StaticLint",
     "SymbolServer",
 )

diff --git a/deps/document.jl b/deps/document.jl
@@ -52,7 +52,6 @@ makedocs(;
         "contracts.md",
         "identify_genes.md",
         "programs.md",
-        "boxes.md",
         "anndata_format.md",
         "defaults.md",
     ],

diff --git a/deps/jet.jl b/deps/jet.jl
@@ -16,8 +16,8 @@ global_logger(detect_problems)
 
 push!(LOAD_PATH, ".")
 
-using JET
 using Metacells
+using JET
 
 println(report_package("Metacells"))
 

diff --git a/deps/test.jl b/deps/test.jl
@@ -14,13 +14,11 @@ end
 global_logger(detect_problems)
 
 using JET
-using SnoopCompile
 
 import Pkg
 Pkg.activate(".")
 
-tinf = @snoopi_deep Pkg.test(; coverage = true, test_args = Base.ARGS)
-report_callees(inference_triggers(tinf))
+Pkg.test(; coverage = true, test_args = Base.ARGS)
 
 if CountWarnings.seen_problems > 1
     exit(1)

diff --git a/docs/v0.1.0/.documenter-siteinfo.json b/docs/v0.1.0/.documenter-siteinfo.json
@@ -0,0 +1 @@
+{"documenter":{"julia_version":"1.10.4","generation_timestamp":"2024-08-05T16:26:59","documenter_version":"1.5.0"}}