fixes

Author: AntonOresten

.github/workflows/CI.yml

@@ -24,7 +24,6 @@ jobs:
       matrix:
         version:
           - '1.10'
-          - 'pre'
         os:
           - ubuntu-latest
         arch:

Project.toml

@@ -1,7 +1,7 @@
 name = "PyBoltz"
 uuid = "0bca4874-a2b8-4dca-bc03-d2d86e344f1f"
 authors = ["Anton Oresten and Aron Stålmarck"]
-version = "0.1.2"
+version = "0.2.0"
 
 [deps]
 Compat = "34da2185-b29b-5c13-b0c7-acf172513d20"
@@ -27,7 +27,7 @@ CondaPkg = "0.2"
 ProteinChains = "0.7"
 PythonCall = "0.9"
 Scratch = "1"
-TMscore = "0.1.0"
+TMscore = "0.1"
 YAML = "0.4"
 julia = "1.10"
 

README.md

@@ -4,9 +4,6 @@
 [![Build Status](https://github.com/MurrellGroup/PyBoltz.jl/actions/workflows/CI.yml/badge.svg?branch=main)](https://github.com/MurrellGroup/PyBoltz.jl/actions/workflows/CI.yml?query=branch%3Amain)
 [![Coverage](https://codecov.io/gh/MurrellGroup/PyBoltz.jl/branch/main/graph/badge.svg)](https://codecov.io/gh/MurrellGroup/PyBoltz.jl)
 
-> [!WARNING]
-> Boltz currently fails when using CPU as accelerator (and thus also GitHub's default CI). See https://github.com/MurrellGroup/PyBoltz.jl/issues/2 for tracker.
-
 Julia bindings for Python's [boltz](https://github.com/jwohlwend/boltz) for biomolecular structure prediction.
 
 ## Installation

test/runtests.jl

@@ -15,7 +15,7 @@ const accelerator = get(ENV, "PyBoltz_TEST_ACCELERATOR", "cpu")
 
     @testset "Single structure run" begin
         mktempdir() do dir
-            structure = retrievepdb("1TIT"; dir)
+            structure = retrievepdb("1EJG"; dir)
             sequence = LongAA(structure["A"], standardselector)
             input = MolecularInput(
                 sequences = [
@@ -34,49 +34,49 @@ const accelerator = get(ENV, "PyBoltz_TEST_ACCELERATOR", "cpu")
                 MolecularInput(
                     name = "Z",
                     sequences = [
-                        protein(; id="A", sequence=randaaseq(10), msa="empty"),
+                        protein(; id="A", sequence=randaaseq(5), msa="empty"),
                     ]
                 ),
                 MolecularInput(
                     name = "X",
                     sequences = [
-                        protein(; id="A", sequence=randaaseq(30), msa="empty"),
+                        protein(; id="A", sequence=randaaseq(15), msa="empty"),
                     ]
                 ),
                 MolecularInput(
                     name = "Y",
                     sequences = [
-                        protein(; id="A", sequence=randaaseq(20), msa="empty"),
+                        protein(; id="A", sequence=randaaseq(10), msa="empty"),
                     ]
                 ),
                 MolecularInput(
                     name = "W",
                     sequences = [
-                        protein(; id="A", sequence=randaaseq(40), msa="empty"),
+                        protein(; id="A", sequence=randaaseq(20), msa="empty"),
                     ]
                 ),
             ]
             predicted_structures = predict(inputs, MolecularStructure; seed=0, accelerator)
             @test predicted_structures isa Vector{Union{Missing,MolecularStructure}}
             @test length(predicted_structures) == 4
             @testset "Order preservation" begin
-                @test countresidues.(predicted_structures) == [10, 30, 20, 40]
+                @test countresidues.(predicted_structures) == [5, 15, 10, 20]
                 @test [predicted_structure.name for predicted_structure in predicted_structures] == ["Z", "X", "Y", "W"]
             end
         end
     end
 
     @testset "MSA run" begin
         mktempdir() do dir
-            sequence = randaaseq(15)
+            sequence = randaaseq(5)
             input = MolecularInput(
                 sequences = [
-                    protein(; id="A", sequence, msa=[sequence; [randaaseq(15) for _ in 1:10]]),
+                    protein(; id="A", sequence, msa=[sequence; [randaaseq(5) for _ in 1:10]]),
                 ]
             )
             predicted_structure = predict(input, MolecularStructure; seed=0, accelerator)
             @test predicted_structure isa MolecularStructure
-            @test predicted_structure |> countresidues == 15
+            @test predicted_structure |> countresidues == 5
         end
     end