Merge pull request #179 from LCSB-BioCore/develop

Develop

Author: laurentheirendt

.github/workflows/TagBot.yml

@@ -1,11 +1,15 @@
 name: TagBot
 on:
-  schedule:
-    - cron: 0 * * * *
+  issue_comment:
+    types:
+      - created
+  workflow_dispatch:
 jobs:
   TagBot:
+    if: github.event_name == 'workflow_dispatch' || github.actor == 'JuliaTagBot'
     runs-on: ubuntu-latest
     steps:
       - uses: JuliaRegistries/TagBot@v1
         with:
           token: ${{ secrets.GITHUB_TOKEN }}
+          ssh: ${{ secrets.DOCUMENTER_KEY }}

.github/workflows/docker.yml

@@ -0,0 +1,22 @@
+name: Publish Docker image
+on:
+  release:
+    types: [published]
+jobs:
+  push_to_registry:
+    name: Push Docker image to GitHub Packages
+    runs-on: ubuntu-latest
+    steps:
+      - name: Check out the repo
+        uses: actions/checkout@v2
+      - name: Login to Registry
+        uses: docker/login-action@v1
+        with:
+          registry: docker.pkg.github.com
+          username: cylon-x
+          password: ${{ secrets.DOCKER_TOKEN }}
+      - uses: docker/build-push-action@v2
+        with:
+         push: true
+         tags: lcsb-biocore/gigasom:latest
+

.github/workflows/docs.yml

@@ -17,7 +17,7 @@ jobs:
       - uses: actions/checkout@v2
       - uses: julia-actions/setup-julia@latest
         with:
-          version: 1.3
+          version: 1.4
       - name: Install dependencies
         run: julia --project=docs/ -e 'using Pkg; Pkg.develop(PackageSpec(path=pwd())); Pkg.instantiate()'
       - name: Build and deploy

Dockerfile

@@ -0,0 +1,5 @@
+FROM julia
+
+RUN julia -e 'import Pkg; Pkg.add("GigaSOM"); Pkg.resolve(); Pkg.status(); Pkg.instantiate(); Pkg.precompile()'
+
+CMD ["julia"]

Project.toml

@@ -1,6 +1,6 @@
 name = "GigaSOM"
 uuid = "a03a9c34-069e-5582-a11c-5c984cab887c"
-version = "0.6.3"
+version = "0.6.4"
 
 [deps]
 CSV = "336ed68f-0bac-5ca0-87d4-7b16caf5d00b"

src/io/process.jl

@@ -62,7 +62,7 @@ function getMetaData(meta::Dict{String,String})::DataFrame
     # create a data frame for the results
     df = Matrix{String}(undef, pars, length(channel_properties))
     df .= defaultValue
-    df = DataFrame(df)
+    df = DataFrame(df, :auto)
     rename!(df, Symbol.(channel_properties))
 
     # collect the data from params

test/testBatch.jl

@@ -26,9 +26,9 @@
         codes = som.codes
         @test size(codes) == (100, 10)
 
-        dfCodes = DataFrame(codes)
+        dfCodes = DataFrame(codes, :auto)
         rename!(dfCodes, Symbol.(antigens))
-        dfEmbed = DataFrame(embed)
+        dfEmbed = DataFrame(embed, :auto)
         CSV.write(genDataPath * "/batchDfCodes.csv", dfCodes)
         CSV.write(genDataPath * "/batchWinners.csv", winners)
         CSV.write(genDataPath * "/batchEmbedded.csv", dfEmbed)

test/testParallel.jl

@@ -23,9 +23,9 @@
         codes = som.codes
         @test size(codes) == (100, 10)
 
-        dfCodes = DataFrame(codes)
+        dfCodes = DataFrame(codes, :auto)
         rename!(dfCodes, Symbol.(antigens))
-        dfEmbed = DataFrame(embed)
+        dfEmbed = DataFrame(embed, :auto)
         CSV.write(genDataPath * "/parallelDfCodes.csv", dfCodes)
         CSV.write(genDataPath * "/parallelWinners.csv", winners)
         CSV.write(genDataPath * "/parallelEmbedded.csv", dfEmbed)