From 4506e35d1af3da43cb2b81e60955219d76d6d4e1 Mon Sep 17 00:00:00 2001
From: Mirek Kratochvil <exa.exa@gmail.com>
Date: Wed, 3 Mar 2021 10:58:02 +0100
Subject: [PATCH 01/25] update tagbot and documenter CI script to current
 recommended version

---
 .github/workflows/TagBot.yml | 8 ++++++--
 .github/workflows/docs.yml   | 2 +-
 2 files changed, 7 insertions(+), 3 deletions(-)

diff --git a/.github/workflows/TagBot.yml b/.github/workflows/TagBot.yml
index d77d3a0c..f49313b6 100644
--- a/.github/workflows/TagBot.yml
+++ b/.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 }}
diff --git a/.github/workflows/docs.yml b/.github/workflows/docs.yml
index a543a85d..a3a79ef9 100644
--- a/.github/workflows/docs.yml
+++ b/.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

From ea188f090b382cb163b94af54c47351d3cd3b36c Mon Sep 17 00:00:00 2001
From: Mirek Kratochvil <exa.exa@gmail.com>
Date: Fri, 19 Mar 2021 13:37:14 +0100
Subject: [PATCH 02/25] remove deprecated DataFrame usage

Closes #165
---
 src/io/process.jl    | 2 +-
 test/testBatch.jl    | 4 ++--
 test/testParallel.jl | 4 ++--
 3 files changed, 5 insertions(+), 5 deletions(-)

diff --git a/src/io/process.jl b/src/io/process.jl
index 75e4d490..52a71eb5 100644
--- a/src/io/process.jl
+++ b/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
diff --git a/test/testBatch.jl b/test/testBatch.jl
index 230a5823..b9b2b308 100644
--- a/test/testBatch.jl
+++ b/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)
diff --git a/test/testParallel.jl b/test/testParallel.jl
index 69fc8fc5..0fc3153e 100644
--- a/test/testParallel.jl
+++ b/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)

From e31fca4e5000cd4b4bdfec901a118b5435a23a44 Mon Sep 17 00:00:00 2001
From: Laurent Heirendt <laurent.heirendt@uni.lu>
Date: Mon, 22 Mar 2021 09:41:51 +0100
Subject: [PATCH 03/25] Create docker.yml

---
 .github/workflows/docker.yml | 19 +++++++++++++++++++
 1 file changed, 19 insertions(+)
 create mode 100644 .github/workflows/docker.yml

diff --git a/.github/workflows/docker.yml b/.github/workflows/docker.yml
new file mode 100644
index 00000000..576c4f63
--- /dev/null
+++ b/.github/workflows/docker.yml
@@ -0,0 +1,19 @@
+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: Push to GitHub Packages
+        uses: docker/build-push-action@v1
+        with:
+          username: ${{ github.actor }}
+          password: ${{ secrets.GITHUB_TOKEN }}
+          registry: docker.pkg.github.com
+          repository: laurentheirendt/GigaSOM.jl/gigasom
+          tag_with_ref: true

From 7396d118efb8726af4ee3d97ed3291d7424f9004 Mon Sep 17 00:00:00 2001
From: Laurent Heirendt <laurent.heirendt@uni.lu>
Date: Mon, 22 Mar 2021 09:45:46 +0100
Subject: [PATCH 04/25] Update docker.yml

---
 .github/workflows/docker.yml | 3 +--
 1 file changed, 1 insertion(+), 2 deletions(-)

diff --git a/.github/workflows/docker.yml b/.github/workflows/docker.yml
index 576c4f63..eef070a3 100644
--- a/.github/workflows/docker.yml
+++ b/.github/workflows/docker.yml
@@ -10,10 +10,9 @@ jobs:
       - name: Check out the repo
         uses: actions/checkout@v2
       - name: Push to GitHub Packages
-        uses: docker/build-push-action@v1
+        uses: docker/build-push-action@v2
         with:
           username: ${{ github.actor }}
           password: ${{ secrets.GITHUB_TOKEN }}
           registry: docker.pkg.github.com
-          repository: laurentheirendt/GigaSOM.jl/gigasom
           tag_with_ref: true

From af53f30721ac3f848c8f46e9b5500f9a5a40cc4d Mon Sep 17 00:00:00 2001
From: Laurent Heirendt <laurent.heirendt@uni.lu>
Date: Mon, 22 Mar 2021 09:46:57 +0100
Subject: [PATCH 05/25] add dockerfile

---
 Dockerfile | 83 ++++++++++++++++++++++++++++++++++++++++++++++++++++++
 1 file changed, 83 insertions(+)
 create mode 100644 Dockerfile

diff --git a/Dockerfile b/Dockerfile
new file mode 100644
index 00000000..93af4bb4
--- /dev/null
+++ b/Dockerfile
@@ -0,0 +1,83 @@
+FROM debian:buster-slim
+
+COPY Project.toml /Project.toml
+
+RUN set -eux; \
+	apt-get update; \
+	apt-get install -y --no-install-recommends \
+		ca-certificates \
+# ERROR: no download agent available; install curl, wget, or fetch
+		curl \
+        unzip \
+        git \
+        git-lfs \
+	; \
+	rm -rf /var/lib/apt/lists/*
+
+ENV JULIA_PATH /usr/local/julia
+ENV PATH $JULIA_PATH/bin:$PATH
+
+# https://julialang.org/juliareleases.asc
+# Julia (Binary signing key) <buildbot@julialang.org>
+ENV JULIA_GPG 3673DF529D9049477F76B37566E3C7DC03D6E495
+
+# https://julialang.org/downloads/
+ENV JULIA_VERSION 1.5.3
+
+RUN set -eux; \
+	\
+	savedAptMark="$(apt-mark showmanual)"; \
+	if ! command -v gpg > /dev/null; then \
+		apt-get update; \
+		apt-get install -y --no-install-recommends \
+			gnupg \
+			dirmngr \
+            unzip \
+            git \
+            git-lfs \
+		; \
+		rm -rf /var/lib/apt/lists/*; \
+	fi; \
+	\
+# https://julialang.org/downloads/#julia-command-line-version
+# https://julialang-s3.julialang.org/bin/checksums/julia-1.4.0.sha256
+# this "case" statement is generated via "update.sh"
+	dpkgArch="$(dpkg --print-architecture)"; \
+	case "${dpkgArch##*-}" in \
+# amd64
+		amd64) tarArch='x86_64'; dirArch='x64'; sha256='f190c938dd6fed97021953240523c9db448ec0a6760b574afd4e9924ab5615f1' ;; \
+# arm64v8
+		arm64) tarArch='aarch64'; dirArch='aarch64'; sha256='3d6641b61b00415fa52a616a61bbd91dbbb1b4e6e9c61b7941710ed6ff720cb4' ;; \
+# i386
+		i386) tarArch='i686'; dirArch='x86'; sha256='b265144f136dcaf2336b5abc8d18ae405ad5834de058a0338a4d020bede2fe47' ;; \
+		*) echo >&2 "error: current architecture ($dpkgArch) does not have a corresponding Julia binary release"; exit 1 ;; \
+	esac; \
+	\
+	folder="$(echo "$JULIA_VERSION" | cut -d. -f1-2)"; \
+	curl -fL -o julia.tar.gz.asc "https://julialang-s3.julialang.org/bin/linux/${dirArch}/${folder}/julia-${JULIA_VERSION}-linux-${tarArch}.tar.gz.asc"; \
+	curl -fL -o julia.tar.gz     "https://julialang-s3.julialang.org/bin/linux/${dirArch}/${folder}/julia-${JULIA_VERSION}-linux-${tarArch}.tar.gz"; \
+	\
+	echo "${sha256} *julia.tar.gz" | sha256sum -c -; \
+	\
+	export GNUPGHOME="$(mktemp -d)"; \
+	gpg --batch --keyserver ha.pool.sks-keyservers.net --recv-keys "$JULIA_GPG"; \
+	gpg --batch --verify julia.tar.gz.asc julia.tar.gz; \
+	command -v gpgconf > /dev/null && gpgconf --kill all; \
+	rm -rf "$GNUPGHOME" julia.tar.gz.asc; \
+	\
+	mkdir "$JULIA_PATH"; \
+	tar -xzf julia.tar.gz -C "$JULIA_PATH" --strip-components 1; \
+	rm julia.tar.gz; \
+	\
+	apt-mark auto '.*' > /dev/null; \
+	[ -z "$savedAptMark" ] || apt-mark manual $savedAptMark; \
+	apt-get purge -y --auto-remove -o APT::AutoRemove::RecommendsImportant=false; \
+	\
+# smoke test
+	julia --version; \
+    mkdir -p ~/.julia/environments/v${folder}; \
+    cd ~/.julia/environments/v${folder}; \
+    cp /Project.toml .; \
+    julia -e "import Pkg; Pkg.resolve(); Pkg.status(); Pkg.instantiate();"
+
+CMD ["julia"]

From 9e3778feb91de635c9eec77fe67b991468e8fca6 Mon Sep 17 00:00:00 2001
From: Laurent Heirendt <laurent.heirendt@uni.lu>
Date: Mon, 22 Mar 2021 10:01:03 +0100
Subject: [PATCH 06/25] Update Dockerfile

---
 Dockerfile | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/Dockerfile b/Dockerfile
index 93af4bb4..7ea53f22 100644
--- a/Dockerfile
+++ b/Dockerfile
@@ -77,7 +77,7 @@ RUN set -eux; \
 	julia --version; \
     mkdir -p ~/.julia/environments/v${folder}; \
     cd ~/.julia/environments/v${folder}; \
-    cp /Project.toml .; \
+    #cp /Project.toml .; \
     julia -e "import Pkg; Pkg.resolve(); Pkg.status(); Pkg.instantiate();"
 
 CMD ["julia"]

From e84590fc4123cd2dfcec189207d8a7a647ebf1bf Mon Sep 17 00:00:00 2001
From: Laurent Heirendt <laurent.heirendt@uni.lu>
Date: Mon, 22 Mar 2021 10:10:08 +0100
Subject: [PATCH 07/25] Update Dockerfile

---
 Dockerfile | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/Dockerfile b/Dockerfile
index 7ea53f22..93af4bb4 100644
--- a/Dockerfile
+++ b/Dockerfile
@@ -77,7 +77,7 @@ RUN set -eux; \
 	julia --version; \
     mkdir -p ~/.julia/environments/v${folder}; \
     cd ~/.julia/environments/v${folder}; \
-    #cp /Project.toml .; \
+    cp /Project.toml .; \
     julia -e "import Pkg; Pkg.resolve(); Pkg.status(); Pkg.instantiate();"
 
 CMD ["julia"]

From 3e23a7440ecf691f153cb00d449ee5a52802ae4c Mon Sep 17 00:00:00 2001
From: Laurent Heirendt <laurent.heirendt@uni.lu>
Date: Mon, 22 Mar 2021 10:22:32 +0100
Subject: [PATCH 08/25] Update docker.yml

---
 .github/workflows/docker.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/docker.yml b/.github/workflows/docker.yml
index eef070a3..602cd699 100644
--- a/.github/workflows/docker.yml
+++ b/.github/workflows/docker.yml
@@ -13,6 +13,6 @@ jobs:
         uses: docker/build-push-action@v2
         with:
           username: ${{ github.actor }}
-          password: ${{ secrets.GITHUB_TOKEN }}
+          password: ${{ secrets.DOCKER_TOKEN }}
           registry: docker.pkg.github.com
           tag_with_ref: true

From 1de49b956f89e2581841d44443837acef6147c78 Mon Sep 17 00:00:00 2001
From: Laurent Heirendt <laurent.heirendt@uni.lu>
Date: Mon, 22 Mar 2021 10:27:45 +0100
Subject: [PATCH 09/25] Update docker.yml

---
 .github/workflows/docker.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/docker.yml b/.github/workflows/docker.yml
index 602cd699..6db0bb82 100644
--- a/.github/workflows/docker.yml
+++ b/.github/workflows/docker.yml
@@ -10,7 +10,7 @@ jobs:
       - name: Check out the repo
         uses: actions/checkout@v2
       - name: Push to GitHub Packages
-        uses: docker/build-push-action@v2
+        uses: docker/build-push-action@v1
         with:
           username: ${{ github.actor }}
           password: ${{ secrets.DOCKER_TOKEN }}

From f24606d020a4142819072add9345249d936b932e Mon Sep 17 00:00:00 2001
From: Laurent Heirendt <laurent.heirendt@uni.lu>
Date: Mon, 22 Mar 2021 10:30:50 +0100
Subject: [PATCH 10/25] Update Dockerfile

---
 Dockerfile | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/Dockerfile b/Dockerfile
index 93af4bb4..7ea53f22 100644
--- a/Dockerfile
+++ b/Dockerfile
@@ -77,7 +77,7 @@ RUN set -eux; \
 	julia --version; \
     mkdir -p ~/.julia/environments/v${folder}; \
     cd ~/.julia/environments/v${folder}; \
-    cp /Project.toml .; \
+    #cp /Project.toml .; \
     julia -e "import Pkg; Pkg.resolve(); Pkg.status(); Pkg.instantiate();"
 
 CMD ["julia"]

From a9af8dc9051d44df7c847170ecc12a19b91c1109 Mon Sep 17 00:00:00 2001
From: Laurent Heirendt <laurent.heirendt@uni.lu>
Date: Mon, 22 Mar 2021 10:34:11 +0100
Subject: [PATCH 11/25] Update Dockerfile

---
 Dockerfile | 3 +--
 1 file changed, 1 insertion(+), 2 deletions(-)

diff --git a/Dockerfile b/Dockerfile
index 7ea53f22..fc3211f1 100644
--- a/Dockerfile
+++ b/Dockerfile
@@ -77,7 +77,6 @@ RUN set -eux; \
 	julia --version; \
     mkdir -p ~/.julia/environments/v${folder}; \
     cd ~/.julia/environments/v${folder}; \
-    #cp /Project.toml .; \
-    julia -e "import Pkg; Pkg.resolve(); Pkg.status(); Pkg.instantiate();"
+    julia -e "import Pkg; Pkg.add('GigaSOM'); Pkg.resolve(); Pkg.status(); Pkg.instantiate();"
 
 CMD ["julia"]

From ea2bc0fd2014ebc4cf9a88c1716c6fa9849c6e22 Mon Sep 17 00:00:00 2001
From: Laurent Heirendt <laurent.heirendt@uni.lu>
Date: Mon, 22 Mar 2021 10:37:07 +0100
Subject: [PATCH 12/25] Update docker.yml

---
 .github/workflows/docker.yml | 1 +
 1 file changed, 1 insertion(+)

diff --git a/.github/workflows/docker.yml b/.github/workflows/docker.yml
index 6db0bb82..7f32b9bd 100644
--- a/.github/workflows/docker.yml
+++ b/.github/workflows/docker.yml
@@ -14,5 +14,6 @@ jobs:
         with:
           username: ${{ github.actor }}
           password: ${{ secrets.DOCKER_TOKEN }}
+          repository: laurentheirendt/GigaSOM.jl/gigasom.jl:latest
           registry: docker.pkg.github.com
           tag_with_ref: true

From d97b4f45371c9ea040835fc326b3c3cb24cb1802 Mon Sep 17 00:00:00 2001
From: Laurent Heirendt <laurent.heirendt@uni.lu>
Date: Mon, 22 Mar 2021 10:39:06 +0100
Subject: [PATCH 13/25] Update docker.yml

---
 .github/workflows/docker.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/docker.yml b/.github/workflows/docker.yml
index 7f32b9bd..33597d04 100644
--- a/.github/workflows/docker.yml
+++ b/.github/workflows/docker.yml
@@ -14,6 +14,6 @@ jobs:
         with:
           username: ${{ github.actor }}
           password: ${{ secrets.DOCKER_TOKEN }}
-          repository: laurentheirendt/GigaSOM.jl/gigasom.jl:latest
+          repository: laurentheirendt/gigasom.jl/latest
           registry: docker.pkg.github.com
           tag_with_ref: true

From c490292ab50b821fa7454fd59838ded61d35b5c7 Mon Sep 17 00:00:00 2001
From: Laurent Heirendt <laurent.heirendt@uni.lu>
Date: Mon, 22 Mar 2021 10:41:17 +0100
Subject: [PATCH 14/25] Update Dockerfile

---
 Dockerfile | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/Dockerfile b/Dockerfile
index fc3211f1..c885e09f 100644
--- a/Dockerfile
+++ b/Dockerfile
@@ -77,6 +77,6 @@ RUN set -eux; \
 	julia --version; \
     mkdir -p ~/.julia/environments/v${folder}; \
     cd ~/.julia/environments/v${folder}; \
-    julia -e "import Pkg; Pkg.add('GigaSOM'); Pkg.resolve(); Pkg.status(); Pkg.instantiate();"
+    julia -e \"import Pkg; Pkg.add("GigaSOM"); Pkg.resolve(); Pkg.status(); Pkg.instantiate();\"
 
 CMD ["julia"]

From 2705dc24823dd4ded02a8ff37b227d41e32592a1 Mon Sep 17 00:00:00 2001
From: Laurent Heirendt <laurent.heirendt@uni.lu>
Date: Mon, 22 Mar 2021 10:41:33 +0100
Subject: [PATCH 15/25] Update Dockerfile

---
 Dockerfile | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/Dockerfile b/Dockerfile
index c885e09f..bc630cde 100644
--- a/Dockerfile
+++ b/Dockerfile
@@ -1,6 +1,6 @@
 FROM debian:buster-slim
 
-COPY Project.toml /Project.toml
+#COPY Project.toml /Project.toml
 
 RUN set -eux; \
 	apt-get update; \

From 05602697281f9e0ee97362f5bc95ef2bf2982a67 Mon Sep 17 00:00:00 2001
From: Laurent Heirendt <laurent.heirendt@uni.lu>
Date: Mon, 22 Mar 2021 10:44:54 +0100
Subject: [PATCH 16/25] Update docker.yml

---
 .github/workflows/docker.yml | 15 ++++++++++-----
 1 file changed, 10 insertions(+), 5 deletions(-)

diff --git a/.github/workflows/docker.yml b/.github/workflows/docker.yml
index 33597d04..ad3de299 100644
--- a/.github/workflows/docker.yml
+++ b/.github/workflows/docker.yml
@@ -7,13 +7,18 @@ jobs:
     name: Push Docker image to GitHub Packages
     runs-on: ubuntu-latest
     steps:
+      - run: echo ::set-env name=IMAGE_TAG::${GITHUB_REF:10}
       - name: Check out the repo
         uses: actions/checkout@v2
-      - name: Push to GitHub Packages
-        uses: docker/build-push-action@v1
+      - name: Login to Registry
+        uses: docker/login-action@v1
         with:
+          registry: docker.pkg.github.com
           username: ${{ github.actor }}
           password: ${{ secrets.DOCKER_TOKEN }}
-          repository: laurentheirendt/gigasom.jl/latest
-          registry: docker.pkg.github.com
-          tag_with_ref: true
+      - uses: docker/build-push-action@v2
+        with:
+         push: true
+         # tags: <org-name>/<repo-name>/<app-name>:${{ env.IMAGE_TAG }}
+         tags: ghcr.io/${{ github.repository_owner }}/<image-name>:${{ env.IMAGE_TAG }}
+

From 0931b8fa757a812db0fc0b7e231089876429eb6b Mon Sep 17 00:00:00 2001
From: Laurent Heirendt <laurent.heirendt@uni.lu>
Date: Mon, 22 Mar 2021 10:46:40 +0100
Subject: [PATCH 17/25] Update docker.yml

---
 .github/workflows/docker.yml | 3 +--
 1 file changed, 1 insertion(+), 2 deletions(-)

diff --git a/.github/workflows/docker.yml b/.github/workflows/docker.yml
index ad3de299..7ed07db9 100644
--- a/.github/workflows/docker.yml
+++ b/.github/workflows/docker.yml
@@ -7,7 +7,6 @@ jobs:
     name: Push Docker image to GitHub Packages
     runs-on: ubuntu-latest
     steps:
-      - run: echo ::set-env name=IMAGE_TAG::${GITHUB_REF:10}
       - name: Check out the repo
         uses: actions/checkout@v2
       - name: Login to Registry
@@ -20,5 +19,5 @@ jobs:
         with:
          push: true
          # tags: <org-name>/<repo-name>/<app-name>:${{ env.IMAGE_TAG }}
-         tags: ghcr.io/${{ github.repository_owner }}/<image-name>:${{ env.IMAGE_TAG }}
+         tags: laurentheirendt/gigasom.jl/gigasom.jl:latest
 

From 4442e296b15d38878db17fee7da52cdeff15159d Mon Sep 17 00:00:00 2001
From: Laurent Heirendt <laurent.heirendt@uni.lu>
Date: Mon, 22 Mar 2021 10:49:43 +0100
Subject: [PATCH 18/25] Update Dockerfile

---
 Dockerfile | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/Dockerfile b/Dockerfile
index bc630cde..3eae9370 100644
--- a/Dockerfile
+++ b/Dockerfile
@@ -77,6 +77,6 @@ RUN set -eux; \
 	julia --version; \
     mkdir -p ~/.julia/environments/v${folder}; \
     cd ~/.julia/environments/v${folder}; \
-    julia -e \"import Pkg; Pkg.add("GigaSOM"); Pkg.resolve(); Pkg.status(); Pkg.instantiate();\"
+    julia -e 'import Pkg; Pkg.add("GigaSOM"); Pkg.resolve(); Pkg.status(); Pkg.instantiate();'
 
 CMD ["julia"]

From 726bb82fa541cba54ecec534231d39e0cc43c1f8 Mon Sep 17 00:00:00 2001
From: Laurent Heirendt <laurent.heirendt@uni.lu>
Date: Mon, 22 Mar 2021 10:54:43 +0100
Subject: [PATCH 19/25] Update docker.yml

---
 .github/workflows/docker.yml | 5 ++---
 1 file changed, 2 insertions(+), 3 deletions(-)

diff --git a/.github/workflows/docker.yml b/.github/workflows/docker.yml
index 7ed07db9..75446b02 100644
--- a/.github/workflows/docker.yml
+++ b/.github/workflows/docker.yml
@@ -13,11 +13,10 @@ jobs:
         uses: docker/login-action@v1
         with:
           registry: docker.pkg.github.com
-          username: ${{ github.actor }}
+          username: cylon-x
           password: ${{ secrets.DOCKER_TOKEN }}
       - uses: docker/build-push-action@v2
         with:
          push: true
-         # tags: <org-name>/<repo-name>/<app-name>:${{ env.IMAGE_TAG }}
-         tags: laurentheirendt/gigasom.jl/gigasom.jl:latest
+         tags: laurentheirendt/gigasom.jl/gigasom:latest
 

From cce1206a9058f9b38c2e49500bb1081e00424ac0 Mon Sep 17 00:00:00 2001
From: Laurent Heirendt <laurent.heirendt@uni.lu>
Date: Mon, 22 Mar 2021 11:02:41 +0100
Subject: [PATCH 20/25] Update docker.yml

---
 .github/workflows/docker.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/docker.yml b/.github/workflows/docker.yml
index 75446b02..4be682e0 100644
--- a/.github/workflows/docker.yml
+++ b/.github/workflows/docker.yml
@@ -18,5 +18,5 @@ jobs:
       - uses: docker/build-push-action@v2
         with:
          push: true
-         tags: laurentheirendt/gigasom.jl/gigasom:latest
+         tags: laurentheirendt/gigasom.jl/latest
 

From 667f9b089677faaa8a1f584b7416c0527ab99b90 Mon Sep 17 00:00:00 2001
From: Laurent Heirendt <laurent.heirendt@uni.lu>
Date: Mon, 22 Mar 2021 11:05:46 +0100
Subject: [PATCH 21/25] Update docker.yml

---
 .github/workflows/docker.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/docker.yml b/.github/workflows/docker.yml
index 4be682e0..17e6aa0f 100644
--- a/.github/workflows/docker.yml
+++ b/.github/workflows/docker.yml
@@ -18,5 +18,5 @@ jobs:
       - uses: docker/build-push-action@v2
         with:
          push: true
-         tags: laurentheirendt/gigasom.jl/latest
+         tags: laurentheirendt/gigasom.jl
 

From f0513bb465321b814862ad8ce35b8f355e5bec0e Mon Sep 17 00:00:00 2001
From: Laurent Heirendt <laurent.heirendt@uni.lu>
Date: Mon, 22 Mar 2021 11:09:33 +0100
Subject: [PATCH 22/25] Update docker.yml

---
 .github/workflows/docker.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/docker.yml b/.github/workflows/docker.yml
index 17e6aa0f..7f605fbc 100644
--- a/.github/workflows/docker.yml
+++ b/.github/workflows/docker.yml
@@ -18,5 +18,5 @@ jobs:
       - uses: docker/build-push-action@v2
         with:
          push: true
-         tags: laurentheirendt/gigasom.jl
+         tags: laurentheirendt/gigasom:latest
 

From 3c0898b28c104fb9b5a256db033c896c4960dbb1 Mon Sep 17 00:00:00 2001
From: laurentheirendt <laurent.heirendt@uni.lu>
Date: Mon, 22 Mar 2021 11:17:51 +0100
Subject: [PATCH 23/25] change org for pushing docker img:

---
 .github/workflows/docker.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/docker.yml b/.github/workflows/docker.yml
index 7f605fbc..c6212333 100644
--- a/.github/workflows/docker.yml
+++ b/.github/workflows/docker.yml
@@ -18,5 +18,5 @@ jobs:
       - uses: docker/build-push-action@v2
         with:
          push: true
-         tags: laurentheirendt/gigasom:latest
+         tags: lcsb-biocore/gigasom:latest
 

From 7ad4a3d664eeef8db221e6261210c54bd16629a3 Mon Sep 17 00:00:00 2001
From: laurentheirendt <laurent.heirendt@uni.lu>
Date: Thu, 25 Mar 2021 14:43:30 +0100
Subject: [PATCH 24/25] use latest julia image

---
 Dockerfile | 81 ++----------------------------------------------------
 1 file changed, 2 insertions(+), 79 deletions(-)

diff --git a/Dockerfile b/Dockerfile
index 3eae9370..ae3999bf 100644
--- a/Dockerfile
+++ b/Dockerfile
@@ -1,82 +1,5 @@
-FROM debian:buster-slim
+FROM julia
 
-#COPY Project.toml /Project.toml
-
-RUN set -eux; \
-	apt-get update; \
-	apt-get install -y --no-install-recommends \
-		ca-certificates \
-# ERROR: no download agent available; install curl, wget, or fetch
-		curl \
-        unzip \
-        git \
-        git-lfs \
-	; \
-	rm -rf /var/lib/apt/lists/*
-
-ENV JULIA_PATH /usr/local/julia
-ENV PATH $JULIA_PATH/bin:$PATH
-
-# https://julialang.org/juliareleases.asc
-# Julia (Binary signing key) <buildbot@julialang.org>
-ENV JULIA_GPG 3673DF529D9049477F76B37566E3C7DC03D6E495
-
-# https://julialang.org/downloads/
-ENV JULIA_VERSION 1.5.3
-
-RUN set -eux; \
-	\
-	savedAptMark="$(apt-mark showmanual)"; \
-	if ! command -v gpg > /dev/null; then \
-		apt-get update; \
-		apt-get install -y --no-install-recommends \
-			gnupg \
-			dirmngr \
-            unzip \
-            git \
-            git-lfs \
-		; \
-		rm -rf /var/lib/apt/lists/*; \
-	fi; \
-	\
-# https://julialang.org/downloads/#julia-command-line-version
-# https://julialang-s3.julialang.org/bin/checksums/julia-1.4.0.sha256
-# this "case" statement is generated via "update.sh"
-	dpkgArch="$(dpkg --print-architecture)"; \
-	case "${dpkgArch##*-}" in \
-# amd64
-		amd64) tarArch='x86_64'; dirArch='x64'; sha256='f190c938dd6fed97021953240523c9db448ec0a6760b574afd4e9924ab5615f1' ;; \
-# arm64v8
-		arm64) tarArch='aarch64'; dirArch='aarch64'; sha256='3d6641b61b00415fa52a616a61bbd91dbbb1b4e6e9c61b7941710ed6ff720cb4' ;; \
-# i386
-		i386) tarArch='i686'; dirArch='x86'; sha256='b265144f136dcaf2336b5abc8d18ae405ad5834de058a0338a4d020bede2fe47' ;; \
-		*) echo >&2 "error: current architecture ($dpkgArch) does not have a corresponding Julia binary release"; exit 1 ;; \
-	esac; \
-	\
-	folder="$(echo "$JULIA_VERSION" | cut -d. -f1-2)"; \
-	curl -fL -o julia.tar.gz.asc "https://julialang-s3.julialang.org/bin/linux/${dirArch}/${folder}/julia-${JULIA_VERSION}-linux-${tarArch}.tar.gz.asc"; \
-	curl -fL -o julia.tar.gz     "https://julialang-s3.julialang.org/bin/linux/${dirArch}/${folder}/julia-${JULIA_VERSION}-linux-${tarArch}.tar.gz"; \
-	\
-	echo "${sha256} *julia.tar.gz" | sha256sum -c -; \
-	\
-	export GNUPGHOME="$(mktemp -d)"; \
-	gpg --batch --keyserver ha.pool.sks-keyservers.net --recv-keys "$JULIA_GPG"; \
-	gpg --batch --verify julia.tar.gz.asc julia.tar.gz; \
-	command -v gpgconf > /dev/null && gpgconf --kill all; \
-	rm -rf "$GNUPGHOME" julia.tar.gz.asc; \
-	\
-	mkdir "$JULIA_PATH"; \
-	tar -xzf julia.tar.gz -C "$JULIA_PATH" --strip-components 1; \
-	rm julia.tar.gz; \
-	\
-	apt-mark auto '.*' > /dev/null; \
-	[ -z "$savedAptMark" ] || apt-mark manual $savedAptMark; \
-	apt-get purge -y --auto-remove -o APT::AutoRemove::RecommendsImportant=false; \
-	\
-# smoke test
-	julia --version; \
-    mkdir -p ~/.julia/environments/v${folder}; \
-    cd ~/.julia/environments/v${folder}; \
-    julia -e 'import Pkg; Pkg.add("GigaSOM"); Pkg.resolve(); Pkg.status(); Pkg.instantiate();'
+RUN julia -e 'import Pkg; Pkg.add("GigaSOM"); Pkg.resolve(); Pkg.status(); Pkg.instantiate(); Pkg.precompile()'
 
 CMD ["julia"]

From a4bec41393d6d52d4c67d1796b5b7cab6ce1f4dd Mon Sep 17 00:00:00 2001
From: laurentheirendt <laurent.heirendt@uni.lu>
Date: Thu, 25 Mar 2021 14:48:09 +0100
Subject: [PATCH 25/25] bump version

---
 Project.toml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/Project.toml b/Project.toml
index a508601a..20cabb8c 100644
--- a/Project.toml
+++ b/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"