From eec5a496089444bb2e66a50828f0d928a9085e8c Mon Sep 17 00:00:00 2001
From: Tom <46992402+ttubb@users.noreply.github.com>
Date: Fri, 5 Apr 2024 16:23:12 +0200
Subject: [PATCH 1/2] name change

---
 .github/workflows/python-app.yml | 26 +++++++++++++-------------
 1 file changed, 13 insertions(+), 13 deletions(-)

diff --git a/.github/workflows/python-app.yml b/.github/workflows/python-app.yml
index 3c63c4a..1f6e4f1 100644
--- a/.github/workflows/python-app.yml
+++ b/.github/workflows/python-app.yml
@@ -30,7 +30,7 @@ jobs:
         python -m pip install .
     - name: Download webin-cli
       run: |
-        synum download_webin
+        submg download_webin
     - name: Lint with flake8
       run: |
         # stop the build if there are Python syntax errors or undefined names
@@ -46,7 +46,7 @@ jobs:
         CFG=01_samples_reads_assembly_bins_mags.yaml
         RANDOM_STR=$(tr -dc 'A-Za-z0-9' </dev/urandom | head -c 5)
         sed -i "s/idx00/${RANDOM_STR}/g" "$CFG"
-        synum submit \
+        submg submit \
           --config $CFG \
           --staging_dir example01/staging \
           --logging_dir example01/logging \
@@ -64,7 +64,7 @@ jobs:
         CFG=02_samples_reads_assembly_bins.yaml
         RANDOM_STR=$(tr -dc 'A-Za-z0-9' </dev/urandom | head -c 5)
         sed -i "s/idx00/${RANDOM_STR}/g" "$CFG"
-        synum submit \
+        submg submit \
           --config $CFG \
           --staging_dir example02/staging \
           --logging_dir example02/logging \
@@ -81,7 +81,7 @@ jobs:
         CFG=03_samples_reads_assembly.yaml
         RANDOM_STR=$(tr -dc 'A-Za-z0-9' </dev/urandom | head -c 5)
         sed -i "s/idx00/${RANDOM_STR}/g" "$CFG"
-        synum submit \
+        submg submit \
           --config $CFG \
           --staging_dir example03/staging \
           --logging_dir example03/logging \
@@ -97,7 +97,7 @@ jobs:
         CFG=04_reads_assembly_bins_mags.yaml
         RANDOM_STR=$(tr -dc 'A-Za-z0-9' </dev/urandom | head -c 5)
         sed -i "s/idx00/${RANDOM_STR}/g" "$CFG"
-        synum submit \
+        submg submit \
           --config $CFG \
           --staging_dir example04/staging \
           --logging_dir example04/logging \
@@ -114,7 +114,7 @@ jobs:
         CFG=05_reads_assembly_bins.yaml
         RANDOM_STR=$(tr -dc 'A-Za-z0-9' </dev/urandom | head -c 5)
         sed -i "s/idx00/${RANDOM_STR}/g" "$CFG"
-        synum submit \
+        submg submit \
           --config $CFG \
           --staging_dir example05/staging \
           --logging_dir example05/logging \
@@ -130,7 +130,7 @@ jobs:
         CFG=06_reads_assembly.yaml
         RANDOM_STR=$(tr -dc 'A-Za-z0-9' </dev/urandom | head -c 5)
         sed -i "s/idx00/${RANDOM_STR}/g" "$CFG"
-        synum submit \
+        submg submit \
           --config $CFG \
           --staging_dir example06/staging \
           --logging_dir example06/logging \
@@ -145,7 +145,7 @@ jobs:
         CFG=07_assembly_bins_mags.yaml
         RANDOM_STR=$(tr -dc 'A-Za-z0-9' </dev/urandom | head -c 5)
         sed -i "s/idx00/${RANDOM_STR}/g" "$CFG"
-        synum submit \
+        submg submit \
           --config $CFG \
           --staging_dir example07/staging \
           --logging_dir example07/logging \
@@ -161,7 +161,7 @@ jobs:
         CFG=08_assembly_bins.yaml
         RANDOM_STR=$(tr -dc 'A-Za-z0-9' </dev/urandom | head -c 5)
         sed -i "s/idx00/${RANDOM_STR}/g" "$CFG"
-        synum submit \
+        submg submit \
           --config $CFG \
           --staging_dir example08/staging \
           --logging_dir example08/logging \
@@ -176,7 +176,7 @@ jobs:
         CFG=09_assembly.yaml
         RANDOM_STR=$(tr -dc 'A-Za-z0-9' </dev/urandom | head -c 5)
         sed -i "s/idx00/${RANDOM_STR}/g" "$CFG"
-        synum submit \
+        submg submit \
           --config $CFG \
           --staging_dir example09/staging \
           --logging_dir example09/logging \
@@ -190,7 +190,7 @@ jobs:
         CFG=10_bins_mags.yaml
         RANDOM_STR=$(tr -dc 'A-Za-z0-9' </dev/urandom | head -c 5)
         sed -i "s/idx00/${RANDOM_STR}/g" "$CFG"
-        synum submit \
+        submg submit \
           --config $CFG \
           --staging_dir example10/staging \
           --logging_dir example10/logging \
@@ -205,7 +205,7 @@ jobs:
         CFG=11_bins.yaml
         RANDOM_STR=$(tr -dc 'A-Za-z0-9' </dev/urandom | head -c 5)
         sed -i "s/idx00/${RANDOM_STR}/g" "$CFG"
-        synum submit \
+        submg submit \
           --config $CFG \
           --staging_dir example11/staging \
           --logging_dir example11/logging \
@@ -219,7 +219,7 @@ jobs:
         CFG=12_mags.yaml
         RANDOM_STR=$(tr -dc 'A-Za-z0-9' </dev/urandom | head -c 5)
         sed -i "s/idx00/${RANDOM_STR}/g" "$CFG"
-        synum submit \
+        submg submit \
           --config $CFG \
           --staging_dir example12/staging \
           --logging_dir example12/logging \

From d8f61215acd966c0f00a077b63d5a145590b1225 Mon Sep 17 00:00:00 2001
From: Tom <46992402+ttubb@users.noreply.github.com>
Date: Wed, 10 Apr 2024 14:23:33 +0200
Subject: [PATCH 2/2] new workflow

pushes / pulls on main will trigger the built of a docker container, which will be uploaded to ttubb/submg on dockerhub
---
 .github/workflows/container.yml | 28 ++++++++++++++++++++++++++++
 1 file changed, 28 insertions(+)
 create mode 100644 .github/workflows/container.yml

diff --git a/.github/workflows/container.yml b/.github/workflows/container.yml
new file mode 100644
index 0000000..4e86558
--- /dev/null
+++ b/.github/workflows/container.yml
@@ -0,0 +1,28 @@
+name: Build and Push Docker Image
+
+on:
+  push:
+    branches: [ "main" ]
+  pull_request:
+    branches: [ "main" ]
+
+jobs:
+  build-and-push:
+    runs-on: ubuntu-latest
+    steps:
+    - name: Check out code
+      uses: actions/checkout@v2
+
+    - name: Log in to Docker Hub
+      uses: docker/login-action@v1
+      with:
+        username: ${{ secrets.DOCKER_USERNAME }}
+        password: ${{ secrets.DOCKER_PASSWORD }}
+
+    - name: Build and push Docker image
+      uses: docker/build-push-action@v2
+      with:
+        context: ./docker
+        file: ./docker/Dockerfile
+        push: true
+        tags: ttubb/submg:latest # You can also use other tags or versioning schemes