Ghcr

.github/workflows/cd.yaml

@@ -13,11 +13,12 @@ jobs:
     steps:
     - name: Checkout source
       uses: actions/checkout@v4
-    - name: Login to DockerHub
+    - name: Login to GHCR
       uses: docker/login-action@v3
       with:
-        username: wjhjgi
-        password: ${{ secrets.DOCKERHUB_TOKEN }}
+        registry: ghcr.io
+        username: ${{ github.repository_owner }}
+        password: ${{ secrets.GITHUB_TOKEN }}
     - name: generate version_info file
       run: python ./docker/most_recent_commits.py > docker/.version_info
     - name: generate time based tag
@@ -32,13 +33,11 @@ jobs:
         context: ./docker
         file: ./docker/Dockerfile.shifter
         platforms: linux/amd64
-        cache-from: type=registry,ref=wjhjgi/metatlas_shifter:latest
+        cache-from: type=registry,ref=ghcr.io/biorack/metatlas/metatlas_shifter:latest
         cache-to: type=inline
         tags: |
-          wjhjgi/metatlas_shifter:${{ steps.timestamp.outputs.date_time }}
-          wjhjgi/metatlas_shifter:latest
-          doejgi/metatlas_shifter:${{ steps.timestamp.outputs.date_time }}
-          doejgi/metatlas_shifter:latest
+          ghcr.io/biorack/metatlas/metatlas_shifter:${{ steps.timestamp.outputs.date_time }}
+          ghcr.io/biorack/metatlas/metatlas_shifter:latest
         push: true
   build_push_metatlas_analysis_image:
     name: Build/push analysis docker image

docker/local_jupyter.sh

@@ -5,7 +5,7 @@ set -euf -o pipefail
 SCRIPT_DIR="$( cd "$( dirname "${BASH_SOURCE[0]}" )" >/dev/null 2>&1 && pwd )"
 REPO_DIR=$(dirname "$SCRIPT_DIR")
 OUT_DIR="${SCRIPT_DIR}/out"
-IMAGE='registry.spin.nersc.gov/metatlas_test/metatlas_ci:1.1.0'
+IMAGE='ghcr.io/biorack/metatlas/metatlas_ci:1.2.0'
 PORT=8888
 
 while [[ "$#" -gt 0 ]]; do

docker/rollback_shifter.sh

@@ -9,7 +9,7 @@
 set -euf -o pipefail
 
 SHORT="metatlas_shifter"
-LONG="doejgi/$SHORT"
+LONG="ghcr.io/biorack/metatlas/$SHORT"
 TAG=""
 
 while [[ "$#" -gt 0 ]]; do

docker/shifter.kernel.json

@@ -1,4 +1,4 @@
 {"argv": ["shifter", "--module=none", "--clearenv", "--entrypoint",
-    "--image=doejgi/metatlas_shifter:latest",
+    "--image=ghcr.io/biorack/metatlas/metatlas_shifter:latest",
     "/usr/local/bin/python", "-m", "ipykernel_launcher", "-f", "{connection_file}"],
     "display_name": "Metatlas Targeted", "language": "python", "metadata": {"debugger": true}}

papermill/submit_slurm_job.sh

@@ -75,7 +75,7 @@ validate_extra_parameters() {
 }
 
 is_valid_yaml() {
-  echo "$1" | shifter --module=none --clearenv --image=doejgi/metatlas_shifter:latest \
+  echo "$1" | shifter --module=none --clearenv --image=ghcr.io/biorack/metatlas/metatlas_shifter:latest \
 	  /src/metatlas/scripts/yaml_validation.py
 }
 

tests/system/test_add_msms_ref.py

@@ -4,7 +4,7 @@
 
 
 def test_add_msms_ref_by_line01(tmp_path):
-    image = "docker.io/doejgi/metatlas_ci:1.2.0"
+    image = "ghcr.io/biorack/metatlas/metatlas_ci:1.2.0"
     expected = {}
     expected[
         str(tmp_path / "updated_refs.tab")

tests/system/test_c18.py

@@ -4,7 +4,7 @@
 
 
 def test_c18_by_line01_with_remove(tmp_path):
-    image = "docker.io/doejgi/metatlas_ci:1.2.0"
+    image = "ghcr.io/biorack/metatlas/metatlas_ci:1.2.0"
     experiment = "20210915_JGI-AK_MK_506588_SoilWaterRep_final_QE-HF_C18_USDAY63680"
     expected = {}
     expected[

tests/system/test_hybrid.py

@@ -4,7 +4,7 @@
 
 
 def test_hybrid_by_line01_with_remove(tmp_path):
-    image = "docker.io/doejgi/metatlas_ci:1.2.0"
+    image = "ghcr.io/biorack/metatlas/metatlas_ci:1.2.0"
     experiment = "20201106_JGI-AK_PS-KM_505892_OakGall_final_QE-HF_HILICZ_USHXG01583"
     expected = {}
     expected[

tests/system/test_rt_alignment.py

@@ -6,7 +6,7 @@
 
 
 def test_rt_alignment_by_line01(tmp_path):
-    image = "docker.io/doejgi/metatlas_ci:1.2.0"
+    image = "ghcr.io/biorack/metatlas/metatlas_ci:1.2.0"
     experiment = "20201106_JGI-AK_PS-KM_505892_OakGall_final_QE-HF_HILICZ_USHXG01583"
     expected = {}
     expected[

tests/system/test_targeted.py

@@ -4,7 +4,7 @@
 
 
 def test_targeted_by_line01_with_remove(tmp_path):
-    image = "docker.io/doejgi/metatlas_ci:1.2.0"
+    image = "ghcr.io/biorack/metatlas/metatlas_ci:1.2.0"
     experiment = "20201106_JGI-AK_PS-KM_505892_OakGall_final_QE-HF_HILICZ_USHXG01583"
     expected = {}
     expected[