build(retrocookie): reflect updates to source template from generated…

… project 'science-institute_brain-lab'
iamamutt · Jun 10, 2022 · 55ba632 · 55ba632
1 parent 44f3061
commit 55ba632
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Showing 20 changed files with 154 additions and 382 deletions.
diff --git a/.gitignore b/.gitignore
@@ -132,4 +132,4 @@ dmypy.json
 .build/
 .DS_Store
 /build
-/science-institute_neuro-lab
+/science-institute_brain-lab
diff --git a/datajoint-workflow/{{cookiecutter.github_repo}}/.github/ISSUE_TEMPLATE/bug_report.yml b/datajoint-workflow/{{cookiecutter.github_repo}}/.github/ISSUE_TEMPLATE/bug_report.yml
@@ -26,7 +26,7 @@ body:
     attributes:
       label: Version
       description: What version of the package were you running?
-      placeholder: "0.0.1"
+      placeholder: "{{cookiecutter._pkg_version}}"
     validations:
       required: true
 

diff --git a/datajoint-workflow/{{cookiecutter.github_repo}}/.github/workflows/package-updates.yml b/datajoint-workflow/{{cookiecutter.github_repo}}/.github/workflows/package-updates.yml
@@ -29,7 +29,7 @@ jobs:
       py_ver: "{{cookiecutter.python_version}}"
       release_branch: main
 
-  call_sciops_docker_images:
+  call_sciops_docker_image_debian:
     needs: call_semantic_versioning
     if: |
       always() &&
@@ -39,14 +39,13 @@ jobs:
       jhub_ver: "1.4.2"
       py_ver: "{{cookiecutter.python_version}}{% raw %}"
       dist: debian
-      env_base_hash: 44c5f19
-      worker_base_hash: fcd8909
+      codebook_base_hash: a7ee3ce
       workflow_version: ${{ needs.call_semantic_versioning.outputs.new_tag }}
       release_upload_url: ${{ needs.call_semantic_versioning.outputs.upload_url }}
     secrets:
-      RAW_DEPLOY_KEY: ${{ secrets.RAW_DEPLOY_KEY }}
-      REGISTRY_USERNAME: ${{ secrets.REGISTRY_USERNAME }}
-      REGISTRY_PASSWORD: ${{ secrets.REGISTRY_PASSWORD }}
+      BOT_SSH_KEY: ${{secrets.BOT_SSH_KEY}}
+      REGISTRY_USERNAME: ${{secrets.REGISTRY_USERNAME}}
+      REGISTRY_PASSWORD: ${{secrets.REGISTRY_PASSWORD}}
 
   if_run_tests_failed:
     if: github.event.workflow_run.conclusion == 'failure'

diff --git a/datajoint-workflow/{{cookiecutter.github_repo}}/README.md b/datajoint-workflow/{{cookiecutter.github_repo}}/README.md
@@ -84,9 +84,48 @@ DataJoint LabBook displays data from your database.
 
 ...
 
-### DataJoint Axon (Data Upload)
+### DataJoint Axon (Data Upload/Download)
+
+
+#### Axon GUI 
+
+1. In the Axon app, on the lower left side, click the 'gear' icon (Config). Enter the following information in each field (See the `Misc` section below for what the generated `json` config file will look like once configured):
+
+- AWS Account ID: `123456789012`
+
+- DataJoint Account Client ID: `xxxxxxxxxxxxxxxxxxxxxx`
+
+- S3 Role: `{{cookiecutter.github_repo}}_researcher_prod`
+
+- S3 Bucket: `dj-sciops`
+
+2. At the top right of the Axon app, click the 'circle arrow' icon (Token). This will open a browser to be able to sign in with your DataJoint account and generate a temporary token.
+
+3. Select the 'S3 Bucket' tab on the left side of the Axon app. Enter the following information to view the current list of files uploaded, the press 'Load':
+
+- S3 Bucket Directory: `{{cookiecutter.github_repo}}/inbox/`
+
+4. To upload a folder to a subfolder within the 'S3 Bucket Directory', for example to upload the subject data folder 'SUBJ100' from your local machine, enter the following path on S3: `{{cookiecutter.github_repo}}/inbox/SUBJ100`
+
+#### Axon CLI
+
+... 
+
+#### Misc
+
+```json
+{
+  "version": "1.2.0",
+  "aws": { "account_id": "123456789012" },
+  "s3":
+    {
+      "role": "{{cookiecutter.github_repo}}_researcher_prod",
+      "bucket": "dj-sciops",
+    },
+  "djauth": { "client_id": "xxxxxxxxxxxxxxxxxxxxxx" },
+}
+```
 
-...
 
 ### DataJoint CodeBook (JupyterHub)
 

diff --git a/datajoint-workflow/{{cookiecutter.github_repo}}/configs/axon.yaml b/datajoint-workflow/{{cookiecutter.github_repo}}/configs/axon.yaml
diff --git a/datajoint-workflow/{{cookiecutter.github_repo}}/docker/.datajoint_config.json b/datajoint-workflow/{{cookiecutter.github_repo}}/docker/.datajoint_config.json
diff --git a/datajoint-workflow/{{cookiecutter.github_repo}}/docker/.devcontainer/.env b/datajoint-workflow/{{cookiecutter.github_repo}}/docker/.devcontainer/.env
@@ -0,0 +1,6 @@
+COMPOSE_PROJECT_NAME=djsciops-devcontainer
+DJ_PASS=simple
+DJ_USER=root
+REPO_OWNER={{cookiecutter.github_user}}
+REPO_NAME={{cookiecutter.github_repo}}
+WORKFLOW_VERSION={{cookiecutter._pkg_version}}
diff --git a/datajoint-workflow/{{cookiecutter.github_repo}}/docker/.devcontainer/devcontainer.json b/datajoint-workflow/{{cookiecutter.github_repo}}/docker/.devcontainer/devcontainer.json
@@ -2,7 +2,7 @@
 {
 	"name": "{{cookiecutter.__project_name}} (devcontainer)",
 	"dockerComposeFile": [
-		"../docker-compose-devcontainer_env.yaml"
+		"./docker-compose.yml"
 	],
 	// Add the IDs of extensions you want installed when the container is created.
 	"extensions": [
@@ -15,7 +15,7 @@
 		"vivaxy.vscode-conventional-commits",
 		"yzhang.markdown-all-in-one"
 	],
-	"initializeCommand": "test -f \"${localWorkspaceFolder}/.env\" || exit 7",
+	"initializeCommand": "test -f \"${localWorkspaceFolder}/.devcontainer/.env\" || exit 7",
 	"service": "devcontainer_env",
 	// Set *default* container specific settings.json values on container create.
 	"settings": {
@@ -35,8 +35,6 @@
 			"module",
 			"docker"
 		],
-		"djcookiecutter.condaExec": "mamba",
-		"djcookiecutter.localPath": "${env:HOME}/Documents/datajoint/dj-cookiecutter",
 		"files.exclude": {
 			"**/.DS_Store": true,
 			"**/.git": true,
@@ -53,7 +51,7 @@
 			"build": true,
 			"src/*.egg-info": true
 		},
-		"jupyter.alwaysScrollOnNewCell": true,
+		"interactiveWindow.alwaysScrollOnNewCell": true,
 		"jupyter.generateSVGPlots": true,
 		"jupyter.interactiveWindowMode": "single",
 		"jupyter.notebookFileRoot": "${workspaceFolder}",
@@ -65,7 +63,7 @@
 			"reportGeneralTypeIssues": "information"
 		},
 		"python.analysis.typeCheckingMode": "basic",
-		"python.defaultInterpreterPath": "/usr/local/bin/python",
+		"python.defaultInterpreterPath": "/opt/local/conda/bin/python",
 		"python.formatting.blackArgs": [
 			"--line-length=88"
 		],
@@ -85,5 +83,5 @@
 		"python.testing.pytestEnabled": true
 	},
 	"shutdownAction": "none",
-	"workspaceFolder": "/home/{{cookiecutter.github_user}}/{{cookiecutter.github_repo}}"
+	"workspaceFolder": "/home/ubuntu/{{cookiecutter.github_repo}}"
 }
diff --git a/...cker/docker-compose-devcontainer_env.yaml → ...}/docker/.devcontainer/docker-compose.yml b/...cker/docker-compose-devcontainer_env.yaml → ...}/docker/.devcontainer/docker-compose.yml
@@ -1,9 +1,9 @@
-#  > docker-compose -f docker/docker-compose-devcontainer_env.yaml up -V --detach --force-recreate --remove-orphans --build
-#  > docker-compose -f docker/docker-compose-devcontainer_env.yaml down --volumes
+#  > docker-compose -f docker/.devcontainer/docker-compose.yml up -V --detach --force-recreate --remove-orphans --build
+#  > docker-compose -f docker/.devcontainer/docker-compose.yml down --volumes
 
 version: "2.4"
 services:
-  mysql_db:
+  mysql_sciops:
     environment:
       MYSQL_ROOT_PASSWORD: ${DJ_PASS:-simple}
     image: datajoint/mysql:5.7
@@ -14,21 +14,21 @@ services:
       - 6603:3306
     restart: always
     volumes:
-      - sqldata:/var/lib/mysql
+      - sciops-sqldata:/var/lib/mysql
 
   devcontainer_env:
     build:
-      context: ../.
-      dockerfile: docker/devcontainer.Dockerfile
+      context: ../../.
+      dockerfile: docker/.devcontainer/build/Dockerfile
       args:
-        REPO_OWNER:
-        REPO_NAME:
-    image: registry.vathes.com/${REPO_OWNER}/devcontainer-${REPO_NAME}:py${PY_VER}-${DIST}-${WORKFLOW_VERSION}
+        REPO_NAME: ${REPO_NAME?}
+        WORKFLOW_VERSION: v${WORKFLOW_VERSION?}
+    image: ghcr.io/${REPO_OWNER?}/${REPO_NAME}:latest
     depends_on:
-      mysql_db:
+      mysql_sciops:
         condition: service_healthy
     environment:
-      DJ_HOST: mysql_db
+      DJ_HOST: mysql_sciops
       DJ_PASS: ${DJ_PASS:-simple}
       DJ_USER: ${DJ_USER:-root}
     init: true
@@ -38,21 +38,20 @@ services:
     ports:
       - 18888:8888
     volumes:
-      - ..:/home/${REPO_OWNER}/${REPO_NAME}
-      - vscode:/home/${REPO_OWNER}/.vscode-server/extensions
-      - vscode-insiders:/home/${REPO_OWNER}/.vscode-server-insiders/extensions
-      - /home/${REPO_OWNER}/${REPO_NAME}/.nox
-      - /home/${REPO_OWNER}/${REPO_NAME}/src/{{cookiecutter.__pkg_import_name}}.egg-info
+      - ../..:/home/ubuntu/${REPO_NAME}
+      - vscode:/home/ubuntu/.vscode-server/extensions
+      - /home/ubuntu/${REPO_NAME}/.nox
+      - /home/ubuntu/${REPO_NAME}/src/{{cookiecutter.__pkg_import_name}}.egg-info
 
   # MySQL GUI --------------
   # http://localhost:8087/
   # System: PostgreSQL
-  # Server: mysql_db
+  # Server: mysql_sciops
   # Username: root
   # Password: simple
   adminer:
     environment:
-      ADMINER_DEFAULT_SERVER: mysql_db
+      ADMINER_DEFAULT_SERVER: mysql_sciops
       ADMINER_DESIGN: nette
     image: adminer
     networks:
@@ -62,17 +61,15 @@ services:
         published: 8087
     restart: always
     depends_on:
-      mysql_db:
+      mysql_sciops:
         condition: service_started
 
 networks:
   {{cookiecutter.__pkg_import_name}}:
     name: {{cookiecutter.__project_name}}-network
 
 volumes:
-  sqldata:
-    name: {{cookiecutter.__project_name}}-vol-sqldata
+  sciops-sqldata:
+    name: {{cookiecutter.__project_name}}-vol-sciops-sqldata
   vscode:
     name: {{cookiecutter.__project_name}}-vol-vscode
-  vscode-insiders:
-    name: {{cookiecutter.__project_name}}-vol-vscode-insiders
diff --git a/datajoint-workflow/{{cookiecutter.github_repo}}/docker/.gitignore b/datajoint-workflow/{{cookiecutter.github_repo}}/docker/.gitignore
@@ -1,3 +1,6 @@
 *.pem
-.env
-!.datajoint_config.json
+*.env
+!build.env
+!run.example.env
+!.devcontainer/.datajoint_config.json
+!.devcontainer/.env