build(retrocookie): reflect updates to source template from generated project 'science-institute_brain-lab'

Author: Joseph Burling

datajoint-workflow/{{cookiecutter.github_repo}}/.dockerignore

@@ -1,16 +1,17 @@
-.git
 .mypy_cache
 .nox
-**/__pycache__/
+.pytest_cache
+**/__pycache__
 **/.DS_Store
 **/.env
-**/.pytest_cache/
+**/.git
+**/.pytest_cache
 **/*.egg-info
-**/*.ipynb_checkpoints/
+**/*.ipynb_checkpoints
 **/*.pem
 **/*cookiecutter*
-build/*
+build
 {{cookiecutter._djconfig}}
-docs/api/*
+docs/api
 environment.lock.yml
-site/*
+site

datajoint-workflow/{{cookiecutter.github_repo}}/docker/.devcontainer/devcontainer.json

@@ -15,6 +15,7 @@
 		"vivaxy.vscode-conventional-commits",
 		"yzhang.markdown-all-in-one"
 	],
+	"initializeCommand": "test -f \"${localWorkspaceFolder}/.env\" || exit 7",
 	"service": "devcontainer_env",
 	// Set *default* container specific settings.json values on container create.
 	"settings": {
@@ -34,38 +35,55 @@
 			"module",
 			"docker"
 		],
+		"djcookiecutter.condaExec": "mamba",
+		"djcookiecutter.localPath": "${env:HOME}/Documents/{{cookiecutter.__org}}/dj-cookiecutter",
 		"files.exclude": {
 			"**/.DS_Store": true,
 			"**/.git": true,
 			"**/.hg": true,
+			"**/.ipynb_checkpoints": true,
 			"**/.svn": true,
 			"**/CVS": true,
 			"**/Thumbs.db": true,
-			"*.command": true
+			"**/__pycache__": true,
+			"*.command": true,
+			".mypy_cache": true,
+			".nox": true,
+			".pytest_cache": true,
+			"build": true,
+			"src/*.egg-info": true
 		},
+		"jupyter.alwaysScrollOnNewCell": true,
 		"jupyter.generateSVGPlots": true,
+		"jupyter.interactiveWindowMode": "single",
+		"jupyter.notebookFileRoot": "${workspaceFolder}",
+		"jupyter.sendSelectionToInteractiveWindow": true,
+		"jupyter.themeMatplotlibPlots": true,
+		"python.analysis.completeFunctionParens": true,
+		"python.analysis.diagnosticMode": "workspace",
+		"python.analysis.diagnosticSeverityOverrides": {
+			"reportGeneralTypeIssues": "information"
+		},
+		"python.analysis.typeCheckingMode": "basic",
 		"python.defaultInterpreterPath": "/usr/local/bin/python",
 		"python.formatting.blackArgs": [
 			"--line-length=88"
 		],
 		"python.formatting.provider": "black",
 		"python.languageServer": "Pylance",
-		"python.linting.enabled": true,
 		"python.linting.flake8Args": [
 			"--max-line-length=88",
 			"--extend-ignore=E203"
 		],
 		"python.linting.flake8Enabled": true,
+		"python.linting.mypyCategorySeverity.error": "Hint",
 		"python.linting.mypyEnabled": true,
-		"python.linting.pylintEnabled": false,
 		"python.sortImports.args": [
-			"--profile",
-			"black"
+			"--profile=black"
 		],
 		"python.terminal.activateEnvInCurrentTerminal": true,
-		"python.terminal.activateEnvironment": true
+		"python.testing.pytestEnabled": true
 	},
 	"shutdownAction": "none",
-	"workspaceFolder": "/home/{{cookiecutter.github_user}}/{{cookiecutter.__org}}_{{cookiecutter.__wf}}",
-	"initializeCommand": "test -f \"${localWorkspaceFolder}/.env\" || exit 1"
+	"workspaceFolder": "/home/{{cookiecutter.github_user}}/{{cookiecutter.__org}}_{{cookiecutter.__wf}}"
 }

datajoint-workflow/{{cookiecutter.github_repo}}/docker/README.md

@@ -58,17 +58,22 @@ docker-compose -f docker-compose-codebook_env.yaml up --detach --force-recreate
 
 ## Standard Workflow Environment
 
+... 
+
+
 ### Docker Compose
 
 Will automatically load environment variables from `.env` file.
 
 ```bash
 cd docker
-docker-compose -f docker-compose-standard_workflow.yaml up --detach --force-recreate --remove-orphans --build
+docker-compose -f docker-compose-standard_worker.yaml up --detach --force-recreate --remove-orphans --build
 ```
 
 ## Devcontainer Environment
 
+> **Note**: Make sure to first set the environment variables file `.env` as outlined at the top of this document, otherwise building the docker image will fail.
+
 ### VSCode
 
 You can either open to the docker folder directly from vscode and it'll prompt you to open the devcontainer, or use the supplied script below. 

datajoint-workflow/{{cookiecutter.github_repo}}/docker/docker-compose-standard_workflow.yaml

@@ -1,7 +1,7 @@
 # docker-compose up --build
 version: "2.4"
 services:
-  standard_workflow:
+  standard_worker:
     build: # only necessary if rebuilding image
       context: .
       dockerfile: standard_worker.Dockerfile