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

… project 'science-institute_brain-lab'
iamamutt · Apr 21, 2022 · 6340195 · 6340195
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Showing 5 changed files with 47 additions and 15 deletions.
diff --git a/datajoint-workflow/{{cookiecutter.github_repo}}/.pre-commit-config.yaml b/datajoint-workflow/{{cookiecutter.github_repo}}/.pre-commit-config.yaml
@@ -23,7 +23,7 @@ repos:
       - id: name-tests-test
         args: ["--django"]
       - id: check-added-large-files
-        args: ["--maxkb=5000"]
+        args: ["--maxkb=25000"]
       - id: end-of-file-fixer
         exclude: LICENSE
       - id: mixed-line-ending
@@ -43,12 +43,11 @@ repos:
     rev: 5.10.1
     hooks:
       - id: isort
-        name: isort (python)
         args:
           - "--settings-file"
           - "./pyproject.toml"
 
-    # Run black on python code blocks in documentation files.
+  # run black on python code blocks in documentation files.
   - repo: https://github.com/asottile/blacken-docs
     rev: v1.12.1
     hooks:
@@ -60,3 +59,17 @@ repos:
     rev: 0.5.0
     hooks:
       - id: nbstripout
+
+  # python linting
+  - repo: https://github.com/pycqa/flake8
+    rev: 4.0.1
+    hooks:
+      - id: flake8
+        exclude: ^tests/(integration/fixtures|unit/data)/
+        args:
+          # making isort line length compatible with black
+          # https://flake8.pycqa.org/en/latest/user/error-codes.html
+          - "--max-line-length=88"
+          - "--max-complexity=18"
+          - "--select=B,C,E,F,W,T4,B9"
+          - "--ignore=E203,E266,E501,W503,F403,F401,E402"
diff --git a/datajoint-workflow/{{cookiecutter.github_repo}}/docker/.devcontainer/devcontainer.json b/datajoint-workflow/{{cookiecutter.github_repo}}/docker/.devcontainer/devcontainer.json
@@ -15,9 +15,6 @@
 		"vivaxy.vscode-conventional-commits",
 		"yzhang.markdown-all-in-one"
 	],
-	"features": {
-		"github": "latest"
-	},
 	"service": "devcontainer_env",
 	// Set *default* container specific settings.json values on container create.
 	"settings": {
@@ -69,5 +66,6 @@
 		"python.terminal.activateEnvironment": true
 	},
 	"shutdownAction": "none",
-	"workspaceFolder": "/home/{{cookiecutter.github_user}}/{{cookiecutter.__org}}_{{cookiecutter.__wf}}"
+	"workspaceFolder": "/home/{{cookiecutter.github_user}}/{{cookiecutter.__org}}_{{cookiecutter.__wf}}",
+	"initializeCommand": "test -f \"${localWorkspaceFolder}/.env\" || exit 1"
 }
diff --git a/datajoint-workflow/{{cookiecutter.github_repo}}/docker/docker-compose-standard_workflow.yaml b/datajoint-workflow/{{cookiecutter.github_repo}}/docker/docker-compose-standard_workflow.yaml
@@ -23,5 +23,5 @@ services:
       - /bin/bash
       - -c
       - |
-        wf_entrypoint --help &
+        {{cookiecutter.__pkg_import_name}}_entrypoint --help &
         tail -f /dev/null
diff --git a/datajoint-workflow/{{cookiecutter.github_repo}}/noxfile.py b/datajoint-workflow/{{cookiecutter.github_repo}}/noxfile.py
@@ -5,6 +5,7 @@
 """
 
 import argparse
+import os
 import re
 
 import nox
@@ -100,6 +101,17 @@ def git_action_bot(
         session.run("git", "push", *push, external=True)
 
 
+@nox.session(python=default_python_version, reuse_venv=True)
+def run_entrypoint(session: nox.Session) -> None:
+    """Install all dependencies then run package entrypoint 'help'.
+
+    nox -s run_entrypoint
+    """
+
+    install_dependencies(session, "dev", "test", "doc", "sciops")
+    session.run("{{cookiecutter.__pkg_import_name}}_entrypoint", "--help")
+
+
 @nox.session(python=default_python_version, reuse_venv=True)
 def write_version(session: nox.Session) -> None:
     """Bump version.py to the latest version.
@@ -137,19 +149,28 @@ def pre_commit(session: nox.Session) -> None:
     install_dependencies(session, "dev")
     session.run("pre-commit", "install")
 
-    failed_hooks = []
+    failed_hooks = {}
+    log_file = ".nox.pre-commit.log"
     for hook in hooks:
         try:
-            session.run("pre-commit", "run", "--all-files", "-v", hook)
+            with open(log_file, "w") as fout:
+                session.run("pre-commit", "run", "--all-files", hook, stdout=fout)
+
         except Exception as err:
             session.log(err)
-            failed_hooks.append(hook)
+            with open(log_file, "r") as fin:
+                failed_hooks[hook] = fin.read()
+
+        finally:
+            os.remove(log_file)
 
     if failed_hooks:
         failed_str = "Failed pre-commit hooks:"
-        failed_str += "".join([f"\n  - {hk}" for hk in failed_hooks])
+        failed_str += "".join(
+            [f"\n::{hk}\n\n{txt}\n" for hk, txt in failed_hooks.items()]
+        )
         if raise_exception:
-            raise SyntaxError(failed_str)
+            session.error(failed_str)
         else:
             session.log(failed_str)
 

diff --git a/datajoint-workflow/{{cookiecutter.github_repo}}/pyproject.toml b/datajoint-workflow/{{cookiecutter.github_repo}}/pyproject.toml
@@ -49,7 +49,7 @@ dependencies = [
 ]
 
 [project.optional-dependencies]
-dev = ["black", "flake8", "pre-commit", "nox", "mypy"]
+dev = ["black", "isort", "flake8", "pre-commit", "nox", "mypy"]
 doc = [
     "mkdocs",
     "mkdocstrings-python",
@@ -65,7 +65,7 @@ test = ["pytest"]
 sciops = ["ipykernel", "djsciops", "datajoint>=0.13.4"]
 
 [project.scripts]
-wf_entrypoint = "{{cookiecutter.__pkg_import_name}}.entrypoint:cli"
+{{cookiecutter.__pkg_import_name}}_entrypoint = "{{cookiecutter.__pkg_import_name}}.entrypoint:cli"
 
 [project.urls]
 Homepage = "{{cookiecutter.homepage_url}}"