15 standardize linting

.github/workflows/mega-linter.yml

@@ -1,3 +1,4 @@
+---
 # MegaLinter GitHub Action configuration file
 # More info at https://megalinter.github.io
 name: MegaLinter
@@ -41,9 +42,13 @@ jobs:
           # https://megalinter.github.io/configuration/
           VALIDATE_ALL_CODEBASE: true  
           # VALIDATE_ALL_CODEBASE: ${{ github.event_name == 'push' && github.ref == 'refs/heads/main' }} # Validates all source when push on main, else just the git diff with main. Override with true if you always want to lint all sources
+          PAT: ${{ secrets.PAT }}
           GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
           # ADD YOUR CUSTOM ENV VARIABLES HERE OR DEFINE THEM IN A FILE .mega-linter.yml AT THE ROOT OF YOUR REPOSITORY
           DISABLE: COPYPASTE,SPELL # Uncomment to disable copy-paste and spell checks
+          PYTHON_FLAKE8_ARGUMENTS: --max-line-length=119 # Uncomment to override Flake8 arguments
+          PYTHON_RUFF_ARGUMENTS: --line-length=119 # Uncomment to override Ruffus arguments
+
 
       # Upload MegaLinter artifacts
       - name: Archive production artifacts

.github/workflows/python-package.yml

@@ -1,3 +1,4 @@
+---
 # This workflow will install Python dependencies and run tests
 name: Python package
 

Makefile

@@ -39,9 +39,12 @@ install: venv/bin/pip-sync requirements.txt
 requirements.txt: venv/bin/pip-compile requirements.in
 	. $(ACTIVATE) && pip-compile requirements.in
 
-test: venv install-dev
+test: venv install-dev lint
 	. $(ACTIVATE) && python3 -m pytest  --cov --cov-report xml:coverage.xml
 
+lint: venv install-dev
+	. $(ACTIVATE) && black .
+
 test-partials: venv install-dev
 	SKIP_PARTIALS=False . $(ACTIVATE) && python3 -m pytest
 

dev-requirements.in

@@ -4,6 +4,7 @@ benchling-sdk ~= 1.6
 botocore ~= 1.31
 jinja2 ~= 3.1
 quilt3 ~=5.3
+black
 pytest
 pytest-coverage
 pytest-watcher

dev-requirements.txt

@@ -24,6 +24,8 @@ benchling-api-client==2.0.167
     # via benchling-sdk
 benchling-sdk==1.7.0
     # via -r dev-requirements.in
+black==23.7.0
+    # via -r dev-requirements.in
 boto3==1.28.27
     # via quilt3
 botocore==1.31.27
@@ -41,6 +43,8 @@ cffi==1.15.1
     # via cryptography
 charset-normalizer==3.2.0
     # via requests
+click==8.1.7
+    # via black
 coverage[toml]==7.3.0
     # via pytest-cov
 cryptography==41.0.3
@@ -89,15 +93,22 @@ markupsafe==2.1.3
 marshmallow==3.20.1
     # via dataclasses-json
 mypy-extensions==1.0.0
-    # via typing-inspect
+    # via
+    #   black
+    #   typing-inspect
 ordered-set==4.1.0
     # via benchling-sdk
 packaging==23.1
     # via
+    #   black
     #   marshmallow
     #   pytest
+pathspec==0.11.2
+    # via black
 platformdirs==3.10.0
-    # via quilt3
+    # via
+    #   black
+    #   quilt3
 pluggy==1.2.0
     # via pytest
 pycparser==2.21
@@ -155,6 +166,7 @@ tenacity==8.2.3
     # via quilt3
 tomli==2.0.1
     # via
+    #   black
     #   coverage
     #   pytest
     #   pytest-watcher
@@ -165,6 +177,7 @@ typing-extensions==4.7.1
     #   aws-lambda-powertools
     #   benchling-api-client
     #   benchling-sdk
+    #   black
     #   typing-inspect
 typing-inspect==0.9.0
     # via dataclasses-json

lambdas/main.py

@@ -51,9 +51,7 @@ def __init__(self, tenant, id, arn):
 
     def get_task(self, entry_id):
         self.task = self.benchling.tasks.wait_for_task(
-            self.benchling.exports.export(
-                benchling_models.ExportItemRequest(id=entry_id)  # type: ignore
-            ).task_id
+            self.benchling.exports.export(benchling_models.ExportItemRequest(id=entry_id)).task_id  # type: ignore
         )
         if self.task.status != benchling_models.AsyncTaskStatus.SUCCEEDED:
             raise Exception(f"Notes export failed: {self.task!r}")
@@ -88,10 +86,10 @@ class BenchlingEntry:
         ]
     )
 
-    FLD = {
-        "URI": "Quilt+ URI",
-        "CAT": "Quilt Catalog URL",
-        "REV": "Quilt Revise URL",
+    FIELDS = {
+        "QUILT_URI": "Quilt+ URI",
+        "CATALOG_URL": "Quilt Catalog URL",
+        "REVISE_URL": "Quilt Revise URL",
     }
 
     ENTRY_FMT = """
@@ -189,11 +187,11 @@ def push_package(self, tmpdir_path):
 
     def field_values(self):
         values = {
-            "URI": f"quilt+s3://{self.DST_BUCKET}#package={self.pkg_name}",
-            "CAT": f"{self.QUILT_PREFIX}/{self.pkg_name}",
-            "REV": f"{self.QUILT_PREFIX}/{self.pkg_name}?{self.REVISE}",
+            "QUILT_URI": f"quilt+s3://{self.DST_BUCKET}#package={self.pkg_name}",
+            "CATALOG_URL": f"{self.QUILT_PREFIX}/{self.pkg_name}",
+            "REVISE_URL": f"{self.QUILT_PREFIX}/{self.pkg_name}?{self.REVISE}",
         }
-        return {f: values.get(k) for k, f in self.FLD.items()}
+        return {f: values.get(k) for k, f in self.FIELDS.items()}
 
     def update_benchling_notebook(self) -> bool:
         values = self.field_values()

make.py

@@ -37,9 +37,7 @@ def make_lambda_environment(**kwargs):
 def get_metadata():
     """build-time metadata for inclusion in template"""
     return {
-        "git_revision": subprocess.run(
-            ("git", "rev-parse", "HEAD"), capture_output=True, text=True
-        ).stdout.rstrip(),
+        "git_revision": subprocess.run(("git", "rev-parse", "HEAD"), capture_output=True, text=True).stdout.rstrip(),
         "git_repository": subprocess.run(
             ("git", "rev-parse", "--show-toplevel"), capture_output=True, text=True
         ).stdout.rstrip(),
@@ -59,9 +57,7 @@ def make_layer(cft: troposphere.Template):
 
 
 def make_template(*, metadata: dict) -> troposphere.Template:
-    description = (
-        "Automatically create a dedicated Quilt package for every Benchling notebook"
-    )
+    description = "Automatically create a dedicated Quilt package for every Benchling notebook"
     cft = troposphere.Template(Description=description)
     troposphere.Output(
         "TemplateBuildMetadata",
@@ -76,17 +72,15 @@ def make_template(*, metadata: dict) -> troposphere.Template:
         Type="String",
         AllowedPattern=r"^aws\.partner(/[\.\-_A-Za-z0-9]+){2,}$",
         Description=(
-            "Name of event bus where Benchling events are emitted, "
-            + "e.g aws.partner/benchling.com/tenant/app-name"
+            "Name of event bus where Benchling events are emitted, " + "e.g aws.partner/benchling.com/tenant/app-name"
         ),
     )
     benchling_tenant = troposphere.Parameter(
         "BenchlingTenant",
         template=cft,
         Type="String",
         AllowedPattern=r"^[^/]+$",
-        Description="Benchling tenant name, i.e. $BenchlingTenant in "
-        + "https://$BenchlingTenant.benchling.com",
+        Description="Benchling tenant name, i.e. $BenchlingTenant in " + "https://$BenchlingTenant.benchling.com",
     )
     benchling_client_id = troposphere.Parameter(
         "BenchlingClientId",

pyproject.toml

@@ -0,0 +1,5 @@
+[tool.black]
+line-length = 119
+target-version = ['py37']
+include = '\.pyi?$'
+# 'extend-exclude' excludes files or directories in addition to the defaults