Merge remote-tracking branch 'origin/12-add-precommit-hook-support' i…

…nto 12-add-precommit-hook-support

.github/workflows/python-package.yml

@@ -63,21 +63,11 @@ jobs:
     - name: Install dependencies
       run: |
         python -m pip install --upgrade pip
-        pip install --use-deprecated=legacy-resolver -e .[dev]
+        make develop
 
     - name: Test with pytest
       run: |
         make test
-
-    - name: Report test-coverage to DeepSource
-      run: |
-        # Install the CLI
-        curl https://deepsource.io/cli | sh
-  
-        # Send the report to DeepSource
-        ./bin/deepsource report --analyzer test-coverage --key python --value-file .coverage
-      env:
-        DEEPSOURCE_DSN: ${{ secrets.DEEPSOURCE_DSN }}
         
   deploy:
     needs:

.github/workflows/stale.yml

@@ -0,0 +1,24 @@
+# https://github.com/actions/stale
+
+name: 'Close stale issues and PRs'
+on:
+  schedule:
+    - cron: '1 1 * * *'
+
+jobs:
+  stale:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/stale@v8
+        with:
+          days-before-issue-stale: 30
+          days-before-issue-close: 7
+          stale-issue-message: 'This issue is stale because it has been open 30 days with no activity. Remove stale label or comment or this will be closed in 7 days.'
+          close-issue-message: 'This issue was closed because it has been stalled for 7 days with no activity.'
+
+          days-before-pr-stale: 30
+          days-before-pr-close: 7
+          stale-pr-message: 'This PR is stale because it has been open 30 days with no activity. Remove stale label or comment or this will be closed in 7 days.'
+          close-pr-message: 'This PR was closed because it has been stalled for 7 days with no activity.'
+
+          exempt-all-pr-assignees: true

Makefile

@@ -8,6 +8,8 @@
 SHELL:=/bin/bash -e -o pipefail -O globstar
 SELF:=$(firstword $(MAKEFILE_LIST))
 
+VE_DIR=venv
+
 TEST_DIRS:=tests
 DOC_TESTS:=src ./README.md
 
@@ -27,17 +29,16 @@ help:
 #=> devready: create venv, install prerequisites, install pkg in develop mode
 .PHONY: devready
 devready:
-	make venv && source venv/bin/activate && make develop
+	make ${VE_DIR} && source ${VE_DIR}/bin/activate && make develop
 	@echo '#################################################################################'
-	@echo '###    Do not forget to `source venv/bin/activate` to use this environment    ###'
+	@echo '###  Do not forget to `source ${VE_DIR}/bin/activate` to use this environment  ###'
 	@echo '#################################################################################'
 
 #=> venv: make a Python 3 virtual environment
-.PHONY: venv
-venv:
+${VE_DIR}:
 	python3 -mvenv $@; \
 	source $@/bin/activate; \
-	python -m ensurepip --upgrade; \
+	python3 -m ensurepip --upgrade; \
 	pip install --upgrade pip setuptools wheel
 
 #=> develop: install package in develop mode
@@ -129,7 +130,7 @@ cleaner: clean
 #=> cleanest: remove files and directories that require more time/network fetches to rebuild
 .PHONY: cleanest
 cleanest: cleaner
-	rm -fr .eggs .tox venv
+	rm -frv .eggs .tox venv
 
 #=> distclean: remove untracked files and other detritus
 .PHONY: distclean

pyproject.toml

@@ -6,7 +6,7 @@ authors = [
 description = "Example Package"
 readme = "README.md"
 license = { file="LICENSE.txt" }
-requires-python = ">=3.8"
+requires-python = ">=3.9"
 classifiers = [
     "Programming Language :: Python :: 3",
     "Programming Language :: Python :: 3.9",
@@ -18,8 +18,8 @@ classifiers = [
 dynamic = ["version"]
 
 [project.urls]
-"Homepage" = "https://github.com/biocommons/example"
-"Bug Tracker" = "https://github.com/biocommons/exmaple/issues"
+"Homepage" = "https://github.com/biocommons/biocommons.example"
+"Bug Tracker" = "https://github.com/biocommons/biocommons.example/issues"
 
 
 [build-system]
@@ -52,7 +52,7 @@ markers = [
 [tool.coverage.run]
 branch = true
 source = ["biocommons.example"]
-omit = ["*_test.py", "*/tests/*"]
+omit = ["*_test.py", "*/test/*", "*/tests/*"]
 
 
 [tool.coverage.report]
@@ -74,7 +74,7 @@ exclude_lines = [
 ]
 
 [tool.black]
-line-length = 120
+line-length = 100
 
 [isort]
 profile = "black"
@@ -91,4 +91,4 @@ disable = "R0913"
 
 
 [tool.pylint.format]
-max-line-length = "120"
+max-line-length = 100

setup.cfg

@@ -9,10 +9,6 @@ install_requires =
     coloredlogs~=15.0
     pyyaml~=6.0
 
-[options.entry_points]
-console_scripts =
-    marvin-quote = biocommons.example.__main__:main
-
 [options.extras_require]
 dev =
     bandit~=1.7
@@ -24,14 +20,18 @@ dev =
     mypy
     pre-commit~=3.4
     pylint~=2.14
-    pytest-cov~=4.0
+    pytest-cov~=4.1
     pytest-optional-tests
     pytest~=7.1
     tox~=3.25
     vcrpy
 docs = 
     mkdocs
 
+[options.entry_points]
+console_scripts =
+    marvin-quote = biocommons.example.__main__:main
+
 [options.packages.find]
 where = src
 exclude =
@@ -43,7 +43,7 @@ exclude =
 
 [flake8]
 ignore = E129,E133,E203,E221,E241,E251,E303,E266,H106,H904,W291
-max-line-length = 120
+max-line-length = 100
 max-complexity = 15
 hang-closing = true
 exclude =