Merge pull request #25 from biocommons/21-tidy-up-biocommons-example-…

…before-updating-repos

update README and Makefile

.github/workflows/python-package.yml

@@ -69,13 +69,14 @@ jobs:
       run: |
         make test
 
-    - name: Report test-coverage to DeepSource
-      run: |
-        # Install the CLI
-        curl https://deepsource.io/cli | sh
+    # #2: I get DEEPSOURCE_DSN not set (or) is empty despite seting. Giving up for now.
+    # - 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
+    #     # Send the report to DeepSource
+    #     ./bin/deepsource report --analyzer test-coverage --key python --value-file .coverage
 
   deploy:
     needs:
@@ -84,7 +85,7 @@ jobs:
     runs-on: ubuntu-latest
 
     steps:
-    - name: hello world
+    - name: Environment
       run: |
         echo "::group::Environment info"
         echo github.event_name = ${{ github.event_name }}

Makefile

@@ -5,12 +5,9 @@
 .PRECIOUS:
 .SUFFIXES:
 
-SHELL:=/bin/bash -e -o pipefail
+SHELL:=/bin/bash -e -o pipefail -O globstar
 SELF:=$(firstword $(MAKEFILE_LIST))
 
-PY_VERSION:=3.10
-VE_DIR=venv/${PY_VERSION}
-
 TEST_DIRS:=tests
 DOC_TESTS:=src ./README.md
 
@@ -30,26 +27,26 @@ help:
 #=> devready: create venv, install prerequisites, install pkg in develop mode
 .PHONY: devready
 devready:
-	make ${VE_DIR} && source ${VE_DIR}/bin/activate && make develop
+	make venv && source venv/bin/activate && make develop
 	@echo '#################################################################################'
-	@echo '###  Do not forget to `source ${VE_DIR}/bin/activate` to use this environment  ###'
+	@echo '###    Do not forget to `source venv/bin/activate` to use this environment    ###'
 	@echo '#################################################################################'
 
 #=> venv: make a Python 3 virtual environment
-venv: ${VE_DIR}
-${VE_DIR}: venv/%:
-	python$* -mvenv $@; \
+.PHONY: venv
+venv:
+	python3 -mvenv $@; \
 	source $@/bin/activate; \
 	python -m ensurepip --upgrade; \
 	pip install --upgrade pip setuptools wheel
 
 #=> develop: install package in develop mode
-.PHONY: develop install
+.PHONY: develop
 develop:
-	@if [ -z "$${VIRTUAL_ENV}" ]; then echo "Not in a virtual environment; see README.md" 1>&2; exit 1; fi
-	pip install -e .[dev,test]
+	pip install -e .[dev]
 
 #=> install: install package
+.PHONY: install
 install:
 	pip install .
 
@@ -76,10 +73,12 @@ cqa:
 .PHONY: test test-code test-docs
 test:
 	pytest
-test-code:
-	pytest src
 test-docs:
 	pytest docs
+test-code:
+	pytest src
+test-%:
+	pytest -m '$*' src
 
 #=> tox -- run all tox tests
 tox:
@@ -102,12 +101,11 @@ reformat:
 rename:
 	./sbin/rename-package
 
-# #=> docs -- make sphinx docs
-# .PHONY: docs
-# docs: develop
-# 	# RTD makes json. Build here to ensure that it works.
-# 	make -C doc html json
-
+#=> docs -- make sphinx docs
+.PHONY: docs
+docs: develop
+	# RTD makes json. Build here to ensure that it works.
+	make -C doc html json
 
 ############################################################################
 #= CLEANUP
@@ -127,10 +125,10 @@ cleaner: clean
 	rm -frv **/*.orig
 	rm -frv **/*.rej
 
-#=> cleanest: remove files and directories that are more expensive to rebuild
+#=> cleanest: remove files and directories that require more time/network fetches to rebuild
 .PHONY: cleanest
 cleanest: cleaner
-	rm -frv .eggs .tox venv
+	rm -fr .eggs .tox venv
 
 #=> distclean: remove untracked files and other detritus
 .PHONY: distclean

README.md

@@ -68,10 +68,3 @@ Try it:
 
 * Quality tools: Code reformatting with black and isort
 * GitHub Actions for testing and packaging
-
-# To Do
-
-* Docs (mkdocs w/mkdocstrings or sphinx)
-* Dockerfile
-* test only certain tags
-* fixture example

pyproject.toml

@@ -1,11 +1,11 @@
 [project]
 name = "biocommons.example"
 authors = [
-  { name="Bob the Builder", email="bob@nowhere.com" },
+  { name="biocommons contributors", email="biocommons-dev@googlegroups.com" },
 ]
 description = "Example Package"
 readme = "README.md"
-license = { file="LICENSE" }
+license = { file="LICENSE.txt" }
 requires-python = ">=3.8"
 classifiers = [
     "Programming Language :: Python :: 3",