add some ci components

epi2me-labs · May 13, 2022 · 29701d7 · 29701d7
1 parent aca9cdc
commit 29701d7
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diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml
@@ -1,25 +1,84 @@
-image: ubuntu:xenial
+include:
+    - project: "epi2melabs/ci-templates"
+      file: "push-github.yaml"
+    - project: "epi2melabs/ci-templates"
+      file: "push-conda.yaml"
+
+image: ${UBUNTUIMAGE}:20.04
+
+.prep-image: &prep-image |
+    export DEBIAN_FRONTEND=noninteractive
+    apt update -qq
+    apt install -y --no-install-recommends make wget python3-all-dev python3-venv 
+
 
 stages:
     - test
-    - pages
+    - build
+    - prerelease
     - release
+    - postrelease
+
+# Insist that the version in __init__.py matches the git tag
+.check-versions: &check-versions |
+    PYVER="v"$(grep "__version__ = " ${CI_PROJECT_NAME}/__init__.py | awk '{gsub("\"","",$3); print $3}')
+    TAGVER=${CI_COMMIT_TAG}
+    if [[ "${PYVER}" != "${TAGVER}" ]]; then
+        echo "Mismatching TAG and PACKAGE versions:"
+        echo " -     TAG:'$TAGVER'"
+        echo " - PACKAGE:'$TAGVER'"
+        exit 1
+    else
+        echo "TAG and PACKAGE versions agree: '${PYVER}'"
+    fi
+
+# Insist a CHANGELOG entry has been made for tags
+.check-changelog: &check-changelog |
+    TAGVER=${CI_COMMIT_TAG}
+    MATCHES=$(grep -c "## \[${TAGVER}\]" CHANGELOG.md || exit 0)
+    if [[ "${MATCHES}" != "1" ]]; then
+        echo "Expected one match to '${CI_COMMIT_TAG}' in CHANGELOG, found ${MATCHES}"
+        exit 1
+    else
+        echo "Found CHANGELOG.md entry for tag"
+    fi
+
+test:
+    stage: test
+    script:
+        - *prep-image #?
+        - make test
+        - make docs
+        - make sdist
+    artifacts:
+        paths:
+            - dist/*.tar.gz
+
+deploy-checks:
+    stage: prerelease
+    script:
+        - *check-versions
+        - *check-changelog
+    rules:
+        - if: '$CI_COMMIT_TAG =~ /^v[[:digit:]]+\.[[:digit:]]+\.[[:digit:]]+$/'
+
+deploy:pypi:
+    stage: release
+    script:
+        - *prep-image
+        - make pypi_build/bin/activate
+        - source pypi_build/bin/activate
+        - twine upload --non-interactive dist/*.tar.gz
+    rules:
+        - if: '$CI_COMMIT_TAG =~ /^v[[:digit:]]+\.[[:digit:]]+\.[[:digit:]]+$/'
+
+conda:
+    extends:
+        - .deploy-conda
+    before_script:
+        - *prep-image
+        - export CONDA_PKG=${CI_PROJECT_NAME}
+        - export CONDA_PKG_VERSION=${CI_COMMIT_TAG/v/}
+        - cd conda
 
-before_script:
-    - apt-get update
-    - apt-get remove python
-    - apt-get install -y python3 python3-pip make python3-numpy python3-matplotlib hmmer 
-    - update-alternatives --install /usr/bin/python python /usr/bin/python3 10
-    - alias python=python3; pip3 install --upgrade pip
-    - hash -r pip3
-    - alias python=python3; pip3 install sphinx sphinx-argparse sphinx_rtd_theme pytest pandas
-    - alias python=python3; pip3 install -e ./
-
-
-do_testing:
-  stage: test
-  script:
-    - alias python=python3; make test
-  except:
-    - tags
-
+# Don't need a mac conda package since the project is pure python
diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -0,0 +1,9 @@
+# Changelog
+All notable changes to this project will be documented in this file.
+
+The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/),
+and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
+
+## [v2.7.0]
+### Added
+- PCS111 cDNA sequencing kit added
diff --git a/Makefile b/Makefile
@@ -1,72 +1,52 @@
-MODULE=pychopper
-
-.PHONY: clean clean-test clean-pyc clean-build docs com help 
-
-.DEFAULT_GOAL := help
-
-define PRINT_HELP_PYSCRIPT
-import re, sys
-
-for line in sys.stdin:
-	match = re.match(r'^([a-zA-Z_-]+):.*?## (.*)$$', line)
-	if match:
-		target, help = match.groups()
-		print("%-20s %s" % (target, help))
-endef
-export PRINT_HELP_PYSCRIPT
-
-help:
-	@python -c "$$PRINT_HELP_PYSCRIPT" < $(MAKEFILE_LIST)
-
-clean: clean-build clean-pyc clean-test ## remove all build, test, coverage and Python artifacts
-
-
-clean-build: ## remove build artifacts
-	rm -fr build/
-	rm -fr dist/
-	rm -fr .eggs/
-	find . -name '*.egg-info' -exec rm -fr {} +
-	find . -name '*.egg' -exec rm -f {} +
-
-clean-pyc: ## remove Python file artifacts
-	find . -name '*.pyc' -exec rm -f {} +
-	find . -name '*.pyo' -exec rm -f {} +
-	find . -name '*~' -exec rm -f {} +
-	find . -name '__pycache__' -exec rm -fr {} +
-
-clean-test: ## remove test and coverage artifacts
-	rm -f .coverage
-	rm -fr htmlcov/
-
-lint: ## check style with flake8
-	@(flake8 --max-line-length=120 $(MODULE) | grep -v "E501 line too long") || true
-	@(flake8 --max-line-length=120 scripts/*.py | grep -v "E501 line too long") || true
-
-test: ## run tests quickly with the default Python
-	py.test
-
-coverage: ## check code coverage quickly with the default Python
-		coverage run --source $(MODULE) --omit="*/tests/*,*__init__.py" `which py.test`
-		coverage report -m --omit="*/tests/*,*__init__.py"
-		coverage html
-
-docs: ## generate Sphinx HTML documentation, including API docs
-	@cd docs; make clean html
-
-servedocs: docs ## compile the docs watching for changes
-	watchmedo shell-command -p '*.rst' -c '$(MAKE) -C docs html' -R -D .
-
-release: clean ## package and upload a release
-	python setup.py sdist upload
-	python setup.py bdist_wheel upload
-
-dist: clean ## builds source and wheel package
-	python setup.py sdist
-	python setup.py bdist_wheel
-	ls -l dist
-
-install: clean ## install the package to the active Python's site-packages
-	python setup.py install
-
-com: ## commit all changes to git
-	git commit -a
+.PHONY: develop docs
+
+PYTHON ?= python3
+
+IN_VENV=. ./venv/bin/activate
+
+venv/bin/activate:
+	test -d venv || $(PYTHON) -m venv venv
+	${IN_VENV} && pip install pip --upgrade
+	${IN_VENV} && pip install -r requirements.txt
+
+develop: venv/bin/activate
+	${IN_VENV} && python setup.py develop
+
+test: venv/bin/activate
+	${IN_VENV} && pip install flake8 flake8-rst-docstrings flake8-docstrings flake8-import-order flake8-forbid-visual-indent
+	${IN_VENV} && flake8 aplanat \
+		--import-order-style google --application-import-names aplanat \
+		--statistics
+	# demo should run without error
+	${IN_VENV} && python setup.py install
+	${IN_VENV} && aplanat demo
+
+IN_BUILD=. ./pypi_build/bin/activate
+pypi_build/bin/activate:
+	test -d pypi_build || $(PYTHON) -m venv pypi_build --prompt "(pypi) "
+	${IN_BUILD} && pip install pip --upgrade
+	${IN_BUILD} && pip install --upgrade pip setuptools twine wheel readme_renderer[md] keyrings.alt
+
+.PHONY: sdist
+sdist: pypi_build/bin/activate
+	${IN_BUILD} && python setup.py sdist
+
+.PHONY: clean
+clean:
+	rm -rf __pycache__ dist build venv aplanat.egg-info tmp docs/_build
+
+# Documentation
+SPHINXOPTS    =
+SPHINXBUILD   = sphinx-build
+BUILDDIR      = _build
+PAPER         =
+PAPEROPT_a4     = -D latex_paper_size=a4
+PAPEROPT_letter = -D latex_paper_size=letter
+ALLSPHINXOPTS   = -d $(BUILDDIR)/doctrees $(PAPEROPT_$(PAPER)) $(SPHINXOPTS) .
+DOCSRC = docs
+docs: venv/bin/activate
+	${IN_VENV} && pip install sphinx sphinx_rtd_theme sphinx-argparse
+	${IN_VENV} && cd $(DOCSRC) && $(SPHINXBUILD) -b html $(ALLSPHINXOPTS) $(BUILDDIR)/html
+	@echo
+	@echo "Build finished. The HTML pages are in $(DOCSRC)/$(BUILDDIR)/html."
+	touch $(DOCSRC)/$(BUILDDIR)/html/.nojekyll
diff --git a/MakefileOld b/MakefileOld
@@ -0,0 +1,72 @@
+MODULE=pychopper
+
+.PHONY: clean clean-test clean-pyc clean-build docs com help 
+
+.DEFAULT_GOAL := help
+
+define PRINT_HELP_PYSCRIPT
+import re, sys
+
+for line in sys.stdin:
+	match = re.match(r'^([a-zA-Z_-]+):.*?## (.*)$$', line)
+	if match:
+		target, help = match.groups()
+		print("%-20s %s" % (target, help))
+endef
+export PRINT_HELP_PYSCRIPT
+
+help:
+	@python -c "$$PRINT_HELP_PYSCRIPT" < $(MAKEFILE_LIST)
+
+clean: clean-build clean-pyc clean-test ## remove all build, test, coverage and Python artifacts
+
+
+clean-build: ## remove build artifacts
+	rm -fr build/
+	rm -fr dist/
+	rm -fr .eggs/
+	find . -name '*.egg-info' -exec rm -fr {} +
+	find . -name '*.egg' -exec rm -f {} +
+
+clean-pyc: ## remove Python file artifacts
+	find . -name '*.pyc' -exec rm -f {} +
+	find . -name '*.pyo' -exec rm -f {} +
+	find . -name '*~' -exec rm -f {} +
+	find . -name '__pycache__' -exec rm -fr {} +
+
+clean-test: ## remove test and coverage artifacts
+	rm -f .coverage
+	rm -fr htmlcov/
+
+lint: ## check style with flake8
+	@(flake8 --max-line-length=120 $(MODULE) | grep -v "E501 line too long") || true
+	@(flake8 --max-line-length=120 scripts/*.py | grep -v "E501 line too long") || true
+
+test: ## run tests quickly with the default Python
+	py.test
+
+coverage: ## check code coverage quickly with the default Python
+		coverage run --source $(MODULE) --omit="*/tests/*,*__init__.py" `which py.test`
+		coverage report -m --omit="*/tests/*,*__init__.py"
+		coverage html
+
+docs: ## generate Sphinx HTML documentation, including API docs
+	@cd docs; make clean html
+
+servedocs: docs ## compile the docs watching for changes
+	watchmedo shell-command -p '*.rst' -c '$(MAKE) -C docs html' -R -D .
+
+release: clean ## package and upload a release
+	python setup.py sdist upload
+	python setup.py bdist_wheel upload
+
+dist: clean ## builds source and wheel package
+	python setup.py sdist
+	python setup.py bdist_wheel
+	ls -l dist
+
+install: clean ## install the package to the active Python's site-packages
+	python setup.py install
+
+com: ## commit all changes to git
+	git commit -a