Upgrade cgap-portal to pytest 7.2 (C4-183)

.github/workflows/main.yml

@@ -1,4 +1,4 @@
-# Build for cgap-portal
+# Main python test suite for cgap-portal
 
 name: CI
 
@@ -17,15 +17,15 @@ on:
 jobs:
   # This workflow contains a single job called "build"
   build:
-    name: Test Suite for cgap-portal (Python 3.8, Node 16)
+    name: cgap-portal tests
 
     # The type of runner that the job will run on
     runs-on: ubuntu-20.04
 
     # Build matrix
     strategy:
       matrix:
-        test_type: ['UNIT', 'NPM', 'Docker']
+        test_type: ['UNIT', 'INDEX', 'DOCKER']
         # We are really not set up for these next two to be multiplicative, so be careful adding more.
         python_version: ['3.8']
         node_version: ['16']
@@ -45,7 +45,7 @@ jobs:
           check-latest: false
 
       - name: Install/Link Postgres
-        if: ${{ matrix.test_type == 'NPM' || matrix.test_type == 'UNIT' }}
+        if: ${{ matrix.test_type == 'UNIT' || matrix.test_type == 'INDEX' }}
         run: |
           sudo apt-get install curl ca-certificates gnupg
           curl https://www.postgresql.org/media/keys/ACCC4CF8.asc | sudo apt-key add -
@@ -55,7 +55,7 @@ jobs:
           echo "/usr/lib/postgresql/14/bin" >> $GITHUB_PATH
           sudo ln -s /usr/lib/postgresql/14/bin/initdb /usr/local/bin/initdb
       - name: Install Deps
-        if: ${{ matrix.test_type == 'NPM' || matrix.test_type == 'UNIT' }}
+        if: ${{ matrix.test_type == 'INDEX' || matrix.test_type == 'UNIT' }}
         run: |
           node --version
           make build
@@ -66,34 +66,28 @@ jobs:
           aws-secret-access-key: ${{ secrets.AWS_SECRET_ACCESS_KEY }}
           aws-region: us-east-1
 
-      - name: QA (NPM)
-        if: ${{ matrix.test_type == 'NPM' }}
+      - name: QA (UNIT)
+        if: ${{ matrix.test_type == 'UNIT' }}
         env:
           S3_ENCRYPT_KEY: ${{ secrets.S3_ENCRYPT_KEY }}
           # The need for this old environment variable name will go away soon.
-          # Once the new snovault is in, we should retain these for a little while to make sure the right
-          # variable is being used, and then this can go away. -kmp 9-Mar-2021
-          # I have named the ID slightly differently so we can see if the old names are in use.
-          TRAVIS_JOB_ID: cgap-npm-x-test-${{ github.run_number }}-
+          TRAVIS_JOB_ID: cgap-unit-x-test-${{ github.run_number }}-
           # This will be the new environment variable name.
-          TEST_JOB_ID: cgap-npm-test-${{ github.run_number }}-
+          TEST_JOB_ID: cgap-unit-test-${{ github.run_number }}-
           GLOBAL_ENV_BUCKET: ${{ secrets.GLOBAL_ENV_BUCKET }}
           ACCOUNT_NUMBER: $ {{ secrets.ACCOUNT_NUMBER }}
         run: |
-          # npm test
+          make remote-test-unit
           make remote-test-npm
 
-      - name: Cleanup (NPM)
-        if: ${{ always() && matrix.test_type == 'NPM' }}
+      - name: Cleanup (UNIT)
+        if: ${{ always() && matrix.test_type == 'UNIT' }}
         env:
           S3_ENCRYPT_KEY: ${{ secrets.S3_ENCRYPT_KEY }}
           # The need for this old environment variable name will go away soon.
-          # Once the new snovault is in, we should retain these for a little while to make sure the right
-          # variable is being used, and then this can go away. -kmp 9-Mar-2021
-          # I have named the ID slightly differently so we can see if the old names are in use.
-          TRAVIS_JOB_ID: cgap-npm-x-test-${{ github.run_number }}-
+          TRAVIS_JOB_ID: cgap-unit-x-test-${{ github.run_number }}-
           # This will be the new environment variable name.
-          TEST_JOB_ID: cgap-npm-test-${{ github.run_number }}-
+          TEST_JOB_ID: cgap-unit-test-${{ github.run_number }}-
           GLOBAL_ENV_BUCKET: ${{ secrets.GLOBAL_ENV_BUCKET }}
           ACCOUNT_NUMBER: $ {{ secrets.ACCOUNT_NUMBER }}
         run: |
@@ -102,27 +96,33 @@ jobs:
           poetry run wipe-test-indices $TRAVIS_JOB_ID search-cgap-unit-testing-opensearch-tcs45cjpwgdzoi7pafr6oewq6u.us-east-1.es.amazonaws.com:443
           poetry run wipe-test-indices cgap-test-$TRAVIS_JOB_ID search-cgap-unit-testing-opensearch-tcs45cjpwgdzoi7pafr6oewq6u.us-east-1.es.amazonaws.com:443
 
-      - name: QA (UNIT)
-        if: ${{ matrix.test_type == 'UNIT' }}
+      - name: QA (INDEX)
+        if: ${{ matrix.test_type == 'INDEX' }}
         env:
           S3_ENCRYPT_KEY: ${{ secrets.S3_ENCRYPT_KEY }}
           # The need for this old environment variable name will go away soon.
-          TRAVIS_JOB_ID: cgap-unit-x-test-${{ github.run_number }}-
+          # Once the new snovault is in, we should retain these for a little while to make sure the right
+          # variable is being used, and then this can go away. -kmp 9-Mar-2021
+          # I have named the ID slightly differently so we can see if the old names are in use.
+          TRAVIS_JOB_ID: cgap-idx-x-test-${{ github.run_number }}-
           # This will be the new environment variable name.
-          TEST_JOB_ID: cgap-unit-test-${{ github.run_number }}-
+          TEST_JOB_ID: cgap-idx-test-${{ github.run_number }}-
           GLOBAL_ENV_BUCKET: ${{ secrets.GLOBAL_ENV_BUCKET }}
           ACCOUNT_NUMBER: $ {{ secrets.ACCOUNT_NUMBER }}
         run: |
-          make remote-test-unit
+          make remote-test-indexing
 
-      - name: Cleanup (UNIT)
-        if: ${{ always() && matrix.test_type == 'UNIT' }}
+      - name: Cleanup (INDEX)
+        if: ${{ always() && matrix.test_type == 'INDEX' }}
         env:
           S3_ENCRYPT_KEY: ${{ secrets.S3_ENCRYPT_KEY }}
           # The need for this old environment variable name will go away soon.
-          TRAVIS_JOB_ID: cgap-unit-x-test-${{ github.run_number }}-
+          # Once the new snovault is in, we should retain these for a little while to make sure the right
+          # variable is being used, and then this can go away. -kmp 9-Mar-2021
+          # I have named the ID slightly differently so we can see if the old names are in use.
+          TRAVIS_JOB_ID: cgap-idx-x-test-${{ github.run_number }}-
           # This will be the new environment variable name.
-          TEST_JOB_ID: cgap-unit-test-${{ github.run_number }}-
+          TEST_JOB_ID: cgap-idx-test-${{ github.run_number }}-
           GLOBAL_ENV_BUCKET: ${{ secrets.GLOBAL_ENV_BUCKET }}
           ACCOUNT_NUMBER: $ {{ secrets.ACCOUNT_NUMBER }}
         run: |
@@ -132,7 +132,7 @@ jobs:
           poetry run wipe-test-indices cgap-test-$TRAVIS_JOB_ID search-cgap-unit-testing-opensearch-tcs45cjpwgdzoi7pafr6oewq6u.us-east-1.es.amazonaws.com:443
 
       - name: Docker Build
-        if: ${{ matrix.test_type == 'Docker' && matrix.node_version == '16' && matrix.python_version == '3.8' }}
+        if: ${{ matrix.test_type == 'DOCKER' && matrix.node_version == '16' && matrix.python_version == '3.8' }}
         run: |
           touch deploy/docker/local/docker_development.ini  # cheap substitute for prepare-docker to make ignored file
           docker build .

CHANGELOG.rst

@@ -6,6 +6,15 @@ cgap-portal
 Change Log
 ----------
 
+
+12.10.2
+=======
+
+* Backport pytest 7.2 support from Fourfront
+* Move to poetry 1.3.2
+* Remove dependence in a pinned version of setuptools
+
+
 12.10.1
 =======
 `PR 702: VEP QC metrics fix <https://github.com/dbmi-bgm/cgap-portal/pull/702>`_

Dockerfile

@@ -43,7 +43,7 @@ RUN apt-get update && apt-get upgrade -y && \
     apt-get install -y --no-install-recommends vim emacs net-tools ca-certificates build-essential \
     gcc zlib1g-dev postgresql-client libpq-dev git make curl libmagic-dev && \
     pip install --upgrade pip && \
-    pip install poetry==1.1.15 && \
+    pip install poetry==1.3.2 && \
     curl -o- https://raw.githubusercontent.com/nvm-sh/nvm/${NVM_VERSION}/install.sh | bash && \
     . "$NVM_DIR/nvm.sh" && nvm install ${NODE_VERSION} && \
     nvm use v${NODE_VERSION} && \

Makefile

@@ -36,7 +36,12 @@ npm-setup:  # runs all front-end setup
 	make aws-ip-ranges
 
 moto-setup:  # optional moto setup that must be done separately
-	pip install "moto[server]==1.3.7"
+	@# This setup was needed here because there was no bracket syntax in pypoetry.com.
+	@# Now that we're using a higher version of moto, and not using the server parts, we don't need this here.
+	@# It's now all done in pyproject.toml, getting a higher version as well.
+	@# This comment and this make target can go away once that's proven effective. -kmp 23-Mar-2023
+	@# pip install "moto[server]==1.3.7"
+	@echo "'moto[server]' not being installed here. Regular 'moto' will be installed by pyproject.toml."
 
 macpoetry-install:  # Same as 'poetry install' except that on OSX Catalina, an environment variable wrapper is needed
 	bin/macpoetry-install
@@ -45,10 +50,11 @@ configure:  # does any pre-requisite installs
 	@#pip install --upgrade pip==21.0.1
 	pip install --upgrade pip
 	@#pip install poetry==1.1.9  # this version is known to work. -kmp 11-Mar-2021
-	# Pin to version 1.1.15 for now to avoid this error:
-	#   Because encoded depends on wheel (>=0.29.0) which doesn't match any versions, version solving failed.
-	pip install poetry==1.1.15
-	pip install setuptools==57.5.0 # this version allows 2to3, any later will break -wrr 20-Sept-2021
+	@# Pin to version 1.1.15 for now to avoid this error:
+	@#   Because encoded depends on wheel (>=0.29.0) which doesn't match any versions, version solving failed.
+	pip install poetry==1.3.2
+	pip install setuptools  # ==57.5.0 # this version allows 2to3, any later will break -wrr 20-Sept-2021
+	pip install wheel
 	poetry config virtualenvs.create false --local # do not create a virtualenv - the user should have already done this -wrr 20-Sept-2021
 
 build-poetry:
@@ -150,46 +156,108 @@ clean-python:
 	pip uninstall encoded
 	pip uninstall -y -r <(pip freeze)
 
-test:
+test-full:
 	@git log -1 --decorate | head -1
 	@date
-	make test-unit || echo "unit tests failed"
+	make test-static-full || echo "static tests failed"
+	make test-unit-full || echo "unit tests failed"
 	make test-npm || echo "npm tests failed"
-	make test-static || echo "static tests failed"
+	make test-indexing-full || echo "indexing tests failed"
+	@git log -1 --decorate | head -1
+	@date
+
+test:
 	@git log -1 --decorate | head -1
 	@date
+	make test-static && make test-unit && make test-npm && make test-indexing
+	@git log -1 --decorate | head -1
+	@date
+
+
+BASE_MARKERS = not manual and not sloppy and not static and not broken
+# Unit tests
+NORM_MARKERS = not performance and not integratedx
+# Performance tests
+PERF_MARKERS = performance and not integratedx
+# Integration tests
+INTG_MARKERS = not performance and (integrated or integratedx)
 
 retest:
 	poetry run python -m pytest -vv -r w --last-failed
 
 test-any:
 	poetry run python -m pytest -xvv -r w --timeout=200
 
-test-npm:
-	poetry run python -m pytest -xvv -r w --durations=25 --timeout=600 -m "not manual and not integratedx and not performance and not broken and not sloppy and not indexing and not static"
-
 test-unit:
-	poetry run python -m pytest -xvv -r w --durations=25 --timeout=200 -m "not manual and not integratedx and not performance and not broken and not sloppy and indexing and not static"
+	poetry run python -m pytest -xvv -r w --durations=25 --timeout=600 -m "${BASE_MARKERS} and ${NORM_MARKERS} and not indexing"
+
+test-unit-full:
+	poetry run python -m pytest -vv  -r w --durations=25 --timeout=600 -m "${BASE_MARKERS} and ${NORM_MARKERS} and not indexing"
+
+test-indexing-full:
+	make test-indexing-es-full
+	make test-indexing-not-es-full
+
+test-indexing-es-full:
+	poetry run python -m pytest -vv  -r w --durations=25 --timeout=300 -m "${BASE_MARKERS} and ${NORM_MARKERS} and indexing and es"
+
+test-indexing-not-es-full:
+	poetry run python -m pytest -vv  -r w --durations=25 --timeout=300 -m "${BASE_MARKERS} and ${NORM_MARKERS} and indexing and not es"
+
+test-indexing:
+	make test-indexing-es && make test-indexing-not-es
+
+test-indexing-es:
+	poetry run python -m pytest -xvv -r w --durations=25 --timeout=200 -m "${BASE_MARKERS} and ${NORM_MARKERS} and indexing and es"
+
+test-indexing-not-es:
+	poetry run python -m pytest -xvv -r w --durations=25 --timeout=200 -m "${BASE_MARKERS} and ${NORM_MARKERS} and indexing and not es"
 
 test-performance:
-	poetry run python -m pytest -xvv -r w --timeout=200 -m "not manual and not integratedx and performance and not broken and not sloppy and not static"
+	poetry run python -m pytest -xvv -r w --timeout=200 -m "${BASE_MARKERS} and ${PERF_MARKERS}"
 
 test-integrated:
-	poetry run python -m pytest -xvv -r w --timeout=200 -m "not manual and (integrated or integratedx) and not performance and not broken and not sloppy and not static"
+	poetry run python -m pytest -xvv -r w --timeout=200 -m "${BASE_MARKERS} and ${INTG_MARKERS}"
 
-test-static:
+test-npm:
+	@#At one point we did 'npm test' here, but now we do separate cypress tests. -kmp 24-Mar-2023
+	@echo "npm tests would run here if they were enabled. Instead we have a separate Cypress test GA workflow."
+
+test-static-full:
 	poetry run python -m pytest -vv -m static
-	make lint
+	make lint-full
+
+test-static:
+	poetry run python -m pytest -vv -m static && make lint
+
+TEST_NAME ?= missing_TEST_NAME_parameter
+
+test-one:
+	poetry run python -m pytest -xvv -r w --durations=25 --timeout=200 -m "${BASE_MARKERS} and ${NORM_MARKERS}" -k "${TEST_NAME}"
+
+REMOTE_ES = search-cgap-unit-testing-opensearch-tcs45cjpwgdzoi7pafr6oewq6u.us-east-1.es.amazonaws.com:443
+REMOTE_MARKERS = ${BASE_MARKERS} and ${NORM_MARKERS} and not broken_remotely
 
 remote-test:  # Actually, we don't normally use this. Instead the GA workflow sets up two parallel tests.
-	make remote-test-unit
-	make remote-test-npm
+	make remote-test-indexing && make remote-test-npm && make remote-test-unit
+
+remote-test-npm:
+	make test-npm
+
+remote-test-unit:
+	make remote-test-indexing-not-es
+
+remote-test-not-indexing:  # Note this only does the 'not indexing' tests
+	poetry run python -m pytest -xvv -r w --durations=25 --timeout=600 -m "${REMOTE_MARKERS} and not indexing" --aws-auth --es ${REMOTE_ES} --instafail --force-flaky --max-runs=2 --durations=20 --cov src/encoded
 
-remote-test-npm:  # Note this only does the 'not indexing' tests
-	poetry run python -m pytest -xvv -r w --instafail --force-flaky --max-runs=2 --timeout=600 -m "not manual and not integratedx and not performance and not broken and not broken_remotely and not sloppy and not indexing and not static" --aws-auth --durations=20 --cov src/encoded --es search-cgap-unit-testing-opensearch-tcs45cjpwgdzoi7pafr6oewq6u.us-east-1.es.amazonaws.com:443
+remote-test-indexing:
+	make remote-test-indexing-es && make remote-test-not-indexing
 
-remote-test-unit:  # Note this does the 'indexing' tests
-	poetry run python -m pytest -xvv -r w --timeout=300 -m "not manual and not integratedx and not performance and not broken and not broken_remotely and not sloppy and indexing and not static" --aws-auth --es search-cgap-unit-testing-opensearch-tcs45cjpwgdzoi7pafr6oewq6u.us-east-1.es.amazonaws.com:443
+remote-test-indexing-es:
+	poetry run python -m pytest -xvv -r w --durations=25 --timeout=300 -m "${REMOTE_MARKERS} and indexing and es" --aws-auth --es ${REMOTE_ES} --cov-append
+
+remote-test-indexing-not-es:
+	poetry run python -m pytest -xvv -r w --durations=25 --timeout=300 -m "${REMOTE_MARKERS} and indexing and not es" --aws-auth --es ${REMOTE_ES} --cov-append
 
 update:  # updates dependencies
 	poetry update
@@ -250,10 +318,13 @@ tag-and-push-docker-production:
 	docker push ${AWS_ACCOUNT}.dkr.ecr.us-east-1.amazonaws.com/${ENV_NAME}:latest
 	date
 
-lint:
+lint-full:
 	@flake8 deploy/ || echo "flake8 failed for deploy/"
 	@flake8 src/encoded/ || echo "flake8 failed for src/encoded"
 
+lint:
+	@flake8 deploy/ && flake8 src/encoded/
+
 help:
 	@make info