From 046b85109be97f98b80fb929bebfea2c75e591d2 Mon Sep 17 00:00:00 2001
From: Christopher Tomkins-Tinch <tomkinsc@broadinstitute.org>
Date: Tue, 4 Jun 2024 09:18:02 -0400
Subject: [PATCH] update coveralls action; bump actions python to 3.10

---
 .coveragerc                 |  3 +--
 .github/workflows/build.yml | 17 ++++++++---------
 .gitignore                  |  3 ++-
 README.md                   |  5 +----
 conftest.py                 |  4 ++++
 5 files changed, 16 insertions(+), 16 deletions(-)

diff --git a/.coveragerc b/.coveragerc
index 6315a274..677d1d14 100644
--- a/.coveragerc
+++ b/.coveragerc
@@ -1,13 +1,12 @@
 # .coveragerc to control test coverage report
-# source is not used here because it is specified in pytest.ini
 [run]
 branch = True
 omit = tools/conda-tools/*
 disable_warnings =
     module-not-imported
+relative_files = True
 
 [report]
-
 exclude_lines =
     pragma: no cover
 
diff --git a/.github/workflows/build.yml b/.github/workflows/build.yml
index 33d764d9..55f058a8 100644
--- a/.github/workflows/build.yml
+++ b/.github/workflows/build.yml
@@ -125,7 +125,7 @@ jobs:
           fi
 
           echo "Building with cache from: $_CACHE_FROM"
-          docker build -t local/build-container:build $_CACHE_FROM .
+          docker build --squash -t local/build-container:build $_CACHE_FROM .
       - name: Deploy docker image
         run: |
           github_actions_ci/deploy-docker.sh
@@ -138,8 +138,8 @@ jobs:
     needs: build_docker
     runs-on: ubuntu-20.04
     env:
-      GITHUB_ACTIONS_PYTHON_VERSION: 3.8
-      PYTEST_ADDOPTS: "-rsxX -n 2 --durations=25 --fixture-durations=10 --junit-xml=pytest.xml --cov-report= --cov kmer_utils --cov metagenomics --cov taxon_filter --cov classify"
+      GITHUB_ACTIONS_PYTHON_VERSION: "3.10"
+      PYTEST_ADDOPTS: "-rsxX --durations=25 --fixture-durations=10 --junit-xml=pytest.xml --cov-config=.coveragerc --cov-report xml:coverage.xml --cov-report= --cov kmer_utils --cov metagenomics --cov taxon_filter --cov classify"
     steps:
       - name: checkout repository
         uses: actions/checkout@v3
@@ -186,12 +186,11 @@ jobs:
           mkdir coverage
       - name: test with docker
         run: |
-          docker run -e _JAVA_OPTIONS -e PYTEST_ADDOPTS -v `pwd`/coverage:/coverage -v `pwd`/test:/opt/viral-ngs/source/test --entrypoint /bin/bash $DOCKER_TAG -c 'set -e; cd /opt/viral-ngs/source; pytest test/unit; cp .coverage /coverage'
-      - name: run coveralls
-        run: |
-          mv coverage/.coverage .
-          pip install coveralls>=1.3.0
-          coveralls --service=github
+          docker run -e _JAVA_OPTIONS -e PYTEST_ADDOPTS -v `pwd`/.coveragerc:/opt/viral-ngs/source/.coveragerc -v `pwd`/coverage:/coverage -v `pwd`/test:/opt/viral-ngs/source/test --entrypoint /bin/bash $DOCKER_TAG -c 'set -e; cd /opt/viral-ngs/source; pytest -n $(nproc) test/unit; cp coverage.xml /coverage;'
+      - name: Run coveralls
+        uses: coverallsapp/github-action@v2
+        with:
+          file: coverage/coverage.xml
 
   ## note: this test_docs job does not actually produce the output on readthedocs
   ## readthedocs does its own build trigger. this job exists simply to alert us
diff --git a/.gitignore b/.gitignore
index 5a3e21a7..eb898c12 100644
--- a/.gitignore
+++ b/.gitignore
@@ -53,7 +53,8 @@ htmlcov/
 nosetests.xml
 pytest.xml
 coverage.xml
-.coverage*
+.coverage
+coverage/
 
 test/input/TestVPhaser2/in.bam.bti
 
diff --git a/README.md b/README.md
index 53b9fb0b..6a468cab 100644
--- a/README.md
+++ b/README.md
@@ -1,10 +1,7 @@
 [![Docker Repository on Quay](https://quay.io/repository/broadinstitute/viral-classify/status "Docker Repository on Quay")](https://quay.io/repository/broadinstitute/viral-classify)
 [![Build Status](https://github.com/broadinstitute/viral-classify/actions/workflows/build.yml/badge.svg?branch=master)](https://github.com/broadinstitute/viral-classify/actions)
 [![Documentation Status](https://readthedocs.org/projects/viral-classify/badge/?version=latest)](https://viral-classify.readthedocs.io/en/latest/?badge=latest)
-<!--
-[![Coverage Status](https://coveralls.io/repos/broadinstitute/viral-ngs/badge.png)](https://coveralls.io/r/broadinstitute/viral-ngs)
-[![Code Health](https://landscape.io/github/broadinstitute/viral-ngs/master/landscape.svg?style=flat)](https://landscape.io/github/broadinstitute/viral-ngs)
--->
+[![Coverage Status](https://coveralls.io/repos/github/broadinstitute/viral-classify/badge.svg)](https://coveralls.io/github/broadinstitute/viral-classify)
 
 viral-classify
 =========
diff --git a/conftest.py b/conftest.py
index 87bd0dc6..fecbbbd1 100644
--- a/conftest.py
+++ b/conftest.py
@@ -43,6 +43,10 @@ def pytest_configure(config):
     reporter = FixtureReporter(config)
     config.pluginmanager.register(reporter, 'fixturereporter')
 
+    config.addinivalue_line(
+        "markers", "slow: marks tests as slow (deselect with '-m \"not slow\"')"
+    )
+
 
 def pytest_collection_modifyitems(config, items):
     if config.getoption("--runslow"):