From 58c1296fd31ee1cfb2009ce05ecfeae3ff433021 Mon Sep 17 00:00:00 2001
From: Christopher Tomkins-Tinch <tomkinsc@broadinstitute.org>
Date: Tue, 4 Jun 2024 09:16:19 -0400
Subject: [PATCH] update coveralls action; bump actions python to 3.10

---
 .coveragerc                 | 21 +++++++++++++++++++++
 .github/workflows/build.yml | 15 +++++++--------
 .gitignore                  |  3 ++-
 README.md                   |  6 +-----
 conftest.py                 |  4 ++++
 5 files changed, 35 insertions(+), 14 deletions(-)
 create mode 100644 .coveragerc

diff --git a/.coveragerc b/.coveragerc
new file mode 100644
index 00000000..19be0727
--- /dev/null
+++ b/.coveragerc
@@ -0,0 +1,21 @@
+# .coveragerc to control test coverage report
+[run]
+branch = True
+omit = tools/conda-tools/*
+disable_warnings =
+    module-not-imported
+relative_files = True
+
+[report]
+
+exclude_lines =
+    pragma: no cover
+
+    #raise AssertionError
+    raise NotImplementedError
+
+    def __repr__
+    if self\.debug
+
+    if 0:
+    if __name__ == .__main__.:
diff --git a/.github/workflows/build.yml b/.github/workflows/build.yml
index a8ce4cf3..8003de2e 100644
--- a/.github/workflows/build.yml
+++ b/.github/workflows/build.yml
@@ -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 assembly --cov assemble"
+      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 assembly --cov assemble"
     steps:
       - name: checkout repository
         uses: actions/checkout@v4
@@ -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 6d867ad3..cfab78f3 100644
--- a/README.md
+++ b/README.md
@@ -1,11 +1,7 @@
 [![Docker Repository on Quay](https://quay.io/repository/broadinstitute/viral-assemble/status "Docker Repository on Quay")](https://quay.io/repository/broadinstitute/viral-assemble)
 [![Build Status](https://github.com/broadinstitute/viral-assemble/actions/workflows/build.yml/badge.svg?branch=master)](https://github.com/broadinstitute/viral-assemble/actions)
 [![Documentation Status](https://readthedocs.org/projects/viral-assemble/badge/?version=latest)](https://viral-assemble.readthedocs.io/en/latest/?badge=latest)
-<!--
-[![broad-viral-badge](https://img.shields.io/badge/install%20from-broad--viral-green.svg?style=flat-square)](https://anaconda.org/broad-viral/viral-ngs)
-[![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-assemble/badge.svg)](https://coveralls.io/github/broadinstitute/viral-assemble)
 
 viral-assemble
 ==============
diff --git a/conftest.py b/conftest.py
index 1274e1d5..a73dc75b 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"):