Hoist coverage setup out of individual cram test files and into the C…

…I workflow This avoids baking in coverage to the tests and lets it remain a separate concern (e.g. CI's concern). In my experience it's better to have coverage tracing happen outside of tests (i.e. the tests are unaware) rather than as integrated into the tests themselves. Partially reverts commit 723d609, which added code for coverage to each cram test file. I chose to use the github.workspace context var in the CI workflow so I could use the "env:" block for the job step. Alternatively, we could use `realpath` to construct an `env AUGUR=… …` call chaining to the `cram …` invocation, but that seemed slightly messier to me.
nextstrain · Apr 28, 2022 · 072404e · 072404e
1 parent ebcdfb8
commit 072404e
Show file tree

Hide file tree

Showing 13 changed files with 17 additions and 25 deletions.
diff --git a/.github/workflows/ci.yaml b/.github/workflows/ci.yaml
@@ -44,6 +44,10 @@ jobs:
     - run: conda list
     - run: pytest -c pytest.python3.ini --cov=augur
     - run: cram --shell=/bin/bash tests/functional/*.t tests/builds/*.t
+      env:
+        AUGUR: coverage run -a ${{ github.workspace }}/bin/augur
+        COVERAGE_FILE: ${{ github.workspace }}/.coverage
+        COVERAGE_RCFILE: ${{ github.workspace }}/.coveragerc
     - run: coverage xml
     - run: bash tests/builds/runner.sh
     - if: github.repository == 'nextstrain/augur' && matrix.python-version == '3.10' && matrix.biopython-version == ''

diff --git a/tests/builds/zika.t b/tests/builds/zika.t
@@ -7,8 +7,7 @@ Running from the test data directory allows us to use relative paths that won't
   $ TEST_DATA_DIR="$TESTDIR/zika"
   $ mkdir -p "$TMP/out"
   $ pushd "$TEST_DATA_DIR" > /dev/null
-  $ export COVERAGE_FILE="$TESTDIR/../../.coverage"
-  $ export AUGUR="coverage run -a --rcfile=$TESTDIR/../../.coveragerc ../../../bin/augur"
+  $ export AUGUR="${AUGUR:-../../../bin/augur}"
 
 Parse a FASTA whose defline contains metadata into separate sequence and metadata files.
 

diff --git a/tests/builds/zika_compressed.t b/tests/builds/zika_compressed.t
@@ -7,8 +7,7 @@ Running from the test data directory allows us to use relative paths that won't
   $ TEST_DATA_DIR="$TESTDIR/zika"
   $ mkdir -p "$TMP/out"
   $ pushd "$TEST_DATA_DIR" > /dev/null
-  $ export COVERAGE_FILE="$TESTDIR/../../.coverage"
-  $ export AUGUR="coverage run -a --rcfile=$TESTDIR/../../.coveragerc ../../../bin/augur"
+  $ export AUGUR="${AUGUR:-../../../bin/augur}"
 
 Parse a FASTA whose defline contains metadata into separate sequence and metadata files.
 

diff --git a/tests/functional/ancestral.t b/tests/functional/ancestral.t
@@ -1,8 +1,7 @@
 Integration tests for augur ancestral.
 
   $ pushd "$TESTDIR" > /dev/null
-  $ export COVERAGE_FILE="$TESTDIR/../../.coverage"
-  $ export AUGUR="coverage run -a --rcfile=$TESTDIR/../../.coveragerc ../../bin/augur"
+  $ export AUGUR="${AUGUR:-../../bin/augur}"
 
 Infer ancestral sequences for the given tree and alignment.
 The default is to infer ambiguous bases, so there should not be N bases in the inferred output sequences.

diff --git a/tests/functional/clades.t b/tests/functional/clades.t
@@ -1,8 +1,7 @@
 Integration tests for augur clades.
 
   $ pushd "$TESTDIR" > /dev/null
-  $ export COVERAGE_FILE="$TESTDIR/../../.coverage"
-  $ export AUGUR="coverage run -a --rcfile=$TESTDIR/../../.coveragerc ../../bin/augur"
+  $ export AUGUR="${AUGUR:-../../bin/augur}"
 
 Test augur clades with simple Zika input files and hierarchical clades.
 
@@ -14,4 +13,4 @@ Test augur clades with simple Zika input files and hierarchical clades.
 
   $ python3 "$TESTDIR/../../scripts/diff_jsons.py"  clades/clades.json "$TMP/clades.json" \
   >   --exclude-paths "root['generated_by']"
-  {}
+  {}
diff --git a/tests/functional/export_v2.t b/tests/functional/export_v2.t
@@ -1,8 +1,7 @@
 Integration tests for augur export v2.
 
   $ pushd "$TESTDIR" > /dev/null
-  $ export COVERAGE_FILE="$TESTDIR/../../.coverage"
-  $ export AUGUR="coverage run -a --rcfile=$TESTDIR/../../.coveragerc ../../bin/augur"
+  $ export AUGUR="${AUGUR:-../../bin/augur}"
 
 Minimal export
 

diff --git a/tests/functional/filter.t b/tests/functional/filter.t
@@ -1,8 +1,7 @@
 Integration tests for augur filter.
 
   $ pushd "$TESTDIR" > /dev/null
-  $ export COVERAGE_FILE="$TESTDIR/../../.coverage"
-  $ export AUGUR="coverage run -a --rcfile=$TESTDIR/../../.coveragerc ../../bin/augur"
+  $ export AUGUR="${AUGUR:-../../bin/augur}"
 
 Filter with exclude query for two regions that comprise all but one strain.
 This filter should leave a single record from Oceania.

diff --git a/tests/functional/frequencies.t b/tests/functional/frequencies.t
@@ -1,8 +1,7 @@
 Integration tests for augur frequencies.
 
   $ pushd "$TESTDIR" > /dev/null
-  $ export COVERAGE_FILE="$TESTDIR/../../.coverage"
-  $ export AUGUR="coverage run -a --rcfile=$TESTDIR/../../.coveragerc ../../bin/augur"
+  $ export AUGUR="${AUGUR:-../../bin/augur}"
 
 Calculate KDE-based tip frequencies from a refined tree.
 Timepoints used to estimate frequencies (i.e., "pivots") get calculated from the range of dates in the given metadata.

diff --git a/tests/functional/mask.t b/tests/functional/mask.t
@@ -1,8 +1,7 @@
 Integration tests for augur mask.
 
   $ pushd "$TESTDIR" > /dev/null
-  $ export COVERAGE_FILE="$TESTDIR/../../.coverage"
-  $ export AUGUR="coverage run -a --rcfile=$TESTDIR/../../.coveragerc ../../bin/augur"
+  $ export AUGUR="${AUGUR:-../../bin/augur}"
 
 Try masking a VCF without any specified mask.
 

diff --git a/tests/functional/parse.t b/tests/functional/parse.t
@@ -1,8 +1,7 @@
 Integration tests for augur parse.
 
   $ pushd "$TESTDIR" > /dev/null
-  $ export COVERAGE_FILE="$TESTDIR/../../.coverage"
-  $ export AUGUR="coverage run -a --rcfile=$TESTDIR/../../.coveragerc ../../bin/augur"
+  $ export AUGUR="${AUGUR:-../../bin/augur}"
 
 Parse Zika sequences into sequences and metadata.
 

diff --git a/tests/functional/refine.t b/tests/functional/refine.t
@@ -1,8 +1,7 @@
 Integration tests for augur refine.
 
   $ pushd "$TESTDIR" > /dev/null
-  $ export COVERAGE_FILE="$TESTDIR/../../.coverage"
-  $ export AUGUR="coverage run -a --rcfile=$TESTDIR/../../.coveragerc ../../bin/augur"
+  $ export AUGUR="${AUGUR:-../../bin/augur}"
 
 Try building a time tree.
 

diff --git a/tests/functional/traits.t b/tests/functional/traits.t
@@ -1,8 +1,7 @@
 Integration tests for augur traits.
 
   $ pushd "$TESTDIR" > /dev/null
-  $ export COVERAGE_FILE="$TESTDIR/../../.coverage"
-  $ export AUGUR="coverage run -a --rcfile=$TESTDIR/../../.coveragerc ../../bin/augur"
+  $ export AUGUR="${AUGUR:-../../bin/augur}"
 
 Infer the ancestral region for a given tree and metadata.
 

diff --git a/tests/functional/tree.t b/tests/functional/tree.t
@@ -1,8 +1,7 @@
 Integration tests for augur tree.
 
   $ pushd "$TESTDIR" > /dev/null
-  $ export COVERAGE_FILE="$TESTDIR/../../.coverage"
-  $ export AUGUR="coverage run -a --rcfile=$TESTDIR/../../.coveragerc ../../bin/augur"
+  $ export AUGUR="${AUGUR:-../../bin/augur}"
 
 Try building a tree with IQ-TREE.