nextstrain · victorlin · May 24, 2022 · Apr 21, 2022 · Apr 21, 2022 · Apr 28, 2022
diff --git a/.github/workflows/ci.yaml b/.github/workflows/ci.yaml
@@ -42,8 +42,13 @@ jobs:
     - run: pip install -e .[dev]
     - run: conda info
     - run: conda list
-    - run: pytest -c pytest.python3.ini  --cov-report=xml --cov=augur
+    - 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 == ''
       uses: codecov/codecov-action@v2

diff --git a/tests/builds/zika.t b/tests/builds/zika.t
@@ -7,7 +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 AUGUR="../../../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
@@ -7,7 +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 AUGUR="../../../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
@@ -1,7 +1,7 @@
 Integration tests for augur ancestral.
 
   $ pushd "$TESTDIR" > /dev/null
-  $ export AUGUR="../../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
@@ -1,7 +1,7 @@
 Integration tests for augur clades.
 
   $ pushd "$TESTDIR" > /dev/null
-  $ export AUGUR="../../bin/augur"
+  $ export AUGUR="${AUGUR:-../../bin/augur}"
 
 Test augur clades with simple Zika input files and hierarchical clades.
 

diff --git a/tests/functional/export_v2.t b/tests/functional/export_v2.t
@@ -1,7 +1,7 @@
 Integration tests for augur export v2.
 
   $ pushd "$TESTDIR" > /dev/null
-  $ export AUGUR="../../bin/augur"
+  $ export AUGUR="${AUGUR:-../../bin/augur}"
 
 Minimal export
 

diff --git a/tests/functional/filter.t b/tests/functional/filter.t
@@ -1,7 +1,7 @@
 Integration tests for augur filter.
 
   $ pushd "$TESTDIR" > /dev/null
-  $ export AUGUR="../../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
@@ -1,7 +1,7 @@
 Integration tests for augur frequencies.
 
   $ pushd "$TESTDIR" > /dev/null
-  $ export AUGUR="../../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
@@ -1,7 +1,7 @@
 Integration tests for augur mask.
 
   $ pushd "$TESTDIR" > /dev/null
-  $ export AUGUR="../../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
@@ -1,7 +1,7 @@
 Integration tests for augur parse.
 
   $ pushd "$TESTDIR" > /dev/null
-  $ export AUGUR="../../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
@@ -1,7 +1,7 @@
 Integration tests for augur refine.
 
   $ pushd "$TESTDIR" > /dev/null
-  $ export AUGUR="../../bin/augur"
+  $ export AUGUR="${AUGUR:-../../bin/augur}"
 
 Try building a time tree.
 

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