ENH: use prodigal in eggnog-diamond-search (#210)

Co-authored-by: Michal Ziemski <[email protected]>

.coveragerc

@@ -2,15 +2,11 @@
 source=q2_moshpit
 branch = True
 omit =
-    */tests*
-    */__init__.py
-    q2_moshpit/_version.py
+    **/test_*.py
+    **/__init__.py
+    **/_version.py
     versioneer.py
+    **/_examples.py
 
 [report]
 fail_under = 90
-omit =
-    */tests*
-    */__init__.py
-    q2_moshpit/_version.py
-    versioneer.py

.github/workflows/ci.yaml

@@ -58,7 +58,7 @@ jobs:
       - name: Setup miniconda
         uses: conda-incubator/setup-miniconda@v3
         with:
-          python-version: 3.9
+          python-version: "3.10"
           mamba-version: 1.5.10
           channels: conda-forge,defaults
           channel-priority: true

Makefile

@@ -12,7 +12,7 @@ test: all
 	py.test
 
 test-cov: all
-	python -m pytest --cov q2_moshpit --cov-report xml:coverage.xml
+	python -m coverage run -m pytest && coverage xml -o coverage.xml
 
 install: all
 	$(PYTHON) setup.py install

ci/recipe/meta.yaml

@@ -43,13 +43,12 @@ requirements:
 test:
   requires:
     - coverage
-    - pytest-cov
     - parameterized
   imports:
     - q2_moshpit
     - qiime2.plugins.moshpit
   commands:
-    - pytest --cov q2_moshpit --cov-report xml:coverage.xml --pyargs q2_moshpit
+    - coverage run --rcfile ./repo/.coveragerc -m pytest && coverage xml -o coverage.xml
 
 about:
   home: https://github.com/bokulich-lab/q2-moshpit

q2_moshpit/eggnog/orthologs/common.py

@@ -121,7 +121,7 @@ def _search_runner(
     """
     cmd = [
         'emapper.py', '-i', str(input_path), '-o', sample_label,
-        '-m', *runner_args,
+        '-m', *runner_args, '--genepred', 'prodigal',
         '--itype', 'metagenome', '--output_dir', output_loc,
         '--cpu', str(num_cpus), '--no_annot'
     ]