From e947429d2d735312d7581369551d7499bf1596e3 Mon Sep 17 00:00:00 2001
From: Liz Gehret <elizabeth.gehret@gmail.com>
Date: Fri, 25 Oct 2024 14:06:27 -0700
Subject: [PATCH 1/2] DEV: 2025.4 [skip ci]


From 6c1bc96ba465503e1af7c169d5978d20cf30c607 Mon Sep 17 00:00:00 2001
From: Doriela Grabocka <50322943+DorielaGrabocka@users.noreply.github.com>
Date: Fri, 1 Nov 2024 20:00:00 +0100
Subject: [PATCH 2/2] ENH: use prodigal in eggnog-diamond-search (#210)

Co-authored-by: Michal Ziemski <mziemski@ethz.ch>
---
 .coveragerc                           | 12 ++++--------
 .github/workflows/ci.yaml             |  2 +-
 Makefile                              |  2 +-
 ci/recipe/meta.yaml                   |  3 +--
 q2_moshpit/eggnog/orthologs/common.py |  2 +-
 5 files changed, 8 insertions(+), 13 deletions(-)

diff --git a/.coveragerc b/.coveragerc
index fde65821..1851da30 100644
--- a/.coveragerc
+++ b/.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
diff --git a/.github/workflows/ci.yaml b/.github/workflows/ci.yaml
index 0bac0874..f9f4261b 100644
--- a/.github/workflows/ci.yaml
+++ b/.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
diff --git a/Makefile b/Makefile
index 24f84ef8..aa008a54 100644
--- a/Makefile
+++ b/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
diff --git a/ci/recipe/meta.yaml b/ci/recipe/meta.yaml
index 262c9416..4ea76e8b 100644
--- a/ci/recipe/meta.yaml
+++ b/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
diff --git a/q2_moshpit/eggnog/orthologs/common.py b/q2_moshpit/eggnog/orthologs/common.py
index 02c8bf45..e230f899 100644
--- a/q2_moshpit/eggnog/orthologs/common.py
+++ b/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'
     ]