add all unit tests

.gitlab-ci.yml

@@ -86,10 +86,10 @@ unit-test-ubuntu:
     - py.test test/test_unit/test_annotate/test_annotation*  -vx
     - py.test test/test_unit/test_annotate/test_format* -v -x
     - py.test test/test_unit/test_pangenome -vx
-    # - py.test test/test_unit/test_corepers -vx
-    # - py.test test/test_unit/test_align -vx
-    # - py.test test/test_unit/test_tree -xv
-    # - mv .coverage .coverage-unit
+    - py.test test/test_unit/test_corepers -vx
+    - py.test test/test_unit/test_align -vx
+    - py.test test/test_unit/test_tree -xv
+    - mv .coverage .coverage-unit
   artifacts:
     paths:
       - .coverage-unit

test/test_unit/test_align/test_alignment.py

@@ -539,8 +539,8 @@ def test_family_align_nomafft_btrempty_errormafft(caplog):
                                    ngenomes, logger)
     assert "Checking extractions for family 8" in caplog.text
     assert "Aligning family 8" in caplog.text
-    assert ("mafft --auto test/data/align/exp_files/exp_aldir-pers/current.8.prt "
-            "does not exist") in caplog.text
+    assert ("command '>mafft --auto test/data/align/exp_files/exp_aldir-pers/current.8.prt' "
+            "is not possible") in caplog.text
     # Check content of mafft and btr files
     assert not os.path.isfile(mafft_file)
     assert not os.path.isfile(btr_file)