Fix three tests

test/test_convert.py

@@ -10,7 +10,7 @@
 from sos.converter import extract_workflow
 
 
-@pytest.mark.skip(reason="temporary skip")
+
 def test_script_to_html(temp_factory, clear_now_and_after):
     '''Test sos show script --html'''
     clear_now_and_after('temp1.sos.html', 'temp2.sos.html')

test/test_dag.py

@@ -828,7 +828,7 @@ def test_reverse_shared_variable(clear_now_and_after):
     assert env.sos_dict['b'] == 1
 
 
-@pytest.mark.skip(reason="temporary skip")
+
 def test_chained_depends(temp_factory):
     '''Test chain dependent'''
     temp_factory('a.bam', 'a.bam.bai', 'a.vcf')

test/test_execute.py

@@ -1775,7 +1775,7 @@ def test_step_id_vars():
         """)
 
 
-@pytest.mark.skip(reason="temporary skip")
+
 def test_reexecution_of_dynamic_depends(clear_now_and_after):
     """Testing the rerun of steps to verify dependency"""
     clear_now_and_after("a.bam", "a.bam.bai")
@@ -1804,7 +1804,7 @@ def test_reexecution_of_dynamic_depends(clear_now_and_after):
     assert res["__completed__"]["__step_skipped__"] == 1
 
 
-@pytest.mark.skip(reason="temporary skip")
+
 def test_traced_function(clear_now_and_after):
     clear_now_and_after("a.bam", "a.bam.bai")
     script = """
@@ -2314,7 +2314,7 @@ def test_remove_empty_groups_empty_named(clear_now_and_after):
         """)
 
 
-@pytest.mark.skip(reason="temporary skip")
+
 def test_multi_depends(clear_now_and_after, temp_factory):
     """Test a step with multiple depdendend steps"""
 
@@ -2596,7 +2596,7 @@ def test_concurrent_running_tasks(script_factory):
     assert ret2.returncode == 0
 
 
-@pytest.mark.skip(reason="temporary skip")
+
 def test_reexecute_task_with_missing_output(clear_now_and_after):
     '''Issue #1493'''
     clear_now_and_after([f'a_{i}.txt' for i in range(10)])

test/test_execute_2.py

@@ -58,7 +58,7 @@ def test_removal_of_output_from_failed_step(clear_now_and_after):
     assert not os.path.isfile("result.csv")
 
 
-@pytest.mark.skip(reason="temporary skip")
+
 def test_error_handling_of_substeps(clear_now_and_after):
     clear_now_and_after(
         [f"test_{i}.txt" for i in range(10)],
@@ -194,7 +194,7 @@ def test_for_each_as_target_property_nested_list(temp_factory):
     ]
 
 
-@pytest.mark.skip(reason="temporary skip")
+
 def test_rerun_with_zap(clear_now_and_after):
     clear_now_and_after([f"zapped_example_{i}.txt.zapped" for i in range(3)])
     clear_now_and_after([f"zapped_example_{i}.bak" for i in range(3)])

test/test_parser.py

@@ -1470,7 +1470,7 @@ def test_cell():
 """)
 
 
-@pytest.mark.skip(reason="temporary skip")
+
 def test_overwrite_keyword(clear_now_and_after):
     """Test overwrite sos keyword with user defined one."""
     clear_now_and_after("a.txt")

test/test_python3_target.py

@@ -61,41 +61,41 @@ def test_py_module_with_version():
 ''')
 
 
-@pytest.mark.skip(reason="temporary skip")
+
 def test_upgrade_py_module():
     '''Test upgrade py module #1246'''
-    # first install tabulate == 0.7.5
+    # first install tabulate == 0.8.5
     execute_workflow(r'''
 [10]
-depends: Py_Module('tabulate==0.7.5', autoinstall=True)
+depends: Py_Module('tabulate==0.8.9', autoinstall=True)
 ''')
     # test should pass
     execute_workflow(r'''
 [10]
-depends: Py_Module('tabulate'), Py_Module('tabulate==0.7.5')
+depends: Py_Module('tabulate'), Py_Module('tabulate==0.8.9')
 ''')
     # test for newer version should fail
 
     with pytest.raises(Exception):
         execute_workflow(r'''
 [10]
-depends: Py_Module('tabulate==0.8.3')
+depends: Py_Module('tabulate==0.9.0')
 ''')
 
     # auto install should work
     execute_workflow(r'''
 [10]
-depends: Py_Module('tabulate==0.8.3', autoinstall=True)
+depends: Py_Module('tabulate==0.9.0', autoinstall=True)
 ''')
 
     # test for old version should fail
     execute_workflow(r'''
         [10]
-        depends: Py_Module('tabulate'), Py_Module('tabulate==0.8.3')
+        depends: Py_Module('tabulate'), Py_Module('tabulate==0.9.0')
         ''')
     # test for old version should fail
     with pytest.raises(Exception):
         execute_workflow(r'''
         [10]
-        depends: Py_Module('tabulate==0.7.5')
+        depends: Py_Module('tabulate==0.8.9')
         ''')

test/test_r_targets.py

@@ -26,7 +26,7 @@ def test_r_library():
         """)
 
 
-@pytest.mark.skip(reason="temporary skip")
+
 @pytest.mark.skipif(not shutil.which("Rscript"), reason="R not installed")
 def test_depends_r_library():
     """Testing depending on R_library"""

test/test_remote.py

@@ -23,7 +23,7 @@
         has_docker = False
 
 
-@pytest.mark.skip(reason="temporary skip")
+
 @pytest.mark.skipif(not has_docker, reason="Docker container not usable")
 def test_to_host_option(clear_now_and_after):
     """Test from_remote option"""
@@ -50,7 +50,7 @@ def test_to_host_option(clear_now_and_after):
         assert lc.read().strip().startswith("100")
 
 
-@pytest.mark.skip(reason="temporary skip")
+
 @pytest.mark.skipif(not has_docker, reason="Docker container not usable")
 def test_to_host_option_with_named_path(clear_now_and_after):
     """Test from_remote option"""
@@ -117,7 +117,7 @@ def test_worker_procs_with_task():
     )
 
 
-@pytest.mark.skip(reason="temporary skip")
+
 @pytest.mark.skipif(not has_docker, reason="Docker container not usable")
 def test_remote_execute(clear_now_and_after, script_factory):
     clear_now_and_after("result_remote.txt", "result_remote1.txt", "local.txt")
@@ -180,7 +180,7 @@ def test_remote_workflow_remote_queue(script_factory):
     assert 0 == subprocess.call(f"sos run {test_r_q} -c ~/docker.yml -r ts -q ts", shell=True)
 
 
-@pytest.mark.skip(reason="temporary skip")
+
 @pytest.mark.skipif(not has_docker, reason="Docker container not usable")
 def test_remote_exec(clear_now_and_after):
     clear_now_and_after("result_exec.txt")
@@ -207,7 +207,7 @@ def test_remote_exec(clear_now_and_after):
         assert f"PWD: {root_dir}" in result
 
 
-@pytest.mark.skip(reason="temporary skip")
+
 @pytest.mark.skipif(not has_docker, reason="Docker container not usable")
 def test_remote_exec_named_path(clear_now_and_after):
     clear_now_and_after("result_named_path.txt")
@@ -236,7 +236,7 @@ def test_remote_exec_named_path(clear_now_and_after):
         assert f"PWD: {root_dir}" in result
 
 
-@pytest.mark.skip(reason="temporary skip")
+
 @pytest.mark.skipif(not has_docker, reason="Docker container not usable")
 def test_remote_exec_workdir_named_path(clear_now_and_after):
     clear_now_and_after(file_target("#home/wd/result_workdir_named_path.txt"))

test/test_signature.py

@@ -754,7 +754,7 @@ def test_signature_with_dependency_tracing_and_vars(clear_signatures,
     assert res['__completed__']['__substep_completed__'] == 2
 
 
-@pytest.mark.skip(reason="temporary skip")
+
 def test_skip_mode(clear_signatures, temp_factory, clear_now_and_after):
     '''Test skipping mode of signature'''
     clear_now_and_after([f'a_{i}.bak' for i in range(4)])

test/test_singularity.py

@@ -25,7 +25,7 @@ def test_bash_in_singularity():
         ''')
 
 
-@pytest.mark.skip(reason="temporary skip")
+
 @pytest.mark.skipif(
     not shutil.which('singularity') or sys.platform == 'win32' or
     'TRAVIS' in os.environ or 'APPVEYOR' in os.environ,
@@ -47,7 +47,7 @@ def test_singularity_build_linux_image(self):
         ''')
 
 
-@pytest.mark.skip(reason="temporary skip")
+
 @pytest.mark.skipif(
     not shutil.which('singularity') or sys.platform == 'win32' or
     'TRAVIS' in os.environ or 'APPVEYOR' in os.environ,
@@ -59,7 +59,7 @@ def test_singularity_build_from_shub(self):
         ''')
 
 
-@pytest.mark.skip(reason="temporary skip")
+
 @pytest.mark.skipif(
     not shutil.which('singularity') or sys.platform == 'win32',
     reason='Skip test because docker is not installed.')

test/test_target.py

@@ -689,7 +689,7 @@ def test_temp_file():
     """)
 
 
-@pytest.mark.skip(reason="temporary skip")
+
 def test_named_path():
     """Test the use of option name of path"""
     execute_workflow(
@@ -707,7 +707,7 @@ def test_named_path():
     )
 
 
-@pytest.mark.skip(reason="temporary skip")
+
 @pytest.mark.skipif(
     sys.platform == 'win32', reason='Graphviz not available under windows')
 def test_to_named_path_path():

test/test_task.py

@@ -482,7 +482,7 @@ def test_max_mem():
         )
 
 
-@pytest.mark.skip(reason="temporary skip")
+
 def test_local_runtime_max_walltime():
     """Test server max_walltime option"""
     # gives warning, but do not kill
@@ -519,7 +519,7 @@ def test_max_cores():
         )
 
 
-@pytest.mark.skip(reason="temporary skip")
+
 @pytest.mark.skipIf(not has_docker, reason="Docker container not usable")
 def test_override_max_cores():
     """Test use queue_args to override server restriction max_cores"""
@@ -540,7 +540,7 @@ def test_override_max_cores():
     )
 
 
-@pytest.mark.skip(reason="temporary skip")
+
 def test_list_hosts():
     """test list hosts using sos status -q"""
     for v in ["0", "1", "3", "4"]:
@@ -652,7 +652,7 @@ def test_task_no_signature(purge_tasks):
         assert time.time() - st > 1
 
 
-@pytest.mark.skip(reason="temporary skip")
+
 def test_task_with_signature(purge_tasks, clear_now_and_after):
     """Test re-execution of tasks"""
     # now with a real signature
@@ -714,7 +714,7 @@ def test_output_in_task():
         options={"default_queue": "localhost"})
 
 
-@pytest.mark.skip(reason="temporary skip")
+
 def test_repeated_tasks():
     """Test statement before task #1142 """
     for i in range(5):
@@ -801,7 +801,7 @@ def test_output_from_master_task():
         options={"default_queue": "localhost"})
 
 
-@pytest.mark.skip(reason="temporary skip")
+
 @pytest.mark.skipIf(not has_docker, reason="Docker container not usable")
 def test_remote_input_target(clear_now_and_after):
     """Test the use of remote target"""
@@ -827,7 +827,7 @@ def test_remote_input_target(clear_now_and_after):
     assert os.path.isfile("vars1.sh")
 
 
-@pytest.mark.skip(reason="temporary skip")
+
 @pytest.mark.skipif(not has_docker, reason="Docker container not usable")
 def test_delayed_interpolation(clear_now_and_after):
     """Test delayed interpolation with expression involving remote objects"""
@@ -860,7 +860,7 @@ def test_delayed_interpolation(clear_now_and_after):
     assert not os.path.isfile("test.py.bak")
 
 
-@pytest.mark.skip(reason="temporary skip")
+
 @pytest.mark.skipif(not has_docker, reason="Docker container not usable")
 def test_remote_output_target(clear_now_and_after):
     """Test the use of remote target"""
@@ -886,7 +886,7 @@ def test_remote_output_target(clear_now_and_after):
     assert not os.path.isfile("vars1.sh")
 
 
-@pytest.mark.skip(reason="temporary skip")
+
 @pytest.mark.skipif(not has_docker, reason="Docker container not usable")
 def test_remote_output_target_with_trunksize(clear_now_and_after):
     clear_now_and_after("vars.sh", "vars1.sh")
@@ -912,7 +912,7 @@ def test_remote_output_target_with_trunksize(clear_now_and_after):
     assert not os.path.isfile("init-d-script")
 
 
-@pytest.mark.skip(reason="temporary skip")
+
 def test_runtime_max_walltime():
     """Test server max_walltime option"""
     with pytest.raises(Exception):
@@ -931,7 +931,7 @@ def test_runtime_max_walltime():
         )
 
 
-@pytest.mark.skip(reason="temporary skip")
+
 @pytest.mark.skipif(not has_docker, reason="Docker container not usable")
 def test_sync_master_task(clear_now_and_after):
     """Test sync input and output with remote host with trunksize"""
@@ -1077,7 +1077,7 @@ def test_trunk_workers_option(clear_now_and_after, purge_tasks):
         assert os.path.isfile(f"{i}.txt")
 
 
-@pytest.mark.skip(reason="temporary skip")
+
 @pytest.mark.skipif(not has_docker, reason="Docker container not usable")
 def test_sync_input_output_and_rerun(clear_now_and_after, purge_tasks):
     """Test sync input and output with remote host"""