Advancing the migration to pytest

conftest.py

@@ -8,4 +8,4 @@
 
 @pytest.fixture(scope='function')
 def raspa_code(aiida_local_code_factory):  # pylint: disable=unused-argument
-    return aiida_local_code_factory("simulate", "raspa")
+    return aiida_local_code_factory("raspa", "simulate")

examples/simple_calculations/test_base.py → examples/simple_calculations/example_base.py

@@ -53,7 +53,7 @@ def example_base(raspa_code, submit=True):
         })
 
     # framework
-    framework = CifData(file=os.path.join(os.path.dirname(os.path.realpath(__file__)), 'files', 'TCC1RS.cif'))
+    framework = CifData(file=os.path.join(os.path.dirname(os.path.realpath(__file__)), '..', 'files', 'TCC1RS.cif'))
 
     # Contructing builder
     builder = raspa_code.get_builder()
@@ -90,14 +90,15 @@ def example_base(raspa_code, submit=True):
 
 @click.command('cli')
 @click.argument('codelabel')
-def cli(codelabel):
+@click.option('--submit', is_flag=True, help='Actually submit calculation')
+def cli(codelabel, submit):
     """Click interface"""
     try:
         code = Code.get_from_string(codelabel)
     except NotExistent:
         print("The code '{}' does not exist".format(codelabel))
         sys.exit(1)
-    example_base(code)
+    example_base(code, submit)
 
 
 if __name__ == '__main__':

examples/simple_calculations/test_restart.py → examples/simple_calculations/example_base_restart.py

@@ -17,17 +17,8 @@
 CifData = DataFactory('cif')  # pylint: disable=invalid-name
 
 
-@click.command('cli')
-@click.argument('codelabel')
-@click.option('--previous_calc', '-p', required=True, type=int, help='PK of test_raspa_base.py calculation')
-@click.option('--submit', is_flag=True, help='Actually submit calculation')
-def main(codelabel, previous_calc, submit):
+def example_base_restart(raspa_code, previous_calc, submit=True):
     """Prepare and submit restart from simple RASPA calculation."""
-    try:
-        code = Code.get_from_string(codelabel)
-    except NotExistent:
-        print("The code '{}' does not exist".format(codelabel))
-        sys.exit(1)
 
     # parameters
     parameters = Dict(
@@ -62,13 +53,13 @@ def main(codelabel, previous_calc, submit):
         })
 
     # framework
-    framework = CifData(file=os.path.join(os.path.dirname(os.path.realpath(__file__)), 'files', 'TCC1RS.cif'))
+    framework = CifData(file=os.path.join(os.path.dirname(os.path.realpath(__file__)), '..', 'files', 'TCC1RS.cif'))
 
     # restart file
     retrieved_parent_folder = load_node(previous_calc).outputs.retrieved
 
     # Contructing builder
-    builder = code.get_builder()
+    builder = raspa_code.get_builder()
     builder.framework = {
         "tcc1rs": framework,
     }
@@ -101,7 +92,21 @@ def main(codelabel, previous_calc, submit):
     print("-----")
 
 
+@click.command('cli')
+@click.argument('codelabel')
+@click.option('--previous_calc', '-p', required=True, type=int, help='PK of example_base.py calculation')
+@click.option('--submit', is_flag=True, help='Actually submit calculation')
+def cli(codelabel, previous_calc, submit):
+    """Click interface"""
+    try:
+        code = Code.get_from_string(codelabel)
+    except NotExistent:
+        print("The code '{}' does not exist".format(codelabel))
+        sys.exit(1)
+    example_base_restart(code, previous_calc, submit)
+
+
 if __name__ == '__main__':
-    main()  # pylint: disable=no-value-for-parameter
+    cli()  # pylint: disable=no-value-for-parameter
 
 # EOF

examples/simple_calculations/test_binary_mixture.py → examples/simple_calculations/example_binary_mixture.py

@@ -11,16 +11,8 @@
 from aiida.orm import Code, Dict
 
 
-@click.command('cli')
-@click.argument('codelabel')
-@click.option('--submit', is_flag=True, help='Actually submit calculation')
-def main(codelabel, submit):
+def example_binary_misture(raspa_code, submit=True):
     """Prepare and submit RASPA calculation with components mixture."""
-    try:
-        code = Code.get_from_string(codelabel)
-    except NotExistent:
-        print("The code '{}' does not exist".format(codelabel))
-        sys.exit(1)
 
     # parameters
     parameters = Dict(
@@ -63,7 +55,7 @@ def main(codelabel, submit):
         })
 
     # Contructing builder
-    builder = code.get_builder()
+    builder = raspa_code.get_builder()
     builder.parameters = parameters
     builder.metadata.options = {
         "resources": {
@@ -93,7 +85,20 @@ def main(codelabel, submit):
     print("-----")
 
 
+@click.command('cli')
+@click.argument('codelabel')
+@click.option('--submit', is_flag=True, help='Actually submit calculation')
+def cli(codelabel, submit):
+    """Click interface"""
+    try:
+        code = Code.get_from_string(codelabel)
+    except NotExistent:
+        print("The code '{}' does not exist".format(codelabel))
+        sys.exit(1)
+    example_binary_misture(code, submit)
+
+
 if __name__ == '__main__':
-    main()  # pylint: disable=no-value-for-parameter
+    cli()  # pylint: disable=no-value-for-parameter
 
 # EOF

examples/simple_calculations/test_binary_restart.py → examples/simple_calculations/example_binary_restart.py

@@ -16,17 +16,8 @@
 CifData = DataFactory('cif')  # pylint: disable=invalid-name
 
 
-@click.command('cli')
-@click.argument('codelabel')
-@click.option('--previous_calc', '-p', required=True, type=int, help='PK of test_raspa_base.py calculation')
-@click.option('--submit', is_flag=True, help='Actually submit calculation')
-def main(codelabel, previous_calc, submit):
+def example_binary_restart(raspa_code, previous_calc, submit=True):
     """Prepare and submit restart from simple RASPA calculation."""
-    try:
-        code = Code.get_from_string(codelabel)
-    except NotExistent:
-        print("The code '{}' does not exist".format(codelabel))
-        sys.exit(1)
 
     # parameters
     parameters = Dict(
@@ -61,13 +52,13 @@ def main(codelabel, previous_calc, submit):
         })
 
     # framework
-    framework = CifData(file=os.path.join(os.path.dirname(os.path.realpath(__file__)), 'files', 'TCC1RS.cif'))
+    framework = CifData(file=os.path.join(os.path.dirname(os.path.realpath(__file__)), '..', 'files', 'TCC1RS.cif'))
 
     # restart file
     parent_folder = load_node(previous_calc).outputs.remote_folder
 
     # Contructing builder
-    builder = code.get_builder()
+    builder = raspa_code.get_builder()
     builder.framework = {
         "tcc1rs": framework,
     }
@@ -100,7 +91,21 @@ def main(codelabel, previous_calc, submit):
     print("-----")
 
 
+@click.command('cli')
+@click.argument('codelabel')
+@click.option('--previous_calc', '-p', required=True, type=int, help='PK of example_raspa_base.py calculation')
+@click.option('--submit', is_flag=True, help='Actually submit calculation')
+def cli(codelabel, previous_calc, submit):
+    """Click interface"""
+    try:
+        code = Code.get_from_string(codelabel)
+    except NotExistent:
+        print("The code '{}' does not exist".format(codelabel))
+        sys.exit(1)
+    example_binary_restart(code, previous_calc, submit)
+
+
 if __name__ == '__main__':
-    main()  # pylint: disable=no-value-for-parameter
+    cli()  # pylint: disable=no-value-for-parameter
 
 # EOF

examples/simple_calculations/test_block_pockets_2frameworks_2molecules.py → examples/simple_calculations/example_block_pockets_2frameworks_2molecules.py

@@ -15,16 +15,9 @@
 CifData = DataFactory('cif')  # pylint: disable=invalid-name
 
 
-@click.command('cli')
-@click.argument('codelabel')
-@click.option('--submit', is_flag=True, help='Actually submit calculation')
-def main(codelabel, submit):
+def example_block_pockets(raspa_code, submit=True):
     """Prepare and submit RASPA calculation with blocked pockets."""
-    try:
-        code = Code.get_from_string(codelabel)
-    except NotExistent:
-        print("The code '{}' does not exist".format(codelabel))
-        sys.exit(1)
+
     # parameters
     parameters = Dict(
         dict={
@@ -88,15 +81,15 @@ def main(codelabel, submit):
 
     # frameworks
     pwd = os.path.dirname(os.path.realpath(__file__))
-    framework_1 = CifData(file=os.path.join(pwd, 'files', 'IRMOF-1.cif'))
-    framework_10 = CifData(file=os.path.join(pwd, 'files', 'IRMOF-10.cif'))
+    framework_1 = CifData(file=os.path.join(pwd, '..', 'files', 'IRMOF-1.cif'))
+    framework_10 = CifData(file=os.path.join(pwd, '..', 'files', 'IRMOF-10.cif'))
 
     # block pocket
-    block_pocket_1 = SinglefileData(file=os.path.join(pwd, 'files', 'IRMOF-1_test.block')).store()
-    block_pocket_10 = SinglefileData(file=os.path.join(pwd, 'files', 'IRMOF-10_test.block')).store()
+    block_pocket_1 = SinglefileData(file=os.path.join(pwd, '..', 'files', 'IRMOF-1_test.block')).store()
+    block_pocket_10 = SinglefileData(file=os.path.join(pwd, '..', 'files', 'IRMOF-10_test.block')).store()
 
     # Contructing builder
-    builder = code.get_builder()
+    builder = raspa_code.get_builder()
     builder.framework = {
         "irmof_1": framework_1,
         "irmof_10": framework_10,
@@ -136,7 +129,20 @@ def main(codelabel, submit):
         print("In order to actually submit, add '--submit'")
 
 
+@click.command('cli')
+@click.argument('codelabel')
+@click.option('--submit', is_flag=True, help='Actually submit calculation')
+def cli(codelabel, submit):
+    """Click interface"""
+    try:
+        code = Code.get_from_string(codelabel)
+    except NotExistent:
+        print("The code '{}' does not exist".format(codelabel))
+        sys.exit(1)
+    example_block_pockets(code, submit)
+
+
 if __name__ == '__main__':
-    main()  # pylint: disable=no-value-for-parameter
+    cli()  # pylint: disable=no-value-for-parameter
 
 # EOF

examples/simple_calculations/test_block_pockets_simple.py → examples/simple_calculations/example_block_pockets_simple.py

@@ -15,16 +15,9 @@
 CifData = DataFactory('cif')  # pylint: disable=invalid-name
 
 
-@click.command('cli')
-@click.argument('codelabel')
-@click.option('--submit', is_flag=True, help='Actually submit calculation')
-def main(codelabel, submit):
+def example_block_pockets(raspa_code, submit=True):
     """Prepare and submit RASPA calculation with blocked pockets."""
-    try:
-        code = Code.get_from_string(codelabel)
-    except NotExistent:
-        print("The code '{}' does not exist".format(codelabel))
-        sys.exit(1)
+
     # parameters
     parameters = Dict(
         dict={
@@ -60,13 +53,13 @@ def main(codelabel, submit):
 
     # framework
     pwd = os.path.dirname(os.path.realpath(__file__))
-    framework = CifData(file=os.path.join(pwd, 'files', 'TCC1RS.cif'))
+    framework = CifData(file=os.path.join(pwd, '..', 'files', 'TCC1RS.cif'))
 
     # block pocket
-    block_pocket_node = SinglefileData(file=os.path.join(pwd, 'files', 'block_pocket.block')).store()
+    block_pocket_node = SinglefileData(file=os.path.join(pwd, '..', 'files', 'block_pocket.block')).store()
 
     # Contructing builder
-    builder = code.get_builder()
+    builder = raspa_code.get_builder()
     builder.framework = {
         "tcc1rs": framework,
     }
@@ -100,7 +93,20 @@ def main(codelabel, submit):
         print("In order to actually submit, add '--submit'")
 
 
+@click.command('cli')
+@click.argument('codelabel')
+@click.option('--submit', is_flag=True, help='Actually submit calculation')
+def cli(codelabel, submit):
+    """Click interface"""
+    try:
+        code = Code.get_from_string(codelabel)
+    except NotExistent:
+        print("The code '{}' does not exist".format(codelabel))
+        sys.exit(1)
+    example_block_pockets(code, submit)
+
+
 if __name__ == '__main__':
-    main()  # pylint: disable=no-value-for-parameter
+    cli()  # pylint: disable=no-value-for-parameter
 
 # EOF

examples/simple_calculations/test_ff_files.py → examples/simple_calculations/example_ff_files.py

@@ -12,16 +12,8 @@
 from aiida.orm import Code, Dict, CifData, SinglefileData
 
 
-@click.command('cli')
-@click.argument('codelabel')
-@click.option('--submit', is_flag=True, help='Actually submit calculation')
-def main(codelabel, submit):
+def example_ff_files(raspa_code, submit=True):
     """Prepare and submit RASPA calculation with components mixture."""
-    try:
-        code = Code.get_from_string(codelabel)
-    except NotExistent:
-        print("The code '{}' does not exist".format(codelabel))
-        sys.exit(1)
 
     # parameters
     parameters = Dict(
@@ -69,17 +61,17 @@ def main(codelabel, submit):
 
     # Contructing builder
     pwd = os.path.dirname(os.path.realpath(__file__))
-    builder = code.get_builder()
+    builder = raspa_code.get_builder()
     builder.framework = {
-        "irmof_1": CifData(file=os.path.join(pwd, 'files', 'IRMOF-1_eqeq.cif')),
+        "irmof_1": CifData(file=os.path.join(pwd, '..', 'files', 'IRMOF-1_eqeq.cif')),
     }
     # Note: Here the SinglefileData in the dict are stored otherwise the dry_run crashes.
     #       However, this is not needed for real calculations (e.g., using --submit), since the work chains stores them.
     builder.file = {
-        "file_1": SinglefileData(file=os.path.join(pwd, 'files', 'force_field_mixing_rules.def')).store(),
-        "file_2": SinglefileData(file=os.path.join(pwd, 'files', 'pseudo_atoms.def')).store(),
-        "file_3": SinglefileData(file=os.path.join(pwd, 'files', 'CO2.def')).store(),
-        "file_4": SinglefileData(file=os.path.join(pwd, 'files', 'N2.def')).store(),
+        "file_1": SinglefileData(file=os.path.join(pwd, '..', 'files', 'force_field_mixing_rules.def')).store(),
+        "file_2": SinglefileData(file=os.path.join(pwd, '..', 'files', 'pseudo_atoms.def')).store(),
+        "file_3": SinglefileData(file=os.path.join(pwd, '..', 'files', 'CO2.def')).store(),
+        "file_4": SinglefileData(file=os.path.join(pwd, '..', 'files', 'N2.def')).store(),
     }
     builder.parameters = parameters
     builder.metadata.options = {
@@ -113,7 +105,20 @@ def main(codelabel, submit):
     print("-----")
 
 
+@click.command('cli')
+@click.argument('codelabel')
+@click.option('--submit', is_flag=True, help='Actually submit calculation')
+def cli(codelabel, submit):
+    """Click interface"""
+    try:
+        code = Code.get_from_string(codelabel)
+    except NotExistent:
+        print("The code '{}' does not exist".format(codelabel))
+        sys.exit(1)
+    example_ff_files(code, submit)
+
+
 if __name__ == '__main__':
-    main()  # pylint: disable=no-value-for-parameter
+    cli()  # pylint: disable=no-value-for-parameter
 
 # EOF