[CI/CD](conf.yml) Update to new tests

.gitignore

@@ -117,3 +117,6 @@ traj_comp.xtc
 
 # Pytest
 .pytest_cache
+
+# MyPy
+.mypy_cache

biobb_cmip/__init__.py

@@ -1,3 +1,4 @@
+from . import cmip
 name = "biobb_cmip"
 __all__ = ["cmip"]
 __version__ = "4.2.0"

biobb_cmip/cmip/__init__.py

@@ -1,2 +1,7 @@
+from . import cmip_titration
+from . import cmip_run
+from . import cmip_prepare_structure
+from . import cmip_prepare_pdb
+from . import cmip_ignore_residues
 name = "cmip"
 __all__ = ["cmip_titration", "cmip_run", "cmip_prepare_structure", "cmip_prepare_pdb", "cmip_ignore_residues"]

biobb_cmip/test/conf.yml

@@ -1,5 +1,5 @@
 global_properties:
-  can_write_console_log: False
+  can_write_console_log: True
   working_dir_path: /tmp/biobb/unitests
 
 cmip_titration:

biobb_cmip/test/unitests/test_cmip/test_cmip_ignore_residues.py

@@ -1,3 +1,4 @@
+# type: ignore
 from biobb_common.tools import test_fixtures as fx
 from biobb_cmip.cmip.cmip_ignore_residues import cmip_ignore_residues
 

biobb_cmip/test/unitests/test_cmip/test_cmip_prepare_pdb.py

@@ -1,3 +1,4 @@
+# type: ignore
 from biobb_common.tools import test_fixtures as fx
 from biobb_cmip.cmip.cmip_prepare_pdb import cmip_prepare_pdb
 

biobb_cmip/test/unitests/test_cmip/test_cmip_prepare_structure.py

@@ -1,3 +1,4 @@
+# type: ignore
 from biobb_common.tools import test_fixtures as fx
 from biobb_cmip.cmip.cmip_prepare_structure import cmip_prepare_structure
 

biobb_cmip/test/unitests/test_cmip/test_cmip_run.py

@@ -1,3 +1,4 @@
+# type: ignore
 from biobb_common.tools import test_fixtures as fx
 from biobb_cmip.cmip.cmip_run import cmip_run
 

biobb_cmip/test/unitests/test_cmip/test_cmip_run_docker.py

@@ -1,3 +1,4 @@
+# type: ignore
 from biobb_common.tools import test_fixtures as fx
 from biobb_cmip.cmip.cmip_run import cmip_run
 

biobb_cmip/test/unitests/test_cmip/test_cmip_run_singularity.py

@@ -1,3 +1,4 @@
+# type: ignore
 from biobb_common.tools import test_fixtures as fx
 from biobb_cmip.cmip.cmip_run import cmip_run
 import pytest

biobb_cmip/test/unitests/test_cmip/test_cmip_titration.py

@@ -1,3 +1,4 @@
+# type: ignore
 from biobb_common.tools import test_fixtures as fx
 from biobb_cmip.cmip.cmip_titration import cmip_titration
 

biobb_cmip/test/unitests/test_cmip/test_cmip_titration_docker.py

@@ -1,3 +1,4 @@
+# type: ignore
 from biobb_common.tools import test_fixtures as fx
 from biobb_cmip.cmip.cmip_titration import cmip_titration
 

biobb_cmip/test/unitests/test_cmip/test_cmip_titration_singularity.py

@@ -1,3 +1,4 @@
+# type: ignore
 from biobb_common.tools import test_fixtures as fx
 from biobb_cmip.cmip.cmip_titration import cmip_titration
 import pytest

jupyter_notebook/Test_CMIP.ipynb

@@ -20,7 +20,7 @@
    "source": [
     "import pytraj as pt\n",
     "\n",
-    "input_topology_filename=\"/Users/pau/projects/biobb_cmip/biobb_cmip/test/data/cmip/egfr_topology.zip\"\n",
+    "input_topology_filename=\"biobb_cmip/biobb_cmip/test/data/cmip/egfr_topology.zip\"\n",
     "top_file = fu.unzip_top(zip_file=input_topology_filename)\n",
     "\n",
     "topology = pt.load_topology(filename=top_file)\n",
@@ -94,7 +94,7 @@
     "            return str(file_path)\n",
     "\n",
     "\n",
-    "input_topology_filename=\"/Users/pau/projects/biobb_cmip/biobb_cmip/test/data/cmip/egfr_topology.zip\"\n",
+    "input_topology_filename=\"biobb_cmip/biobb_cmip/test/data/cmip/egfr_topology.zip\"\n",
     "top_file = fu.unzip_top(zip_file=input_topology_filename)\n",
     "\n",
     "with open(top_file) as tf:\n",
@@ -140,10 +140,10 @@
    "source": [
     "import functools\n",
     "import math\n",
-    " \n",
-    "if functools.reduce(lambda x, y : x and y, map(lambda p, q: math.isclose(p,q, abs_tol=0.0001),pt_charges,mda_charges), True): \n",
-    "    print (\"The lists l1 and l2 are the same\") \n",
-    "else: \n",
+    "\n",
+    "if functools.reduce(lambda x, y : x and y, map(lambda p, q: math.isclose(p,q, abs_tol=0.0001),pt_charges,mda_charges), True):\n",
+    "    print (\"The lists l1 and l2 are the same\")\n",
+    "else:\n",
     "    print (\"The lists l1 and l2 are not the same\")\n",
     "print(pt_charges[:10])\n",
     "print(mda_charges[:10])"
@@ -168,10 +168,10 @@
    "source": [
     "import functools\n",
     "import math\n",
-    " \n",
-    "if functools.reduce(lambda x, y : x and y, map(lambda p, q: p == q,pt_atom_types,mda_atom_types), True): \n",
-    "    print (\"The lists l1 and l2 are the same\") \n",
-    "else: \n",
+    "\n",
+    "if functools.reduce(lambda x, y : x and y, map(lambda p, q: p == q,pt_atom_types,mda_atom_types), True):\n",
+    "    print (\"The lists l1 and l2 are the same\")\n",
+    "else:\n",
     "    print (\"The lists l1 and l2 are not the same\")\n",
     "print(pt_atom_types[:10])\n",
     "print(mda_atom_types[:10])"

setup.py

@@ -35,7 +35,7 @@
             "cmip_ignore_residues = biobb_cmip.cmip.cmip_ignore_residues:main"
         ]
     },
-    classifiers=(
+    classifiers=[
         "Development Status :: 5 - Production/Stable",
         "Programming Language :: Python :: 3.8",
         "Programming Language :: Python :: 3.9",
@@ -44,5 +44,5 @@
         "Operating System :: MacOS :: MacOS X",
         "Operating System :: POSIX",
         "Operating System :: Unix"
-    ),
+    ],
 )