Fix typing errror

bioexcel · Oct 23, 2024 · b85b306 · b85b306
1 parent 3fd7ef7
commit b85b306
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Showing 9 changed files with 45 additions and 45 deletions.
diff --git a/.github/env.yaml b/.github/env.yaml
@@ -4,7 +4,7 @@ channels:
   - bioconda
   - anaconda
 dependencies:
-  - biobb_common ==4.2.0
+  - biobb_common ==5.0.0
   - imods
   - prody
   - concoord

diff --git a/biobb_flexdyn/flexdyn/concoord_disco.py b/biobb_flexdyn/flexdyn/concoord_disco.py
@@ -133,43 +133,45 @@ def launch(self):
         # MARGINS_li.DAT, MARGINS_oplsaa.DAT, MARGINS_oplsua.DAT, MARGINS_oplsx.DAT, MARGINS_repel.DAT, MARGINS_yamber2.DAT
         # 1 (OPLS-UA -united atoms- parameters), 2 (OPLS-AA -all atoms- parameters), 3 (PROLSQ repel parameters), 4 (Yamber2 parameters), 5 (Li et al. parameters), 6 (OPLS-X parameters -recommended for NMR structure determination-).
         vdw_values = ["vdw_values", "oplsua", "oplsaa", "repel", "yamber2", "li", "oplsx"]
+        if self.vdw is None:
+            raise ValueError("The 'vdw' property cannot be None")
         vdw_index = int(self.vdw)
-        margins_file = concoord_lib + "/MARGINS_" + vdw_values[vdw_index] + ".DAT"
-        atoms_file = concoord_lib + "/ATOMS_" + vdw_values[vdw_index] + ".DAT"
-        bonds_file = concoord_lib + "/BONDS.DAT"
-        shutil.copy2(margins_file, self.stage_io_dict.get("unique_dir"))
-        shutil.copy2(margins_file, self.stage_io_dict.get("unique_dir")+"/MARGINS.DAT")
-        shutil.copy2(atoms_file, self.stage_io_dict.get("unique_dir"))
-        shutil.copy2(bonds_file, self.stage_io_dict.get("unique_dir"))
+        margins_file = str(concoord_lib) + "/MARGINS_" + vdw_values[vdw_index] + ".DAT"
+        atoms_file = str(concoord_lib) + "/ATOMS_" + vdw_values[vdw_index] + ".DAT"
+        bonds_file = str(concoord_lib) + "/BONDS.DAT"
+        shutil.copy2(margins_file, self.stage_io_dict.get("unique_dir", ""))
+        shutil.copy2(margins_file, self.stage_io_dict.get("unique_dir", "")+"/MARGINS.DAT")
+        shutil.copy2(atoms_file, self.stage_io_dict.get("unique_dir", ""))
+        shutil.copy2(bonds_file, self.stage_io_dict.get("unique_dir", ""))
 
         # Command line
         # (concoord) OROZCO67:biobb_flexdyn hospital$ disco -d biobb_flexdyn/test/reference/flexdyn/dist.dat
         # -p biobb_flexdyn/test/reference/flexdyn/dist.pdb  -op patata.pdb
-        self.cmd = ["cd ", self.stage_io_dict.get('unique_dir'), ";", self.binary_path,
+        self.cmd = ["cd ", self.stage_io_dict.get('unique_dir', ''), ";", self.binary_path,
                     #  "-p", str(Path(self.stage_io_dict["in"]["input_pdb_path"]).relative_to(Path.cwd())),
                     #  "-d", str(Path(self.stage_io_dict["in"]["input_dat_path"]).relative_to(Path.cwd())),
                     #  "-or", str(Path(self.stage_io_dict["out"]["output_rmsd_path"]).relative_to(Path.cwd())),
                     #  "-of", str(Path(self.stage_io_dict["out"]["output_bfactor_path"]).relative_to(Path.cwd()))
-                    "-p", str(Path(self.stage_io_dict["in"]["input_pdb_path"]).relative_to(Path(self.stage_io_dict.get('unique_dir')))),
-                    "-d", str(Path(self.stage_io_dict["in"]["input_dat_path"]).relative_to(Path(self.stage_io_dict.get('unique_dir')))),
-                    "-or", str(Path(self.stage_io_dict["out"]["output_rmsd_path"]).relative_to(Path(self.stage_io_dict.get('unique_dir')))),
-                    "-of", str(Path(self.stage_io_dict["out"]["output_bfactor_path"]).relative_to(Path(self.stage_io_dict.get('unique_dir'))))
+                    "-p", str(Path(self.stage_io_dict["in"]["input_pdb_path"]).relative_to(Path(self.stage_io_dict.get('unique_dir', '')))),
+                    "-d", str(Path(self.stage_io_dict["in"]["input_dat_path"]).relative_to(Path(self.stage_io_dict.get('unique_dir', '')))),
+                    "-or", str(Path(self.stage_io_dict["out"]["output_rmsd_path"]).relative_to(Path(self.stage_io_dict.get('unique_dir', '')))),
+                    "-of", str(Path(self.stage_io_dict["out"]["output_bfactor_path"]).relative_to(Path(self.stage_io_dict.get('unique_dir', ''))))
                     ]
 
         # Output structure formats:
         file_extension = Path(self.stage_io_dict["out"]["output_traj_path"]).suffix
         if file_extension == ".pdb":
             self.cmd.append('-on')  # NMR-PDB format (multi-model)
 #            self.cmd.append(str(Path(self.stage_io_dict["out"]["output_traj_path"]).relative_to(Path.cwd())))
-            self.cmd.append(str(Path(self.stage_io_dict["out"]["output_traj_path"]).relative_to(Path(self.stage_io_dict.get('unique_dir')))))
+            self.cmd.append(str(Path(self.stage_io_dict["out"]["output_traj_path"]).relative_to(Path(self.stage_io_dict.get('unique_dir', '')))))
         elif file_extension == ".gro":
             self.cmd.append('-ot')
 #            self.cmd.append(str(Path(self.stage_io_dict["out"]["output_traj_path"]).relative_to(Path.cwd())))
-            self.cmd.append(str(Path(self.stage_io_dict["out"]["output_traj_path"]).relative_to(Path(self.stage_io_dict.get('unique_dir')))))
+            self.cmd.append(str(Path(self.stage_io_dict["out"]["output_traj_path"]).relative_to(Path(self.stage_io_dict.get('unique_dir', '')))))
         elif file_extension == ".xtc":
             self.cmd.append('-ox')
 #            self.cmd.append(str(Path(self.stage_io_dict["out"]["output_traj_path"]).relative_to(Path.cwd())))
-            self.cmd.append(str(Path(self.stage_io_dict["out"]["output_traj_path"]).relative_to(Path(self.stage_io_dict.get('unique_dir')))))
+            self.cmd.append(str(Path(self.stage_io_dict["out"]["output_traj_path"]).relative_to(Path(self.stage_io_dict.get('unique_dir', '')))))
         else:
             fu.log("ERROR: output_traj_path ({}) must be a PDB, GRO or XTC formatted file ({})".format(self.io_dict["out"]["output_traj_path"], file_extension), self.out_log, self.global_log)
 

diff --git a/biobb_flexdyn/flexdyn/concoord_dist.py b/biobb_flexdyn/flexdyn/concoord_dist.py
@@ -111,8 +111,8 @@ def launch(self):
         # Copy auxiliary file (HBONDS) to the working dir
         concoord_lib = os.getenv("CONCOORDLIB")
 
-        hbonds_file = concoord_lib + "/HBONDS.DAT"
-        shutil.copy2(hbonds_file, self.stage_io_dict.get("unique_dir"))
+        hbonds_file = str(concoord_lib) + "/HBONDS.DAT"
+        shutil.copy2(hbonds_file, self.stage_io_dict.get("unique_dir", ""))
 
         # Command line
         # (concoord) OROZCO67:biobb_flexdyn hospital$ dist -p biobb_flexdyn/test/data/flexdyn/structure.pdb
@@ -135,25 +135,25 @@ def launch(self):
         # Selected parameter set 1
         # copying /opt/anaconda3/envs/concoord/share/concoord/lib/BONDS.DAT.noeh to BONDS.DAT in current working directory
 
-        self.cmd = ["cd ", self.stage_io_dict.get('unique_dir'), ";", self.binary_path,
+        self.cmd = ["cd ", self.stage_io_dict.get('unique_dir', ''), ";", self.binary_path,
                     #  "-op", self.stage_io_dict["out"]["output_pdb_path"],
                     #  "-og", self.stage_io_dict["out"]["output_gro_path"],
                     #  "-od", self.stage_io_dict["out"]["output_dat_path"]
-                    "-op", str(Path(self.stage_io_dict["out"]["output_pdb_path"]).relative_to(Path(self.stage_io_dict.get('unique_dir')))),
-                    "-og", str(Path(self.stage_io_dict["out"]["output_gro_path"]).relative_to(Path(self.stage_io_dict.get('unique_dir')))),
-                    "-od", str(Path(self.stage_io_dict["out"]["output_dat_path"]).relative_to(Path(self.stage_io_dict.get('unique_dir'))))
+                    "-op", str(Path(self.stage_io_dict["out"]["output_pdb_path"]).relative_to(Path(self.stage_io_dict.get('unique_dir', '')))),
+                    "-og", str(Path(self.stage_io_dict["out"]["output_gro_path"]).relative_to(Path(self.stage_io_dict.get('unique_dir', '')))),
+                    "-od", str(Path(self.stage_io_dict["out"]["output_dat_path"]).relative_to(Path(self.stage_io_dict.get('unique_dir', ''))))
                     ]
         # If input structure in pdb format:
         file_extension = Path(self.stage_io_dict["in"]["input_structure_path"]).suffix
         if file_extension == ".pdb":
             self.cmd.append('-p')
             # self.cmd.append(self.stage_io_dict["in"]["input_structure_path"])
-            self.cmd.append(str(Path(self.stage_io_dict["in"]["input_structure_path"]).relative_to(Path(self.stage_io_dict.get('unique_dir')))))
+            self.cmd.append(str(Path(self.stage_io_dict["in"]["input_structure_path"]).relative_to(Path(self.stage_io_dict.get('unique_dir', '')))))
 
         elif file_extension == ".gro":
             self.cmd.append('-g')
             # self.cmd.append(self.stage_io_dict["in"]["input_structure_path"])
-            self.cmd.append(str(Path(self.stage_io_dict["in"]["input_structure_path"]).relative_to(Path(self.stage_io_dict.get('unique_dir')))))
+            self.cmd.append(str(Path(self.stage_io_dict["in"]["input_structure_path"]).relative_to(Path(self.stage_io_dict.get('unique_dir', '')))))
 
         else:
             fu.log("ERROR: input_structure_path ({}) must be a PDB or a GRO formatted file ({})".format(self.io_dict["in"]["input_structure_path"], file_extension), self.out_log, self.global_log)
@@ -182,7 +182,7 @@ def launch(self):
         # Add stdin input file
         self.cmd.append('<')
         # self.cmd.append(self.stage_io_dict["in"]["stdin_file_path"])
-        self.cmd.append(str(Path(self.stage_io_dict["in"]["stdin_file_path"]).relative_to(Path(self.stage_io_dict.get('unique_dir')))))
+        self.cmd.append(str(Path(self.stage_io_dict["in"]["stdin_file_path"]).relative_to(Path(self.stage_io_dict.get('unique_dir', '')))))
 
         # Run Biobb block
         self.run_biobb()
@@ -193,7 +193,7 @@ def launch(self):
         # remove temporary folder(s)
         self.tmp_files.extend([
             self.stage_io_dict.get("unique_dir", ""),
-            self.io_dict['in'].get("stdin_file_path")
+            self.io_dict['in'].get("stdin_file_path", "")
         ])
         self.remove_tmp_files()
 

diff --git a/biobb_flexdyn/flexdyn/imod_imc.py b/biobb_flexdyn/flexdyn/imod_imc.py
@@ -102,8 +102,8 @@ def launch(self):
         shutil.copy2(self.io_dict["in"]["input_dat_path"], self.tmp_folder)
 
         # Output temporary file
-        # out_file_prefix = Path(self.stage_io_dict.get("unique_dir")).joinpath("imod_ensemble")
-        # out_file = Path(self.stage_io_dict.get("unique_dir")).joinpath("imod_ensemble.pdb")
+        # out_file_prefix = Path(self.stage_io_dict.get("unique_dir", "")).joinpath("imod_ensemble")
+        # out_file = Path(self.stage_io_dict.get("unique_dir", "")).joinpath("imod_ensemble.pdb")
         out_file_prefix = "imod_ensemble"  # Needed as imod is appending the .pdb extension
         out_file = "imod_ensemble.pdb"
 
@@ -149,7 +149,7 @@ def launch(self):
 
         # remove temporary folder(s)
         self.tmp_files.extend([
-            # self.stage_io_dict.get("unique_dir")
+            # self.stage_io_dict.get("unique_dir", "")
             self.tmp_folder
         ])
         self.remove_tmp_files()

diff --git a/biobb_flexdyn/flexdyn/imod_imode.py b/biobb_flexdyn/flexdyn/imod_imode.py
@@ -95,8 +95,8 @@ def launch(self):
         shutil.copy2(self.io_dict["in"]["input_pdb_path"], self.tmp_folder)
 
         # Output temporary file
-        # out_file_prefix = Path(self.stage_io_dict.get("unique_dir")).joinpath("imods_evecs")
-        # out_file = Path(self.stage_io_dict.get("unique_dir")).joinpath("imods_evecs_ic.evec")
+        # out_file_prefix = Path(self.stage_io_dict.get("unique_dir", "")).joinpath("imods_evecs")
+        # out_file = Path(self.stage_io_dict.get("unique_dir", "")).joinpath("imods_evecs_ic.evec")
         out_file_prefix = "imods_evecs"  # Needed as imod is appending the _ic.evec extension
         out_file = "imods_evecs_ic.evec"
 
@@ -129,7 +129,7 @@ def launch(self):
 
         # remove temporary folder(s)
         self.tmp_files.extend([
-            # self.stage_io_dict.get("unique_dir")
+            # self.stage_io_dict.get("unique_dir", "")
             self.tmp_folder
         ])
         self.remove_tmp_files()

diff --git a/biobb_flexdyn/flexdyn/imod_imove.py b/biobb_flexdyn/flexdyn/imod_imove.py
@@ -132,7 +132,7 @@ def launch(self):
 
         # remove temporary folder(s)
         self.tmp_files.extend([
-            # self.stage_io_dict.get("unique_dir")
+            # self.stage_io_dict.get("unique_dir", "")
             self.tmp_folder
         ])
         self.remove_tmp_files()

diff --git a/biobb_flexdyn/flexdyn/nolb_nma.py b/biobb_flexdyn/flexdyn/nolb_nma.py
@@ -87,8 +87,8 @@ def launch(self):
         self.stage_files()
 
         # Output temporary file
-        out_file_prefix = Path(self.stage_io_dict.get("unique_dir")).joinpath("nolb_ensemble")
-        out_file = Path(self.stage_io_dict.get("unique_dir")).joinpath("nolb_ensemble_nlb_decoys.pdb")
+        out_file_prefix = Path(self.stage_io_dict.get("unique_dir", "")).joinpath("nolb_ensemble")
+        out_file = Path(self.stage_io_dict.get("unique_dir", "")).joinpath("nolb_ensemble_nlb_decoys.pdb")
 
         # Command line
         # ./NOLB 1ake_monomer.pdb -s 100 --rmsd 5 -m  -o patata # Output: patata_nlb_decoys.pdb

diff --git a/biobb_flexdyn/flexdyn/prody_anm.py b/biobb_flexdyn/flexdyn/prody_anm.py
@@ -3,7 +3,7 @@
 """Module containing the prody_anm class and the command line interface."""
 import argparse
 from typing import Optional
-import prody
+import prody  # type: ignore
 from biobb_common.generic.biobb_object import BiobbObject
 from biobb_common.configuration import settings
 from biobb_common.tools.file_utils import launchlogger
@@ -91,7 +91,7 @@ def launch(self):
         prot = prody.parsePDB(self.stage_io_dict["in"]["input_pdb_path"],)
 
         # http://prody.csb.pitt.edu/manual/reference/atomic/select.html
-        prot_sel = prot.select(self.selection)
+        prot_sel = prot.select(self.selection)  # type: ignore
 
         enm = prody.ANM('BioBB_flexdyn Prody ANM ensemble generator')
 

diff --git a/setup.py b/setup.py
@@ -5,7 +5,7 @@
 
 setuptools.setup(
     name="biobb_flexdyn",
-    version="4.2.0",
+    version="5.0.0",
     author="Biobb developers",
     author_email="[email protected]",
     description="biobb_flexdyn is a BioBB category for studies on the conformational landscape of native proteins.",
@@ -20,8 +20,8 @@
     packages=setuptools.find_packages(exclude=['docs', 'test']),
     package_data={'biobb_flexdyn': ['py.typed']},
     include_package_data=True,
-    install_requires=['biobb_common==4.2.0'],
-    python_requires='>=3.8',
+    install_requires=['biobb_common==5.0.0'],
+    python_requires='>=3.9',
     entry_points={
         "console_scripts": [
             "concoord_dist = biobb_flexdyn.flexdyn.concoord_dist:main",
@@ -33,13 +33,11 @@
             "prody_anm = biobb_flexdyn.flexdyn.prody_anm:main"
         ]
     },
-    classifiers=(
-        "Development Status :: 3 - Alpha",
-        "Programming Language :: Python :: 3.8",
+    classifiers=[
+        "Development Status :: 5 - Production/Stable",
         "Programming Language :: Python :: 3.9",
-        "Programming Language :: Python :: 3.10",
         "License :: OSI Approved :: Apache Software License",
         "Operating System :: MacOS :: MacOS X",
         "Operating System :: POSIX",
-    ),
+    ],
 )