fix typos, better doc string format in atomate/qchem/fireworks/core.py

Author: janosh

atomate/common/firetasks/glue_tasks.py

@@ -344,8 +344,8 @@ def setup_copy(
                 (e.g., rename 'INCAR' to 'INCAR.precondition')
             continue_on_missing(bool): Whether to continue copying when a file
                 in filenames is missing. Defaults to False.
-            from_path_dict (dict): dict specification of the path. If specified must contain atleast
-                the key "path" that specifies the path to the from_dir.
+            from_path_dict (dict): dict specification of the path. If specified must contain at
+                least the key "path" that specifies the path to the from_dir.
         """
         from_path_dict = from_path_dict or {}
         from_dir = env_chk(from_dir, fw_spec, strict=False) or from_path_dict.get(

atomate/feff/firetasks/glue_tasks.py

@@ -18,7 +18,7 @@ class CopyFeffOutputs(CopyFiles):
             search for the most recent calc_loc with the matching name.
         calc_dir (str): path to dir that contains VASP output files.
         filesystem (str): remote filesystem. e.g. username@host
-        exclude_files (list): list fo filenames to be excluded when copying.
+        exclude_files (list): list of filenames to be excluded when copying.
     """
 
     optional_params = ["calc_loc", "calc_dir", "filesystem", "exclude_files"]

atomate/feff/firetasks/parse_outputs.py

@@ -103,7 +103,7 @@ class AddPathsToFilepadTask(FiretaskBase):
     Optional_params:
         labels (list): list of labels to tag the inserted files. Useful for querying later.
         filepad_file (str): path to the filepad connection settings file.
-        compress (bool): wether or not to compress the file contents before insertion.
+        compress (bool): Whether or not to compress the file contents before insertion.
         metadata (dict): metadata.
     """
 

atomate/feff/firetasks/tests/test_tasks.py

@@ -27,18 +27,18 @@ def setUp(self):
     def test_copy_feff_outputs_task(self):
         t = CopyFeffOutputs(calc_dir=os.path.join(module_dir, "..", "..", "test_files"))
         t.run_task({})
-        ans = ["Co2O2.cif", "feff_eels.inp", "feo_781777.json"]
+        answer = ["Co2O2.cif", "feff_eels.inp", "feo_781777.json"]
         files = glob("*")
-        self.assertEqual(sorted(ans), sorted(files))
+        self.assertEqual(sorted(answer), sorted(files))
 
     def test_write_paths_task(self):
         exafs = MPEXAFSSet(0, self.struct, edge="K", radius=10)
         t = WriteEXAFSPaths(feff_input_set=exafs, paths=[[249, 0], [85, 0]])
         paths = Paths(exafs.atoms, [[249, 0], [85, 0]])
-        paths.write_file("paths_ans.dat")
+        paths.write_file("paths_answer.dat")
         t.run_task({})
-        with open("paths_ans.dat") as ans, open("paths.dat") as tmp:
-            self.assertEqual(ans.readlines(), tmp.readlines())
+        with open("paths_answer.dat") as answer, open("paths.dat") as tmp:
+            self.assertEqual(answer.readlines(), tmp.readlines())
 
 
 if __name__ == "__main__":

atomate/feff/fireworks/tests/test_fireworks.py

@@ -24,14 +24,14 @@ def test_exafs_paths_fw(self):
         fw = EXAFSPathsFW(0, self.struct, [[249, 0], [85, 0]])
         fw_dict = fw.as_dict()
         self.assertEqual(len(fw_dict["spec"]["_tasks"]), 5)
-        ans = [
+        answer = [
             "{{atomate.feff.firetasks.glue_tasks.CopyFeffOutputs}}",
             "{{atomate.feff.firetasks.write_inputs.WriteFeffFromIOSet}}",
             "{{atomate.feff.firetasks.write_inputs.WriteEXAFSPaths}}",
             "{{atomate.feff.firetasks.run_calc.RunFeffDirect}}",
             "{{atomate.feff.firetasks.parse_outputs.AddPathsToFilepadTask}}",
         ]
-        self.assertEqual(ans, [ft["_fw_name"] for ft in fw_dict["spec"]["_tasks"]])
+        self.assertEqual(answer, [ft["_fw_name"] for ft in fw_dict["spec"]["_tasks"]])
 
 
 if __name__ == "__main__":

atomate/feff/workflows/tests/test_exafs_scattering_paths.py

@@ -29,8 +29,8 @@ def setUp(self):
 
     def test_wflow_composition(self):
         self.assertEqual(len(self.wf_dict["fws"]), 2)
-        ans = sorted(["FeO-EXAFS-K-0", "FeO-EXAFS Paths"])
-        self.assertEqual(ans, sorted(ft["name"] for ft in self.wf_dict["fws"]))
+        answer = sorted(["FeO-EXAFS-K-0", "FeO-EXAFS Paths"])
+        self.assertEqual(answer, sorted(ft["name"] for ft in self.wf_dict["fws"]))
 
     def test_feff_input_sets(self):
         ans_fis_fw1 = {

atomate/lammps/drones.py

@@ -68,7 +68,7 @@ def assimilate(
             path (str): path to the run folder
             input_filename (str): just the name of the input file
             log_filename (str): lammps log file name
-            is_forcefield (bool): whether or not ot parse forcefield info
+            is_forcefield (bool): whether or not to parse forcefield info
             data_filename (str): name of the data file
             dump_files ([str]): list of dump file names
 

atomate/lammps/firetasks/glue_tasks.py

@@ -18,8 +18,8 @@ class CopyPackmolOutputs(CopyFiles):
             search for the most recent calc_loc with the matching name.
         calc_dir (str): path to dir that contains VASP output files.
         filesystem (str): remote filesystem. e.g. username@host
-        exclude_files (list): list fo filenames to be excluded when copying.
-            NOte: by default nothing is excluded.
+        exclude_files (list): list of filenames to be excluded when copying.
+            Note: by default nothing is excluded.
     """
 
     optional_params = ["calc_loc", "calc_dir", "filesystem", "exclude_files"]

atomate/lammps/workflows/core.py

@@ -31,7 +31,7 @@ def get_wf_basic(
     Args:
         input_file (str): path to lammps input file.
             Note: It could be a template file too, then the user_settings must be set.
-        user_settings ([dict] or dict): list of settings dict. if the input_file is a tempalte file
+        user_settings ([dict] or dict): list of settings dict. if the input_file is a template file
             then each dict contains the key value pairs for the template file.
         lammps_data (string/LammpsData/LammpsForceFieldData): path to the data file or
             an appropriate object.
@@ -110,7 +110,7 @@ def get_packmol_wf(
 
     Args:
         input_file (str):  path to lammps input(or template) file.
-        user_settings ([dict] or dict): list of settings dict. if the input_file is a tempalte file
+        user_settings ([dict] or dict): list of settings dict. if the input_file is a template file
             then each dict contains the key value pairs for the template file.
         constituent_molecules ([Molecules]): list of pymatgen Molecule objects
         packing_config ([dict]): list of configuration dictionaries, one for each constituent molecule.

atomate/qchem/drones.py

@@ -63,7 +63,7 @@ def __init__(self, runs=None, additional_fields=None):
         """
         Initialize a QChem drone to parse qchem calculations
         Args:
-            runs (list): Naming scheme for multiple calcuations in one folder
+            runs (list): Naming scheme for multiple calculations in one folder
             additional_fields (dict): dictionary of additional fields to add to output document
         """
         self.runs = runs or list(
@@ -151,7 +151,7 @@ def generate_doc(self, dir_name, qcinput_files, qcoutput_files, multirun):
             d["schema"] = {"code": "atomate", "version": QChemDrone.__version__}
             d["dir_name"] = fullpath
 
-            # If a saved "orig" input file is present, parse it incase the error handler made changes
+            # If a saved "orig" input file is present, parse it in case the error handler made changes
             # to the initial input molecule or rem params, which we might want to filter for later
             if len(qcinput_files) > len(qcoutput_files):
                 orig_input = QCInput.from_file(