Merge pull request #736 from janosh/random

Squash a few more issues

Author: itsduowang

.circleci/images/py3/Dockerfile

@@ -3,4 +3,4 @@ FROM python:3.6.4
 RUN apt-get update && apt-get install -y gfortran python-openbabel python-vtk python3-tk
 RUN wget https://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh
 RUN bash Miniconda3-latest-Linux-x86_64.sh -b
-RUN export PATH=$HOME/miniconda3/bin:$PATH
+RUN export PATH=$HOME/miniconda3/bin:$PATH

.github/PULL_REQUEST_TEMPLATE.md

@@ -1,6 +1,6 @@
 ## Summary
 
-<Short few sentences, and summary of the major changes in bullet 
+<Short few sentences, and summary of the major changes in bullet
 points>
 
 * Feature 1
@@ -10,7 +10,7 @@ points>
 
 ## TODO (if any)
 
-<If this is a work-in-progress, write something about what else needs 
+<If this is a work-in-progress, write something about what else needs
 to be done>
 
-* Feature 1 supports a, but not b.
+* Feature 1 supports a, but not b.

.pre-commit-config.yaml

@@ -1,3 +1,5 @@
+exclude: ^(docs/|.*test_files/|.*tests/)
+
 repos:
   - repo: https://github.com/myint/autoflake
     rev: v1.4

CHANGES.txt

@@ -1 +1 @@
-(see changelog in the docs) 
+(see changelog in the docs)

LICENSE

@@ -43,4 +43,4 @@ for such Enhancements, then you hereby grant the following license:
 a  non-exclusive, royalty-free perpetual license to install, use,
 modify, prepare derivative works, incorporate into other computer
 software, distribute, and sublicense such enhancements or derivative
-works thereof, in binary and source code form.
+works thereof, in binary and source code form.

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__":