Refactor SnB_input_files

Former-commit-id: d88b00f

.pre-commit-config.yaml

@@ -1,6 +1,6 @@
 # See https://pre-commit.com for more information
 # See https://pre-commit.com/hooks.html for more hooks
-exclude: ^(docs|tests|SnB_input_files|.github|shakenbreak/scripts|CITATION*|MANIFEST*)
+exclude: ^(docs|tests|shakenbreak/SnB_input_files|.github|CITATION*|MANIFEST*)
 repos:
   # Lint and format, isort, docstrings...
   - repo: https://github.com/charliermarsh/ruff-pre-commit

docs/Generation.rst

@@ -32,7 +32,7 @@ we'll get a warning and we'll need to specify the defect site with the ``--defec
 
 .. NOTE::
     To specify additional distortion parameters, we can use a
-    `config.yaml <https://github.com/SMTG-Bham/ShakeNBreak/blob/main/SnB_input_files/example_generate_config.yaml>`_
+    `config.yaml <https://github.com/SMTG-Bham/ShakeNBreak/blob/main/shakenbreak/SnB_input_files/example_generate_config.yaml>`_
     file like the one below and use the ``--config`` flag to specify its path (i.e. ``snb-generate --config ./my_config.yaml``).
     A detailed description of all the parameters is available in the Python API section
     (:ref:`shakenbreak.input.Distortions class <api_input>`).
@@ -122,7 +122,7 @@ the following directory structures will be parsed correctly:
 
 .. NOTE::
     To specify the charge state range for each defect, as well as other optional arguments, we can use a
-    `config.yaml <https://github.com/SMTG-Bham/ShakeNBreak/blob/main/SnB_input_files/example_generate_all_config.yaml>`_ file
+    `config.yaml <https://github.com/SMTG-Bham/ShakeNBreak/blob/main/shakenbreak/SnB_input_files/example_generate_all_config.yaml>`_ file
     like the one below. A detailed description of all the parameters is available in the
     Python API section (:ref:`shakenbreak.input.Distortions class <api_input>`).
 

setup.py

@@ -114,17 +114,6 @@ def run(self):
         _install_custom_font()
 
 
-# https://stackoverflow.com/questions/27664504/how-to-add-package-data-recursively-in-python-setup-py
-def package_files(directory):
-    """Include package data."""
-    paths = []
-    for path, _dir, filenames in os.walk(directory):
-        paths.extend(os.path.join("..", path, filename) for filename in filenames)
-    return paths
-
-
-input_files = package_files("SnB_input_files/")
-
 with open("README.md", encoding="utf-8") as file:
     long_description = file.read()
 
@@ -192,7 +181,7 @@ def package_files(directory):
     },
     # Specify any non-python files to be distributed with the package
     package_data={
-        "shakenbreak": ["shakenbreak/*", *input_files],
+        "shakenbreak": ["shakenbreak/*"],
     },
     include_package_data=True,
     # Specify the custom installation class

shakenbreak/cli.py

@@ -150,8 +150,8 @@ def snb():
 @click.option(
     "--config",
     "-conf",
-    help="Config file for advanced distortion settings. See example in"
-    " SnB_input_files/example_generate_config.yaml",
+    help="Config file for advanced distortion settings. See example in "
+    "shakenbreak/SnB_input_files/example_generate_config.yaml",
     default=None,
     type=click.Path(exists=True, dir_okay=False),
     show_default=True,
@@ -426,7 +426,7 @@ def generate(
     "--config",
     "-conf",
     help="Config file for advanced distortion settings. See example in "
-    "/SnB_input_files/example_generate_all_config.yaml",
+    "shakenbreak/SnB_input_files/example_generate_all_config.yaml",
     default=None,
     type=click.Path(exists=True, dir_okay=False, file_okay=True),
     show_default=True,

shakenbreak/input.py

@@ -40,9 +40,9 @@
 from shakenbreak import analysis, distortions, io
 
 MODULE_DIR = os.path.dirname(os.path.abspath(__file__))
-default_potcar_dict = loadfn(f"{MODULE_DIR}/../SnB_input_files/default_POTCARs.yaml")
+default_potcar_dict = loadfn(f"{MODULE_DIR}/SnB_input_files/default_POTCARs.yaml")
 # Load default INCAR settings for the ShakeNBreak geometry relaxations
-default_incar_settings = loadfn(os.path.join(MODULE_DIR, "../SnB_input_files/incar.yaml"))
+default_incar_settings = loadfn(os.path.join(MODULE_DIR, "SnB_input_files/incar.yaml"))
 
 
 _ignore_pmg_warnings()  # Ignore pymatgen POTCAR warnings
@@ -305,7 +305,7 @@ def _create_vasp_input(
             Dictionary of user VASP POTCAR settings, to overwrite/update
             the `doped` defaults (e.g. {'Fe': 'Fe_pv', 'O': 'O'}}). Highly
             recommended to look at output `POTCAR`s, or `shakenbreak`
-            `SnB_input_files/default_POTCARs.yaml`, to see what the default
+            `shakenbreak/SnB_input_files/default_POTCARs.yaml`, to see what the default
             `POTCAR` settings are. (Default: None)
         output_path (:obj:`str`):
             Path to directory in which to write distorted defect structures and
@@ -2466,7 +2466,7 @@ def write_vasp_files(
                 Dictionary of user VASP INCAR settings (e.g.
                 {"ENCUT": 300, ...}), to overwrite the `ShakenBreak` defaults
                 for those tags. Highly recommended to look at output `INCAR`s,
-                or `SnB_input_files/incar.yaml` to see what the default `INCAR`
+                or `shakenbreak/SnB_input_files/incar.yaml` to see what the default `INCAR`
                 settings are. Note that any flags that aren't numbers or
                 True/False need to be input as strings with quotation marks
                 (e.g. `{"ALGO": "All"}`). (Default: None)
@@ -2477,7 +2477,7 @@ def write_vasp_files(
                 Dictionary of user VASP POTCAR settings, to overwrite/update
                 the `doped` defaults (e.g. {'Fe': 'Fe_pv', 'O': 'O'}}). Highly
                 recommended to look at output `POTCAR`s, or `shakenbreak`
-                `SnB_input_files/default_POTCARs.yaml`, to see what the default
+                `shakenbreak/SnB_input_files/default_POTCARs.yaml`, to see what the default
                 `POTCAR` settings are. (Default: None)
             write_files (:obj:`bool`):
                 Whether to write output files (Default: True)
@@ -2575,11 +2575,11 @@ def write_espresso_files(
             input_parameters (:obj:`dict`, optional):
                 Dictionary of user Quantum Espresso input parameters, to
                 overwrite/update `shakenbreak` default ones (see
-                `SnB_input_files/qe_input.yaml`).
+                `shakenbreak/SnB_input_files/qe_input.yaml`).
                 (Default: None)
             input_file (:obj:`str`, optional):
                 Path to Quantum Espresso input file, to overwrite/update
-                `shakenbreak` default ones (see `SnB_input_files/qe_input.yaml`).
+                `shakenbreak` default ones (see `shakenbreak/SnB_input_files/qe_input.yaml`).
                 If both `input_parameters` and `input_file` are provided,
                 the input_parameters will be used.
                 (Default: None)
@@ -2619,7 +2619,7 @@ def write_espresso_files(
 
         # Update default parameters with user defined values
         if pseudopotentials and not write_structures_only:
-            default_input_parameters = loadfn(os.path.join(MODULE_DIR, "../SnB_input_files/qe_input.yaml"))
+            default_input_parameters = loadfn(os.path.join(MODULE_DIR, "SnB_input_files/qe_input.yaml"))
             if input_file and not input_parameters:
                 input_parameters = io.parse_qe_input(input_file)
             if input_parameters:
@@ -2693,7 +2693,7 @@ def write_espresso_files(
 
     def write_cp2k_files(
         self,
-        input_file: Optional[str] = f"{MODULE_DIR}/../SnB_input_files/cp2k_input.inp",
+        input_file: Optional[str] = f"{MODULE_DIR}/SnB_input_files/cp2k_input.inp",
         write_structures_only: Optional[bool] = False,
         output_path: str = ".",
         verbose: Optional[bool] = None,
@@ -2725,15 +2725,13 @@ def write_cp2k_files(
         """
         if os.path.exists(input_file) and not write_structures_only:
             cp2k_input = Cp2kInput.from_file(input_file)
-        elif (
-            os.path.exists(f"{MODULE_DIR}/../SnB_input_files/cp2k_input.inp") and not write_structures_only
-        ):
+        elif os.path.exists(f"{MODULE_DIR}/SnB_input_files/cp2k_input.inp") and not write_structures_only:
             warnings.warn(
                 f"Specified input file {input_file} does not exist! Using"
                 " default CP2K input file "
                 "(see shakenbreak/shakenbreak/cp2k_input.inp)"
             )
-            cp2k_input = Cp2kInput.from_file(f"{MODULE_DIR}/../SnB_input_files/cp2k_input.inp")
+            cp2k_input = Cp2kInput.from_file(f"{MODULE_DIR}/SnB_input_files/cp2k_input.inp")
 
         distorted_defects_dict, self.distortion_metadata = self.apply_distortions(
             verbose=verbose,
@@ -2757,7 +2755,7 @@ def write_cp2k_files(
 
     def write_castep_files(
         self,
-        input_file: Optional[str] = f"{MODULE_DIR}/../SnB_input_files/castep.param",
+        input_file: Optional[str] = f"{MODULE_DIR}/SnB_input_files/castep.param",
         write_structures_only: Optional[bool] = False,
         output_path: str = ".",
         verbose: Optional[bool] = None,