Cleanup package structure (#66)

* Add isort as development tool
* Add import order to CI and makefile
* Separate public/private for control package
* Sort import in util and third_party
* Separate public/private in data package
* Rename exceptions to exception
* Separate public/private in raw package
* Separate calculation in private and public part

.github/workflows/test.yml

@@ -1,6 +1,6 @@
 name: tests
 
-on: 
+on:
   push:
     branches: [master]
   pull_request:
@@ -32,6 +32,9 @@ jobs:
         poetry run pytest --cov=py4vasp --cov-report term
     - name: Check code style
       run: |
+        poetry run isort --version
+        poetry run isort --check src
+        poetry run isort --check tests
         poetry run black --version
         poetry run black --check src
         poetry run black --check tests
@@ -62,6 +65,9 @@ jobs:
         poetry run pytest --cov=py4vasp --cov-report term
     - name: Check code style
       run: |
+        poetry run isort --version
+        poetry run isort --check src
+        poetry run isort --check tests
         poetry run black --version
         poetry run black --check src
         poetry run black --check tests

makefile

@@ -1,12 +1,17 @@
 # Copyright © VASP Software GmbH,
 # Licensed under the Apache License 2.0 (http://www.apache.org/licenses/LICENSE-2.0)
-.PHONY: test format
+.PHONY: test format style import
 
 TEST ?= tests
 
 test:
 	poetry run pytest $(TEST)
 
 
-format:
-	poetry run black .
+format: import style
+
+style:
+	poetry run black .
+
+import:
+	poetry run isort .

pyproject.toml

@@ -36,6 +36,7 @@ pylint = "^2.14.3"
 Sphinx = "^5.0.2"
 black = "^22.6.0"
 hypothesis = "^6.48.1"
+isort = "^5.10.1"
 
 [tool.poetry.scripts]
 error-analysis = "py4vasp.scripts.error_analysis:main"
@@ -57,6 +58,8 @@ pytest = {channel = "anaconda"}
 sphinx = {channel = "anaconda"}
 black = {channel = "conda-forge"}
 
+[tool.isort]
+profile = "black"
 
 [tool.dephell.main]
 from = {format = "poetry", path = "pyproject.toml"}

src/py4vasp/__init__.py

@@ -1,8 +1,8 @@
 # Copyright © VASP Software GmbH,
 # Licensed under the Apache License 2.0 (http://www.apache.org/licenses/LICENSE-2.0)
-from .calculation import Calculation
-from py4vasp._third_party.interactive import set_error_handling
+from py4vasp._calculation import Calculation
 from py4vasp._third_party.graph import plot
+from py4vasp._third_party.interactive import set_error_handling
 
 __version__ = "0.5.1"
 set_error_handling("Minimal")

src/py4vasp/calculation.py → src/py4vasp/_calculation.py

@@ -13,12 +13,11 @@
 >>> calc.structure.print()  # to print the structure in a POSCAR format
 """
 import inspect
-import py4vasp.data
-import py4vasp.exceptions as exception
-import py4vasp.control
-import py4vasp._util.convert as _convert
 import pathlib
 
+from py4vasp import _data, control, data, exception
+from py4vasp._util import convert
+
 
 class Calculation:
     """Manage access to input and output of VASP calculations.
@@ -114,15 +113,15 @@ def POSCAR(self, poscar):
 
 
 def _add_all_refinement_classes(calc, add_single_class):
-    for name, class_ in inspect.getmembers(py4vasp.data, inspect.isclass):
-        if issubclass(class_, py4vasp.data._base.Refinery):
+    for name, class_ in inspect.getmembers(data, inspect.isclass):
+        if issubclass(class_, _data.base.Refinery):
             calc = add_single_class(calc, name, class_)
     return calc
 
 
 def _add_attribute_from_path(calc, name, class_):
     instance = class_.from_path(calc.path())
-    setattr(calc, _convert.to_snakecase(name), instance)
+    setattr(calc, convert.to_snakecase(name), instance)
     return calc
 
 
@@ -132,7 +131,7 @@ def __init__(self, file_name):
 
     def __call__(self, calc, name, class_):
         instance = class_.from_file(self._file_name)
-        setattr(calc, _convert.to_snakecase(name), instance)
+        setattr(calc, convert.to_snakecase(name), instance)
         return calc
 
 
@@ -141,7 +140,7 @@ def _add_to_documentation(calc, name, class_):
     functions = inspect.getmembers(class_, inspect.isfunction)
     names = [name for name, _ in functions if not name.startswith("_")]
     calc.__doc__ += f"""
-    {_convert.to_snakecase(name)}
+    {convert.to_snakecase(name)}
         {first_line}
 
 """
@@ -154,7 +153,7 @@ def _add_to_documentation(calc, name, class_):
 
 
 def _add_input_files(calc):
-    calc._INCAR = py4vasp.control.INCAR(calc.path())
-    calc._KPOINTS = py4vasp.control.KPOINTS(calc.path())
-    calc._POSCAR = py4vasp.control.POSCAR(calc.path())
+    calc._INCAR = control.INCAR(calc.path())
+    calc._KPOINTS = control.KPOINTS(calc.path())
+    calc._POSCAR = control.POSCAR(calc.path())
     return calc

src/py4vasp/control/_base.py → src/py4vasp/_control/base.py

@@ -3,7 +3,7 @@
 from pathlib import Path
 
 
-class InputBase:
+class InputFile:
     def __init__(self, path):
         self._path = path
 

src/py4vasp/control/incar.py → src/py4vasp/_control/incar.py

@@ -1,9 +1,9 @@
 # Copyright © VASP Software GmbH,
 # Licensed under the Apache License 2.0 (http://www.apache.org/licenses/LICENSE-2.0)
-from py4vasp.control._base import InputBase
+from py4vasp._control import base
 
 
-class INCAR(InputBase):
+class INCAR(base.InputFile):
     """The INCAR file defining the input parameters of a VASP calculation.
 
     Parameters

src/py4vasp/control/kpoints.py → src/py4vasp/_control/kpoints.py

@@ -1,9 +1,9 @@
 # Copyright © VASP Software GmbH,
 # Licensed under the Apache License 2.0 (http://www.apache.org/licenses/LICENSE-2.0)
-from py4vasp.control._base import InputBase
+from py4vasp._control import base
 
 
-class KPOINTS(InputBase):
+class KPOINTS(base.InputFile):
     """The KPOINTS file defining the **k**-point grid for the VASP calculation.
 
     Parameters

src/py4vasp/control/poscar.py → src/py4vasp/_control/poscar.py

@@ -1,10 +1,10 @@
 # Copyright © VASP Software GmbH,
 # Licensed under the Apache License 2.0 (http://www.apache.org/licenses/LICENSE-2.0)
-from py4vasp.control._base import InputBase
+from py4vasp._control import base
 from py4vasp.data import Structure
 
 
-class POSCAR(InputBase):
+class POSCAR(base.InputFile):
     """The POSCAR file defining the structure used in the VASP calculation.
 
     Parameters

src/py4vasp/data/band.py → src/py4vasp/_data/band.py

@@ -2,21 +2,18 @@
 # Licensed under the Apache License 2.0 (http://www.apache.org/licenses/LICENSE-2.0)
 import numpy as np
 import pandas as pd
-from py4vasp import data
-import py4vasp._util.sanity_check as _check
-import py4vasp._util.documentation as _documentation
 from IPython.lib.pretty import pretty
-from .projector import Projector as _Projector, _selection_doc, _selection_examples
-from .kpoint import Kpoint, _kpoints_opt_source
-from py4vasp.data import _base
-import py4vasp.data._export as _export
+
+from py4vasp import data
+from py4vasp._data import base, export, kpoint, projector
+from py4vasp._util import check, documentation
 
 _to_dict_doc = f"""Read the data into a dictionary.
 
 Parameters
 ----------
-{_selection_doc}
-{_kpoints_opt_source}
+{projector.selection_doc}
+{kpoint.kpoints_opt_source}
 
 Returns
 -------
@@ -26,14 +23,14 @@
     and a selection is passed, the projections of these bands on the
     selected projectors are included.
 
-{_selection_examples("band", "to_dict")}"""
+{projector.selection_examples("band", "to_dict")}"""
 
 _to_frame_doc = f"""Read the data into a DataFrame.
 
 Parameters
 ----------
-{_selection_doc}
-{_kpoints_opt_source}
+{projector.selection_doc}
+{kpoint.kpoints_opt_source}
 
 Returns
 -------
@@ -42,16 +39,16 @@
     bands. If a selection string is given, in addition the orbital projections
     on these bands are returned.
 
-{_selection_examples("band", "to_frame")}"""
+{projector.selection_examples("band", "to_frame")}"""
 
 _plot_doc = f"""Read the data and generate a graph.
 
 Parameters
 ----------
-{_selection_doc}
+{projector.selection_doc}
 width : float
     Specifies the width of the flatbands if a selection of projections is specified.
-{_kpoints_opt_source}
+{kpoint.kpoints_opt_source}
 
 Returns
 -------
@@ -60,17 +57,17 @@
     is provided the width of the bands represents the projections of the
     bands onto the specified projectors.
 
-{_selection_examples("band", "plot")}"""
+{projector.selection_examples("band", "plot")}"""
 
 
 _to_plotly_doc = f"""Read the data and generate a plotly figure.
 
 Parameters
 ----------
-{_selection_doc}
+{projector.selection_doc}
 width : float
     Specifies the width of the flatbands if a selection of projections is specified.
-{_kpoints_opt_source}
+{kpoint.kpoints_opt_source}
 
 Returns
 -------
@@ -79,10 +76,10 @@
     is provided the width of the bands represents the projections of the
     bands onto the specified projectors.
 
-{_selection_examples("band", "to_plotly")}"""
+{projector.selection_examples("band", "to_plotly")}"""
 
 
-class Band(_base.Refinery, _export.Image):
+class Band(base.Refinery, export.Image):
     """The electronic band structure.
 
     The most common use case of this class is to produce the electronic band
@@ -92,7 +89,7 @@ class Band(_base.Refinery, _export.Image):
     **k**-point distances that are calculated are meaningless.
     """
 
-    @_base.data_access
+    @base.data_access
     def __str__(self):
         return f"""
 {"spin polarized" if self._spin_polarized() else ""} band data:
@@ -101,8 +98,8 @@ def __str__(self):
 {pretty(self._projector)}
     """.strip()
 
-    @_base.data_access
-    @_documentation.add(_to_dict_doc)
+    @base.data_access
+    @documentation.add(_to_dict_doc)
     def to_dict(self, selection=None):
         dispersion = self._dispersion.read()
         return {
@@ -114,22 +111,22 @@ def to_dict(self, selection=None):
             "projections": self._read_projections(selection),
         }
 
-    @_base.data_access
-    @_documentation.add(_plot_doc)
+    @base.data_access
+    @documentation.add(_plot_doc)
     def plot(self, selection=None, width=0.5):
         projections = self._projections(selection, width)
         graph = self._dispersion.plot(projections)
         graph = self._shift_series_by_fermi_energy(graph)
         graph.ylabel = "Energy (eV)"
         return graph
 
-    @_base.data_access
-    @_documentation.add(_to_plotly_doc)
+    @base.data_access
+    @documentation.add(_to_plotly_doc)
     def to_plotly(self, selection=None, width=0.5):
         return self.plot(selection, width).to_plotly()
 
-    @_base.data_access
-    @_documentation.add(_to_frame_doc)
+    @base.data_access
+    @documentation.add(_to_frame_doc)
     def to_frame(self, selection=None):
         index = self._setup_dataframe_index()
         data = self._extract_relevant_data(selection)
@@ -143,17 +140,17 @@ def _dispersion(self):
         return data.Dispersion.from_data(self._raw_data.dispersion)
 
     def _kpoints(self):
-        return Kpoint.from_data(self._raw_data.dispersion.kpoints)
+        return data.Kpoint.from_data(self._raw_data.dispersion.kpoints)
 
     @property
     def _projector(self):
-        return _Projector.from_data(self._raw_data.projectors)
+        return data.Projector.from_data(self._raw_data.projectors)
 
     def _projections(self, selection, width):
         if selection is None:
             return None
         error_message = "Width of fat band structure must be a number."
-        _check.raise_error_if_not_number(width, error_message)
+        check.raise_error_if_not_number(width, error_message)
         return {
             name: width * projection
             for name, projection in self._read_projections(selection).items()