diff --git a/.github/workflows/test_core.yml b/.github/workflows/test_core.yml new file mode 100644 index 00000000..25ae2330 --- /dev/null +++ b/.github/workflows/test_core.yml @@ -0,0 +1,61 @@ +name: test-core + +on: + push: + branches: [master] + pull_request: + branches: [master] + +jobs: + tests: + runs-on: ${{ matrix.os }} + strategy: + matrix: + os: [ubuntu-latest, macos-latest] + python-version: ["3.8", "3.9", "3.10"] + + steps: + - uses: actions/checkout@v3 + - name: Set up Python ${{ matrix.python-version }} + uses: actions/setup-python@v4 + with: + python-version: ${{ matrix.python-version }} + - name: Install dependencies + run: | + python -m pip install --upgrade pip + pip install "poetry!=1.4.1" + cp core/* . + poetry --version + poetry install + - name: Test with pytest + run: | + poetry run pytest --version + poetry run pytest + + + test-windows: + runs-on: windows-latest + strategy: + matrix: + python-version: ["3.8", "3.9", "3.10"] + + steps: + - uses: actions/checkout@v3 + - uses: conda-incubator/setup-miniconda@v2 + with: + auto-update-conda: true + python-version: ${{ matrix.python-version }} + - name: Install dependencies with conda + run: | + conda info + conda install -c conda-forge mdtraj + - name: Install py4vasp + run: | + python -m pip install --upgrade pip + cp core/* . + pip install . + - name: Test with pytest + run: | + pip install pytest pytest-cov hypothesis + pytest --version + pytest diff --git a/.github/workflows/test.yml b/.github/workflows/test_full.yml similarity index 64% rename from .github/workflows/test.yml rename to .github/workflows/test_full.yml index 273e866d..3d956a1d 100644 --- a/.github/workflows/test.yml +++ b/.github/workflows/test_full.yml @@ -1,4 +1,4 @@ -name: tests +name: test-full on: push: @@ -10,7 +10,6 @@ jobs: tests: runs-on: ${{ matrix.os }} strategy: - fail-fast: false matrix: os: [ubuntu-latest, macos-latest] python-version: ["3.8", "3.9", "3.10"] @@ -43,13 +42,16 @@ jobs: test-windows: runs-on: windows-latest + strategy: + matrix: + python-version: ["3.8", "3.9", "3.10"] steps: - uses: actions/checkout@v3 - uses: conda-incubator/setup-miniconda@v2 with: auto-update-conda: true - python-version: 3.8 + python-version: ${{ matrix.python-version }} - name: Install dependencies with conda run: | conda info @@ -58,7 +60,6 @@ jobs: run: | python -m pip install --upgrade pip pip install . - pip install ipykernel # missing dependecy of nglview - name: Test with pytest run: | pip install pytest pytest-cov hypothesis @@ -73,24 +74,3 @@ jobs: black --version black --check src black --check tests - # - name: Install poetry - # run: | - # python -m pip install --upgrade pip - # pip install "poetry!=1.4.1" - # poetry --version - # - name: Install py4vasp - # run: | - # poetry config virtualenvs.create false --local - # poetry install - # - name: Test with pytest - # run: | - # poetry run pytest --version - # 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 diff --git a/README.md b/README.md index 0158e030..80f74230 100644 --- a/README.md +++ b/README.md @@ -11,7 +11,7 @@ We use the [poetry dependency manager](https://python-poetry.org/) which takes care of all dependencies and maintains a virtual environment to check the code. If you want to -test something in the virtual environment, just use e.g. ```poetry run jupyter-notebook```. +test something in the virtual environment, just use e.g. `poetry run jupyter-notebook`. Using poetry installing and the code requires the following steps. The last step will test whether everything worked @@ -35,15 +35,38 @@ conda create --name py4vasp-env python=3.8 conda activate py4vasp-env conda install -c conda-forge poetry conda install -c conda-forge mdtraj -poetry config virtualenvs.create false --local poetry install poetry run pytest ~~~ +## py4vasp core + +If you want to use py4vasp to develop your own scripts, you may want to limit the amount +of external dependencies. To this end, we provide alternative configuration files that +only install numpy, h5py, and the development dependencies. To install this core package +replace the configurations files in the root folder with the ones in the `core` folder +~~~shell +cp core/* . +~~~ +Then you can install py4vasp with the same steps as above. Note that some tests will be +skipped because they require the external packages to run. + +If you want to exclude even the development dependencies, you can run +~~~shell +poetry install --without dev +~~~ +for the minimal installation. + ## Code style Code style is enforced, but is not something the developer should spend time on, so we -decided on using the black formatter. Please run ```black .``` before committing the code. +decided on using black and isort. Please run +~~~shell +black src tests +isort src tests +~~~ +before committing the code. This will autoformat your code and sort the import +statements in a consistent order. ## Contributing to py4vasp diff --git a/core/poetry.lock b/core/poetry.lock new file mode 100644 index 00000000..7d3e8083 --- /dev/null +++ b/core/poetry.lock @@ -0,0 +1,670 @@ +# This file is automatically @generated by Poetry 1.5.1 and should not be changed by hand. + +[[package]] +name = "astroid" +version = "2.15.5" +description = "An abstract syntax tree for Python with inference support." +optional = false +python-versions = ">=3.7.2" +files = [ + {file = "astroid-2.15.5-py3-none-any.whl", hash = "sha256:078e5212f9885fa85fbb0cf0101978a336190aadea6e13305409d099f71b2324"}, + {file = "astroid-2.15.5.tar.gz", hash = "sha256:1039262575027b441137ab4a62a793a9b43defb42c32d5670f38686207cd780f"}, +] + +[package.dependencies] +lazy-object-proxy = ">=1.4.0" +typing-extensions = {version = ">=4.0.0", markers = "python_version < \"3.11\""} +wrapt = [ + {version = ">=1.11,<2", markers = "python_version < 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a/pyproject.toml b/pyproject.toml index 3a1f138d..2777b8ca 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -18,63 +18,37 @@ repository = "https://github.com/vasp-dev/py4vasp" [tool.poetry.urls] "Support Forum" = "https://vasp.at/forum/" + [tool.poetry.dependencies] -# We actually do not want the <4 restriction here. This is due to requests 2.28.2 having -# this restriction, which will hopefully be released in a future release there -#python = ">=3.8" -python = ">=3.8,<4" -numpy = ">=1.23.0" +python = ">=3.8" +numpy = ">=1.23" h5py = ">=3.7.0" pandas = ">=1.4.3" -nglview = ">=3.0.3" -# nglview is not compatible with recent ipywidgets, so we need to set the constraint here -# this should be removed again, once this is fixed in nglview and the broken version of -# nglview should be excluded -ipywidgets = "^7.7" +nglview = ">=3.0.5" ase = ">=3.22.1" -mdtraj = ">=1.9.6" mrcfile = ">=1.3.0" plotly = ">=5.9.0" -kaleido = "!=0.2.1.post1,>=0.2.1" +kaleido = ">=0.2.1,<0.2.1.post1 || >0.2.1.post1" ipython = "^8.12" +mdtraj = ">=1.9.6" -[tool.poetry.dev-dependencies] +[tool.poetry.group.dev.dependencies] pytest = ">=7.1.2" pytest-cov = ">=3.0.0" -pylint = ">=2.14.3" -Sphinx = ">=5.0.2" -black = ">=22.6.0" +pylint = ">=2.15" hypothesis = ">=6.48.1" +black = ">=22.6.0" isort = ">=5.10.1" -sphinx-automodapi = ">=0.14.1" -[tool.poetry.scripts] -error-analysis = "py4vasp.scripts.error_analysis:main" - -[tool.poetry2conda] -name = "py4vasp-env" +[tool.poetry.group.doc.dependencies] +sphinx = ">=5.0.2" +sphinx-automodapi = ">=0.14.1" -[tool.poetry2conda.dependencies] -python = {channel = "anaconda"} -h5py = {channel = "conda-forge"} -numpy = {channel = "anaconda"} -pandas = {channel = "conda-forge"} -nglview = {channel = "conda-forge"} -ase = {channel = "conda-forge"} -mdtraj = {channel = "conda-forge"} -plotlt = {channel = "conda-forge"} -mrcfile = {channel = "conda-forge"} -pytest = {channel = "anaconda"} -sphinx = {channel = "anaconda"} -black = {channel = "conda-forge"} [tool.isort] profile = "black" -[tool.dephell.main] -from = {format = "poetry", path = "pyproject.toml"} -to = {format = "setuppy", path = "setup.py"} [build-system] -requires = ["poetry-core>=1.0.0"] +requires = ["poetry-core"] build-backend = "poetry.core.masonry.api" diff --git a/src/py4vasp/_data/band.py b/src/py4vasp/_data/band.py index 9b2e407d..3b484655 100644 --- a/src/py4vasp/_data/band.py +++ b/src/py4vasp/_data/band.py @@ -1,13 +1,14 @@ # Copyright © VASP Software GmbH, # Licensed under the Apache License 2.0 (http://www.apache.org/licenses/LICENSE-2.0) import numpy as np -import pandas as pd -from IPython.lib.pretty import pretty from py4vasp import data from py4vasp._data import base, projector from py4vasp._third_party import graph -from py4vasp._util import check, documentation +from py4vasp._util import check, documentation, import_ + +pd = import_.optional("pandas") +pretty = import_.optional("IPython.lib.pretty") class Band(base.Refinery, graph.Mixin): @@ -26,7 +27,7 @@ def __str__(self): {"spin polarized" if self._spin_polarized() else ""} band data: {self._raw_data.dispersion.eigenvalues.shape[1]} k-points {self._raw_data.dispersion.eigenvalues.shape[2]} bands -{pretty(self._projector)} +{pretty.pretty(self._projector)} """.strip() @base.data_access diff --git a/src/py4vasp/_data/density.py b/src/py4vasp/_data/density.py index 0591918e..99d72722 100644 --- a/src/py4vasp/_data/density.py +++ b/src/py4vasp/_data/density.py @@ -1,9 +1,10 @@ # Copyright © VASP Software GmbH, # Licensed under the Apache License 2.0 (http://www.apache.org/licenses/LICENSE-2.0) -from IPython.lib.pretty import pretty - from py4vasp import data, exception from py4vasp._data import base, structure +from py4vasp._util import import_ + +pretty = import_.optional("IPython.lib.pretty") class _ViewerWrapper: @@ -27,8 +28,9 @@ class Density(base.Refinery, structure.Mixin): def __str__(self): _raise_error_if_no_data(self._raw_data.charge) grid = self._raw_data.charge.shape[1:] + topology = data.Topology.from_data(self._raw_data.structure.topology) return f"""density: - structure: {pretty(data.Topology.from_data(self._raw_data.structure.topology))} + structure: {pretty.pretty(topology)} grid: {grid[0]}, {grid[1]}, {grid[2]} {"spin polarized" if self._spin_polarized() else ""} """.strip() diff --git a/src/py4vasp/_data/dos.py b/src/py4vasp/_data/dos.py index 93474923..cc7684c5 100644 --- a/src/py4vasp/_data/dos.py +++ b/src/py4vasp/_data/dos.py @@ -1,12 +1,12 @@ # Copyright © VASP Software GmbH, # Licensed under the Apache License 2.0 (http://www.apache.org/licenses/LICENSE-2.0) -import pandas as pd -from IPython.lib.pretty import pretty - from py4vasp import data from py4vasp._data import base, projector from py4vasp._third_party import graph -from py4vasp._util import documentation +from py4vasp._util import documentation, import_ + +pd = import_.optional("pandas") +pretty = import_.optional("IPython.lib.pretty") class Dos(base.Refinery, graph.Mixin): @@ -27,7 +27,7 @@ def __str__(self): return f""" {"spin polarized" if self._spin_polarized() else ""} Dos: energies: [{energies[0]:0.2f}, {energies[-1]:0.2f}] {len(energies)} points -{pretty(self._projectors())} +{pretty.pretty(self._projectors())} """.strip() @base.data_access diff --git a/src/py4vasp/_data/kpoint.py b/src/py4vasp/_data/kpoint.py index 5530803e..cfaf4f17 100644 --- a/src/py4vasp/_data/kpoint.py +++ b/src/py4vasp/_data/kpoint.py @@ -91,7 +91,8 @@ def number_lines(self): Returns ------- int - The number of lines the band structure contains. For regular meshes this is set to 1.""" + The number of lines the band structure contains. For regular meshes this is set to 1. + """ return self.number_kpoints() // self.line_length() @base.data_access diff --git a/src/py4vasp/_data/structure.py b/src/py4vasp/_data/structure.py index d2ed96aa..6da2816b 100644 --- a/src/py4vasp/_data/structure.py +++ b/src/py4vasp/_data/structure.py @@ -4,15 +4,16 @@ from collections import Counter from dataclasses import dataclass -import ase.io -import mdtraj import numpy as np -from IPython.lib.pretty import pretty from py4vasp import data, exception, raw from py4vasp._data import base, slice_, topology from py4vasp._data.viewer3d import Viewer3d -from py4vasp._util import documentation, reader +from py4vasp._util import documentation, import_, reader + +ase = import_.optional("ase") +ase_io = import_.optional("ase.io") +mdtraj = import_.optional("mdtraj") @dataclass @@ -24,7 +25,7 @@ class _Format: newline: str = "" def comment_line(self, topology, step_string): - return f"{pretty(topology)}{step_string}{self.newline}" + return f"{topology}{step_string}{self.newline}" def scaling_factor(self): return f"1.0{self.newline}" @@ -67,7 +68,7 @@ def from_POSCAR(cls, poscar, *, elements=None): """Generate a structure from string in POSCAR format.""" poscar = _replace_or_set_elements(str(poscar), elements) poscar = io.StringIO(poscar) - structure = ase.io.read(poscar, format="vasp") + structure = ase_io.read(poscar, format="vasp") return cls.from_ase(structure) @classmethod diff --git a/src/py4vasp/_data/topology.py b/src/py4vasp/_data/topology.py index e03e0696..41687cd0 100644 --- a/src/py4vasp/_data/topology.py +++ b/src/py4vasp/_data/topology.py @@ -2,14 +2,15 @@ # Licensed under the Apache License 2.0 (http://www.apache.org/licenses/LICENSE-2.0) import itertools -import mdtraj import numpy as np -import pandas as pd from py4vasp import raw from py4vasp._data import base from py4vasp._data.selection import Selection -from py4vasp._util import check, convert, select +from py4vasp._util import check, convert, import_, select + +mdtraj = import_.optional("mdtraj") +pd = import_.optional("pandas") _subscript = "_" diff --git a/src/py4vasp/_data/viewer3d.py b/src/py4vasp/_data/viewer3d.py index 705e1cd0..94204a74 100644 --- a/src/py4vasp/_data/viewer3d.py +++ b/src/py4vasp/_data/viewer3d.py @@ -5,11 +5,13 @@ import tempfile from typing import NamedTuple -import mrcfile -import nglview import numpy as np from py4vasp import exception +from py4vasp._util import import_ + +mrcfile = import_.optional("mrcfile") +nglview = import_.optional("nglview") class _Arrow3d(NamedTuple): diff --git a/src/py4vasp/_third_party/graph/__init__.py b/src/py4vasp/_third_party/graph/__init__.py index 5a9d6102..783f9255 100644 --- a/src/py4vasp/_third_party/graph/__init__.py +++ b/src/py4vasp/_third_party/graph/__init__.py @@ -1,14 +1,16 @@ # Copyright © VASP Software GmbH, # Licensed under the Apache License 2.0 (http://www.apache.org/licenses/LICENSE-2.0) -import plotly.graph_objects as go -import plotly.io as pio - from py4vasp._config import VASP_COLORS +from py4vasp._util import import_ from .graph import Graph from .mixin import Mixin from .plot import plot from .series import Series -pio.templates["vasp"] = go.layout.Template(layout={"colorway": VASP_COLORS}) -pio.templates.default = "ggplot2+vasp" +go = import_.optional("plotly.graph_objects") +pio = import_.optional("plotly.io") + +if import_.is_imported(go) and import_.is_imported(pio): + pio.templates["vasp"] = go.layout.Template(layout={"colorway": VASP_COLORS}) + pio.templates.default = "ggplot2+vasp" diff --git a/src/py4vasp/_third_party/graph/graph.py b/src/py4vasp/_third_party/graph/graph.py index 25f15605..5c3f7bc8 100644 --- a/src/py4vasp/_third_party/graph/graph.py +++ b/src/py4vasp/_third_party/graph/graph.py @@ -5,12 +5,14 @@ from dataclasses import dataclass, fields, replace import numpy as np -import plotly.graph_objects as go -from plotly.subplots import make_subplots from py4vasp import exception from py4vasp._config import VASP_COLORS from py4vasp._third_party.graph.series import Series +from py4vasp._util import import_ + +go = import_.optional("plotly.graph_objects") +subplots = import_.optional("plotly.subplots") @dataclass @@ -118,11 +120,11 @@ def _make_plotly_figure(self): def _figure_with_one_or_two_y_axes(self): if self._subplot_on: max_row = max(series.subplot for series in self) - figure = make_subplots(rows=max_row, cols=1) + figure = subplots.make_subplots(rows=max_row, cols=1) figure.update_layout(showlegend=False) return figure elif any(series.y2 for series in self): - return make_subplots(specs=[[{"secondary_y": True}]]) + return subplots.make_subplots(specs=[[{"secondary_y": True}]]) else: return go.Figure() diff --git a/src/py4vasp/_third_party/graph/series.py b/src/py4vasp/_third_party/graph/series.py index 57aa71fd..946051f3 100644 --- a/src/py4vasp/_third_party/graph/series.py +++ b/src/py4vasp/_third_party/graph/series.py @@ -3,9 +3,11 @@ from dataclasses import dataclass, fields import numpy as np -import plotly.graph_objects as go from py4vasp import exception +from py4vasp._util import import_ + +go = import_.optional("plotly.graph_objects") @dataclass diff --git a/src/py4vasp/_third_party/interactive.py b/src/py4vasp/_third_party/interactive.py index 4e3b21e9..5d057549 100644 --- a/src/py4vasp/_third_party/interactive.py +++ b/src/py4vasp/_third_party/interactive.py @@ -3,11 +3,32 @@ import contextlib import os -import IPython +from py4vasp._util import import_ + +IPython = import_.optional("IPython") +_ERROR_VERBOSITY = "Minimal" def set_error_handling(verbosity): - ipython = IPython.get_ipython() - if ipython is not None: + global _ERROR_VERBOSITY + ipython = _get_ipython() + if ipython is None: + _ERROR_VERBOSITY = verbosity + else: with open(os.devnull, "w") as ignore, contextlib.redirect_stdout(ignore): ipython.magic(f"xmode {verbosity}") + + +def error_handling(): + ipython = _get_ipython() + if ipython is None: + return _ERROR_VERBOSITY + else: + return ipython.xmode + + +def _get_ipython(): + if import_.is_imported(IPython): + return IPython.get_ipython() + else: + return None diff --git a/src/py4vasp/_util/import_.py b/src/py4vasp/_util/import_.py new file mode 100644 index 00000000..93db5e4d --- /dev/null +++ b/src/py4vasp/_util/import_.py @@ -0,0 +1,27 @@ +# Copyright © VASP Software GmbH, +# Licensed under the Apache License 2.0 (http://www.apache.org/licenses/LICENSE-2.0) +import importlib + +from py4vasp import exception + + +class _ModulePlaceholder: + def __init__(self, name): + self._name = name + + def __getattr__(self, attr): + raise exception.ModuleNotInstalled( + "You use an optional part of py4vasp that relies on the package " + f"'{self._name}'. Please install the package to use this functionality." + ) + + +def optional(name): + try: + return importlib.import_module(name) + except: + return _ModulePlaceholder(name) + + +def is_imported(module): + return not isinstance(module, _ModulePlaceholder) diff --git a/src/py4vasp/exception.py b/src/py4vasp/exception.py index 2742b238..6c4f5deb 100644 --- a/src/py4vasp/exception.py +++ b/src/py4vasp/exception.py @@ -36,6 +36,11 @@ class OutdatedVaspVersion(Py4VaspError): used version of Vasp.""" +class ModuleNotInstalled(Py4VaspError): + """Exception raised when a functionality is used that relies on an optional + dependency of py4vasp but that dependency is not installed.""" + + class StopExecution(Py4VaspError): """Exception raised when an error occurred in the user interface. This prevents further cells from being executed.""" diff --git a/tests/conftest.py b/tests/conftest.py index 8bdc7473..0f4f2b7b 100644 --- a/tests/conftest.py +++ b/tests/conftest.py @@ -1,5 +1,6 @@ # Copyright © VASP Software GmbH, # Licensed under the Apache License 2.0 (http://www.apache.org/licenses/LICENSE-2.0) +import importlib.metadata import itertools import numpy as np @@ -22,6 +23,27 @@ number_modes = axes * number_atoms +@pytest.fixture(scope="session") +def is_core(): + try: + importlib.metadata.distribution("py4vasp-core") + return True + except importlib.metadata.PackageNotFoundError: + return False + + +@pytest.fixture() +def only_core(is_core): + if not is_core: + pytest.skip("This test checks py4vasp-core functionality not used by py4vasp.") + + +@pytest.fixture() +def not_core(is_core): + if is_core: + pytest.skip("This test requires features not present in py4vasp-core.") + + class _Assert: @staticmethod def allclose(actual, desired): diff --git a/tests/control/test_base.py b/tests/control/test_base.py index 4ad5b367..f8ca32c4 100644 --- a/tests/control/test_base.py +++ b/tests/control/test_base.py @@ -5,7 +5,11 @@ from pathlib import Path from unittest.mock import mock_open, patch -from IPython.lib.pretty import pretty +import pytest + +from py4vasp._util import import_ + +pretty = import_.optional("IPython.lib.pretty") class AbstractTest: @@ -55,7 +59,11 @@ def test_print_instance(self): instance.print() assert buffer.getvalue().strip() == text + @pytest.mark.skipif( + not import_.is_imported(pretty), + reason="This test requires pretty from IPython.", + ) def test_pretty_instance(self): text = "! comment line" instance = self.tested_class.from_string(text) - assert pretty(instance) == text + assert pretty.pretty(instance) == text diff --git a/tests/control/test_poscar.py b/tests/control/test_poscar.py index 13e04135..93cc57bf 100644 --- a/tests/control/test_poscar.py +++ b/tests/control/test_poscar.py @@ -13,7 +13,7 @@ class TestPoscar(AbstractTest): tested_class = POSCAR -def test_plot_poscar(): +def test_plot_poscar(not_core): text = """! comment line 5.43 0.0 0.5 0.5 diff --git a/tests/data/conftest.py b/tests/data/conftest.py index 5cad2364..33d3a2b6 100644 --- a/tests/data/conftest.py +++ b/tests/data/conftest.py @@ -4,10 +4,11 @@ from unittest.mock import MagicMock, patch import pytest -from IPython.core.formatters import DisplayFormatter from py4vasp import exception -from py4vasp._util import convert +from py4vasp._util import convert, import_ + +formatters = import_.optional("IPython.core.formatters") TEST_FILENAME = "read_data_from_this_file" SELECTION = "alternative" @@ -22,7 +23,7 @@ def mock_schema(): @pytest.fixture -def check_factory_methods(mock_schema): +def check_factory_methods(mock_schema, not_core): def inner(cls, data, parameters={}): instance = cls.from_path() check_instance_accesses_data(instance, data, parameters) @@ -90,5 +91,5 @@ def check_mock_called(mock_access, quantity, file, selection=None): @pytest.fixture -def format_(): - return DisplayFormatter().format +def format_(not_core): + return formatters.DisplayFormatter().format diff --git a/tests/data/test_band.py b/tests/data/test_band.py index 83e72d4e..03510e17 100644 --- a/tests/data/test_band.py +++ b/tests/data/test_band.py @@ -5,7 +5,6 @@ import numpy as np import pytest -from IPython.lib.pretty import pretty from py4vasp import exception from py4vasp.data import Band, Kpoint, Projector @@ -93,7 +92,7 @@ def spin_projectors(raw_data): band.ref.Fe_d_down = np.sum(raw_band.projections[1, 0:3, 2, :, :], axis=0) band.ref.O_up = np.sum(raw_band.projections[0, 3:7, :, :, :], axis=(0, 1)) band.ref.O_down = np.sum(raw_band.projections[1, 3:7, :, :, :], axis=(0, 1)) - band.ref.projectors_string = pretty(Projector.from_data(raw_band.projectors)) + band.ref.projectors_string = str(Projector.from_data(raw_band.projectors)) return band @@ -160,14 +159,14 @@ def test_more_projections_style(raw_data, Assert): Assert.allclose(band["projections"]["g_down"], zero) -def test_single_polarized_to_frame(single_band, Assert): +def test_single_polarized_to_frame(single_band, Assert, not_core): actual = single_band.to_frame() assert all(actual.index == single_band.ref.index) Assert.allclose(actual.bands, single_band.ref.bands[:, 0]) Assert.allclose(actual.occupations, single_band.ref.occupations[:, 0]) -def test_multiple_bands_to_frame(multiple_bands, Assert): +def test_multiple_bands_to_frame(multiple_bands, Assert, not_core): actual = multiple_bands.to_frame() assert actual.index[0] == "[0.00 0.00 0.12] 1" assert actual.index[1] == "2" @@ -177,13 +176,13 @@ def test_multiple_bands_to_frame(multiple_bands, Assert): Assert.allclose(actual.occupations, multiple_bands.ref.occupations.T.flatten()) -def test_with_projectors_to_frame(with_projectors, Assert): +def test_with_projectors_to_frame(with_projectors, Assert, not_core): actual = with_projectors.to_frame("Sr p") Assert.allclose(actual.Sr, with_projectors.ref.Sr.T.flatten()) Assert.allclose(actual.p, with_projectors.ref.p.T.flatten()) -def test_spin_polarized_to_frame(spin_polarized, Assert): +def test_spin_polarized_to_frame(spin_polarized, Assert, not_core): actual = spin_polarized.to_frame() ref = spin_polarized.ref Assert.allclose(actual.bands_up, ref.bands_up.T.flatten()) @@ -192,7 +191,7 @@ def test_spin_polarized_to_frame(spin_polarized, Assert): Assert.allclose(actual.occupations_down, ref.occupations_down.T.flatten()) -def test_spin_projectors_to_frame(spin_projectors, Assert): +def test_spin_projectors_to_frame(spin_projectors, Assert, not_core): actual = spin_projectors.to_frame(selection="O Fe(d)") Assert.allclose(actual.O_up, spin_projectors.ref.O_up.T.flatten()) Assert.allclose(actual.O_down, spin_projectors.ref.O_down.T.flatten()) diff --git a/tests/data/test_density.py b/tests/data/test_density.py index 5e352a63..bc7d9339 100644 --- a/tests/data/test_density.py +++ b/tests/data/test_density.py @@ -43,7 +43,7 @@ def test_read(collinear_density, Assert): Assert.allclose(actual["magnetization"], collinear_density.ref.magnetization) -def test_charge_plot(collinear_density, Assert): +def test_charge_plot(collinear_density, Assert, not_core): obj = viewer3d.Viewer3d cm_init = patch.object(obj, "__init__", autospec=True, return_value=None) cm_cell = patch.object(obj, "show_cell") @@ -59,7 +59,7 @@ def test_charge_plot(collinear_density, Assert): assert kwargs == {"isolevel": 0.2, "color": "yellow", "opacity": 0.6} -def test_magnetization_plot(collinear_density, Assert): +def test_magnetization_plot(collinear_density, Assert, not_core): obj = viewer3d.Viewer3d cm_init = patch.object(obj, "__init__", autospec=True, return_value=None) cm_cell = patch.object(obj, "show_cell") @@ -88,14 +88,14 @@ def test_charge_only(charge_only_density, Assert): assert actual["magnetization"] is None -def test_missing_element(charge_only_density, Assert): +def test_missing_element(charge_only_density, Assert, not_core): with pytest.raises(exception.IncorrectUsage): charge_only_density.plot("unknown tag") with pytest.raises(exception.NoData): charge_only_density.plot("magnetization") -def test_color_specified_for_magnetism(collinear_density, Assert): +def test_color_specified_for_magnetism(collinear_density, Assert, not_core): with pytest.raises(exception.NotImplemented): collinear_density.plot("magnetization", color="brown") diff --git a/tests/data/test_dos.py b/tests/data/test_dos.py index 0335c161..a14f1d85 100644 --- a/tests/data/test_dos.py +++ b/tests/data/test_dos.py @@ -118,14 +118,14 @@ def test_read_excess_orbital_types(raw_data, Assert): Assert.allclose(actual["g_down"], zero) -def test_Sr2TiO4_to_frame(Sr2TiO4, Assert): +def test_Sr2TiO4_to_frame(Sr2TiO4, Assert, not_core): actual = Sr2TiO4.to_frame() Assert.allclose(actual.energies, Sr2TiO4.ref.energies) Assert.allclose(actual.total, Sr2TiO4.ref.dos) assert actual.fermi_energy == Sr2TiO4.ref.fermi_energy -def test_Fe3O4_to_frame(Fe3O4, Assert): +def test_Fe3O4_to_frame(Fe3O4, Assert, not_core): actual = Fe3O4.to_frame() Assert.allclose(actual.energies, Fe3O4.ref.energies) Assert.allclose(actual.up, Fe3O4.ref.dos_up) @@ -133,7 +133,7 @@ def test_Fe3O4_to_frame(Fe3O4, Assert): assert actual.fermi_energy == Fe3O4.ref.fermi_energy -def test_Sr2TiO4_projectors_to_frame(Sr2TiO4_projectors, Assert): +def test_Sr2TiO4_projectors_to_frame(Sr2TiO4_projectors, Assert, not_core): equivalent_selections = [ "s Sr(d) Ti O(px,dxy) 2(p) 4 3(dz2) 1:2(p)", "2( p), dz2(3) Sr(d) p(1:2), s, 4 Ti px(O) O(dxy)", diff --git a/tests/data/test_structure.py b/tests/data/test_structure.py index 09cce967..10be3ff7 100644 --- a/tests/data/test_structure.py +++ b/tests/data/test_structure.py @@ -101,7 +101,7 @@ def test_to_poscar(Sr2TiO4): Sr2TiO4[steps].to_POSCAR() -def test_from_poscar(Sr2TiO4, Assert): +def test_from_poscar(Sr2TiO4, Assert, not_core): structure = Structure.from_POSCAR(REF_POSCAR) check_Sr2TiO4_structure(structure.read(), Sr2TiO4.ref, -1, Assert) structure = Structure.from_POSCAR(REF_POSCAR, elements=["Ba", "Zr", "S"]) @@ -112,7 +112,7 @@ def test_from_poscar(Sr2TiO4, Assert): assert actual["names"] == ["Ba_1", "Ba_2", "Zr_1", "S_1", "S_2", "S_3", "S_4"] -def test_from_poscar_without_elements(Sr2TiO4, Assert): +def test_from_poscar_without_elements(Sr2TiO4, Assert, not_core): poscar = """\ POSCAR without elements 1.0 @@ -134,7 +134,7 @@ def test_from_poscar_without_elements(Sr2TiO4, Assert): check_Sr2TiO4_structure(structure.read(), Sr2TiO4.ref, -1, Assert) -def test_to_ase_Sr2TiO4(Sr2TiO4, Assert): +def test_to_ase_Sr2TiO4(Sr2TiO4, Assert, not_core): check_Sr2TiO4_ase(Sr2TiO4.to_ase(), Sr2TiO4.ref, -1, Assert) check_Sr2TiO4_ase(Sr2TiO4[0].to_ase(), Sr2TiO4.ref, 0, Assert) for steps in (slice(None), slice(1, 3)): @@ -149,7 +149,7 @@ def check_Sr2TiO4_ase(structure, reference, steps, Assert): assert all(structure.pbc) -def test_to_ase_Fe3O4(Fe3O4, Assert): +def test_to_ase_Fe3O4(Fe3O4, Assert, not_core): check_Fe3O4_ase(Fe3O4.to_ase(), Fe3O4.ref, -1, Assert) check_Fe3O4_ase(Fe3O4[0].to_ase(), Fe3O4.ref, 0, Assert) @@ -162,12 +162,12 @@ def check_Fe3O4_ase(structure, reference, steps, Assert): assert all(structure.pbc) -def test_from_ase(Sr2TiO4, Assert): +def test_from_ase(Sr2TiO4, Assert, not_core): structure = Structure.from_ase(Sr2TiO4.to_ase()) check_Sr2TiO4_structure(structure.read(), Sr2TiO4.ref, -1, Assert) -def test_to_mdtraj(Sr2TiO4, Assert): +def test_to_mdtraj(Sr2TiO4, Assert, not_core): for steps in (slice(None), slice(1, 3)): trajectory = Sr2TiO4[steps].to_mdtraj() check_Sr2TiO4_mdtraj(trajectory, Sr2TiO4.ref, steps, Assert) @@ -188,7 +188,7 @@ def check_Sr2TiO4_mdtraj(trajectory, reference, steps, Assert): Assert.allclose(trajectory.unitcell_vectors, unitcell_vectors) -def test_supercell_scale_all(Sr2TiO4, Assert): +def test_supercell_scale_all(Sr2TiO4, Assert, not_core): number_atoms = 7 scale = 2 supercell = Sr2TiO4.to_ase(supercell=scale) @@ -197,7 +197,7 @@ def test_supercell_scale_all(Sr2TiO4, Assert): assert list(supercell.symbols) == 16 * ["Sr"] + 8 * ["Ti"] + 32 * ["O"] -def test_supercell_scale_individual(Sr2TiO4, Assert): +def test_supercell_scale_individual(Sr2TiO4, Assert, not_core): number_atoms = 7 scale = (2, 1, 3) supercell = Sr2TiO4.to_ase(supercell=scale) @@ -205,14 +205,14 @@ def test_supercell_scale_individual(Sr2TiO4, Assert): Assert.allclose(supercell.cell.array, np.diag(scale) @ Sr2TiO4.ref.lattice_vectors) -def test_supercell_wrong_size(Sr2TiO4): +def test_supercell_wrong_size(Sr2TiO4, not_core): with pytest.raises(exception.IncorrectUsage): Sr2TiO4.to_ase("foo") with pytest.raises(exception.IncorrectUsage): Sr2TiO4.to_ase([1, 2]) -def test_cartesian_positions(Sr2TiO4, Fe3O4, Assert): +def test_cartesian_positions(Sr2TiO4, Fe3O4, Assert, not_core): check_cartesian_positions(Sr2TiO4, Assert) check_cartesian_positions(Fe3O4, Assert) check_cartesian_positions(Fe3O4[0], Assert) @@ -246,13 +246,13 @@ def test_number_steps(Sr2TiO4): assert Sr2TiO4[1:3].number_steps() == 2 -def test_plot_Sr2TiO4(Sr2TiO4): +def test_plot_Sr2TiO4(Sr2TiO4, not_core): check_plot_structure(Sr2TiO4) for steps in (slice(None), slice(1, 3), 0): check_plot_structure(Sr2TiO4[steps]) -def test_plot_Fe3O4(Fe3O4): +def test_plot_Fe3O4(Fe3O4, not_core): check_plot_structure(Fe3O4) for steps in (slice(None), slice(1, 3), 0): check_plot_structure(Fe3O4[steps]) diff --git a/tests/data/test_topology.py b/tests/data/test_topology.py index 9a9805c9..8efb9493 100644 --- a/tests/data/test_topology.py +++ b/tests/data/test_topology.py @@ -1,14 +1,15 @@ # Copyright © VASP Software GmbH, # Licensed under the Apache License 2.0 (http://www.apache.org/licenses/LICENSE-2.0) -import ase -import pandas as pd import pytest from py4vasp import exception from py4vasp._data.selection import Selection -from py4vasp._util import select +from py4vasp._util import import_, select from py4vasp.data import Topology +ase = import_.optional("ase") +pd = import_.optional("pandas") + class Base: def test_read(self): @@ -19,13 +20,13 @@ def test_read(self): assert topology[str(i + 1)] == expected self.check_ion_indices(topology) - def test_to_frame(self): + def test_to_frame(self, not_core): actual = self.topology.to_frame() ref_data = {"name": self.names, "element": self.elements} reference = pd.DataFrame(ref_data) assert reference.equals(actual) - def test_to_mdtraj(self): + def test_to_mdtraj(self, not_core): actual, _ = self.topology.to_mdtraj().to_dataframe() num_atoms = self.topology.number_atoms() ref_data = { @@ -53,7 +54,7 @@ def test_names(self): def test_number_atoms(self): assert self.topology.number_atoms() == 7 - def test_from_ase(self): + def test_from_ase(self, not_core): structure = ase.Atoms("".join(self.elements)) topology = Topology.from_ase(structure) assert topology.elements() == self.elements diff --git a/tests/data/test_viewer3d.py b/tests/data/test_viewer3d.py index 25e51292..e12bd6f5 100644 --- a/tests/data/test_viewer3d.py +++ b/tests/data/test_viewer3d.py @@ -3,15 +3,17 @@ import types from unittest.mock import patch -import ipykernel.jsonutil as json -import nglview import numpy as np import pytest from py4vasp import exception from py4vasp._data.viewer3d import Viewer3d, _Arrow3d, _x_axis, _y_axis, _z_axis +from py4vasp._util import import_ from py4vasp.data import Structure +json = import_.optional("ipykernel.jsonutil") +nglview = import_.optional("nglview") + @pytest.fixture def assert_arrow_message(Assert): @@ -30,7 +32,7 @@ def _assert_arrow_message(message, arrow): @pytest.fixture -def viewer3d(raw_data): +def viewer3d(raw_data, not_core): structure = Structure.from_data(raw_data.structure("Sr2TiO4")) return make_viewer(structure) @@ -107,7 +109,7 @@ def test_arrows(viewer3d, assert_arrow_message): viewer3d.hide_arrows_at_atoms() -def test_supercell(raw_data, assert_arrow_message): +def test_supercell(raw_data, assert_arrow_message, not_core): structure = Structure.from_data(raw_data.structure("Sr2TiO4")) number_atoms = structure.number_atoms() supercell = (1, 2, 3) @@ -132,13 +134,13 @@ def create_arrows(viewer, number_atoms): return arrows -def test_serializable(): +def test_serializable(not_core): arrow = _Arrow3d(np.zeros(3), np.ones(3), np.ones(1)) for element in arrow.to_serializable(): json.json_clean(element) -def test_standard_form(raw_data, Assert): +def test_standard_form(raw_data, Assert, not_core): # TODO: this test should be changed to make the intention clearer # The issue is that the positions of the arrows are incorrect if we pass a structure # which has not been transformed to standard form. @@ -150,7 +152,7 @@ def test_standard_form(raw_data, Assert): Assert.allclose(viewer._positions, raw_structure.positions) -def test_isosurface(raw_data): +def test_isosurface(raw_data, not_core): raw_density = raw_data.density("Fe3O4 collinear") viewer = make_viewer(Structure.from_data(raw_density.structure)) viewer.show_isosurface(raw_density.charge) @@ -164,7 +166,7 @@ def test_isosurface(raw_data): assert_add_surface(messages[1], kwargs) -def test_trajectory(raw_data): +def test_trajectory(raw_data, not_core): structure = Structure.from_data(raw_data.structure("Sr2TiO4")) viewer = structure[:].plot() viewer.default_messages = 0 diff --git a/tests/test_calculation.py b/tests/test_calculation.py index 661da92e..4f526750 100644 --- a/tests/test_calculation.py +++ b/tests/test_calculation.py @@ -1,6 +1,7 @@ # Copyright © VASP Software GmbH, # Licensed under the Apache License 2.0 (http://www.apache.org/licenses/LICENSE-2.0) import inspect +import os from pathlib import Path from unittest.mock import mock_open, patch @@ -16,7 +17,7 @@ def test_creation_from_path(mock_access, mock_from_path): absolute_path = Path(__file__) calc = Calculation.from_path(absolute_path) assert calc.path() == absolute_path - relative_path = absolute_path.relative_to(Path.cwd()) + relative_path = os.path.relpath(absolute_path, Path.cwd()) calc = Calculation.from_path(relative_path) assert calc.path() == absolute_path calc = Calculation.from_path("~") @@ -33,7 +34,7 @@ def test_creation_from_file(mock_access, mock_from_file): absolute_file = absolute_path / "example.h5" calc = Calculation.from_file(absolute_file) assert calc.path() == absolute_path - relative_file = absolute_file.relative_to(Path.cwd()) + relative_file = os.path.relpath(absolute_file, Path.cwd()) calc = Calculation.from_file(relative_file) assert calc.path() == absolute_path calc = Calculation.from_file("~/example.h5") diff --git a/tests/third_party/graph/test_graph.py b/tests/third_party/graph/test_graph.py index d3c7999e..1663d3ce 100644 --- a/tests/third_party/graph/test_graph.py +++ b/tests/third_party/graph/test_graph.py @@ -59,14 +59,14 @@ def subplot(): return Series(x1, y1, subplot=1), Series(x2, y2, subplot=2) -def test_basic_graph(parabola, Assert): +def test_basic_graph(parabola, Assert, not_core): graph = Graph(parabola) fig = graph.to_plotly() assert len(fig.data) == 1 compare_series(fig.data[0], parabola, Assert) -def test_two_series(parabola, sine, Assert): +def test_two_series(parabola, sine, Assert, not_core): for graph in (Graph([parabola, sine]), Graph(parabola) + Graph(sine)): fig = graph.to_plotly() assert len(fig.data) == 2 @@ -80,7 +80,7 @@ def compare_series(converted, original, Assert): assert converted.name == original.name -def test_axis_label(parabola): +def test_axis_label(parabola, not_core): graph = Graph(parabola) graph.xlabel = "xaxis label" graph.ylabel = "yaxis label" @@ -89,7 +89,7 @@ def test_axis_label(parabola): assert fig.layout.yaxis.title.text == graph.ylabel -def test_secondary_yaxis(parabola, sine, Assert): +def test_secondary_yaxis(parabola, sine, Assert, not_core): sine.y2 = True graph = Graph([parabola, sine]) graph.y2label = "secondary yaxis label" @@ -104,7 +104,7 @@ def check_legend_group(converted, original, first_trace): assert converted.showlegend == first_trace -def test_two_lines(two_lines, Assert): +def test_two_lines(two_lines, Assert, not_core): graph = Graph(two_lines) fig = graph.to_plotly() assert len(fig.data) == 2 @@ -135,13 +135,13 @@ def compare_series_with_width(converted, original, Assert): assert converted.opacity == 0.5 -def test_fatband(fatband, Assert): +def test_fatband(fatband, Assert, not_core): graph = Graph(fatband) fig = graph.to_plotly() compare_series_with_width(fig.data[0], fatband, Assert) -def test_two_fatbands(two_fatbands, Assert): +def test_two_fatbands(two_fatbands, Assert, not_core): graph = Graph(two_fatbands) fig = graph.to_plotly() assert len(fig.data) == 2 @@ -157,7 +157,7 @@ def test_two_fatbands(two_fatbands, Assert): first_trace = False -def test_simple_with_marker(sine): +def test_simple_with_marker(sine, not_core): graph = Graph(sine) fig = graph.to_plotly() assert len(fig.data) == 1 @@ -165,7 +165,7 @@ def test_simple_with_marker(sine): assert fig.data[0].marker.size is None -def test_fatband_with_marker(fatband, Assert): +def test_fatband_with_marker(fatband, Assert, not_core): with_marker = dataclasses.replace(fatband, marker="o") graph = Graph(with_marker) fig = graph.to_plotly() @@ -177,7 +177,7 @@ def test_fatband_with_marker(fatband, Assert): Assert.allclose(fig.data[0].marker.size, fatband.width) -def test_two_fatband_with_marker(two_fatbands, Assert): +def test_two_fatband_with_marker(two_fatbands, Assert, not_core): with_marker = dataclasses.replace(two_fatbands, marker="o") graph = Graph(with_marker) fig = graph.to_plotly() @@ -190,7 +190,7 @@ def test_two_fatband_with_marker(two_fatbands, Assert): Assert.allclose(converted.marker.size, w) -def test_custom_xticks(parabola): +def test_custom_xticks(parabola, not_core): graph = Graph(parabola) graph.xticks = {0.1: "X", 0.3: "Y", 0.4: "", 0.8: "Z"} fig = graph.to_plotly() @@ -200,7 +200,7 @@ def test_custom_xticks(parabola): # empty ticks should be replace by " " because otherwise plotly will replace them -def test_title(parabola): +def test_title(parabola, not_core): graph = Graph(parabola) graph.title = "title" fig = graph.to_plotly() @@ -230,7 +230,7 @@ def test_merging_of_fields_of_graph(sine, parabola): dataclasses.replace(graph2, **{field.name: "other"}) + graph1 -def test_subplot(subplot): +def test_subplot(subplot, not_core): graph = Graph(subplot) graph.xlabel = ("first x-axis", "second x-axis") graph.ylabel = ("first y-axis", "second y-axis") @@ -257,7 +257,7 @@ def test_mixture_subplot_raises_error(parabola, subplot): Graph((parabola,) + subplot) -def test_non_numpy_data(non_numpy, Assert): +def test_non_numpy_data(non_numpy, Assert, not_core): graph = Graph(non_numpy) fig = graph.to_plotly() assert len(fig.data) == len(non_numpy) @@ -287,14 +287,14 @@ def test_add_label_to_multiple_lines(parabola, sine, Assert): @patch("plotly.graph_objs.Figure._ipython_display_") -def test_ipython_display(mock_display, parabola): +def test_ipython_display(mock_display, parabola, not_core): graph = Graph(parabola) graph._ipython_display_() mock_display.assert_called_once() @patch("plotly.graph_objs.Figure.show") -def test_show(mock_show, parabola): +def test_show(mock_show, parabola, not_core): graph = Graph(parabola) graph.show() mock_show.assert_called_once() diff --git a/tests/third_party/test_interactive.py b/tests/third_party/test_interactive.py index f041b976..1142ec1c 100644 --- a/tests/third_party/test_interactive.py +++ b/tests/third_party/test_interactive.py @@ -6,11 +6,12 @@ def test_no_error_handling_outside_ipython(): - with patch("IPython.get_ipython", return_value=None) as mock: - interactive.set_error_handling("Minimal") + assert interactive.error_handling() == "Minimal" # default + interactive.set_error_handling("Plain") + assert interactive.error_handling() == "Plain" -def test_set_error_handling(capsys): +def test_set_error_handling(capsys, not_core): with patch("IPython.get_ipython") as mock: interactive.set_error_handling("Minimal") mock.return_value.magic.assert_called_once_with("xmode Minimal") diff --git a/tests/util/test_import.py b/tests/util/test_import.py new file mode 100644 index 00000000..1528a90b --- /dev/null +++ b/tests/util/test_import.py @@ -0,0 +1,18 @@ +# Copyright © VASP Software GmbH, +# Licensed under the Apache License 2.0 (http://www.apache.org/licenses/LICENSE-2.0) +import pytest + +from py4vasp import exception +from py4vasp._util import import_ + + +def test_import_not_available(): + module = import_.optional("_name_which_does_not_exist_") + assert not import_.is_imported(module) + with pytest.raises(exception.ModuleNotInstalled): + module.attribute + + +def test_import_for_existing_module(): + module = import_.optional("py4vasp") + assert import_.is_imported(module)