Installation and Usage
There are a number of possible ways to install dials_data
.
From the simplest to the most involved these are:
As an end user
Quite simply: You do not need to install dials_data
.
It does not add any functionality to end users.
As a developer to run tests with dials_data
You may want to install dials_data
so that you can run regression tests locally.
Or you might say that continuous integration should take care of this.
Both are valid opinions.
However you do not need to install dials_data
from source. You can simply run:
pip install -U dials-data
or, in a conda environment:
conda install -c conda-forge dials-data
This will install or update an existing installation of dials_data
.
You can then run your tests as usual using:
pytest
although, depending on the configuration of the code under test, you probably need to run it as:
pytest --regression
to actually enable those tests depending on files from dials_data
.
As a developer to write tests with dials_data
Install dials_data
as above.
If your test is written in pytest and you use the fixture provided by
dials_data
then you can use regression datasets in your test by
adding the dials_data
fixture to your test, ie:
def test_accessing_a_dataset(dials_data):
location = dials_data("x4wide", pathlib=True)
The fixture/variable dials_data
in the test is a
dials_data.download.DataFetcher
instance, which can be called with
the name of the dataset you want to access (here: x4wide
). If the
files are not present on the machine then they will be downloaded.
If either the download fails or --regression
is not specified then
the test is skipped.
The return value (location
) is a pathlib.Path
object pointing
to the directory containing the requested dataset.
To get a python py.path.local
object instead you can call:
def test_accessing_a_dataset(dials_data):
location = dials_data("x4wide", pathlib=False)
However, please note that the py.path
support is deprecated, and
will be removed at some point in the future. Currently, if you do not
specify the pathlib=
argument a py.path
object is returned.
You can see a list of all available datasets by running:
dials.data list
or by going through the dataset definition files in the repository.
If you want the tests on your project to be runnable even when
dials_data
is not installed in the environment you could add a
dummy fixture to your conftest.py
, for example:
import pytest
try:
import dials_data as _ # noqa: F401
except ModuleNotFoundError:
@pytest.fixture(scope="session")
def dials_data():
pytest.skip("Test requires python package dials_data")
As a developer who wants to add files to dials_data
Follow the steps in Contributing to install dials_data
into a
virtual environment.
You can install dials_data
using pip
as above unless you want to
immediately use your dataset definition in tests without waiting for your
pull request to be accepted. In this case you can follow the instructions
in the next step.
As a developer who wants to extend dials_data
Have a look at the Contributing page.
Install your own fork of dials_data
by running:
pip install -e path/to/fork
in a cctbx/DIALS environment use libtbx.pip
respectively, followed by
a round of libtbx.configure
or make reconf
.
If you made substantial changes or updated your source copy you may also have to run:
python setup.py develop
This will update your python package index and install/update any
dials_data
dependencies if necessary.
To switch back from using your checked out version to the ‘official’
version of dials_data
you can uninstall it with:
pip uninstall dials_data
and then reinstall it following the instructions at the top of this page.
Where are the regression datasets stored?
In order of evaluation:
If the environment variable
DIALS_DATA
is set and exists or can be created then use that location.If the file path
/dls/science/groups/scisoft/DIALS/dials_data
exists and is readable then use this location. This is a shared directory specific to Diamond Light Source.If the environment variable
LIBTBX_BUILD
is set and the directorydials_data
exists or can be created underneath that location then use that.Use
~/.cache/dials_data
if it exists or can be created.Otherwise
dials_data
will fail with a RuntimeError.