Installation

Using pip

Optional but recommended step: install a conda environment:

conda create -n <cosipy_env_name> python=3.10 pip
conda activate <cosipy_env_name>

Note: currently cosipy is not compatible with Python 3.12 due to installation issues with dependencies (threeML and astromodels)

Install with pip:

pip install --use-pep517 cosipy

Note: --use-pep517 is a temporary workaround to install astromodels with new setuptools versions.

Note: The tutorials, examples, and other documentation are not shipped with the PyPi (pip) release —only the embedded docstrings. You can see this information in the main repository (“docs” folder).

From source (for developers)

Optional but recommended step: install a conda environment:

conda create -n <cosipy_env_name> python=3.10 pip
conda activate <cosipy_env_name>

Also optional but recommended: before installing cosipy, install the main dependencies from the source (similar procedure as for cosipy below). These are histpy, mhealpy, scoords, threeml and astromodels. The reason is that these libraries might be changing rapidly to accommodate new features in cosipy.

Do the following (preferably inside a conda environment):

git clone git@github.com:cositools/cosipy.git
cd cosipy
pip install --use-pep517 -e .

The flag -e (--editable) allows you to make changes and try them without having to run pip again.

Troubleshooting

ERROR:: Could not find a local HDF5 installation.

This error is caused by missing h5py wheels for M1 chips.

See https://github.com/h5py/h5py/issues/1810 and https://github.com/h5py/h5py/issues/1800

Currently, the best workaround for M1 users is to install h5py using conda before the cosipy installation:

conda install h5py

Example error log:

× Getting requirements to build wheel did not run successfully.
│ exit code: 1
╰─> [13 lines of output]
    /var/folders/5p/wnc17p7s0gz1vd3krp7gly60v5n_5p/T/H5close39c45pt5.c:1:10: fatal error: 'H5public.h' file not found
    #include "H5public.h"
             ^~~~~~~~~~~~
    1 error generated.
    cpuinfo failed, assuming no CPU features: 'flags'
    * Using Python 3.10.12 | packaged by conda-forge | (main, Jun 23 2023, 22:41:52) [Clang 15.0.7 ]
    * Found cython 3.0.10
    * USE_PKGCONFIG: True
    * Found conda env: ``/Users/mjmoss/miniforge3``
    .. ERROR:: Could not find a local HDF5 installation.
       You may need to explicitly state where your local HDF5 headers and
       library can be found by setting the ``HDF5_DIR`` environment
       variable or by using the ``--hdf5`` command-line option.

OSError: Could not find library XSFunctions. Impossible to compile Xspec

This error can occur while installing astromodels:

Xspec is detected. Will compile the Xspec extension.
[...]
Could not find library XSFunctions. Impossible to compile Xspec

While astromodels support Xspec functions, these are generally not currently relevant for the use and development of cosipy. The most straightforward workaround is to temporarily hide your Xspec installation so that astromodels does not try to link to it. Before running pip, run:

unset HEADAS ASTRO_XSPEC_VERSION

Testing

Warning

Under construction. Unit tests are not ready.

When you make a change, check that it didn’t break something by running:

pytest --cov=cosipy --cov-report term --cov-report html:tests/coverage_report

Open tests/coverage_report/index.html in a browser and check the coverage. This is the percentage of lines that were executed during the tests. The goal is to have a 100% coverage!

You can install pytest and pytest-cov with:

conda install -c conda-forge pytest pytest-cov

Compiling the docs

You need pandoc, sphinx, nbsphinx, sphinx_rtd_theme and mock. Using conda:

conda install -c conda-forge pandoc=3.1.3 nbsphinx=0.9.3 sphinx_rtd_theme=2.0.0 mock=5.1.0

Other versions might work was well.

Once you have these requirements, run:

cd docs
make html

To read the documentation, open docs/_build/html/index.html in a browser.