diff --git a/.circleci/config.yml b/.circleci/config.yml index b8abef3d6..89da9592c 100644 --- a/.circleci/config.yml +++ b/.circleci/config.yml @@ -36,7 +36,7 @@ commands: deactivate python -m venv /home/circleci/simple source /home/circleci/simple/bin/activate - pip install git+https://github.com/FCP-INDI/cpac.git@81c33b52d72478bef54ccfdce05577d52ebf714c semver + pip install cpac semver deactivate run-cpac-commands: diff --git a/docs/_sources/user/cpac.rst b/docs/_sources/user/cpac.rst index 922056c05..9c8761a13 100644 --- a/docs/_sources/user/cpac.rst +++ b/docs/_sources/user/cpac.rst @@ -3,12 +3,26 @@ cpac (Python package) `cpac `_ is available so that you can easily run analyses without needing interact with the container platform that allows you to run C-PAC without installing all of the underlying software. -cpac requires Python 3.6 or greater. To get cpac, simply +``cpac`` requires Python 3.8 or greater. To get cpac, simply .. code-block:: console pip install cpac +Run extra packages with cpac +```````````````````````````` +Beginning with v1.8.5, ``cpac`` can run |ba_timeseries_gradients|_ and/or |tsconcat|_ in addition to C-PAC. If either package is already installed, ``cpac`` will use the installed version. You can install them with the relevant extras, like one of the following lines: + +.. code-block:: console + + pip install cpac[ba_timeseries_gradients] + pip install cpac[tsconcat] + pip install cpac[ba_timeseries_gradients,tsconcat] + +.. note:: + + ``ba_timeseries_gradients`` and ``tsconcat`` may have more specific dependency requirements than C-PAC. If you run into unclear installation issues when installing these extras, please see the documentation for those packages. + Download / Upgrade C-PAC with cpac `````````````````````````````````` @@ -117,4 +131,13 @@ Note that any of the optional arguments above will over-ride any pipeline settin * The ``participant_label`` and ``participant_ndx`` arguments allow the user to specify which of the many datasets should be processed, which is useful when parallelizing the run of multiple participants. * If you want to pass runtime options to your container plaform (Docker or Singularity), you can pass them with ``-o`` or ``--container_options``. + .. TODO: Update cpac to handle `-`s and `_`s like C-PAC + +.. |ba_timeseries_gradients| replace:: ``ba_timeseries_gradients`` + +.. _ba_timeseries_gradients: https://cmi-dair.github.io/ba-timeseries-gradients/ba_timeseries_gradients.html + +.. |tsconcat| replace:: ``tsconcat`` + +.. _tsconcat: https://cmi-dair.github.io/tsconcat/tsconcat.html