diff --git a/data b/data index ddcc619a0..c86c573b8 160000 --- a/data +++ b/data @@ -1 +1 @@ -Subproject commit ddcc619a0e29f246ed3416f7e28e748cb554c0f1 +Subproject commit c86c573b8a3eee7b0676451c3275d3acc0a7a2d5 diff --git a/docs/source/contributing.rst b/docs/source/contributing.rst index ea021b719..cfeb2b72b 100644 --- a/docs/source/contributing.rst +++ b/docs/source/contributing.rst @@ -58,7 +58,7 @@ Installing a Development Version conda activate scico -6. Navigate to the root of the cloned repository: +6. Change directory to the root of the cloned repository: :: @@ -77,11 +77,15 @@ Installing a Development Version :: pip install -r requirements.txt # Installs basic requirements + pip install -r dev_requirements.txt # Installs developer requirements pip install -r docs/docs_requirements.txt # Installs documentation requirements - pip install -r examples/examples_requirements.txt # Installs example requirements pip install -e . # Installs SCICO from the current directory in editable mode + For installing dependencies related to the examples please see :ref:`example_notebooks`. + Installing these are neccessary for the successfull running of the tests. + + 9. The SCICO project uses the `black `_, `isort `_ and `pylint `_ code formatting utilities. It is important to set up a `pre-commit hook `_ to @@ -104,13 +108,26 @@ Installing a Development Version Building Documentation ---------------------- -To build a local copy of the docs, from the repo root directory, do +Before building the documentation, one must install the documentation specific dependencies by running + +:: + + pip install -r docs_requirements.txt + +Then, a local copy of the documentation can be built from the respository root directory by running :: python setup.py build_sphinx +Alternatively, one can also build the documentation by running the following from the `docs/` directory + +:: + + make html + + Contributing Code ----------------- @@ -203,7 +220,7 @@ scico-data repositories must be updated and kept in sync. 1. Add the ``new_data.npz`` file to the ``scico/data`` directory. -2. Navigate to the ``data`` directory and add/commit the new data file: +2. Change directory to the ``data`` directory and add/commit the new data file: :: diff --git a/docs/source/examples.rst b/docs/source/examples.rst index 1729dfbdd..5ac2c28a8 100644 --- a/docs/source/examples.rst +++ b/docs/source/examples.rst @@ -6,6 +6,21 @@ Usage Examples .. toctree:: :maxdepth: 1 +.. _example_dependencies: + +Example Dependencies +-------------------- + +Some examples use additional dependencies, which are listed in `examples_requirements.txt `_. +The additional requirements should be installed via pip, with the exception of ``astra-toolbox``, +which should be installed via conda: + + :: + + conda install -c astra-toolbox astra-toolbox + pip install -r examples/examples_requirements.txt # Installs other example requirements + +The dependencies can also be installed individually as required. Organized by Application ------------------------ diff --git a/docs/source/install.rst b/docs/source/install.rst index 3e7fff1f2..066506014 100644 --- a/docs/source/install.rst +++ b/docs/source/install.rst @@ -54,26 +54,14 @@ The instructions above install a CPU-only version of SCICO. To install a version :: - pip install --upgrade "jaxlib==0.1.70+cuda110" -f https://storage.googleapis.com/jax-releases/jax_releases.html + pip install --upgrade "jaxlib==0.1.75+cuda110" -f https://storage.googleapis.com/jax-releases/jax_releases.html Additional Dependencies ----------------------- -We use the `ASTRA Toolbox `_ for tomographic projectors. We currently require the development version of ASTRA, as suggested by the package maintainers. - -The development version of ASTRA can be installed using conda: - -:: - - conda install -c astra-toolbox/label/dev astra-toolbox - -Alternatively, it can be `built from source `_. - -We also support the `Super-Voxel Model-Based Iterative Reconstruction `_ package as an alternative tomographic projector. Since this package can be installed via ``pip``, it is -included in the list of package dependencies (``requirements.txt``), and need -not be separately installed. +For instructions on installing dependencies related to the examples please see :ref:`example_notebooks`. For Developers @@ -81,29 +69,3 @@ For Developers For installing a version of SCICO suitable for development, see the instructions in :ref:`scico_dev_contributing`. - - -Building Documentation ----------------------- - -The documentation can be built from the respository root directory by doing - -:: - - python setup.py build_sphinx - -Alternatively: - -1. Navigate to the docs directory ``docs/`` - -2. Install dependencies - - :: - - pip install -r docs_requirements.txt - -3. Build documentation - - :: - - make html diff --git a/examples/README.rst b/examples/README.rst index 731ee9bab..e7c36865e 100644 --- a/examples/README.rst +++ b/examples/README.rst @@ -102,7 +102,7 @@ A number of files in this directory assist in the mangement of the usage example `examples_requirements.txt `_ Requirements file (as used by ``pip``) listing additional dependencies for running the usage example scripts. -`notebooks_requirements.txt `_ +`notebooks_requirements.txt `_ Requirements file (as used by ``pip``) listing additional dependencies for building the Jupyter notebooks from the usage example scripts. `makenotebooks.py `_ diff --git a/examples/examples_requirements.txt b/examples/examples_requirements.txt index 9dfa3cce2..c76f94e24 100644 --- a/examples/examples_requirements.txt +++ b/examples/examples_requirements.txt @@ -1,4 +1,5 @@ astra-toolbox +cached_property colour_demosaicing xdesign ray[tune]