mfixstsci / jwst

Python library for science observations from the James Webb Space Telescope

Home Page:https://jwst-pipeline.readthedocs.io/en/latest/

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JWST Calibration Pipeline

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JWST requires Python 3.6 or above and a C compiler for dependencies.

Installation

The jwst package can be installed into a virtualenv or conda environment via pip. We recommend creating a fresh environment with only python installed. Via conda:

conda create -n jwst_env python=3.7
conda activate jwst_env

Installing for end-users

To install a released (tagged) version, you can install directly from Github. To install tagged release jwst 0.14.2:

pip install git+https://github.com/spacetelescope/jwst@0.14.2

The latest development version (from master) can also be installed from Github:

pip install git+https://github.com/spacetelescope/jwst

As can a particular commit hash:

pip install git+https://github.com/spacetelescope/jwst@3f03323c

Installing a DMS release

We still package our releases to DMS via environment snapshots that specify the exact versions of all packages to be installed.

The latest release 0.14.2 may be installed in two stages by running the following commands:

Stage 1:

conda create -n jwstdp-0.14.2 --file https://ssb.stsci.edu/releases/jwstdp/0.14.2/[env_file]
source activate jwstdp-0.14.2

Where [env_file] = conda_python_stable-deps.txt for Linux and [env_file] = conda_python_macos-stable-deps.txt for Macos

Stage 2:

pip install -r https://ssb.stsci.edu/releases/jwstdp/0.14.2/[pkgs_file]

Where [pkgs_file] = reqs_stable-deps.txt for Linux and [pkgs_file] = reqs_macos-stable-deps.txt for Macos

Each such delivery has its own installation instructions which may be found in the corresponding release documentation linked from this page: https://github.com/astroconda/astroconda-releases/tree/master/jwstdp

The version values shown there are the JWSTDP releases available to install. Installation procedures for each version are in the README.md file for that version. See the "Software vs DMS build version map" table below for a list of version tags corresponding to particular releases.

The installation procedures may change from time to time, so consulting the documentation page for the specific version in question is the best way to get that version installed.

Installing for developers

Fork and clone the repo:

git clone https://github.com/spacetelescope/jwst
cd jwst

Note: python setup.py install and python setup.py develop commands do not work.

Install from your local checked out copy as an "editable" install:

pip install -e .

If you want to run the tests and/or build the docs, you can make sure those dependencies are installed too:

pip install -e .[test]
pip install -e .[docs]
pip install -e .[test,docs]

Note: If you wish to install directly from github, but also include the extra dependencies, the syntax is as follows:

pip install "jwst[test] @ git+https://github.com/spacetelescope/jwst"

Need other useful packages in your development environment?

pip install ipython flake8 pytest-xdist

CRDS Setup

Inside the STScI network, the pipeline works with default CRDS setup with no modifications. To run the pipeline outside the STScI network, CRDS must be configured by setting two environment variables:

export CRDS_PATH=$HOME/crds_cache
export CRDS_SERVER_URL=https://jwst-crds.stsci.edu

Documentation

Documentation (built daily from master) is available at:

https://jwst-pipeline.readthedocs.io/en/latest/

To build the docs yourself, clone this repository and build the documentation with:

pip install -e .[docs]
cd docs
make html
make latexpdf

Contributions and Feedback

We welcome contributions and feedback on the project. Please follow the contributing guidelines to submit an issue or a pull request.

We strive to provide a welcoming community to all of our users by abiding to the Code of Conduct.

If you have questions or concerns regarding the software, please open an issue at https://github.com/spacetelescope/jwst/issues or contact the JWST Help Desk.

Software vs DMS build version map

jwst tag DMS build CRDS_CONTEXT Date Notes
0.14.2 B7.4 0570 11/18/2019 Final release candidate for B7.4
0.14.1 B7.4rc2 0568 11/11/2019 Second release candidate for B7.4
0.14.0 B7.4rc1 0563 10/25/2019 First release candidate for B7.4
0.13.8 B7.3.1 0541 09/05/2019 Patch for Build 7.3 released as Build 7.3.1
0.13.7 B7.3 0535 06/21/2019 Final release candidate for Build 7.3
0.13.6 B7.3rc4 0534 06/20/2019 Fourth release candidate for Build 7.3
0.13.5 B7.3rc3 0534 06/19/2019 Third release candidate for Build 7.3
0.13.4 B7.3rc2 0534 06/18/2019 Second release candidate for Build 7.3
0.13.3 B7.3rc1 0532 06/04/2019 First release candidate for Build 7.3
0.13.2 0500* 05/14/2019 DMS test, no delivery to I&T
0.13.1 0500* 03/08/2019 DMS test, no delivery to I&T
0.13.0 0500 02/15/2019 DMS test, no delivery to I&T
0.12.3 B7.2.1 0500 01/15/2019 DMS Build 7.2.1 patch release
0.12.2 B7.2 0495 11/07/2018 Final release candidate for Build 7.2
0.12.1 B7.2rc2 0495 11/01/2018 Second release candidate for Build 7.2
0.12.0 B7.2rc1 0493* 10/09/2018 First release candidate for Build 7.2
0.11.0 0482* 09/10/2018 DMS test, no delivery to I&T
0.10.0 0477* 07/31/2018 DMS test, no delivery to I&T
0.9.6 B7.1.3 0468 06/08/2018 Final release candidate for Build 7.1.3
0.9.5 B7.1.3rc3 0468 06/06/2018 Third release candidate for Build 7.1.3
0.9.4 B7.1.3rc2 0463* 05/29/2018 Second release candidate for Build 7.1.3
0.9.3 B7.1.3rc1 0457* 05/11/2018 First release candidate for Build 7.1.3
0.9.2 0441* 03/28/2018 DMS test, no delivery to I&T
0.9.1 0432* 02/16/2018 DMS test, no delivery to I&T
0.9.0 B7.1.2 0422 12/22/2017 DMS patch release to I&T 02/15/2018
0.8.0 B7.1.1 0422 DMS patch release to I&T 01/17/2018
0.8.0 B7.1 0422 11/14/2017 Final, delivered to I&T 11/17/2017
0.7.0rc7 B7.0 0303 12/13/2016 Final, delivered to I&T

Note: CRDS_CONTEXT values flagged with an asterisk in the above table are estimates (formal CONTEXT deliveries are only provided with final builds).

Unit Tests

Unit tests can be run via pytest. Within the top level of your local jwst repo checkout:

pip install -e .[test]
pytest

Need to parallelize your test runs over 8 cores?

pip install pytest-xdist
pytest -n 8

Regression Tests

Latest regression test results can be found here (STScI staff only):

https://plwishmaster.stsci.edu:8081/job/RT/job/JWST/

The test builds start at 6pm local Baltimore time Monday through Saturday on jwcalibdev.

To run the regression tests on your local machine, get the test dependencies and set the environment variable TEST_BIGDATA to our Artifactory server (STSci staff members only)

pip install -e .[test]
export TEST_BIGDATA=https://bytesalad.stsci.edu/artifactory

To run all the regression tests:

pytest --bigdata jwst/tests_nightly

You can control where the test results are written with the --basetemp=<PATH> arg to pytest. Note that pytest will wipe this directory clean for each test session, so make sure it is a scratch area.

If you would like to run a specific test, find its name or ID and use the -k option:

pytest --bigdata --basetemp=<PATH> jwst/tests_nightly -k image3_pipeline

If developers need to update the truth files in our nightly regression tests, there are instructions in the repository wiki.

https://github.com/spacetelescope/jwst/wiki/Maintaining-Regression-Tests

JupyterHub Access

Note: This is currently still in research-and-development stage and is subject to change.

To run a pre-installed pipeline in JupyterHub:

Latest release of any packages is not guaranteed in this environment. Amazon Web Services charges may apply.

About

Python library for science observations from the James Webb Space Telescope

https://jwst-pipeline.readthedocs.io/en/latest/

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