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CRDS

CRDS is a package used for working with astronomical reference files for the HST and JWST telescopes. CRDS is useful for performing various operations on reference files or reference file assignment rules. CRDS is used to assign, check, and compare reference files and rules, and also to predict those datasets which should potentially be reprocessed due to changes in reference files or assignment rules. CRDS has versioned rules which define the assignment of references for each type and instrument configuration. CRDS has web sites corresponding to each project (http://hst-crds.stsci.edu or https://jwst-crds.stsci.edu/) which record information about reference files and provide related services.

CRDS development is occuring at:: Project's github page.
CRDS is also available for installation as part of stenv:: stenv.

Basic CRDS Installation

For many roles, CRDS is automatically installed as a dependency of the calibration software. This default installation supports running calibrations but not more advanced CRDS activities like submitting files or development.

You can test for an existing installation of CRDS like this:

$ crds list --status
CRDS Version = '7.4.0, b7.4.0, daf308e24c8dd37e70c89012e464058861417245'
CRDS_MODE = 'auto'
CRDS_PATH = 'undefined'
CRDS_SERVER_URL = 'undefined'
Cache Locking = 'enabled, multiprocessing'
Effective Context = 'jwst_0541.pmap'
Last Synced = '2019-08-26 07:30:09.254136'
Python Executable = '/Users/homer/miniconda3/envs/crds-env/bin/python'
Python Version = '3.7.4.final.0'
Readonly Cache = False

This output indicates CRDS is installed and configured for processing onsite using a pre-built cache of CRDS rules and references at /grp/crds/cache.

File Submission Installation

For performing the file submission role, CRDS includes additional dependencies and can be trickier to install.

Addding CRDS to an Existing Environment

You can install/upgrade CRDS and it's dependencies in your current environment like this:

git clone https://github.com/spacetelescope/crds.git
cd crds
./crds_setup_crds

It is recommended that you only do this in an environment dedicated to file submissions. This may be suitable for e.g. installing/upgrading CRDS in an active redcatconda environment.

Full Environment Install

Sometimes it's expedient to install an entirely new environment including a baseline conda, CRDS, and all of it's dependencies. To start from scratch, you can:

git clone https://github.com/spacetelescope/crds.git
cd crds
./crds_setup_all

# open a new terminal window
conda activate crds-env

To customize a bit more, crds_setup_all and crds_setup_env support parameters which can be used to specify OS, shell, and install location. Substitute the below to specify Linux, c-shell, and a non-default install location:

./crds_setup_all   Linux  csh   $HOME/miniconda_crds

Advanced Install

Below are the current sub-tasks used conceptually for a full featured CRDS install. These can serve as an alternative to cloning the CRDS repo and running the install script(s). If you already have a python environment supporting pip,

1. Installing Conda / Astroconda

Alternate / definitive installation instructions for installing a baseline conda can be found here:

https://spacetelescope.github.io/training-library/computer_setup.html#installing-conda

2. Create crds-env Environment

The CRDS software and basic conda dependencies should be installed in an isolated conda environment:

conda create -n crds-env
conda activate crds-env

You can substitute the environment name of your choice, e.g. redcatconda vs. crds-env.

3. Add JWST CAL S/W and Dependencies

Installing the JWST CAL S/W will also automatically install many dendencies of a numerical computing environment:

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

Note that these commands also install the latest version of CRDS from pip which may not be current enough for ongoing reference file testing and troubleshooting.

4. Install CRDS and Dependencies

This sequence first removes the CRDS installed automatically as part of installing the jwst package and then installs the latest available CRDS from github with advanced dependencies not needed for basic operation:

pip uninstall --yes crds
pip install --upgrade  git+https://github.com/spacetelescope/crds.git#egg=crds["submission","test"]

A more full featured CRDS install is:

pip install --upgrade  git+https://github.com/spacetelescope/crds.git#egg=crds["submission","dev","test","docs"]

5. Install Fitsverify

Since it is a C-based package fitsverify is not available using pip but is available via conda on the astroconda channel:

conda config --add channels http://ssb.stsci.edu/astroconda
conda install --yes fitsverify

As part of an end-user setup installation of fitsverify is optional, CRDS certify will run without it after issuing a warning, the CRDS server will run fitsverify as part of its checks unless/until we stop using it altogether.

User's Guide

More documentation about CRDS is available here:

https://jwst-crds.stsci.edu/static/users_guide/index.html

	CRDS_CONFIG_URI = StrConfigItem("CRDS_CONFIG_URI", None,
	"Defines the URL/URI from which CRDS config files are downloaded.",
	lower=True)

	CRDS_MAPPING_URI = StrConfigItem("CRDS_MAPPING_URI", None,
	"Defines the URL/URI from which CRDS mapping files are downloaded.",
	lower=True)

	CRDS_REFERENCE_URI = StrConfigItem("CRDS_REFERENCE_URI", None,
	"Defines the URL/URI from which CRDS reference files are downloaded.",
	lower=True)

	CRDS_PICKLE_URI = StrConfigItem("CRDS_PICKLE_URI", None,
	"Defines the URL/URI from which CRDS pickle files are downloaded.",
	lower=True)

	if get_cache_readonly(): # message and quit
	func("READONLY CACHE", args, *keys)
	return False
	else:
	return True
	func_check_writable.__name__ = "wrapped_writable_" + func.__name__
	func_check_writable._wrapped_writable = True

	@mark.multimission
	@mark.certify
	def test_tpn_repr():
	# typical subtle expression error, "=" vs. "=="
	info = generic_tpn.TpnInfo('DETECTOR','H', 'C', 'R', ("FOO","BAR","BAZ"))
	repr(validators.validator(info))

	@mark.hst
	@mark.core
	@mark.rmap
	def test_rmap_match_not_applicable(default_shared_state, hst_data):
	r = rmap.get_cached_mapping(f"{hst_data}/hst_acs_darkfile_na_omit.rmap")
	r.get_best_ref({
	"DETECTOR" : "SBC",
	"CCDAMP" : "A",
	"CCDGAIN" : "1.0",
	"DATE-OBS" : "1993-01-01",
	"TIME-OBS" : "12:00:00",
	}) == "NOT FOUNT n/a"

	def download_core(self, name, localpath):
	"""Download and verify file `name` under context `pipeline_context` to `localpath`."""
	if config.get_download_plugin():
	self.plugin_download(name, localpath)
	else:
	generator = self.get_data_http(name)
	self.generator_download(generator, localpath)
	self.verify_file(name, localpath)

	if info["state"] not in ["archived", "operational"]:
	log.warning("File", repr(base), "has an unusual CRDS file state", repr(info["state"]))

spacetelescope / crds Goto Github PK

crds's Introduction

CRDS

Basic CRDS Installation

File Submission Installation

Addding CRDS to an Existing Environment

Full Environment Install

Advanced Install

1. Installing Conda / Astroconda

2. Create crds-env Environment

3. Add JWST CAL S/W and Dependencies

4. Install CRDS and Dependencies

5. Install Fitsverify

User's Guide

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