rename sdss-astra to astra; update docs; put astra to bin/

bin/astra

@@ -1,47 +1,77 @@
 #!/usr/bin/env python
 # encoding: utf-8
-#
-# @Author: José Sánchez-Gallego
-# @Date: Dec 1, 2017
-# @Filename: astra
-# @License: BSD 3-Clause
-# @Copyright: José Sánchez-Gallego
 
+import click
+import os
+from shutil import rmtree
+from astra import log
+from logging import DEBUG, INFO
+from astra.db.connection import Base, engine
+from sqlalchemy_utils import database_exists, create_database
 
-from __future__ import division
-from __future__ import print_function
-from __future__ import absolute_import
-from __future__ import unicode_literals
+from astra.tools.sdss_astra import (data, subset, component, execute, 
+                                    query_execute, schedule)
 
-import argparse
-import os
-import sys
+# Common options.
+@click.group()
+@click.option("-v", "verbose", default=False, is_flag=True,
+              help="verbose mode")
+@click.pass_context
+def cli(context, verbose):
+    context.ensure_object(dict)
+    context.obj["verbose"] = verbose
+
+    # TODO: This isn't correctly followed for sqlalchemy output. 
+    # It defaults to verbose!
+    log.set_level(DEBUG if verbose else INFO)
+
+
+@cli.command()
+@click.option("-y", "confirm", default=False, is_flag=True,
+              help="drop the database if it already exists")
+@click.pass_context
+def setup(context, confirm):
+    r""" Setup databases using the current configuration. """
+
+    log.debug("Running setup")
+
+    if not database_exists(engine.url):
+        log.info(f"Creating database {engine.url}")
+        create_database(engine.url)
+
+    elif not confirm \
+         and click.confirm("Database already exists. This will wipe the database, including all "\
+                           "downloaded components, and start again. Are you sure?", abort=True):
+        None
+
+    log.debug("Dropping all tables")
+    Base.metadata.drop_all(engine)
 
-from astra.main import math
+    log.debug("Creating all tables")
+    Base.metadata.create_all(engine)
 
+    log.debug("Removing old components")
+    component_dir = os.getenv("ASTRA_COMPONENT_DIR", None)
+    if component_dir is not None:
+        if os.path.exists(component_dir):
+            rmtree(component_dir)
+        os.makedirs(component_dir, exist_ok=True)
 
-if __name__ == '__main__':
 
-    # An example of how to write a command line parser that works with the
-    # main.math function. For more details on how to use argparse, start with
-    # this tutorial: https://kapeli.com/dash_share?docset_file=Python%203&docset_name=Python%203&path=doc/howto/argparse.html%23id1&platform=python&repo=Main&version=3.6.3
+    log.info("Astra is ready.")
+    return None
 
-    parser = argparse.ArgumentParser(
-        prog=os.path.basename(sys.argv[0]),
-        description='Performs an arithmetic operation.')
 
-    parser.add_argument('VALUE1', type=float, help='The first operand')
-    parser.add_argument('OPERATOR', type=str, help='The operator [+, -, *, /]')
-    parser.add_argument('VALUE2', type=float, help='The second operand')
+# Add various commands
+cli.add_command(data.data)
+cli.add_command(subset.subset)
+cli.add_command(component.component)
+cli.add_command(execute.execute)
+cli.add_command(query_execute.query_execute)
+cli.add_command(schedule.schedule)
 
-    parser.add_argument('-v', '--verbose', action='store_true', default=False,
-                        help='sets verbose mode')
 
-    args = parser.parse_args()
 
-    result = math(args.VALUE1, args.VALUE2, arith_operator=args.OPERATOR)
 
-    if args.verbose:
-        print('{} {} {} = {}'.format(args.VALUE1, args.OPERATOR, args.VALUE2, result))
-    else:
-        print(result)
+if __name__ == "__main__":
+    cli(obj=dict())

docs/sphinx/components.rst

@@ -94,9 +94,9 @@ now you will need to supply the relevant information in a `YAML-formatted
   owner_email_address: andrew.casey@monash.edu
 
 
-To add this component to Astra, use the ``sdss-astra`` shell utility::
+To add this component to Astra, use the ``astra`` shell utility::
 
-  sdss-astra component create --from-path my-component.yml
+  astra component create --from-path my-component.yml
 
 Most keywords in the above example are self-explanatory. The most important
 terms are the ``github_repo_slug`` and the ``component_cli``, which should 
@@ -189,9 +189,9 @@ Updating components
 ===================
 
 All attributes relating to a component can be updated **except** the
-``github_repo_slug``. Attribuets can be updated using the ``sdss-astra`` tool::
+``github_repo_slug``. Attribuets can be updated using the ``astra`` tool::
 
-  sdss-astra component update {github_repo_slug} --active true
+  astra component update {github_repo_slug} --active true
 
 [TBD: more examples of things to alter]
 
@@ -206,17 +206,17 @@ You will rarely need to delete components because you can just mark them as
 inactive and they will no longer be run on any observations. If you do need
 to delete a component you can do so using::
 
-  sdss-astra component delete {github_repo_slug}
+  astra component delete {github_repo_slug}
 
 It will ask you if you are sure. You can use the ``-y`` flag to indicate yes and
 skip this question.
 
 Executing components
 ====================
 
-You can directly execute a component using the ``sdss-astra`` utility. For example::
+You can directly execute a component using the ``astra`` utility. For example::
 
-  sdss-astra execute the-cannon -i training-paths.txt -o tmp/ --train --data-release 16
+  astra execute the-cannon -i training-paths.txt -o tmp/ --train --data-release 16
 
 will train a Cannon model using the data files listed in the text file 
 (``training-paths.txt``) and use Data Release 16 labels for those 

docs/sphinx/data.rst

@@ -23,19 +23,19 @@ a database that records the data files present in each directory in order to
 identify new or updated files. When new or updated data are detected, Astra will
 schedule all *active* components to be executed. Once new observations have been 
 processed by all active components, they will only be re-processed once a new 
-component is added. To watch a folder you can use the ``sdss-astra`` shell 
+component is added. To watch a folder you can use the ``astra`` shell 
 utility::
 
-  sdss-astra data watch -r /path/to/SDSS/data --interval 3600
+  astra data watch -r /path/to/SDSS/data --interval 3600
 
-[TBD: link to full docs for ``sdss-astra`` CLI]
+[TBD: link to full docs for ``astra`` CLI]
 
 Unwatching folders
 ==================
 
-You can use the ``sdss-astra`` shell utility to stop watching a folder::
+You can use the ``astra`` shell utility to stop watching a folder::
 
-  sdss-astra data unwatch /path/to/SDSS/data
+  astra data unwatch /path/to/SDSS/data
 
 
 Force refresh
@@ -44,7 +44,7 @@ Force refresh
 If you want to forcibly refresh all watched folders instead of waiting until
 the next interval, you can do so with::
 
-  sdss-astra data refresh
+  astra data refresh
 
 
 Subsets
@@ -56,9 +56,9 @@ allow for multiple components to run on something like 'calibration sets'
 (or 'science verification set', etc). Named subsets are available to any 
 component through the functions in  ``astra.utils``.
 
-Use the ``sdss-astra`` utility to create a named subset::
+Use the ``astra`` utility to create a named subset::
 
-  sdss-astra subset create dr20.science-verification -i paths.txt
+  astra subset create dr20.science-verification -i paths.txt
 
 Data products can be part of many subsets (data products have a many-to-many 
 relationship with subsets), and subsets can be created to automatically add 

docs/sphinx/index.rst

@@ -48,7 +48,6 @@ then you can simply enter the following command in a terminal window::
 
   sdss_install -G astra
 
-
 Development version
 ^^^^^^^^^^^^^^^^^^^
 
@@ -64,9 +63,16 @@ The configuration for Astra is currently specified in the ``python/astra/etc/ast
 file. Once those configuration settings are updated, you can set Astra up by
 running the following command from the terminal::
 
-  sdss-astra setup
+  astra setup
+
 
+Using modules on the Utah system
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
 
+TBD some docs::
+
+  sdss_install -G astra
+  module load astra
 
 
 

docs/sphinx/tools.rst

@@ -11,16 +11,16 @@
 .. rubric:: :header_no_toc:`Tools`
 
 
-``sdss-astra``
+``astra``
 ========
 
-The ``sdss-astra`` command line tool provides most of the functionality needed
+The ``astra`` command line tool provides most of the functionality needed
 to manage data flows, analysis components, scheduling and monitoring of analysis 
 tasks, and bookkeeping the outputs from those analysis tasks.
 
 This documentation page will be automatically generated using the help strings
 of each function, but for now you can see a list of commands that are expected
-to be available in the ``sdss-astra`` tool (e.g., ``sdss-astra data watch``):
+to be available in the ``astra`` tool (e.g., ``astra data watch``):
 
 =====================  =============
    Command              Description