sdsstools 1.8.2

Small tools for SDSS products

sdsstools

sdsstools provides several common tools for logging, configuration handling, version parsing, packaging, etc. Its main purpose is to consolidate some of the utilities originally found in the python_template, allowing them to become dependencies that can be updated.

This is not intended to be a catch-all repository for astronomical tools. sdsstools itself aims to have minimal dependencies (i.e., mainly the Python standard library and setuptools).

Using sdsstools

To use sdsstools simply install it with

pip install sdsstools

Most likely, you'll want to include sdsstools as a dependency for your library. To do so, either add to your setup.cfg

[options]
install_requires =
    sdsstools>=0.1.0

(this is equivalent of passing install_requires=['sdsstools>=0.1.0'] to setuptools.setup), or if you are using poetry run poetry add sdsstools, which should add this line to your pyproject.toml

[tool.poetry.dependencies]
sdsstools = { version="^0.1.0" }

Logging

sdsstools includes the sdsstools.logger.SDSSLogger class, which provides a wrapper around the standard Python logging module. SDSSLoger provides the following features:

• A console handler (accessible via the .sh attribute) with nice colouring.
• Automatic capture of warnings and exceptions, which are formatted and redirected to the logger. For the console handler, this means that once the logger has been created, all warnings and exceptions are output normally but are clearer and more aesthetic.
• A TimedRotatingFileHandler (accessible via the .fh attribute) that rotates at midnight UT, with good formatting.
• A version of the logger that uses rich log handling.

To get a new logger for your application, simply do

from sdsstools.logger import get_logger

NAME = 'myrepo'
log = get_logger(NAME)

You can get a logger using the rich RichHandler by passing use_rich_handler=True.

The file logger is disabled by default and can be started by calling log.start_file_logger(path). By default a TimedRotatingFileHandler is created. If you want a normal FileHandler use rotating=False. The file mode defaults to mode='a' (append). The TimedRotatingFileHandler options when, utc, and at_time are available to log.start_file_logger for controlling aspects of the rollover time.

By default, the file logger is formatted to output a human-readble log file. To output a JSON log instead, set as_json=True, when calling log.start_file_logger. This will create a .json log file which can machine-read and more easily parsed for content. To output both a human-readable (.log) and JSON log (.json), set with_json=True.

The SDSSLogger instance also include an asyncio_exception_handler method that can be added to the asyncio event loop to handle exceptions; for example loop.set_exception_handler(log.asyncio_exception_handler).

Console logging uses the standard StreamHandler. It's possible to use the rich library RichHandler instead by passing use_rich_handler=True to get_logger(). Additional keyword arguments to RichHandler can be passed as a rich_handler_kwargs dictionary. In the future the rich handler may become the default console logger.

Configuration

The sdsstools.configuration module contains several utilities to deal with configuration files. The most useful one is get_config, which allows to read a YAML configuration file. For example

from sdsstools.configuration import get_config

NAME = 'myrepo'
config = get_config(NAME, allow_user=True)

get_config assumes that the file is located in etc/<NAME>.yml relative from the file that calls get_config, but that can be changed by passing config_file=<config-file-path>. Additionally, if allow_user=True and a file exists in ~/.config/sdss/<NAME>.yaml, this file is read and merged with the default configuration, overriding any parameter that is present in the user file. This allows to create a default configuration that lives with the library but that can be overridden by a user.

In addition to the (recommended) location ~/.config/sdss/<NAME>.yaml, get_config also looks for user configuration files in ~/.config/sdss/<NAME>.yml, ~/.config/sdss/<NAME>/<NAME>.y(a)ml, and ~/.<NAME>/<NAME>.y(a)ml.

get_config returns an instance of Configuration, which behaves as a dictionary but allows to dynamically reload the configuration from a new user file by calling load().

sdsstools.configuration includes two other tools, merge_config, that allows to merge dictionaries recursively, and read_yaml_file to read a YAML file.

Extending a YAML file

read_yaml_file provides a non-standard feature that allows you to extend one YAML file with another. To achieve this you need to add the tag !extends <base-file> at the top of the file that you want to extend. For example, if you have a file base.yaml

cat1:
  key1: value2

cat2:
  key2: 1

that you want to use as a template for extendable.yaml

#!extends base.yaml

cat1:
  key1: value1

you can use read_yaml_file to parse the result

>>> read_yaml_file('extendable.yaml')
{'cat1': {'key1': 'value2'}, 'cat2': {'key2': 1}}

The path to the base file must be absolute or relative to the location of the file to be extended.

The Configuration class

By default get_config() and read_yaml_file() return a Configuration instance. For the most part a Configuration object is the same as a dictionary, and it can be used as such. It has two main differences:

• When a Configuration object is initialised from a file (or a base and custom configuration files) as with get_config(), the object keeps the information about the file paths. It's then possible to call Configuration.reload() to hot-reload the contents of the file after it has changed.
• It is possible to recursively get a nested configuration value, for example config['a.b'], which is equivalent to dd['a']['b'] but will return None if a key does not exist anywhere in the chain. This behaviour can be disabled by setting config.strict_mode=True. Note that this syntax is not valid for assignement and attempting to do d['a.b'] = 1 will raise an error.

Metadata

sdsscore provides tools to locate and parse metadata files (pyproject.toml, setup.cfg, setup.py). get_metadata_files locates the path of the metadata file relative to a given path. get_package_version tries to find the version of the package by looking for a version string in the metadata file or in the egg/wheel metadata file, if the package has been installed. To use it

from sdsstools.metadata import get_package_version

__version__ = get_package_version(path=__file__, package_name='sdss-camera') or 'dev'

This will try to find and parse the version from the metadata file (we pass __file__ to indicate where to start looking); if that fails, it will try to get the version from the installed package sdss-camera. If all fails, it will set the fallback version 'dev'.

Command Line Interface

sdsstools provides the command line tool sdss, which is just a thin wrapper around some commonly used Invoke tasks. sdsstools does not automatically install all the dependencies for the tasks, which need to be added manually.

sdss provides the following tasks

Task	Options	Description
clean		Removes files produces during build and packaging.
deploy	--test	Builds and deploys to PyPI (or the test server). Requires twine and wheel.
install-deps	--extras	Installs dependencies from a setup.cfg file
docs.build	--target	Builds the Sphinx documentation. Requires Sphinx.
docs.show	--target	Shows the documentation in the browser. Requires Sphinx.
docs.clean	--target	Cleans the documentation build. Requires Sphinx.

sdss assumes that the documentation lives in docs/sphinx relative to the root of the repository. This can be changed by setting the sphinx.target configuration in an invoke.yaml file, for example

sphinx:
  target: docs

Click daemon command

The daemonizer module implements a Click command group that allows to spawn a daemon, and to stop and restart it. Internally the module uses daemonocle (the package is not installed with sdsstools and needs to be pip-installed manually).

A simple example of how to use daemonizer is

import time
import click
from sdsstools.daemonizer import DaemonGroup

@click.group(cls=DaemonGroup, prog='hello', pidfile='/var/tmp/hello.pid')
@click.argument('NAME', type=str)
@click.option('--file', type=str, default='hello.dat')
def daemon(name):

    with open(file, 'w') as unit:
        while True:
            unit.write(f'Hi {name}!\n')
            unit.flush()
            time.sleep(1)

if __name__ == '__main__':
    daemon()

This will create a new group hello with four subcommands

Usage: daemon [OPTIONS] NAME COMMAND [ARGS]...

Options:
  --file
  --help  Show this message and exit.

Commands:
  restart  Restart the daemon.
  start    Start the daemon.
  status   Report if the daemon is running.
  stop     Stop the daemon.

Now we can run daemon --file ~/hello.dat John start and a new background process will start, writing to the file every second. We can stop it with daemon stop. In general the behaviour is identical to the daemonocle Click implementation but the internal are slightly different to allow the group callback to accept arguments. If the callback is a coroutine, it can be wrapped with the cli_coro decorator

import asyncio
import signal
import click
from sdsstools.daemonizer import DaemonGroup, cli_coro

def shutdown(signal):
    if signal == signal.SIGTERM:
        cancel_something()

@click.group(cls=DaemonGroup, prog='hello', pidfile='/var/tmp/hello.pid')
@click.argument('NAME', type=str)
@click.option('--file', type=str, default='hello.dat')
@cli_coro(shutdown_func=shutdown, signals=(signal.SIGTERM, signal.SIGINT))
async def daemon(name):

    with open(file, 'w') as unit:
        while True:
            unit.write(f'Hi {name}!\n')
            unit.flush()
            await asyncio.sleep(1)

cli_coro can accept a shutdown_func function that is called when the coroutine receives a signal. The default signals handled are (SIGHUP, SIGTERM, SIGINT).

Daemonizing a command

To execute any command as a daemon you can use the daemonize script that is installed with sdsstools. To start the process as a daemon do daemonize start NAME COMMAND when NAME is the name associated to the daemon (so that it can be stopped later) and COMMAND is the command to run, for example:

daemonize start apoActor python ./apoActor_main.py

To stop the daemon do daemonize stop NAME. See daemonize --help for more options.

Date functions

The function sdsstools.time.get_sjd() returns the integer with the SDSS-style Modified Julian Day. The function accepts an observatory ('APO' or 'LCO') but otherwise will try to determine the current location from environment variables or the fully qualified domain name.

Bundled packages

For convenience, sdsstools bundles the following products:

• (Up to version 1.0.0) A copy of releases that fixes some issues with recent versions of semantic-version. This copy is not available in sdsstools>=1.0.0. releases is not maintained anymore, so use at your own risk.
• A copy of toml to read TOML files (used by the metadata submodule).
• An adapted version of Astropy's color_print.
• A copy of the pydl's yanny module.

You can access them directly from the top-level namespace, sdsstools.toml, sdsstools.releases. To use releases with sphinx, simply add the following to your config.py

extensions += ['sdsstools.releases']