.. include:: ../references.txt .. _dev_howto: **************** Developer How To **************** This page is a collection of notes for Gammapy contributors and maintainers, in the form of short "How To" or "Q&A" entries. .. _dev-python2and3: Python version support ---------------------- In Gammapy we currently support Python 3.7 or later. .. _dev_import: Where should I import from? --------------------------- You should import from the "end-user namespaces", not the "implementation module". .. testcode:: from gammapy.data import EventList # good from gammapy.data.event_list import EventList # bad from gammapy.stats import cash # good from gammapy.stats.fit_statistics import cash # bad The end-user namespace is the location that is shown in the API docs, i.e. you can use the Sphinx full-text search to quickly find it. To make code maintenance easier, the implementation of the functions and classes is spread across multiple modules (``.py`` files), but the user shouldn't care about their names, that would be too much to remember. The only reason to import from a module directly is if you need to access a private function, class or variable (something that is not listed in ``__all__`` and thus not imported into the end-user namespace. Note that this means that in the definition of an "end-user namespace", e.g. in the ``gammapy/data/__init__.py`` file, the imports have to be sorted in a way such that modules in ``gammapy/data`` are loaded when imported from other modules in that sub-package. .. _dev-result_object: Functions returning several values ---------------------------------- It is up to the developer to decide how to return multiple things from functions and methods. For up to three things, if callers usually will want access to several things, using a ``tuple`` or ``collections.namedtuple`` is OK. For three or more things, using a Python ``dict`` instead should be preferred. Check Python code present in RST files -------------------------------------- Most of the documentation of Gammapy is present in RST files that are converted into HTML pages with Sphinx during the build documentation process. You may include snippets of Python code in these RST files within blocks labelled with ``.. code-block:: python`` Sphinx directive. However this code could not be tested and it will not be possible to know if it fails in following versions of Gammapy. That's why we recommend to use the ``.. testcode::`` directive to enclose code that will be tested against the results present in a block labelled with ``.. testoutput::`` directive. If not ``.. testoutput::`` directive is provided, only execution tests will be performed. For example, we could check that the code below does not fail, since it does not provide any output. .. code-block:: text .. testcode:: from gammapy.astro import source from gammapy.astro import population from gammapy.astro import darkmatter On the contrary, we could check the execution of the following code as well as the output values produced. .. code-block:: text .. testcode:: from astropy.time import Time time = Time(['1999-01-01T00:00:00.123456789', '2010-01-01T00:00:00']) print(time.mjd) .. testoutput:: [51179.00000143 55197. ] In order to perform tests of these snippets of code present in RST files, you may run the following command. .. code-block:: bash pytest --doctest-glob="*.rst" docs/ Check Python code present in docstrings of Python files ------------------------------------------------------- It is also advisable to add code snippets within the docstrings of the classes and functions present in Python files. These snippets show how to use the function or class that is documented, and are written in the docstrings using the following syntax. .. code-block:: text Examples -------- >>> from astropy.units import Quantity >>> from gammapy.data import EventList >>> event_list = EventList.read('events.fits') # doctest: +SKIP In the case above, we could check the execution of the first two lines importing the ``Quantity`` and ``EventList`` modules, whilst the third line will be skipped. On the contrary, in the example below we could check the execution of the code as well as the output value produced. .. code-block:: text Examples -------- >>> from regions import Regions >>> regions = Regions.parse("galactic;circle(10,20,3)", format="ds9") >>> print(regions[0]) Region: CircleSkyRegion center: radius: 3.0 deg In order to perform tests of these snippets of code present in the docstrings of the Python files, you may run the following command. .. code-block:: bash pytest --doctest-modules --ignore-glob=*/tests gammapy .. _dev-skip_tests: Skip unit tests for some Astropy versions ----------------------------------------- .. testcode:: import astropy import pytest ASTROPY_VERSION = (astropy.version.major, astropy.version.minor) @pytest.mark.xfail(ASTROPY_VERSION < (0, 4), reason="Astropy API change") def test_something(): ... Assert convention ----------------- When performing tests, the preferred numerical assert method is `numpy.testing.assert_allclose`. Use .. testcode:: from numpy.testing import assert_allclose at the top of the file and then just use ``assert_allclose`` for the tests. This makes the lines shorter, i.e. there is more space for the arguments. ``assert_allclose`` covers all use cases for numerical asserts, so it should be used consistently everywhere instead of using the dozens of other available asserts from pytest or numpy in various places. For assertions on `~astropy.units.Quantity` objects, you can do this to assert on the unit and value separately: .. testcode:: from numpy.testing import assert_allclose import astropy.units as u actual = 1 / 3 * u.deg assert actual.unit == 'deg' assert_allclose(actual.value, 0.33333333) Note that `~astropy.units.Quantity` can be compared to unit strings directly. Also note that the default for ``assert_allclose`` is ``atol=0`` and ``rtol=1e-7``, so when using it, you have to give the reference value with a precision of ``rtol ~ 1e-8``, i.e. 8 digits to be on the safe side (or pass a lower ``rtol`` or set an ``atol``). The use of `~astropy.tests.helper.assert_quantity_allclose` is discouraged, because it only requires that the values match after unit conversions. This is not so bad, but units in test cases should not change randomly, so asserting on unit and value separately establishes more behaviour. If you don't like the two separate lines, you can use `gammapy.utils.testing.assert_quantity_allclose`, which does assert that units are equal, and calls `numpy.testing.assert_equal` for the values. Testing of plotting functions ----------------------------- Many of the data classes in Gammapy implement ``.plot()`` or ``.peek()`` methods to allow users a quick look in the data. Those methods should be tested using the `mpl_check_plot()` context manager. The context manager will take care of creating a new figure to plot on and writing the plot to a byte-stream to trigger the rendering of the plot, which can raise errors as well. Here is a short example: .. testcode:: from gammapy.utils.testing import mpl_plot_check def test_plot(): with mpl_plot_check(): plt.plot([1., 2., 3., 4., 5.]) With this approach we make sure that the plotting code is at least executed once and runs completely (up to saving the plot to file) without errors. In future we will maybe change to something like https://github.com/matplotlib/pytest-mpl to ensure that correct plots are produced. Making a pull request with new or modified datasets --------------------------------------------------- Datasets used in tests are hosted in the `gammapy-data `__ Github repository. It is recommended that developers have `$GAMMAPY_DATA` environment variable pointing to the local folder where they have fetched the `gammapy-data `__ Github repository, so they can push and pull eventual modification of its content. Making a pull request which skips GitHub Actions ------------------------------------------------- For minor PRs (eg: correcting typos in doc-strings) we can skip GitHub Actions. Adding ``[ci skip]`` in a specific commit message will skip CI for that specific commit which can be useful for draft or incomplete PR. For details, `see here. `__ Fix non-Unix line endings ------------------------- In the past we had non-Unix (i.e. Mac or Windows) line endings in some files. This can be painful, e.g. git diff and autopep8 behave strangely. Here's to commands to check for and fix this (see `here `__): .. code-block:: bash $ git clean -fdx $ find . -type f -print0 | xargs -0 -n 1 -P 4 dos2unix -c mac $ find . -type f -print0 | xargs -0 -n 1 -P 4 dos2unix -c ascii $ git status $ cd astropy_helpers && git checkout -- . && cd .. What checks and conversions should I do for inputs? --------------------------------------------------- In Gammapy we assume that `"we're all consenting adults" `__, which means that when you write a function you should write it like this: .. testcode:: def do_something(data, option): """Do something. Parameters ---------- data : `numpy.ndarray` Data option : {'this', 'that'} Option """ if option == 'this': out = 3 * data elif option == 'that': out = data ** 5 else: ValueError('Invalid option: {}'.format(option)) return out * **Don't always add `isinstance` checks for everything** ... assume the caller passes valid inputs, ... in the example above this is not needed:: assert isinstance(option, str) * **Don't always add `numpy.asanyarray` calls for all array-like inputs** ... the caller can do this if it's really needed ... in the example above document ``data`` as type `~numpy.ndarray` instead of array-like and don't put this line:: data = np.asanyarray(data) * **Do always add an `else` clause to your `if`-`elif` clauses** ... this is boilerplate code, but not adding it would mean users get this error if they pass an invalid option:: UnboundLocalError: local variable 'out' referenced before assignment Now if you really want, you can add the `numpy.asanyarray` and `isinstance` checks for functions that end-users might often use for interactive work to provide them with better exception messages, but doing it everywhere would mean 1000s of lines of boilerplate code and take the fun out of Python programming. Float data type: 32 bit or 64 bit? ---------------------------------- Most of the time what we want is to use 32 bit to store data on disk and 64 bit to do computations in memory. Using 64 bit to store data and results (e.g. large images or cubes) on disk would mean a factor ~2 increase in file sizes and slower I/O, but I'm not aware of any case where we need that precision. On the other hand, doing computations with millions and billions of pixels very frequently results in inaccurate results ... e.g. the likelihood is the sum over per-pixel likelihoods and using 32-bit will usually result in erratic and hard-to-debug optimizer behaviour and even if the fit works incorrect results. Now you shouldn't put this line at the top of every function ... assume the caller passes 64-bit data:: data = np.asanyarray(data, dtype='float64') But you should add explicit type conversions to 64 bit when reading float data from files and explicit type conversions to 32 bit before writing to file. Clobber or overwrite? --------------------- In Gammapy we consistently use an ``overwrite`` bool option for `gammapy.scripts` and functions that write to files. This is in line with Astropy, which had a mix of ``clobber`` and ``overwrite`` in the past, and has switched to uniform ``overwrite`` everywhere. The default value should be ``overwrite=False``, although we note that this decision was very controversial, several core developers would prefer to use ``overwrite=True``. For discussion on this, see `GH 1396 `__. Pixel coordinate convention --------------------------- All code in Gammapy should follow the Astropy pixel coordinate convention that the center of the first pixel has pixel coordinates ``(0, 0)`` (and not ``(1, 1)`` as shown e.g. in ds9). You should use ``origin=0`` when calling any of the pixel to world or world to pixel coordinate transformations in `astropy.wcs`. Performance ----------- Currently Gammapy is 99% Python and scientific Python code. Most memory used is in Numpy arrays, since most Gammapy and Astropy objects hold the data in Numpy arrays, and there's some fraction of memory in Python objects. We have 1% of Cython code, although it's not really needed in those cases, we could rewrite that using just Numpy. In the future, we plan to benchmark and improve the performance both of our existing code (e.g. avoid temp copies of Numpy arrays, better algorithms), and also to introduce parallel execution that can take advantage of multi-core CPUs (and maybe even multiple machines). There's many options how to do that, e.g. using Numba, Cython, Dask, Ray, multiprocessing to name a few. Also, parallelism can be introduced for different tasks and at different levels, e.g. during data reduction, or at the dataset or model component or at the function level. This is planned for 2020, but really prototyping and pull requests on performance are welcome any time. .. _dev_random: Caplog fixture -------------- Inside tests, we have the possibility to change the log level for the captured log messages using the ``caplog`` fixture which allow you to access and control log capturing. When logging is part of your function and you want to verify the right message is logged with the expected logging level: .. testcode:: import pytest def test_something(caplog): """Test something. Parameters ---------- caplog : caplog fixture that give you access to the log level, the logger, etc., """ assert "WARNING" in [_.levelname for _ in caplog.records] assert "warning message" in [_.message for _ in caplog.records] Random numbers -------------- All functions that need to call a random number generator should take a ``random_state`` input parameter and call the `~gammapy.utils.random.get_random_state` utility function like this (you can copy & paste the three docstring lines and the first code line to the function you're writing): .. testcode:: from gammapy.utils.random import get_random_state def make_random_stuff(X, random_state='random-seed'): """... Parameters ---------- random_state : {int, 'random-seed', 'global-rng', `~numpy.random.RandomState`} Defines random number generator initialisation. Passed to `~gammapy.utils.random.get_random_state`. """ random_state = get_random_state(random_state) data = random_state.uniform(low=0, high=3, size=10) return data This allows callers flexible control over which random number generator (i.e. which `numpy.random.RandomState` instance) is used and how it's initialised. The default ``random_state='random-seed'`` means "create a new RNG, seed it in a random way", i.e. different random numbers will be generated on every call. There's a few ways to get deterministic results from a script that call functions that generate random numbers. One option is to create a single `~numpy.random.RandomState` object seeded with an integer and then pass that ``random_state`` object to every function that generates random numbers: .. code-block:: python from numpy.random import RandomState random_state = RandomState(seed=0) stuff1 = make_some_random_stuff(random_state=random_state) stuff2 = make_more_random_stuff(random_state=random_state) Another option is to pass an integer seed to every function that generates random numbers: .. code-block:: python seed = 0 stuff1 = make_some_random_stuff(random_state=seed) stuff2 = make_more_random_stuff(random_state=seed) This pattern was inspired by the way `scikit-learn handles random numbers `__. We have changed the ``None`` option of ``sklearn.utils.check_random_state`` to ``'global-rng'``, because we felt that this meaning for ``None`` was confusing given that `numpy.random.RandomState` uses a different meaning (for which we use the option ``'global-rng'``). Logging ------- Gammapy is a library. This means that it should never contain print statements, because with print statements the library users have no easy way to configure where the print output goes (e.g. to ``stdout`` or ``stderr`` or a log file) and what the log level (``warning``, ``info``, ``debug``) and format is (e.g. include timestamp and log level?). So logging is much better than printing. But also logging is only rarely needed. Many developers use print or log statements to debug some piece of code while they write it. Once it's written and works, it's rare that callers want it to be chatty and log messages all the time. Print and log statements should mostly be contained in end-user scripts that use Gammapy, not in Gammapy itself. That said, there are cases where emitting log messages can be useful. E.g. a long-running algorithm with many steps can log info or debug statements. In a function that reads and writes several files it can make sense to include info log messages for normal operation, and warning or error log messages when something goes wrong. Also, command line tools that are included in Gammapy **should** contain log messages, informing the user about what they are doing. Gammapy uses the Python standard library `logging` module. This module is extremely flexible, but also quite complex. But our logging needs are very modest, so it's actually quite simple ... It is worth mentioning that important logs returned to the user should be captured and tested using caplog fixture, see the section Caplog fixture above Generating log messages +++++++++++++++++++++++ To generate log messages from any file in Gammapy, include these two lines at the top: .. testcode:: import logging log = logging.getLogger(__name__) This creates a module-level `logging.Logger` object called ``log``, and you can then create log messages like this from any function or method: .. testcode:: def process_lots_of_data(infile, outfile): log.info('Starting processing data ...') # do lots of work log.info('Writing {}'.format(outfile)) You should never log messages from the module level (i.e. on import) or configure the log level or format in Gammapy, that should be left to callers ... except from command line tools ... There is also the rare case of functions or classes with the main job to check and log things. For these you can optionally let the caller pass a logger when constructing the class to make it easier to configure the logging. See the `~gammapy.data.EventListDatasetChecker` as an example. Command line tools using click ------------------------------ Command line tools that use the `click `__ module should disable the unicode literals warnings to clean up the output of the tool: .. testcode:: import click click.disable_unicode_literals_warning = True See `here `__ for further information. BSD or GPL license? ------------------- Gammapy is BSD licensed (same license as Numpy, Scipy, Matplotlib, scikit-image, Astropy, photutils, yt, ...). We prefer this over the GPL3 or LGPL license because it means that the packages we are most likely to share code with have the same license, e.g. we can take a function or class and "upstream" it, i.e. contribute it e.g. to Astropy or Scipy if it's generally useful. Some optional dependencies of Gammapy (i.e. other packages like Sherpa or Gammalib or ROOT that we import in some places) are GPL3 or LGPL licensed. Now the GPL3 and LGPL license contains clauses that other package that copy or modify it must be released under the same license. We take the standpoint that Gammapy is independent from these libraries, because we don't copy or modify them. This is a common standpoint, e.g. ``astropy.wcs`` is BSD licensed, but uses the LGPL-licensed WCSLib. Note that if you distribute Gammapy together with one of the GPL dependencies, the whole distribution then falls under the GPL license. Changelog --------- In Gammapy we keep a :ref:`changelog` with a list of pull requests. We sort by release and within the release by PR number (largest first). As explained in the :ref:`astropy:changelog-format` section in the Astropy docs, there are (at least) two approaches for adding to the changelog, each with pros and cons. We've had some pain due to merge conflicts in the changelog and having to wait until the contributor rebases (and having to explain git rebase to new contributors). So our recommendation is that changelog entries are not added in pull requests, but that the core developer adds a changelog entry after right after having merged a pull request (you can add ``[skip ci]`` on this commit). File and directory path handling -------------------------------- In Gammapy use `pathlib.Path` objects to handle file and directory paths. Bundled gammapy.extern code --------------------------- We bundle some code in ``gammapy.extern``. This is external code that we don't maintain or modify in Gammapy. We only bundle small pure-Python files (currently all single-file modules) purely for convenience, because having to explain about these modules as Gammapy dependencies to end-users would be annoying. And in some cases the file was extracted from some other project, i.e. can't be installed separately as a dependency. For ``gammapy.extern`` we don't generate Sphinx API docs. To see what is there, check out the ``gammapy/extern`` directory locally or on `Github `__. Notes on the bundled files are kept in the docstring of `gammapy/extern/__init__.py `__. .. _interpolation-extrapolation: Interpolation and extrapolation ------------------------------- In Gammapy, we use interpolation a lot, e.g. to evaluate instrument response functions (IRFs) on data grids, or to reproject diffuse models on data grids. The default interpolator we use is `scipy.interpolate.RegularGridInterpolator` because it's fast and robust (more fancy interpolation schemes can lead to unstable response in some cases, so more careful checking across all of parameter space would be needed). You should use this pattern to implement a function of method that does interpolation: .. code-block:: python def do_something(..., interp_kwargs=None): """Do something. Parameters ---------- interp_kwargs : dict or None Interpolation parameter dict passed to `scipy.interpolate.RegularGridInterpolator`. If you pass ``None``, the default ``interp_params=dict(bounds_error=False)`` is used. """ if not interp_kwargs: interp_kwargs = dict(bounds_error=False) interpolator = RegularGridInterpolator(..., **interp_kwargs) Since the other defaults are ``method='linear'`` and ``fill_value=nan``, this implies that linear interpolation is used and `NaN`_ values are returned for points outside of the interpolation domain. This is a compromise between the alternatives: * ``bounds_error=True`` -- Very "safe", refuse to return results for any points if one of the points is outside the valid domain. Can be annoying for the caller to not get any result. * ``bounds_error=False, fill_value=nan`` -- Medium "safe". Always return a result, but put NaN values to make it easy for analysers to spot that there's an issue in their results (if pixels with NaN are used, that will usually lead to NaN values in high level analysis results. * ``bounds_error=False, fill_value=0`` -- Less "safe". Extrapolate with zero. Can be very convenient for the caller to avoid dealing with NaN, but if the data values can also be zero you will lose track of invalid pixels. * ``bounds_error=False, fill_value=None`` -- "Unsafe". If fill_value is None, values outside the domain are extrapolated. Can lead to errors where e.g. stacked high level analysis results aren't quite correct because IRFs or background models or ... were used outside their valid range. Methods that use interpolation should provide an option to the caller to pass interpolation options on to ``RegularGridInterpolator`` in case the default behaviour doesn't suit the application. TODO: we have some classes (aeff2d and edisp2d) that pre-compute an interpolator, currently in the constructor. In those cases the ``interp_kwargs`` would have to be exposed e.g. also on the ``read`` and other constructors. Do we want / need that? Locate origin of warnings ------------------------- By default, warnings appear on the console, but often it's not clear where a given warning originates (e.g. when building the docs or running scripts or tests) or how to fix it. Sometimes putting this in ``gammapy/__init__.py`` can help: .. testcode:: import numpy as np np.seterr(all='raise') Following the advice `here `__, putting this in ``docs/conf.py`` can also help sometimes: .. code:: import traceback import warnings import sys def warn_with_traceback(message, category, filename, lineno, file=None, line=None): traceback.print_stack() log = file if hasattr(file,'write') else sys.stderr log.write(warnings.formatwarning(message, category, filename, lineno, line)) warnings.showwarning = warn_with_traceback Object text repr, str and info ------------------------------ In Python, by default objects don't have a good string representation. This section explains how Python repr, str and print work, and gives guidelines for writing ``__repr__``, ``__str__`` and ``info`` methods on Gammapy classes. Let's use this as an example:: class Person: def __init__(self, name='Anna', age=8): self.name = name self.age = age The default ``repr`` and ``str`` are this:: p = Person() repr(p) '<__main__.Person object at 0x105fe3b70>' p.__repr__() '<__main__.Person object at 0x105fe3b70>' str(p) '<__main__.Person object at 0x105fe3b70>' p.__str__() Users will see that. If they just give an object in the Python REPL, the ``repr`` is shown. If they print the object, the ``str`` is shown. In both cases without the quotes seen above. p <__main__.Person at 0x105fd0cf8> print(p) <__main__.Person object at 0x105fe3b70> There are ways to make this better and avoid writing boilerplate code, specifically `attrs `__ and `dataclasses `__. We might use those in the future in Gammapy, but for now, we don't. If you want a better repr or str for a given object, you have to add ``__repr__`` and / or ``__str__`` methods when writing the class. Note that you don't have to do that, it's mainly useful for objects users interact with a lot. For classes that are mainly used internally, developers can e.g. just do this to see the attributes printed nicely:: p.__dict__ {'name': 'Anna', 'age': 8} Here's an example how to write ``__repr__``:: def __repr__(self): return '{}(name={!r}, age={!r})'.format( self.__class__.__name__, self.name, self.age ) Note how we use ``{!r}`` in the format string to fill in the ``repr`` of the object being formatted, and how we used ``self.__class__.__name__`` to avoid duplicating the class name (easier to refactor code, and shows sub-class name if repr is inherited). This will give a nice string representation. The same one for ``repr`` and ``str``, you don't have to write ``__str__``:: p = Person(name='Anna', age=8) p Person(name='Anna', age=8) print(p) Person(name='Anna', age=8) The string representation is usually used for more informal or longer printout. Here's an example:: def __str__(self): return ( "Hi, my name is {} and I'm {} years old.\n" "I live in Heidelberg." ).format(self.name, self.age) If you need text representation that is configurable, i.e. tables arguments what to show, you should add a method called ``info``. To avoid code duplication, you should then call ``info`` from ``__str__``. Example:: class Person: def __init__(self, name='Anna', age=8): self.name = name self.age = age def __repr__(self): return '{}(name={!r}, age={!r})'.format( self.__class__.__name__, self.name, self.age ) def __str__(self): return self.info(add_location=False) def info(self, add_location=True): s = ("Hi, my name is {} and I'm {} years old." ).format(self.name, self.age) if add_location: s += "\nI live in Heidelberg" return s This pattern of returning a string from ``info`` has some pros and cons. It's easy to get the string, and do what you like with it, e.g. combine it with other text, or store it in a list and write it to file later. The main con is that users have to call ``print(p.info())`` to see a nice printed version of the string instead of ``\n``:: p = Person() p.info() "Hi, my name is Anna and I'm 8 years old.\nI live in Heidelberg" print(p.info()) Hi, my name is Anna and I'm 8 years old. I live in Heidelberg To make ``info`` print by default, and be re-usable from ``__str__`` and make it possible to get a string (without having to monkey-patch ``sys.stdout``), would require adding this ``show`` option and if-else at the end of every ``info`` method:: def __str__(self): return self.info(add_location=False, show=False) def info(self, add_location=True, show=True): s = ("Hi, my name is {} and I'm {} years old." ).format(self.name, self.age) if add_location: s += "\nI live in Heidelberg" if show: print(s) else: return s To summarise: start without adding and code for text representation. If there's a useful short text representation, you can add a ``__repr__``. If really useful, add a ``__str__``. If you need it configurable, add an ``info`` and call ``info`` from ``str``. If ``repr`` and ``str`` are similar, it's not really useful: delete the ``__str__`` and only keep the ``__repr__``. It is common to have bugs in ``__repr__``, ``__str__`` and ``info`` that are not tested. E.g. a ``NameError`` or ``AttributeError`` because some attribute name changed, and updating the repr / str / info was forgotten. So tests should be added that execute these methods once. You can write the reference string in the output, but that is not required (and actually very hard for cases where you have floats or Numpy arrays or str, where formatting differs across Python or Numpy version. Example what to put as a test:: def test_person_txt(): p = Person() assert repr(p).startswith('Person') assert str(p).startswith('Hi') assert p.info(add_location=True).endswith('Heidelberg') .. _use-nddata: Coordinate and axis names ------------------------- In Gammapy, the following coordinate and axis names should be used. This applies to most of the code, ranging from IRFs to maps to sky models, for function parameters and variable names. * ``time`` - time * ``energy`` - energy * ``ra``, ``dec`` - sky coordinates, ``radec`` frame (i.e. ``icrs`` to be precise) * ``glon``, ``glat`` - sky coordinates, ``galactic`` frame * ``az``, ``alt`` - sky coordinates, ``altaz`` frame * ``lon``, ``lat`` for spherical coordinates that aren't in a specific frame. For angular sky separation angles: * ``psf_theta`` - offset wrt. PSF center position * ``fov_theta`` - offset wrt. field of view (FOV) center * ``theta`` - when no PSF is involved, e.g. to evaluate spatial sky models For the general case of FOV coordinates that depend on angular orientation of the FOV coordinate frame: * ``fov_{frame}_lon``, ``fov_{frame}_lat`` - field of view coordinates * ``fov_theta``, ``fov_{frame}_phi`` - field of view polar coordinates where ``{frame}`` can be one of ``radec``, ``galactic`` or ``altaz``, depending on with which frame the FOV coordinate frame is aligned. Notes: * In cases where it's unclear if the value is for true or reconstructed event parameters, a postfix ``_true`` or ``_reco`` should be added. In Gammapy, this mostly occurs for ``energy_true`` and ``energy_reco``, e.g. the background IRF has an axis ``energy_reco``, but effective area usually ``energy_true``, and energy dispersion has both axes. We are not pedantic about adding ``_true`` and ``_reco`` everywhere. Note that this would quickly become annoying (e.g. source models use true parameters, and it's not clear why one should write ``ra_true``). E.g. the property on the event list ``energy`` matches the ``ENERGY`` column from the event list table, which is for real data always reco energy. * Currently, no sky frames centered on the source, or non-radially symmetric PSFs are in use, and thus the case of "source frames" that have to be with a well-defined alignment, like we have for the "FOV frames" above, doesn't occur and thus doesn't need to be defined yet (but it would be natural to use the same naming convention as for FOV if it eventually does occur). * These definitions are mostly in agreement with the `format spec `_. We do not achieve 100% consistency everywhere in the spec and Gammapy code. Achieving this seems unrealistic, because legacy formats have to be supported, we are not starting from scratch and have time to make all formats consistent. Our strategy is to do renames on I/O where needed, to and from the internal Gammapy names defined here, to the names used in the formats. Of course, where formats are not set in stone yet, we advocate and encourage the use of the names chosen here. * Finally, we realise that eventually probably CTA will define this, and Gammapy is only a prototype. So if CTA chooses something else, probably we will follow suite and do one more backward-incompatible change at some point to align with CTA. Documentation guidelines ------------------------ Like almost all Python projects, the Gammapy documentation is written in a format called `restructured text (RST)`_ and built using `Sphinx`_. We mostly follow the :ref:`Astropy documentation guidelines `, which are based on the `Numpy docstring standard`_, which is what most scientific Python packages use. .. _restructured text (RST): http://sphinx-doc.org/rest.html .. _Sphinx: http://sphinx-doc.org/ .. _Numpy docstring standard: https://github.com/numpy/numpy/blob/master/doc/HOWTO_DOCUMENT.rst.txt There's a few details that are not easy to figure out by browsing the Numpy or Astropy documentation guidelines, or that we actually do differently in Gammapy. These are listed here so that Gammapy developers have a reference. Usually the quickest way to figure out how something should be done is to browse the Astropy or Gammapy code a bit (either locally with your editor or online on Github or via the HTML docs), or search the Numpy or Astropy documentation guidelines mentioned above. If that doesn't quickly turn up something useful, please ask by putting a comment on the issue or pull request you're working on on Github, or send an email to the Gammapy mailing list. Functions or class methods that return a single object ++++++++++++++++++++++++++++++++++++++++++++++++++++++ For functions or class methods that return a single object, following the Numpy docstring standard and adding a *Returns* section usually means that you duplicate the one-line description and repeat the function name as return variable name. See `astropy.cosmology.LambdaCDM.w` or `astropy.time.Time.sidereal_time` as examples in the Astropy codebase. Here's a simple example: .. testcode:: def circle_area(radius): """Circle area. Parameters ---------- radius : `~astropy.units.Quantity` Circle radius Returns ------- area : `~astropy.units.Quantity` Circle area """ return 3.14 * (radius ** 2) In these cases, the following shorter format omitting the *Returns* section is recommended: .. testcode:: def circle_area(radius): """Circle area (`~astropy.units.Quantity`). Parameters ---------- radius : `~astropy.units.Quantity` Circle radius """ return 3.14 * (radius ** 2) Usually the parameter description doesn't fit on the one line, so it's recommended to always keep this in the *Parameters* section. A common case where the short format is appropriate are class properties, because they always return a single object. As an example see `gammapy.data.EventList.radec`, which is reproduced here: .. testcode:: @property def radec(self): """Event RA / DEC sky coordinates (`~astropy.coordinates.SkyCoord`). """ lon, lat = self['RA'], self['DEC'] return SkyCoord(lon, lat, unit='deg', frame='icrs') Class attributes ++++++++++++++++ Class attributes (data members) and properties are currently a bit of a mess. Attributes are listed in an *Attributes* section because I've listed them in a class-level docstring attributes section as recommended `here `__. Properties are listed in separate *Attributes summary* and *Attributes Documentation* sections, which is confusing to users ("what's the difference between attributes and properties?"). One solution is to always use properties, but that can get very verbose if we have to write so many getters and setters. We could start using descriptors. TODO: make a decision on this and describe the issue / solution here. Sphinx docs build ----------------- Generating the HTML docs for Gammapy is straight-forward:: make docs-all make docs-show Generating the PDF docs is more complex. This should work:: python setup.py build_docs -b latex cd docs/_build/latex makeindex -s python.ist gammapy.idx pdflatex -interaction=nonstopmode gammapy.tex open gammapy.pdf You need a bunch or LaTeX stuff, specifically ``texlive-fonts-extra`` is needed. Jupyter notebooks present in Gammapy documentation have stripped output cells. All notebooks are code clean formatted, tested, and filled during the process of documentation building. They are also converted to Sphinx formatted HTML files and ``.py`` scripts. The Sphinx formatted versions of the notebooks provide links to the raw ``.ipynb`` Jupyter files and ``.py`` script versions stored in ``docs/_static/notebooks`` folder, as well as a link pointing to its specific Binder space in the `gammapy-webpage `__ repository. Since notebooks are evolving with Gammapy features and documentation, the different versions of the notebooks are linked to versioned Binder environments. Once the documentation is built you can optimize the speed of eventual re-building, for example in case you are modifying or creating new docs and you would like to check these changes are displayed nicely. For that purpose, if your modified RST file does not contain links to notebooks, you may run ``make docs-sphinx`` so that notebooks are not executed during the docs build. In the case one single notebook is modified or added to the documentation, you can execute the build doc process with the ``src`` parameter with value the name of the considered notebook. i.e. ``make docs-all src=docs/tutorials/my-notebook.ipynb`` Sphinx gallery extension ------------------------ The documentation built-in process uses the `sphinx-gallery `__ extension to build galleries of illustrated examples on how to use Gammapy (i.e. :ref:`model-gallery`). The Python scripts used to produce the model gallery are placed in ``examples/models`` and the configuration of the ``sphinx-gallery`` module is done in ``docs/conf.py``. Add a notebook in a folder different than tutorials folder ---------------------------------------------------------- Most of the Gammapy notebooks are placed in the ``tutorials`` folder, and are are displayed in a :ref:`tutorials` Gallery. However, we can choose to place a notebook in a different folder of the documentation folder structure. In this way we can write some parts of the documentation as notebooks instead of RST files. Once we have placed the notebook in the folder we choose we can link it from the ``index.rst`` file using the name of the notebook filename **without the extension** and the Sphinx ``toctree`` directive as shown below. .. code-block:: text .. toctree:: mynotebook .. _skip-nb-execution: Skip notebooks from being executed ---------------------------------- You may choose if a notebook is not executed during the documentation building process, and hence it will be published without the output cells in its static HTML version. To do this you may add the following code to the notebook metadata: .. code-block:: javascript "gammapy": { "skip_run": true } Choose a thumbnail and tooltip for the tutorials gallery -------------------------------------------------------- The Gammapy :ref:`tutorials` are Jupyter notebooks that are displayed as a gallery with picture thumbnails and tooltips. You can choose the thumbnail for the tutorial and add the tooltip editing the metadata of the code cell that produces the picture that you've chosen. You can open the notebook in a text editor, and edit the internal code there. It may sound risky, but it is much simpler. Then, find the code cell that produces the figure that you would like for the gallery, and then replace the ``"metadata": {},`` bit above the code cell with the snippet below: .. code-block:: javascript "metadata": { "nbsphinx-thumbnail": { "tooltip": "Learn how to do perform a Fit in gammapy." }}, Note that you may write whatever you like after "tooltip". Dealing with links and notebooks -------------------------------- All Jupyter notebooks in Gammpay documentation are converted to HTML files using `nb_sphinx `__ Sphinx extension which provides a source parser for ``.ipynb`` files. Links to notebooks ++++++++++++++++++ From docstrings and RST documentation files in Gammapy you can link to the built fixed-text HTML formatted versions of the notebooks and subsections providing its filename with the ``.ipynb`` file extension and the relative path to the folder where they are placed:: `Maps section in Gammapy overview tutorial <../tutorials/overview.ipynb#Maps>`__ Links within notebooks ++++++++++++++++++++++ From MD cells in notebooks you can link to other notebooks, as well as to RST documentation files, and subsections using the markdown syntax to declare links to resources, as shown in the examples below: .. code-block:: rst - [Maps section in Gammapy overview tutorial](overview.ipynb#Maps) - [Help!](../getting-started.rst#help) You can also link to the Gammapy API reference documentation using the same Sphinx syntax that is used when writing RST files. All links to the API reference classes and methods should start with ``~gammapy.`` and enclosed within quotation marks. This syntax will be translated into relative links to the API in the HTML formatted versions of the notebooks, and to absolute links pointing to the on-line Gammapy documentation in the ``.ipynb`` notebook files available to download. During the documentation building process a warning will be raised for each detected broken link to the API. Examples: - `gammapy.maps` - `gammapy.maps.Geom` - `gammapy.maps.Geom.is_image` - `gammapy.maps.Geom.is_image()` The example links above could be created within MD cells in notebooks with the syntax below: .. code-block:: rst - `~gammapy.maps` - `~gammapy.maps.Geom` - `~gammapy.maps.Geom.is_image` - `~gammapy.maps.Geom.is_image()` When building the documentation of a release, the links declared in the MD cells as absolute links pointing to the ``dev`` version of the on-line Gammapy documentation will be transformed to relative links in the built HTML formatted notebooks and to absolute links pointing to that specific released version of the on-line docs in the downloadable ``.ipynb`` files. Include png files as images in the notebooks -------------------------------------------- You may include static images in notebooks using the following markdown directive: .. code-block:: rst ![](images/my_static_image.png) Please note that your images should be placed inside an `images` folder, accessed with that relative path from your notebook. Include images from gammapy-data into the docs ---------------------------------------------- Gammapy has a ``gp-image`` directive to include an image from ``$GAMMAPY_DATA/figures/``, use the ``gp-image`` directive instead of the usual Sphinx ``image`` directive like this: .. code-block:: rst .. gp-image:: detect/fermi_ts_image.png :scale: 100% More info on the `image directive `__. .. _dev-check_html_links: Check broken links ------------------ To check for broken external links from the Sphinx documentation: .. code-block:: bash $ python setup.py install $ cd docs; make linkcheck You may also use `brök `__ software, which will also check the links present in the notebooks files. .. code-block:: bash $ brok docs/tutorials/*.ipynb | grep "Failed|Could"