This version fixes many bugs in the Python 3 support. Moreover, it includes a significant
refactoring of the `Fit` and `Stat` classes that made it possible to fix several bugs
related to the recent `wstat` implementation while making these classes more maintainable
and extensible.
Note that this version deprecates the use of `load_table_model` for XSPEC models.
Sherpa/XSPEC users should use the new `load_xstable_model` function instead.
Details
Infrastructure and minor non-functional changes have been omitted.
242 Avoid use of inspect.getargspec in Python3
Finish off the replacement of inspect.getargspec by inspect.signature.
263 List_data_ids() fails on py3 with mixed id types (Fix 262).
Sherpa was sorting the list of dataset IDs in a non-python3 compliant fashion,
which resulted in issues when using strings and integers together as dataset
IDs. This has now been fixed.
267 add wstat tests
Add several regression tests for wstat.
282 Parallel_map not working on py3 with numcores=1 (Fix 277).
The `utils` function `parallel_map` failed on Python 3 when called with `numcores=1`,
i.e. on systems with only one processor/core. This has been fixed.
283 Sample flux and numpy deprecations (Fix 273 and 276).
The `sample_flux` function was not working under Python 3 if the `scales` argument
was provided. This has been fixed. Also, a `DeprecationWarning` was issued by
`numpy` because during the `sample_flux` execution values were extracted from
an array with non-integer indices. This has also been fixed.
284 String representation of data classes under py3 (Fix 275).
Data classes `DataPHA`, `DataARF`, `DataRMF`, `DataIMG`, and `DataIMGInt` in
`sherpa.astro.data` would throw an exception if users tried to print them as
strings, under Python 3. This has been fixed.
287 Rewrite sherpa.stats.Stat.calc_stat and simplify sherpa.fit.Fit (fix 227 248 289 292).
In order to fix several issues related to the WStat support, and in order to
make the code more maintainable, the `sherpa.stats.Stat.calc_stat` and
`sherpa.fit.Fit` classes have gone through a round of refactoring. This fixes
the following issues: 227 Issues using wstat when grouping/filtering data; 248
backscal column not treated properly for WStat; 289 calc_stat does not error out
if background subtracted data is used with Likelihood statistics; 292 stat info
does not include reduced stat/qval for wstat.
295 Fix display of pileup model in Python 3.5 (Fix 294).
Fix display of instances of `sherpa.astro.models.JDPileup` so that, in Python 3.5,
they can be displayed after the model has been evaluated.
304 replace file -> open (Fix 297).
The `save` and `restore` functions used to use the `file` function which is not
compatible with Python 3. This has now been fixed.
305 Fix python 3 issues with some session commands (Fix 303).
The `set_xlog`, `set_ylog`, and `show_bkg_model` functions were not compatible
with Python 3. This has now been fixed (Issue 303).
307 Move XSPEC table support to load_xstable_model and deprecate its support
in load_table_model (Fix 270).
Add the `load_xstable_model` routine to the `sherpa.astro.ui` module, which
supports loading XSPEC additive or multiplicative (atable and mtable) models.
The support for these models is still available via `load_table_model` in this
release, but it is deprecated. The `read_xstable_model` routine has been added
to the `sherpa.astro.xspec` module.
312 Fix over-zealous code clean up in PR 287 affecting sigmarej.
Fits using the sigmarej iterated-fit method were broken if a filter had been
applied to the data before the fit and there are any bins that get ignored at
larger bin values than the filtered-out data. (This fixes a subtle regression
introduced by 287).
313 Allow sequence=None when using gridsearch and Python 3.5 (Fix 309).
Allow the `gridsearch` optimiser to be used with the `sequence` option set
to `None` for Python 3.5.
Caveats
The requirements for Sherpa are to build with Python 2.7 and 3.5. There has been limited testing with Python 3.6, for which we distribute conda binaries. If in doubt, please install Sherpa in 2.7 or 3.5 environments only. Support for Python versions 3.3 and 3.4 is possible but would require community support.
It has been reported during testing that some versions of the matplotlib conda package do not install properly because of a pyqt v5 dependency. If you encounter this issue, please pin down pyqt to version 4, e.g. `conda install matplotlib pyqt=4`.
The `sherpatest` package is not distributed as a conda package anymore. This will probably be true for the foreseeable future. The `sherpatest` package contains data and functional tests that relies on external datasets, so it allows users and developers to run the entire regression tests suite. If you want to install `sherpatest`, please use pip and github:
$ pip install https://github.com/sherpa/sherpa-test-data/archive/4.9.0.tar.gz
If you decide to run the full regression tests suite you should also have matplotlib installed. If matplotlib is not installed a test will run and fail rather than being skipped. This issue will be fixed in the next release.
ciao4.9
This is a CIAO release.
Binaries will be provided with the next standalone release.
Release notes are collected for all changes since CIAO 4.8, which may be included from multiple standalone releases.
Release Notes
Sherpa 4.9 now runs under both Python 2.7 and Python 3.5. The test infrastructure
has been modified including simplification of the smoke test. Several bug fixes and
enhancements are also included. Specific details are identified below.
14361: Sherpa and Chips wrapper need to replace execfile for python 3 compatibility
This fix modifies the sherpa and chips wrapper scripts to replace the
'execfile' command with an 'exec' command sequence that allows the
wrapper script to be utilized by python 2.7 or python 3.5. Without the
change, the option to specify a command script at the sherpa or chips
command prompt (ie. 'chips /pool1/runme.py') will not work on python 3.5
since the execfile does not exist in python 3.5.
107: Normalize plot labels.
Plots created with `plot_source` used a different format to other
plots when analysis=wavelength, in that LaTeX symbols were used for
Angstrom and lambda (in other plots the string 'Angstrom' is used
instead). The source plots now match the other plots.
138: improve and fix issues in `save_all` function.
- added a new argument to `save_all`: if `outfile` is `None` then the `outfh`
argument is used
to define the output handle (the argument can be any file-like argument, such
as a file
handle like `sys.stdout` or the output of `open`, or a `StringIO` object)
- setting the `clobber` argument to `save_all` now means that the output file
(the `outfile`
argument, if not `None`) is deleted if it already exists; prior to this, the
file would be
appended to instead
- the source expression is now saved correctly for most cases (e.g. when not
using `set_full_model`); this is bug 97 but also affects non-PHA data sets
- the background model expression was not always written out correctly when
using PHA
data sets
- quality and grouping arrays of PHA data sets are now stored as 16-byte
integers rather
than a floating-point value (this has no affect on the results, but matches
the OGIP standard)
- fixed up saving the grouping and quality arrays of background PHA data sets
(this would only
be an issue if the background is being fit, rather than subtracted)
- basic data sets created with the `load_arrays` function are now written out by
`save_all`
as part of the script; this is intended for small datasets and may have
problems with
precision if used with floating-point arrays
- calls to `load_psf` are now correctly restored (they may not have been written
out correctly
if multiple data sets were loaded)
- user models are now written out to disk; this consists of two parts:
- writing out the function that defines the model, which may or may not be
possible (if
not, a place-holder function is added to the output and a warning
displayed).
- the necessary calls to `load_user_model` and `add_user_pars` are now
included in the output
- the Python code created by `save` all has undergone several minor changes:
- it now explicitly imports the `sherpa.astro.ui` module, so that it can be
run from the
IPython prompt using the `%run <filename>` command, or directly as `python <filename>`
- it uses the `create_model_component` function rather than `eval` to create
model
components (this is CXC bug 12146)
- many optional arguments to functions are now given as `name=value` rather
than
being a positional argument, to make it clearer what the script is doing.
- calls to `load_data` have been replaced by more-specific versions - e.g.
`load_pha`
and `load_image` - if appropriate
- there have been several minor syntactic clean ups to better follow the
suggestions from PEP8
When writing out code that defines a user-model, there is no attempt to make
sure that
modules used by the function are available. These will need to be added, either
directly
or imported, manually to the output.
153: Minor bug with calc_chi2datavar_errors (Fix 148).
Make comparison test in `calc_chi2datavar_errors` less stringent, so to
include the case where `sqrt(x)=0`.
155: Add argument to get_draws for supplying a covariance matrix.
The `get_draws` function now accepts a user-provided covariance matrix. If
no covariance matrix is provided, the covariance matrix computed by the default
implementation is used. Note that `covar()` must be invoked before invoking
`get_draws` if no covariance matrix is provided, otherwise `get_draws` will exit
with an error.
165: Remove usage of deprecated numpy API.
185: Protect XPA command to avoid shell confusion.
Fix the problem where if the working directory contained a file called
`x` or `y` then the `sherpa.astro.ui.image_data()` function would fail with the message
DS9Err: Could not display image
187: Issue a more meaningful message when
`sherpa.astro.io` is imported directly and no fits backends are available. (Fix 92).
190: Datastack can be used if no plotter available.
The datastack package can now be used even if there is no
available plotting backend. In this case, plotting functions will not be
available, but the rest of the datastack functionality will. (Fix 22).
195 Generalize calc_stat API + example of how to have several datasets with
different fit statistics. Attempts to generalize the `calc_stat` API and
enable simultaneous fits with different statistics for different data sets.
209: Fix docstrings for `group_snr()` and `group_adapt_snr()`.
Updates to the docstrings for clarity.
210: New Smoke Test
The smoke test has been greatly simplified: rather than running all the unit and regression tests that do not require test data, the smoke test now simply ensures that the basic installation works, i.e. that basic commands can be run and that dependencies can be reached.
211: Cleanup of documentation and code in `sherpa.astro.utils`.
The `calc_kcorr` function is now exported by sherpa.astro.utils. Minor
changes to the documentation in `sherpa.astro.utils` were also made to conform
to Sphinx standards.
221 Add model documentation (Fix 217).
Integrate existing model documentation (from external sources and the CIAO
ahelp documentation system) into the model classes.
229: Code is both Python 2.7 and 3.5 compliant. (Fix 76).
242: Avoid use of `inspect.argspec` in Python 3
This change replaces the deprecated 'inspect.argspec' call with 'inspect.signature'.
252: Fix `plot_photon_flux` function. (Fix 241).
A bug where plotting photon flux was fixed by adding a missing argument to the `sample_photon_flux` call.
253 Make sure background is taken into account in calc_stat_info (Fix 147).
`calc_stat_info` call failed when `wstat` was selected, as the background
was not taken into account. This issue has now been fixed.
254 Fix the documentation for set_rmf (Fix 236).
The documentation for `set_rmf` incorrectly referred to ARF rather than RMF.
256 Fix docstring in set_quality (Fix 205).
The docstring in `set_quality` now correctly indicates the quality flags.
The previous documentation didn't describe the values of such flags properly.
257 Fix docstring for levmar tolerance (Fix 257).
The documentation string for the Levenberg-Marquardt optimization function now
correctly states that the parameter default values are equal to the single
precision epsilon, rather than the square root of the double precision epsilon.
263 List_data_ids() fails on py3 with mixed id types (Fix 262).
Sherpa was sorting the list of dataset IDs in a non-python3 compliant fashion,
which resulted in issues when using strings and integers together as dataset
IDs. This has now been fixed.
267 add wstat tests
Add several regression tests for wstat.
282 Parallel_map not working on py3 with numcores=1 (Fix 277).
The `utils` function `parallel_map` failed on Python 3 when called with `numcores=1`,
i.e. on systems with only one processor/core. This has been fixed.
283 Sample flux and numpy deprecations (Fix 273 and 276).
The `sample_flux` function was not working under Python 3 if the `scales` argument
was provided. This has been fixed. Also, a `DeprecationWarning` was issued by
`numpy` because during the `sample_flux` execution values were extracted from
an array with non-integer indices. This has also been fixed.
284 String representation of data classes under py3 (Fix 275).
Data classes `DataPHA`, `DataARF`, `DataRMF`, `DataIMG`, and `DataIMGInt` in
`sherpa.astro.data` would throw an exception if users tried to print them as
strings, under Python 3. This has been fixed.
287 Rewrite sherpa.stats.Stat.calc_stat and simplify sherpa.fit.Fit (fix 227 248 289 292).
In order to fix several issues related to the WStat support, and in order to
make the code more maintainable, the `sherpa.stats.Stat.calc_stat` and
`sherpa.fit.Fit` classes have gone through a round of refactoring. This fixes
the following issues: 227 Issues using wstat when grouping/filtering data; 248
backscal column not treated properly for WStat; 289 calc_stat does not error out
if background subtracted data is used with Likelihood statistics; 292 stat info
does not include reduced stat/qval for wstat.
295 Fix display of pileup model in Python 3.5 (Fix 294).
Fix display of instances of `sherpa.astro.models.JDPileup` so that, in Python 3.5,
they can be displayed after the model has been evaluated.
304 replace file -> open (Fix 297).
The `save` and `restore` functions used to use the `file` function which is not
compatible with Python 3. This has now been fixed.
305 Fix python 3 issues with some session commands (Fix 303).
The `set_xlog`, `set_ylog`, and `show_bkg_model` functions were not compatible
with Python 3. This has now been fixed (Issue 303).
307 Move XSPEC table support to load_xstable_model and deprecate its support
in load_table_model (Fix 270).
Add the `load_xstable_model` routine to the `sherpa.astro.ui` module, which
supports loading XSPEC additive or multiplicative (atable and mtable) models.
The support for these models is still available via `load_table_model` in this
release, but it is deprecated. The `read_xstable_model` routine has been added
to the `sherpa.astro.xspec` module.
312 Fix over-zealous code clean up in PR 287 affecting sigmarej.
Fits using the sigmarej iterated-fit method were broken if a filter had been
applied to the data before the fit and there are any bins that get ignored at
larger bin values than the filtered-out data. (This fixes a subtle regression
introduced by 287).
313 Allow sequence=None when using gridsearch and Python 3.5 (Fix 309).
Allow the `gridsearch` optimiser to be used with the `sequence` option set
to `None` for Python 3.5.
Caveats
319: `image_getregion` returns byte string on Py3.
SH-2: The new `test_save_restore` test in the CIAO regression tests suite is failing on all platforms. We are investigating the reasons of the failure. The failure is triggered when the test is not run in isolation, and only when certain other tests are run before it. Also, this only applies to CIAO and not to standalone Sherpa.
SH-3: Some tests are skipped during the CIAO regression tests.
SH-4: Several OS X regression tests are failing.
Note: The SH-2/3/4 caveats are issues with the tests themselves, not with the code, and only appear when running the full CIAO regression tests suite. User will not be affected by the above issues unless they run the full CIAO regression tests suite.