Reasons to update to Sherpa 4.10.0 (fun with conda)

A quick note about our conda packages for Sherpa

It looks like the conda environment has changed again, which means that the Sherpa 4.9.1 (and earlier) packages we provide for Sherpa may stop working. At least if you are using macOS with Python 3.5 or Python 3.6.

An example of the problem

On macOS (any version), create a new conda environment with sherpa 4.9.1 and the latest version of python:

$ conda create -n sherpa-macos-issue -c sherpa \
          python=3.6.5 sherpa=4.9.1
$ source activate sherpa-macos-issue

At this point, trying to load a Sherpa module will result in the following:

$ python -c "from sherpa.astro.ui import *"
Fatal Python error: PyThreadState_Get: no current thread

Abort trap: 6

This is obviously "not good"™.

This does not appear to be a problem for people using Python 2.7, but we suggest updating to Python 3.5 (or later) as we will be dropping support for Python 2.7 in the not too-distant future.

Solutions

The preferred solution is to update to Sherpa 4.10.0, since they were built with a recent conda installation, and so do not suffer this problem.

$ conda install -c sherpa sherpa=4.10

For users with a source build of Sherpa within a conda environment, remove the original build before re-building, or switch to the binary install above.

If upgrading is not possible, then downgrading the Python version appears to work - that is, use Python version 3.6.1 or 3.5.3.

$ conda install python=3.6.1

$ conda install python=3.5.3

Please let the Sherpa team know, via the Sherpa GitHub page, if there are problems with either of the above approaches.

Happy fitting and modelling!

Sherpa 4.10 Release

Sherpa 4.10.0  has now been released and is available via our Conda channel (https://conda.anaconda.org/sherpa), 
pip (https://pypi.python.org/pypi/sherpa/4.10.0), 
Zenodo (https://zenodo.org/record/1245678#.WvsNVlNAnUI), 
and GitHub (https://github.com/sherpa/sherpa/tree/4.10.0). 
This release supports Python 2.7, 3.5, and 3.6.

We thank everyone who contributed to this release with feature requests, bug reports, testing, code contributions, or questions.  Please join in the fun on GitHub: https://github.com/sherpa/sherpa/

OVERVIEW

Sherpa 4.10.0 fixes several bugs related to the support of instrumental responses, including improved support of XMM and Swift responses. Also, this release fixes a significant bug in the support of user statistics, improvements to the Python 3 compatibility, more robust usage of the numpy API, as well as several other minor bug fixes and new tests.

Additionally, this release introduces support for XSPEC 12.9.1n models, as well as the ability to use aliases for parameter names. Some parameter names have been deprecated and may be removed in a future release. We reviewed the parameter limits for many models and updated them to reflect the latest XSPEC specification. Also, multiple versions of XSPEC are now supported, through optional models and version-dependent low-level function calls. This feature is for advanced users building Sherpa from source. Note that Sherpa has been tested against XSPEC 12.9.0i, 12.9.0o, and 12.9.1n. Note that XSPEC is not directly supported by the standalone binary builds, and users are expected to build Sherpa from sources if they want to link it against their version of XSPEC. These changes make it easier for user to link different versions of XSPEC with the same Sherpa code base. Also note, however, that XSPEC 12.10 is not currently supported.

Sherpa now requires pytest-3.3 or later for running the tests.

Details

#451 Release/4.10.0
Testing code now works with pip 10 as well, despite a change in the pip 10 API. Also, the README is now properly rendered as markdown in PyPI.

#438 Change from error to warning for OGIP violations
Given that users can not easily change a response file, and previous versions of Sherpa would allow the responses to be used, this commit changes some of the errors recently introduced (in PR #383) into warnings. The errors for the first bin edge being <= 0 are still left in because users of the sherpa.astro.ui module will find that these files are auto-corrected for them (by PR #383).

#430 Update XSPEC parameters
XSPEC model parameter default values, limits, and properties were reviewed and updated to reflect changes in or mismatches with the model.dat file shipped with XSPEC 12.9.1n.

#428 handle function name changes in XSPEC 12.9.1
Sherpa now supports multiple versions of the XSPEC models from the 12.9.0 and 12.9.1 series. Some models recommend using the C-style interface over the older FORTRAN one, which may also resolve some memory access issues. For CIAO 4.10 users this means the interfaces to XSPEC models have been updated to the 12.9.1n versions. For Standalone Sherpa users this means they can build and run Sherpa against a larger range of XSPEC versions, and Sherpa will pick the XSPEC low level model function accordingly. Note that Sherpa has been tested against XSPEC 12.9.0i, 12.9.0o, and 12.9.1n.
The 14 models that have been changed are: apec, bapec, bvapec, bvvapec, gaussian, lorentz, meka, mekal, raymond, vapec, vmeka, vmekal, vraymond, and vvapec.

#427 Add support for XSPEC models added in 12.9.1 (fix #331)
Add support for models added in XSPEC 12.9.1: bvtapec, bvvtapec, tapec, vtapec, vvtapec, carbatm, hatm, ismabs, slimbh, snapec, TBfeo, TBgas, TBpcf, TBrel, voigt, xscat.
Version 12.9.0 of XSPEC can still be used, in which case the models can be generated - e.g. a user can say xstapec.mdl to create a Python object - but it will error out when evaluated.
The Si and S elemental parameters for the ismabs model have been renamed from the XSPEC versions since they are not unique using the caseinsensitive matching used by Sherpa: so SI, SII, SIII and SiI, SiII, SiIII have been renamed S_I, S_II, S_III and Si_I, Si_II, and Si_III respectively.
Low level support for the following convolution models from XSPEC 12.9.1 has also been added, but there is no Python model support for these: clumin, rfxconv, vashift, vmshift, xilconv.

#412 support ROSAT PSPC (and similar) RMF files with AstroPy
Add explicit tests for reading in, and using, ROSAT PSPC PHA and RMF files. Fix a bug in the AstroPy back-end handling of the ROSAT RMF file.

#409 EmissionGaussian model when skew parameter is not unity (fix #403)
The sherpa.astro.optical.EmissionGaussian code has been fixed for the case when the skew parameter is not unity. The documentation has also been updated.

#399 Python 3 fixes and new tests for pha2 datasets
Fixed several problems when using Sherpa with Python 3: failures when calling list_bkg_ids and list_response_ids and the parameter querying after paramprompt(True) has been called.
There is also a change to avoid a FutureWarning being raised in the astropy backend when reading in PHA2 data files.
Tests have been added to test the reading of a PHA2 format dataset, and new files added to the sherpa-test-data repository for this purpose.

#398 Check that list_samplers returns a list (fix #397)
The list_samplers function now returns a list in Python 3 as well.

#396 Fix set_xlog and related commands using Python 3 (fix #393)
Fix use of commands that set the plot state using the sherpa.astro.ui module, such as set_xlogand set_xlinear, when using Python 3.

#395 Add xspec optional models
Sherpa has new infrastructure for supporting multiple versions of XSPEC at the same time, with models that are built and enabled conditionally depending on the version of XSPEC being linked. Models are assumed to have the same parameters and low level functions across supported versions.

#394 XSPEC build and functionality improvements
Add support for reading and changing the path to the XSPEC "manager" directory, and reading the current XSPEC "model" directory (get_xspath_manager, set_xspath_manager, and get_xspath_model). These are intended for the power user and so require an explicit import from sherpa.astro.xspec.
There are several improvements to the build and interface to the XSPEC model library: these have no user-visible changes.

#390 Add nlapec model
The nlapec XSpec model has been added. Note that XSPEC 12.9.0 is now required.

#385 DS9 calls return string in Python 2 and 3 (fix #319)
Some low lever xpa calls were returning byte strings rather than strings in Python 3. This had particular impact on the image_getregion function. This has now been fixed.

#383 Replace 0-energy bins in ARF and RMFs (fix #332)
Sherpa now performs some validation of the energy ranges of ARF and RMF files against the OGIP standard. If the ranges are inconsistent then the code will return with an error. If one energy bound is 0 the bound is replaced with a small number to avoid numerical issues like division by zero. A new configuration option minimum_energy, if present, allows users to override Sherpa's default behavior.

#379 Use a line not span to draw horizontal line (fix #378)
Ensure that the line at y=0 (residual) or y=1 (ratio) is drawn for residual or ratio plots when using matplotlib 2.0.

#373 Make sure ds9 properly works with Python 2.7 (fix #368)
For Python versions prior to 3.2 add in explicit code to make _Popen work as a context manager.

#352 Add low-level support for the XSPEC rgsxsrc convolution model
Add low-level support for the rgsxsrc convolution model in XSPEC. This is intended for R&D into fully supporting XSPEC convolution models in Sherpa.

#255 Add aliases for parameter names so to support new xspec names (fix #74)
The XSPEC models have been updated to use parameter names that match the new XSPEC naming scheme introduced in XSPEC 12.9.0. The old parameter names can still be used as aliases for the new name, but are deprecated and may be removed in a next major release. Note this allows any models to define aliases for their parameters.

Sherpa 4.9.1 Release

Sherpa 4.9.1 - an incremental improvement over the Sherpa 4.9 release - has now been released and is available via our Conda channel (https://conda.anaconda.org/sherpa), pip (https://pypi.python.org/pypi/sherpa/4.9.1), Zenodo (http://doi.org/10.5281/zenodo.838686), and GitHub (https://github.com/sherpa/sherpa/tree/4.9.1). This release supports Python 2.7, 3.5, and 3.6.

We thank everyone who contributed to this release with feature requests, bug reports, testing, code contributions, or questions.  Please join in the fun on GitHub: https://github.com/sherpa/sherpa/

Overview

This version introduces full support for Python 3.6. It also fixes issues with non-Chandra response files, correctly handles the AREASCAL column in PHA files, and fixes a significant regression that was preventing user statistics from working in v4.8.2. It also introduces a number of smaller improvements and fixes. In particular, quite a few improvements have been made to the documentation and to the testing framework, including several new tests to improve stability.

Details

Infrastructure and minor non-functional changes have been omitted.

#335 Fix `setup.py` install command

The `setup.py install` command was not enforcing the installation of the dependencies listed in `setup.py`. This has been fixed.

#368 Remove ds9 warnings when run under Python 3.6

Update the DS9 code so that external processes are cleaned up properly, so to remove the potential ResourceWarning warnings when running DS9 on Python 3.6.

#351 fix handling of AREASCAL column in PHA files (fix #350)

Add support for handling the AREASCAL value (either scalar of vector) for PHA data sets. This array is used in XMM RGS data to handle missing chips.

#358 Properly handle Swift RMF when using Astropy backend (fix #357)

A Swift RMF could not be read in when the AstroPy back end was in use. The problem was that the code did not support RMF matrices that were not stored as variable-length arrays. This has now been fixed, and new tests have been added for this kind of file.

#343 Fix user statistics regression (fix #341)

A number of regressions were introduced in version 4.8.1 up to version 4.9.0, so user statistics that were properly working in version 4.7 have not been working any more. This has been fixed, and a number of regression tests have been added.

#381 Fix `bdist_wheel` command

We reviewed our customization of the setuptools commands as we realized that a recent bug fix (#335) introduced a regression in the bdist_wheel command used by pip to build Sherpa from source distributions. Both commands should now properly work.

SABA  Sherpa Bridge to Astropy

Sherpa can be used as part of astropy.modeling thanks to SABA - Sherpa Bridge to Astropy

https://saba.readthedocs.io/en/latest/

The development of this package was made possible by the generous support of the Google Summer of Code program in 2016 under the OpenAstronomy by Michele Costa with the support and advice of mentors Tom Aldcroft, Omar Laurino, Moritz Guenther, and Doug Burke.

Sherpa 4.9 Release 

Sherpa 4.9 was just released this week. It now runs in Python 2.7 and Python 3.5. There has been minimal testing with Python 3.6. Support for versions 3.3 and 3.4 would require community support.

Check our GitHub page:
https://github.com/sherpa/sherpa/

Jupyter Notebooks are available on the wiki:

https://github.com/sherpa/sherpa/wiki

Sherpa 4.8.2 Release with Python 3.5 Beta

Sherpa 4.8.2 was released on September 22, 2016. This is the first release for both Python 2.7 and Python 3.5 (Beta release). The 4.8.2 release is available for Python 2.7 and for the first time (as a beta release) for Python 3.5 The Python 3.5 release is considered a Beta designed to maintain backwards compatibility with Python 2.7.

Check our GitHub page:
https://github.com/sherpa/sherpa/

A few IPython notebooks

I have started to collect together a few IPython notebooks highlighting a few features of Sherpa - in particular the standalone version. They can be found on GitHub at https://github.com/DougBurke/sherpa-standalone-notebooks/ and the current collection contains:

•  A simple fit
•  Writing your own user model
•  An integrated user model
•  How can I plot data and models using the lower-level interface

The first one is the same as referenced in my
How do I use the standalone build of Sherpa to fit my data?
post from last year, but the last three are *new*.

We will soon have a better location for this style of information, as we continue work on our "Open Sherpa" project. Please come along and help out!