Docs/reporting bugs

docs/bugs.rst

@@ -0,0 +1,133 @@
+Reporting Bugs
+**************
+
+Despite our best efforts TARDIS contains bugs. We want to make sure that fixing
+these is quick and painless for users and developers.
+
+When reporting bugs please use the mailing list
+(`tardis-sn-user <http://groups.google.com/forum/#!forum/tardis-sn-users>`_) or
+create an issue for TARDIS on github (??? ;preferred).
+
+If there are very long ouputs needed to debug the problem, please use a website like
+`pastebin <http://pastebin.com>`_ that way it is easier for us to look through it.
+
+
+One of the major problems that we see are mismatches in installed versions of
+third-party libraries (that's where virtualenvs really help -
+see :doc:`workflow/python_environment`). To make sure that we can test this properly
+please tell us the installed version of third party packages. The easiest way is::
+
+
+    $ pip freeze
+    Cython==0.20.2
+    Jinja2==2.7.2
+    MarkupSafe==0.21
+    PyYAML==3.11
+    Pygments==1.6
+    Sphinx==1.2.2
+    astropy==1.0.dev10065
+    astropy-helpers==0.4.2
+    backports.ssl-match-hostname==3.4.0.2
+    cov-core==1.11
+    coverage==3.7.1
+    docutils==0.11
+    execnet==1.2.0
+    h5py==2.4.0a0
+    ipdb==0.8
+    ipython==1.2.1
+    latexcodec==0.3.2
+    matplotlib==1.4.0
+    mock==1.0.1
+    nose==1.3.4
+    numexpr==2.4
+    numpy==1.9.0
+    numpydoc==0.4
+    oset==0.1.3
+    pandas==0.14.1
+    pep8==1.5.6
+    py==1.4.20
+    pybtex==0.17
+    pybtex-docutils==0.2.0
+    pyparsing==2.0.2
+    pytest==2.5.2
+    pytest-cache==1.0
+    pytest-cov==1.6
+    pytest-ipdb==0.1-prerelease
+    pytest-pep8==1.0.6
+    python-dateutil==2.2
+    pytz==2014.7
+    pyzmq==14.2.0
+    scipy==0.13.3
+    six==1.8.0
+    sphinx-bootstrap-theme==0.4.0
+    sphinxcontrib-bibtex==0.2.9
+    sphinxcontrib-tikz==0.4.1
+    tables==3.1.1
+    tornado==3.2
+    tox==1.7.1
+    virtualenv==1.11.6
+    wsgiref==0.1.2
+
+
+and pasting the output in your error report, this will show us what packages are
+installed and used.
+
+The next thing that is useful to do if TARDIS is downloaded in a directory is to run
+the test suites and find if any of the tests fail::
+
+    python setup.py test
+    running test
+    running build
+    running build_py
+    copying tardis/./macro_atom.c -> build/lib.macosx-10.9-x86_64-2.7/tardis/.
+    copying tardis/./montecarlo.c -> build/lib.macosx-10.9-x86_64-2.7/tardis/.
+    running build_ext
+    skipping 'tardis/montecarlo.c' Cython extension (up-to-date)
+    skipping 'tardis/macro_atom.c' Cython extension (up-to-date)
+    running build_scripts
+    ============================= test session starts ==============================
+    platform darwin -- Python 2.7.8 -- pytest-2.5.1
+
+    Running tests in tardis /Users/wkerzend/scripts/python/tardis/docs.
+
+    Platform: Darwin-13.4.0-x86_64-i386-64bit
+
+    Executable: /Users/wkerzend/.virtualenvs/tardis-devel/bin/python
+
+    Full Python Version:
+    2.7.8 (default, Oct 15 2014, 22:04:42)
+    [GCC 4.2.1 Compatible Apple LLVM 5.1 (clang-503.0.40)]
+
+    encodings: sys: ascii, locale: UTF-8, filesystem: utf-8, unicode bits: 15
+    byteorder: little
+    float info: dig: 15, mant_dig: 15
+
+    Numpy: 1.9.1
+    Scipy: 0.13.3
+    astropy: 1.0.dev10065
+    yaml: 3.11
+    cython: 0.20.2
+    h5py: 2.4.0a0
+    Matplotlib: 1.4.0
+    ipython: 1.2.1
+
+    plugins: cache, cov, ipdb, pep8
+    collected 107 items
+
+    tardis/io/tests/test_ascii_readers.py .......
+    tardis/io/tests/test_config_reader.py .............................
+    tardis/io/tests/test_config_validator.py ........................
+    tardis/io/tests/test_configuration_namespace.py .........
+    tardis/tests/test_atomic.py .....s
+    tardis/tests/test_lte_plasma.py ssssssssss
+    tardis/tests/test_plasma_nlte.py .....
+    tardis/tests/test_plasma_simple.py .
+    tardis/tests/test_tardis_full.py s
+    tardis/tests/test_util.py ...............
+
+    ==================== 95 passed, 12 skipped in 8.53 seconds =====================
+
+
+
+This will hopefully help us to identify us the problem. We will continue to
+update this document with other techniques.

docs/index.rst

@@ -17,6 +17,7 @@ rapid spectral modelling of supernovae. The code is described in this documentat
     installation
     running
     uses
+    bugs
     configuration/index
     examples/examples
     testing
@@ -45,7 +46,7 @@ please mention the website and cite Kerzendorf & Sim 2014.
 User modifications and additions that lead to publications need to be handed back to the community by incorporating them
 into this publicly available version of TARDIS.
 
-The current stable version of TARDIS is 0.9 and can be downloaded `here <https://pypi.python.org/pypi/tardis-sn>`_, further installation instructions are
+The current stable version of TARDIS is 0.9.2 and can be downloaded `here <https://pypi.python.org/pypi/tardis-sn>`_, further installation instructions are
 available here :ref:`installation`.
 
 A file containing an example configuration file and an atomic database can be found in the section :ref:`running`

tardis/conftest.py

@@ -27,3 +27,105 @@ def pytest_addoption(parser):
                   default=False)
 
     parser.addoption("--atomic-dataset", dest='atomic-dataset', default=None, help="filename for atomic dataset")
+
+def pytest_report_header(config):
+
+    stdoutencoding = getattr(sys.stdout, 'encoding') or 'ascii'
+
+    s = "\n"
+    if six.PY2:
+        args = [x.decode('utf-8') for x in config.args]
+    elif six.PY3:
+        args = config.args
+    s += "Running tests in {0}.\n\n".format(" ".join(args))
+
+    from platform import platform
+    plat = platform()
+    if isinstance(plat, bytes):
+        plat = plat.decode(stdoutencoding, 'replace')
+    s += "Platform: {0}\n\n".format(plat)
+    s += "Executable: {0}\n\n".format(sys.executable)
+    s += "Full Python Version: \n{0}\n\n".format(sys.version)
+
+    s += "encodings: sys: {0}, locale: {1}, filesystem: {2}".format(
+        sys.getdefaultencoding(),
+        locale.getpreferredencoding(),
+        sys.getfilesystemencoding())
+    if sys.version_info < (3, 3, 0):
+        s += ", unicode bits: {0}".format(
+            int(math.log(sys.maxunicode, 2)))
+    s += '\n'
+
+    s += "byteorder: {0}\n".format(sys.byteorder)
+    s += "float info: dig: {0.dig}, mant_dig: {0.dig}\n\n".format(
+        sys.float_info)
+
+    import numpy
+    s += "Numpy: {0}\n".format(numpy.__version__)
+
+    try:
+        import scipy
+        s += "Scipy: {0}\n".format(scipy.__version__)
+    except:
+        s += "Scipy: not available\n"
+
+    try:
+        import astropy
+    except:
+        s += "astropy: not available\n"
+    else:
+        s += "astropy: {0}\n".format(astropy.__version__)
+
+    try:
+        import yaml
+    except:
+        s += "yaml: not available\n"
+    else:
+        s += "yaml: {0}\n".format(yaml.__version__)
+
+
+    try:
+        import cython
+    except:
+        s += "cython: not available\n"
+    else:
+        s += "cython: {0}\n".format(cython.__version__)
+
+
+
+    try:
+        import h5py.version
+        s += "h5py: {0}\n".format(h5py.version.version)
+    except:
+        s += "h5py: not available\n"
+
+
+    try:
+        import matplotlib
+        s += "Matplotlib: {0}\n".format(matplotlib.__version__)
+    except:
+        s += "Matplotlib: not available\n"
+
+    try:
+        import IPython
+    except:
+        s += "ipython: not available\n"
+    else:
+        s += "ipython: {0}\n".format(IPython.__version__)
+
+
+    special_opts = ["remote_data", "pep8"]
+    opts = []
+    for op in special_opts:
+        if getattr(config.option, op, None):
+            opts.append(op)
+    if opts:
+        s += "Using Astropy options: {0}.\n".format(" ".join(opts))
+
+    if six.PY3 and (config.getini('doctest_rst') or config.option.doctest_rst):
+        s += "Running doctests in .rst files is not supported on Python 3.x\n"
+
+    if not six.PY3:
+        s = s.encode(stdoutencoding, 'replace')
+
+    return s