tardis-sn · wkerzendorf · Feb 13, 2015 · Feb 2, 2015 · Feb 2, 2015 · Feb 3, 2015
diff --git a/.travis.yml b/.travis.yml
@@ -12,7 +12,7 @@ env:
         - CYTHON_VERSION=0.21
         - NUMPY_VERSION=1.8
         - PANDAS_VERSION=0.12
-        - ASTROPY_VERSION=0.4
+        - ASTROPY_VERSION=0.4.4
         - ASTROPY_USE_SYSTEM_PYTEST=1
         - SETUP_CMD='test'
         - TEST_MODE='normal'
@@ -55,13 +55,11 @@ before_install:
     - if [[ $TEST_MODE == 'spectrum' ]]; then mv kurucz_cd23_chianti_H_He.h5 $HOME/; fi
 
 install:
-   - conda create --yes -n tardis-travis --file pip-requirements python=$TRAVIS_PYTHON_VERSION
+   - conda create --yes -n tardis-travis --file pip-requirements pip python=$TRAVIS_PYTHON_VERSION
    - source activate tardis-travis
    - if [[ $NUMPY_VERSION == 'latest' ]]; then conda install --yes  numpy; else conda install --yes "numpy==$NUMPY_VERSION"; fi
    - if [[ $PANDAS_VERSION == 'latest' ]]; then conda install --yes pandas; else conda install --yes "pandas=$PANDAS_VERSION"; fi
-   - conda install --yes pytables
-   #- conda install --yes cython
-   - if [[ $ASTROPY_VERSION == 'development' ]]; then pip install git+https://github.com/astropy/astropy; else conda install --yes "astropy==$ASTROPY_VERSION"; fi
+   - if [[ $ASTROPY_VERSION == 'development' ]]; then pip install git+https://github.com/astropy/astropy; else conda install --yes "astropy=$ASTROPY_VERSION"; fi
    - conda install --yes pytest
 
    - if [[ $SETUP_CMD == 'test --coverage' ]]; then pip install -q coveralls; fi

diff --git a/CHANGELOG.rst b/CHANGELOG.rst
@@ -1,7 +1,39 @@
 1.0.0 (unreleased)
 ------------------
 
-- Nothing changed yet.
+New Features
+^^^^^^^^^^^^
+- the main feature is the re-write of the montecarlo code to C, which comes
+with a 4x speed increase.
+
+Pull Requests
+^^^^^^^^^^^^^
+
+- [#210](https://github.com/tardis-sn/tardis/pull/210) a restructure of the C-file file structure (@wkerzendorf, @mklauser)
+- [#7](https://github.com/tardis-sn/tardis/pull/7) include .c in montecarlo/src/ for the randomkit files (@mklauser)
+- [#209](https://github.com/tardis-sn/tardis/pull/209) Testing/pandas version info (@wkerzendorf)
+- [#205](https://github.com/tardis-sn/tardis/pull/205) As simpler `run_tardis` (@wkerzendorf)
+- [#206](https://github.com/tardis-sn/tardis/pull/206) Minor but critical fix to binary search (reverse) (@ssim)
+- [#199](https://github.com/tardis-sn/tardis/pull/199) Gnuify cmontecarlo.c and cmontecarlo.h files (@orbitfold)
+- [#203](https://github.com/tardis-sn/tardis/pull/203) Docs/reporting bugs (@wkerzendorf)
+- [#201](https://github.com/tardis-sn/tardis/pull/201) A critical warning was added to the model indicating that no packet has left the simulation through the outer boundary. (@mklauser)
+- [#200](https://github.com/tardis-sn/tardis/pull/200) added a new location for the atomic data. (@wkerzendorf)
+- [#196](https://ggithub.com/tardis-sn/tardis/pull/196) New binary search added (@mklauser)
+- [#169](https://github.com/tardis-sn/tardis/pull/169) fix for #168 (@mklauser)
+- [#194](https://github.com/tardis-sn/tardis/pull/194) Setup/fix requirements (@wkerzendorf)
+- [#188](https://github.com/tardis-sn/tardis/pull/188) A macro to automagically fix inline issues (@orbitfold)
+- [#190](https://github.com/tardis-sn/tardis/pull/190) General/fixing unit problems (@wkerzendorf)
+- [#179](https://github.com/tardis-sn/tardis/pull/179) making sure that if last_no_of_packets is not specified that it is set t... (@wkerzendorf)
+- [#178](https://github.com/tardis-sn/tardis/pull/178) Atomic/fix reprepare (@wkerzendorf)
+- [#177](https://github.com/tardis-sn/tardis/pull/177) added from_yaml and from_config_dict to ConfigurationNameSpace (@wkerzendorf)
+- [#175](https://github.com/tardis-sn/tardis/pull/175) Fix a few problems in cmontecarlo.c (@orbitfold, @wkerzendorf)
+- [#174](https://github.com/tardis-sn/tardis/pull/174) fixes added for clang compile on mac (@wkerzendorf)
+- [#171](https://github.com/tardis-sn/tardis/pull/171) Fix issues when using clang compiler (issue #170) (@orbitfold)
+- [#167](https://github.com/tardis-sn/tardis/pull/167) fix for #165 (@mklauser, @wkerzendorf)
+- [#3](https://github.com/tardis-sn/tardis/pull/3) testing the new t_inner fix (@wkerzendorf)
+- [#164](https://github.com/tardis-sn/tardis/pull/164) Config/toggle validation (@wkerzendorf)
+- [#151](https://github.com/tardis-sn/tardis/pull/151) WIP Montecarlo C Rewrite (@orbitfold)
+- [#160](https://github.com/tardis-sn/tardis/pull/160) how to get constant density? broken? (@wkerzendorf)
 
 
 0.9.2 (2014-06-12)

diff --git a/MANIFEST.in b/MANIFEST.in
@@ -1,26 +1,22 @@
 include README.rst
-include pip-requirements
+include CHANGES.rst
 
 include ez_setup.py
 include ah_bootstrap.py
 include setup.cfg
 
-recursive-include astropy_helpers *
-exclude astropy_helpers/.git
-exclude astropy_helpers/.gitignore
-exclude tardis/_compiler.c
-
-
-recursive-include tardis *.pyx *.c *.h
-recursive-include tardis/randomkit *.c *.h
-include tardis/tardis.cfg
-
+recursive-include *.pyx *.c *.pxd
 recursive-include docs *
 recursive-include licenses *
 recursive-include cextern *
 recursive-include scripts *
 
-exclude *.pyc *.o
-prune docs/_build
 prune build
+prune docs/_build
+prune docs/api
+
+recursive-include astropy_helpers *
+exclude astropy_helpers/.git
+exclude astropy_helpers/.gitignore
 
+global-exclude *.pyc *.o
diff --git a/README.rst b/README.rst
@@ -1,6 +1,6 @@
-======
+******
 TARDIS
-======
+******
 
 .. image:: https://pypip.in/v/tardis-sn/badge.png
   :target: https://pypi.python.org/pypi/tardis-sn

diff --git a/Vagrantfile b/Vagrantfile
@@ -12,7 +12,7 @@ Vagrant.configure(VAGRANTFILE_API_VERSION) do |config|
   # Every Vagrant virtual environment requires a box to build off of.
   config.vm.box = "ubuntu/trusty64"
 
-  config.vm.provision :shell, path: "bootstrap_trusty64.sh"
+  config.vm.provision :shell, path: "bootstrap_trusty64.sh", privileged:false
 
   # Disable automatic box update checking. If you disable this, then
   # boxes will only be checked for updates when the user runs

diff --git a/astropy_helpers b/astropy_helpers
diff --git a/bootstrap_trusty64.sh b/bootstrap_trusty64.sh
@@ -1,8 +1,17 @@
 #!/usr/bin/env bash
 
-apt-get update
-apt-get install -y python-virtualenv python-numpy python-pandas python-scipy python-h5py python-yaml ipython python-matplotlib cython git
-virtualenv --system-site-packages tardis.ve
-chmod -R a+rwX tardis.ve
-source tardis.ve/bin/activate
-pip install -r /vagrant/pip-requirements
+sudo apt-get install git --yes
+
+sudo apt-get install git
+wget http://repo.continuum.io/miniconda/Miniconda-latest-Linux-x86_64.sh -O miniconda.sh
+bash miniconda.sh -b
+
+export PATH=/home/vagrant/miniconda/bin:$PATH
+conda update --yes conda
+
+conda create --yes -n tardis --file /vagrant/pip-requirements pip
+
+echo "export PATH=/home/vagrant/miniconda/bin:$PATH" >> .bashrc
+
+wget https://www.dropbox.com/s/svvyr5i7m8ouzdt/tardis_example.tar.gz
+tar zxvf tardis_example.tar.gz
diff --git a/docs/atomic/current_public_table.rst b/docs/atomic/current_public_table.rst
@@ -2,7 +2,7 @@
 | file name                                                                                                                       | uuid1                                                                                                                           | data sources                                                                                                                    | macroatom                                                                                                                       | zeta                                                                                                                            | synpp references                                                                                                                | database version                                                                                                                |
 |                                                                                                                                 |                                                                                                                                 |                                                                                                                                 |                                                                                                                                 |                                                                                                                                 |                                                                                                                                 |                                                                                                                                 |
 +=================================================================================================================================+=================================================================================================================================+=================================================================================================================================+=================================================================================================================================+=================================================================================================================================+=================================================================================================================================+=================================================================================================================================+
-| `kurucz_cd23_chianti_H_He.zip <http://moria.astro.utoronto.ca/~wkerzend/tardis_atomic_databases/kurucz_cd23_chianti_H_He.zip>`_ | 5ca3035ca8b311e3bb684437e69d75d7                                                                                                | **kurucz:**                                                                                                                     | True                                                                                                                            | True                                                                                                                            | True                                                                                                                            | v0.9                                                                                                                            |
+| `kurucz_cd23_chianti_H_He.zip <https://www.dropbox.com/s/4uohu65g9bd2iwr/kurucz_cd23_chianti_H_He.zip?dl=0>`_                   | 5ca3035ca8b311e3bb684437e69d75d7                                                                                                | **kurucz:**                                                                                                                     | True                                                                                                                            | True                                                                                                                            | True                                                                                                                            | v0.9                                                                                                                            |
 |                                                                                                                                 |                                                                                                                                 |                                                                                                                                 |                                                                                                                                 |                                                                                                                                 |                                                                                                                                 |                                                                                                                                 |
 |                                                                                                                                 |                                                                                                                                 | Li I-II, Be I-IV, C I-IV, N I-VI                                                                                                |                                                                                                                                 |                                                                                                                                 |                                                                                                                                 |                                                                                                                                 |
 |                                                                                                                                 |                                                                                                                                 | O I-VI, F I-VI, Ne I-VI, Na I-VI                                                                                                |                                                                                                                                 |                                                                                                                                 |                                                                                                                                 |                                                                                                                                 |

diff --git a/docs/bugs.rst b/docs/bugs.rst
@@ -1,3 +1,4 @@
+**************
 Reporting Bugs
 **************
 

diff --git a/docs/glossary.rst b/docs/glossary.rst
@@ -1,5 +1,6 @@
+********
 Glossary
-========
+********
 
 .. glossary::
     meta-stable

diff --git a/docs/testing.rst b/docs/testing.rst
@@ -1,5 +1,6 @@
+**************
 Testing TARDIS
---------------
+**************
 
 Testing a code like TARDIS is an important step to making sure that the output is trustworthy. The TARDIS team has opted
 to use the py.test testing framework for use with TARDIS (and some astropy extensions of it). To run the tests download

diff --git a/docs/workflow/development_workflow.rst b/docs/workflow/development_workflow.rst
@@ -14,7 +14,7 @@ explains how to do that.
 
 
 General Workflow to add a new feature
--------------------------------------
+=====================================
 
 In TARDIS we aim to stick to a test driven development. This uses the testing
 framework extensively starting with a test that shows this feature lacking via
@@ -24,7 +24,6 @@ repository.
 In most cases we try to break down big features into small, quantifiable goals
 which are then acted upon.
 
-
  * Document feature to be added in an issue and maybe ask the mailing
    list if this feature exists
  * Write a test that demonstrates what feature will be added.
@@ -37,3 +36,6 @@ which are then acted upon.
  * Run the test to verify that it passes.
  * Write documentation about your feature.
  * close issue/partial PR and add to changelog.
+
+
+.. include:: release_workflow.inc
diff --git a/docs/workflow/release_workflow.rst b/docs/workflow/release_workflow.rst
@@ -0,0 +1,24 @@
+*******
+Release
+*******
+
+This is documentation is mainly intended for core developers of TARDIS. There
+are several steps to do a release.
+
+
+Update the Changelog
+====================
+
+The changelog is located in ``CHANGELOG.rst`` in the root directory of TARDIS and contains
+a description of changes between versions. One useful idea is to mention all the
+pull requests, which can be accomplished with the tool
+`github-changes <https://www.npmjs.com/package/github-changes>` and invoke it with
+``github-changes -o tardis-sn -r tardis --only-pulls --use-commit-body -f tmp_changelog.md``
+which will write the pull requests into ``tmp_changelog.md``. This can be used to put into
+the actual ``CHANGELOG.rst``.
+
+Doing the actual release
+========================
+
+This is best done in a clean environment (so a fresh checkout from the master).
+We again use the astropy instructions: `<http://astropy.readthedocs.org/en/latest/development/releasing.html>`_
diff --git a/docs/zreferences.rst b/docs/zreferences.rst
@@ -1,5 +1,6 @@
+**********
 References
-==========
+**********
 
 .. bibliography:: tardis.bib
     :encoding: utf8
diff --git a/pip-requirements b/pip-requirements
@@ -1,9 +1,11 @@
 numpy>=1.4.0
 scipy>=0.10
 pandas>=0.12
+pytables
 h5py>=2.0
 matplotlib>=1.1
 astropy>=0.4
 PyYAML>=3.0
 numexpr>=2.0.0
 Cython>=0.21
+jinja2
diff --git a/setup.py b/setup.py
@@ -36,15 +36,14 @@
 # Get the long description from the package's docstring
 #__import__(PACKAGENAME)
 #package = sys.modules[PACKAGENAME]
-#LONG_DESCRIPTION = package.__doc__
-LONG_DESCRIPTION = ""
+LONG_DESCRIPTION = "" #package.__doc__
 
 # Store the package name in a built-in variable so it's easy
 # to get from other parts of the setup infrastructure
 builtins._ASTROPY_PACKAGE_NAME_ = PACKAGENAME
 
 # VERSION should be PEP386 compatible (http://www.python.org/dev/peps/pep-0386)
-VERSION = '1.0.0.dev'
+VERSION = '1.0.dev'
 
 # Indicates if this version is a release version
 RELEASE = 'dev' not in VERSION
@@ -79,6 +78,12 @@
 package_info['package_data'].setdefault(PACKAGENAME, [])
 package_info['package_data'][PACKAGENAME].append('data/*')
 
+# Define entry points for command-line scripts
+entry_points = {}
+entry_points['console_scripts'] = [
+    'astropy-package-template-example = packagename.example_mod:main',
+]
+
 # Include all .c files, recursively, including those generated by
 # Cython, since we can not do this in MANIFEST.in with a "dynamic"
 # directory name.
@@ -106,5 +111,6 @@
       cmdclass=cmdclassd,
       zip_safe=False,
       use_2to3=True,
+      entry_points=entry_points,
       **package_info
 )
diff --git a/tardis/conftest.py b/tardis/conftest.py
@@ -26,7 +26,11 @@ def pytest_addoption(parser):
                   "Run the doctests in the rst documentation",
                   default=False)
 
-    parser.addoption("--atomic-dataset", dest='atomic-dataset', default=None, help="filename for atomic dataset")
+    parser.addoption('--repeat', action='store',
+                     help='Number of times to repeat each test')
+
+    parser.addoption("--atomic-dataset", dest='atomic-dataset', default=None,
+                     help="filename for atomic dataset")
 
 def pytest_report_header(config):
+5 −0		.gitignore
+35 −18		.travis.yml
+135 −1		CHANGES.rst
+20 −0		CONTRIBUTING.md
+1 −1		LICENSE.rst
+23 −21		README.rst
+575 −370		ah_bootstrap.py
+52 −0		appveyor.yml
+2 −0		astropy_helpers/__init__.py
+0 −0		astropy_helpers/commands/__init__.py
+179 −0		astropy_helpers/commands/build_ext.py
+39 −0		astropy_helpers/commands/build_py.py
+215 −0		astropy_helpers/commands/build_sphinx.py
+14 −0		astropy_helpers/commands/install.py
+14 −0		astropy_helpers/commands/install_lib.py
+53 −0		astropy_helpers/commands/register.py
+257 −0		astropy_helpers/distutils_helpers.py
+71 −29		astropy_helpers/git_helpers.py
+151 −823		astropy_helpers/setup_helpers.py
+21 −33		astropy_helpers/sphinx/conf.py
+24 −3		astropy_helpers/sphinx/ext/astropyautosummary.py
+56 −0		astropy_helpers/sphinx/ext/autodoc_enhancements.py
+3 −3		astropy_helpers/sphinx/ext/automodapi.py
+23 −6		astropy_helpers/sphinx/ext/automodsumm.py
+14 −2		astropy_helpers/sphinx/ext/changelog_links.py
+5 −0		astropy_helpers/sphinx/ext/doctest.py
+2 −1		astropy_helpers/sphinx/ext/edit_on_github.py
+25 −2		astropy_helpers/sphinx/ext/smart_resolver.py
+70 −0		astropy_helpers/sphinx/ext/tests/__init__.py
+56 −0		astropy_helpers/sphinx/ext/tests/test_autodoc_enhancements.py
+51 −8		astropy_helpers/sphinx/ext/tests/test_automodapi.py
+34 −3		astropy_helpers/sphinx/ext/tests/test_automodsumm.py
+1 −1		astropy_helpers/sphinx/ext/tests/test_utils.py
+12 −5		astropy_helpers/sphinx/ext/viewcode.py
+ −		astropy_helpers/sphinx/local/python3links.inv
+7 −0		astropy_helpers/sphinx/local/python3links.txt
+17 −5		astropy_helpers/sphinx/themes/bootstrap-astropy/static/bootstrap-astropy.css
+140 −94		astropy_helpers/test_helpers.py
+44 −55		astropy_helpers/tests/__init__.py
+104 −21		astropy_helpers/tests/test_ah_bootstrap.py
+141 −23		astropy_helpers/tests/test_git_helpers.py
+147 −10		astropy_helpers/tests/test_setup_helpers.py
+434 −5		astropy_helpers/utils.py
+54 −6		astropy_helpers/version_helpers.py
+71 −0		continuous-integration/appveyor/install-miniconda.ps1
+47 −0		continuous-integration/appveyor/windows_sdk.cmd
+7 −0		continuous-integration/travis/install_conda_linux.sh
+7 −0		continuous-integration/travis/install_conda_osx.sh
+4 −0		continuous-integration/travis/install_graphviz_linux.sh
+4 −0		continuous-integration/travis/install_graphviz_osx.sh
+5 −2		setup.py
+3 −1		tox.ini