diff --git a/README.rst b/README.rst index 13a0942..eaa5840 100644 --- a/README.rst +++ b/README.rst @@ -24,8 +24,8 @@ modification, separation, for any purpose and without a charge. :scale: 100% :target: https://alchemtest.readthedocs.io/en/latest/ -.. |doi| image:: https://zenodo.org/badge/XXXXX.svg +.. |doi| image:: https://zenodo.org/badge/83470847.svg :alt: Zenodo DOI :scale: 100% - :target: https://zenodo.org/badge/latestdoi/XXXXX + :target: https://zenodo.org/badge/latestdoi/83470847 diff --git a/docs/conf.py b/docs/conf.py index e89a811..3317ee4 100644 --- a/docs/conf.py +++ b/docs/conf.py @@ -58,9 +58,22 @@ # built documents. # # The short X.Y version. -version = u'0.1.0-dev' +#version = u'0.2' # The full version, including alpha/beta/rc tags. -release = u'0.1.0-dev' +#release = u'0.2.0' + +# automatically get the version information (requires that +# alchemtest is installed) +# We always display the full release string; if something else is +# desired, see the commented out code + +from alchemtest._version import get_versions +release = get_versions()['version'] +del get_versions + +version = release +#version = release.split("+")[0] # only major.minor.patch +#version = "."join(release.split(".")[:2]) # only major.minor # The language for content autogenerated by Sphinx. Refer to documentation # for a list of supported languages. diff --git a/docs/index.rst b/docs/index.rst index f5902ed..516ae34 100644 --- a/docs/index.rst +++ b/docs/index.rst @@ -6,6 +6,8 @@ alchemtest: the simple alchemistry test set =========================================== +|doi| + **alchemtest** is a collection of test datasets for alchemical free energy calculations. The datasets come from a variety of software packages, primarily molecular dynamics engines, and are used as the test set for `alchemlyb`_. The @@ -23,6 +25,10 @@ suite it may contain bugs. Please raise any issues or questions in the `Issue Tracker`_. `Contributions of data sets`_ and code in the form of pull requests are very welcome. +.. |doi| image:: https://zenodo.org/badge/83470847.svg + :alt: Zenodo DOI + :scale: 100% + :target: https://zenodo.org/badge/latestdoi/83470847 .. _`alchemlyb`: https://github.com/alchemistry/alchemlyb .. _`open license`: diff --git a/src/alchemtest/namd/access.py b/src/alchemtest/namd/access.py index 72f4c3f..cb1b921 100644 --- a/src/alchemtest/namd/access.py +++ b/src/alchemtest/namd/access.py @@ -21,8 +21,8 @@ def load_tyr2ala(): """ module_path = dirname(__file__) - data = {'forward': glob(join(module_path, 'tyr2ala/in-aqua/forward/*.fepout')), - 'backward': glob(join(module_path, 'tyr2ala/in-aqua/backward/*.fepout'))} + data = {'forward': glob(join(module_path, 'tyr2ala/in-aqua/forward/*.fepout.bz2')), + 'backward': glob(join(module_path, 'tyr2ala/in-aqua/backward/*.fepout.bz2'))} with open(join(module_path, 'tyr2ala', 'descr.rst')) as rst_file: fdescr = rst_file.read() diff --git a/src/alchemtest/namd/tyr2ala/descr.rst b/src/alchemtest/namd/tyr2ala/descr.rst index 0996e68..960744f 100644 --- a/src/alchemtest/namd/tyr2ala/descr.rst +++ b/src/alchemtest/namd/tyr2ala/descr.rst @@ -24,5 +24,6 @@ Data Set Characteristics: :License: `CC0 `_ Public Domain Dedication -This dataset was generated using the `NAMD `_ -molecular dynamics engine. +This dataset was generated using the `NAMD +`_ molecular dynamics +engine.