niprov: February 2015

819d4f8 Bumped version to 0.1 80034fa [doc] Docstring for discovery. 610cf4b Discovery now ignores known files (and tells the listener about them). 232670e Storage test will no longer write to production database, but to temporary files. 300ddd2 Log() will only attempt to copy fields from the parent's provenance that are available. 594908a Log() now complains if it doesn't know the primary parent. 5683249 Record() now passes the args and kwargs for python operations to log() as custom provenance fields. 23444bd Record() now obtains the code file location, and log() accepts the it as 'script' parameter. ab16ef3 log() and record() now accept both a single string or a list of strings for the new and parent files. 6d10e30 Record() now passes None values for unavailable args to log(). 3f37d40 Tentative support for record() on python code. d6067cf Record() now also works on a single string instead of a list. ad9cd7e Log() raises IOError if the new file doesn't exist. 782428b Report() now warns when the file is not found. 0638c63 Record() will inform about the way it interprets the code. 508c8a8 Implemented a Nifti file class which supports injecting an extension as a way to attach provenance. c035137 [doc] Transient field now in provenance fields table. 16a7766 New function 'add()' registers a file for reference. f31edc1 [doc] Fixed arg type in log() aa9831d New 'transient' argument to log() and record() indicates a temporary file. 3c49d1d Adapted README to new order of args for log(). dc35a92 Log() and record() now accept multiple parent files. The first file is assumed to be the primary. 9a11ed2 Changed the order of arguments to log() to emphasize the new file. d625bec Default location for the json file database is no in the user home directory. f182f74 New 'version' command prints niprov package version. 798abec Commandline version of log() now accepts --code argument. 72421e6 record() now accepts optional arguments to override the paths of the new and parent file. ad8759e Finished templates. 2cfab90 Further testing of the usage of the Mako templating interface by the HtmlExporter dc409f9 Revamping html reporting to use Mako templates. e1493fe Nifti test skeleton and comments. 7894dcf Filesystem wrapper can now create text files. Provenance attachment files ignored. ca63ad4 Implemented a simple method to attach() provenance to the BaseFile. 4f9485d [docs] Documented fields supported for .fif files and listed mne as an optional dependency. 22bf7da Raw MEG .fif files now supported. 699e12e Refactored; files are now represented by a hierarchy of objects, specifically able to deal with a certain file and data type. d95f13e [docs] Link to pdf in README 940e355 [docs] Added new classes to index. 095302c Each type of file for which provenance is handled will be represented by it's own class. An object of the right class is created by a call to the cf5b26e [docs] Fixed bug in fields table. c836265 Renamed 'ancestor' field to 'parent'. 5c4d58e Documentation of individual provenance attributes. 75abc07 Documentation now has a table with provenance attributes/fields. d6af9c3 File hash added to provenance during inspection. b2c49c6 Added a 'created' field which reflects the timestamp of the file. 7014f88 File size now in provenance b2339c2 [docs] Added niprov.hashing to the module index a428642 Merge branch 'master' of github.com:ilogue/niprov ea68ad7 Implemented file content hashing to be able to uniquely identify files. 1631d73 Updated the list of scripts. 8f92bd4 Made selected variables private so as not to show up in docs. 764d6dd Two new provenance fields: code and logtext. Both are extracted by record(). Html export now possible for the provenance of a single image file. abaa036 Commandline interface changed; all 'sub' commands are now preceded by 'provenance'. Record() became a valid subcommand. 6eba5c4 Introduced new 'recording' functionality; run a command and extract provenance from it. 32083ef Updated docs after changing record() to log() 9e89e23 Renamed record() to log() since record() in the future will refer to logging while executing a transformation b140d99 Adapted html test to source formatting with newlines 002f3a7 Improved html markup 12380ac Added path to html output 629f98c Added code highlighting to readme. d6aa702 Small fix in Readme f519a4e Documented new record() functionality. 27df817 [docs] Documented JsonFile.knowsByPath() 70dc8d5 Created a commandline executable for recording transformations. 4f8f608 Provenance for new files record()ed now inherit fields from ancestor. c3bf648 Now saving recorded transformations. ac6e411 [docs] Added documentation template for record(). eab6063 Added a record() function which will compile provenance for a new image created from an existing image 35c337b Reporting of single item or all items for subject c6e36ab Saving file location along with provenance d7deb8b Added html header and formatting to the html output 77e5077 Fixed error in docs 8b6be6d Revamped storage, now using serializer class, and adding records one by one. 992c1e2 Minor improvement of inline docs for JsonSerializer 239d0ce [docs] New documentation for JsonSerializer aeb9b86 Improved serializer 85040e8 Implemented a JsonSerializer 610d8fc Added docs entry for Externals. 5e5a7e4 Added a utility that wraps standard library subprocesses. a895ff1 Html exporter enabled and opens html in firefox. dd711fa Html class now writes each item out as a list item. 13b30ae Added two custom pages to documentation. Improved table of contents. 355fbab Added sphinx to requirements to get readthedocs to use the napoleon sphinx extension b216918 Switched to 'sphinxcontrib.napoleon'as readthedocs uses Sphinx 1.2 5e6425c Fixed documentation, apidoc now stores files in docs/source instead of docs/source/_templates. Index contains links to modules. 8ba05ac Switched to google-style docstrings. These are parsed by sphinx.ext.napoleon 3f16182 Documented Filefilter.include() 4bfa6b4 Added into line to documentation home page. 98ed896 Made sure that creating a Filefilter object does not raise an exception if filter file is not available. This happens e.g. on readthedocs.org bd289d7 Automated API documentation and documentation README file added 09010bd Started on the html exporter cb43643 Linked to pypi in README.md 218378a Release 0.0 configured and uploaded to pypi. 98917e3 Added Zenodo DOI badge