Ecosyste.ms: Issues

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GitHub / bskinn/h5cube issues and pull requests

#85 - Could mmap accelerate the CUBE read/write?

Issue - State: open - Opened by bskinn over 4 years ago
Labels: enhancement, question

#84 - ID and set up 3rd-party tool to sanity-check CUBE contents

Issue - State: open - Opened by bskinn about 5 years ago
Labels: needs tests, investigate

#83 - Remove 'module not executable' blocks

Issue - State: open - Opened by bskinn almost 6 years ago
Labels: administrative

#82 - Consider handling entire data block load in numpy, for speed

Issue - State: open - Opened by bskinn over 6 years ago
Labels: enhancement, maybe, performance

#81 - Implement "quick" pre-check of CUBE file contents for faster rejection at cmdline

Issue - State: open - Opened by bskinn about 7 years ago
Labels: enhancement, performance

#80 - Bump sphinx &c. versions and eliminate sphinxcontrib-napoleon

Issue - State: open - Opened by bskinn over 7 years ago
Labels: doc, administrative

#79 - Consider Cython as a means to accelerate exponential format conversion from the strings

Issue - State: open - Opened by bskinn over 7 years ago
Labels: enhancement, maybe, performance

#78 - To-string conversions for CUBE writing could be faster with printf-style formatting

Issue - State: open - Opened by bskinn over 7 years ago - 1 comment
Labels: enhancement, performance

#77 - Add import-time checks for h5py, numpy presence

Issue - State: open - Opened by bskinn over 7 years ago
Labels: todo

#76 - Convert CHANGELOG to .md; update format/content

Issue - State: open - Opened by bskinn over 7 years ago
Labels: administrative

#75 - Implement interface for setting/retrieving metadata

Issue - State: open - Opened by bskinn over 7 years ago
Labels: future, cmdline, api

#74 - Enable modification of single datasets stored in an h5cube

Issue - State: open - Opened by bskinn over 7 years ago
Labels: maybe, future, cmdline, api

#73 - Explicitly detect and enforce a prohibition on zero values of {NATOMS} and [NATOMS]

Issue - State: open - Opened by bskinn almost 8 years ago
Labels: bug, todo

#72 - Update file description in h5cube.py

Issue - State: open - Opened by bskinn almost 8 years ago
Labels: cleanup

#71 - Fix comment with wrong nAXIS information

Issue - State: open - Opened by bskinn almost 8 years ago
Labels: cleanup

#70 - Add copyright statement and LICENSE link to README

Issue - State: open - Opened by bskinn almost 8 years ago
Labels: administrative

#69 - Convert h5cube.py into a proper subdivided package

Issue - State: open - Opened by bskinn almost 8 years ago
Labels: refactor, todo

#68 - Add h5cube file specification version number information into cmdline help in some fashion

Issue - State: open - Opened by bskinn almost 8 years ago
Labels: administrative, cmdline

#67 - Add options in cmdline and API to allow writing to specific version of h5cube spec

Issue - State: open - Opened by bskinn almost 8 years ago
Labels: maybe, cmdline, api

#66 - Change to strict cmdline matching

Issue - State: open - Opened by bskinn about 8 years ago
Labels: todo, administrative, future, cmdline

#65 - Add Python 3.6 to tox

Issue - State: open - Opened by bskinn about 8 years ago
Labels: needs tests, administrative

#64 - CUBE interpolation

Issue - State: open - Opened by bskinn about 8 years ago
Labels: enhancement, maybe

#63 - Invalid command line inputs need to be caught and exec halted right away

Issue - State: open - Opened by bskinn about 8 years ago
Labels: performance, cmdline

#62 - API call to h5_to_cube with nonexistent file is not trapped

Issue - State: open - Opened by bskinn about 8 years ago
Labels: bug

#61 - Decompression to CUBE is slow

Issue - State: open - Opened by bskinn about 8 years ago - 1 comment
Labels: performance

#60 - Add version display to help menu.

Issue - State: open - Opened by bskinn about 8 years ago
Labels: administrative, cmdline

#59 - Utility to extract orbital dataset(s) from a file

Issue - State: open - Opened by bskinn about 8 years ago
Labels: maybe, future

#58 - Split command line parsing into multiple sub-parsers

Issue - State: open - Opened by bskinn about 8 years ago
Labels: maybe, future, cmdline

#57 - h5cube validity checking against specification

Issue - State: open - Opened by bskinn about 8 years ago
Labels: todo

#56 - Interpolated deskewing of non-orthogonal CUBEs

Issue - State: open - Opened by bskinn over 8 years ago
Labels: enhancement, maybe

#55 - Support for nonscalar / multi-quantity CUBE fields?

Issue - State: open - Opened by bskinn over 8 years ago - 1 comment
Labels: todo

#54 - Add option for adjusting number of digits in the exponent on decompression

Issue - State: open - Opened by bskinn over 8 years ago
Labels: enhancement, maybe

#53 - Benchmark compression factors against gzip and bzip2

Issue - State: open - Opened by bskinn over 8 years ago
Labels: doc

#52 - Create profiling suite and document

Issue - State: open - Opened by bskinn over 8 years ago
Labels: doc, todo

#51 - Correct thresholding behavior of zero values

Issue - State: closed - Opened by bskinn over 8 years ago - 1 comment
Labels: bug

#50 - Optional status text/bar during (de)compression

Issue - State: open - Opened by bskinn over 8 years ago
Labels: enhancement, future

#49 - Rich, granular error handling within cube_to_h5 and h5_to_cube

Issue - State: open - Opened by bskinn over 8 years ago
Labels: enhancement, maybe, future

#48 - Chunk-wise serialization of decompression (and defined chunk sizing)

Issue - State: closed - Opened by bskinn over 8 years ago - 1 comment
Labels: enhancement, wontfix

#47 - Very large number of orbitals in a MO cube --> multi-line MO index listing

Issue - State: closed - Opened by bskinn over 8 years ago - 1 comment
Labels: bug

#46 - Inconsistent compressed filesize for multi-orbital files?

Issue - State: closed - Opened by bskinn over 8 years ago - 1 comment
Labels: bug

#45 - Implement serialized read of CUBE files

Issue - State: closed - Opened by bskinn over 8 years ago - 1 comment
Labels: enhancement, wontfix

#44 - For orbital data files, make the dataset always print substantially in six-element rows

Issue - State: closed - Opened by bskinn over 8 years ago - 1 comment
Labels: todo

#43 - Need to test proper handling of negative signs on axes/grid dimensions

Issue - State: closed - Opened by bskinn over 8 years ago - 1 comment
Labels: needs tests

#42 - Auxiliary functionality for merging orbital CUBEs

Issue - State: open - Opened by bskinn over 8 years ago - 1 comment
Labels: enhancement, maybe

#41 - Writeup of the CUBE format as understood by h5cube

Issue - State: closed - Opened by bskinn over 8 years ago - 4 comments
Labels: doc

#40 - Number of atoms can be negative to indicate various things

Issue - State: closed - Opened by bskinn over 8 years ago - 1 comment
Labels: bug

#39 - Number of voxels can be negative to indicate Angstrom units

Issue - State: closed - Opened by bskinn over 8 years ago - 1 comment
Labels: bug

#38 - Ensure axes aren't being stored wrong

Issue - State: closed - Opened by bskinn over 8 years ago - 1 comment
Labels: bug, maybe

#37 - Change main so that it is the only place that returns an exit value

Issue - State: closed - Opened by bskinn over 8 years ago - 1 comment
Labels: refactor

#36 - Store compression option values in the h5cube file format

Issue - State: open - Opened by bskinn over 8 years ago
Labels: todo

#35 - Expand data &c. checking in h5_to_cube to handle other applications writing to .h5cube

Issue - State: open - Opened by bskinn over 8 years ago
Labels: needs tests, todo

#34 - Convert the _validate functions to boolean returns and refactor/reimplement their use

Issue - State: closed - Opened by bskinn over 8 years ago - 2 comments
Labels: needs tests, refactor

#33 - Investigate parallelization

Issue - State: open - Opened by bskinn over 8 years ago
Labels: maybe, future

#32 - Add bug reporting/feature request blurb to commandline help display

Issue - State: closed - Opened by bskinn over 8 years ago - 1 comment
Labels: administrative

#31 - Single-sided thresholding

Issue - State: open - Opened by bskinn over 8 years ago
Labels: enhancement, maybe

#30 - Add special handling of zero data values

Issue - State: closed - Opened by bskinn over 8 years ago - 2 comments
Labels: bug

#29 - Examine gains from making the signs dataset integer-typed, and scale-offset compressed

Issue - State: closed - Opened by bskinn over 8 years ago - 1 comment
Labels: todo

#28 - Evaluation of compression/speed tradeoff of the gzip compression level

Issue - State: open - Opened by bskinn over 8 years ago
Labels: doc

#26 - Add link to h5py doc page to README

Issue - State: closed - Opened by bskinn over 8 years ago - 1 comment
Labels: administrative

#25 - Exception handling around OS interactions

Issue - State: open - Opened by bskinn over 8 years ago
Labels: todo

#24 - Demonstration of the effects of thresholding on volumetric integration

Issue - State: open - Opened by bskinn over 8 years ago
Labels: doc

#23 - Fix thresholding cmdline args - behavior not accurate

Issue - State: closed - Opened by bskinn over 8 years ago
Labels: bug

#22 - Study of error dependence of threshold values

Issue - State: closed - Opened by bskinn over 8 years ago - 1 comment
Labels: doc

#21 - Add zero threshold option

Issue - State: closed - Opened by bskinn over 8 years ago - 1 comment
Labels: enhancement

#20 - Fully serialize the decompression operation

Issue - State: closed - Opened by bskinn over 8 years ago - 1 comment
Labels: enhancement, wontfix

#19 - Instead of just from-file CUBE input, allow streaming or string or etc. input

Issue - State: open - Opened by bskinn over 8 years ago
Labels: enhancement, refactor, maybe

#18 - Instead of just to-file CUBE output, allow streaming or string or etc. output

Issue - State: open - Opened by bskinn over 8 years ago
Labels: enhancement, refactor, maybe

#17 - Search .cube for its data precision to use as default truncation

Issue - State: open - Opened by bskinn over 8 years ago
Labels: enhancement, maybe

#16 - Set up tox runner

Issue - State: closed - Opened by bskinn over 8 years ago - 1 comment
Labels: needs tests

#15 - Create test suite

Issue - State: closed - Opened by bskinn over 8 years ago - 1 comment
Labels: needs tests, in progress

#14 - Docstrings

Issue - State: open - Opened by bskinn over 8 years ago
Labels: doc

#13 - Add & configure setup.py

Issue - State: closed - Opened by bskinn over 8 years ago - 1 comment
Labels: todo

#12 - Cull addition of extra leading zero in the exponents of the data block

Issue - State: closed - Opened by bskinn over 8 years ago - 1 comment
Labels: todo

#11 - Increase file extension flexibility

Issue - State: closed - Opened by bskinn over 8 years ago - 1 comment
Labels: todo

#10 - Reference various writeups of CUBE format

Issue - State: open - Opened by bskinn over 8 years ago
Labels: doc

#9 - Change clobber default to noclobber; cmdline option for clobber?

Issue - State: open - Opened by bskinn over 8 years ago - 1 comment
Labels: enhancement, maybe

#8 - Neaten the help 'choices' display for the numerical arguments

Issue - State: closed - Opened by bskinn over 8 years ago - 1 comment
Labels: refactor

#7 - Refactor into proper package to allow programmatic access to the conversion functions

Issue - State: closed - Opened by bskinn over 8 years ago - 2 comments
Labels: refactor, todo

#5 - Initial README.md and README.rst

Issue - State: closed - Opened by bskinn over 8 years ago - 2 comments
Labels: administrative

#4 - Implement max/min data value thresholding for enhanced compression

Issue - State: closed - Opened by bskinn over 8 years ago - 1 comment
Labels: enhancement

#3 - Implement parsing/processing of multiple filenames on the commandline

Issue - State: open - Opened by bskinn over 8 years ago
Labels: enhancement, maybe, cmdline

#2 - Allow user-specified (de)compression on the command line, regardless of file extension

Issue - State: open - Opened by bskinn over 8 years ago
Labels: enhancement, maybe, cmdline

#1 - Restructure data block iteration to avoid materialization

Issue - State: closed - Opened by bskinn over 8 years ago - 1 comment
Labels: refactor, todo