General + Implement tests for all modules and functions. + Update all situations to use 'filter' instead of 'positive'/'nonzero' + More tests. For plotting stuff, add tests just to make sure nothing breaks. + Setup automatic testing (e.g. nightly?)
astro/ + Separate GW stuff into its own submodule
math/ + math_core.py
around + Does this work correctly for negative decimal values?? + Implement 'dir' relative to zero --- i.e. round up/down the absolute values.
spacing + Add endpoint keyword argument to decide whether end-point(s) are included
in returned range.
str_array_2d() - Finish this method and then incorporate into str_array()
interp_func() - Finish developing function.
numeric.py - monotonic_smooth
- BUG: fix shitty edge effects after many iterations.
statistic.py - percentiles()
- BUG: method failed when multidimensional arrays were used. Now it flattens the data before calculation.
- random_power() - BUG: negative extrema values break
pdf_index=-1plot/ + Hist2D.py
- Add ability to plot central axes as scatter plot, with projected histograms (instead of just the central 2D histogram).
- plot_core.py - Finish 'set_ticks' method.
'astro/' - 'gws.py'
- gw_hardening_timescale() [NEW-FUNCTION]
'astro/' - astro_core.py
- binary_circular_vels() [NEW-FUNCTION]
- inclinations_uniform() <== uniform_inclinations() [DEPRECATION]
- Convert args to arrays as needed in eddington_luminosity() and schwarzschild_radius()
'obs.py' - mag_to_flux_zero() [NEW-FUNCTION]
- Calculate flux based on magnitude and given zero-point in Jansky
'math/' - reordered functions by broad-category (API, utils, deprecated), and alphabetically. - math_core.py
- around() - Enabled for array values. - Deprecate argument sigfigs [bool] <== scale [str] - Use decimals argument to correctly refer to number of significant figures (when using sigfigs=True)
- around_str() [NEW-FUNCTION] - Perform rounding and also format as appropriate type of string value
- frexp10() - Handle the case of 0.0 values. Set mantissa to 0.0 and exp to np.nan.
- midpoints() - Allow sequences to be given to specify multiple axes. Also axis=None means midpoints along all axes. - Separated core functionality to new _midpoints_1d() function.
- minmax() - Add fraction argument to set one extrema to a fraction of the other.
- rescale() [NEW-FUNCTION] - Rescale given array range to new span.
- slice_for_axis() <=== sliceForAxis [DEPRECATION]
- spacing() - When creating 'intergers' spacings, allow integers to be subdivided some number of times, specified by an integer value to the intergers argument.
'plot/' - 'plot_core.py'
- color_lightness() [NEW-FUNCTION] - Adjust the lightness (in HLS sense) of the given color.
- scientific_notation() - BUG: fix boolean logic for determining when to include exponent and mantissa
- smap() - New default cmap is 'Spectral'
- unify_axes_limits() <== unifyAxesLimits() [DEPRECATION]
Moved notebooks from inside internal zcode/ to root directory.
notebooks/ - math_numeric.ipynb [NEW-FILE]
- New notebook for testing math/numeric.py functions.
- Added tests for regress().
constants.py - SIGMA_TO_FWHM [NEW-VARIABLE]
- Converting from (normal-)standard deviation to full-width at half-maximum (FWHM)
- inout/
- inout_core.py
- backup_existing() [NEW-METHOD] - If the given filename already exists, move it to a backup file.
- notebooks.py [NEW-FILE]
- Methods specifically for jupyter notebooks
- math/
- interpolate.py [NEW-FILE]
- New submodule for interpolation and extrapolation.
- interp_axis [NEW-FUNCTION]
- Method to perform fast, array-based linear interpolation of ndarrays over a single axis.
- Added unittests.
- math_core.py
- interp() [MOVED TO interpolate.py]
- interp_func() [MOVED TO interpolate.py]
- isnumeric() [NEW-FUNCTION]
- Check if a value is a numeric scalar.
- str_array()
- BUG: Flatten multi-dimensional arrays before processing.
- within()
- Allow two elements to be given where a None value for either of them means infinity in that direction.
- BUG: TEMPORARY: raise error if extrema bounds are non-increasing. Not sure how this should be handled in the future. This could be used as shorthand to do the inverse (i.e. look for things outside of bounds)? Or should the extrema just be sorted within the function?
- numeric.py
- cumtrapz_loglog()
- BUG: when power-law index is near -1, integral should be nat-log
- regress() [NEW-FUNCTION]
- Perform linear regression on ND data.
- Tests added to math_numeric.ipynb.
- rk4_step()
- Allow additional args to be passed to integration function.
- statistic.py
- percentiles() [DEPRECATED ==> quantiles()]
- quantiles() [<== percentiles()]
- BUG: error in multidimensional arrays when axis=0.
- random_power()
- Allow power-law index to be array valued.
- LH_Sampler [NEW-CLASS]
- Latin Hypercube Sampler class
- plot/
- draw.py
- plot_contiguous()
- Add a scatter argument to plot the NON-contiguous elements as scatter points.
- plot_segmented_line()
- Pass all additional kwargs to LineCollection constructor.
- Improve color handling.
- Hist2D.py
- draw_hist2d()
- Removed edges from pcolor
- Allow log argument for normalization of pcolor.
- plot_core.py
- figax()
- BUG: fix error when grid value was False.
- smap() <=== colormap() [DEPRECATION]
- utils.py
- dep_warn_var() [NEW-METHOD]
- Standardized method for handling deprecated variables.
- astro/
- astro_core.py
- eddington_accretion()
- BUG: 'epsilon' (radiative efficiency) factor was being double counted in accretion calculation, as it was also being used in the luminosity.
- orbital_velocities() [NEW-METHOD]
- Orbital velocity of both objects given mtot and mrat.
- rad_hill [NEW-METHOD]
- Hill radius equation from Murray & Dermott
- rad_isco_spin() [NEW-FUNCTION]
- Return the radius of the ISCO for a BH with the given spin.
- rad_roche [NEW-METHOD]
- Average roche-lobe radius from Eggleton-1983
- uniform_inclinations() [NEW-FUNCTION]
- New function to draw random, uniform inclination angles.
- obs.py
- Added SDSS AB ugriz magnitude to conversion tables.
- fnu_to_flambda() & flambda_to_fnu() [NEW-FUNCTION]
- Functions to convert spectral flux from wavelength to frequency and visa-versa.
- lum_to_abs_mag()
- BUG: standard distance is 10 pc
- inout/
- stats_str() ==> moved to math.statistic.stats_str()
- inout_core.py
- unzip() [NEW-METHOD]
- Function to extract an inner-iterable from an outer-iterable; analogous to the transpose of a 2D numpy-array.
- math/
- tests/
- test_math_core.py
- Fixed numerous tests.
- Added new tests for interpolation methods.
- Tests for edges_from_cents
- Tests for broadcast
- test_statistic.py
- New test for percentiles.
- math_core.py
- argfirst() [NEW-FUNCTION]
- Return the index of the first true element of the given array.
- argfirstlast() [NEW-FUNCTION]
- Return the indices of the first and last true elements of the given array.
- arglast() [NEW-FUNCTION]
- Return the index of the last true element of the given array.
- array_str() [NEW-FUNCTION]
- Alias of str_array()
- broadcast() [NEW-FUNCTION]
- Expand N, 1D arrays into N, ND arrays each with the same shape.
- Scalars do not contribute dimensions.
- Unit tests added.
- broadcastable() [NEW-FUNCTION]
- Method to expand N, 1D arrays into N, ND arrays which can be broadcasted together.
- edges_from_cents() [NEW-FUNCTION]
- Method to estimate bin-edges given the local of bin-centers.
- interp()
- BUG: fix issue where 'left' and 'right' bounds were being taken to ten-to-the-power-of.
- interp_func()
- Implement optional 'xlog' and 'ylog' scalings.
- Implement 'mono' option for interpolation kind to use PchipInterpolator which enforced monotonicity.
- minmax()
- BUG: Jagged input arrays would fail in comparison_filter. FIX: pre-flatten input data.
- roll() [NEW-FUNCTION]
- Roll an array along a target axis by varying amounts for each index.
- rotation_matrix_about() [NEW-FUNCTION]
- Construct a rotation matrix about the given axis (vector) by the given angle.
- rpt_to_xyz() [NEW-FUNCTION]
- Convert from spherical to cartesian coordinates.
- rtp_to_xyz() [NEW-FUNCTION]
- Convert from spherical to cartesian coordinates (uses rpt_to_xyz())
- spacing()
- Pass along endpoint argument to numpy functions
- spacing_composite() [NEW-FUNCTION]
- New function to create composite (stacked) spacings with different ranges.
- str_array_neighbors() [NEW-FUNCTION]
- Use 'str_array' to print particular indices, and its neighbors, in an array.
- within()
- Add new close argument to allow np.isclose comparisons to bin edges.
- xyz_to_rpt() [NEW-FUNCTION]
- Convert from cartesian to spherical coordinates.
- xyz_to_rtp() [NEW-FUNCTION]
- Convert from spherical to cartesian coordinates (uses xyz_to_rpt())
- zenumerate() <== zenum() [DEPRECATION]
- _guess_str_format_from_range()
- BUG: fix issue where exponential notation was only being used for positive-definite values
- numeric.py
- cumtrapz_loglog()
- Previous version of this function used an algorithm found online. New version uses a similar algorithm -- which is basically the trapezoid rule in log-log space (i.e. for power-laws) -- with some minor improvements and niceties.
- kde() [DEPRECATED]
- Use new functionality from kde.py
- kde_hist() [DEPRECATED]
- Use new functionality from kde.py
- rk4_step() [NEW-FUNCTION]
- Take a Fourth-order Runge-Kutta step.
- Adapt time-step size to avoid nan-values.
- statistic.py
- confidenceBands() [DELETED-METHOD]
- confidence_intervals()
- percs <== confInts [DEPRECATION-VARIABLE]
- confidenceIntervals() [DELETED-METHOD]
- confidence_intervals()
- New argument sigma which is converted into percentiles
- New argument weights for performing weighted percentiles
- mean() [NEW-METHOD]
- Method for calculating distribution mean, optionally with weights.
- percentiles()
- New argument, sigmas which is used to calculate percentiles from sigma values.
- percs <== ci [DEPRECATION-VARIABLE]
- percs_from_sigma() <== sigma() [DEPRECATION]
- random_power() [NEW-FUNCTION]
- Draw random numbers from a power-law PDF, allows negative indices unlike numpy.
- stats_str() <=== moved from inout_core.stats_str()
- New argument label which determines whether the percentiles are listed.
- std() [NEW-METHOD]
- Method for calculating distribution standard-deviations, optionally with weights.
- plot/
- draw.py
- plot_carpet() [NEW-METHOD]
- New method for drawing carpet-plots (i.e. tick marks)
- Hist2D.py
- draw_hist2d() [NEW-METHOD]
- New 2D histogram plotting method from corner.hist2d method by 'Dan Foreman-Mackey'.
- corner() [NEW-METHOD]
- New corner plotting method.
- plot_const.py [FILE-DELETED]
- Constant values moved to zcode.plot.__init__.py
- plot_core.py
- colormap()
- New midpoint argument and functionality to allow colormaps's colors to be centered at particular values in either log or linear space. Uses new classes MidpointNormalize and MidpointLogNormalize.
- draw_colorbar_contours() [NEW-FUNCTION]
- Add contour marks on the given colorbar.
- figax()
- New scale argument to set the scale of both x and y axes.
- Default to grid on.
- Pass along kwargs to plt.subplots.
- BUG: xlim and ylim were not being broadcast correctly
- get_norm() [NEW-METHOD]
- Separated out from colormap(), same functionality.
astro/ - astro_core.py
- distance() [NEW-FUNCTION] - Calculate the cartesian distance between vectors
- kepler_vel_from_freq() [NEW-FUNCTION] - Calculate keplerian velocity from frequency
- mtmr_from_m1m2() [NEW-FUNCTION] - Convert from primary and secondary masses to total-mass and mass-ratio
inout/ - inout_core.py
- count_lines <== countLines [DEPRECATION]
- BUG: lists of files were being screwed up somehow
- frac_str [NEW-FUNCTION] - New function to nicely format a string of the form '{}/{} = {}' given a numerator and denominator. Chooses appropriate formatting given the values.
log.py - Have log to stream go to stdout (instead of stderr) by default. - get_logger()
- Setup StreamHandler to log to stdout instead of stderr by default.
plot/ - draw.py
- draw_hist_bars() - Update to allow for horizontal or vertical plotting. - [BUG]: Single confidence-interval cause error with shape of returned values.
- plot_conf_fill() - [BUG]: bad function call using filter. - [BUG]: filter/floor/ceil parameters were not correctly selecting elements. Improved using masked arrays.
- plot_segmented_line() - Utilize colormap() method
layout.py - extent() [NEW-FUNCTION]
- Function for calculating the extent of an object. Currently only axes work.
plot_core.py - [BUG]: _LINE_STYLE_SET did not match new linestyle format for matplotlib - colormap()
- First argument args is now optional, defaults to [0.0, 1.0]
- figax() [NEW-FUNCTION] - New method for conveniently creating and adjusting plots using plt.subplots()
- invert_color() [NEW-FUNCTION] - Invert the given named or RGB(A) color.
- legend() - New argument 'prev' for previous artists (i.e. legends) to be readded to axis after creating new legend.
- set_axis() - Catch 'fs' keyword-argument and replace with 'labelsize'
- text() - Do not set default fontsize fs
math/ - math_core.py
- argnearest()
- Add side argument to select if a particular side should be chosen, otherwise find the nearest on either side (default and previous behavior). Tests Added.
comparison_filter() - Use numpy masked arrays, instead of flattening multi-dimensional arrays.
midpoints() - Add option to use a scale argument instead of log boolean
- minmax()
- Allow (2,) values to be given for stretch and log_stretch to apply to left and right sides respectively.
rotation_matrix_between_vectors() [NEW-FUNCTION] - Function that uses Rodriguez' formula to create a rotation matrix that will rotate one vector to another.
slice_with_inds_for_axis() [NEW-FUNCTION] - Slice an N-dimensional array using an N-1 dimensional array, with indices for the remaining axis.
spacing() - New agument dex to set the number of points per decade when using log spacing.
str_array() - Guess default format based on array values (use _guess_str_format_from_range)
- zenum() [NEW-FUNCTION]
- Method to perform enumerate(zip(*args))
_guess_str_format_from_range() [NEW-FUNCTION] - Based on the dynamical (logarithmic) range of an array, guess the appropriate string formatting (i.e. 'f' vs 'e')
numeric.py - kde() [NEW-FUNCTION]
- Construct a custom KDE object, optionally in log-space.
- kde_hist() [NEW-FUNCTION] - Construct a KDE "histogram" resampling from the KDE distribution.
statistic.py - confidence_intervals()
- Implement a kludge to allow percentile calculation with masked arrays.
- percentiles() - BUG: when integer values were being used, percentiles were converted to [0, 1].
constants.py - Added electron-charge QELC - Added Jansky unit JY
astro/ [NEW-SUBMODULE] - New submodule for astrophysics specific functions and relations. - astro_core.py [NEW-FILE]
- chirp_mass [NEW-FUNCTION]
- dynamical_time [NEW-FUNCTION]
- eddington_accretion [NEW-FUNCTION]
- eddington_luminosity [NEW-FUNCTION]
- gw_hardening_rate_dadt [NEW-FUNCTION] - GW hardening rate (da/dt) function.
- gw_strain_source_circ [NEW-FUNCTION] - GW Strain from a single source in a circular orbit.
- kepler_freq_from_sep [NEW-FUNCTION]
- kepler_sep_from_freq [NEW-FUNCTION]
- m1m2_from_mtmr() [NEW-FUNCTION] - Convert from total-mass and mass-ratio to primary and secondary binary masses.
- rad_isco() [NEW-FUNCTION] - Calculate the inner-most stable circular-orbit.
- schwarzschild_radius [NEW-FUNCTION]
- sep_to_merge_in_time() [NEW-FUNCTION] - Limiting binary separation to merge by GW in a given time.
- time_to_merge_at_sep() [NEW-FUNCTION] - Time it will take for a binary to merger form GW from the given separation.
scalings.py [NEW-FILE] - New submodule for common astrophysical scaling relations. - mbh_sigma()
- From a stellar-bulge velocity dispersion, get the MBH mass
- mbh_sigma_inv() - From an MBH mass, get the stellar-bulge velocity dispersion
obs.py [NEW-FILE] - New submodule for observational calculations (especially magnititudes). - ABmag_to_flux() [NEW-FUNCTION] - mag_to_flux() [NEW-FUNCTION] - flux_to_mag() [NEW-FUNCTION] - abs_mag_to_lum() [NEW-FUNCTION] - lum_to_abs_mag() [NEW-FUNCTION]
inout/ - inout_core.py
- BUG: some print statements were lying around causing issues with checking files.
- environment_is_jupyter() [NEW-FUNCTION] - Return 'True' if the current environment is a jupyter notebook.
- python_environment() [NEW-FUNCTION] - Determine the current python environment (e.g. 'jupyter') and return string.
math/ + math_core.py
- argnearest - Add assume_sorted option so that method can handle either sorted or unsorted. - Check if input is scalar, if so return scalar output (instead of list).
- interp_func() [NEW-FUNCTION] - Started version of interp that will return an interpolating method. Needs lots of work.
- spacing - Added kwargs arguments which are passed on to minmax function. Allows for (e.g.) log_stretch to be used to expand the spacing.
- str_array_2d [NEW-FUNCTION] - Support printing 2D arrays... not finished but basic functionality working.
statistic.py - log_normal_base_10 [NEW-FUNCTION]
- Method to draw from a log-normal distribution with given base-ten variance.
- Added 'shift' parameter to shift the center of the distribution some amount (in dex).
- sigma() - BUG: scipy.stats wasnt being imported
- stats_str() - Improve default formatting choice based on extrema of input values.
plot/ - draw.py
- conf_fill() [NEW-FUNCTION] - Method combining math.confidence_intervals and draw.plot_conf_fill.
- plot_bg() [NEW-FUNCTION] - Method to plot a line and a broader background-line behind it.
Hist2D.py - plot2DHist()
- Fixed documentation to reflect all return parameters.
plot_core.py - colormap
- If there are no valid elements for a given colormap, set the extrema to [0.0, 0.0] instead of an error being raised.
- color_cycle() - [BUG] In recent matplotlib upgrade mpl.cm.spectral changed to mpl.cm.Spectral.
- legend() - [BUG] loc argument no longer overrides x and y.
- scientific_notation() - [BUG] Values could be rounded up to a higher exponent (i.e. 9.9e-5 ==> 10e-5 instead of 1e-4).
- set_axis() - [BUG] Raise error if additions kwargs are passed (they arent used) - [BUG] Error when color was None, set to black as default
- `text() - [BUG] Transform argument was getting lost in kwargs.
- _color_from_kwargs() - Add option to pop (remove) color argument from dictionary.
- _setAxis_scale() - [BUG] Update linthreshx and linthreshy arguments seem to be deprecated, at least when not using 'symlog' specifically.
inout/ - inout_core.py
- BUG: modify_exists and modify_filename would fail for directories (at least of certain name patterns. Introduced new internal method _path_fname_split and some minor tweaks to deal with this. Seems to be working.
- bytes_string <== bytesString [DEPRECATION]
log.py - Add option info_file to create a second log-file at the INFO level. - Added log method clear_files() to erase existing contents of log files. - log_memory [NEW-FUNCTION]
- Log the current memory usage (taken from mbh-mergers.constants code).
math/ - math_core.py
- minmax() - Improved how 'stretch' is handled, and added separate 'log_stretch' parameter to stretch in log-space (as apposed to linear). - Add parameter to convert types (can be issue when ints are passed in)
- interp() [NEW-FUNCTION] - Interpolation function which can deal with log-log.
numeric.py - Deprecating old smooth function, its not very good. - even_selection [NEW-FUNCTION]
- Given an array_like of size N, select M evenly spaced elements (or as nearly as possible).
- monotonic_smooth [NEW-FUNCTION] - Find locations of non-monotonicities and run the smooth_convolve method on them. Do this iteratively. - NOTE: causes some suboptimal edge-effects.
- smooth_convolve [NEW-FUNCTION] - New method (from scipy cookbook) for smoothing a 1D array with convolution.
- sample_inverse <== sampleInverse [DEPRECATION]
statistic.py - percentiles
- BUG: issue with data type incompatibilities between input data and the percentiles.
- BUG: fixed issue where peercentiles wouldn't work for int type data.
- confidence_bands - BUG: x-scaling parameter was not being passed to asBinEdges
- confidence_intervals - BUG: filter and axis arguments incompatbile with eachother. For now, added an explicite error message not to use them together. Added to to-do list (above).
- stats_str - Choose a default formatting based on whether log is set to True or not.
plot/ - Deprecated lots of old camel-case function names. - draw.py [NEW-FILE]
- New file for organizing methods for actually drawing stuff onto axes.
- Moved these methods from plot_core.py to here: - "plot_hist_line", "plot_segmented_line", "plot_scatter", "plot_hist_bars", "plot_conf_fill"
- New method plot_contiguous to plot line-sections with contigous points.
Hist2D.py - BUG: 'fs' parameter was not being used properly in plot2DHist(). - Improved usage of fs parameter to that None values do not alter defaults. - New options and settings for contours.
layout.py [NEW-FILE] - New file for containing methods relating to layout, spacing, etc. - Moved these methods from plot_core.py to here:
- "backdrop", "full_extent", "position_to_extent", "rect_for_inset", "transform"
plot_const.py [NEW-FILE] - New file for containing plotting constants previously in plot_core.py.
plot_core.py - Moved lots of methods to new files: draw.py, layout.py and constants to plot_const.py. - Added kwargs parameter to set_axis and twin_axis, set some additional default values for aesthetics. - label_line()
- Add rotation parameter and interpolation that can be log-spaced.
- line_style_set() - Added 'solid' argument to determine if solid lines are included in the set.
- text() - Upgrade the pad parameter to work for a single value or tuple, if the latter, the first applies to x and the second to y. - Change also applies to _loc_str_to_pars().
- _loc_str_to_pars() - See note in text().
tools/ [NEW-SUBMODULE] - singleton.py [NEW-FILE]
- Singleton - Singleton implementation using a decorator.
constants.py - Added derived constant EDDC, for the Eddington (Luminosity) constant, in units of erg/s/g. I.e. the Eddington luminosity for an object of mass M would be EDDC*M. - Added new physical constants. - Added ARCSEC arcsecond constant.
inout/ - inout_core.py
- check_path() <== checkPath [DEPRECATION]
- getFileSize() [DELETED] - Use get_file_size() instead.
- modify_exists() - If, for some reason, the new filename already exists, raise a warning and then bootstrap to modify the filename again. Previously the code would raise an error. - BUG: fix issue where special characters (e.g. +) were interfering with regex match.
- modify_filename() <== modifyFilename [DEPRECATION]
log.py - Add method after() to logger objects which report a message and duration for execution. - Add method frac() to logger objects which report a fraction. - Changed parameters for logging methods to use underscores instead of camel-case. - get_logger() <== getLogger [DEPRECATION] - default_logger() <== defaultLogger [DEPRECATION] - Added docstrings to after(), raise_error(), and copy() added-on methods. - IndentFormatter
- BUG: sometimes the initial depth of the stack is too high, resulting in a missing indent. In IndentFormatter.format(), reset the depth as needed.
plot/ - plot_core.py
- text() - Add a shift argument which allows for adjusting the (x,y) position of the text more dynamically.
- _loc_str_to_pars() - Check the location specifier for validity.
- set_grid() <== setGrid [DEPRECATION]
- set_lim() <== setLim [DEPRECATION]
- scientific_notation() <== strSciNot() [DEPRECATION] - Also change from precman and precexp to just man and exp.
- line_style_set() [new-function] - Retrieve a list of line-style specifications to be used with Line2D.set_dashes.
math/ - statistic.py
- stats_str - Re-enabled the label argument for backwards compatibility. If used, a warning is raised. But it works.
math_core.py - str_array()
- Changed the arguments to this function to use a single sides parameter which encodes information about both the beginning and end.
- Improved the function to properly handle the number of elements at the end, and what to do if the number of requested elements equals or exceeds the array length.
- Added tests to tests.test_math_core.TestMathCore.test_str_array().
- Added log argument, to convert input values to log10 first.
time.py [new-submodule] - New submodule for dealing with general time related functions.
- to_decimal_year() [new-function] - New function to convert from a datetime object (or string datetime specification) to a decimal year. - Added precision down to milliseconds.
- to_datetime [new-function] - Convert a general datetime specification into a datetime.datetime instance.
- to_str [new-function] - Convert a datetime specification into an arbitrarily formatted string representation (by way of a datetime instance).
tests/ - test_time.py [new-submodule]
- Unit tests for the new time.py submodule.
- So far, only rests for the time.to_datetime method.
requirements.txt [new-file] - Started to add requirements file, nearly empty at the moment.
inout/ + inout_core.py
- npzToDict + BUG: issue loading npz across python2-python3 transition. Attempt to resolve.
- str_format_dict [new-function] - New function to pretty-print a dictionary object into a string (uses json).
- getFileSize ==> get_file_size [deprecation] - Also improve behavior to accept single or list of filenames.
- getProgressBar [DELETED] - Should use tqdm functions instead.
- par_dir [new-function]
- !!NOTE: not sure if this is a good one... commented out for now!!
- Method which returns the parent directory of the given path.
- top_dir [new-function]
- Method which returns the top-most directory from the given path.
- underline [new-function]
- Append a newline to the given string with repeated characters (e.g. '-')
- warn_with_traceback [new-function] - Used to override builtin warnings.showwarning method, will include traceback information in warning report.
log.py - getLogger
- Attached a function to new logger instances which will both log an error and raise one. Just call log.raise_error(msg) on the returned log instance.
- Attached a function log.after(msg, beg) to report how long something took (automatically calculated).
math/ + math_core.py
- argnearest [new-function] + Find the arguments in one array closest to those in another.
- limit [new-function] + Limit the given value(s) to the given extrema.
- str_array <== strArray
statistic.py - confidence_intervals
- BUG: fixed issue where multidimensional array input was leading to incorrectly shaped output arrays.
- sigma + ENH: added new parameter 'boundaries' to determine whether a pair of boundaries are given for the confidence interval, or for normal behavior where the area is given. Also added tests.
- percentiles [new-function] - Function which calculates percentiles (like np.percentile) but with optional weighting of values.
- stats_str - Changes to use local percentiles function instead of np.percentile. Added weights argument, and converted from using input percentile arguments in [0, 100] range to fractions: [0.0, 1.0] range. - Set ave=False, and remove label parameter. Should be added manually on str is used from the calling code.
tests/ - test_math_core.py
- test_argnearest [new-function] - Test the new argnearest function.
plot/ + Hist2D.py
- plot2DHist + BUG: fixed issue where grid indices were reversed -- caused errors in non-square grids. + BUG: contour lines were using a different grid for some reason (unknown), was messing up edges and spacings. + BUG: default fs=None to not change the preset font size.
- plot2DHistProj + BUG: errors when x and y projection axes were turned off.
plot_core.py - colormap
- ENH: added left and right parameters to allow truncation of colormaps.
- cut_colormap [new-function] - ENH: new function to truncate the given colormap.
- label_line [new-function] + ENH: new function to add an annotation to a given line with the appropriate placement and rotation.
- plotConfFill - ENH: convert passed confidence intervals to np.array as needed.
- text + ENH: Add pad parameter. + ENH: now accepts a loc argument, a two-letter string which describes the location at which the text will be placed. + ENH: halign and valign are now passed through the new _parse_align() method which will process/filter the alignment strings. e.g. 'l' is now converted to 'left' as required for matplotlib.
- setGrid + ENH: added new arguments for color and alpha.
- _loc_str_to_pars - [BUG]: Was using 'lower' instead of 'bottom', triggering warning.
constants.py - Added DAY (in seconds) variable.
utils.py [new-file] - New file for general purpose, internal methods, etc. - dep_warn [new-function]
- Function for sending deprecation warnings.
math/ + math_core.py
Moved many methods to new files, 'numeric.py' and 'stats.py'
around [new-function] + Round in linear or log-space, in any direction (up, down, nearest).
This function deprecates other rounding methods (ceil_log, floor_log, round_log).
- When rounding in log-space, a negative value for decimals means rounding to an order of magnitude (in any direction).
ceil_log [DEPRECATED] ---> around
floor_log [DEPRECATED] ---> around
minmax + Added rounding functionality using new around method. + Added round_scale parameter for interface with around method.
ordered_groups [new-function] + Find the locations in an array of indices which sort the input array into groups
based on target locations.
round_log [DEPRECATED] ---> around
spacing + Added integers parameter, if true, will create spacing in integers (linear or log)
between the given extrema.
numeric.py [new-file] - Moved 'numerical' methods from 'math_core.py' to here.
statistic.py [new-file] - Moved 'statistical' methods from 'math_core.py' to here. - confidenceBands [DEPRECATED] --> confidence_bands [new-function] - confidenceIntervals [DEPRECATED] --> confidence_intervals [new-function] - sigma [new-function]
- Convert from standard deviations to percentiles (inside or outside) of the normal distribution.
tests/ - 'test_math_core.py'
- Functions split off into 'test_numeric.py' and 'test_statistic.py'.
- Added tests for new-function around.
- Added tests for new functionality (integers) of spacing().
- 'test_numeric.py' [new-file] + Tests for numerical functions.
- 'test_statistic.py' [new-file] + Tests for statistical functions. + Tests for sigma function.
plot/ + Hist2D.py
plot2DHist + [MAINT] minor, allow different types of overlayed values; (see plot2DHistProj).
plot2DHistProj + [ENH] Allow central plot to be scatter instead of 2D histogram.
Use type argument.
- [ENH] Add fourth subplot in the top-right corner for additional (especially cumulative) plots. Still needs fine tuning, but working okay.
- [ENH] Add ability to overlay (write) either 'counts' or 'values' on 2D hist. Optional formatting available also.
- [ENH] Ability to plot cumulative statistics --- i.e. consider values in all bins (e.g.) up and to the right of the target bin, works for counts, medians, etc.
_constructFigure + [ENH] Add fourth subplot in the top-right corner, if desired.
plot_core.py - backdrop
- [ENH] Add option draw to determine if patch should be added to figure or only returned.
color_cycle + [ENH] Allow single color to be passed, from which a cycle is created by
using seaborn.light_palette or seaborn.dark_palette.
color_set + [ENH] Added new set of colors based on seaborn.xkcd_palette colors.
full_extent + [ENH] Improve to work with legends (matplotlib.legend.Legend).
legend + [ENH] Added loc parameter to automatically set x,y positions and alignment
based on a two-character string.
- [ENH] Added mono parameter to set font as monospaced.
strSciNot + [ENH] Added options one and zero to decide whether to include mantissa values
of '1.0' and whether to write '0.0' as just '0.0' (instead of 10^-inf).
test + [ENH] Now works with either matplotlib.axes.Axes or matplotlib.figure.Figure.
inout/ + inout_core.py
ascii_table + [ENH] passing
out = Nonewill make the function return a string version of thetable.
checkPath + [ENH] added parameter create to choose whether missing directories are created
or not.
- [DOC] added docstrings.
iterable_notstring [new-function] + Return 'True' if the argument is an iterable and not a string type.
timer.py - [ENH] Timings.report() will return the results as a string if the parameter,
out = None.math/ + math_core.py
_comparisonFunction [DEPRECATED] ---> _comparison_function [new-function] + [ENH] Returned function takes a single parameter, instead of needing the comparison
value in each call. Instead the comparison value is passed once to _comparison_function, just during initialization.
_comparisonFilter [DEPRECATED] ---> comparison_filter [new-function] + [ENH] Added options to return indices (instead of values), compare with non-zero
comparison values, and check for finite (or not).
ceil_log [new-function] + Round up to the nearest integer in the the log10 mantissa (e.g. 23400 --> 30000)
floor_log [new-function] + Round down to the nearest integer in the the log10 mantissa (e.g. 23400 --> 20000)
frexp10 + [ENH] Updated to work with negative and non-finite values.
minmax + [ENH] Extend the prev argument to allow for either minimum or maximum comparison
to be None.
- [ENH] Added limit keyword argument to place limits on low/high extrema.
- [MAINT] Fully deprecated (removed) positive, nonzero keywords.
round_log [new-function] + Wrapper for ceil_log and floor_log, round in log-space in either direction.
stats_str + [ENH] Added parameter label to give to the output string.
tests/ - test_math_core.py
- [ENH] Added some tests for _comparison_function and _comparison_filter.
plot/ + Hist2D.py
plot2DHist + [ENH] Added options for overplotting contour lines. Basics work, might need some
fine tuning.
plot2DHistProj + [ENH] added parameters to adjust the size / location of axes composing plots. + [BUG] fixed issue where log-color-scales projected axes with zero values would
fail. Seems to be working fine.
- [BUG] fixed issue in right projection where the x-axis scaling would be set incorrectly.
- [BUG] fixed issue with trying to set numerous axes variables in colorbar.
- [ENH] updated with cmap and smap parameters passed to plot2DHist.
- [ENH] improved the way extrema are handled, especially in xprojection axis.
plot_core.py - backdrop [new-function]
- [ENH] Add rectangular patches behind the content of the given axes.
colormap + [ENH] Added grey colors for 'under' and 'over' (i.e. outside colormap limits).
full_extent [new-function] + [ENH] Find the bbox (or set of bbox) which contain the given axes and its contents.
legend + [BUG] fixed issue where 'center' could be repeated for valign and halign. + [ENH] change the argument fig to be art -- either an axes or fig object. + [ENH] added default for handlelength parameter; removed monospace fonts default.
line_label [new-function] + Function which draws a vertical or horizontal line, and adds an annotation to it.
plotConfFill + [ENH] Added edges argument to control drawing the edges of each confidence
interval explicitly.
- [ENH] Added 'floor' and 'ceil' parameters to set absolute minima and maxima.
plotHistBars + [ENH] Added improved default parameters for bar plot. Missing parameter bug fix.
plotHistLine + [ENH] Added invert argument to allow switching the x and y data.
position_to_extent [new-function] + [ENH] Reposition an axes object so that its 'full_extent' (see above) is at the
intended position.
saveFigure + [ENH] check that figures saved properly.
strSciNot + [ENH] enable None precision --- i.e. dont show mantissa or exponent. + [ENH] Updated to work with negative and non-finite values.
constants.py + Bug-fix where SIGMA_T wasn't loading properly from astropy. + Added Electron-Scattering opacity, KAPPA_ES.
README.rst + Added more information about contents and structure of package.
inout/ + inout_core.py
ascii_table [new-function] + New function which prints a table of values to the given output. + Added linewise and prepend arguments, allowing the table to be printed
line-by-line or as a single block, and for the print to be prepended with an additional string.
modify_exists [new-function] + Function which modifies the given filename if it already exists. The modifications
is appending an integer to the filename.
- Added tests for this function.
timer.py [new-file] - Provides the classes Timer and Timings which are used to time code execution and
provided summaries of the results. The Timer class is used to calculate repeated durations of execution for the same (type of) calculation, while the Timings class will manage the timing of many different calculations/chunks of code.
tests/ - test_inout_core.py
- Fixed some issues with cleaning up (deleting) files/directories created for the tests.
- test_timer.py [new-file] + Test for the classes in the new inout/timer.py file. Basics tests in place.
math/ + math_core.py
- groupDigitized + [Docs]: improved documentation clarifying input parameters.
- stats_str [new-function] + [ENH]: Return a string with the statistics of the given array.
- _comparisonFilter + [ENH]: always filter for finite values (regardless of the function arguments).
plot/ + plot_core.py
plotConfFill + [Bug]: fixed default value of outline which was still set to a boolean instead of
a color string. Caused failure when trying to save images.
colorCycle [DEPRECATED] ---> color_cycle [new-function] + [Docs]: added method documentation.
Hist2D.py - plot2DHistProj
- [ENH]: Check to make input arguments are the correct (consistent) shapes.
- [ENH]: Added flag 'write_counts' which overlays a string of the number of values in each bin of the 2D histogram. Uses the new counts parameter of plot2DHist.
plot2DHist + [ENH]: Added parameter 'counts' for numbers to be overlaid on each bin, used by
the write_counts of plot2DHistProj.
inout/ + inout_core.py
dictToNPZ + Added optional log parameter for a
logging.Loggerobject. + Instead of raising an error for scalar parameters, cast them into arrays andprint a warning.
tests/ - test_inout_core.py [new-file]
- Tests for the inout_core.py submodule.
- Added tests for npzToDict and dictToNPZ.
math/ + math_core.py
confidenceBands + Added filter argument to select points based on how their y values compare to
zero, e.g. to select for only
y >= 0.0etc.minmax + Added a filter argument to replace usage of nonzero (use '!=') and
positive (use '>'). Left both of the arguments in place, but usage of them will print a deprecation warning.
spacing + Updated to use filter argument.
plot/ + plot_core.py
plotConfFill + Added a filter argument to filter the values to be plotted. + Added an outline argument to optional draw a line with a different color
behind the median line, to make it more visible.
text + [Bug]: fixed issue where regardless of what transformation was passed, only the
figure transformation was used. Solution is to call
plt.textinstead offig.text.
color2d.py [new-file] - New file with classes and functions to provide color-mappings from 2D parameter spaces
to RGB color-space. ScalarMappable2D is the class which handles this mapping, analogous to the matplotlib.cm.ScalarMappable class. Similarly, the function to create an instance is zplot.color2d.colormap2d, analogous to the zcode.plot.plot_core.colormap function.
constants.py + Added sigma_T -- the Thomson-scattering cross-section in units of cm^2.
General + Can now run tests through python via
>>> zcode.test().inout/ + inout_core.py
- mpiError [new-method] + New method to raise an error across an MPI communicator
log.py - getLogger
- Added the log output filename as a member variable to the newly created logger object.
math/ + math_core.py
argextrema [new-method] + Method to find the index of the extrema (either 'min' or 'max') with filtering
criteria (e.g. 'ge' = filter for values
>= 0.0).really1d [new-method] + Test whether a list or array is purely 1D, i.e. make sure it is not a 'jagged'
list (or array) of lists (or arrays).
asBinEdges [new-method] + Convert a bin-specification to a list of bin-edges. I.e. given either a set of
bin-edges, or a number of bins (in N-dimensions), return or create those bin-edges.
confidenceIntervals [new-method] + For a pair of x and y data, bin the values by x to construct confidence intervals
in y.
tests/ - test_math_core.py [new-file]
- New location and standard for math tests using 'nose'.
- Moved over one of the tests for 'smooth' from previous location, 'zcode/testing/test_Math.py' [deleted], and simplified.
test.sh [new-file] + Bash script containing the single command to use for running nosetests.
testing/ [Deleted] + Moved and reformatted test into new 'zcode/math/tests/test_math_core.py' file.
Overall + Restructured module to use subdirectories per topic (e.g. 'math') instead of single files. + Implemented python3 styles into all files, with backwards compatibility.
CHANGES.rst [new-file] + Track changes.
MANIFEST.in [new-file] + Track files required for module.
version.py [new-file] + Current version information loaded from 'zcode.__init__'. + Should be expanded to include git commit SHA, etc.
math/ + math_core.py
- Enhanced the spline function, and removed the secondary functions logSpline and logSpline_resample. The former is included in the new functionality of spline, and the latter is too simple to warrant its own function.
- strArray [new-function] + Creates a string representation of a numerical array.
- indsWIthin [new-function] + Finds the indices of an array within the bounds of the given extrema.
- midpoints + Enhanced to find the midpoints along an arbitrary axis.
plot/ + plot_core.py
legend [new-method] + Similar to 'text' --- just a wrapper for matplotlib.pyplot.legend.
plotConfFill [new-method] + Draws a median line and filled-regions for associated confidence intervals
(e.g. generated by zcode.math.confidenceIntervals).
Hist2D.py - Plotted histograms now use the scipy.stats.binned_statistic function so that more
complicated statistics can be used. The projected histograms are now colored to match the 2D main histogram.
inout/ + inout_core.py
MPI_TAGS [new-class] + A Keys subclass used for passing tags/status between different processors when
using MPI. Commonly used in the master-slave(s) paradigm.