Plotter and CLI fix #49
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The plotter module has been reorganized (#25). Now it contains all the plot functions. A `Plotter` subclass can be defined by simply importing the relevant functions. `CurrentPlotter` has been defined: it contains all the plot functions used by `Current`. The `Current` class has a `_default_plotter` attribute (`CurrentPlotter`). The plot methods are defined dynamically by the `set_plotter` method. This method takes all the 'plot_*' functions contained in the `plotter` input parameter (or the default plotter, e.g. `CurrentPlotter`) and converts them into methods of `Current`. This is obtained thanks to a decorator (`add_method`) that was defined. The first argument of the plot functions (`current`) becomes `self` when converted into a class method. The plotter of `Current` is initialized by default to `CurrentPlotter` when importing the library. It is possible to change it dynamically by calling the `set_plotter` method. This is a class method, hence it will change the plotter assigned to the `Current` class and affect all the current object already defined. (Notice that calling `set_plotter` from a subclass will modify also the plotter of the `Current` base class. If this behavior might be confusing, if it is not wanted in some applications, we should change it.) It seems that #40 is not the case anymore. TODO: - check and remove the commented plot methods from `mdsample` (#43). - fix the analysis CLI. It is broken now. In order to close #25 : - should we define other plotters for the CLI and GUI? In case, evaluate shared functionalities. - how to define plots customizations?
Working on #25. The function `plotter.style.use_plot_style` sets the plot style of Matplotlib. Each `Plotter` subclass define its default plot style (e.g. Current defines 'api_style.mplstyle', the CLI defines 'cli_style.mplstyle', etc.). New plot styles can be added in the `plotter/styles/` folder, or simply set via the function mentioned above. This allows one to define/use different plot style for different uses, such as the API, CLI, and GUI, if needed. The `Current.set_plotter` method will call `use_plot_style` when setting up the plotter. TODO: - the styles need to be revised (especially the CLI's)
- A new `MDSamplePlotter` for the `MDSample` base class has been created. The `set_plotter` class method has been moved into it, and it will be inherited by `Current`. - The old plot functions in `mdsample.py` have been removed; `plot_trajectory` was added to the `plotter.py` module. - Any reference to `thermocepstrum.utils.plt` & `plotAfterPlt` has been removed. - `md.resample.resample_timeseries` now calls the `plotter.plot_resample` method (#43) - `plotter.plot_resample` now accepts a `MDSample` (sub)-class object and returns only axes. TODO: - fix the `analysis.py` script. There are problems calling the plotter functions
TODO: check if it is possible to merge CLIPlotter functions with the API's ones.
Some tests were failing due to old numpy/scipy/pytest versions. Dependencies updated to numpy>=0.16, scipy>=1.2, pytest>=5.1. TODO: - The imaginary part of the cospectrum is not checked. We should add a check for complex arrays. - Update the examples' reference results.
a factor was missing
…into the command line
to generate the doc, goto into the docs directory and type make html or make latexpdf or whathever you want to generate
it works
added a decorator to wun function in specific directory
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Closes #25, fixes #40, closes #43
Status as of today:
Plottermodule has been reorganized. Now it contains all the plot functions.Plottersubclass can be defined by simply importing the relevant functions.MDSamplePlotter,CurrentPlotterandCLIPlotterhave been defined: they contain all the plot functions used by the API and the CLI. TheCurrentclass has a_default_plotterattribute (CurrentPlotter).set_plottermethod. This method takes all the 'plot_*' functions contained in thePlotterobject and converts them into methods ofCurrent(orMDSample). This is obtained thanks to a decorator (add_method) that was defined (utils.decorators). The first argument of any plot function (current) becomesselfwhen converted into a class method.Currentis initialized by default toCurrentPlotterwhen importing the library. It is possible to change it dynamically by calling theset_plottermethod. This is a class method, hence it will change the plotter assigned to theCurrentclass and affect all the current objects already defined.set_plotterfrom a subclass will modify also the plotter of theCurrentbase class. If this behavior is confusing, or not desirable in some applications, we should change it.MDSampleuses its own plotterMDSamplePlotter, however it is independent of the Current's plotter chosen.To Do (in order of importance)
utils.pltinmd/mdsample.pyandmd/resample.pythermocepstrum.utils.loadAfterPltandpltfromutils/__init__.py.analysis.py, with calls to the plotter methods where needed.