bioverse.classes module

Contains class definitions.

class bioverse.classes.Object(label=None)

Bases: object

This class allows the Generator and Survey classes to be saved as .pkl files under the Objects/ directory.

Parameters:

label (str, optional) – Name of the Generator or Survey. Default is to create a new object.

save(label=None)

Saves the Object as a template in a .pkl file under ./<object type>s/.

get_filename_from_label(label)
class bioverse.classes.Table(*args, **kwargs)

Bases: dict

Class for storing numpy arrays in a table-like format. Inherits dict. Each key is treated as a separate table column.

split_key(key)

Splits a key such as ‘Planets:Atmosphere:O2’ into (‘Planets’,’Atmosphere:O2’) and ensures that the first key refers to a dict-like object.

keys()

Returns an array of keys instead of a dict_keys object, because I prefer it this way.

sort_by(key, inplace=False, ascending=True)

Sorts the table by the values in one column.

Parameters:

  • key (str) – Name of the column by which to sort the table.

  • inplace (bool, optional) – If True, sort the table in-place. Otherwise return a new sorted Table.

  • ascending (bool, optional) – If True, sort from least to greatest.

Returns:

sortd – A sorted copy of this table. Only returned if inplace is True.

Return type:

Table

get_stars()

Returns just the first entry for each star in the Table.

legend(keys=None, filename='/home/docs/checkouts/readthedocs.org/user_builds/bioverse/envs/stable/lib/python3.11/site-packages/bioverse/Data/legend.dat')

Prints the description of parameter(s) in the Table.

Parameters:

  • keys (str or str array, optional) – Key or list of keys to describe. If not specified, every key is described.

  • filename (str, optional) – CSV file containing the list of parameter descriptions. Default is ./legend.dat.

copy()

Returns a deep copy of the Table instead of a shallow copy (as in dict.copy). This way, if a column is filled by objects (such as Atmosphere objects), a copy of those is returned instead of a reference.

append(table, inplace=True)

Appends another table onto this table in-place. The second table must have the same columns, unless this table is empty, in which case the columns are copied over.

Parameters:

  • table (Table) – Table to be appended onto this one.

  • inplace (bool, optional) – If True, append inplace and return None. If False, return a new Table.

compute(key, force=False)

Computes the value of key using other values in the dictionary and a pre-defined formula. Useful for translating measured values (e.g. ‘a’, ‘L_st’) into secondary data products (e.g., ‘S’). Will also propagate uncertainties contained in self.error.

shuffle(inplace=True)

Re-orders rows in the Table. If inplace is False, return a new re-ordered Table instead.

pdshow()

If pandas is installed, show the Table represented as a DataFrame. Otherwise return an error.

to_pandas()

export Table into a pandas DataFrame

observed(key)

Returns the subset of rows for which self[key] is not nan.

class bioverse.classes.Stopwatch

Bases: object

This class uses the time module to profile chunks of code. Use the start() and stop() methods to start and stop the Stopwatch, and the mark() methods to record a time. stop() and read() will report the total time elapsed as well as the time between each step.

clear()
mark(flag=None)
stop(flag=None)
read()