Configuration

pyplate.yaml location

pyplate.yaml controls package behavior. PyPlate will search for pyplate.yaml in the following locations in this order:

  • The directory specified by the environment variable PYPLATE_CONFIG

  • The current working directory

  • The user’s home directory

  • The package directory

The configuration file that is found first will take precedence.

Precision

The number of digits to display in the output can be controlled using the precisions option. Different precisions can be set for different units.

# How many digits of precision to return to the user
precisions:
  default: 3
  uL: 0
  umol: 1
  mg: 1

The default precision is 3 digits. The precision for units uL is set to 0 because it is impossible to measure less than 1 uL. umol, and mg are set to 1 digit.

Internal Precision

Because floating point numbers are not exact, some rounding of numbers during intermediate calculations should occur. The number of digits to retain during intermediate calculations can be controlled using the internal_precision option.

# How many digits of precision to maintain in internal calculations
internal_precision: 10

Storage Units

Amounts of substances and volumes can be stored with different units. The default units for these can be set using the moles_storage_units and volume_storage_units options.

# How to store volumes and moles internally
# uL means we will store volumes as microliters
volume_storage_unit: uL

# umol means we will store moles as micromoles
moles_storage_unit: umol

Display Units

In many of PyPlate’s functions, the user can specify which units to return data in.

  • volume_display_unit specifies the default unit for displaying volumes.

  • moles_display_unit specifies the default unit for displaying moles.

  • concentration_display_unit specifies the default unit for displaying concentrations.

# uL means we will return volumes as microliters
volume_display_unit: uL

# umol means we will return moles as micromoles
moles_display_unit: umol

# Default concentration unit for get_concentration()
concentration_display_unit: M

Concentration Units

When specifying concentration in ‘%w/v’, a default for the units for weight and volume is set using the default_weight_volume_units option.

# units for %w/v
default_weight_volume_units: g/mL

Default Densities

Solids and enzymes have the same default densities for all objects.

  • The default density for solids is set using the default_solid_density option.

  • The default density for enzymes is set using the default_enzyme_density option.

# density for solids/enzymes in g/mL or U/mL. Can be set to float('inf') to give solids and enzymes zero volume.
default_solid_density: 1
default_enzyme_density: 1

Colormaps

For functions that return a styled DataFrame, the colormap can be set using the colormap option.

# default colormap to be used in visualizations
default_colormap: Purples
default_diverging_colormap: PuOr

The diverging colormap is used for functions that return a DataFrame with both positive and negative values.