Feature: Separate pyplate.py into Multiple Files (Merge pull request #32

 from ekwan/feature_separate_files)

Created separate files for the various classes of PyPlate. Some which were closely paired (e.g. Recipe and RecipeStep) were kept in the same file, whereas most others were given their own files.

examples/Example.py

@@ -1,6 +1,6 @@
 from operator import itemgetter
 
-from pyplate.pyplate import Substance, Container, Plate, Recipe
+from pyplate import Substance, Container, Plate, Recipe
 
 # testing #
 

examples/Test_Example.py

@@ -1,4 +1,4 @@
-from pyplate.pyplate import Substance, Container, Recipe, Plate
+from pyplate import Substance, Container, Recipe, Plate
 
 
 water = Substance.liquid('H2O', mol_weight=18.0153, density=1)

pyplate/__init__.py

@@ -1,49 +1,39 @@
-from pathlib import Path
-import os
-import yaml
-
-
-class Config:
-    def __init__(self):
-        file_path = None
-        for path in [Path(os.environ.get('PYPLATE_CONFIG', '')), Path.home(), Path(os.path.dirname(__file__))]:
-            path = path.joinpath('pyplate.yaml')
-            if path.is_file():
-                file_path = path
-                break
-
-        if file_path is None:
-            raise RuntimeError("pyplate.yaml not found.")
-
-        try:
-            with file_path.open('r') as config_file:
-                yaml_config = yaml.safe_load(config_file)
-        except yaml.YAMLError as exc:
-            raise RuntimeError("Config file could not be read.") from exc
-
-        self.internal_precision = yaml_config['internal_precision']
-        self.moles_storage_unit = yaml_config['moles_storage_unit']
-        assert self.moles_storage_unit[-3:] == 'mol'
-        self.moles_display_unit = yaml_config['moles_display_unit']
-        assert self.moles_display_unit[-3:] == 'mol'
-        self.volume_storage_unit = yaml_config['volume_storage_unit']
-        assert self.volume_storage_unit[-1] == 'L'
-        self.volume_display_unit = yaml_config['volume_display_unit']
-        assert self.volume_display_unit[-1] == 'L'
-
-        self.concentration_display_unit = yaml_config['concentration_display_unit']
-        # we can't use Unit to do a full check of the unit, so we just do a cursory check
-        assert ('/' in self.concentration_display_unit or self.concentration_display_unit[-1] == 'm' or
-                self.concentration_display_unit[-1] == 'M')
-        self.default_solid_density = float(yaml_config['default_solid_density'])
-        self.default_enzyme_density = float(yaml_config['default_enzyme_density'])
-        self.default_weight_volume_units = yaml_config['default_weight_volume_units']
-
-        self.default_colormap = yaml_config['default_colormap']
-        self.default_diverging_colormap = yaml_config['default_diverging_colormap']
-        self.precisions = yaml_config['precisions']
-
-
-# This has to be imported after Config is defined, otherwise there will be a circular import.
-from .pyplate import Substance, Container, Plate, Recipe, Unit, RecipeStep  # noqa: E402
-__all__ = ['Substance', 'Container', 'Plate', 'Recipe', 'Unit', 'Config', 'RecipeStep']
+"""
+pyplate: a tool for designing chemistry experiments in plate format
+
+Substance: An abstract chemical or biological entity (e.g., reagent, solvent, etc.).
+           Immutable. 
+
+Container: Stores specified quantities of Substances in a vessel with a given maximum volume. Immutable.
+
+Plate: A spatially ordered collection of Containers, like a 96 well plate.
+       The spatial arrangement must be rectangular. Immutable.
+
+Recipe: A list of instructions for transforming one set of containers into another.
+
+Storage format is defined in pyplate.yaml for volumes and moles.
+
+    Example:
+        # 1e-6 means we will store volumes as microliters
+        volume_storage: 'uL'
+
+        # 1e-6 means we will store moles as micromoles.
+        moles_storage: 'umol'
+
+All classes in this package are friends and use private methods of other classes freely.
+
+All internal computations are rounded to config.internal_precision to maintain sanity.
+    Rounding errors quickly compound.
+All values returned to the user are rounded to config.precisions for ease of use.
+"""
+
+# This is necessary to instantiate the config instance; the unit tests fail without it
+from pyplate.config import config, Config
+
+from pyplate.container import Container
+from pyplate.plate import Plate
+from pyplate.recipe import Recipe, RecipeStep
+from pyplate.substance import Substance
+from pyplate.unit import Unit 
+  # noqa: E402
+__all__ = ['Substance', 'Container', 'Plate', 'Recipe', 'Unit', 'RecipeStep']

pyplate/config.py

@@ -0,0 +1,45 @@
+from pathlib import Path
+import os
+import yaml
+
+class Config:
+    def __init__(self):
+        file_path = None
+        for path in [Path(os.environ.get('PYPLATE_CONFIG', '')), Path.home(), Path(os.path.dirname(__file__))]:
+            path = path.joinpath('pyplate.yaml')
+            if path.is_file():
+                file_path = path
+                break
+
+        if file_path is None:
+            raise RuntimeError("pyplate.yaml not found.")
+
+        try:
+            with file_path.open('r') as config_file:
+                yaml_config = yaml.safe_load(config_file)
+        except yaml.YAMLError as exc:
+            raise RuntimeError("Config file could not be read.") from exc
+
+        self.internal_precision = yaml_config['internal_precision']
+        self.moles_storage_unit = yaml_config['moles_storage_unit']
+        assert self.moles_storage_unit[-3:] == 'mol'
+        self.moles_display_unit = yaml_config['moles_display_unit']
+        assert self.moles_display_unit[-3:] == 'mol'
+        self.volume_storage_unit = yaml_config['volume_storage_unit']
+        assert self.volume_storage_unit[-1] == 'L'
+        self.volume_display_unit = yaml_config['volume_display_unit']
+        assert self.volume_display_unit[-1] == 'L'
+
+        self.concentration_display_unit = yaml_config['concentration_display_unit']
+        # we can't use Unit to do a full check of the unit, so we just do a cursory check
+        assert ('/' in self.concentration_display_unit or self.concentration_display_unit[-1] == 'm' or
+                self.concentration_display_unit[-1] == 'M')
+        self.default_solid_density = float(yaml_config['default_solid_density'])
+        self.default_enzyme_density = float(yaml_config['default_enzyme_density'])
+        self.default_weight_volume_units = yaml_config['default_weight_volume_units']
+
+        self.default_colormap = yaml_config['default_colormap']
+        self.default_diverging_colormap = yaml_config['default_diverging_colormap']
+        self.precisions = yaml_config['precisions']
+
+config = Config()