Bugfix: include expr in variable definitions when writing to file (#87)

* correct release date for v0.4.2

* Fix equation generator and activate test.

* Fix and activate second test.

* Add get_parents to utils.

* Rename writer.eq and writer.var to neweq and newvar.

* Fix VariableWriter and add test.

* Replace value by default in VariableWriter

* Add VariableWriter.var and test

* Add EquationWriter.eq and failing test.

* Add imports of functions.

* Remove eval from utils.

* fix utils.

* Clean up test

* Replace domain by assumptions

* Fix to _generator.py

* Fix examples in _generator.

* Fix examples in _generator.

* Update jupyter examples

* update docu

* Fix spaces.

* Update jupyter examples

* Fix pydocstyle

* Add failing test of VariableWriter with expr in variable.

* Fix VariableWriter and move test to test_variable_writer.py

* Remove unused function.

* Update CHANGES.rst

CHANGES.rst

@@ -1,6 +1,26 @@
 Changes
 =======
 
+``v0.4.3``
+----------
+*released 2020-06-18*
+
+Bug Fixes
+~~~~~~~~~
+- **utils:**  Include expr in variable definitions when writing to file 
+  (`PR #87 <https://github.com/environmentalscience/essm/pull/87>`__)
+
+
+Features
+~~~~~~~~
+
+- **documentation:** Add use examples as Jupyter notebooks and integrate in documentation
+  (`PR #83 <https://github.com/environmentalscience/essm/pull/83>`__)
+
+- **utils:**  Enable writers of .py files for re-import of variable and equation definitions 
+  (`PR #84 <https://github.com/environmentalscience/essm/pull/84>`__)
+
+
 ``v0.4.2``
 ----------
 *released 2020-04-28*

essm/_generator.py

@@ -78,6 +78,7 @@ class {name}(Variable):
     assumptions = {assumptions!r}
     latex_name = {latex_name!r}
     {default}
+    {expr}
 """
 
 # CONSTANTS = re.compile(r'\b(e|pi)\b')
@@ -96,38 +97,6 @@ def _lint_content(content):
     return content
 
 
-def create_module(name, doc=None, folder=None, overwrite=False):
-    """Create folder with init file."""
-    name_path = (name.replace('.', os.path.sep), ) \
-        if not isinstance(name, (tuple, list)) \
-        else name
-    folder = folder or pkg_resources.resource_filename('essm', '')
-    path = os.path.join(folder, *name_path)
-    try:
-        os.makedirs(path)
-        logger.info('Created new folder: {0}'.format(path))
-    except OSError as e1:
-        logger.error('Could not create new folder: {0}'.format(path))
-
-    init_path = os.path.join(path, '__init__.py')
-
-    if os.path.isfile(init_path):
-        logger.info(
-            '{0} already exists. Use `overwrite=True` to overwrite.'.
-            format(init_path)
-        )
-
-    if overwrite or not os.path.isfile(init_path):
-        with open(init_path, 'w') as file_out:
-            file_out.write(
-                LICENSE_TPL.format(year=datetime.datetime.now().year)
-            )
-            file_out.write('"""{0}"""\n'.format(doc))
-        logger.debug('Created file {0}.'.format(init_path))
-
-    return path
-
-
 def extract_functions(expr):
     """Traverse through expression and return set of functions."""
     return {
@@ -207,22 +176,30 @@ def newvar(
             units=None,
             assumptions={'real': True},
             latex_name=None,
-            default=None
+            default=None,
+            expr=None
     ):
         """Add new variable."""
         if not latex_name:
             latex_name = name
         if default is None:
-            default = ''
+            default = 'default = None'
         else:
             default = 'default = ' + str(default)
+        if expr is None:
+            expr = ''
+        else:
+            expr = 'expr = ' + str(expr)
+
         context = {
             "name": name,
             "doc": doc,
             "units": str(units).replace('^', '**') if units else '1/1',
             "assumptions": assumptions,
             "latex_name": latex_name,
-            "default": default
+            "default": default,
+            "expr": expr
+
         }
         self.vars.append(context)
 
@@ -252,7 +229,8 @@ def var(self, var1):
         assumptions = dict_attr.get('assumptions')
         latex_name = dict_attr.get('latex_name')
         value = dict_attr.get('default')
-        self.newvar(name, doc, units, assumptions, latex_name, value)
+        expr = dict_attr.get('expr')
+        self.newvar(name, doc, units, assumptions, latex_name, value, expr)
 
     def write(self, filename):
         """Serialize itself to a filename."""

tests/test_equations.py

@@ -303,26 +303,6 @@ def test_solve():
     ) == [0.031 * demo_d - 1.68e-7 * demo_d2]
 
 
-def test_variable_writer(tmpdir):
-    """VariableWriter creates importable file with variable definitions."""
-    from essm.variables.physics.thermodynamics import c_pa
-    g = {}
-    writer_td = VariableWriter(docstring='Test of Variable_writer.')
-    writer_td.newvar(
-        'g',
-        'meter / second ^ 2',
-        'default = 9.81'
-    )
-    writer_td.var(c_pa)
-    eq_file = tmpdir.mkdir('test').join('test_variables.py')
-    writer_td.write(eq_file.strpath)
-    with open(eq_file, "rb") as source_file:
-        code = compile(eq_file.read(), eq_file, "exec")
-    exec(code, g)
-    assert g['g'].definition.default == 9.81
-    assert g['c_pa'].definition.unit == c_pa.definition.unit
-
-
 def test_equation_writer(tmpdir):
     """EquationWriter creates importable file with internal variables."""
     from sympy import var

tests/test_variables.py

@@ -4,6 +4,7 @@
 import pytest
 
 from essm.variables import Variable
+from essm._generator import VariableWriter
 from essm.variables.units import (derive_baseunit, derive_unit, joule,
                                   kilogram, markdown, meter, second)
 from essm.variables.utils import generate_metadata_table
@@ -179,3 +180,27 @@ def test_generate_metadata_table():
             'Test expression variable.', '$2 demo_variable$', '-', 'm'),
             ('$E_l$', 'E_l',
             'Latent heat flux from leaf.', '', '-', 'J s$^{-1}$ m$^{-2}$')]
+
+
+def test_variable_writer(tmpdir):
+    """VariableWriter creates importable file with variable definitions."""
+    from essm.variables.physics.thermodynamics import c_pa
+    g = {}
+    writer_td = VariableWriter(docstring='Test of Variable_writer.')
+    writer_td.newvar(
+        'g',
+        units=meter / second ** 2,
+        default=9.81
+    )
+    writer_td.var(c_pa)
+    writer_td.var(demo_variable)
+    writer_td.var(demo_expression_variable)
+    eq_file = tmpdir.mkdir('test').join('test_variables.py')
+    writer_td.write(eq_file.strpath)
+    with open(eq_file, "rb") as source_file:
+        code = compile(eq_file.read(), eq_file, "exec")
+    exec(code, g)
+    assert g['g'].definition.default == 9.81
+    assert g['c_pa'].definition.unit == c_pa.definition.unit
+    assert g['demo_expression_variable'].definition.expr \
+        == demo_expression_variable.definition.expr