finish implementation of review to #11

src/ixdat/backends/backend_base.py

@@ -21,6 +21,7 @@ class BackendBase:
 
     backend_type = "none"
     address = "none"
+    """A location uniquely identifying the backend together with its type"""
 
     def __init__(self):
         """Initialize the backend with dict for {table_name (str): id_counter (int)}"""

src/ixdat/backends/directory_backend.py

@@ -78,7 +78,7 @@ def __init__(
 
     @property
     def address(self):
-        """"""
+        """The directory containing the tables (folders) and rows (.ix files)"""
         return str(self.project_directory)
 
     def save(self, obj, force=False, no_updates=True):

src/ixdat/db.py

@@ -349,8 +349,8 @@ def get_object(self):
         return self.cls.get(self.id, backend=self.backend)
 
     @property
-    def identity(self):
-        """Placeholder also has an short_identity to check equivalence without loading"""
+    def short_identity(self):
+        """Placeholder also has a short_identity to check equivalence without loading"""
         if self.backend is DB.backend:
             return self.id
         return self.backend, self.id

src/ixdat/exporters/csv_exporter.py

@@ -5,10 +5,10 @@
 class CSVExporter:
     """The default exporter, which writes delimited measurement data row-wise to file"""
 
-    def __init__(self, measurement=None, delim=",\t", default_v_list=None):
+    def __init__(self, measurement=None, delimiter=",\t", default_v_list=None):
         """Initiate the exported with a measurement (Measurement) and delimiter (str)"""
         self.measurement = measurement
-        self.delim = delim
+        self.delimiter = delimiter
         self._default_v_list = default_v_list
 
     @property
@@ -49,7 +49,9 @@ def export_measurement(self, measurement, path_to_file, v_list=None, tspan=None)
             s_list.append(v_name)
 
         header_line = (
-            "".join([s_name + self.delim for s_name in s_list])[: -len(self.delim)]
+            "".join([s_name + self.delimiter for s_name in s_list])[
+                : -len(self.delimiter)
+            ]
             + "\n"
         )
 
@@ -61,10 +63,10 @@ def export_measurement(self, measurement, path_to_file, v_list=None, tspan=None)
             for s_name in s_list:
                 if len(columns_data[s_name]) > n:
                     # Then put the data there:
-                    line = line + str(columns_data[s_name][n]) + self.delim
+                    line = line + str(columns_data[s_name][n]) + self.delimiter
                 else:
                     # No more data in this column. Just hold alignment:
-                    line = line + self.delim
+                    line = line + self.delimiter
             line = line + "\n"
             lines.append(line)
 

src/ixdat/exporters/ec_exporter.py

@@ -8,7 +8,7 @@ class ECExporter(CSVExporter):
     def default_v_list(self):
         """The default v_list for ECExporter is V_str, J_str, and sel_str"""
         return [
-            # self.measurement.t_str,
+            # self.measurement.t_name,
             self.measurement.v_name,
             self.measurement.j_name,
             self.measurement.selector_name,

src/ixdat/measurements.py

@@ -493,7 +493,7 @@ def t(self):
         return self[self.control_series_name].t
 
     @property
-    def t_str(self):
+    def t_name(self):
         return self[self.control_series_name].tseries.name
 
     def _build_file_number_series(self):
@@ -580,12 +580,12 @@ def data_cols(self):
         """Return a set of the names of all of the measurement's VSeries and TSeries"""
         return set([s.name for s in (self.value_series + self.time_series)])
 
-    def get_original_m_id_of_series(self, series):
+    def get_original_m_ids_of_series(self, series):
         """Return a list of id's of component measurements to which `series` belongs."""
         m_id_list = []
         for m in self.component_measurements:
             if series.short_identity in m.s_ids:
-                # FIXME: the whole id vs identity issue
+                # FIXME: the whole id vs short_identity issue
                 #   see https://github.com/ixdat/ixdat/pull/11#discussion_r746632897
                 m_id_list.append(m.id)
         return m_id_list
@@ -807,6 +807,10 @@ def select(self, *args, tspan=None, **kwargs):
             new_measurement = new_measurement.select_values(*args, **kwargs)
         return new_measurement
 
+    def copy(self):
+        """Make a copy of the Measurement via its dictionary representation"""
+        return self.__class__.from_dict(self.as_dict())
+
     def __add__(self, other):
         """Addition of measurements appends the series and component measurements lists.
 

tests/test_biologic_ec_measurement.py

@@ -10,28 +10,16 @@
 
 path_to_file = Path(__file__).parent.parent / "test_data/biologic/Pt_poly_cv.mpt"
 change_database("directory", project_name="test_biologic_ec_measurement")
+# TODO: Use a temporary directory.
+#   see: https://github.com/ixdat/ixdat/pull/11#discussion_r677567528
 
-
-class TestLog:
-    def __init__(self, path_to_file="~/git/ixdat_test_output.txt"):
-        self.path_to_file = Path(path_to_file).expanduser()
-        with open(self.path_to_file, "w") as f:
-            f.write("\n" + "-" * 80 + "\n")
-            f.write(f"RUNNING MODULE {__file__} AT t={time.time()}\n")
-            f.write("-" * 80 + "\n")
-
-    def print(self, s):
-        with open(self.path_to_file, "a") as f:
-            f.write(s + "\n")
-
-
-log = TestLog()
-log.print(f"cwd = {Path('.').absolute().resolve()}")
+print(f"cwd = {Path('.').absolute().resolve()}")
 
 
 def test_append_essential_series():
+    # TODO: break this up into functions testing specific things.
     meas = Measurement.read(path_to_file, reader="biologic")
-    log.print(f"successfully read {meas}")
+    print(f"successfully read {meas}")
 
     assert meas.technique == "EC"
     assert len(meas["potential"].data) == len(meas["time/s"].data)
@@ -55,8 +43,9 @@ def test_append_essential_series():
 
 
 def test_save_load():
+    # TODO: break this up into functions testing specific things.
     meas = Measurement.read(path_to_file, reader="biologic")
-    log.print(f"successfully read {meas}")
+    print(f"successfully read {meas}")
 
     # To make it complex, we first select a couple cycles, this time with select(),
     # and append them:
@@ -107,8 +96,10 @@ def test_save_load():
 
 
 if __name__ == "__main__":
+    # TODO: probably doesn't beling here.
+    #   See https://github.com/ixdat/ixdat/pull/11#discussion_r677996529
     meas = Measurement.read(path_to_file, reader="biologic")
-    log.print(f"successfully read {meas}")
+    print(f"successfully read {meas}")
 
     # To make it complex, we first select a couple cycles, this time with select(),
     # and append them: