apmtools 0.2.13__tar.gz → 0.2.15__tar.gz

{apmtools-0.2.13 → apmtools-0.2.15}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.5
 Name: apmtools
-Version: 0.2.013
+Version: 0.2.015
 Summary: A collection of tools for processing air pollution monitoring data
 Project-URL: Homepage, https://github.com/federlorenz/apmtools
 Author-email: Federico Lorenzetti <lorenzetti.federico@gmail.com>

{apmtools-0.2.13 → apmtools-0.2.15}/pyproject.toml

@@ -4,7 +4,7 @@ build-backend = "hatchling.build"
 
 [project]
 name = "apmtools"
-version = "0.2.013"
+version = "0.2.015"
 authors = [
   { name="Federico Lorenzetti", email="lorenzetti.federico@gmail.com" },
 ]

{apmtools-0.2.13 → apmtools-0.2.15}/src/apmtools/classes.py

@@ -39,9 +39,9 @@ class DictionaryPlus(dict):
         """
         Return a subset of a DictionaryPlus, specified in the parameter filter_dict (itself a dictionary) or condition (a function that takes at minimum a value from the dictionary as an input parameter, and return True/False if some condition specified in the function is met. Typically a lambda function of the form lambda x: True if condition else False)
         filter_dict is {attrib:["attrib_value_x","attrib_value_y",..]}, where 
-            attrib is an attribute of the elements of dictionary, and attrib_value is a list
+            attrib is an attribute of the elements of dictionary, and attrib_value is a value or list
             of the values of such attrib that the elements of returned dictionary can have
-        specify filter_style='all' if all conditions should be met to be included in the return dictionary, specify filter_style='any' for including when any condition is met. Default is 'all'.
+        specify filter_style='all' if all conditions should be met to be included in the return dictionary, other filters allowed are 'any', 'negative all', 'negative any'.
         """
         if type(filter_dict) != type(dict()):
             print("subset function error: type filter_dict should be dict")
@@ -49,14 +49,17 @@ class DictionaryPlus(dict):
         return_dict = copy.deepcopy(self)
         a = {}
 
+        if filter_style not in {'all', 'any', 'negative all', 'negative any'}:
+            return return_dict
+
         if filter_style == 'all':
             a = {key: value for key, value in return_dict.items()}
             for key, value in return_dict.items():
                 for i, j in filter_dict.items():
                     if hasattr(value, i):
                         try:
-                            if type(j) == type(""):
-                                if not eval("value.__getattr__(\""+i+"\")" + j):
+                            if type(j) is not list:
+                                if getattr(value, i) not in [j]:
                                     del a[key]
                                     break
                             else:
@@ -67,8 +70,8 @@ class DictionaryPlus(dict):
                             pass
                     elif hasattr(value, 'm') & (type(value.m) == type({})) & (i in value.m.keys()):
                         try:
-                            if type(j) == type(""):
-                                if not eval("value.__getattr__('m')[\""+i+"\"]" + j):
+                            if type(j) is not list:
+                                if getattr(value, 'm')[i] not in [j]:
                                     del a[key]
                                     break
                             else:
@@ -86,8 +89,8 @@ class DictionaryPlus(dict):
                 for i, j in filter_dict.items():
                     if hasattr(value, 'm') & (type(value.m) == type({})) & (i in value.m.keys()):
                         try:
-                            if type(j) == type(""):
-                                if eval("value.__getattr__('m')[\""+i+"\"]" + j):
+                            if type(j) is not list:
+                                if getattr(value, 'm')[i] in [j]:
                                     a[key] = value
                                     break
                             else:
@@ -98,8 +101,8 @@ class DictionaryPlus(dict):
                             pass
                     else:
                         try:
-                            if type(j) == type(""):
-                                if eval("value.__getattr__(\""+i+"\")" + j):
+                            if type(j) is not list:
+                                if getattr(value, i) in [j]:
                                     a[key] = value
                                     break
                             else:
@@ -109,14 +112,14 @@ class DictionaryPlus(dict):
                         except:
                             pass
 
-        if filter_style == 'negative':
+        if filter_style == 'negative all':
             a = {key: value for key, value in return_dict.items()}
             for key, value in return_dict.items():
                 for i, j in filter_dict.items():
                     if hasattr(value, i):
                         try:
-                            if type(j) == type(""):
-                                if eval("value.__getattr__(\""+i+"\")" + j):
+                            if type(j) is not list:
+                                if getattr(value, i) in [j]:
                                     del a[key]
                                     break
                             else:
@@ -127,8 +130,8 @@ class DictionaryPlus(dict):
                             pass
                     elif hasattr(value, 'm') & (type(value.m) == type({})) & (i in value.m.keys()):
                         try:
-                            if type(j) == type(""):
-                                if eval("value.__getattr__('m')[\""+i+"\"]" + j):
+                            if type(j) is not list:
+                                if getattr(value, 'm')[i] in [j]:
                                     del a[key]
                                     break
                             else:
@@ -140,6 +143,40 @@ class DictionaryPlus(dict):
                     else:
                         break
 
+        if filter_style == 'negative any':
+            b = {key: value for key, value in return_dict.items()}
+            for key, value in return_dict.items():
+                for i, j in filter_dict.items():
+                    if hasattr(value, i):
+                        try:
+                            if type(j) is not list:
+                                if getattr(value, i) not in [j]:
+                                    del b[key]
+                                    break
+                            else:
+                                if getattr(value, i) not in j:
+                                    del b[key]
+                                    break
+                        except:
+                            pass
+                    elif hasattr(value, 'm') & (type(value.m) == type({})) & (i in value.m.keys()):
+                        try:
+                            if type(j) is not list:
+                                if getattr(value, 'm')[i] not in [j]:
+                                    del b[key]
+                                    break
+                            else:
+                                if getattr(value, 'm')[i] not in j:
+                                    del b[key]
+                                    break
+                        except:
+                            pass
+                    else:
+                        del b[key]
+                        break
+            a = {key: value for key, value in return_dict.items()
+                 if key not in b.keys()}
+
         if condition != None:
             if a == {}:
                 for key, value in return_dict.items():
@@ -264,14 +301,17 @@ class Dataset(DictionaryPlus):
         return_dict = copy.deepcopy(self)
         a = {}
 
+        if filter_style not in {'all', 'any', 'negative all', 'negative any'}:
+            return return_dict
+
         if filter_style == 'all':
             a = {key: value for key, value in return_dict.items()}
             for key, value in return_dict.items():
                 for i, j in filter_dict.items():
                     if hasattr(value, i):
                         try:
-                            if type(j) == type(""):
-                                if not eval("value.__getattr__(\""+i+"\")" + j):
+                            if type(j) is not list:
+                                if getattr(value, i) not in [j]:
                                     del a[key]
                                     break
                             else:
@@ -282,8 +322,8 @@ class Dataset(DictionaryPlus):
                             pass
                     elif hasattr(value, 'm') & (type(value.m) == type({})) & (i in value.m.keys()):
                         try:
-                            if type(j) == type(""):
-                                if not eval("value.__getattr__('m')[\""+i+"\"]" + j):
+                            if type(j) is not list:
+                                if getattr(value, 'm')[i] not in [j]:
                                     del a[key]
                                     break
                             else:
@@ -301,8 +341,8 @@ class Dataset(DictionaryPlus):
                 for i, j in filter_dict.items():
                     if hasattr(value, 'm') & (type(value.m) == type({})) & (i in value.m.keys()):
                         try:
-                            if type(j) == type(""):
-                                if eval("value.__getattr__('m')[\""+i+"\"]" + j):
+                            if type(j) is not list:
+                                if getattr(value, 'm')[i] in [j]:
                                     a[key] = value
                                     break
                             else:
@@ -313,8 +353,8 @@ class Dataset(DictionaryPlus):
                             pass
                     else:
                         try:
-                            if type(j) == type(""):
-                                if eval("value.__getattr__(\""+i+"\")" + j):
+                            if type(j) is not list:
+                                if getattr(value, i) in [j]:
                                     a[key] = value
                                     break
                             else:
@@ -324,14 +364,14 @@ class Dataset(DictionaryPlus):
                         except:
                             pass
 
-        if filter_style == 'negative':
+        if filter_style == 'negative all':
             a = {key: value for key, value in return_dict.items()}
             for key, value in return_dict.items():
                 for i, j in filter_dict.items():
                     if hasattr(value, i):
                         try:
-                            if type(j) == type(""):
-                                if eval("value.__getattr__(\""+i+"\")" + j):
+                            if type(j) is not list:
+                                if getattr(value, i) in [j]:
                                     del a[key]
                                     break
                             else:
@@ -342,8 +382,8 @@ class Dataset(DictionaryPlus):
                             pass
                     elif hasattr(value, 'm') & (type(value.m) == type({})) & (i in value.m.keys()):
                         try:
-                            if type(j) == type(""):
-                                if eval("value.__getattr__('m')[\""+i+"\"]" + j):
+                            if type(j) is not list:
+                                if getattr(value, 'm')[i] in [j]:
                                     del a[key]
                                     break
                             else:
@@ -355,6 +395,39 @@ class Dataset(DictionaryPlus):
                     else:
                         break
 
+        if filter_style == 'negative any':
+            b = {key: value for key, value in return_dict.items()}
+            for key, value in return_dict.items():
+                for i, j in filter_dict.items():
+                    if hasattr(value, i):
+                        try:
+                            if type(j) is not list:
+                                if getattr(value, i) not in [j]:
+                                    del b[key]
+                                    break
+                            else:
+                                if getattr(value, i) not in j:
+                                    del b[key]
+                                    break
+                        except:
+                            pass
+                    elif hasattr(value, 'm') & (type(value.m) == type({})) & (i in value.m.keys()):
+                        try:
+                            if type(j) is not list:
+                                if getattr(value, 'm')[i] not in [j]:
+                                    del b[key]
+                                    break
+                            else:
+                                if getattr(value, 'm')[i] not in j:
+                                    del b[key]
+                                    break
+                        except:
+                            pass
+                    else:
+                        del b[key]
+                        break
+            a = {key:value for key,value in return_dict.items() if key not in b.keys()}
+
         if condition != None:
             if a == {}:
                 for key, value in return_dict.items():
@@ -703,7 +776,6 @@ class Dataset(DictionaryPlus):
             return pd.concat([out[k] for k in out.keys()]).reset_index()
         return out
 
-
     def save_data(self, directory="./saved/", levels=[]):
         def get_specific_level(v, j):
             if hasattr(v, j):
@@ -919,6 +991,8 @@ class Summary(pd.DataFrame):
         # Only conditions referring to existing columns can be evaluated.
         conditions = []
         for column, values in filter_dict.items():
+            if type(values) is not list:
+                values = [values]
             if column in return_dict.columns:
                 conditions.append(return_dict[column].isin(values).to_numpy())
 

{apmtools-0.2.13 → apmtools-0.2.15}/src/apmtools/shiny/summary.py

@@ -44,7 +44,10 @@ def _default_x(data: pd.DataFrame) -> str:
         for column in data.columns
         if pd.api.types.is_datetime64_any_dtype(data[column])
     ]
-    return str(datetime_columns[0] if datetime_columns else data.columns[0])
+    if "time" in datetime_columns:
+        return "time"
+    else:
+        return str(datetime_columns[0] if datetime_columns else data.columns[0])
 
 def _default_group(data: pd.DataFrame) -> str | None:
     """Return ``identifier`` when available."""
@@ -58,7 +61,6 @@ def _numeric_columns(data: pd.DataFrame) -> list[str]:
         if pd.api.types.is_numeric_dtype(data[column])
     ]
 
-
 def _normalise_y(data: pd.DataFrame, x: str, y: str | Sequence[str] | None) -> list[str]:
     """Validate and normalise an initial Y selection."""
     numeric = _numeric_columns(data)
@@ -71,6 +73,25 @@ def _normalise_y(data: pd.DataFrame, x: str, y: str | Sequence[str] | None) -> l
     return [str(column) for column in values]
 
 
+def _categorical_columns(data: pd.DataFrame) -> list[str]:
+    """Return columns suitable for a boxplot categorical X axis."""
+    return sorted(
+        [
+            str(column)
+            for column in data.columns
+            if not pd.api.types.is_numeric_dtype(data[column])
+            and not pd.api.types.is_datetime64_any_dtype(data[column])
+        ],
+        key=str.casefold,
+    )
+
+
+def _alphabetical(values) -> list[str]:
+    """Return string values sorted alphabetically, case-insensitively."""
+    return sorted((str(value) for value in values), key=str.casefold)
+
+
+
 def _subset_choices(data: pd.DataFrame, column: str) -> tuple[dict[str, str], dict[str, object]]:
     """Build stable Shiny choices and their corresponding original values."""
     values = pd.unique(data[column].dropna())
@@ -250,9 +271,10 @@ def create_summary_app(
         raise ValueError(
             "Cannot create a Shiny application from an empty Summary.")
 
-    columns = [str(c) for c in summary.columns]
+    columns = _alphabetical(summary.columns)
     column_map = {str(c): c for c in summary.columns}
-    numeric_columns = _numeric_columns(summary)
+    numeric_columns = _alphabetical(_numeric_columns(summary))
+    categorical_columns = _categorical_columns(summary)
 
     x = _default_x(summary) if x is None else str(x)
     if x not in column_map:
@@ -281,12 +303,8 @@ def create_summary_app(
             ui.h4("Plot controls"),
             ui.input_select("plot_type", "Plot type",
                             choices=PLOT_TYPES, selected=plot_type),
-            ui.input_select("x", "X-axis / category",
-                            choices=columns, selected=x),
-            ui.input_selectize(
-                "y", "Y-axis / variable", choices=numeric_columns,
-                selected=initial_y, multiple=True,
-            ),
+            ui.output_ui("x_control"),
+            ui.output_ui("y_control"),
             ui.input_selectize(
                 "group_by", "Group by",
                 choices={c: c for c in columns},
@@ -338,6 +356,43 @@ def create_summary_app(
     )
 
     def server(input, output, session):
+        @render.ui
+        def x_control():
+            """Use categorical X choices for boxplots; all columns otherwise."""
+            if input.plot_type() == "box":
+                if not categorical_columns:
+                    return ui.help_text(
+                        "Boxplots require at least one categorical column for the X axis."
+                    )
+                selected = x if x in categorical_columns else categorical_columns[0]
+                return ui.input_select(
+                    "x", "X-axis / category",
+                    choices={c: c for c in categorical_columns},
+                    selected=selected,
+                )
+            return ui.input_select(
+                "x", "X-axis / category",
+                choices={c: c for c in columns},
+                selected=x,
+            )
+
+        @render.ui
+        def y_control():
+            """Boxplots accept one numeric Y variable; other plots accept many."""
+            if input.plot_type() == "box":
+                selected = initial_y[0] if initial_y else (
+                    numeric_columns[0] if numeric_columns else None)
+                return ui.input_select(
+                    "y", "Y-axis / variable",
+                    choices={c: c for c in numeric_columns},
+                    selected=selected,
+                )
+            return ui.input_selectize(
+                "y", "Y-axis / variable",
+                choices={c: c for c in numeric_columns},
+                selected=initial_y, multiple=True,
+            )
+
         @render.ui
         def subset_filters():
             """Render one value selector for every selected subset column."""
@@ -395,7 +450,9 @@ def create_summary_app(
         @reactive.calc
         def selected_data():
             current = filtered_summary()
-            selected_y = list(input.y())
+            y_input = input.y()
+            selected_y = ([y_input] if isinstance(
+                y_input, str) else list(y_input or []))
             if not selected_y:
                 return pd.DataFrame()
 
@@ -405,9 +462,18 @@ def create_summary_app(
             frequency = FREQUENCIES[input.frequency()]
             aggregate = AGGREGATES[input.aggregate()]
 
+            # A boxplot's categorical X must survive group_stat(). Include it
+            # as a statistical grouping key when frequency aggregation is used,
+            # without turning it into a colour/group selection in the UI.
+            if input.plot_type() == "box":
+                selected_x = input.x()
+                if selected_x in column_map:
+                    box_x = column_map[selected_x]
+                    if box_x not in grouping_by:
+                        grouping_by = [*grouping_by, box_x]
+
             # All selected grouping columns are passed directly to
-            # Summary.group_stat() when a frequency is selected.  With raw
-            # data they remain plotting-only grouping columns.
+            # Summary.group_stat() when a frequency is selected.
             if frequency is not None:
                 current = _aggregate(current, y_columns,
                                      frequency, grouping_by, aggregate)
@@ -419,7 +485,9 @@ def create_summary_app(
             plot_df = selected_data()
             selected_plot = input.plot_type()
             selected_x = input.x()
-            selected_y = list(input.y())
+            y_input = input.y()
+            selected_y = ([y_input] if isinstance(
+                y_input, str) else list(y_input or []))
             selected_groups = list(input.group_by())
             frequency = FREQUENCIES[input.frequency()]
 
@@ -441,7 +509,12 @@ def create_summary_app(
                 y_columns = _aggregated_value_columns(
                     plot_df, selected_y_columns, aggregate
                 )
-                x_column = frequency
+                if selected_plot == "box":
+                    if selected_x not in column_map:
+                        return px.scatter(title="Select a categorical X variable for the boxplot")
+                    x_column = column_map[selected_x]
+                else:
+                    x_column = frequency
 
                 if x_column not in plot_df.columns:
                     return px.scatter(
@@ -511,18 +584,23 @@ def create_summary_app(
                         opacity=0.65 if len(y_columns) > 1 else 1.0,
                     )
             elif selected_plot == "box":
-                if not group_columns:
-                    long_df = plot_df[y_columns].melt(
-                        var_name="variable", value_name="value")
-                    fig = px.box(long_df, x="variable",
-                                 y="value", points="outliers")
+                # Boxplots are distributions of one numerical variable across
+                # categories. X is therefore always the selected categorical
+                # column and Y is exactly one numerical variable.
+                if x_column not in categorical_columns:
+                    return px.scatter(
+                        title="Boxplots require a categorical variable on the X axis"
+                    )
+                y_column = y_columns[0]
+                if group_columns:
+                    fig = px.box(
+                        plot_df, x=x_column, y=y_column,
+                        color="__plot_group", points="outliers",
+                    )
                 else:
-                    group_column = "__plot_group"
-                    long_df = plot_df[[group_column, *y_columns]].melt(
-                        id_vars=[group_column], var_name="variable", value_name="value",
+                    fig = px.box(
+                        plot_df, x=x_column, y=y_column, points="outliers"
                     )
-                    fig = px.box(long_df, x="variable", y="value",
-                                 color=group_column, points="outliers")
             elif selected_plot == "bar":
                 if not group_columns:
                     fig = px.bar(plot_df, x=x_column,