plot-misc 2.0.4__tar.gz → 2.2.0__tar.gz

{plot_misc-2.0.4/plot_misc.egg-info → plot_misc-2.2.0}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: plot-misc
-Version: 2.0.4
+Version: 2.2.0
 Summary: Various plotting templates built on top of matplotlib
 Author-email: A Floriaan Schmidt <floriaanschmidt@gmail.com>
 License-Expression: GPL-3.0-or-later
@@ -18,7 +18,6 @@ License-File: LICENSE
 Requires-Dist: pandas>=1.3
 Requires-Dist: numpy>=1.21
 Requires-Dist: matplotlib>=3.5
-Requires-Dist: seaborn>=0.11
 Requires-Dist: scipy>=1.5
 Requires-Dist: statsmodels>=0.1
 Requires-Dist: scikit-learn>=1.4
@@ -32,11 +31,14 @@ Requires-Dist: pytest>=6; extra == "dev"
 Requires-Dist: pytest-mock>=3; extra == "dev"
 Requires-Dist: pytest-dependency>=0.5; extra == "dev"
 Requires-Dist: bump2version>=1; extra == "dev"
+Requires-Dist: codespell; extra == "dev"
 Requires-Dist: jupyter; extra == "dev"
 Dynamic: license-file
 
+<img src="https://schmidtaf.gitlab.io/plot-misc/_images/icon.png" alt="plot-misc icon" width="250"/>
+
 # A collection of plotting functions
-__version__: `2.0.4`
+__version__: `2.2.0`
 
 This repository collects plotting modules written on top of `matplotlib`.
 The functions are intended to set up light-touch, basic illustrations that
@@ -46,7 +48,8 @@ covering forest plots, volcano plots, incidence matrices/bubble charts,
 illustrations to evaluate prediction models (e.g. feature importance, net benefit, calibration plots),
 and more.
 
-The documentation for plot-misc can be found [here](https://SchmidtAF.gitlab.io/plot-misc/). 
+The documentation for plot-misc can be found 
+[here](https://SchmidtAF.gitlab.io/plot-misc/). 
 
 ## Installation 
 The package is available on PyPI, and conda, with the latest source code 
@@ -56,7 +59,7 @@ available on gitlab.
 
 To install the package from PyPI, run:
 
-```sh
+```bash
 pip install plot-misc
 ```
 
@@ -68,49 +71,94 @@ A Conda package is maintained in my personal Conda channel.
 To install from this channel, run:
 
 
-```sh
-conda install afschmidt::plot_misc
+```bash
+conda install afschmidt::plot-misc
 ```
 
 ### Installation using gitlab
 
-If you require the latest updates, potentially not yet formally released, you can install the package directly from GitLab.
+If you require the latest updates, potentially not yet formally released,
+you can install the package directly from GitLab.
 
 First, clone the repository and move into its root directory:
 
-```sh
+```bash
 git clone git@gitlab.com:SchmidtAF/plot-misc.git
 cd plot-misc
 ```
 
 Install the dependencies:
 
-```sh
+```bash
 # From the root of the repository
 conda env create --file ./resources/conda/envs/conda_create.yaml
 ```
 
 To add to an existing environment use:
 
-```sh
+```bash
 # From the root of the repository
 conda env update --file ./resources/conda/envs/conda_update.yaml
 ```
 
 Next the package can be installed: 
 
-```sh
-python -m pip install .
+```bash
+make install
 ```
 
-Or for an editable (developer) install run the command below from the 
-root of the repository.
-The difference with this is that you can just run `git pull` to 
-update repository, or switch branches without re-installing:
+#### Development
+For development work, install the package in editable mode with Git commit 
+hooks configured:
+
+```bash
+make install-dev
+```
+This command installs the package in editable mode and configures Git commit 
+hooks, allowing you to run `git pull` to update the repository or switch 
+branches without reinstalling.
 
-```sh
+Alternatively, you can install manually:
+```bash
 python -m pip install -e .
+python .setup_git_hooks.py
+```
+
+#### Git Hooks Configuration
+
 
+When setting up a development environment, the `setup-hooks` command 
+configures Git hooks to enforce conventional commit message formatting and 
+spell check using `codespell`.
+
+To view the commit message format requirements, run:
+
+```bash
+./.githooks/commit-msg -help
+```
+
+For frequent use, add this function to your shell configuration (`~/.bashrc` 
+or `~/.zshrc`):
+
+```bash
+commit-format-help() {
+    local git_root
+    git_root=$(git rev-parse --show-toplevel 2>/dev/null)
+    
+    if [ -z "$git_root" ]; then
+        echo "Error: Not inside a git repository"
+        return 1
+    fi
+    
+    local hook_path="$git_root/.githooks/commit-msg"
+    
+    if [ ! -f "$hook_path" ]; then
+        echo "Error: commit-msg hook not found"
+        return 1
+    fi
+    
+    "$hook_path" --help
+}
 ```
 
 #### Validating the package
@@ -118,7 +166,7 @@ python -m pip install -e .
 After installing the package from GitLab, you may wish to run the test
 suite to confirm everything is working as expected:
 
-```sh
+```bash
 # From the root of the repository
 pytest tests
 ```
@@ -129,3 +177,4 @@ Please have a look at the examples in
 [resources](https://gitlab.com/SchmidtAF/plot-misc/-/tree/master/resources/examples)
 for some possible recipes. 
 
+

{plot_misc-2.0.4 → plot_misc-2.2.0}/README.md

@@ -1,5 +1,7 @@
+<img src="https://schmidtaf.gitlab.io/plot-misc/_images/icon.png" alt="plot-misc icon" width="250"/>
+
 # A collection of plotting functions
-__version__: `2.0.4`
+__version__: `2.2.0`
 
 This repository collects plotting modules written on top of `matplotlib`.
 The functions are intended to set up light-touch, basic illustrations that
@@ -9,7 +11,8 @@ covering forest plots, volcano plots, incidence matrices/bubble charts,
 illustrations to evaluate prediction models (e.g. feature importance, net benefit, calibration plots),
 and more.
 
-The documentation for plot-misc can be found [here](https://SchmidtAF.gitlab.io/plot-misc/). 
+The documentation for plot-misc can be found 
+[here](https://SchmidtAF.gitlab.io/plot-misc/). 
 
 ## Installation 
 The package is available on PyPI, and conda, with the latest source code 
@@ -19,7 +22,7 @@ available on gitlab.
 
 To install the package from PyPI, run:
 
-```sh
+```bash
 pip install plot-misc
 ```
 
@@ -31,49 +34,94 @@ A Conda package is maintained in my personal Conda channel.
 To install from this channel, run:
 
 
-```sh
-conda install afschmidt::plot_misc
+```bash
+conda install afschmidt::plot-misc
 ```
 
 ### Installation using gitlab
 
-If you require the latest updates, potentially not yet formally released, you can install the package directly from GitLab.
+If you require the latest updates, potentially not yet formally released,
+you can install the package directly from GitLab.
 
 First, clone the repository and move into its root directory:
 
-```sh
+```bash
 git clone git@gitlab.com:SchmidtAF/plot-misc.git
 cd plot-misc
 ```
 
 Install the dependencies:
 
-```sh
+```bash
 # From the root of the repository
 conda env create --file ./resources/conda/envs/conda_create.yaml
 ```
 
 To add to an existing environment use:
 
-```sh
+```bash
 # From the root of the repository
 conda env update --file ./resources/conda/envs/conda_update.yaml
 ```
 
 Next the package can be installed: 
 
-```sh
-python -m pip install .
+```bash
+make install
 ```
 
-Or for an editable (developer) install run the command below from the 
-root of the repository.
-The difference with this is that you can just run `git pull` to 
-update repository, or switch branches without re-installing:
+#### Development
+For development work, install the package in editable mode with Git commit 
+hooks configured:
+
+```bash
+make install-dev
+```
+This command installs the package in editable mode and configures Git commit 
+hooks, allowing you to run `git pull` to update the repository or switch 
+branches without reinstalling.
 
-```sh
+Alternatively, you can install manually:
+```bash
 python -m pip install -e .
+python .setup_git_hooks.py
+```
+
+#### Git Hooks Configuration
+
 
+When setting up a development environment, the `setup-hooks` command 
+configures Git hooks to enforce conventional commit message formatting and 
+spell check using `codespell`.
+
+To view the commit message format requirements, run:
+
+```bash
+./.githooks/commit-msg -help
+```
+
+For frequent use, add this function to your shell configuration (`~/.bashrc` 
+or `~/.zshrc`):
+
+```bash
+commit-format-help() {
+    local git_root
+    git_root=$(git rev-parse --show-toplevel 2>/dev/null)
+    
+    if [ -z "$git_root" ]; then
+        echo "Error: Not inside a git repository"
+        return 1
+    fi
+    
+    local hook_path="$git_root/.githooks/commit-msg"
+    
+    if [ ! -f "$hook_path" ]; then
+        echo "Error: commit-msg hook not found"
+        return 1
+    fi
+    
+    "$hook_path" --help
+}
 ```
 
 #### Validating the package
@@ -81,7 +129,7 @@ python -m pip install -e .
 After installing the package from GitLab, you may wish to run the test
 suite to confirm everything is working as expected:
 
-```sh
+```bash
 # From the root of the repository
 pytest tests
 ```
@@ -92,3 +140,4 @@ Please have a look at the examples in
 [resources](https://gitlab.com/SchmidtAF/plot-misc/-/tree/master/resources/examples)
 for some possible recipes. 
 
+

plot_misc-2.2.0/plot_misc/_version.py

@@ -0,0 +1 @@
+__version__ = '2.2.0'

{plot_misc-2.0.4 → plot_misc-2.2.0}/plot_misc/barchart.py

@@ -21,9 +21,9 @@ group_bar(data, label, columns, ...)
     Plot a grouped bar chart with multiple bars per group, optionally
     with error bars.
 """
-import matplotlib.pyplot as plt
 import pandas as pd
 import numpy as np
+import matplotlib.pyplot as plt
 from plot_misc.utils.utils import _update_kwargs
 from plot_misc.errors import (
     is_type,
@@ -56,7 +56,7 @@ def bar(data:pd.DataFrame, label:str, column:str,
         The column name for the bar height values.
     error_max : `str`, default `NoneType`
         column name for the upper value of the error line segment.
-    error_min : ``str` default `NoneType`
+    error_min : `str`, default `NoneType`
         column name for the lower value of the error line segment.
     colours : `list` [`str`], default ['tab:blue', 'tab:pink']
         Colours for the bars; recycled if shorter than the number of bars.
@@ -233,7 +233,7 @@ def stack_bar(data:pd.DataFrame, label:str, columns:list[str],
         f, ax = plt.subplots(figsize=figsize)
     else:
         f = ax.figure
-    # ### should not be any missings
+    # ### should not be any missing
     # NOTE consider making this into a function
     if any(data.isna().any()):
         raise ValueError(Error_MSG.MISSING_DF.format('data'))

{plot_misc-2.0.4 → plot_misc-2.2.0}/plot_misc/errors.py

@@ -111,7 +111,7 @@ def is_type(param: Any, types: tuple[Type] | Type,
         if param_name is None:
             param_name = _get_param_name(param)
         else:
-            warnings.warn('`param_name` will be depricated.',
+            warnings.warn('`param_name` will be deprecated.',
                           DeprecationWarning,
                           stacklevel=2,
                           )
@@ -207,7 +207,7 @@ def is_series_type(column: pd.Series | pd.DataFrame, types: tuple[Type] | Type,
     ----------
     column : `pd.Series` or `pd.DataFrame`
         Data structure to validate.
-    types : `type` or `tuple` [`tupe`]
+    types : `type` or `tuple` [`type`]
         Allowed types for individual elements.
     
     Returns
@@ -232,7 +232,7 @@ def is_series_type(column: pd.Series | pd.DataFrame, types: tuple[Type] | Type,
         [is_type(col, types) for col in column]
     elif isinstance(column, pd.DataFrame):
         if version.parse('2.0.3') <= version.parse(pd.__version__):
-            # iteritems got depricated.
+            # iteritems got deprecated.
             column.iteritems = column.items
         for _, col in column.items():
             [is_type(co, types) for co in col]

{plot_misc-2.0.4 → plot_misc-2.2.0}/plot_misc/example_data/examples.py

@@ -635,3 +635,92 @@ def load_mace_associations(**kwargs):
     )
     # return
     return df
+
+# ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+def create_survival_data(nrows:int = 50,
+                         survival_rate:float = 0.02,
+                         ci_width:float=0.15,
+                         random_seed:int = 42,
+                         initial_n:int = 1000) -> pd.DataFrame:
+    """
+    Create pilot survival analysis data for testing.
+    
+    Parameters
+    ----------
+    nrows : int, default 50
+        Number of time points to generate
+    random_seed : int, default 42
+        Random seed for reproducibility
+    initial_n : int, default 1000
+        Initial number of subjects at risk at time zero
+        
+    Returns
+    -------
+    pd.DataFrame
+        DataFrame with survival data including survival estimates,
+        confidence intervals, and at-risk counts
+    """
+    np.random.seed(random_seed)
+    
+    # Create time points
+    time_points = np.linspace(0, 100, nrows)
+    
+    # Generate decreasing survival function with some noise
+    base_survival = np.exp(-time_points * survival_rate)  # Exponential decay
+    noise = np.random.normal(0, 0.01, nrows)
+    survival = np.clip(base_survival + noise, 0, 1)
+    
+    # Ensure monotonic decrease
+    survival = np.minimum.accumulate(survival)
+    
+    # Generate confidence intervals
+    ci_width = ci_width * survival  # CI width proportional to survival
+    lower_ci = np.clip(survival - ci_width, 0, 1)
+    upper_ci = np.clip(survival + ci_width, 0, 1)
+    
+    # Generate at-risk numbers directly from survival probabilities
+    at_risk = (survival * initial_n).astype(int)
+    
+    # Create DataFrame
+    df = pd.DataFrame({
+        'survival_estimate': survival,
+        'lower_ci_95': lower_ci,
+        'upper_ci_95': upper_ci,
+        'at_risk': at_risk,
+        'time': time_points
+    })
+    
+    df.set_index('time', inplace=True)
+    return df
+
+# ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+@dataset
+def load_survival_table(**kwargs):
+    """
+    Returns a survival table with information on the `time` (in days) an event
+    occurred the cumulative events per discordancy group. The time per year
+    is provided as the time_format column.
+    
+    Returns
+    -------
+    pd.DataFrame
+    """
+    # data
+    table = pd.DataFrame(
+        {
+            'time': [0, 365, 730, 1095, 1461, 1826, 2191, 2556, 2922, 3287,
+                     3652, 4017, 4383, 4748, 5113, 5478],
+            'Not Discordant': ['268,196', '263,426', '258,484', '254,009',
+                               '249,315', '244,907', '240,562', '236,574',
+                               '233,347', '230,368', '227,648', '224,916',
+                               '222,169', '172,545', '95,987', '15,280'],
+            'Discordant': ['5,749', '5,629', '5,494', '5,374',
+                                 '5,245', '5,129', '5,029', '4,935',
+                                 '4,863', '4,777', '4,714', '4,634',
+                                 '4,558', '3,586', '2,030', '346'],
+            'time_format': [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15]
+        }, **kwargs,
+    )
+    # return
+    return table
+

{plot_misc-2.0.4 → plot_misc-2.2.0}/plot_misc/forest.py

@@ -394,9 +394,9 @@ class ForestPlot(object):
         - 'max' : float
             The upper bound of the span in data coordinates.
         - 'kwargs' : dict
-        A dictionary of keyword arguments to be passed to the span plotting
-        function (e.g., `ax.axhspan()`), such as `facecolor`, `alpha`,
-        `zorder`, etc.
+            A dictionary of keyword arguments to be passed to the span plotting
+            function (e.g., `ax.axhspan()`), such as `facecolor`, `alpha`,
+            `zorder`, etc.
     
     Notes
     -----
@@ -587,7 +587,7 @@ class ForestPlot(object):
         is_type(span_colour, list)
         is_type(reverse_y, bool)
         is_type(ylim, (type(None), tuple))
-        # ### set defauls
+        # ### set defaults
         # replace None by empty dict
         kwargs_scatter_dict = kwargs_scatter_dict or {}
         kwargs_plot_ci_dict = kwargs_plot_ci_dict or {}
@@ -701,7 +701,7 @@ class ForestPlot(object):
         y_mid.insert(0, y_locations.iloc[0][FNames.min])
         y_mid[-1] = self.ax.get_ylim()[1] # replace with y-axis limit
         # ################### Add horizontal segments
-        # to store the span y-axis coordiniates, colours
+        # to store the span y-axis coordinates, colours
         if span ==True:
             span_dict = {}
             # add segments
@@ -767,7 +767,7 @@ def plot_table(
     Parameters
     ----------
     data : `pd.DataFrame`
-        Pandas DataFrame containg `string_col` that should be plotted.
+        Pandas DataFrame containing `string_col` that should be plotted.
         margin of error, etc.
     ax : plt.axes
             Axes to operate on.
@@ -858,7 +858,7 @@ def plot_table(
     kwargs_yticklabel_dict = kwargs_yticklabel_dict or {}
     # ################### remove spines
     ax.spines[['top', 'right', 'bottom', 'left']].set_visible(False)
-    # remove lables
+    # remove labels
     ax.xaxis.set_ticklabels([])
     # remove ticks
     ax.set_xticks([])
@@ -869,7 +869,7 @@ def plot_table(
         raise ValueError('`yticklabel` should be supplied if `ytickloc` is defined.')
     if (not yticklabel is None) and (not ytickloc is None):
         if len(yticklabel) != len(ytickloc):
-            raise IndexError('`yticklabel` and `ytickloc` containts distinct values.')
+            raise IndexError('`yticklabel` and `ytickloc` contains distinct values.')
         # add optional label padding
         if not l_yticklab_pad is None:
             yticklabel = [l_yticklab_pad + str(s) for s in yticklabel]
@@ -1000,15 +1000,15 @@ class EmpericalSupport(object):
     -----
     This implementation is based on the concept of compatibility (or
     confidence) curves, which visualise the range of parameter values supported
-    by the data across a continuum of alpha levels [1]_, [2]_.
+    by the data across a continuum of alpha levels [ES1]_, [ES2]_.
     
     References
     ----------
-    .. [1] Amrhein, V., Greenland, S., & McShane, B. B. (2019).
+    .. [ES1] Amrhein, V., Greenland, S., & McShane, B. B. (2019).
        Scientists rise up against statistical significance.
        *Nature*, 567(7748), 305–307. https://doi.org/10.1038/d41586-019-00857-9
     
-    .. [2] Van der Burg, S. H., & Gelman, A. (2020).
+    .. [ES2] Van der Burg, S. H., & Gelman, A. (2020).
        Empirical support plots and compatibility intervals.
        *BMC Medical Research Methodology*, 20, Article 109.
        https://doi.org/10.1186/s12874-020-01105-9
@@ -1026,7 +1026,7 @@ class EmpericalSupport(object):
         is_type(estimate, (int, float))
         is_type(standard_error, (int, float))
         is_type(alpha, (list, np.ndarray))
-        # asign
+        # assign
         self.estimate=estimate
         self.standard_error=standard_error
         self.alpha=alpha
@@ -1304,10 +1304,10 @@ class EmpericalSupport(object):
                   kwargs_text:dict[Any,Any] | None = None,
                   )-> tuple[plt.Figure, plt.Axes]:
         """
-        Plots an Emperical Support graph based on either `coverage` (iterating
+        Plots an Empirical Support graph based on either `coverage` (iterating
         the confidence interval coverage percentage), or `compatibility`
         (iterating the p-value). Due to its Christmas tree like shape this
-        type of illustration is refered to as a `tree plot`.
+        type of illustration is referred to as a `tree plot`.
         
         Parameters
         ----------