plot-misc 2.0.2__tar.gz → 2.0.4__tar.gz

plot_misc-2.0.4/MANIFEST.in

@@ -0,0 +1,16 @@
+# include top-level metadata
+include README.md LICENSE
+include requirements.txt
+include requirements-dev.txt
+
+# ship the example datasets explicitly
+recursive-include plot_misc/example_data/example_datasets *.tsv.gz *.txt
+
+# drop these 
+prune tests
+prune resources
+
+# drop the rest
+global-exclude .*
+global-exclude *.py[cod]
+global-exclude __pycache__/*

{plot_misc-2.0.2 → plot_misc-2.0.4}/PKG-INFO

@@ -1,10 +1,11 @@
 Metadata-Version: 2.4
 Name: plot-misc
-Version: 2.0.2
+Version: 2.0.4
 Summary: Various plotting templates built on top of matplotlib
 Author-email: A Floriaan Schmidt <floriaanschmidt@gmail.com>
 License-Expression: GPL-3.0-or-later
 Project-URL: Homepage, https://gitlab.com/SchmidtAF/plot-misc
+Project-URL: Documentation, https://schmidtaf.gitlab.io/plot-misc/
 Classifier: Programming Language :: Python
 Classifier: Programming Language :: Python :: 3
 Classifier: Programming Language :: Python :: 3.10
@@ -14,46 +15,68 @@ Classifier: Programming Language :: Python :: Implementation :: PyPy
 Requires-Python: <3.13,>=3.10
 Description-Content-Type: text/markdown
 License-File: LICENSE
-Requires-Dist: numpy
-Requires-Dist: pandas
-Requires-Dist: matplotlib
-Requires-Dist: seaborn
-Requires-Dist: scipy
-Requires-Dist: scikit-learn
-Requires-Dist: adjustText
+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
+Requires-Dist: adjustText>=1.3
 Provides-Extra: dev
+Requires-Dist: python-build; extra == "dev"
 Requires-Dist: twine; extra == "dev"
-Requires-Dist: build; extra == "dev"
+Requires-Dist: setuptools; extra == "dev"
+Requires-Dist: wheel; extra == "dev"
+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: jupyter; extra == "dev"
 Dynamic: license-file
 
 # A collection of plotting functions
-__version__: `2.0.2`
+__version__: `2.0.4`
 
+This repository collects plotting modules written on top of `matplotlib`.
+The functions are intended to set up light-touch, basic illustrations that
+can be customised using the standard matplotlib interface via axes and figures.
+Functionality is included to create illustrations commonly used in medical research,
+covering forest plots, volcano plots, incidence matrices/bubble charts,
+illustrations to evaluate prediction models (e.g. feature importance, net benefit, calibration plots),
+and more.
 
-This repository collects plotting modules written on top of `matplotlib` or
-`seaborn`. 
-The functions are intended to set-up a light-touch basic illustration which 
-can be customised using the normal matplotlib interface using axes and figures. 
+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 
+available on gitlab. 
 
-The documentation for plot-misc can be found [here](https://SchmidtAF.gitlab.io/plot-misc/). 
+### Installation using PyPI
 
+To install the package from PyPI, run:
 
-## Installation 
-At present, this package is undergoing development and no packages exist yet on PyPI.
-Therefore it is recommended that you install in either of the two ways below.
+```sh
+pip install plot-misc
+```
+
+This installs the latest stable release along with its dependencies.
 
 ### Installation using conda
-I maintain a conda package in my personal conda channel. To install from this please run:
 
-```
+A Conda package is maintained in my personal Conda channel.
+To install from this channel, run:
+
+
+```sh
 conda install afschmidt::plot_misc
 ```
 
-### Installation using pip
+### Installation using gitlab
+
+If you require the latest updates, potentially not yet formally released, you can install the package directly from GitLab.
 
-You can install using pip from the root of the cloned repository,
-first clone and cd into the repository root:
+First, clone the repository and move into its root directory:
 
 ```sh
 git clone git@gitlab.com:SchmidtAF/plot-misc.git
@@ -80,8 +103,8 @@ Next the package can be installed:
 python -m pip install .
 ```
 
-Or for an editable (developer) install run the command below from the root of 
-the repository.
+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:
 
@@ -90,9 +113,10 @@ python -m pip install -e .
 
 ```
 
-## Next steps...
-After installation you might wish to try the `pytest` to confirm 
-everything is in working order. 
+#### Validating the package
+
+After installing the package from GitLab, you may wish to run the test
+suite to confirm everything is working as expected:
 
 ```sh
 # From the root of the repository

plot_misc-2.0.4/README.md

@@ -0,0 +1,94 @@
+# A collection of plotting functions
+__version__: `2.0.4`
+
+This repository collects plotting modules written on top of `matplotlib`.
+The functions are intended to set up light-touch, basic illustrations that
+can be customised using the standard matplotlib interface via axes and figures.
+Functionality is included to create illustrations commonly used in medical research,
+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/). 
+
+## Installation 
+The package is available on PyPI, and conda, with the latest source code 
+available on gitlab. 
+
+### Installation using PyPI
+
+To install the package from PyPI, run:
+
+```sh
+pip install plot-misc
+```
+
+This installs the latest stable release along with its dependencies.
+
+### Installation using conda
+
+A Conda package is maintained in my personal Conda channel.
+To install from this channel, run:
+
+
+```sh
+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.
+
+First, clone the repository and move into its root directory:
+
+```sh
+git clone git@gitlab.com:SchmidtAF/plot-misc.git
+cd plot-misc
+```
+
+Install the dependencies:
+
+```sh
+# From the root of the repository
+conda env create --file ./resources/conda/envs/conda_create.yaml
+```
+
+To add to an existing environment use:
+
+```sh
+# 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 .
+```
+
+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:
+
+```sh
+python -m pip install -e .
+
+```
+
+#### Validating the package
+
+After installing the package from GitLab, you may wish to run the test
+suite to confirm everything is working as expected:
+
+```sh
+# From the root of the repository
+pytest tests
+```
+
+## Usage
+
+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/_version.py

@@ -0,0 +1 @@
+__version__ = '2.0.4'

{plot_misc-2.0.2 → plot_misc-2.0.4}/plot_misc/barchart.py

@@ -83,6 +83,14 @@ def bar(data:pd.DataFrame, label:str, column:str,
         Matplotlib figure object.
     ax : plt.Axes
         Matplotlib axes with the rendered bar plot.
+    
+    Notes
+    -----
+    This function is essentially a helper function for the more complicated
+    bar charts in this module and simply wraps matplotlib's bar function.
+    It is included as a public function to allow people to use the same
+    interface when working with plot-misc. If one is exclusively looking to
+    use `bar` it is advisable to simply revert to matplotlib's offering.
     """
     # check input
     is_df(data)
@@ -235,30 +243,30 @@ def stack_bar(data:pd.DataFrame, label:str, columns:list[str],
                              'number of colours ({1}).'.format(
                                  len(columns), len(colours)))
     # get labels
-    labels = data[label]
+    # labels = data[label]
     # get columns
     fields=columns
     # actual plotting
     left = len(data) * [0]
     for idx, name in enumerate(fields):
+        new_kwargs = _update_kwargs(update_dict=kwargs,
+                                    edgecolor=edgecolour,
+                                    color=colours[idx],
+                                    alpha=transparency,
+                                    )
         if horizontal == False:
-            # plotting vertical bar chart
-            new_kwargs = _update_kwargs(update_dict=kwargs,
-                                        edgecolor=edgecolour,
-                                        width=wd, color=colours[idx],
-                                        alpha=transparency,
+            new_kwargs = _update_kwargs(new_kwargs, bottom=left,
                                         )
-            ax.bar(labels, height=data[name], bottom=left, **new_kwargs,
-                   )
         else:
-            # horizontal bar chart
-            new_kwargs = _update_kwargs(update_dict=kwargs, edgecolor=edgecolour,
-                                        height=wd, color=colours[idx],
-                                        alpha=transparency,
+            new_kwargs = _update_kwargs(new_kwargs, left=left,
                                         )
-            ax.barh(labels, width=data[name], left=left, **new_kwargs,
+        # The actual plotting
+        # NOTE adding wd here because it bar assigns it to either width or
+        # height depending on horizontal.
+        _, ax = bar(data=data, label=label, column=name, horizontal=horizontal,
+                    wd=wd, ax=ax, kwargs_bar=new_kwargs,
                     )
-        # update the locations
+        # updating the coordinate where the last bar stops
         left = left + data[name]
     # removing spines
     ax.spines['right'].set_visible(False)

{plot_misc-2.0.2 → plot_misc-2.0.4}/plot_misc/volcano.py

@@ -113,6 +113,15 @@ def plot_volcano(data:DataFrame, y_column:str, x_column:str,
         The created figure (if `ax` was not provided).
     ax : `matplotlib.axes.Axes`
         The matplotlib axis containing the plot.
+    
+    Notes
+    -----
+    When `adjust=True`, text labels are repositioned using the `adjustText`
+    package to reduce overlaps. This is particularly helpful when multiple
+    points are labelled in a crowded region. Additional options can be passed
+    to `adjustText` via `label_kwargs_dict`.
+    
+    Please see the module documentation `here <https://pypi.org/project/adjustText/>`_.
     """
     FT_FAM = 'font.family'
     # ###### Check input

{plot_misc-2.0.2 → plot_misc-2.0.4}/plot_misc.egg-info/PKG-INFO

@@ -1,10 +1,11 @@
 Metadata-Version: 2.4
 Name: plot-misc
-Version: 2.0.2
+Version: 2.0.4
 Summary: Various plotting templates built on top of matplotlib
 Author-email: A Floriaan Schmidt <floriaanschmidt@gmail.com>
 License-Expression: GPL-3.0-or-later
 Project-URL: Homepage, https://gitlab.com/SchmidtAF/plot-misc
+Project-URL: Documentation, https://schmidtaf.gitlab.io/plot-misc/
 Classifier: Programming Language :: Python
 Classifier: Programming Language :: Python :: 3
 Classifier: Programming Language :: Python :: 3.10
@@ -14,46 +15,68 @@ Classifier: Programming Language :: Python :: Implementation :: PyPy
 Requires-Python: <3.13,>=3.10
 Description-Content-Type: text/markdown
 License-File: LICENSE
-Requires-Dist: numpy
-Requires-Dist: pandas
-Requires-Dist: matplotlib
-Requires-Dist: seaborn
-Requires-Dist: scipy
-Requires-Dist: scikit-learn
-Requires-Dist: adjustText
+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
+Requires-Dist: adjustText>=1.3
 Provides-Extra: dev
+Requires-Dist: python-build; extra == "dev"
 Requires-Dist: twine; extra == "dev"
-Requires-Dist: build; extra == "dev"
+Requires-Dist: setuptools; extra == "dev"
+Requires-Dist: wheel; extra == "dev"
+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: jupyter; extra == "dev"
 Dynamic: license-file
 
 # A collection of plotting functions
-__version__: `2.0.2`
+__version__: `2.0.4`
 
+This repository collects plotting modules written on top of `matplotlib`.
+The functions are intended to set up light-touch, basic illustrations that
+can be customised using the standard matplotlib interface via axes and figures.
+Functionality is included to create illustrations commonly used in medical research,
+covering forest plots, volcano plots, incidence matrices/bubble charts,
+illustrations to evaluate prediction models (e.g. feature importance, net benefit, calibration plots),
+and more.
 
-This repository collects plotting modules written on top of `matplotlib` or
-`seaborn`. 
-The functions are intended to set-up a light-touch basic illustration which 
-can be customised using the normal matplotlib interface using axes and figures. 
+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 
+available on gitlab. 
 
-The documentation for plot-misc can be found [here](https://SchmidtAF.gitlab.io/plot-misc/). 
+### Installation using PyPI
 
+To install the package from PyPI, run:
 
-## Installation 
-At present, this package is undergoing development and no packages exist yet on PyPI.
-Therefore it is recommended that you install in either of the two ways below.
+```sh
+pip install plot-misc
+```
+
+This installs the latest stable release along with its dependencies.
 
 ### Installation using conda
-I maintain a conda package in my personal conda channel. To install from this please run:
 
-```
+A Conda package is maintained in my personal Conda channel.
+To install from this channel, run:
+
+
+```sh
 conda install afschmidt::plot_misc
 ```
 
-### Installation using pip
+### Installation using gitlab
+
+If you require the latest updates, potentially not yet formally released, you can install the package directly from GitLab.
 
-You can install using pip from the root of the cloned repository,
-first clone and cd into the repository root:
+First, clone the repository and move into its root directory:
 
 ```sh
 git clone git@gitlab.com:SchmidtAF/plot-misc.git
@@ -80,8 +103,8 @@ Next the package can be installed:
 python -m pip install .
 ```
 
-Or for an editable (developer) install run the command below from the root of 
-the repository.
+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:
 
@@ -90,9 +113,10 @@ python -m pip install -e .
 
 ```
 
-## Next steps...
-After installation you might wish to try the `pytest` to confirm 
-everything is in working order. 
+#### Validating the package
+
+After installing the package from GitLab, you may wish to run the test
+suite to confirm everything is working as expected:
 
 ```sh
 # From the root of the repository

{plot_misc-2.0.2 → plot_misc-2.0.4}/plot_misc.egg-info/SOURCES.txt

@@ -1,6 +1,9 @@
 LICENSE
+MANIFEST.in
 README.md
 pyproject.toml
+requirements-dev.txt
+requirements.txt
 plot_misc/__init__.py
 plot_misc/_version.py
 plot_misc/barchart.py

plot_misc-2.0.4/plot_misc.egg-info/requires.txt

@@ -0,0 +1,19 @@
+pandas>=1.3
+numpy>=1.21
+matplotlib>=3.5
+seaborn>=0.11
+scipy>=1.5
+statsmodels>=0.1
+scikit-learn>=1.4
+adjustText>=1.3
+
+[dev]
+python-build
+twine
+setuptools
+wheel
+pytest>=6
+pytest-mock>=3
+pytest-dependency>=0.5
+bump2version>=1
+jupyter

{plot_misc-2.0.2 → plot_misc-2.0.4}/pyproject.toml

@@ -4,22 +4,14 @@ build-backend = "setuptools.build_meta"
 
 [project]
 name = "plot-misc"
-version = "2.0.2"
+version = "2.0.4"
 description = "Various plotting templates built on top of matplotlib"
 readme = "README.md"
 authors = [{ name = "A Floriaan Schmidt", email = "floriaanschmidt@gmail.com" }]
 license = "GPL-3.0-or-later"
 license-files = ["LICENSE"]
 requires-python = ">=3.10, <3.13"
-dependencies = [
-    "numpy",
-    "pandas",
-    "matplotlib",
-    "seaborn",
-    "scipy",
-    "scikit-learn",
-    "adjustText"
-]
+dynamic = ["dependencies", "optional-dependencies"]
 classifiers = [
     "Programming Language :: Python",
     "Programming Language :: Python :: 3",
@@ -29,11 +21,15 @@ classifiers = [
     "Programming Language :: Python :: Implementation :: PyPy"
 ]
 
-[project.optional-dependencies]
-dev = ["twine", "build"]
-
 [project.urls]
 Homepage = "https://gitlab.com/SchmidtAF/plot-misc"
+Documentation = "https://schmidtaf.gitlab.io/plot-misc/"
+
+[tool.setuptools.dynamic]
+dependencies = { file = ["requirements.txt"] }
+
+[tool.setuptools.dynamic.optional-dependencies]
+dev = { file = ["requirements-dev.txt"] }
 
 [tool.setuptools.packages.find]
 include = ["plot_misc*"]

plot_misc-2.0.4/requirements-dev.txt

@@ -0,0 +1,9 @@
+python-build
+twine
+setuptools
+wheel
+pytest>=6
+pytest-mock>=3
+pytest-dependency>=0.5
+bump2version>=1
+jupyter

plot_misc-2.0.4/requirements.txt

@@ -0,0 +1,9 @@
+pandas>=1.3
+numpy>=1.21
+matplotlib>=3.5
+seaborn>=0.11
+scipy>=1.5
+statsmodels>=0.1
+scikit-learn>=1.4
+adjustText>=1.3
+

plot_misc-2.0.2/README.md

@@ -1,79 +0,0 @@
-# A collection of plotting functions
-__version__: `2.0.2`
-
-
-This repository collects plotting modules written on top of `matplotlib` or
-`seaborn`. 
-The functions are intended to set-up a light-touch basic illustration which 
-can be customised using the normal matplotlib interface using axes and figures. 
-
-
-The documentation for plot-misc can be found [here](https://SchmidtAF.gitlab.io/plot-misc/). 
-
-
-## Installation 
-At present, this package is undergoing development and no packages exist yet on PyPI.
-Therefore it is recommended that you install in either of the two ways below.
-
-### Installation using conda
-I maintain a conda package in my personal conda channel. To install from this please run:
-
-```
-conda install afschmidt::plot_misc
-```
-
-### Installation using pip
-
-You can install using pip from the root of the cloned repository,
-first clone and cd into the repository root:
-
-```sh
-git clone git@gitlab.com:SchmidtAF/plot-misc.git
-cd plot-misc
-```
-
-Install the dependencies:
-
-```sh
-# From the root of the repository
-conda env create --file ./resources/conda/envs/conda_create.yaml
-```
-
-To add to an existing environment use:
-
-```sh
-# 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 .
-```
-
-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:
-
-```sh
-python -m pip install -e .
-
-```
-
-## Next steps...
-After installation you might wish to try the `pytest` to confirm 
-everything is in working order. 
-
-```sh
-# From the root of the repository
-pytest tests
-```
-
-## Usage
-
-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-2.0.2/plot_misc/_version.py

@@ -1 +0,0 @@
-__version__ = '2.0.2'

plot_misc-2.0.2/plot_misc.egg-info/requires.txt

@@ -1,11 +0,0 @@
-numpy
-pandas
-matplotlib
-seaborn
-scipy
-scikit-learn
-adjustText
-
-[dev]
-twine
-build