remove seaborn dependency

.github/workflows/deploy-conda.yml

@@ -50,6 +50,6 @@ jobs:
                   conda config --set anaconda_upload yes
                   export PATH=$(conda info --root):$PATH
                   export PATH=$(conda info --root)/bin:$PATH
-                  conda-build --output-folder . .
+                  conda build --output-folder conda-bld .
               env:
                   ANACONDA_API_TOKEN: ${{ secrets.ANACONDA_TOKEN }}

.github/workflows/deploy-pypi.yml

@@ -33,7 +33,7 @@ jobs:
                   python setup.py bdist_wheel
                   twine check dist/*
 
-            - name: Publish to PyPi
+            - name: Publish to PyPI
               uses: pypa/gh-action-pypi-publish@release/v1
               with:
                   verbose: true

.gitignore

@@ -12,9 +12,15 @@
 # cache
 __pycache__/
 *.py[cod]
+.ipynb_checkpoints/
+.pytest_cache/
 
-# C extentions
+# C extensions
 *.so
+*.o
+
+# Build
+.mesonpy-*
 
 # Distribution
 bin/
@@ -23,6 +29,7 @@ develop-eggs/
 dist/
 eggs/
 sdist/
+tmp/
 .eggs/
 *.egg-info/
 .installed.cfg
@@ -36,4 +43,10 @@ nosetests.xml
 coverage.xml
 
 # Sphinx documentation
-docs/_build/
+docs/build/
+
+# Lint
+.ruff_cache/
+
+# Conda
+conda-bld/

MANIFEST.in

@@ -3,50 +3,28 @@ global-exclude *.so *.dll *.dylib
 global-exclude *.o
 global-exclude *.swp
 
-recursive-include docs *.bat
-recursive-include docs *.css
-recursive-include docs *.py
-recursive-include docs *.rst
-recursive-include docs *.svg
-recursive-include docs *.png
-recursive-include docs *.ico
-recursive-include docs *.js
-recursive-include docs *.ttf
-recursive-include docs Makefile
-recursive-include docs *.bib
-recursive-include docs *.in
-recursive-include docs *.txt
-recursive-exclude docs *.html
-recursive-exclude docs *.pdf
-recursive-include docs/source *.html
-
 recursive-include ortho *.rst
-recursive-include examples *.py
-recursive-include examples *.rst
-recursive-include notebooks *.ipynb
-recursive-include tests *.py
-recursive-include tests *.rst
-recursive-exclude tests *.svg
-recursive-include tests *.txt
-
 include CHANGELOG.rst
 include README.rst
 include AUTHORS.txt
 include LICENSE.txt
 include requirements.txt
 include pyproject.toml
-include .coveragerc
-include tox.ini
-include environment.yml
 
+exclude tox.ini
+exclude environment.yml
 exclude TODO.rst
 exclude .coverage
+exclude .coveragerc
 exclude .gitattributes
+exclude .tokeignore
 
-prune docs/build
-prune .git
+prune docs
 prune tmp
-prune .tox
-prune .github
 prune conda-recipe
-prune benchmark
+prune notebooks
+prune examples
+prune tests
+prune .git
+prune .github
+prune .tox

README.rst

@@ -20,9 +20,9 @@ ortho
 
 A python package to generate a set of orthogonal functions.
 
-* `Documentation <https://ameli.github.io/ortho/index.html>`_
-* `API Reference <https://ameli.github.io/ortho/api.html>`_
-* `Github <https://ameli.github.io/ortho>`_
+* `Documentation <https://ameli.github.io/ortho/index.html>`__
+* `API Reference <https://ameli.github.io/ortho/api.html>`__
+* `Github <https://ameli.github.io/ortho>`__
 
 -----------
 Description
@@ -100,7 +100,7 @@ Install using the package available on `PyPi <https://pypi.org/project/ortho>`__
 
 |conda-version| |conda-platform|
 
-Install using `Anaconda cloud <https://anaconda.org/s-ameli/traceinv>`_ by
+Install using `Anaconda cloud <https://anaconda.org/s-ameli/traceinv>`__ by
 
 ::
 

conda-recipe/meta.yaml

@@ -26,7 +26,6 @@ requirements:
         - numpy
         - sympy
         - matplotlib
-        - seaborn
 
 test:
     imports:

ortho/__version__.py

@@ -1 +1 @@
-__version__ = "0.3.7"
+__version__ = "0.4.0"

ortho/_orthogonal_functions/display_utilities.py

@@ -0,0 +1,29 @@
+# SPDX-FileCopyrightText: Copyright 2021, Siavash Ameli <sameli@berkeley.edu>
+# SPDX-License-Identifier: BSD-3-Clause
+# SPDX-FileType: SOURCE
+#
+# This program is free software: you can redistribute it and/or modify it
+# under the terms of the license found in the LICENSE.txt file in the root
+# directory of this source tree.
+
+
+# ===========
+# is notebook
+# ===========
+
+def is_notebook():
+    """
+    Returns ``True`` if this script is running in a jupyter notebook. Returns
+    ``False`` otherwise, including both ipython and python.
+    """
+
+    try:
+        shell = get_ipython().__class__.__name__
+        if shell == 'ZMQInteractiveShell':
+            return True   # Jupyter notebook or qtconsole
+        elif shell == 'TerminalInteractiveShell':
+            return False  # Terminal running IPython
+        else:
+            return False  # Other type
+    except NameError:
+        return False      # Probably standard Python interpreter

ortho/_orthogonal_functions/orthogonal_functions.py

@@ -16,7 +16,7 @@
 from .orthogonalization_utilities import check_mutual_orthonormality
 from .orthogonalization_utilities import get_symbolic_coeffs
 from .orthogonalization_utilities import get_numeric_coeffs
-from .plot_utilities import plot_functions
+from .plot_functions import plot_functions
 
 
 # ====================

ortho/_orthogonal_functions/plot_functions.py

@@ -0,0 +1,93 @@
+# SPDX-FileCopyrightText: Copyright 2021, Siavash Ameli <sameli@berkeley.edu>
+# SPDX-License-Identifier: BSD-3-Clause
+# SPDX-FileType: SOURCE
+#
+# This program is free software: you can redistribute it and/or modify it under
+# the terms of the license found in the LICENSE.txt file in the root directory
+# of this source tree.
+
+
+# =======
+# Imports
+# =======
+
+import numpy
+import sympy
+import os
+from .plot_utilities import plt, matplotlib, get_custom_theme, save_plot
+from .declarations import t
+
+__all__ = ['plot_functions']
+
+
+# ==============
+# Plot Functions
+# ==============
+
+@matplotlib.rc_context(get_custom_theme(font_scale=1.2))
+def plot_functions(phi_orthonormalized_list, start_index, interval):
+    """
+    Plots the generated functions, also saves the plots as both ``svg`` and
+    ``pdf`` format.
+
+    :param phi_orthonormalized_list: The list of generated functions. Each
+        entry is a ``sympy`` object.
+    :param: list
+
+    :param start_index: The indet of the first function.
+    :type start_index: int
+
+    :param Interval: The right side of the interval of the domain of the
+        functions.
+    :param Interval: float
+    """
+
+    # Axis
+    t_array = numpy.logspace(-7, numpy.log10(interval[1]), 1000)
+
+    # Evaluate functions
+    num_functions = len(phi_orthonormalized_list)
+
+    f = numpy.zeros((num_functions, t_array.size), dtype=float)
+    for j in range(num_functions):
+        f_lambdify = sympy.lambdify(t, phi_orthonormalized_list[j], 'numpy')
+        f[j, :] = f_lambdify(t_array)
+
+    # Plot
+    fig, ax = plt.subplots(figsize=(7, 4.8))
+    for j in range(num_functions):
+        ax.semilogx(t_array, f[j, :],
+                    label=r'$i = %d$' % (j+start_index))
+
+    ax.legend(ncol=3, loc='lower left', borderpad=0.5, frameon=False)
+    ax.set_xlim([t_array[0], t_array[-1]])
+    ax.set_ylim([-1, 1])
+    ax.set_yticks([-1, 0, 1])
+    ax.set_xlabel(r'$t$')
+    ax.set_ylabel(r'$\phi_i^{\perp}(t)$')
+    ax.set_title('Orthogonalized inverse-monomial functions')
+    ax.grid(axis='y')
+
+    # Get the root directory of the package (parent directory of this script)
+    file_dir = os.path.dirname(os.path.realpath(__file__))
+    parent_dir = os.path.dirname(file_dir)
+    second_parent_dir = os.path.dirname(parent_dir)
+
+    # Try to save in the docs/images directory. Check if exists and writable
+    save_dir = os.path.join(second_parent_dir, 'docs', 'images')
+    if (not os.path.isdir(save_dir)) or (not os.access(save_dir, os.W_OK)):
+
+        # Write in the current working directory
+        save_dir = os.getcwd()
+
+    # Save plot in both svg and pdf format
+    if os.access(save_dir, os.W_OK):
+        save_filename = 'orthogonal_functions'
+        save_plot(plt, save_filename, save_dir=save_dir,
+                  transparent_background=True)
+    else:
+        print('Cannot save plot to %s. Directory is not writable.' % save_dir)
+
+    # If no display backend is enabled, do not plot in the interactive mode
+    if matplotlib.get_backend() != 'agg':
+        plt.show()