Fix formatting issues

ghiggi · Feb 3, 2024 · b7bb3da · b7bb3da
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diff --git a/CONTRIBUTING.rst b/CONTRIBUTING.rst
@@ -303,19 +303,19 @@ In the table below, some CI tools are mentioned for your information, but does n
 They are automatically run when you push your changes to the main repository via a GitHub Pull Request.
 
 
-+----------------------------------------------------+-----------------------------------------------------------------------------------------------------------------------------------+
-| Tool                                               | Aim                                                                                                                               |
-+====================================================+===================================================================================================================================+
-| `pre-commit.ci <https://pre-commit.ci/>`__         | Run pre-commit (as defined in `.pre-commit-config.yaml <https://github.com/ghiggi/pycolorbar/blob/main/.pre-commit-config.yaml>`_ ) |
-+----------------------------------------------------+-----------------------------------------------------------------------------------------------------------------------------------+
-| `CodeBeat <https://codebeat.co/>`__                | Automated code review and analysis tools                                                                                          |
-+----------------------------------------------------+-----------------------------------------------------------------------------------------------------------------------------------+
-| `CodeScene <https://codescene.com/>`__             | Automated code review and analysis tools                                                                                          |
-+----------------------------------------------------+-----------------------------------------------------------------------------------------------------------------------------------+
-| `CodeFactor <https://www.codefactor.io/>`__        | Automated code review and analysis tools                                                                                          |
-+----------------------------------------------------+-----------------------------------------------------------------------------------------------------------------------------------+
-| `Snyk Code <https://snyk.io/product/snyk-code/>`__ | Automated code security checks                                                                                                    |
-+----------------------------------------------------+-----------------------------------------------------------------------------------------------------------------------------------+
++----------------------------------------------------+-------------------------------------------------------------------------------------------------------------------------------------+
+| Tool                                               | Aim                                                                                                                                 |
++====================================================+=====================================================================================================================================+
+| `pre-commit.ci <https://pre-commit.ci/>`__         | Run pre-commit (as defined in `.pre-commit-config.yaml <https://github.com/ghiggi/pycolorbar/blob/main/.pre-commit-config.yaml>`__) |
++----------------------------------------------------+-------------------------------------------------------------------------------------------------------------------------------------+
+| `CodeBeat <https://codebeat.co/>`__                | Automated code review and analysis tools                                                                                            |
++----------------------------------------------------+-------------------------------------------------------------------------------------------------------------------------------------+
+| `CodeScene <https://codescene.com/>`__             | Automated code review and analysis tools                                                                                            |
++----------------------------------------------------+-------------------------------------------------------------------------------------------------------------------------------------+
+| `CodeFactor <https://www.codefactor.io/>`__        | Automated code review and analysis tools                                                                                            |
++----------------------------------------------------+-------------------------------------------------------------------------------------------------------------------------------------+
+| `Snyk Code <https://snyk.io/product/snyk-code/>`__ | Automated code security checks                                                                                                      |
++----------------------------------------------------+-------------------------------------------------------------------------------------------------------------------------------------+
 
 
 

diff --git a/README.md b/README.md
@@ -10,7 +10,7 @@
 | Build Status         | [![Tests](https://github.com/ghiggi/pycolorbar/actions/workflows/tests.yml/badge.svg?style=flat)](https://github.com/ghiggi/pycolorbar/actions/workflows/tests.yml) [![Lint](https://github.com/ghiggi/pycolorbar/actions/workflows/lint.yml/badge.svg?style=flat)](https://github.com/ghiggi/pycolorbar/actions/workflows/lint.yml) [![Docs](https://readthedocs.org/projects/pycolorbar/badge/?version=latest&style=flat)](https://pycolorbar.readthedocs.io/en/latest/) |
 | Linting              | [![Black](https://img.shields.io/badge/code%20style-black-000000.svg?style=flat)](https://github.com/psf/black) [![Ruff](https://img.shields.io/endpoint?url=https://raw.githubusercontent.com/astral-sh/ruff/main/assets/badge/v2.json&style=flat)](https://github.com/astral-sh/ruff) [![Codespell](https://img.shields.io/badge/Codespell-enabled-brightgreen?style=flat)](https://github.com/codespell-project/codespell) |
 | Code Coverage        | [![Coveralls](https://coveralls.io/repos/github/ghiggi/pycolorbar/badge.svg?branch=main&style=flat)](https://coveralls.io/github/ghiggi/pycolorbar?branch=main) [![Codecov](https://codecov.io/gh/ghiggi/pycolorbar/branch/main/graph/badge.svg?style=flat)](https://codecov.io/gh/ghiggi/pycolorbar) |
-| Code Quality         | [![Codefactor](https://www.codefactor.io/repository/github/ghiggi/pycolorbar/badge?style=flat)](https://www.codefactor.io/repository/github/ghiggi/pycolorbar) [![Codebeat](https://codebeat.co/badges/236abcf2-cbae-4ca9-8a2d-3b70495bb16b?style=flat)](https://codebeat.co/projects/github-com-ghiggi-pycolorbar-main) [![Codacy](https://app.codacy.com/project/badge/Grade/bee842cb10004ad8bb9288256f2fc8af?style=flat)](https://app.codacy.com/gh/ghiggi/pycolorbar/dashboard?utm_source=gh&utm_medium=referral&utm_content=&utm_campaign=Badge_grade) [![Codescene](https://codescene.io/projects/36767/status-badges/code-health?style=flat)](https://codescene.io/projects/36767) |
+| Code Quality         | [![Codefactor](https://www.codefactor.io/repository/github/ghiggi/pycolorbar/badge?style=flat)](https://www.codefactor.io/repository/github/ghiggi/pycolorbar) [![Codebeat](https://codebeat.co/badges/236abcf2-cbae-4ca9-8a2d-3b70495bb16b?style=flat)](https://codebeat.co/projects/github-com-ghiggi-pycolorbar-main) [![Codacy](https://app.codacy.com/project/badge/Grade/bee842cb10004ad8bb9288256f2fc8af?style=flat)](https://app.codacy.com/gh/ghiggi/pycolorbar/dashboard?utm_source=gh&utm_medium=referral&utm_content=&utm_campaign=Badge_grade) [![Codescene](https://codescene.io/projects/41870/status-badges/code-health?style=flat)](https://codescene.io/projects/41870) |
 | License              | [![License](https://img.shields.io/github/license/ghiggi/pycolorbar?style=flat)](https://github.com/ghiggi/pycolorbar/blob/main/LICENSE) |
 | Community            | [![Slack](https://img.shields.io/badge/Slack-pycolorbar-green.svg?logo=slack&style=flat)](https://join.slack.com/t/pycolorbar/shared_invite/zt-2bxdsywo3-368GbufPyb8vNJ1GC9aT3g) [![GitHub Discussions](https://img.shields.io/badge/GitHub-Discussions-green?logo=github&style=flat)](https://github.com/ghiggi/pycolorbar/discussions) |
 | Citation             | [![DOI](https://zenodo.org/badge/286664485.svg?style=flat)](https://doi.org/10.5281/zenodo.10255084) |

diff --git a/docs/environment.yaml b/docs/environment.yaml
@@ -0,0 +1,8 @@
+name: build-doc-pycolorbar
+channels:
+  - conda-forge
+dependencies:
+  - python>=3.9
+  - pip
+  - pip:
+    - -r file:requirements.txt
diff --git a/docs/requirements.txt b/docs/requirements.txt
@@ -1,46 +1,5 @@
-cftime==1.6.1
-click==8.1.3
-cloudpickle==2.1.0
-colorama==0.4.5
-donfig==0.8.1.post0
-fsspec==2022.11.0
-locket==1.0.0
-netCDF4==1.6.2
-packaging==21.3
-partd==1.3.0
-pyarrow==14.0.1
-pyparsing==3.0.9
-python-dateutil==2.8.2
-pytz==2022.6
-PyYAML==6.0
-six==1.16.0
-toolz==0.12.0
-xarray==2022.6.0
 nbsphinx==0.8.9
-jupyter==1.0.0
-setuptools==65.5.1
-dask[distributed]==2023.11.0
-pre-commit==2.20.0
-importlib==1.0.4
-importlib-metadata==5.1.0
-trollsift==0.5.0
-coverage==7.2.2
-pooch==1.7.0
-pydantic==2.5.2
-pytest-cov==4.0.0
-pytest-mock==3.10.0
-pytest==7.2.0
-requests-mock==1.10.0
-requests==2.31.0
 sphinx==5.1.1
 sphinx_book_theme==1.0.1
 sphinx-mdinclude==0.5.3
-tqdm==4.65.0
-pycolorbar==0.0.17
-ipython>=8.10.0 # not directly required, pinned by Snyk to avoid a vulnerability
-jupyter-core>=4.11.2 # not directly required, pinned by Snyk to avoid a vulnerability
-mistune>=2.0.3 # not directly required, pinned by Snyk to avoid a vulnerability
-nbconvert>=6.3.0b0 # not directly required, pinned by Snyk to avoid a vulnerability
-notebook>=6.4.12 # not directly required, pinned by Snyk to avoid a vulnerability
-pygments>=2.15.0 # not directly required, pinned by Snyk to avoid a vulnerability
-tornado>=6.3.3 # not directly required, pinned by Snyk to avoid a vulnerability
+pycolorbar
diff --git a/docs/source/api/modules.rst b/docs/source/api/modules.rst
@@ -0,0 +1,7 @@
+pycolorbar
+==========
+
+.. toctree::
+   :maxdepth: 4
+
+   pycolorbar
diff --git a/docs/source/api/pycolorbar.colors.rst b/docs/source/api/pycolorbar.colors.rst
@@ -0,0 +1,21 @@
+pycolorbar.colors package
+=========================
+
+Submodules
+----------
+
+pycolorbar.colors.colors\_io module
+-----------------------------------
+
+.. automodule:: pycolorbar.colors.colors_io
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+Module contents
+---------------
+
+.. automodule:: pycolorbar.colors
+   :members:
+   :undoc-members:
+   :show-inheritance:
diff --git a/docs/source/api/pycolorbar.rst b/docs/source/api/pycolorbar.rst
@@ -0,0 +1,21 @@
+pycolorbar package
+==================
+
+Subpackages
+-----------
+
+.. toctree::
+   :maxdepth: 4
+
+   pycolorbar.colors
+   pycolorbar.settings
+   pycolorbar.tests
+   pycolorbar.utils
+
+Module contents
+---------------
+
+.. automodule:: pycolorbar
+   :members:
+   :undoc-members:
+   :show-inheritance:
diff --git a/docs/source/api/pycolorbar.settings.rst b/docs/source/api/pycolorbar.settings.rst
@@ -0,0 +1,101 @@
+pycolorbar.settings package
+===========================
+
+Submodules
+----------
+
+pycolorbar.settings.colorbar\_io module
+---------------------------------------
+
+.. automodule:: pycolorbar.settings.colorbar_io
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+pycolorbar.settings.colorbar\_registry module
+---------------------------------------------
+
+.. automodule:: pycolorbar.settings.colorbar_registry
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+pycolorbar.settings.colorbar\_utility module
+--------------------------------------------
+
+.. automodule:: pycolorbar.settings.colorbar_utility
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+pycolorbar.settings.colorbar\_validator module
+----------------------------------------------
+
+.. automodule:: pycolorbar.settings.colorbar_validator
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+pycolorbar.settings.colorbar\_visualization module
+--------------------------------------------------
+
+.. automodule:: pycolorbar.settings.colorbar_visualization
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+pycolorbar.settings.colormap\_io module
+---------------------------------------
+
+.. automodule:: pycolorbar.settings.colormap_io
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+pycolorbar.settings.colormap\_registry module
+---------------------------------------------
+
+.. automodule:: pycolorbar.settings.colormap_registry
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+pycolorbar.settings.colormap\_utility module
+--------------------------------------------
+
+.. automodule:: pycolorbar.settings.colormap_utility
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+pycolorbar.settings.colormap\_validator module
+----------------------------------------------
+
+.. automodule:: pycolorbar.settings.colormap_validator
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+pycolorbar.settings.colormap\_visualization module
+--------------------------------------------------
+
+.. automodule:: pycolorbar.settings.colormap_visualization
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+pycolorbar.settings.utils module
+--------------------------------
+
+.. automodule:: pycolorbar.settings.utils
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+Module contents
+---------------
+
+.. automodule:: pycolorbar.settings
+   :members:
+   :undoc-members:
+   :show-inheritance:
diff --git a/docs/source/api/pycolorbar.tests.rst b/docs/source/api/pycolorbar.tests.rst
@@ -0,0 +1,21 @@
+pycolorbar.tests package
+========================
+
+Submodules
+----------
+
+pycolorbar.tests.test\_foo module
+---------------------------------
+
+.. automodule:: pycolorbar.tests.test_foo
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+Module contents
+---------------
+
+.. automodule:: pycolorbar.tests
+   :members:
+   :undoc-members:
+   :show-inheritance:
diff --git a/docs/source/api/pycolorbar.utils.rst b/docs/source/api/pycolorbar.utils.rst
@@ -0,0 +1,37 @@
+pycolorbar.utils package
+========================
+
+Submodules
+----------
+
+pycolorbar.utils.directories module
+-----------------------------------
+
+.. automodule:: pycolorbar.utils.directories
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+pycolorbar.utils.mpl module
+---------------------------
+
+.. automodule:: pycolorbar.utils.mpl
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+pycolorbar.utils.yaml module
+----------------------------
+
+.. automodule:: pycolorbar.utils.yaml
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+Module contents
+---------------
+
+.. automodule:: pycolorbar.utils
+   :members:
+   :undoc-members:
+   :show-inheritance:
diff --git a/docs/source/index.rst b/docs/source/index.rst
@@ -4,7 +4,7 @@
    contain the root `toctree` directive.
 
 Welcome to pycolorbar !
-======================
+========================
 
 
 Motivation

diff --git a/docs/source/installation.rst b/docs/source/installation.rst
@@ -167,7 +167,7 @@ The latter is recommended since it indicates if the commit contained any formatt
 
 
 Run pycolorbar on Jupyter Notebooks
-==================================
+=====================================
 
 If you want to run pycolorbar on a `Jupyter Notebook <https://jupyter.org/>`__,
 you have to take care to set up the IPython kernel environment where pycolorbar is installed.