From 3089b2ceea35edaf0c8e0d36012933e41b6c548c Mon Sep 17 00:00:00 2001 From: JantineSmit Date: Fri, 21 Jun 2024 13:44:51 +0200 Subject: [PATCH 01/18] Removed documentation --- docs/Makefile | 20 ------- docs/_templates/.gitignore | 0 docs/conf.py | 111 ------------------------------------- docs/developers.rst | 5 -- docs/index.rst | 40 ------------- docs/make.bat | 36 ------------ 6 files changed, 212 deletions(-) delete mode 100644 docs/Makefile delete mode 100644 docs/_templates/.gitignore delete mode 100644 docs/conf.py delete mode 100644 docs/developers.rst delete mode 100644 docs/index.rst delete mode 100644 docs/make.bat diff --git a/docs/Makefile b/docs/Makefile deleted file mode 100644 index d86a3e7d0..000000000 --- a/docs/Makefile +++ /dev/null @@ -1,20 +0,0 @@ -# Minimal makefile for Sphinx documentation -# - -# You can set these variables from the command line. -SPHINXOPTS = -SPHINXBUILD = sphinx-build -SPHINXPROJ = eitprocessing -SOURCEDIR = . -BUILDDIR = _build - -# Put it first so that "make" without argument is like "make help". -help: - @$(SPHINXBUILD) -M help "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O) - -.PHONY: help Makefile - -# Catch-all target: route all unknown targets to Sphinx using the new -# "make mode" option. $(O) is meant as a shortcut for $(SPHINXOPTS). -%: Makefile - @$(SPHINXBUILD) -M $@ "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O) diff --git a/docs/_templates/.gitignore b/docs/_templates/.gitignore deleted file mode 100644 index e69de29bb..000000000 diff --git a/docs/conf.py b/docs/conf.py deleted file mode 100644 index 05327db3a..000000000 --- a/docs/conf.py +++ /dev/null @@ -1,111 +0,0 @@ -# Configuration file for the Sphinx documentation builder. -# -# This file only contains a selection of the most common options. For a full -# list see the documentation: -# https://www.sphinx-doc.org/en/master/usage/configuration.html -# - -# -- Path setup -------------------------------------------------------------- - -# If extensions (or modules to document with autodoc) are in another directory, -# add these directories to sys.path here. If the directory is relative to the -# documentation root, use os.path.abspath to make it absolute, like shown here. - -import os -import subprocess -import sys - - -sys.path.insert(0, os.path.abspath(os.path.join(os.path.dirname(__file__), ".."))) - -# -- Project information ----------------------------------------------------- - -project = "eitprocessing" -copyright = "2023, Netherlands eScience Center, Erasmus MC" -author = "Dani Bodor" - -# The version info for the project you're documenting, acts as replacement for -# |version| and |release|, also used in various other places throughout the -# built documents. -# -# The short X.Y version. -##version = "0.0.0" -# The full version, including alpha/beta/rc tags. -##release = version - -try: - tag = ( - subprocess.check_output( - [ - "git", - "--no-pager", - "describe", - "--abbrev=0", - "--tags", - ] - ) - .strip() - .decode() - ) -except subprocess.CalledProcessError as e: - print(e.output) - tag = "v0.0.0" - -release = tag[1:] -# -- General configuration ------------------------------------------------ - -# Add any Sphinx extension module names here, as strings. They can be -# extensions coming with Sphinx (named "sphinx.ext.*") or your custom -# ones. -extensions = [ - "sphinx.ext.autodoc", - "sphinx.ext.coverage", - "sphinx.ext.doctest", - "sphinx.ext.intersphinx", - "sphinx.ext.mathjax", - "sphinx.ext.napoleon", - "sphinx.ext.todo", - "sphinx.ext.viewcode", - "autoapi.extension", - "myst_parser", -] - -# Add any paths that contain templates here, relative to this directory. -templates_path = ["_templates"] - -# List of patterns, relative to source directory, that match files and -# directories to ignore when looking for source files. -# This patterns also effect to html_static_path and html_extra_path -exclude_patterns = ["_build", "Thumbs.db", ".DS_Store"] - -# If true, `todo` and `todoList` produce output, else they produce nothing. -todo_include_todos = False - -# -- Use autoapi.extension to run sphinx-apidoc ------- - -autoapi_dirs = ["../eitprocessing"] - -# -- Options for HTML output ---------------------------------------------- - -# The theme to use for HTML and HTML Help pages. See the documentation for -# a list of builtin themes. -# -html_theme = "nature" - -# Theme options are theme-specific and customize the look and feel of a theme -# further. For a list of options available for each theme, see the -# documentation. -# -# html_theme_options = {} - -# -- Options for Intersphinx - -intersphinx_mapping = { - "python": ("https://docs.python.org/3", None), - # Commonly used libraries, uncomment when used in package - # 'numpy': ('http://docs.scipy.org/doc/numpy/', None), - # 'scipy': ('http://docs.scipy.org/doc/scipy/reference/', None), - # 'scikit-learn': ('https://scikit-learn.org/stable/', None), - # 'matplotlib': ('https://matplotlib.org/stable/', None), - # 'pandas': ('http://pandas.pydata.org/docs/', None), -} diff --git a/docs/developers.rst b/docs/developers.rst deleted file mode 100644 index 761a88db0..000000000 --- a/docs/developers.rst +++ /dev/null @@ -1,5 +0,0 @@ -================= -Developer's Guide -================= - -Please refer to https://github.com/EIT-ALIVE/eitprocessing/blob/main/README.dev.md diff --git a/docs/index.rst b/docs/index.rst deleted file mode 100644 index 0eafaad3e..000000000 --- a/docs/index.rst +++ /dev/null @@ -1,40 +0,0 @@ -.. eitprocessing documentation master file, created by - sphinx-quickstart on Wed May 5 22:45:36 2021. - You can adapt this file completely to your liking, but it should at least - contain the root `toctree` directive. - - - -Welcome to eitprocessing's documentation! -========================================= - -Here is some general information about the eitprocessing package. We are working on -documentation, stay tuned. - - -The API Documentation / Guide ------------------------------ - -If you are looking for information on a specific function, class, or method, -this part of the documentation is for you. - -.. toctree:: - :maxdepth: 2 - :caption: Contents: - - modules - developers - -Developer's Guide ------------------ - -:doc:`Developer's Guide <../developers>` - - - -Indices and tables -================== - -* :ref:`genindex` -* :ref:`modindex` -* :ref:`search` diff --git a/docs/make.bat b/docs/make.bat deleted file mode 100644 index 71ce7e98a..000000000 --- a/docs/make.bat +++ /dev/null @@ -1,36 +0,0 @@ -@ECHO OFF - -pushd %~dp0 - -REM Command file for Sphinx documentation - -if "%SPHINXBUILD%" == "" ( - set SPHINXBUILD=sphinx-build -) -set SOURCEDIR=. -set BUILDDIR=_build -set SPHINXPROJ=eitprocessing - -if "%1" == "" goto help - -%SPHINXBUILD% >NUL 2>NUL -if errorlevel 9009 ( - echo. - echo.The 'sphinx-build' command was not found. Make sure you have Sphinx - echo.installed, then set the SPHINXBUILD environment variable to point - echo.to the full path of the 'sphinx-build' executable. Alternatively you - echo.may add the Sphinx directory to PATH. - echo. - echo.If you don't have Sphinx installed, grab it from - echo.http://sphinx-doc.org/ - exit /b 1 -) - -%SPHINXBUILD% -M %1 %SOURCEDIR% %BUILDDIR% %SPHINXOPTS% -goto end - -:help -%SPHINXBUILD% -M help %SOURCEDIR% %BUILDDIR% %SPHINXOPTS% - -:end -popd From 203b156e170cf881efa4101770092ee3c10bd474 Mon Sep 17 00:00:00 2001 From: JantineSmit Date: Fri, 21 Jun 2024 13:40:23 +0200 Subject: [PATCH 02/18] Remove sphinx dependencies and add mkdocs dependencies --- pyproject.toml | 13 +++++++++---- 1 file changed, 9 insertions(+), 4 deletions(-) diff --git a/pyproject.toml b/pyproject.toml index e2111f347..9ebd59da6 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -49,12 +49,17 @@ dev = [ "pytest-cov", "pytest-runner", "coveralls", - "sphinx", - "sphinx_rtd_theme", - "sphinx-autoapi", "tox", "ruff < 0.6", - "myst_parser", +] +docs = [ + "mkdocs", + "mkdocs-material", + "mkdocstrings", + "mkdocstrings-python", + "mkdocs-exclude", + "mike", + "pymdown-extensions", ] notebooks = [ "ipykernel >= 6.15.2", From 20f6634e42bdb953ae5504c6ceac8f5ff06a893d Mon Sep 17 00:00:00 2001 From: JantineSmit Date: Thu, 4 Jul 2024 13:57:14 +0200 Subject: [PATCH 03/18] Format license file for markdown --- LICENSE | 402 ++++++++++++++++++++++++++++---------------------------- 1 file changed, 201 insertions(+), 201 deletions(-) diff --git a/LICENSE b/LICENSE index cedf1b60b..42be5f23f 100644 --- a/LICENSE +++ b/LICENSE @@ -1,204 +1,204 @@ - Apache License - Version 2.0, January 2004 - http://www.apache.org/licenses/ - - TERMS AND CONDITIONS FOR USE, REPRODUCTION, AND DISTRIBUTION - - 1. Definitions. - - "License" shall mean the terms and conditions for use, reproduction, - and distribution as defined by Sections 1 through 9 of this document. - - "Licensor" shall mean the copyright owner or entity authorized by - the copyright owner that is granting the License. - - "Legal Entity" shall mean the union of the acting entity and all - other entities that control, are controlled by, or are under common - control with that entity. For the purposes of this definition, - "control" means (i) the power, direct or indirect, to cause the - direction or management of such entity, whether by contract or - otherwise, or (ii) ownership of fifty percent (50%) or more of the - outstanding shares, or (iii) beneficial ownership of such entity. - - "You" (or "Your") shall mean an individual or Legal Entity - exercising permissions granted by this License. - - "Source" form shall mean the preferred form for making modifications, - including but not limited to software source code, documentation - source, and configuration files. - - "Object" form shall mean any form resulting from mechanical - transformation or translation of a Source form, including but - not limited to compiled object code, generated documentation, - and conversions to other media types. - - "Work" shall mean the work of authorship, whether in Source or - Object form, made available under the License, as indicated by a - copyright notice that is included in or attached to the work - (an example is provided in the Appendix below). - - "Derivative Works" shall mean any work, whether in Source or Object - form, that is based on (or derived from) the Work and for which the - editorial revisions, annotations, elaborations, or other modifications - represent, as a whole, an original work of authorship. For the purposes - of this License, Derivative Works shall not include works that remain - separable from, or merely link (or bind by name) to the interfaces of, - the Work and Derivative Works thereof. - - "Contribution" shall mean any work of authorship, including - the original version of the Work and any modifications or additions - to that Work or Derivative Works thereof, that is intentionally - submitted to Licensor for inclusion in the Work by the copyright owner - or by an individual or Legal Entity authorized to submit on behalf of - the copyright owner. For the purposes of this definition, "submitted" - means any form of electronic, verbal, or written communication sent - to the Licensor or its representatives, including but not limited to - communication on electronic mailing lists, source code control systems, - and issue tracking systems that are managed by, or on behalf of, the - Licensor for the purpose of discussing and improving the Work, but - excluding communication that is conspicuously marked or otherwise - designated in writing by the copyright owner as "Not a Contribution." - - "Contributor" shall mean Licensor and any individual or Legal Entity - on behalf of whom a Contribution has been received by Licensor and - subsequently incorporated within the Work. - - 2. Grant of Copyright License. Subject to the terms and conditions of - this License, each Contributor hereby grants to You a perpetual, - worldwide, non-exclusive, no-charge, royalty-free, irrevocable - copyright license to reproduce, prepare Derivative Works of, - publicly display, publicly perform, sublicense, and distribute the - Work and such Derivative Works in Source or Object form. - - 3. Grant of Patent License. Subject to the terms and conditions of - this License, each Contributor hereby grants to You a perpetual, - worldwide, non-exclusive, no-charge, royalty-free, irrevocable - (except as stated in this section) patent license to make, have made, - use, offer to sell, sell, import, and otherwise transfer the Work, - where such license applies only to those patent claims licensable - by such Contributor that are necessarily infringed by their - Contribution(s) alone or by combination of their Contribution(s) - with the Work to which such Contribution(s) was submitted. If You - institute patent litigation against any entity (including a - cross-claim or counterclaim in a lawsuit) alleging that the Work - or a Contribution incorporated within the Work constitutes direct - or contributory patent infringement, then any patent licenses - granted to You under this License for that Work shall terminate - as of the date such litigation is filed. - - 4. Redistribution. You may reproduce and distribute copies of the - Work or Derivative Works thereof in any medium, with or without - modifications, and in Source or Object form, provided that You - meet the following conditions: - - (a) You must give any other recipients of the Work or - Derivative Works a copy of this License; and - - (b) You must cause any modified files to carry prominent notices - stating that You changed the files; and - - (c) You must retain, in the Source form of any Derivative Works - that You distribute, all copyright, patent, trademark, and - attribution notices from the Source form of the Work, - excluding those notices that do not pertain to any part of - the Derivative Works; and - - (d) If the Work includes a "NOTICE" text file as part of its - distribution, then any Derivative Works that You distribute must - include a readable copy of the attribution notices contained - within such NOTICE file, excluding those notices that do not - pertain to any part of the Derivative Works, in at least one - of the following places: within a NOTICE text file distributed - as part of the Derivative Works; within the Source form or - documentation, if provided along with the Derivative Works; or, - within a display generated by the Derivative Works, if and - wherever such third-party notices normally appear. The contents - of the NOTICE file are for informational purposes only and - do not modify the License. You may add Your own attribution - notices within Derivative Works that You distribute, alongside - or as an addendum to the NOTICE text from the Work, provided - that such additional attribution notices cannot be construed - as modifying the License. - - You may add Your own copyright statement to Your modifications and - may provide additional or different license terms and conditions - for use, reproduction, or distribution of Your modifications, or - for any such Derivative Works as a whole, provided Your use, - reproduction, and distribution of the Work otherwise complies with - the conditions stated in this License. - - 5. Submission of Contributions. Unless You explicitly state otherwise, - any Contribution intentionally submitted for inclusion in the Work - by You to the Licensor shall be under the terms and conditions of - this License, without any additional terms or conditions. - Notwithstanding the above, nothing herein shall supersede or modify - the terms of any separate license agreement you may have executed - with Licensor regarding such Contributions. - - 6. Trademarks. This License does not grant permission to use the trade - names, trademarks, service marks, or product names of the Licensor, - except as required for reasonable and customary use in describing the - origin of the Work and reproducing the content of the NOTICE file. - - 7. Disclaimer of Warranty. Unless required by applicable law or - agreed to in writing, Licensor provides the Work (and each - Contributor provides its Contributions) on an "AS IS" BASIS, - WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or - implied, including, without limitation, any warranties or conditions - of TITLE, NON-INFRINGEMENT, MERCHANTABILITY, or FITNESS FOR A - PARTICULAR PURPOSE. You are solely responsible for determining the - appropriateness of using or redistributing the Work and assume any - risks associated with Your exercise of permissions under this License. - - 8. Limitation of Liability. In no event and under no legal theory, - whether in tort (including negligence), contract, or otherwise, - unless required by applicable law (such as deliberate and grossly - negligent acts) or agreed to in writing, shall any Contributor be - liable to You for damages, including any direct, indirect, special, - incidental, or consequential damages of any character arising as a - result of this License or out of the use or inability to use the - Work (including but not limited to damages for loss of goodwill, - work stoppage, computer failure or malfunction, or any and all - other commercial damages or losses), even if such Contributor - has been advised of the possibility of such damages. - - 9. Accepting Warranty or Additional Liability. While redistributing - the Work or Derivative Works thereof, You may choose to offer, - and charge a fee for, acceptance of support, warranty, indemnity, - or other liability obligations and/or rights consistent with this - License. However, in accepting such obligations, You may act only - on Your own behalf and on Your sole responsibility, not on behalf - of any other Contributor, and only if You agree to indemnify, - defend, and hold each Contributor harmless for any liability - incurred by, or claims asserted against, such Contributor by reason - of your accepting any such warranty or additional liability. - - END OF TERMS AND CONDITIONS - - APPENDIX: How to apply the Apache License to your work. - - To apply the Apache License to your work, attach the following - boilerplate notice, with the fields enclosed by brackets "{}" - replaced with your own identifying information. (Don't include - the brackets!) The text should be enclosed in the appropriate - comment syntax for the file format. We also recommend that a - file or class name and description of purpose be included on the - same "printed page" as the copyright notice for easier - identification within third-party archives. - - Copyright [yyy] [name of copyright owner] - - Licensed under the Apache License, Version 2.0 (the "License"); - you may not use this file except in compliance with the License. - You may obtain a copy of the License at - - http://www.apache.org/licenses/LICENSE-2.0 - - Unless required by applicable law or agreed to in writing, software - distributed under the License is distributed on an "AS IS" BASIS, - WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. - See the License for the specific language governing permissions and - limitations under the License. +Apache License +Version 2.0, January 2004 +http://www.apache.org/licenses/ + +TERMS AND CONDITIONS FOR USE, REPRODUCTION, AND DISTRIBUTION + +1. Definitions. + + "License" shall mean the terms and conditions for use, reproduction, + and distribution as defined by Sections 1 through 9 of this document. + + "Licensor" shall mean the copyright owner or entity authorized by + the copyright owner that is granting the License. + + "Legal Entity" shall mean the union of the acting entity and all + other entities that control, are controlled by, or are under common + control with that entity. For the purposes of this definition, + "control" means (i) the power, direct or indirect, to cause the + direction or management of such entity, whether by contract or + otherwise, or (ii) ownership of fifty percent (50%) or more of the + outstanding shares, or (iii) beneficial ownership of such entity. + + "You" (or "Your") shall mean an individual or Legal Entity + exercising permissions granted by this License. + + "Source" form shall mean the preferred form for making modifications, + including but not limited to software source code, documentation + source, and configuration files. + + "Object" form shall mean any form resulting from mechanical + transformation or translation of a Source form, including but + not limited to compiled object code, generated documentation, + and conversions to other media types. + + "Work" shall mean the work of authorship, whether in Source or + Object form, made available under the License, as indicated by a + copyright notice that is included in or attached to the work + (an example is provided in the Appendix below). + + "Derivative Works" shall mean any work, whether in Source or Object + form, that is based on (or derived from) the Work and for which the + editorial revisions, annotations, elaborations, or other modifications + represent, as a whole, an original work of authorship. For the purposes + of this License, Derivative Works shall not include works that remain + separable from, or merely link (or bind by name) to the interfaces of, + the Work and Derivative Works thereof. + + "Contribution" shall mean any work of authorship, including + the original version of the Work and any modifications or additions + to that Work or Derivative Works thereof, that is intentionally + submitted to Licensor for inclusion in the Work by the copyright owner + or by an individual or Legal Entity authorized to submit on behalf of + the copyright owner. For the purposes of this definition, "submitted" + means any form of electronic, verbal, or written communication sent + to the Licensor or its representatives, including but not limited to + communication on electronic mailing lists, source code control systems, + and issue tracking systems that are managed by, or on behalf of, the + Licensor for the purpose of discussing and improving the Work, but + excluding communication that is conspicuously marked or otherwise + designated in writing by the copyright owner as "Not a Contribution." + + "Contributor" shall mean Licensor and any individual or Legal Entity + on behalf of whom a Contribution has been received by Licensor and + subsequently incorporated within the Work. + +2. Grant of Copyright License. Subject to the terms and conditions of + this License, each Contributor hereby grants to You a perpetual, + worldwide, non-exclusive, no-charge, royalty-free, irrevocable + copyright license to reproduce, prepare Derivative Works of, + publicly display, publicly perform, sublicense, and distribute the + Work and such Derivative Works in Source or Object form. + +3. Grant of Patent License. Subject to the terms and conditions of + this License, each Contributor hereby grants to You a perpetual, + worldwide, non-exclusive, no-charge, royalty-free, irrevocable + (except as stated in this section) patent license to make, have made, + use, offer to sell, sell, import, and otherwise transfer the Work, + where such license applies only to those patent claims licensable + by such Contributor that are necessarily infringed by their + Contribution(s) alone or by combination of their Contribution(s) + with the Work to which such Contribution(s) was submitted. If You + institute patent litigation against any entity (including a + cross-claim or counterclaim in a lawsuit) alleging that the Work + or a Contribution incorporated within the Work constitutes direct + or contributory patent infringement, then any patent licenses + granted to You under this License for that Work shall terminate + as of the date such litigation is filed. + +4. Redistribution. You may reproduce and distribute copies of the + Work or Derivative Works thereof in any medium, with or without + modifications, and in Source or Object form, provided that You + meet the following conditions: + + (a) You must give any other recipients of the Work or + Derivative Works a copy of this License; and + + (b) You must cause any modified files to carry prominent notices + stating that You changed the files; and + + (c) You must retain, in the Source form of any Derivative Works + that You distribute, all copyright, patent, trademark, and + attribution notices from the Source form of the Work, + excluding those notices that do not pertain to any part of + the Derivative Works; and + + (d) If the Work includes a "NOTICE" text file as part of its + distribution, then any Derivative Works that You distribute must + include a readable copy of the attribution notices contained + within such NOTICE file, excluding those notices that do not + pertain to any part of the Derivative Works, in at least one + of the following places: within a NOTICE text file distributed + as part of the Derivative Works; within the Source form or + documentation, if provided along with the Derivative Works; or, + within a display generated by the Derivative Works, if and + wherever such third-party notices normally appear. The contents + of the NOTICE file are for informational purposes only and + do not modify the License. You may add Your own attribution + notices within Derivative Works that You distribute, alongside + or as an addendum to the NOTICE text from the Work, provided + that such additional attribution notices cannot be construed + as modifying the License. + + You may add Your own copyright statement to Your modifications and + may provide additional or different license terms and conditions + for use, reproduction, or distribution of Your modifications, or + for any such Derivative Works as a whole, provided Your use, + reproduction, and distribution of the Work otherwise complies with + the conditions stated in this License. + +5. Submission of Contributions. Unless You explicitly state otherwise, + any Contribution intentionally submitted for inclusion in the Work + by You to the Licensor shall be under the terms and conditions of + this License, without any additional terms or conditions. + Notwithstanding the above, nothing herein shall supersede or modify + the terms of any separate license agreement you may have executed + with Licensor regarding such Contributions. + +6. Trademarks. This License does not grant permission to use the trade + names, trademarks, service marks, or product names of the Licensor, + except as required for reasonable and customary use in describing the + origin of the Work and reproducing the content of the NOTICE file. + +7. Disclaimer of Warranty. Unless required by applicable law or + agreed to in writing, Licensor provides the Work (and each + Contributor provides its Contributions) on an "AS IS" BASIS, + WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or + implied, including, without limitation, any warranties or conditions + of TITLE, NON-INFRINGEMENT, MERCHANTABILITY, or FITNESS FOR A + PARTICULAR PURPOSE. You are solely responsible for determining the + appropriateness of using or redistributing the Work and assume any + risks associated with Your exercise of permissions under this License. + +8. Limitation of Liability. In no event and under no legal theory, + whether in tort (including negligence), contract, or otherwise, + unless required by applicable law (such as deliberate and grossly + negligent acts) or agreed to in writing, shall any Contributor be + liable to You for damages, including any direct, indirect, special, + incidental, or consequential damages of any character arising as a + result of this License or out of the use or inability to use the + Work (including but not limited to damages for loss of goodwill, + work stoppage, computer failure or malfunction, or any and all + other commercial damages or losses), even if such Contributor + has been advised of the possibility of such damages. + +9. Accepting Warranty or Additional Liability. While redistributing + the Work or Derivative Works thereof, You may choose to offer, + and charge a fee for, acceptance of support, warranty, indemnity, + or other liability obligations and/or rights consistent with this + License. However, in accepting such obligations, You may act only + on Your own behalf and on Your sole responsibility, not on behalf + of any other Contributor, and only if You agree to indemnify, + defend, and hold each Contributor harmless for any liability + incurred by, or claims asserted against, such Contributor by reason + of your accepting any such warranty or additional liability. + +END OF TERMS AND CONDITIONS + +APPENDIX: How to apply the Apache License to your work. + +To apply the Apache License to your work, attach the following +boilerplate notice, with the fields enclosed by brackets "{}" +replaced with your own identifying information. (Don't include +the brackets!) The text should be enclosed in the appropriate +comment syntax for the file format. We also recommend that a +file or class name and description of purpose be included on the +same "printed page" as the copyright notice for easier +identification within third-party archives. + +Copyright [yyy] [name of copyright owner] + +Licensed under the Apache License, Version 2.0 (the "License"); +you may not use this file except in compliance with the License. +You may obtain a copy of the License at + +http://www.apache.org/licenses/LICENSE-2.0 + +Unless required by applicable law or agreed to in writing, software +distributed under the License is distributed on an "AS IS" BASIS, +WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. +See the License for the specific language governing permissions and +limitations under the License. From e089b2eb4dc4286c1a65c79051afbad32660ec57 Mon Sep 17 00:00:00 2001 From: JantineSmit Date: Fri, 21 Jun 2024 14:21:48 +0200 Subject: [PATCH 04/18] Write new documentation --- README.md | 8 +-- docs/APIindex.md | 4 ++ docs/basic_example.md | 1 + docs/code_of_conduct_doc.md | 3 + docs/contributing_doc.md | 3 + docs/index.md | 23 +++++++ docs/installation.md | 1 + docs/license_doc.md | 3 + docs/team.md | 12 ++++ mkdocs.yml | 118 ++++++++++++++++++++++++++++++++++++ 10 files changed, 171 insertions(+), 5 deletions(-) create mode 100644 docs/APIindex.md create mode 100644 docs/basic_example.md create mode 100644 docs/code_of_conduct_doc.md create mode 100644 docs/contributing_doc.md create mode 100644 docs/index.md create mode 100644 docs/installation.md create mode 100644 docs/license_doc.md create mode 100644 docs/team.md create mode 100644 mkdocs.yml diff --git a/README.md b/README.md index 66e19125d..d6c7445c9 100644 --- a/README.md +++ b/README.md @@ -11,17 +11,15 @@ # Contents -- [What is eitprocessing?](#what-is-eitprocessing) -- [Installation](#installation) +- [Installation](#installation-1) - [Virtual environment](#virtual-environment) - [Install using `pip`](#install-using-pip) - [Documentation](#documentation) - [Contributing](#contributing) - [Credits](#credits) -# What is eitprocessing? - -Processing of data from electrical impedance tomography and other respiratory monitoring tools. +The project setup is documented in [project_setup](/project_setup.md). Feel free to remove this document (and/or the link to this document) if you don't need it. +## Installation [Electrical Impedance Tomography](https://en.wikipedia.org/wiki/Electrical_impedance_tomography) (EIT) is a noninvasive and radiation-free continuous imaging tool for monitoring respiratory mechanics. eitprocessing aims to provide a diff --git a/docs/APIindex.md b/docs/APIindex.md new file mode 100644 index 000000000..ec6c4bca7 --- /dev/null +++ b/docs/APIindex.md @@ -0,0 +1,4 @@ +## Classes +::: eitprocessing.datahandling + options: + show_submodels: true \ No newline at end of file diff --git a/docs/basic_example.md b/docs/basic_example.md new file mode 100644 index 000000000..b9c4d8d1f --- /dev/null +++ b/docs/basic_example.md @@ -0,0 +1 @@ +Under construction \ No newline at end of file diff --git a/docs/code_of_conduct_doc.md b/docs/code_of_conduct_doc.md new file mode 100644 index 000000000..16b8f7e3d --- /dev/null +++ b/docs/code_of_conduct_doc.md @@ -0,0 +1,3 @@ + + +--8<-- "CODE_OF_CONDUCT.md" diff --git a/docs/contributing_doc.md b/docs/contributing_doc.md new file mode 100644 index 000000000..17267ed86 --- /dev/null +++ b/docs/contributing_doc.md @@ -0,0 +1,3 @@ + + +--8<-- "CONTRIBUTING.md" \ No newline at end of file diff --git a/docs/index.md b/docs/index.md new file mode 100644 index 000000000..5f19972c6 --- /dev/null +++ b/docs/index.md @@ -0,0 +1,23 @@ + +# Welcome to EITprocessing + +# Introduction + +Welcome to the documentation of the ALIVE software tool designed to load, analyze, and extract parameters from Electrical Impedance Tomography (EIT) data. +This software was designed by a joined effort of the Rotterdam Advanced Respiratory Care research group (ROTARC) of the Intensive Care of the Erasmus Medical Center and the Netherlands e-Science center. [Grant ID: NLESC.OEC.2022.002](https://research-software-directory.org/projects/alive) + +EIT is a bedside non-invasive lung imaging tool: it continuously and real-time visualizes changes in lung volume. Our software tool serves as a comprehensive solution for handling EIT data from multiple leading manufacturers, including Sentec, Dräger, and Timpel. + +The software tool includes a back-end for researchers that are familair with programming [eitprocessing](https://github.com/EIT-ALIVE/eitprocessing) and also a user-friendly dashboard [eit_dash](https://github.com/EIT-ALIVE/eit_dash) for clinical researchers allowing to quickly import datasets from various formats and sources and perform processing and analysis. This documentation page concerns eitprocessing. + +Our tool offers robust analysis features. From basic filters to advanced signal processing techniques, you can extract meaningful parameters from your EIT data. With our dashboard we aim to provide default analysis pipelines and many opportunities for customization according to the user needs. Visualizations and interactive graphs make it easy to interpret the results and understand the underlying physiological processes. + +It is important to note that the software tool is a work in progress, so not all fuctionalities are available yet. If you would like to contribute to coding you can reach out to us. + +## Getting Started +To start using our software you can you use the [installation](installation.md) guide to set up the software on your system. Once installed, you can load your first dataset and explore the basic features. +We are committed to supporting your journey with EIT data analysis and extraction. If you encounter any issues or have questions you can put a pull request via github or emailadres. + + + + diff --git a/docs/installation.md b/docs/installation.md new file mode 100644 index 000000000..4ab0748ee --- /dev/null +++ b/docs/installation.md @@ -0,0 +1 @@ +--8<-- "README.md" \ No newline at end of file diff --git a/docs/license_doc.md b/docs/license_doc.md new file mode 100644 index 000000000..0e1d3e825 --- /dev/null +++ b/docs/license_doc.md @@ -0,0 +1,3 @@ + + +--8<-- "LICENSE" \ No newline at end of file diff --git a/docs/team.md b/docs/team.md new file mode 100644 index 000000000..e27aa76f7 --- /dev/null +++ b/docs/team.md @@ -0,0 +1,12 @@ +## Our team: + +# eScience Center +- Dani Bodor, Lead RSE +- Walter Baccinelli, RSE +- Pablo Lopez-Tarifa, Programme Manager + +# Erasmus Medical Center +- Annemijn H. Jonkman, Lead Applicant +- Peter Somhorst +- Juliette Francovich +- Jantine Wisse \ No newline at end of file diff --git a/mkdocs.yml b/mkdocs.yml new file mode 100644 index 000000000..6914c9be5 --- /dev/null +++ b/mkdocs.yml @@ -0,0 +1,118 @@ +site_name: EITprocessing +site_description: ALIVE project +strict: false + +theme: + name: 'material' + palette: + - media: "(prefers-color-scheme: light)" + scheme: default + primary: darkblue + accent: pink + toggle: + icon: material/weather-sunny + name: "Switch to dark mode" + - media: "(prefers-color-scheme: dark)" + scheme: slate + primary: darkblue + accent: pink + toggle: + icon: material/weather-night + name: "Switch to light mode" + features: + - announce.dismiss + - content.action.view + - content.code.annotate + - content.code.copy + - content.tabs.link + - navigation.indexes + - navigation.path + - navigation.sections + - navigation.tabs + - navigation.tabs.sticky + icon: + logo: 'material/home' + next: fontawesome/solid/angle-right + previous: fontawesome/solid/angle-left + repo: fontawesome/brands/github-alt + view: material/eye + + +repo_url: https://github.com/EIT-ALIVE/eitprocessing +repo_name: EIT-ALIVE/eitprocessing +edit_uri: edit/main/docs/ + +# Page tree +nav: +- Home: index.md +- Getting started: + - Installation: installation.md + - Basic example: basic_example.md +- API Documentation: APIindex.md +- About: + - Contributing: contributing_doc.md + - Code of Conduct: code_of_conduct_doc.md + - License: license_doc.md + - Our team: team.md + +extra: + version: + provider: mike + +# https://www.mkdocs.org/user-guide/configuration/#validation +validation: + omitted_files: warn + absolute_links: warn + unrecognized_links: warn + +markdown_extensions: +- tables +- toc: + permalink: true + title: Page contents +- admonition +- pymdownx.details +- pymdownx.superfences +- pymdownx.highlight: + anchor_linenums: true + pygments_lang_class: true +- pymdownx.extra +- pymdownx.tabbed: + alternate_style: true +- pymdownx.magiclink +- pymdownx.snippets: + base_path: ["docs","."] + +watch: +- docs + +plugins: +- mike: + alias_type: symlink + canonical_version: latest +- search +- exclude: + glob: + - __pycache__/* +- mkdocstrings: + handlers: + python: + paths: [src] + import: + - https://docs.python.org/3/objects.inv + - https://numpy.org/doc/stable/objects.inv + - https://docs.scipy.org/doc/scipy/objects.inv + - https://pandas.pydata.org/docs/objects.inv + options: + members_order: source + inherited_members: true + filters: ["!^_"] + merge_init_into_class: true + show_root_heading: true + show_root_full_path: false + show_signature_annotations: true + signature_crossrefs: true + separate_signature: true + show_symbol_type_heading: true + show_symbol_type_toc: true + show_submodules: true From 512e3c6ea19e850afd78973674f455aba0a37920 Mon Sep 17 00:00:00 2001 From: Peter Somhorst Date: Wed, 9 Oct 2024 16:49:59 +0200 Subject: [PATCH 05/18] Add /site to .gitignore --- .gitignore | 2 ++ 1 file changed, 2 insertions(+) diff --git a/.gitignore b/.gitignore index 742af0463..879ee622d 100644 --- a/.gitignore +++ b/.gitignore @@ -36,3 +36,5 @@ venv3 **/test_data/* .helpers/dock_test_data/* .helpers/dock_test_add/* + +/site/ From 028830e93491a88a43c50224406845d306a14080 Mon Sep 17 00:00:00 2001 From: Peter Somhorst Date: Wed, 9 Oct 2024 20:24:36 +0200 Subject: [PATCH 06/18] Update README.md --- README.md | 43 +++++++++++++++++++++---------------------- 1 file changed, 21 insertions(+), 22 deletions(-) diff --git a/README.md b/README.md index d6c7445c9..9d6b714c7 100644 --- a/README.md +++ b/README.md @@ -6,20 +6,20 @@ | License | [![github license badge](https://img.shields.io/github/license/EIT-ALIVE/eitprocessing)](git@github.com:EIT-ALIVE/eitprocessing) | | Citation | [![DOI](https://zenodo.org/badge/617944717.svg)](https://zenodo.org/badge/latestdoi/617944717) | | Fairness | [![OpenSSF Best Practices](https://www.bestpractices.dev/projects/9147/badge)](https://www.bestpractices.dev/projects/9147) [![fair-software badge](https://img.shields.io/badge/fair--software.eu-%E2%97%8F%20%20%E2%97%8F%20%20%E2%97%8F%20%20%E2%97%8F%20%20%E2%97%8B-yellow)](https://fair-software.eu) | -| GitHub Actions | ![build](https://github.com/EIT-ALIVE/eitprocessing/actions/workflows/build.yml/badge.svg) ![dash_actions](https://github.com/EIT-ALIVE/eitprocessing/actions/workflows/dash_actions.yml/badge.svg) ![lint](https://github.com/EIT-ALIVE/eitprocessing/actions/workflows/lint.yml/badge.svg) ![documentation](https://github.com/EIT-ALIVE/eitprocessing/actions/workflows/documentation.yml/badge.svg) ![cffconvert](https://github.com/EIT-ALIVE/eitprocessing/actions/workflows/cffconvert.yml/badge.svg) | +| GitHub Actions | ![build](https://github.com/EIT-ALIVE/eitprocessing/actions/workflows/build.yml/badge.svg) ![lint](https://github.com/EIT-ALIVE/eitprocessing/actions/workflows/lint.yml/badge.svg) ![documentation](https://github.com/EIT-ALIVE/eitprocessing/actions/workflows/documentation.yml/badge.svg) ![cffconvert](https://github.com/EIT-ALIVE/eitprocessing/actions/workflows/cffconvert.yml/badge.svg) | | Python | ![Python](https://img.shields.io/badge/python-3.10-blue.svg) | # Contents -- [Installation](#installation-1) - - [Virtual environment](#virtual-environment) - - [Install using `pip`](#install-using-pip) +- [Introduction](#introduction) +- [Installation](#installation) + - [Install from PyPi](#install-from-pypi) + - [Developer install](#developer-install) - [Documentation](#documentation) - [Contributing](#contributing) - [Credits](#credits) -The project setup is documented in [project_setup](/project_setup.md). Feel free to remove this document (and/or the link to this document) if you don't need it. -## Installation +# Introduction [Electrical Impedance Tomography](https://en.wikipedia.org/wiki/Electrical_impedance_tomography) (EIT) is a noninvasive and radiation-free continuous imaging tool for monitoring respiratory mechanics. eitprocessing aims to provide a @@ -34,40 +34,39 @@ and Timpel, as well as data from other sources. Several pre-processing tools and [eit_dash](https://github.com/EIT-ALIVE/eit_dash) provides an accompanying GUI. -We welcome any [contributions or suggestions](CONTRIBUTING.md) -# Installation -## Virtual environment +# Installation It is advised to install eitprocessing in a dedicated virtual environment. See e.g. [Install packages in a virtual environment using pip and venv](https://packaging.python.org/en/latest/guides/installing-using-pip-and-virtual-environments/) or [Getting started with conda](https://docs.conda.io/projects/conda/en/stable/user-guide/getting-started.html). -For conda (using 'eit-alive' as example environment name; you can choose your own): +## Install from PyPi + +eitprocessing can be installed from PyPi as follows: + ``` -conda create -n eit-alive python=3.10 -conda activate eit-alive +pip install eitprocessing ``` -## Install using `pip` +### Developer install +For full developer options (testing, etc): -eitprocessing can be installed from PyPi as follows: - -- For basic use: `pip install eitprocessing` -- For full developer options (testing, etc): - - `git clone git@github.com:EIT-ALIVE/eitprocessing.git` - - `cd eitprocessing` - - `pip install -e ".[dev]"` +``` +git clone git@github.com:EIT-ALIVE/eitprocessing.git +cd eitprocessing +pip install -e ".[dev]" +``` # Documentation -Please see our [usage documentation](https://eit-alive.github.io/eitprocessing/) for a detailed explanation of the package. +Please see our [user documentation](https://eit-alive.github.io/eitprocessing/) for a detailed explanation of the package. # Contributing -If you want to contribute to the development of eitprocessing, +We welcome any contributions or suggestions. If you want to contribute to the development of eitprocessing, have a look at the [contribution guidelines](CONTRIBUTING.md) and the [developer documentation](README.dev.md). # Credits From 18db2f381a78035e21807d18f668a47429f2acee Mon Sep 17 00:00:00 2001 From: Peter Somhorst Date: Wed, 9 Oct 2024 20:24:47 +0200 Subject: [PATCH 07/18] Extract only Installation section from README --- docs/installation.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/docs/installation.md b/docs/installation.md index 4ab0748ee..491329a16 100644 --- a/docs/installation.md +++ b/docs/installation.md @@ -1 +1 @@ ---8<-- "README.md" \ No newline at end of file +--8<-- "README.md:39:62" From 1b25ecfa7a6b8e7b4b8a2efb4e40146aa7f0a980 Mon Sep 17 00:00:00 2001 From: Peter Somhorst Date: Wed, 9 Oct 2024 21:20:18 +0200 Subject: [PATCH 08/18] Add black dependency for signature formatting --- pyproject.toml | 1 + 1 file changed, 1 insertion(+) diff --git a/pyproject.toml b/pyproject.toml index 9ebd59da6..1b4972041 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -60,6 +60,7 @@ docs = [ "mkdocs-exclude", "mike", "pymdown-extensions", + "black", ] notebooks = [ "ipykernel >= 6.15.2", From bc1e5f43c7c10f0dee9071f1fd00dbf1c2cb6bf3 Mon Sep 17 00:00:00 2001 From: Peter Somhorst Date: Wed, 9 Oct 2024 21:20:41 +0200 Subject: [PATCH 09/18] Add TypeVar to sequence datacollections --- eitprocessing/datahandling/sequence.py | 14 ++++++++++---- 1 file changed, 10 insertions(+), 4 deletions(-) diff --git a/eitprocessing/datahandling/sequence.py b/eitprocessing/datahandling/sequence.py index 30d21880f..c56a1301b 100644 --- a/eitprocessing/datahandling/sequence.py +++ b/eitprocessing/datahandling/sequence.py @@ -42,10 +42,16 @@ class Sequence(Equivalence, SelectByTime): label: str | None = field(default=None, compare=False) name: str | None = field(default=None, compare=False, repr=False) description: str = field(default="", compare=False, repr=False) - eit_data: DataCollection = field(default_factory=lambda: DataCollection(EITData), repr=False) - continuous_data: DataCollection = field(default_factory=lambda: DataCollection(ContinuousData), repr=False) - sparse_data: DataCollection = field(default_factory=lambda: DataCollection(SparseData), repr=False) - interval_data: DataCollection = field(default_factory=lambda: DataCollection(IntervalData), repr=False) + eit_data: DataCollection[EITData] = field(default_factory=lambda: DataCollection(EITData), repr=False) + continuous_data: DataCollection[ContinuousData] = field( + default_factory=lambda: DataCollection(ContinuousData), + repr=False, + ) + sparse_data: DataCollection[SparseData] = field(default_factory=lambda: DataCollection(SparseData), repr=False) + interval_data: DataCollection[IntervalData] = field( + default_factory=lambda: DataCollection(IntervalData), + repr=False, + ) def __post_init__(self): if not self.label: From 8521e75ef7ae36fec70064b9af6f9600cb7c9735 Mon Sep 17 00:00:00 2001 From: Peter Somhorst Date: Wed, 9 Oct 2024 21:27:31 +0200 Subject: [PATCH 10/18] Change mkdocs settings for better readability --- mkdocs.yml | 7 ++++++- 1 file changed, 6 insertions(+), 1 deletion(-) diff --git a/mkdocs.yml b/mkdocs.yml index 6914c9be5..05bfed2f0 100644 --- a/mkdocs.yml +++ b/mkdocs.yml @@ -109,10 +109,15 @@ plugins: filters: ["!^_"] merge_init_into_class: true show_root_heading: true - show_root_full_path: false + show_root_full_path: true show_signature_annotations: true signature_crossrefs: true separate_signature: true show_symbol_type_heading: true show_symbol_type_toc: true show_submodules: true + heading_level: 2 + show_bases: false + show_source: false + docstring_section_style: spacy + line_length: 80 From aa433b08e2545392e326579666683a6f015c9397 Mon Sep 17 00:00:00 2001 From: Peter Somhorst Date: Wed, 9 Oct 2024 21:27:53 +0200 Subject: [PATCH 11/18] Add custom CSS (from mkdocstrings website) --- docs/css/material.css | 5 +++++ mkdocs.yml | 3 +++ 2 files changed, 8 insertions(+) create mode 100644 docs/css/material.css diff --git a/docs/css/material.css b/docs/css/material.css new file mode 100644 index 000000000..bf35afa80 --- /dev/null +++ b/docs/css/material.css @@ -0,0 +1,5 @@ +/* Indentation. */ +div.doc-contents:not(.first) { + padding-left: 25px; + border-left: .1rem solid var(--md-typeset-table-color); +} diff --git a/mkdocs.yml b/mkdocs.yml index 05bfed2f0..f3166c541 100644 --- a/mkdocs.yml +++ b/mkdocs.yml @@ -121,3 +121,6 @@ plugins: show_source: false docstring_section_style: spacy line_length: 80 + +extra_css: +- css/material.css From deb948cef644c1af52e59f845221342fa4c7c4ba Mon Sep 17 00:00:00 2001 From: Peter Somhorst Date: Wed, 9 Oct 2024 21:28:49 +0200 Subject: [PATCH 12/18] Split API --- docs/APIindex.md | 4 ---- docs/api/categories.md | 3 +++ docs/api/datacontainers.md | 17 +++++++++++++++++ docs/api/features.md | 6 ++++++ docs/api/filters.md | 12 ++++++++++++ docs/api/loading.md | 3 +++ docs/api/parameters.md | 3 +++ mkdocs.yml | 8 +++++++- 8 files changed, 51 insertions(+), 5 deletions(-) delete mode 100644 docs/APIindex.md create mode 100644 docs/api/categories.md create mode 100644 docs/api/datacontainers.md create mode 100644 docs/api/features.md create mode 100644 docs/api/filters.md create mode 100644 docs/api/loading.md create mode 100644 docs/api/parameters.md diff --git a/docs/APIindex.md b/docs/APIindex.md deleted file mode 100644 index ec6c4bca7..000000000 --- a/docs/APIindex.md +++ /dev/null @@ -1,4 +0,0 @@ -## Classes -::: eitprocessing.datahandling - options: - show_submodels: true \ No newline at end of file diff --git a/docs/api/categories.md b/docs/api/categories.md new file mode 100644 index 000000000..075fc5153 --- /dev/null +++ b/docs/api/categories.md @@ -0,0 +1,3 @@ +# Categories + +::: eitprocessing.categories.Category diff --git a/docs/api/datacontainers.md b/docs/api/datacontainers.md new file mode 100644 index 000000000..f8367aac2 --- /dev/null +++ b/docs/api/datacontainers.md @@ -0,0 +1,17 @@ +# Data containers + +::: eitprocessing.datahandling.sequence.Sequence + +::: eitprocessing.datahandling.eitdata.EITData + +::: eitprocessing.datahandling.continuousdata.ContinuousData + +::: eitprocessing.datahandling.sparsedata.SparseData + +::: eitprocessing.datahandling.intervaldata.IntervalData + +::: eitprocessing.datahandling.datacollection.DataCollection + +::: eitprocessing.datahandling.breath.Breath + +::: eitprocessing.datahandling.event.Event diff --git a/docs/api/features.md b/docs/api/features.md new file mode 100644 index 000000000..a25fd4f43 --- /dev/null +++ b/docs/api/features.md @@ -0,0 +1,6 @@ +# Feature extraction + +::: eitprocessing.features.breath_detection.BreathDetection + + +::: eitprocessing.features.moving_average.MovingAverage diff --git a/docs/api/filters.md b/docs/api/filters.md new file mode 100644 index 000000000..9d939765c --- /dev/null +++ b/docs/api/filters.md @@ -0,0 +1,12 @@ +# Filters + +::: eitprocessing.filters.butterworth_filters.LowPassFilter + +::: eitprocessing.filters.butterworth_filters.HighPassFilter + +::: eitprocessing.filters.butterworth_filters.BandStopFilter + +::: eitprocessing.filters.butterworth_filters.BandPassFilter + +::: eitprocessing.filters.butterworth_filters.ButterworthFilter + diff --git a/docs/api/loading.md b/docs/api/loading.md new file mode 100644 index 000000000..168ce6498 --- /dev/null +++ b/docs/api/loading.md @@ -0,0 +1,3 @@ +# Loading functions + +::: eitprocessing.datahandling.loading.load_eit_data diff --git a/docs/api/parameters.md b/docs/api/parameters.md new file mode 100644 index 000000000..7bb2f738c --- /dev/null +++ b/docs/api/parameters.md @@ -0,0 +1,3 @@ +# Parameters + +::: eitprocessing.parameters.eeli.EELI diff --git a/mkdocs.yml b/mkdocs.yml index f3166c541..d06ff1e4b 100644 --- a/mkdocs.yml +++ b/mkdocs.yml @@ -48,7 +48,13 @@ nav: - Getting started: - Installation: installation.md - Basic example: basic_example.md -- API Documentation: APIindex.md +- API Documentation: + - api/loading.md + - api/datacontainers.md + - api/filters.md + - api/features.md + - api/parameters.md + - api/categories.md - About: - Contributing: contributing_doc.md - Code of Conduct: code_of_conduct_doc.md From 179020bcb522a29406e552b9683b8c2ded6ef3a0 Mon Sep 17 00:00:00 2001 From: Peter Somhorst Date: Wed, 9 Oct 2024 21:29:07 +0200 Subject: [PATCH 13/18] Remove unnecessary title overwrites --- mkdocs.yml | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/mkdocs.yml b/mkdocs.yml index d06ff1e4b..41f78aee5 100644 --- a/mkdocs.yml +++ b/mkdocs.yml @@ -46,8 +46,8 @@ edit_uri: edit/main/docs/ nav: - Home: index.md - Getting started: - - Installation: installation.md - - Basic example: basic_example.md + - installation.md + - basic_example.md - API Documentation: - api/loading.md - api/datacontainers.md @@ -58,8 +58,8 @@ nav: - About: - Contributing: contributing_doc.md - Code of Conduct: code_of_conduct_doc.md - - License: license_doc.md - - Our team: team.md + - license_doc.md + - team.md extra: version: From 06d6bc5873fa25736a628529e1d8b8120637be2e Mon Sep 17 00:00:00 2001 From: Peter Somhorst Date: Wed, 9 Oct 2024 21:29:15 +0200 Subject: [PATCH 14/18] Fix headings --- docs/team.md | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/docs/team.md b/docs/team.md index e27aa76f7..9d0351c80 100644 --- a/docs/team.md +++ b/docs/team.md @@ -1,12 +1,12 @@ -## Our team: +# Our team -# eScience Center +## eScience Center - Dani Bodor, Lead RSE - Walter Baccinelli, RSE - Pablo Lopez-Tarifa, Programme Manager -# Erasmus Medical Center +## Erasmus Medical Center Rotterdam - Annemijn H. Jonkman, Lead Applicant - Peter Somhorst - Juliette Francovich -- Jantine Wisse \ No newline at end of file +- Jantine Wisse From 3b7657608221701e2a47f80e1932ce8842b0d295 Mon Sep 17 00:00:00 2001 From: Peter Somhorst Date: Wed, 9 Oct 2024 21:29:19 +0200 Subject: [PATCH 15/18] Add heading --- docs/license_doc.md | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/docs/license_doc.md b/docs/license_doc.md index 0e1d3e825..0e8c6fcab 100644 --- a/docs/license_doc.md +++ b/docs/license_doc.md @@ -1,3 +1,3 @@ +# License - ---8<-- "LICENSE" \ No newline at end of file +--8<-- "LICENSE" From 181cf5625cd00483dad3f92d369cdcb5636984e7 Mon Sep 17 00:00:00 2001 From: Peter Somhorst Date: Wed, 9 Oct 2024 21:39:04 +0200 Subject: [PATCH 16/18] Update github action for mkdocs --- .github/workflows/documentation.yml | 26 ++++++++------------------ 1 file changed, 8 insertions(+), 18 deletions(-) diff --git a/.github/workflows/documentation.yml b/.github/workflows/documentation.yml index be9a5fdeb..f65ac6a43 100644 --- a/.github/workflows/documentation.yml +++ b/.github/workflows/documentation.yml @@ -3,25 +3,21 @@ permissions: contents: write on: + workflow_dispatch: push: branches: - main - - drcandacemakedamoore/improve_docu - pull_request: - types: [opened, synchronize, reopened, ready_for_review] - branches: - - main - - drcandacemakedamoore/improve_docu jobs: build-documentation: - if: github.event.pull_request.draft == false name: Build documentation runs-on: ubuntu-latest strategy: fail-fast: false steps: - - uses: actions/checkout@v2 + - uses: actions/checkout@v4 + with: + fetch-depth: 0 - name: Set up Python 3.10 uses: actions/setup-python@v2 with: @@ -34,14 +30,8 @@ jobs: - name: Upgrade pip and install dependencies run: | python3 -m pip install --upgrade pip setuptools - python3 -m pip install .[dev,publishing] - - name: Install pandoc using apt - run: sudo apt install pandoc + python3 -m pip install .[docs] - name: Build documentation - run: make html - working-directory: docs - - name: Publish Docs to Pages - uses: JamesIves/github-pages-deploy-action@4.1.1 - with: - branch: gh-pages - folder: docs/_build/html + run: mkdocs build + - name: Deploy documentation + run: mkdocs gh-deploy From b5738d0aa0b21a6e6d456581e10518a8651b2c6a Mon Sep 17 00:00:00 2001 From: Peter Somhorst Date: Wed, 9 Oct 2024 22:07:36 +0200 Subject: [PATCH 17/18] Add pyyaml to dependencies Probably, pyyaml was a dependency of sphinx, but not explicitly of eitprocessing. --- pyproject.toml | 1 + 1 file changed, 1 insertion(+) diff --git a/pyproject.toml b/pyproject.toml index 1b4972041..9496f1bca 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -37,6 +37,7 @@ dependencies = [ "strenum >= 0.4.10", "anytree >= 2.12.1 ", "typing_extensions", + "pyyaml", ] [project.optional-dependencies] From c946919a098a7769b6ca4cbacf6aaedfca52b90e Mon Sep 17 00:00:00 2001 From: Peter Somhorst Date: Thu, 10 Oct 2024 09:58:56 +0200 Subject: [PATCH 18/18] Use lowercase naming --- mkdocs.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/mkdocs.yml b/mkdocs.yml index 41f78aee5..21680c0df 100644 --- a/mkdocs.yml +++ b/mkdocs.yml @@ -1,4 +1,4 @@ -site_name: EITprocessing +site_name: eitprocessing site_description: ALIVE project strict: false