Merge pull request #67 from Proteobench/add_more_formats

Added Proline and Custom formats, as well as a first documentation

.github/workflows/build_docs.yml

@@ -0,0 +1,37 @@
+name: Build and Deploy Documentation
+
+on:
+  push:
+    branches:
+      - main  # Adjust to your default branch
+
+jobs:
+  build-docs:
+    runs-on: ubuntu-latest
+
+    steps:
+      - name: Checkout repository
+        uses: actions/checkout@v2
+
+      - name: Set up Python
+        uses: actions/setup-python@v2
+        with:
+          python-version: 3.x  # Use the appropriate Python version
+
+      - name: Install dependencies
+        run: |
+          python -m pip install --upgrade pip
+          pip install -r docs/requirements.txt  # Adjust path if needed
+
+      - name: Build documentation
+        run: |
+          cd docs
+          make html  # Or your Sphinx build command
+        env:
+          READTHEDOCS: 'True'
+
+      - name: Deploy to Read the Docs
+        uses: readthedocs/github-action@master
+        with:
+          sphinx-version: latest  # Use the appropriate version
+

.vscode/settings.json

@@ -2,9 +2,12 @@
     "[python]": {
         "editor.formatOnSave": true,
         "editor.codeActionsOnSave": {"source.organizeImports": true},
-        "editor.rulers": [88]
+        "editor.rulers": [
+            88
+        ],
+        "editor.defaultFormatter": "ms-python.black-formatter"
     },
-    "python.formatting.provider": "black",
+    "python.formatting.provider": "none",
     "python.testing.unittestArgs": [
         "-v",
         "-s",

README.md

@@ -3,3 +3,8 @@
 [TODO]
 
 See **Contributing** for installation instructions
+
+
+## Documenation
+
+You find the documentation in docs/_build/html

docs/Makefile

@@ -0,0 +1,20 @@
+# Minimal makefile for Sphinx documentation
+#
+
+# You can set these variables from the command line, and also
+# from the environment for the first two.
+SPHINXOPTS    ?=
+SPHINXBUILD   ?= sphinx-build
+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)

docs/changelog.rst

@@ -1 +1,5 @@
-.. mdinclude:: ../CHANGELOG.md
+=================
+Change log
+=================
+
+TODO

docs/conf.py

@@ -1,55 +1,44 @@
+# Configuration file for the Sphinx documentation builder.
+#
+# For the full list of built-in configuration values, see the documentation:
+# https://www.sphinx-doc.org/en/master/usage/configuration.html
+
 import os
 import sys
 
-sys.path.insert(0, os.path.abspath('..'))
+# -- Project information -----------------------------------------------------
+# https://www.sphinx-doc.org/en/master/usage/configuration.html#project-information
 
-from proteobench import __version__
+project = "ProteoBench"
+copyright = "2023, EuBIC-MS"
+author = "EuBIC-MS"
+description = "A Python-base platform for benchmarking data analysis in proteomics."
 
-project = 'ProteoBench'
-author = 'EuBIC-MS'
-release = __version__
-github_project_url = "https://github.com/proteobench/proteobench/"
-github_doc_root = "https://github.com/proteobench/proteobench/tree/main/docs/"
+# Add source folder to path for autodoc
+sys.path.insert(0, os.path.abspath(".."))
 
-extensions = [
-    'sphinx.ext.autodoc',
-    "sphinx.ext.autosectionlabel",
-    'sphinx.ext.autosummary',
-    "sphinx.ext.napoleon",
-    'sphinx.ext.intersphinx',
-    'sphinx.ext.viewcode',
-    "sphinx_rtd_theme",
-    'sphinx_autodoc_typehints',
-    "sphinx_mdinclude",
-]
-source_suffix = [".rst", ".md"]
-master_doc = "index"
+# Add path for documentation including the main project path
 
-intersphinx_mapping = {
-    "python": ("https://docs.python.org/3/", None),
-    "numpy": ('https://numpy.org/doc/stable/', None),
-    "pandas": ('https://pandas.pydata.org/docs/', None),
-}
+# -- General configuration ---------------------------------------------------
+# https://www.sphinx-doc.org/en/master/usage/configuration.html#general-configuration
 
-autosummary_generate = True
-autoclass_content = "both"
-html_show_sourcelink = False
-autodoc_inherit_docstrings = True
-set_type_checking_flag = True
-add_module_names = False
+extensions = []
 
-templates_path = ['_templates']
-exclude_patterns = ["_build"]
+templates_path = ["_templates"]
+exclude_patterns = ["_build", "Thumbs.db", ".DS_Store"]
 
-html_theme = "sphinx_rtd_theme"
-html_static_path = ["_static"]
-html_css_files = ["css/custom.css"]
 
-autodoc_member_order = "bysource"
-autoclass_content = "init"
+# -- Options for HTML output -------------------------------------------------
+# https://www.sphinx-doc.org/en/master/usage/configuration.html#options-for-html-output
 
+html_theme = "sphinx_rtd_theme"
+html_static_path = ["_static"]
 
-def setup(app):
-    config = {
-        "enable_eval_rst": True,
-    }
+extensions = [
+    "sphinx.ext.napoleon",
+    "sphinx.ext.autodoc",
+    "sphinx.ext.autosummary",
+    "sphinx.ext.viewcode",
+    "sphinx.ext.todo",
+    "sphinx.ext.githubpages",
+]

docs/index.rst

@@ -1,12 +1,36 @@
-.. mdinclude:: ../README.md
+.. ProteoBench documentation master file, created by
+   sphinx-quickstart on Fri Jun 16 09:58:17 2023.
+   You can adapt this file completely to your liking, but it should at least
+   contain the root `toctree` directive.
+
+Welcome
+=======================================
 
 .. toctree::
-   :hidden:
-   :includehidden:
-   :glob:
-   :maxdepth: 2
-
-   About<self>
-   Reference<_autosummary/proteobench>
-   Changelog<changelog>
-   Contributing<contributing>
+    :maxdepth: 1
+
+    user_guide/index
+    changelog
+    proteobench/modules
+    webinterface/webinterface
+
+Project Overview
+------------------
+
+The ProteoBench project is divided into two main parts:
+
+Modules for Data Processing and Reporting
+-----------------------------------------
+These :doc:`proteobench/modules` process the data and generate reports.
+
+Web Interface for Result Visualization
+--------------------------------------
+The :doc:`webinterface/webinterface` displays the results and allows comparison with publicly available data.
+
+
+Indices and tables
+==================
+
+* :ref:`genindex`
+* :ref:`modindex`
+* :ref:`search`

docs/make.bat

@@ -0,0 +1,35 @@
+@ECHO OFF
+
+pushd %~dp0
+
+REM Command file for Sphinx documentation
+
+if "%SPHINXBUILD%" == "" (
+	set SPHINXBUILD=sphinx-build
+)
+set SOURCEDIR=.
+set BUILDDIR=_build
+
+%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.https://www.sphinx-doc.org/
+	exit /b 1
+)
+
+if "%1" == "" goto help
+
+%SPHINXBUILD% -M %1 %SOURCEDIR% %BUILDDIR% %SPHINXOPTS% %O%
+goto end
+
+:help
+%SPHINXBUILD% -M help %SOURCEDIR% %BUILDDIR% %SPHINXOPTS% %O%
+
+:end
+popd

docs/proteobench/dda_quant.rst

@@ -0,0 +1,29 @@
+DDA_Quant
+======================================
+
+Module for quantitative DDA data
+---------------------------------
+
+.. autosummary::
+    :toctree: DDA_Quant
+
+.. automodule:: proteobench.modules.dda_quant.parse_settings
+   :members:
+   :undoc-members:
+   :show-inheritance:
+.. automodule:: proteobench.modules.dda_quant.parse
+   :members:
+   :undoc-members:
+   :show-inheritance:
+.. automodule:: proteobench.modules.dda_quant.module
+   :members:
+   :undoc-members:
+   :show-inheritance:
+.. automodule:: proteobench.modules.dda_quant.datapoint
+   :members:
+   :undoc-members:
+   :show-inheritance:
+.. automodule:: proteobench.modules.dda_quant.plot
+   :members:
+   :undoc-members:
+   :show-inheritance:

docs/proteobench/modules.rst

@@ -0,0 +1,21 @@
+Modules
+===========================
+
+The different modules correpond to code to read the different input files and
+to create the benchmarking metrics for visualization and comparison in the :doc:`../webinterface/webinterface`
+
+.. toctree::
+   :maxdepth: 1
+
+   dda_id
+   dda_quant
+   dia_id
+   dia_quant
+   metaproteomics
+   template
+   .. proteobench.modules.rescoring
+
+
+The template module contains all needed files to create a new module. It is
+recommended to copy the template module and rename it to the new module name.
+

docs/proteobench/template.rst

@@ -0,0 +1,29 @@
+Template
+======================================
+
+Template for module
+---------------------------------
+
+.. autosummary::
+    :toctree: template
+
+.. automodule:: proteobench.modules.template.parse_settings
+   :members:
+   :undoc-members:
+   :show-inheritance:
+.. automodule:: proteobench.modules.template.parse
+   :members:
+   :undoc-members:
+   :show-inheritance:
+.. automodule:: proteobench.modules.template.module
+   :members:
+   :undoc-members:
+   :show-inheritance:
+.. automodule:: proteobench.modules.template.datapoint
+   :members:
+   :undoc-members:
+   :show-inheritance:
+.. automodule:: proteobench.modules.template.plot
+   :members:
+   :undoc-members:
+   :show-inheritance: