Autodocs

.github/workflows/build_documentation.yml

@@ -0,0 +1,27 @@
+name: documentation
+
+on: [push, pull_request, workflow_dispatch]
+
+permissions:
+  contents: write
+
+jobs:
+  docs:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+      - uses: actions/setup-python@v5
+      - name: Install dependencies
+        run: |
+          pip install sphinx sphinx_rtd_theme myst_parser sphinx-autoapi
+      - name: Sphinx build
+        run: |
+          sphinx-build doc/sphinx _build
+      - name: Deploy to GitHub Pages
+        uses: peaceiris/actions-gh-pages@v4
+        if: ${{ github.event_name == 'push' }}
+        with:
+          publish_branch: gh-pages
+          github_token: ${{ secrets.GITHUB_TOKEN }}
+          publish_dir: _build/
+          force_orphan: true 

.github/workflows/check-code-formatting.yml

@@ -8,7 +8,7 @@ jobs:
     env:
       CLANG_FORMAT: clang-format-15
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v4
       - name: Install clang-format
         run: sudo apt-get update && sudo apt-get install -y --no-install-recommends $CLANG_FORMAT && $CLANG_FORMAT --version
       - name: Run clang-format
@@ -29,8 +29,8 @@ jobs:
   cmake-formatting:
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v2
-      - uses: actions/setup-python@v2
+      - uses: actions/checkout@v4
+      - uses: actions/setup-python@v5
         with:
           python-version: '3.x'
       - name: Install cmake-format
@@ -53,8 +53,8 @@ jobs:
   python-formatting:
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v2
-      - uses: actions/setup-python@v2
+      - uses: actions/checkout@v4
+      - uses: actions/setup-python@v5
         with:
           python-version: '3.x'
       - name: Install ruff

.github/workflows/codeql-analysis.yml

@@ -30,7 +30,7 @@ jobs:
 
     steps:
     - name: Checkout repository
-      uses: actions/checkout@v2
+      uses: actions/checkout@v4
       with:
         # We must fetch at least the immediate parents so that if this is
         # a pull request then we can checkout the head.
@@ -43,7 +43,7 @@ jobs:
 
     # Initializes the CodeQL tools for scanning.
     - name: Initialize CodeQL
-      uses: github/codeql-action/init@v1
+      uses: github/codeql-action/init@v3
       with:
         languages: ${{ matrix.language }}
         # If you wish to specify custom queries, you can do so here or in a config file.
@@ -54,7 +54,7 @@ jobs:
     # Autobuild attempts to build any compiled languages  (C/C++, C#, or Java).
     # If this step fails, then you should remove it and run the build manually (see below)
     - name: Autobuild
-      uses: github/codeql-action/autobuild@v1
+      uses: github/codeql-action/autobuild@v3
 
     # ℹ️ Command-line programs to run using the OS shell.
     # 📚 https://git.io/JvXDl
@@ -68,4 +68,4 @@ jobs:
     #   make release
 
     - name: Perform CodeQL Analysis
-      uses: github/codeql-action/analyze@v1
+      uses: github/codeql-action/analyze@v3

.github/workflows/compile-without-helpers.yml

@@ -7,10 +7,10 @@ jobs:
     name: Compile without helpers
     runs-on: ubuntu-latest
     steps:
-    - uses: actions/checkout@v2
+    - uses: actions/checkout@v4
 
     - name: Setup conda
-      uses: conda-incubator/setup-miniconda@v2
+      uses: conda-incubator/setup-miniconda@v3
       with:
         auto-update-conda: true
         miniconda-version: "latest"

.github/workflows/run-tests.yml

@@ -19,10 +19,10 @@ jobs:
       fail-fast: false
 
     steps:
-    - uses: actions/checkout@v2
+    - uses: actions/checkout@v4
 
     - name: Setup conda
-      uses: conda-incubator/setup-miniconda@v2
+      uses: conda-incubator/setup-miniconda@v3
       with:
         auto-update-conda: true
         miniconda-version: "latest"
@@ -39,5 +39,5 @@ jobs:
       run: pytest -v --color=yes --cov=hdtv --cov-report=xml tests
 
     - name: Post Coverage
-      uses: codecov/codecov-action@v1
+      uses: codecov/codecov-action@v3
       if: matrix.python-version == '3.12' && matrix.root-version == '6.32.2'

.gitignore

@@ -25,6 +25,7 @@ var/
 *.egg-info/
 .installed.cfg
 *.egg
+.spyproject/
 
 # PyInstaller
 #  Usually these files are written by a python script from a template
@@ -56,7 +57,7 @@ junit.xml
 *.log
 
 # Sphinx documentation
-docs/_build/
+doc/sphinx/_build/
 
 # PyBuilder
 target/

doc/guide/hdtv-tutorial.rst

@@ -309,6 +309,31 @@ To write all existing calibrations into a calibration list file, use
 
     hdtv> calibration position list write <filename>
 
+Alternatively, the calibration can be done with some known calibration
+sources automatically:
+
+.. code-block::
+
+    hdtv> calibration position nuclide Eu-152 -d IAEA -a
+
+To calibrate the efficiency also the built-in calibration sources can
+be used.
+.. code-block::
+
+    hdtv> calibration efficiency fit -d IAEA 0,152Eu
+
+NORMALIZE SPECTRA
+=================
+Spectra can be normalized with a coefficient with
+
+.. code-block::
+
+    hdtv> spectrum normalize <specID> <coefficient>
+
+Afterwards, go to the spectrum and press ``shift``+``1`` to apply the normalization.
+Press the key combination again to unapply it.
+
+
 WORKING WITH MULTIPLE SPECTRA
 =============================
 
@@ -348,6 +373,51 @@ a <specID>
 The currently visible spectra and their corresponding colors are shown in
 the top left corner of the GUI spectra window.
 
+Spectra can be also deleted, or copied:
+
+.. code-block::
+
+    hdtv> spectrum copy <specID>
+    hdtv> spectrum delete <specID>
+
+Add several spectra by first specifying the specID of the resulting summed
+spectrum:
+
+.. code-block::
+
+    hdtv> spectrum add <specID_sum> <specID1> <specID2> ...
+
+
+OPEN ROOT FILES
+=============== 
+
+To open a ROOT histogram:
+
+.. code-block::
+
+    hdtv> root get path/to/rootfile.root/histogram
+
+To open an asymmetric ROOT matrix:
+
+.. code-block::
+
+    hdtv> root matrix get asym path/to/rootfile.root/matrix
+
+For symmetric matrices use ``sym`` instead of ``asym``.
+Opening a matrix gives two spectra 0.0 and 0.1 which are the X and Y projections.
+
+PEAK SEARCH
+===========
+Find peaks automatically between start and end bin:
+
+.. code-block::
+
+    hdtv> fit peakfind startbin endbin  [-a] [-r] [-s] [-t]
+
+The option [-a] automatically fits the found peaks. [-r] rejects peaks. 
+With [-s] sigma and with [-t] the threshold for the search can be specified.
+
+
 SEE ALSO
 ========
 

doc/sphinx/Makefile

@@ -0,0 +1,16 @@
+# 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     = source
+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)

doc/sphinx/README

@@ -0,0 +1,6 @@
+Build the autoapi documentation with
+ sphinx-build -b html . _build
+inside this directory.
+Dependencies for this documentation:
+ sphinx-autoapi
+ sphinx-rtd-theme

doc/sphinx/conf.py

@@ -0,0 +1,29 @@
+"""
+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
+"""
+
+# -- Project information -----------------------------------------------------
+# https://www.sphinx-doc.org/en/master/usage/configuration.html#project-information
+
+project = "hdtv"
+project_copyright = "2024, IKP"
+author = "IKP"
+
+# -- General configuration ---------------------------------------------------
+# https://www.sphinx-doc.org/en/master/usage/configuration.html#general-configuration
+
+extensions = ["autoapi.extension"]
+autoapi_dirs = ["../../hdtv"]
+
+templates_path = ["_templates"]
+exclude_patterns = ["_build", "Thumbs.db", ".DS_Store"]
+
+
+# -- 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"]

doc/sphinx/include_guide.rst

@@ -0,0 +1 @@
+.. include:: ../guide/hdtv.rst

doc/sphinx/include_tutorial.rst

@@ -0,0 +1 @@
+.. include:: ../guide/hdtv-tutorial.rst

doc/sphinx/index.rst

@@ -0,0 +1,22 @@
+.. hdtv documentation master file, created by
+   sphinx-quickstart on Thu Apr 11 16:12:11 2024.
+   You can adapt this file completely to your liking, but it should at least
+   contain the root `toctree` directive.
+
+Welcome to hdtv's documentation!
+================================
+
+.. toctree::
+   :maxdepth: 3
+   :caption: Contents:
+
+   Documentation <include_guide.rst>
+   Tutorial <include_tutorial.rst>
+
+
+Indices and tables
+==================
+
+* :ref:`genindex`
+* :ref:`modindex`
+* :ref:`search`

doc/sphinx/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

hdtv/hsluv.py

@@ -270,7 +270,10 @@ def lch_to_hpluv(_hx_tuple):
 
 
 def rgb_to_hex(_hx_tuple):
-    return f"#{int(_math.floor(_hx_tuple[0] * 255 + 0.5)):02x}{int(_math.floor(_hx_tuple[1] * 255 + 0.5)):02x}{int(_math.floor(_hx_tuple[2] * 255 + 0.5)):02x}"
+    r = int(_math.floor(_hx_tuple[0] * 255 + 0.5))
+    g = int(_math.floor(_hx_tuple[1] * 255 + 0.5))
+    b = int(_math.floor(_hx_tuple[2] * 255 + 0.5))
+    return f"#{r:02x}{g:02x}{b:02x}"
 
 
 def hex_to_rgb(_hex):

pyproject.toml

@@ -12,7 +12,7 @@ lint.ignore = [
     "RUF012",  # enforces type annotations on a codebase that lacks type annotations
     "B904",
     "ISC001",
-    "UP031",
+    "UP031",  # Use format specifiers instead of percent format
 ]
 lint.select = [
     "E",