From e4c1d39247c801b415edda6e290a0f6a31b19dff Mon Sep 17 00:00:00 2001
From: Benedikt Moneke <67148916+bmoneke@users.noreply.github.com>
Date: Wed, 12 Jul 2023 14:35:03 +0200
Subject: [PATCH 01/29] First version for CI, similar to pymeasure.

---
 .github/pytest.json             |  23 +++
 .github/sphinx.json             |  38 +++++
 .github/workflows/pyleco_CI.yml | 105 ++++++++++++++
 docs/Makefile                   | 177 +++++++++++++++++++++++
 docs/index.rst                  |   3 +
 docs/make.bat                   | 242 ++++++++++++++++++++++++++++++++
 environment.yml                 |  16 ++-
 pyleco/__init__.py              |  51 +++++++
 pyproject.toml                  |  14 +-
 setup.cfg                       |   6 +
 10 files changed, 665 insertions(+), 10 deletions(-)
 create mode 100644 .github/pytest.json
 create mode 100644 .github/sphinx.json
 create mode 100644 .github/workflows/pyleco_CI.yml
 create mode 100644 docs/Makefile
 create mode 100644 docs/index.rst
 create mode 100644 docs/make.bat
 create mode 100644 setup.cfg

diff --git a/.github/pytest.json b/.github/pytest.json
new file mode 100644
index 000000000..7f010d1e9
--- /dev/null
+++ b/.github/pytest.json
@@ -0,0 +1,23 @@
+{
+    "problemMatcher": [
+        {
+            "owner": "pytest-warnings",
+            "severity": "warning",
+            "pattern": [
+                {
+                    "regexp": "^=+ warnings summary =+$"
+                },
+                {
+                    "regexp": "^(?<path>.+?):(?<line>\\d+)$",
+                    "file": 1,
+                    "line": 2
+                },
+                {
+                    "regexp": "^  (?<message>.+)$",
+                    "message": 1,
+                    "loop": true
+                }
+            ]
+        }
+    ]
+}
diff --git a/.github/sphinx.json b/.github/sphinx.json
new file mode 100644
index 000000000..2f12378da
--- /dev/null
+++ b/.github/sphinx.json
@@ -0,0 +1,38 @@
+{
+    "problemMatcher": [
+        {
+            "owner": "sphinx-docstring",
+            "pattern": [
+                {
+                    "regexp": "^(?<path>.+?):(?<message>.*? (?<severity>WARNING|ERROR): .+)$",
+                    "file": 1,
+                    "severity": 3,
+                    "message": 2
+                }
+            ]
+        },
+        {
+            "owner": "sphinx-doctest",
+            "pattern": [
+                {
+                    "regexp": "^File \\\"(?<path>.+?)\\\", line (?<line>\\d+|\\?), (?<msg>.*$)",
+                    "file": 1,
+                    "line": 2,
+                    "message": 3
+                }
+            ]
+        },
+        {
+            "owner": "sphinx-extension",
+            "pattern": [
+                {
+                    "regexp": "^(?<severity>WARNING|ERROR): (?<code>\\S+): (?<message>.+)(?<dummy_file_entry>)$",
+                    "severity": 1,
+                    "code": 2,
+                    "message": 3,
+                    "file": 4
+                }
+            ]
+        }
+    ]
+}
diff --git a/.github/workflows/pyleco_CI.yml b/.github/workflows/pyleco_CI.yml
new file mode 100644
index 000000000..b7a575caa
--- /dev/null
+++ b/.github/workflows/pyleco_CI.yml
@@ -0,0 +1,105 @@
+name: PyLECO CI
+on:
+  push:
+    branches:
+      - main
+  pull_request:
+
+jobs:
+  docs_lint:
+    name: Docs and Linting
+    runs-on: "ubuntu-latest"
+    defaults:
+      run:
+        shell: bash -l {0}
+    steps:
+      - uses: actions/checkout@v3
+        with:
+          fetch-depth: 0
+      - name: Cache conda
+        uses: actions/cache@v3
+        env:
+          CACHE_NUMBER: 0  # Increase to reset the cache
+        with:
+          path: ~/conda_pkgs_dir
+          key: py3.10-ubuntu-latest-conda-${{ env.CACHE_NUMBER }}-${{ hashFiles('environment.yml') }}
+      - name: Install pyleco requirements
+        uses: conda-incubator/setup-miniconda@v2
+        with:
+          python-version: "3.10"
+          environment-file: environment.yml
+          activate-environment: pyleco
+          auto-update-conda: true
+          use-only-tar-bz2: true  # for caching to work properly
+      - name: Conda info & list
+        run: |
+          conda info
+          conda list
+      - name: Set up flake8 annotations
+        uses: rbialon/flake8-annotations@v1
+      - name: Lint with flake8
+        run: |
+          # Be sure to check for Python syntax errors or undefined names
+          flake8 . --count --extend-select=E9,F63,F7,F82 --show-source --statistics
+      - uses: ammaraskar/sphinx-problem-matcher@master
+      - name: Generate docs
+        if: always()  # run even if the previous step failed
+        working-directory: ./docs
+        run: |
+          echo "::add-matcher::.github/sphinx.json"
+          make html SPHINXOPTS="-W --keep-going"
+      - name: Run doctests
+        if: always()  # run even if the previous step failed
+        working-directory: ./docs
+        run: |
+          echo "::add-matcher::.github/sphinx.json"
+          make doctest SPHINXOPTS="-W --keep-going"
+  test:
+    name: Python ${{ matrix.python-version }}, ${{ matrix.os }}
+    runs-on: ${{ matrix.os }}
+    defaults:
+      run:
+        shell: bash -l {0}
+    strategy:
+      fail-fast: true
+      matrix:
+        os: ["ubuntu-latest", "macos-latest", "windows-latest"]
+        python-version: ["3.10", "3.11"]
+    steps:
+      - uses: actions/checkout@v3
+        with:
+          fetch-depth: 0
+      - name: Cache conda
+        uses: actions/cache@v3
+        env:
+          CACHE_NUMBER: 0  # Increase to reset the cache
+        with:
+          path: ~/conda_pkgs_dir
+          key: py${{ matrix.python-version }}-${{ matrix.os }}-conda-${{ env.CACHE_NUMBER }}-${{ hashFiles('environment.yml') }}
+      - name: Install pyleco requirements
+        uses: conda-incubator/setup-miniconda@v2
+        with:
+          python-version: ${{ matrix.python-version }}
+          environment-file: environment.yml
+          activate-environment: pyleco
+          auto-update-conda: true
+          use-only-tar-bz2: true  # for caching to work properly
+      - name: Install Pyleco
+        # If the pytest problem matcher stops working because of bad paths, do an editable install
+        run: pip install .[dev]
+      - name: Pyleco version
+        run: python -c "import pyleco;print(pyleco.__version__)"
+      - name: Conda info & list
+        run: |
+          conda info
+          conda list
+      - name: Run pytest with xvfb
+        if: runner.os == 'Linux'
+        run: |
+          echo "::add-matcher::.github/pytest.json"
+          xvfb-run -a pytest
+      - name: Run pytest
+        if: runner.os != 'Linux'
+        run: |
+          echo "::add-matcher::.github/pytest.json"
+          pytest
diff --git a/docs/Makefile b/docs/Makefile
new file mode 100644
index 000000000..97c821792
--- /dev/null
+++ b/docs/Makefile
@@ -0,0 +1,177 @@
+# Makefile for Sphinx documentation
+#
+
+# You can set these variables from the command line.
+SPHINXOPTS    =
+SPHINXBUILD   = sphinx-build
+PAPER         =
+BUILDDIR      = _build
+
+# User-friendly check for sphinx-build
+ifeq ($(shell which $(SPHINXBUILD) >/dev/null 2>&1; echo $$?), 1)
+$(error The '$(SPHINXBUILD)' command was not found. Make sure you have Sphinx installed, then set the SPHINXBUILD environment variable to point to the full path of the '$(SPHINXBUILD)' executable. Alternatively you can add the directory with the executable to your PATH. If you don't have Sphinx installed, grab it from http://sphinx-doc.org/)
+endif
+
+# Internal variables.
+PAPEROPT_a4     = -D latex_paper_size=a4
+PAPEROPT_letter = -D latex_paper_size=letter
+ALLSPHINXOPTS   = -d $(BUILDDIR)/doctrees $(PAPEROPT_$(PAPER)) $(SPHINXOPTS) .
+# the i18n builder cannot share the environment and doctrees with the others
+I18NSPHINXOPTS  = $(PAPEROPT_$(PAPER)) $(SPHINXOPTS) .
+
+.PHONY: help clean html dirhtml singlehtml pickle json htmlhelp qthelp devhelp epub latex latexpdf text man changes linkcheck doctest gettext
+
+help:
+	@echo "Please use \`make <target>' where <target> is one of"
+	@echo "  html       to make standalone HTML files"
+	@echo "  dirhtml    to make HTML files named index.html in directories"
+	@echo "  singlehtml to make a single large HTML file"
+	@echo "  pickle     to make pickle files"
+	@echo "  json       to make JSON files"
+	@echo "  htmlhelp   to make HTML files and a HTML help project"
+	@echo "  qthelp     to make HTML files and a qthelp project"
+	@echo "  devhelp    to make HTML files and a Devhelp project"
+	@echo "  epub       to make an epub"
+	@echo "  latex      to make LaTeX files, you can set PAPER=a4 or PAPER=letter"
+	@echo "  latexpdf   to make LaTeX files and run them through pdflatex"
+	@echo "  latexpdfja to make LaTeX files and run them through platex/dvipdfmx"
+	@echo "  text       to make text files"
+	@echo "  man        to make manual pages"
+	@echo "  texinfo    to make Texinfo files"
+	@echo "  info       to make Texinfo files and run them through makeinfo"
+	@echo "  gettext    to make PO message catalogs"
+	@echo "  changes    to make an overview of all changed/added/deprecated items"
+	@echo "  xml        to make Docutils-native XML files"
+	@echo "  pseudoxml  to make pseudoxml-XML files for display purposes"
+	@echo "  linkcheck  to check all external links for integrity"
+	@echo "  doctest    to run all doctests embedded in the documentation (if enabled)"
+
+clean:
+	rm -rf $(BUILDDIR)/*
+
+html:
+	$(SPHINXBUILD) -b html $(ALLSPHINXOPTS) $(BUILDDIR)/html
+	@echo
+	@echo "Build finished. The HTML pages are in $(BUILDDIR)/html."
+
+dirhtml:
+	$(SPHINXBUILD) -b dirhtml $(ALLSPHINXOPTS) $(BUILDDIR)/dirhtml
+	@echo
+	@echo "Build finished. The HTML pages are in $(BUILDDIR)/dirhtml."
+
+singlehtml:
+	$(SPHINXBUILD) -b singlehtml $(ALLSPHINXOPTS) $(BUILDDIR)/singlehtml
+	@echo
+	@echo "Build finished. The HTML page is in $(BUILDDIR)/singlehtml."
+
+pickle:
+	$(SPHINXBUILD) -b pickle $(ALLSPHINXOPTS) $(BUILDDIR)/pickle
+	@echo
+	@echo "Build finished; now you can process the pickle files."
+
+json:
+	$(SPHINXBUILD) -b json $(ALLSPHINXOPTS) $(BUILDDIR)/json
+	@echo
+	@echo "Build finished; now you can process the JSON files."
+
+htmlhelp:
+	$(SPHINXBUILD) -b htmlhelp $(ALLSPHINXOPTS) $(BUILDDIR)/htmlhelp
+	@echo
+	@echo "Build finished; now you can run HTML Help Workshop with the" \
+	      ".hhp project file in $(BUILDDIR)/htmlhelp."
+
+qthelp:
+	$(SPHINXBUILD) -b qthelp $(ALLSPHINXOPTS) $(BUILDDIR)/qthelp
+	@echo
+	@echo "Build finished; now you can run "qcollectiongenerator" with the" \
+	      ".qhcp project file in $(BUILDDIR)/qthelp, like this:"
+	@echo "# qcollectiongenerator $(BUILDDIR)/qthelp/PyMeasure.qhcp"
+	@echo "To view the help file:"
+	@echo "# assistant -collectionFile $(BUILDDIR)/qthelp/PyMeasure.qhc"
+
+devhelp:
+	$(SPHINXBUILD) -b devhelp $(ALLSPHINXOPTS) $(BUILDDIR)/devhelp
+	@echo
+	@echo "Build finished."
+	@echo "To view the help file:"
+	@echo "# mkdir -p $$HOME/.local/share/devhelp/PyMeasure"
+	@echo "# ln -s $(BUILDDIR)/devhelp $$HOME/.local/share/devhelp/PyMeasure"
+	@echo "# devhelp"
+
+epub:
+	$(SPHINXBUILD) -b epub $(ALLSPHINXOPTS) $(BUILDDIR)/epub
+	@echo
+	@echo "Build finished. The epub file is in $(BUILDDIR)/epub."
+
+latex:
+	$(SPHINXBUILD) -b latex $(ALLSPHINXOPTS) $(BUILDDIR)/latex
+	@echo
+	@echo "Build finished; the LaTeX files are in $(BUILDDIR)/latex."
+	@echo "Run \`make' in that directory to run these through (pdf)latex" \
+	      "(use \`make latexpdf' here to do that automatically)."
+
+latexpdf:
+	$(SPHINXBUILD) -b latex $(ALLSPHINXOPTS) $(BUILDDIR)/latex
+	@echo "Running LaTeX files through pdflatex..."
+	$(MAKE) -C $(BUILDDIR)/latex all-pdf
+	@echo "pdflatex finished; the PDF files are in $(BUILDDIR)/latex."
+
+latexpdfja:
+	$(SPHINXBUILD) -b latex $(ALLSPHINXOPTS) $(BUILDDIR)/latex
+	@echo "Running LaTeX files through platex and dvipdfmx..."
+	$(MAKE) -C $(BUILDDIR)/latex all-pdf-ja
+	@echo "pdflatex finished; the PDF files are in $(BUILDDIR)/latex."
+
+text:
+	$(SPHINXBUILD) -b text $(ALLSPHINXOPTS) $(BUILDDIR)/text
+	@echo
+	@echo "Build finished. The text files are in $(BUILDDIR)/text."
+
+man:
+	$(SPHINXBUILD) -b man $(ALLSPHINXOPTS) $(BUILDDIR)/man
+	@echo
+	@echo "Build finished. The manual pages are in $(BUILDDIR)/man."
+
+texinfo:
+	$(SPHINXBUILD) -b texinfo $(ALLSPHINXOPTS) $(BUILDDIR)/texinfo
+	@echo
+	@echo "Build finished. The Texinfo files are in $(BUILDDIR)/texinfo."
+	@echo "Run \`make' in that directory to run these through makeinfo" \
+	      "(use \`make info' here to do that automatically)."
+
+info:
+	$(SPHINXBUILD) -b texinfo $(ALLSPHINXOPTS) $(BUILDDIR)/texinfo
+	@echo "Running Texinfo files through makeinfo..."
+	make -C $(BUILDDIR)/texinfo info
+	@echo "makeinfo finished; the Info files are in $(BUILDDIR)/texinfo."
+
+gettext:
+	$(SPHINXBUILD) -b gettext $(I18NSPHINXOPTS) $(BUILDDIR)/locale
+	@echo
+	@echo "Build finished. The message catalogs are in $(BUILDDIR)/locale."
+
+changes:
+	$(SPHINXBUILD) -b changes $(ALLSPHINXOPTS) $(BUILDDIR)/changes
+	@echo
+	@echo "The overview file is in $(BUILDDIR)/changes."
+
+linkcheck:
+	$(SPHINXBUILD) -b linkcheck $(ALLSPHINXOPTS) $(BUILDDIR)/linkcheck
+	@echo
+	@echo "Link check complete; look for any errors in the above output " \
+	      "or in $(BUILDDIR)/linkcheck/output.txt."
+
+doctest:
+	$(SPHINXBUILD) -b doctest $(ALLSPHINXOPTS) $(BUILDDIR)/doctest
+	@echo "Testing of doctests in the sources finished, look at the " \
+	      "results in $(BUILDDIR)/doctest/output.txt."
+
+xml:
+	$(SPHINXBUILD) -b xml $(ALLSPHINXOPTS) $(BUILDDIR)/xml
+	@echo
+	@echo "Build finished. The XML files are in $(BUILDDIR)/xml."
+
+pseudoxml:
+	$(SPHINXBUILD) -b pseudoxml $(ALLSPHINXOPTS) $(BUILDDIR)/pseudoxml
+	@echo
+	@echo "Build finished. The pseudo-XML files are in $(BUILDDIR)/pseudoxml."
diff --git a/docs/index.rst b/docs/index.rst
new file mode 100644
index 000000000..c23b467a1
--- /dev/null
+++ b/docs/index.rst
@@ -0,0 +1,3 @@
+######
+PyLeco
+######
diff --git a/docs/make.bat b/docs/make.bat
new file mode 100644
index 000000000..aefe0b35c
--- /dev/null
+++ b/docs/make.bat
@@ -0,0 +1,242 @@
+@ECHO OFF
+
+REM Command file for Sphinx documentation
+
+if "%SPHINXBUILD%" == "" (
+	set SPHINXBUILD=sphinx-build
+)
+set BUILDDIR=_build
+set ALLSPHINXOPTS=-d %BUILDDIR%/doctrees %SPHINXOPTS% .
+set I18NSPHINXOPTS=%SPHINXOPTS% .
+if NOT "%PAPER%" == "" (
+	set ALLSPHINXOPTS=-D latex_paper_size=%PAPER% %ALLSPHINXOPTS%
+	set I18NSPHINXOPTS=-D latex_paper_size=%PAPER% %I18NSPHINXOPTS%
+)
+
+if "%1" == "" goto help
+
+if "%1" == "help" (
+	:help
+	echo.Please use `make ^<target^>` where ^<target^> is one of
+	echo.  html       to make standalone HTML files
+	echo.  dirhtml    to make HTML files named index.html in directories
+	echo.  singlehtml to make a single large HTML file
+	echo.  pickle     to make pickle files
+	echo.  json       to make JSON files
+	echo.  htmlhelp   to make HTML files and a HTML help project
+	echo.  qthelp     to make HTML files and a qthelp project
+	echo.  devhelp    to make HTML files and a Devhelp project
+	echo.  epub       to make an epub
+	echo.  latex      to make LaTeX files, you can set PAPER=a4 or PAPER=letter
+	echo.  text       to make text files
+	echo.  man        to make manual pages
+	echo.  texinfo    to make Texinfo files
+	echo.  gettext    to make PO message catalogs
+	echo.  changes    to make an overview over all changed/added/deprecated items
+	echo.  xml        to make Docutils-native XML files
+	echo.  pseudoxml  to make pseudoxml-XML files for display purposes
+	echo.  linkcheck  to check all external links for integrity
+	echo.  doctest    to run all doctests embedded in the documentation if enabled
+	goto end
+)
+
+if "%1" == "clean" (
+	for /d %%i in (%BUILDDIR%\*) do rmdir /q /s %%i
+	del /q /s %BUILDDIR%\*
+	goto end
+)
+
+
+%SPHINXBUILD% 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
+)
+
+if "%1" == "html" (
+	%SPHINXBUILD% -b html %ALLSPHINXOPTS% %BUILDDIR%/html
+	if errorlevel 1 exit /b 1
+	echo.
+	echo.Build finished. The HTML pages are in %BUILDDIR%/html.
+	goto end
+)
+
+if "%1" == "dirhtml" (
+	%SPHINXBUILD% -b dirhtml %ALLSPHINXOPTS% %BUILDDIR%/dirhtml
+	if errorlevel 1 exit /b 1
+	echo.
+	echo.Build finished. The HTML pages are in %BUILDDIR%/dirhtml.
+	goto end
+)
+
+if "%1" == "singlehtml" (
+	%SPHINXBUILD% -b singlehtml %ALLSPHINXOPTS% %BUILDDIR%/singlehtml
+	if errorlevel 1 exit /b 1
+	echo.
+	echo.Build finished. The HTML pages are in %BUILDDIR%/singlehtml.
+	goto end
+)
+
+if "%1" == "pickle" (
+	%SPHINXBUILD% -b pickle %ALLSPHINXOPTS% %BUILDDIR%/pickle
+	if errorlevel 1 exit /b 1
+	echo.
+	echo.Build finished; now you can process the pickle files.
+	goto end
+)
+
+if "%1" == "json" (
+	%SPHINXBUILD% -b json %ALLSPHINXOPTS% %BUILDDIR%/json
+	if errorlevel 1 exit /b 1
+	echo.
+	echo.Build finished; now you can process the JSON files.
+	goto end
+)
+
+if "%1" == "htmlhelp" (
+	%SPHINXBUILD% -b htmlhelp %ALLSPHINXOPTS% %BUILDDIR%/htmlhelp
+	if errorlevel 1 exit /b 1
+	echo.
+	echo.Build finished; now you can run HTML Help Workshop with the ^
+.hhp project file in %BUILDDIR%/htmlhelp.
+	goto end
+)
+
+if "%1" == "qthelp" (
+	%SPHINXBUILD% -b qthelp %ALLSPHINXOPTS% %BUILDDIR%/qthelp
+	if errorlevel 1 exit /b 1
+	echo.
+	echo.Build finished; now you can run "qcollectiongenerator" with the ^
+.qhcp project file in %BUILDDIR%/qthelp, like this:
+	echo.^> qcollectiongenerator %BUILDDIR%\qthelp\PyMeasure.qhcp
+	echo.To view the help file:
+	echo.^> assistant -collectionFile %BUILDDIR%\qthelp\PyMeasure.ghc
+	goto end
+)
+
+if "%1" == "devhelp" (
+	%SPHINXBUILD% -b devhelp %ALLSPHINXOPTS% %BUILDDIR%/devhelp
+	if errorlevel 1 exit /b 1
+	echo.
+	echo.Build finished.
+	goto end
+)
+
+if "%1" == "epub" (
+	%SPHINXBUILD% -b epub %ALLSPHINXOPTS% %BUILDDIR%/epub
+	if errorlevel 1 exit /b 1
+	echo.
+	echo.Build finished. The epub file is in %BUILDDIR%/epub.
+	goto end
+)
+
+if "%1" == "latex" (
+	%SPHINXBUILD% -b latex %ALLSPHINXOPTS% %BUILDDIR%/latex
+	if errorlevel 1 exit /b 1
+	echo.
+	echo.Build finished; the LaTeX files are in %BUILDDIR%/latex.
+	goto end
+)
+
+if "%1" == "latexpdf" (
+	%SPHINXBUILD% -b latex %ALLSPHINXOPTS% %BUILDDIR%/latex
+	cd %BUILDDIR%/latex
+	make all-pdf
+	cd %BUILDDIR%/..
+	echo.
+	echo.Build finished; the PDF files are in %BUILDDIR%/latex.
+	goto end
+)
+
+if "%1" == "latexpdfja" (
+	%SPHINXBUILD% -b latex %ALLSPHINXOPTS% %BUILDDIR%/latex
+	cd %BUILDDIR%/latex
+	make all-pdf-ja
+	cd %BUILDDIR%/..
+	echo.
+	echo.Build finished; the PDF files are in %BUILDDIR%/latex.
+	goto end
+)
+
+if "%1" == "text" (
+	%SPHINXBUILD% -b text %ALLSPHINXOPTS% %BUILDDIR%/text
+	if errorlevel 1 exit /b 1
+	echo.
+	echo.Build finished. The text files are in %BUILDDIR%/text.
+	goto end
+)
+
+if "%1" == "man" (
+	%SPHINXBUILD% -b man %ALLSPHINXOPTS% %BUILDDIR%/man
+	if errorlevel 1 exit /b 1
+	echo.
+	echo.Build finished. The manual pages are in %BUILDDIR%/man.
+	goto end
+)
+
+if "%1" == "texinfo" (
+	%SPHINXBUILD% -b texinfo %ALLSPHINXOPTS% %BUILDDIR%/texinfo
+	if errorlevel 1 exit /b 1
+	echo.
+	echo.Build finished. The Texinfo files are in %BUILDDIR%/texinfo.
+	goto end
+)
+
+if "%1" == "gettext" (
+	%SPHINXBUILD% -b gettext %I18NSPHINXOPTS% %BUILDDIR%/locale
+	if errorlevel 1 exit /b 1
+	echo.
+	echo.Build finished. The message catalogs are in %BUILDDIR%/locale.
+	goto end
+)
+
+if "%1" == "changes" (
+	%SPHINXBUILD% -b changes %ALLSPHINXOPTS% %BUILDDIR%/changes
+	if errorlevel 1 exit /b 1
+	echo.
+	echo.The overview file is in %BUILDDIR%/changes.
+	goto end
+)
+
+if "%1" == "linkcheck" (
+	%SPHINXBUILD% -b linkcheck %ALLSPHINXOPTS% %BUILDDIR%/linkcheck
+	if errorlevel 1 exit /b 1
+	echo.
+	echo.Link check complete; look for any errors in the above output ^
+or in %BUILDDIR%/linkcheck/output.txt.
+	goto end
+)
+
+if "%1" == "doctest" (
+	%SPHINXBUILD% -b doctest %ALLSPHINXOPTS% %BUILDDIR%/doctest
+	if errorlevel 1 exit /b 1
+	echo.
+	echo.Testing of doctests in the sources finished, look at the ^
+results in %BUILDDIR%/doctest/output.txt.
+	goto end
+)
+
+if "%1" == "xml" (
+	%SPHINXBUILD% -b xml %ALLSPHINXOPTS% %BUILDDIR%/xml
+	if errorlevel 1 exit /b 1
+	echo.
+	echo.Build finished. The XML files are in %BUILDDIR%/xml.
+	goto end
+)
+
+if "%1" == "pseudoxml" (
+	%SPHINXBUILD% -b pseudoxml %ALLSPHINXOPTS% %BUILDDIR%/pseudoxml
+	if errorlevel 1 exit /b 1
+	echo.
+	echo.Build finished. The pseudo-XML files are in %BUILDDIR%/pseudoxml.
+	goto end
+)
+
+:end
diff --git a/environment.yml b/environment.yml
index 5f5bb44e6..551e9401d 100644
--- a/environment.yml
+++ b/environment.yml
@@ -2,12 +2,16 @@ name: pyleco
 channels:
   - conda-forge
 dependencies:
-  - pyzmq=25.0.0
+  - pyzmq=25.1.0
+  - pip  # don't pin, to gain newest conda compatibility fixes
+  - pip:
+    - jsonrpc2-pyclient==2.2.12
+    - openrpc==6.3.17
+    - uuid7==0.1.0
 # Development dependencies below
   - pytest=7.2.0
+  - pytest-runner=6.0.0
+  - flake8=6.0.0
   - setuptools_scm # don't pin, to get newest features
-  - sphinx=6.1.3
-  - sphinx_rtd_theme=1.0.0
-  # - pip  # don't pin, to gain newest conda compatibility fixes
-  # - pip:
-  #   - xxx
+  # - sphinx=6.1.3
+  # - sphinx_rtd_theme=1.0.0
diff --git a/pyleco/__init__.py b/pyleco/__init__.py
index e69de29bb..1c806830c 100644
--- a/pyleco/__init__.py
+++ b/pyleco/__init__.py
@@ -0,0 +1,51 @@
+#
+# This file is part of the PyLECO package.
+#
+# Copyright (c) 2023-2023 PyLECO Developers
+#
+# Permission is hereby granted, free of charge, to any person obtaining a copy
+# of this software and associated documentation files (the "Software"), to deal
+# in the Software without restriction, including without limitation the rights
+# to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+# copies of the Software, and to permit persons to whom the Software is
+# furnished to do so, subject to the following conditions:
+#
+# The above copyright notice and this permission notice shall be included in
+# all copies or substantial portions of the Software.
+#
+# THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+# IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+# FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+# AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+# LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+# OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
+# THE SOFTWARE.
+#
+
+import warnings
+
+# Maximally flexible approach to obtain version numbers, based on this approach:
+# https://github.com/pypa/setuptools_scm/issues/143#issuecomment-672878863
+# Sadly, this does not work with editable installs, which bake in version info on installation.
+# see also https://github.com/pyusb/pyusb/pull/307#issuecomment-650797688
+try:
+    # If a user has setuptools_scm installed, assume they want the most up to date version string.
+    # Alternatively, we could use a dummy dev module that is never packaged whose presence signals
+    # that we are in an editable install/repo, see https://github.com/pycalphad/pycalphad/pull/341
+    import setuptools_scm
+    __version__ = setuptools_scm.get_version(root='..', relative_to=__file__)
+    del setuptools_scm
+except (ImportError, LookupError):
+    # Setuptools_scm was not found, or it could not find a version, so use installation metadata.
+    from importlib.metadata import version, PackageNotFoundError
+    try:
+        __version__ = version("pyleco")
+        # Alternatively, if the current approach is too slow, we could add
+        # 'write_to = "pyleco/_version.py"' in pyproject.toml and use the generated file here:
+        # from ._version import version as __version__
+    except PackageNotFoundError:
+        warnings.warn('Could not find pyleco version, it does not seem to be installed. '
+                      'Either install it (editable or full) or install setuptools_scm')
+        __version__ = '0.0.0'
+    finally:
+        del version, PackageNotFoundError
diff --git a/pyproject.toml b/pyproject.toml
index 405e9fc1c..0576cb558 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -16,10 +16,10 @@ classifiers = [
 
 requires-python = ">=3.10"
 dependencies = [
-  "pyzmq",
-  "openrpc",
-  "jsonrpc2-pyclient",
-  "uuid7",
+  "pyzmq" >= 22.3.0,
+  "openrpc" >= 6.3.17,
+  "jsonrpc2-pyclient" >= 2.2.12,
+  "uuid7" >= 0.1.0,
 ]
 
 [project.optional-dependencies]
@@ -39,3 +39,9 @@ build-backend = "setuptools.build_meta"
 
 [tool.setuptools_scm]
 # write_to = "pyleco/_version.py"
+
+[tool.black]
+line-length = 100
+
+[tool.isort]
+profile = "black"
diff --git a/setup.cfg b/setup.cfg
new file mode 100644
index 000000000..5a05141a8
--- /dev/null
+++ b/setup.cfg
@@ -0,0 +1,6 @@
+[flake8]
+exclude = .git,__pycache__,docs/conf.py,build,dist
+max-line-length = 100
+max-complexity = 15
+per-file-ignores =
+    __init__.py:F401

From c26b7e4fce41567e432f25c0084ad6142b90aae4 Mon Sep 17 00:00:00 2001
From: Benedikt Moneke <67148916+bmoneke@users.noreply.github.com>
Date: Wed, 12 Jul 2023 15:47:23 +0200
Subject: [PATCH 02/29] Add sphinx dependency and fix pyproject.toml dependency
 declaration.

---
 environment.yml | 5 +++--
 pyproject.toml  | 8 ++++----
 2 files changed, 7 insertions(+), 6 deletions(-)

diff --git a/environment.yml b/environment.yml
index 551e9401d..1e256530c 100644
--- a/environment.yml
+++ b/environment.yml
@@ -13,5 +13,6 @@ dependencies:
   - pytest-runner=6.0.0
   - flake8=6.0.0
   - setuptools_scm # don't pin, to get newest features
-  # - sphinx=6.1.3
-  # - sphinx_rtd_theme=1.0.0
+  - pip:
+    - sphinx==6.1.3
+    - sphinx_rtd_theme==1.2.2
diff --git a/pyproject.toml b/pyproject.toml
index 0576cb558..1c86cbbba 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -16,10 +16,10 @@ classifiers = [
 
 requires-python = ">=3.10"
 dependencies = [
-  "pyzmq" >= 22.3.0,
-  "openrpc" >= 6.3.17,
-  "jsonrpc2-pyclient" >= 2.2.12,
-  "uuid7" >= 0.1.0,
+  "pyzmq >= 22.3.0",
+  "openrpc >= 6.3.17",
+  "jsonrpc2-pyclient >= 2.2.12",
+  "uuid7 >= 0.1.0",
 ]
 
 [project.optional-dependencies]

From a56025a945f80f3d8cbf24d766b24913a224ddb1 Mon Sep 17 00:00:00 2001
From: Benedikt Moneke <67148916+bmoneke@users.noreply.github.com>
Date: Wed, 12 Jul 2023 16:38:13 +0200
Subject: [PATCH 03/29] conf.py added and message made python 3.10 compatible.

---
 docs/conf.py           | 271 +++++++++++++++++++++++++++++++++++++++++
 pyleco/core/message.py |   4 +-
 2 files changed, 273 insertions(+), 2 deletions(-)
 create mode 100644 docs/conf.py

diff --git a/docs/conf.py b/docs/conf.py
new file mode 100644
index 000000000..b1978cc2d
--- /dev/null
+++ b/docs/conf.py
@@ -0,0 +1,271 @@
+#
+# PyLeco documentation build configuration file, created by
+# sphinx-quickstart on Mon Apr  6 13:06:00 2015.
+#
+# This file is execfile()d with the current directory set to its
+# containing dir.
+#
+# Note that not all possible configuration values are present in this
+# autogenerated file.
+#
+# All configuration values have a default; values that are commented out
+# serve to show the default.
+
+import sys
+import os
+
+sys.path.insert(0, os.path.abspath('..'))  # Allow modules to be found
+from pyleco import __version__
+
+# Include Read the Docs formatting
+on_rtd = os.environ.get('READTHEDOCS', None) == 'True'
+
+if not on_rtd:  # only import and set the theme if we're building docs locally
+    import sphinx_rtd_theme
+
+    html_theme = 'sphinx_rtd_theme'
+    html_theme_path = [sphinx_rtd_theme.get_html_theme_path()]
+
+# 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.
+# sys.path.insert(0, os.path.abspath('.'))
+
+# -- General configuration ------------------------------------------------
+
+# If your documentation needs a minimal Sphinx version, state it here.
+# needs_sphinx = '1.0'
+
+# 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.autosummary', 'sphinx.ext.doctest'
+]
+
+# Add any paths that contain templates here, relative to this directory.
+templates_path = ['_templates']
+
+# The suffix of source filenames.
+source_suffix = '.rst'
+
+# The encoding of source files.
+# source_encoding = 'utf-8-sig'
+
+# The master toctree document.
+master_doc = 'index'
+
+# General information about the project.
+project = 'PyLeco'
+copyright = '2013-2023, PyMeasure Developers'
+
+# 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.
+#
+release = __version__
+version = '.'.join(release.split('.')[:3])
+
+# The language for content autogenerated by Sphinx. Refer to documentation
+# for a list of supported languages.
+# language = None
+
+# There are two options for replacing |today|: either, you set today to some
+# non-false value, then it is used:
+# today = ''
+# Else, today_fmt is used as the format for a strftime call.
+# today_fmt = '%B %d, %Y'
+
+# List of patterns, relative to source directory, that match files and
+# directories to ignore when looking for source files.
+exclude_patterns = ['_build']
+
+# The reST default role (used for this markup: `text`) to use for all
+# documents.
+# default_role = None
+
+# If true, '()' will be appended to :func: etc. cross-reference text.
+# add_function_parentheses = True
+
+# If true, the current module name will be prepended to all description
+# unit titles (such as .. function::).
+# add_module_names = True
+
+# If true, sectionauthor and moduleauthor directives will be shown in the
+# output. They are ignored by default.
+# show_authors = False
+
+# The name of the Pygments (syntax highlighting) style to use.
+pygments_style = 'sphinx'
+
+# A list of ignored prefixes for module index sorting.
+# modindex_common_prefix = []
+
+# If true, keep warnings as "system message" paragraphs in the built documents.
+# keep_warnings = False
+
+
+# -- 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 = 'sphinx_rtd_theme'
+
+# 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 = {}
+
+# Add any paths that contain custom themes here, relative to this directory.
+# html_theme_path = []
+
+# The name for this set of Sphinx documents.  If None, it defaults to
+# "<project> v<release> documentation".
+# html_title = None
+
+# A shorter title for the navigation bar.  Default is the same as html_title.
+# html_short_title = None
+
+# The name of an image file (relative to this directory) to place at the top
+# of the sidebar.
+# html_logo = None
+
+# The name of an image file (within the static path) to use as favicon of the
+# docs.  This file should be a Windows icon file (.ico) being 16x16 or 32x32
+# pixels large.
+# html_favicon = None
+
+# Add any paths that contain custom static files (such as style sheets) here,
+# relative to this directory. They are copied after the builtin static files,
+# so a file named "default.css" will overwrite the builtin "default.css".
+# html_static_path = ['_static']
+
+# Add any extra paths that contain custom files (such as robots.txt or
+# .htaccess) here, relative to this directory. These files are copied
+# directly to the root of the documentation.
+# html_extra_path = []
+
+# If not '', a 'Last updated on:' timestamp is inserted at every page bottom,
+# using the given strftime format.
+# html_last_updated_fmt = '%b %d, %Y'
+
+# If true, SmartyPants will be used to convert quotes and dashes to
+# typographically correct entities.
+# html_use_smartypants = True
+
+# Custom sidebar templates, maps document names to template names.
+# html_sidebars = {}
+
+# Additional templates that should be rendered to pages, maps page names to
+# template names.
+# html_additional_pages = {}
+
+# If false, no module index is generated.
+# html_domain_indices = True
+
+# If false, no index is generated.
+# html_use_index = True
+
+# If true, the index is split into individual pages for each letter.
+# html_split_index = False
+
+# If true, links to the reST sources are added to the pages.
+# html_show_sourcelink = True
+
+# If true, "Created using Sphinx" is shown in the HTML footer. Default is True.
+# html_show_sphinx = True
+
+# If true, "(C) Copyright ..." is shown in the HTML footer. Default is True.
+# html_show_copyright = True
+
+# If true, an OpenSearch description file will be output, and all pages will
+# contain a <link> tag referring to it.  The value of this option must be the
+# base URL from which the finished HTML is served.
+# html_use_opensearch = ''
+
+# This is the file name suffix for HTML files (e.g. ".xhtml").
+# html_file_suffix = None
+
+# Output file base name for HTML help builder.
+htmlhelp_basename = 'PyLecodoc'
+
+# -- Options for LaTeX output ---------------------------------------------
+
+latex_elements = {
+    # The paper size ('letterpaper' or 'a4paper').
+    # 'papersize': 'letterpaper',
+
+    # The font size ('10pt', '11pt' or '12pt').
+    # 'pointsize': '10pt',
+
+    # Additional stuff for the LaTeX preamble.
+    # 'preamble': '',
+}
+
+# Grouping the document tree into LaTeX files. List of tuples
+# (source start file, target name, title,
+#  author, documentclass [howto, manual, or own class]).
+latex_documents = [
+    ('index', 'PyMeasure.tex', 'PyLeco Documentation',
+     'PyMeasure Developers', 'manual'),
+]
+
+# The name of an image file (relative to this directory) to place at the top of
+# the title page.
+# latex_logo = None
+
+# For "manual" documents, if this is true, then toplevel headings are parts,
+# not chapters.
+# latex_use_parts = False
+
+# If true, show page references after internal links.
+# latex_show_pagerefs = False
+
+# If true, show URL addresses after external links.
+# latex_show_urls = False
+
+# Documents to append as an appendix to all manuals.
+# latex_appendices = []
+
+# If false, no module index is generated.
+# latex_domain_indices = True
+
+
+# -- Options for manual page output ---------------------------------------
+
+# One entry per manual page. List of tuples
+# (source start file, name, description, authors, manual section).
+man_pages = [
+    ('index', 'pyleco', 'PyLeco Documentation',
+     ['PyMeasure Developers'], 1)
+]
+
+# If true, show URL addresses after external links.
+# man_show_urls = False
+
+
+# -- Options for Texinfo output -------------------------------------------
+
+# Grouping the document tree into Texinfo files. List of tuples
+# (source start file, target name, title, author,
+#  dir menu entry, description, category)
+texinfo_documents = [
+    ('index', 'PyLeco', 'PyLeco Documentation',
+     'PyMeasure Developers', 'PyLeco', 'One line description of project.',
+     'Miscellaneous'),
+]
+
+# Documents to append as an appendix to all manuals.
+# texinfo_appendices = []
+
+# If false, no module index is generated.
+# texinfo_domain_indices = True
+
+# How to display URL addresses: 'footnote', 'no', or 'inline'.
+# texinfo_show_urls = 'footnote'
+
+# If true, do not generate a @detailmenu in the "Top" node's menu.
+# texinfo_no_detailmenu = False
+
+# Automatically mock optional packages
+# autodoc_mock_imports = ['zmq']
diff --git a/pyleco/core/message.py b/pyleco/core/message.py
index 016c68d93..ecda04beb 100644
--- a/pyleco/core/message.py
+++ b/pyleco/core/message.py
@@ -23,7 +23,7 @@
 #
 
 from json import JSONDecodeError
-from typing import Any, Optional, Self
+from typing import Any, Optional
 
 
 from . import VERSION_B
@@ -81,7 +81,7 @@ def __init__(self, receiver: bytes | str, sender: bytes | str = b"",
 
     @classmethod
     def from_frames(cls, version: bytes, receiver: bytes, sender: bytes, header: bytes,
-                    *payload: bytes) -> Self:
+                    *payload: bytes):  # -> typing.Self for py>=3.11
         """Create a message from a frames list, for example after reading from a socket.
 
         .. code::

From 6d3dd0d0a0a14eb9ddde3517f8950d723ada282e Mon Sep 17 00:00:00 2001
From: Benedikt Moneke <67148916+bmoneke@users.noreply.github.com>
Date: Thu, 13 Jul 2023 10:42:10 +0200
Subject: [PATCH 04/29] Switching to mamba.

---
 .github/workflows/pyleco_CI.yml | 35 ++++++++-------------------------
 1 file changed, 8 insertions(+), 27 deletions(-)

diff --git a/.github/workflows/pyleco_CI.yml b/.github/workflows/pyleco_CI.yml
index b7a575caa..5011dc0eb 100644
--- a/.github/workflows/pyleco_CI.yml
+++ b/.github/workflows/pyleco_CI.yml
@@ -16,25 +16,14 @@ jobs:
       - uses: actions/checkout@v3
         with:
           fetch-depth: 0
-      - name: Cache conda
-        uses: actions/cache@v3
-        env:
-          CACHE_NUMBER: 0  # Increase to reset the cache
-        with:
-          path: ~/conda_pkgs_dir
-          key: py3.10-ubuntu-latest-conda-${{ env.CACHE_NUMBER }}-${{ hashFiles('environment.yml') }}
       - name: Install pyleco requirements
-        uses: conda-incubator/setup-miniconda@v2
+        uses: mamba-org/setup-micromamba@v1
         with:
           python-version: "3.10"
           environment-file: environment.yml
-          activate-environment: pyleco
-          auto-update-conda: true
-          use-only-tar-bz2: true  # for caching to work properly
-      - name: Conda info & list
-        run: |
-          conda info
-          conda list
+          cache-environment-key: py3.10-ubuntu-latest-mamba-${{ env.CACHE_NUMBER }}-${{ hashFiles('environment.yml') }}
+          cache-downloads: false
+
       - name: Set up flake8 annotations
         uses: rbialon/flake8-annotations@v1
       - name: Lint with flake8
@@ -69,21 +58,13 @@ jobs:
       - uses: actions/checkout@v3
         with:
           fetch-depth: 0
-      - name: Cache conda
-        uses: actions/cache@v3
-        env:
-          CACHE_NUMBER: 0  # Increase to reset the cache
-        with:
-          path: ~/conda_pkgs_dir
-          key: py${{ matrix.python-version }}-${{ matrix.os }}-conda-${{ env.CACHE_NUMBER }}-${{ hashFiles('environment.yml') }}
       - name: Install pyleco requirements
-        uses: conda-incubator/setup-miniconda@v2
+        uses: mamba-org/setup-micromamba@v1
         with:
-          python-version: ${{ matrix.python-version }}
+          python-version: "3.10"
           environment-file: environment.yml
-          activate-environment: pyleco
-          auto-update-conda: true
-          use-only-tar-bz2: true  # for caching to work properly
+          cache-environment-key: py3.10-ubuntu-latest-mamba-${{ env.CACHE_NUMBER }}-${{ hashFiles('environment.yml') }}
+          cache-downloads: false
       - name: Install Pyleco
         # If the pytest problem matcher stops working because of bad paths, do an editable install
         run: pip install .[dev]

From 6f989ddfc7b92c89eecaa9bc8314f40b0478bbc8 Mon Sep 17 00:00:00 2001
From: Benedikt Moneke <67148916+bmoneke@users.noreply.github.com>
Date: Thu, 13 Jul 2023 10:47:54 +0200
Subject: [PATCH 05/29] Fixing mamba command.

---
 .github/workflows/pyleco_CI.yml | 11 +++++++----
 1 file changed, 7 insertions(+), 4 deletions(-)

diff --git a/.github/workflows/pyleco_CI.yml b/.github/workflows/pyleco_CI.yml
index 5011dc0eb..ca483ac72 100644
--- a/.github/workflows/pyleco_CI.yml
+++ b/.github/workflows/pyleco_CI.yml
@@ -23,7 +23,10 @@ jobs:
           environment-file: environment.yml
           cache-environment-key: py3.10-ubuntu-latest-mamba-${{ env.CACHE_NUMBER }}-${{ hashFiles('environment.yml') }}
           cache-downloads: false
-
+      - name: Mamba info & list
+        run: |
+          mamba info
+          mamba list
       - name: Set up flake8 annotations
         uses: rbialon/flake8-annotations@v1
       - name: Lint with flake8
@@ -70,10 +73,10 @@ jobs:
         run: pip install .[dev]
       - name: Pyleco version
         run: python -c "import pyleco;print(pyleco.__version__)"
-      - name: Conda info & list
+      - name: Mamba info & list
         run: |
-          conda info
-          conda list
+          mamba info
+          mamba list
       - name: Run pytest with xvfb
         if: runner.os == 'Linux'
         run: |

From 80762a93ce2ffbc495b9be8fea9d3d936d52053e Mon Sep 17 00:00:00 2001
From: Benedikt Moneke <67148916+bmoneke@users.noreply.github.com>
Date: Thu, 13 Jul 2023 10:53:54 +0200
Subject: [PATCH 06/29] Adding ruff.

---
 .github/workflows/pyleco_CI.yml | 1 +
 pyproject.toml                  | 5 +++++
 2 files changed, 6 insertions(+)

diff --git a/.github/workflows/pyleco_CI.yml b/.github/workflows/pyleco_CI.yml
index ca483ac72..34a1edf50 100644
--- a/.github/workflows/pyleco_CI.yml
+++ b/.github/workflows/pyleco_CI.yml
@@ -34,6 +34,7 @@ jobs:
           # Be sure to check for Python syntax errors or undefined names
           flake8 . --count --extend-select=E9,F63,F7,F82 --show-source --statistics
       - uses: ammaraskar/sphinx-problem-matcher@master
+      - uses: chartboost/ruff-action@v1
       - name: Generate docs
         if: always()  # run even if the previous step failed
         working-directory: ./docs
diff --git a/pyproject.toml b/pyproject.toml
index 1c86cbbba..bba9c4c69 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -45,3 +45,8 @@ line-length = 100
 
 [tool.isort]
 profile = "black"
+
+[tool.ruff]
+select = ["E", "F", "W"]
+line-length = 100
+per-file-ignores = {"__init__.py": ["F401"]}
\ No newline at end of file

From e6fe0e95867239ea31884b3a8cd3e9913b68923b Mon Sep 17 00:00:00 2001
From: Benedikt Moneke <67148916+bmoneke@users.noreply.github.com>
Date: Thu, 13 Jul 2023 10:57:37 +0200
Subject: [PATCH 07/29] Fixing mamba and ruff configuration.

---
 .github/workflows/pyleco_CI.yml | 8 --------
 pyproject.toml                  | 4 +++-
 2 files changed, 3 insertions(+), 9 deletions(-)

diff --git a/.github/workflows/pyleco_CI.yml b/.github/workflows/pyleco_CI.yml
index 34a1edf50..708fa0c69 100644
--- a/.github/workflows/pyleco_CI.yml
+++ b/.github/workflows/pyleco_CI.yml
@@ -23,10 +23,6 @@ jobs:
           environment-file: environment.yml
           cache-environment-key: py3.10-ubuntu-latest-mamba-${{ env.CACHE_NUMBER }}-${{ hashFiles('environment.yml') }}
           cache-downloads: false
-      - name: Mamba info & list
-        run: |
-          mamba info
-          mamba list
       - name: Set up flake8 annotations
         uses: rbialon/flake8-annotations@v1
       - name: Lint with flake8
@@ -74,10 +70,6 @@ jobs:
         run: pip install .[dev]
       - name: Pyleco version
         run: python -c "import pyleco;print(pyleco.__version__)"
-      - name: Mamba info & list
-        run: |
-          mamba info
-          mamba list
       - name: Run pytest with xvfb
         if: runner.os == 'Linux'
         run: |
diff --git a/pyproject.toml b/pyproject.toml
index bba9c4c69..49a2a68d6 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -49,4 +49,6 @@ profile = "black"
 [tool.ruff]
 select = ["E", "F", "W"]
 line-length = 100
-per-file-ignores = {"__init__.py": ["F401"]}
\ No newline at end of file
+
+[tool.ruff.per-file-ignores]
+"__init__.py" = ["F401"]
\ No newline at end of file

From 141b659a60413f5f3c7952aab3715017322b03e1 Mon Sep 17 00:00:00 2001
From: Benedikt Moneke <67148916+bmoneke@users.noreply.github.com>
Date: Thu, 13 Jul 2023 11:07:59 +0200
Subject: [PATCH 08/29] Remove flake from CI and make ruff similar to previous
 flake configuration.

---
 .github/workflows/pyleco_CI.yml | 11 ++++-------
 environment.yml                 |  1 -
 pyproject.toml                  |  9 +++++++++
 setup.cfg                       |  6 ------
 4 files changed, 13 insertions(+), 14 deletions(-)
 delete mode 100644 setup.cfg

diff --git a/.github/workflows/pyleco_CI.yml b/.github/workflows/pyleco_CI.yml
index 708fa0c69..90051b1e2 100644
--- a/.github/workflows/pyleco_CI.yml
+++ b/.github/workflows/pyleco_CI.yml
@@ -23,14 +23,11 @@ jobs:
           environment-file: environment.yml
           cache-environment-key: py3.10-ubuntu-latest-mamba-${{ env.CACHE_NUMBER }}-${{ hashFiles('environment.yml') }}
           cache-downloads: false
-      - name: Set up flake8 annotations
-        uses: rbialon/flake8-annotations@v1
-      - name: Lint with flake8
-        run: |
-          # Be sure to check for Python syntax errors or undefined names
-          flake8 . --count --extend-select=E9,F63,F7,F82 --show-source --statistics
+      - name: Lint with ruff
+        uses: chartboost/ruff-action@v1
+        with:
+          args: --extend-select=E9,F63,F7,F82 --show-source --statistics
       - uses: ammaraskar/sphinx-problem-matcher@master
-      - uses: chartboost/ruff-action@v1
       - name: Generate docs
         if: always()  # run even if the previous step failed
         working-directory: ./docs
diff --git a/environment.yml b/environment.yml
index 1e256530c..0daa87a2d 100644
--- a/environment.yml
+++ b/environment.yml
@@ -11,7 +11,6 @@ dependencies:
 # Development dependencies below
   - pytest=7.2.0
   - pytest-runner=6.0.0
-  - flake8=6.0.0
   - setuptools_scm # don't pin, to get newest features
   - pip:
     - sphinx==6.1.3
diff --git a/pyproject.toml b/pyproject.toml
index 49a2a68d6..a48a01730 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -49,6 +49,15 @@ profile = "black"
 [tool.ruff]
 select = ["E", "F", "W"]
 line-length = 100
+exclude = [
+    ".git",
+    ".venv",
+    "__pypackages__",
+    "__pycache__",
+    "build",
+    "dist",
+    "docs/conf.py",
+]
 
 [tool.ruff.per-file-ignores]
 "__init__.py" = ["F401"]
\ No newline at end of file
diff --git a/setup.cfg b/setup.cfg
deleted file mode 100644
index 5a05141a8..000000000
--- a/setup.cfg
+++ /dev/null
@@ -1,6 +0,0 @@
-[flake8]
-exclude = .git,__pycache__,docs/conf.py,build,dist
-max-line-length = 100
-max-complexity = 15
-per-file-ignores =
-    __init__.py:F401

From b301f65b9a4bde9f706e444bfee8512fbdc9544a Mon Sep 17 00:00:00 2001
From: Benedikt Moneke <67148916+bmoneke@users.noreply.github.com>
Date: Thu, 13 Jul 2023 11:15:04 +0200
Subject: [PATCH 09/29] Fix ruff (--show-source and --statistics exclude each
 other).

---
 .github/workflows/pyleco_CI.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/pyleco_CI.yml b/.github/workflows/pyleco_CI.yml
index 90051b1e2..74f99d13a 100644
--- a/.github/workflows/pyleco_CI.yml
+++ b/.github/workflows/pyleco_CI.yml
@@ -26,7 +26,7 @@ jobs:
       - name: Lint with ruff
         uses: chartboost/ruff-action@v1
         with:
-          args: --extend-select=E9,F63,F7,F82 --show-source --statistics
+          args: --extend-select=E9,F63,F7,F82 --show-source
       - uses: ammaraskar/sphinx-problem-matcher@master
       - name: Generate docs
         if: always()  # run even if the previous step failed

From 2efd1879967845725cb8bf0065c1d0db19f31ae2 Mon Sep 17 00:00:00 2001
From: Benedikt Moneke <67148916+bmoneke@users.noreply.github.com>
Date: Thu, 13 Jul 2023 11:15:27 +0200
Subject: [PATCH 10/29] Add mypy.

---
 .github/workflows/pyleco_CI.yml | 6 ++++++
 1 file changed, 6 insertions(+)

diff --git a/.github/workflows/pyleco_CI.yml b/.github/workflows/pyleco_CI.yml
index 74f99d13a..3b6efdc3f 100644
--- a/.github/workflows/pyleco_CI.yml
+++ b/.github/workflows/pyleco_CI.yml
@@ -27,6 +27,12 @@ jobs:
         uses: chartboost/ruff-action@v1
         with:
           args: --extend-select=E9,F63,F7,F82 --show-source
+      - name: Install mypy
+        run: pip install mypy
+      - name: Run mypy
+        uses: sasanquaneuf/mypy-github-action@releases/v1
+        with:
+          checkName: 'docs_lint'  # NOTE: this needs to be the same as the job name
       - uses: ammaraskar/sphinx-problem-matcher@master
       - name: Generate docs
         if: always()  # run even if the previous step failed

From a497ccfd175ff77f5f22d3070c85c6af9afd0881 Mon Sep 17 00:00:00 2001
From: Benedikt Moneke <67148916+bmoneke@users.noreply.github.com>
Date: Thu, 13 Jul 2023 11:21:15 +0200
Subject: [PATCH 11/29] Test whether linting and mypy find errors.

---
 pyleco/core/message.py     | 4 ++--
 tests/core/test_message.py | 4 ++--
 2 files changed, 4 insertions(+), 4 deletions(-)

diff --git a/pyleco/core/message.py b/pyleco/core/message.py
index ecda04beb..92aa7e334 100644
--- a/pyleco/core/message.py
+++ b/pyleco/core/message.py
@@ -44,13 +44,13 @@ class Message:
         - 0 or more `payload` frames
 
     If you do not specify a sender, the sending program shall add it itself.
-    The :attr:`data` attribute is the content of the first :attr:`payload` frame. It can be set with
+    The :attr:`data` attribute is the content of the first :attr:`payload` frame. It can be set with asfd asd
     the corresponding argument.
     All attributes, except the official frames, are for convenience.
     """
 
     version: bytes = VERSION_B
-    receiver: bytes
+    receiver: str
     sender: bytes
     header: bytes
     payload: list[bytes]
diff --git a/tests/core/test_message.py b/tests/core/test_message.py
index 6b276b7c4..6f159f7d9 100644
--- a/tests/core/test_message.py
+++ b/tests/core/test_message.py
@@ -28,7 +28,7 @@
 
 from pyleco.core.message import Message
 
-
+#                                                 asdf                                   asdf               asfd
 cid = b"conversation_id;"
 
 
@@ -85,7 +85,7 @@ def test_message_data_str_to_binary_data(self):
 
 
 class Test_Message_from_frames:
-    def test_message_from_frames(self, message: Message):
+    def test_message_from_frames(self, message: str):
         message.version = b"diff"  # also if the version is different
         assert Message.from_frames(*message.to_frames()) == message
 

From 18e1d4b4b4dff622fffe914ca4e6b7adac960737 Mon Sep 17 00:00:00 2001
From: Benedikt Moneke <67148916+bmoneke@users.noreply.github.com>
Date: Thu, 13 Jul 2023 11:25:10 +0200
Subject: [PATCH 12/29] Moving mypy to its own job.

---
 .github/workflows/pyleco_CI.yml | 29 +++++++++++++++++++++++------
 1 file changed, 23 insertions(+), 6 deletions(-)

diff --git a/.github/workflows/pyleco_CI.yml b/.github/workflows/pyleco_CI.yml
index 3b6efdc3f..d78660835 100644
--- a/.github/workflows/pyleco_CI.yml
+++ b/.github/workflows/pyleco_CI.yml
@@ -27,12 +27,6 @@ jobs:
         uses: chartboost/ruff-action@v1
         with:
           args: --extend-select=E9,F63,F7,F82 --show-source
-      - name: Install mypy
-        run: pip install mypy
-      - name: Run mypy
-        uses: sasanquaneuf/mypy-github-action@releases/v1
-        with:
-          checkName: 'docs_lint'  # NOTE: this needs to be the same as the job name
       - uses: ammaraskar/sphinx-problem-matcher@master
       - name: Generate docs
         if: always()  # run even if the previous step failed
@@ -46,6 +40,29 @@ jobs:
         run: |
           echo "::add-matcher::.github/sphinx.json"
           make doctest SPHINXOPTS="-W --keep-going"
+  type_checking:
+    name: Static Type Checking
+    runs-on: "ubuntu-latest"
+    defaults:
+      run:
+        shell: bash -l {0}
+    steps:
+      - uses: actions/checkout@v3
+        with:
+          fetch-depth: 0
+      - name: Install pyleco requirements
+        uses: mamba-org/setup-micromamba@v1
+        with:
+          python-version: "3.10"
+          environment-file: environment.yml
+          cache-environment-key: py3.10-ubuntu-latest-mamba-${{ env.CACHE_NUMBER }}-${{ hashFiles('environment.yml') }}
+          cache-downloads: false
+      - name: Install mypy
+        run: pip install mypy
+      - name: Run mypy
+        uses: sasanquaneuf/mypy-github-action@releases/v1
+        with:
+          checkName: 'type_checking'  # NOTE: this needs to be the same as the job name
   test:
     name: Python ${{ matrix.python-version }}, ${{ matrix.os }}
     runs-on: ${{ matrix.os }}

From 8b021760ce2724a251fd7b0121f5aa8a0b9f5a11 Mon Sep 17 00:00:00 2001
From: Benedikt Moneke <67148916+bmoneke@users.noreply.github.com>
Date: Thu, 13 Jul 2023 12:03:10 +0200
Subject: [PATCH 13/29] Improve mypy testing.

---
 .github/workflows/pyleco_CI.yml | 4 +---
 1 file changed, 1 insertion(+), 3 deletions(-)

diff --git a/.github/workflows/pyleco_CI.yml b/.github/workflows/pyleco_CI.yml
index d78660835..b032b01fa 100644
--- a/.github/workflows/pyleco_CI.yml
+++ b/.github/workflows/pyleco_CI.yml
@@ -60,9 +60,7 @@ jobs:
       - name: Install mypy
         run: pip install mypy
       - name: Run mypy
-        uses: sasanquaneuf/mypy-github-action@releases/v1
-        with:
-          checkName: 'type_checking'  # NOTE: this needs to be the same as the job name
+        run: mypy .
   test:
     name: Python ${{ matrix.python-version }}, ${{ matrix.os }}
     runs-on: ${{ matrix.os }}

From 75c9d10adc11356f112a00e1fff2eb5b8f68ce82 Mon Sep 17 00:00:00 2001
From: Benedikt Moneke <67148916+bmoneke@users.noreply.github.com>
Date: Thu, 13 Jul 2023 12:04:17 +0200
Subject: [PATCH 14/29] Revert introduced errors in message and test_message
 and fix more mypy issues.

---
 docs/conf.py                 | 1 +
 pyleco/__init__.py           | 2 +-
 pyleco/core/message.py       | 4 ++--
 pyleco/core/rpc_generator.py | 4 ++--
 pyleco/core/serialization.py | 2 +-
 tests/core/test_message.py   | 4 ++--
 6 files changed, 9 insertions(+), 8 deletions(-)

diff --git a/docs/conf.py b/docs/conf.py
index b1978cc2d..840235b32 100644
--- a/docs/conf.py
+++ b/docs/conf.py
@@ -1,3 +1,4 @@
+# mypy: ignore-errors
 #
 # PyLeco documentation build configuration file, created by
 # sphinx-quickstart on Mon Apr  6 13:06:00 2015.
diff --git a/pyleco/__init__.py b/pyleco/__init__.py
index 1c806830c..e0ff630b8 100644
--- a/pyleco/__init__.py
+++ b/pyleco/__init__.py
@@ -32,7 +32,7 @@
     # If a user has setuptools_scm installed, assume they want the most up to date version string.
     # Alternatively, we could use a dummy dev module that is never packaged whose presence signals
     # that we are in an editable install/repo, see https://github.com/pycalphad/pycalphad/pull/341
-    import setuptools_scm
+    import setuptools_scm  # type: ignore
     __version__ = setuptools_scm.get_version(root='..', relative_to=__file__)
     del setuptools_scm
 except (ImportError, LookupError):
diff --git a/pyleco/core/message.py b/pyleco/core/message.py
index 92aa7e334..ecda04beb 100644
--- a/pyleco/core/message.py
+++ b/pyleco/core/message.py
@@ -44,13 +44,13 @@ class Message:
         - 0 or more `payload` frames
 
     If you do not specify a sender, the sending program shall add it itself.
-    The :attr:`data` attribute is the content of the first :attr:`payload` frame. It can be set with asfd asd
+    The :attr:`data` attribute is the content of the first :attr:`payload` frame. It can be set with
     the corresponding argument.
     All attributes, except the official frames, are for convenience.
     """
 
     version: bytes = VERSION_B
-    receiver: str
+    receiver: bytes
     sender: bytes
     header: bytes
     payload: list[bytes]
diff --git a/pyleco/core/rpc_generator.py b/pyleco/core/rpc_generator.py
index d18320ef0..98408fba3 100644
--- a/pyleco/core/rpc_generator.py
+++ b/pyleco/core/rpc_generator.py
@@ -24,7 +24,7 @@
 
 from typing import Any
 
-from jsonrpc2pyclient._irpcclient import IRPCClient
+from jsonrpc2pyclient._irpcclient import IRPCClient  # type: ignore
 
 
 class RPCGenerator(IRPCClient):
@@ -45,4 +45,4 @@ def get_result_from_response(self, data: bytes | str) -> Any:
 
     def clear_id_list(self) -> None:
         """Reset the list of created ids."""
-        self._ids = {}
+        self._ids: dict[int, int] = {}
diff --git a/pyleco/core/serialization.py b/pyleco/core/serialization.py
index f02bd9dc4..075afa2a1 100644
--- a/pyleco/core/serialization.py
+++ b/pyleco/core/serialization.py
@@ -25,7 +25,7 @@
 import json
 from typing import Optional, NamedTuple
 
-from uuid_extensions import uuid7  # as long as uuid does not yet support UUIDv7
+from uuid_extensions import uuid7  # type: ignore  #  as long as uuid does not yet support UUIDv7
 from jsonrpcobjects.objects import (RequestObject, RequestObjectParams,
                                     ResultResponseObject,
                                     ErrorResponseObject,
diff --git a/tests/core/test_message.py b/tests/core/test_message.py
index 6f159f7d9..6b276b7c4 100644
--- a/tests/core/test_message.py
+++ b/tests/core/test_message.py
@@ -28,7 +28,7 @@
 
 from pyleco.core.message import Message
 
-#                                                 asdf                                   asdf               asfd
+
 cid = b"conversation_id;"
 
 
@@ -85,7 +85,7 @@ def test_message_data_str_to_binary_data(self):
 
 
 class Test_Message_from_frames:
-    def test_message_from_frames(self, message: str):
+    def test_message_from_frames(self, message: Message):
         message.version = b"diff"  # also if the version is different
         assert Message.from_frames(*message.to_frames()) == message
 

From e5ebaa7ffc5f6eee50c761d1e35d50106c7b7336 Mon Sep 17 00:00:00 2001
From: Benedikt Moneke <67148916+bmoneke@users.noreply.github.com>
Date: Thu, 13 Jul 2023 12:22:08 +0200
Subject: [PATCH 15/29] Coverage added.

---
 .github/workflows/pyleco_CI.yml | 17 +++++++++++++++++
 environment.yml                 |  1 +
 pyproject.toml                  |  5 ++++-
 3 files changed, 22 insertions(+), 1 deletion(-)

diff --git a/.github/workflows/pyleco_CI.yml b/.github/workflows/pyleco_CI.yml
index b032b01fa..7fa03df6d 100644
--- a/.github/workflows/pyleco_CI.yml
+++ b/.github/workflows/pyleco_CI.yml
@@ -61,6 +61,23 @@ jobs:
         run: pip install mypy
       - name: Run mypy
         run: mypy .
+      - name: Coverage
+        run: pytest --junitxml=pytest.xml --cov-report=term-missing:skip-covered --cov=pyleco | tee pytest-coverage.txt
+      - name: Pytest coverage comment
+        uses: MishaKav/pytest-coverage-comment@main
+        with:
+          pytest-coverage-path: ./pytest-coverage.txt
+          title: Coverage Report
+          badge-title: PyLECO Coverage
+          hide-badge: false
+          hide-report: false
+          create-new-comment: false
+          hide-comment: false
+          report-only-changed-files: false
+          remove-link-from-badge: false
+          unique-id-for-comment: python3.8
+          junitxml-path: ./pytest.xml
+          junitxml-title: Coverage Summary
   test:
     name: Python ${{ matrix.python-version }}, ${{ matrix.os }}
     runs-on: ${{ matrix.os }}
diff --git a/environment.yml b/environment.yml
index 0daa87a2d..775e8dd6f 100644
--- a/environment.yml
+++ b/environment.yml
@@ -10,6 +10,7 @@ dependencies:
     - uuid7==0.1.0
 # Development dependencies below
   - pytest=7.2.0
+  - pytest-cov=4.1.0
   - pytest-runner=6.0.0
   - setuptools_scm # don't pin, to get newest features
   - pip:
diff --git a/pyproject.toml b/pyproject.toml
index a48a01730..5f3452034 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -25,6 +25,7 @@ dependencies = [
 [project.optional-dependencies]
 dev = [
   'pytest',
+  'pytest-cov',
   'sphinx',
   'sphinx_rtd_theme',
 ]
@@ -60,4 +61,6 @@ exclude = [
 ]
 
 [tool.ruff.per-file-ignores]
-"__init__.py" = ["F401"]
\ No newline at end of file
+"__init__.py" = ["F401"]
+
+[mypy]

From 86b116abc6db3be881c1d370518d9414d6bd83a8 Mon Sep 17 00:00:00 2001
From: Benedikt Moneke <67148916+bmoneke@users.noreply.github.com>
Date: Thu, 13 Jul 2023 12:45:38 +0200
Subject: [PATCH 16/29] Fix coverage report.

---
 .github/workflows/pyleco_CI.yml | 7 +++++--
 1 file changed, 5 insertions(+), 2 deletions(-)

diff --git a/.github/workflows/pyleco_CI.yml b/.github/workflows/pyleco_CI.yml
index 7fa03df6d..61afaba45 100644
--- a/.github/workflows/pyleco_CI.yml
+++ b/.github/workflows/pyleco_CI.yml
@@ -61,9 +61,12 @@ jobs:
         run: pip install mypy
       - name: Run mypy
         run: mypy .
-      - name: Coverage
+      - name: Install Pyleco
+        # If the pytest problem matcher stops working because of bad paths, do an editable install
+        run: pip install .[dev]
+      - name: Test for Coverage
         run: pytest --junitxml=pytest.xml --cov-report=term-missing:skip-covered --cov=pyleco | tee pytest-coverage.txt
-      - name: Pytest coverage comment
+      - name: Pytest Coverage Comment
         uses: MishaKav/pytest-coverage-comment@main
         with:
           pytest-coverage-path: ./pytest-coverage.txt

From 159e4f1e2ff61c09d21062efbc057faf6423f54e Mon Sep 17 00:00:00 2001
From: Benedikt Moneke <67148916+bmoneke@users.noreply.github.com>
Date: Thu, 13 Jul 2023 12:58:27 +0200
Subject: [PATCH 17/29] Add __init__.py for coverage.

---
 tests/__init__.py      | 0
 tests/core/__init__.py | 0
 2 files changed, 0 insertions(+), 0 deletions(-)
 create mode 100644 tests/__init__.py
 create mode 100644 tests/core/__init__.py

diff --git a/tests/__init__.py b/tests/__init__.py
new file mode 100644
index 000000000..e69de29bb
diff --git a/tests/core/__init__.py b/tests/core/__init__.py
new file mode 100644
index 000000000..e69de29bb

From 3d18efe332f20c27f9e5e492ac75edfe587153b2 Mon Sep 17 00:00:00 2001
From: Benedikt Moneke <67148916+bmoneke@users.noreply.github.com>
Date: Thu, 13 Jul 2023 13:15:59 +0200
Subject: [PATCH 18/29] Exclude LECO definitions from coverage reports.

---
 .github/workflows/pyleco_CI.yml | 6 +++---
 pyproject.toml                  | 8 ++++++++
 2 files changed, 11 insertions(+), 3 deletions(-)

diff --git a/.github/workflows/pyleco_CI.yml b/.github/workflows/pyleco_CI.yml
index 61afaba45..37aa54998 100644
--- a/.github/workflows/pyleco_CI.yml
+++ b/.github/workflows/pyleco_CI.yml
@@ -41,7 +41,7 @@ jobs:
           echo "::add-matcher::.github/sphinx.json"
           make doctest SPHINXOPTS="-W --keep-going"
   type_checking:
-    name: Static Type Checking
+    name: Static Type Checking and Code Coverage
     runs-on: "ubuntu-latest"
     defaults:
       run:
@@ -53,9 +53,9 @@ jobs:
       - name: Install pyleco requirements
         uses: mamba-org/setup-micromamba@v1
         with:
-          python-version: "3.10"
+          python-version: "3.11"
           environment-file: environment.yml
-          cache-environment-key: py3.10-ubuntu-latest-mamba-${{ env.CACHE_NUMBER }}-${{ hashFiles('environment.yml') }}
+          cache-environment-key: py3.11-ubuntu-latest-mamba-${{ env.CACHE_NUMBER }}-${{ hashFiles('environment.yml') }}
           cache-downloads: false
       - name: Install mypy
         run: pip install mypy
diff --git a/pyproject.toml b/pyproject.toml
index 5f3452034..a5bc9ec2a 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -64,3 +64,11 @@ exclude = [
 "__init__.py" = ["F401"]
 
 [mypy]
+
+[tool.coverage.run]
+branch = true
+omit = [
+    # Omit LECO definitions
+    "pyleco/errors.py",
+    "pyleco/core/leco_protocols.py",
+]

From 77e1c20b9d627604ffba199dad324c11487ae280 Mon Sep 17 00:00:00 2001
From: Benedikt Moneke <67148916+bmoneke@users.noreply.github.com>
Date: Thu, 13 Jul 2023 13:24:38 +0200
Subject: [PATCH 19/29] Move (slow) code coverage to its own job.

---
 .github/workflows/pyleco_CI.yml | 19 ++++++++++++++++++-
 1 file changed, 18 insertions(+), 1 deletion(-)

diff --git a/.github/workflows/pyleco_CI.yml b/.github/workflows/pyleco_CI.yml
index 37aa54998..a458b7660 100644
--- a/.github/workflows/pyleco_CI.yml
+++ b/.github/workflows/pyleco_CI.yml
@@ -41,7 +41,7 @@ jobs:
           echo "::add-matcher::.github/sphinx.json"
           make doctest SPHINXOPTS="-W --keep-going"
   type_checking:
-    name: Static Type Checking and Code Coverage
+    name: Static Type Checking
     runs-on: "ubuntu-latest"
     defaults:
       run:
@@ -61,6 +61,23 @@ jobs:
         run: pip install mypy
       - name: Run mypy
         run: mypy .
+  test_coverage:
+    name: Code Coverage
+    runs-on: "ubuntu-latest"
+    defaults:
+      run:
+        shell: bash -l {0}
+    steps:
+      - uses: actions/checkout@v3
+        with:
+          fetch-depth: 0
+      - name: Install pyleco requirements
+        uses: mamba-org/setup-micromamba@v1
+        with:
+          python-version: "3.11"
+          environment-file: environment.yml
+          cache-environment-key: py3.11-ubuntu-latest-mamba-${{ env.CACHE_NUMBER }}-${{ hashFiles('environment.yml') }}
+          cache-downloads: false
       - name: Install Pyleco
         # If the pytest problem matcher stops working because of bad paths, do an editable install
         run: pip install .[dev]

From 36a8af96a7a37748c38c474c1338656a7d9a12be Mon Sep 17 00:00:00 2001
From: Benedikt Moneke <67148916+bmoneke@users.noreply.github.com>
Date: Fri, 14 Jul 2023 09:18:24 +0200
Subject: [PATCH 20/29] Improve coverage (and introduce a type error for mypy).

---
 .github/workflows/pyleco_CI.yml | 2 +-
 pyleco/core/message.py          | 2 +-
 tests/__init__.py               | 0
 tests/core/__init__.py          | 0
 4 files changed, 2 insertions(+), 2 deletions(-)
 delete mode 100644 tests/__init__.py
 delete mode 100644 tests/core/__init__.py

diff --git a/.github/workflows/pyleco_CI.yml b/.github/workflows/pyleco_CI.yml
index a458b7660..68636160d 100644
--- a/.github/workflows/pyleco_CI.yml
+++ b/.github/workflows/pyleco_CI.yml
@@ -80,7 +80,7 @@ jobs:
           cache-downloads: false
       - name: Install Pyleco
         # If the pytest problem matcher stops working because of bad paths, do an editable install
-        run: pip install .[dev]
+        run: pip install -e .[dev]  # editable for covtest
       - name: Test for Coverage
         run: pytest --junitxml=pytest.xml --cov-report=term-missing:skip-covered --cov=pyleco | tee pytest-coverage.txt
       - name: Pytest Coverage Comment
diff --git a/pyleco/core/message.py b/pyleco/core/message.py
index ecda04beb..04a7212ed 100644
--- a/pyleco/core/message.py
+++ b/pyleco/core/message.py
@@ -51,7 +51,7 @@ class Message:
 
     version: bytes = VERSION_B
     receiver: bytes
-    sender: bytes
+    sender: str
     header: bytes
     payload: list[bytes]
 
diff --git a/tests/__init__.py b/tests/__init__.py
deleted file mode 100644
index e69de29bb..000000000
diff --git a/tests/core/__init__.py b/tests/core/__init__.py
deleted file mode 100644
index e69de29bb..000000000

From f31d2aabc847af4f3458c96742eef6e41f182149 Mon Sep 17 00:00:00 2001
From: Benedikt Moneke <67148916+bmoneke@users.noreply.github.com>
Date: Fri, 14 Jul 2023 09:23:43 +0200
Subject: [PATCH 21/29] Revert introduced error to message and adding no cover
 to global init.

---
 pyleco/__init__.py     | 2 +-
 pyleco/core/message.py | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/pyleco/__init__.py b/pyleco/__init__.py
index e0ff630b8..a5c01b1f8 100644
--- a/pyleco/__init__.py
+++ b/pyleco/__init__.py
@@ -35,7 +35,7 @@
     import setuptools_scm  # type: ignore
     __version__ = setuptools_scm.get_version(root='..', relative_to=__file__)
     del setuptools_scm
-except (ImportError, LookupError):
+except (ImportError, LookupError):  # pragma: no cover
     # Setuptools_scm was not found, or it could not find a version, so use installation metadata.
     from importlib.metadata import version, PackageNotFoundError
     try:
diff --git a/pyleco/core/message.py b/pyleco/core/message.py
index 04a7212ed..ecda04beb 100644
--- a/pyleco/core/message.py
+++ b/pyleco/core/message.py
@@ -51,7 +51,7 @@ class Message:
 
     version: bytes = VERSION_B
     receiver: bytes
-    sender: str
+    sender: bytes
     header: bytes
     payload: list[bytes]
 

From 6671f07d6fa79241d509934c7cdf33dcfbe1fa4b Mon Sep 17 00:00:00 2001
From: Benedikt Moneke <67148916+bmoneke@users.noreply.github.com>
Date: Fri, 14 Jul 2023 09:47:41 +0200
Subject: [PATCH 22/29] Fix python versions for tests.

---
 .github/workflows/pyleco_CI.yml | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/.github/workflows/pyleco_CI.yml b/.github/workflows/pyleco_CI.yml
index 68636160d..59206daac 100644
--- a/.github/workflows/pyleco_CI.yml
+++ b/.github/workflows/pyleco_CI.yml
@@ -116,9 +116,9 @@ jobs:
       - name: Install pyleco requirements
         uses: mamba-org/setup-micromamba@v1
         with:
-          python-version: "3.10"
+          python-version: ${{ matrix.python-version }}
           environment-file: environment.yml
-          cache-environment-key: py3.10-ubuntu-latest-mamba-${{ env.CACHE_NUMBER }}-${{ hashFiles('environment.yml') }}
+          cache-environment-key: py${{ matrix.python-version }}-${{ matrix.os }}-mamba-${{ env.CACHE_NUMBER }}-${{ hashFiles('environment.yml') }}
           cache-downloads: false
       - name: Install Pyleco
         # If the pytest problem matcher stops working because of bad paths, do an editable install

From 49672775c4b1f5d07a7703d630093e3936817596 Mon Sep 17 00:00:00 2001
From: Benedikt Moneke <67148916+bmoneke@users.noreply.github.com>
Date: Fri, 14 Jul 2023 18:46:03 +0200
Subject: [PATCH 23/29] Update pyleco_CI.yml

---
 .github/workflows/pyleco_CI.yml | 20 ++++++++++++++------
 1 file changed, 14 insertions(+), 6 deletions(-)

diff --git a/.github/workflows/pyleco_CI.yml b/.github/workflows/pyleco_CI.yml
index 59206daac..941f4c82a 100644
--- a/.github/workflows/pyleco_CI.yml
+++ b/.github/workflows/pyleco_CI.yml
@@ -19,10 +19,13 @@ jobs:
       - name: Install pyleco requirements
         uses: mamba-org/setup-micromamba@v1
         with:
-          python-version: "3.10"
           environment-file: environment.yml
-          cache-environment-key: py3.10-ubuntu-latest-mamba-${{ env.CACHE_NUMBER }}-${{ hashFiles('environment.yml') }}
+          cache-environment-key: pylatest-ubuntu-latest-mamba-${{ env.CACHE_NUMBER }}-${{ hashFiles('environment.yml') }}
           cache-downloads: false
+      - name: Python and Mamba version
+        run: |
+          python --version
+          micromamba info
       - name: Lint with ruff
         uses: chartboost/ruff-action@v1
         with:
@@ -53,10 +56,11 @@ jobs:
       - name: Install pyleco requirements
         uses: mamba-org/setup-micromamba@v1
         with:
-          python-version: "3.11"
           environment-file: environment.yml
-          cache-environment-key: py3.11-ubuntu-latest-mamba-${{ env.CACHE_NUMBER }}-${{ hashFiles('environment.yml') }}
+          cache-environment-key: pylatest-ubuntu-latest-mamba-${{ env.CACHE_NUMBER }}-${{ hashFiles('environment.yml') }}
           cache-downloads: false
+      - name: Python version
+        run: python --version
       - name: Install mypy
         run: pip install mypy
       - name: Run mypy
@@ -74,10 +78,11 @@ jobs:
       - name: Install pyleco requirements
         uses: mamba-org/setup-micromamba@v1
         with:
-          python-version: "3.11"
           environment-file: environment.yml
-          cache-environment-key: py3.11-ubuntu-latest-mamba-${{ env.CACHE_NUMBER }}-${{ hashFiles('environment.yml') }}
+          cache-environment-key: pylatest-ubuntu-latest-mamba-${{ env.CACHE_NUMBER }}-${{ hashFiles('environment.yml') }}
           cache-downloads: false
+      - name: Python version
+        run: python --version
       - name: Install Pyleco
         # If the pytest problem matcher stops working because of bad paths, do an editable install
         run: pip install -e .[dev]  # editable for covtest
@@ -118,8 +123,11 @@ jobs:
         with:
           python-version: ${{ matrix.python-version }}
           environment-file: environment.yml
+          create-args: python=${{ matrix.python-version }}
           cache-environment-key: py${{ matrix.python-version }}-${{ matrix.os }}-mamba-${{ env.CACHE_NUMBER }}-${{ hashFiles('environment.yml') }}
           cache-downloads: false
+      - name: Python version
+        run: python --version
       - name: Install Pyleco
         # If the pytest problem matcher stops working because of bad paths, do an editable install
         run: pip install .[dev]

From 54c529cdbe6c7104faaaab47759f786f16f91bcb Mon Sep 17 00:00:00 2001
From: Benedikt Moneke <67148916+bmoneke@users.noreply.github.com>
Date: Wed, 19 Jul 2023 15:58:43 +0200
Subject: [PATCH 24/29] Remove superfluos entry in CI file.

---
 .github/workflows/pyleco_CI.yml | 1 -
 1 file changed, 1 deletion(-)

diff --git a/.github/workflows/pyleco_CI.yml b/.github/workflows/pyleco_CI.yml
index 941f4c82a..3e8ed1b39 100644
--- a/.github/workflows/pyleco_CI.yml
+++ b/.github/workflows/pyleco_CI.yml
@@ -121,7 +121,6 @@ jobs:
       - name: Install pyleco requirements
         uses: mamba-org/setup-micromamba@v1
         with:
-          python-version: ${{ matrix.python-version }}
           environment-file: environment.yml
           create-args: python=${{ matrix.python-version }}
           cache-environment-key: py${{ matrix.python-version }}-${{ matrix.os }}-mamba-${{ env.CACHE_NUMBER }}-${{ hashFiles('environment.yml') }}

From 50f3a68ab72c8b6244dae9f822ae051a895fc39a Mon Sep 17 00:00:00 2001
From: Benedikt Moneke <67148916+bmoneke@users.noreply.github.com>
Date: Thu, 20 Jul 2023 10:16:02 +0200
Subject: [PATCH 25/29] Move Coordinator error codes to range with less
 conflicts.

---
 pyleco/errors.py | 11 ++++++-----
 1 file changed, 6 insertions(+), 5 deletions(-)

diff --git a/pyleco/errors.py b/pyleco/errors.py
index 196d962f8..1cbf2310b 100644
--- a/pyleco/errors.py
+++ b/pyleco/errors.py
@@ -30,11 +30,12 @@
 # -32000 to -32099  Server error    reserved for implementation-defined server-errors
 
 # TODO define valid error codes: Proposal:
-# Routing errors (Coordinator) between -32000 and -32009
-NOT_SIGNED_IN = ErrorObject(code=-32000, message="You did not sign in!")
-DUPLICATE_NAME = ErrorObject(code=-32001, message="The name is already taken.")
-NODE_UNKNOWN = ErrorObject(code=-32002, message="Node is not known.")
-RECEIVER_UNKNOWN = ErrorObject(code=-32003, message="Receiver is not in addresses list.")
+# general error: -32000
+# Routing errors (Coordinator) between -32090 and -32099
+NOT_SIGNED_IN = ErrorObject(code=-32090, message="You did not sign in!")
+DUPLICATE_NAME = ErrorObject(code=-32091, message="The name is already taken.")
+NODE_UNKNOWN = ErrorObject(code=-32092, message="Node is not known.")
+RECEIVER_UNKNOWN = ErrorObject(code=-32093, message="Receiver is not in addresses list.")
 
 
 def generate_error_with_data(error: ErrorObject, data: Any) -> ErrorObjectData:

From 64a6a00f778a7851989ffc91eba8a9fcf54062dc Mon Sep 17 00:00:00 2001
From: Benedikt Moneke <67148916+bmoneke@users.noreply.github.com>
Date: Sun, 23 Jul 2023 08:20:00 +0200
Subject: [PATCH 26/29] Change to pyleco developers.

Co-authored-by: Christoph Buchner <bilderbuchi@users.noreply.github.com>
---
 docs/conf.py | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/docs/conf.py b/docs/conf.py
index 840235b32..f196b6e1b 100644
--- a/docs/conf.py
+++ b/docs/conf.py
@@ -58,7 +58,7 @@
 
 # General information about the project.
 project = 'PyLeco'
-copyright = '2013-2023, PyMeasure Developers'
+copyright = '2023, pyLECO Developers'
 
 # The version info for the project you're documenting, acts as replacement for
 # |version| and |release|, also used in various other places throughout the
@@ -238,7 +238,7 @@
 # (source start file, name, description, authors, manual section).
 man_pages = [
     ('index', 'pyleco', 'PyLeco Documentation',
-     ['PyMeasure Developers'], 1)
+     ['PyLECO Developers'], 1)
 ]
 
 # If true, show URL addresses after external links.
@@ -252,7 +252,7 @@
 #  dir menu entry, description, category)
 texinfo_documents = [
     ('index', 'PyLeco', 'PyLeco Documentation',
-     'PyMeasure Developers', 'PyLeco', 'One line description of project.',
+     'PyLECO Developers', 'PyLeco', 'Python implementation of the Laboratory Experiment COntrol (LECO) protocol.',
      'Miscellaneous'),
 ]
 

From 78799a856a5331575249b53cd97b5501aea07645 Mon Sep 17 00:00:00 2001
From: Benedikt Moneke <67148916+bmoneke@users.noreply.github.com>
Date: Sun, 23 Jul 2023 19:15:29 +0200
Subject: [PATCH 27/29] rename to PyLECO

---
 docs/conf.py   | 18 +++++++++---------
 docs/index.rst |  2 +-
 2 files changed, 10 insertions(+), 10 deletions(-)

diff --git a/docs/conf.py b/docs/conf.py
index f196b6e1b..eb5a78bd1 100644
--- a/docs/conf.py
+++ b/docs/conf.py
@@ -1,6 +1,6 @@
 # mypy: ignore-errors
 #
-# PyLeco documentation build configuration file, created by
+# PyLECO documentation build configuration file, created by
 # sphinx-quickstart on Mon Apr  6 13:06:00 2015.
 #
 # This file is execfile()d with the current directory set to its
@@ -57,8 +57,8 @@
 master_doc = 'index'
 
 # General information about the project.
-project = 'PyLeco'
-copyright = '2023, pyLECO Developers'
+project = 'PyLECO'
+copyright = '2023, PyLECO Developers'
 
 # The version info for the project you're documenting, acts as replacement for
 # |version| and |release|, also used in various other places throughout the
@@ -188,7 +188,7 @@
 # html_file_suffix = None
 
 # Output file base name for HTML help builder.
-htmlhelp_basename = 'PyLecodoc'
+htmlhelp_basename = 'PyLECOdoc'
 
 # -- Options for LaTeX output ---------------------------------------------
 
@@ -207,8 +207,8 @@
 # (source start file, target name, title,
 #  author, documentclass [howto, manual, or own class]).
 latex_documents = [
-    ('index', 'PyMeasure.tex', 'PyLeco Documentation',
-     'PyMeasure Developers', 'manual'),
+    ('index', 'PyLECO.tex', 'PyLECO Documentation',
+     'PyLECO Developers', 'manual'),
 ]
 
 # The name of an image file (relative to this directory) to place at the top of
@@ -237,7 +237,7 @@
 # One entry per manual page. List of tuples
 # (source start file, name, description, authors, manual section).
 man_pages = [
-    ('index', 'pyleco', 'PyLeco Documentation',
+    ('index', 'pyleco', 'PyLECO Documentation',
      ['PyLECO Developers'], 1)
 ]
 
@@ -251,8 +251,8 @@
 # (source start file, target name, title, author,
 #  dir menu entry, description, category)
 texinfo_documents = [
-    ('index', 'PyLeco', 'PyLeco Documentation',
-     'PyLECO Developers', 'PyLeco', 'Python implementation of the Laboratory Experiment COntrol (LECO) protocol.',
+    ('index', 'PyLECO', 'PyLECO Documentation',
+     'PyLECO Developers', 'PyLECO', 'Python implementation of the Laboratory Experiment COntrol (LECO) protocol.',
      'Miscellaneous'),
 ]
 
diff --git a/docs/index.rst b/docs/index.rst
index c23b467a1..8d0c79014 100644
--- a/docs/index.rst
+++ b/docs/index.rst
@@ -1,3 +1,3 @@
 ######
-PyLeco
+PyLECO
 ######

From 4676ed627752f830ac3352cca189e8fda3a157be Mon Sep 17 00:00:00 2001
From: Benedikt Moneke <67148916+bmoneke@users.noreply.github.com>
Date: Sun, 23 Jul 2023 19:18:34 +0200
Subject: [PATCH 28/29] Test with conda-forge instead of pip in CI.

---
 environment.yml | 5 ++---
 1 file changed, 2 insertions(+), 3 deletions(-)

diff --git a/environment.yml b/environment.yml
index 775e8dd6f..8c0d7316f 100644
--- a/environment.yml
+++ b/environment.yml
@@ -13,6 +13,5 @@ dependencies:
   - pytest-cov=4.1.0
   - pytest-runner=6.0.0
   - setuptools_scm # don't pin, to get newest features
-  - pip:
-    - sphinx==6.1.3
-    - sphinx_rtd_theme==1.2.2
+  - sphinx=6.1.3
+  - sphinx_rtd_theme=1.2.2

From 76f475b8efb8900b30eddb41fc6367fbbeb7ece7 Mon Sep 17 00:00:00 2001
From: Benedikt Moneke <67148916+bmoneke@users.noreply.github.com>
Date: Sun, 23 Jul 2023 20:22:26 +0200
Subject: [PATCH 29/29] Test different sphinx version.

---
 environment.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/environment.yml b/environment.yml
index 8c0d7316f..945da579a 100644
--- a/environment.yml
+++ b/environment.yml
@@ -13,5 +13,5 @@ dependencies:
   - pytest-cov=4.1.0
   - pytest-runner=6.0.0
   - setuptools_scm # don't pin, to get newest features
-  - sphinx=6.1.3
+  - sphinx=5.3.0
   - sphinx_rtd_theme=1.2.2