Merge dev to master

.github/auto_assign.yml

@@ -2,9 +2,7 @@ addReviewers: true
 addAssignees: true
 reviewers:
   - MKoesters
-
 skipKeywords:
   - wip
   - WIP
-
 numberOfReviewers: 0

.github/workflows/cd.yml

@@ -1,5 +1,4 @@
 name: Publish to pypi
-
 on:
   push:
     tags:
@@ -8,11 +7,11 @@ jobs:
   deploy:
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v4
+      - uses: actions/checkout@v6
       - name: Set up Python
-        uses: actions/setup-python@v5
+        uses: actions/setup-python@v6
         with:
-          python-version: '3.9'
+          python-version: '3.13'
       - name: Install dependencies
         run: |
           python -m pip install --upgrade pip

.github/workflows/sphinx.yml

@@ -0,0 +1,24 @@
+# For reference: https://github.com/JamesIves/github-pages-deploy-action
+name: Build Sphinx docu.
+on:
+  release:
+    types: [published]
+  workflow_dispatch:
+
+permissions:
+  contents: write
+jobs:
+  build-and-deploy:
+    runs-on: ubuntu-latest
+    steps:
+      - name: Checkout
+        uses: actions/checkout@v6
+      - name: Install and Build HTML
+        run: |
+          pip install --upgrade pip
+          pip install ".[test]"
+          python -m sphinx.cmd.build ./docs/source ./docs/build
+      - name: Deploy HTML
+        uses: JamesIves/github-pages-deploy-action@v4
+        with:
+          folder: docs/build/ # The folder the action should deploy.

.github/workflows/tox_ci.yml

@@ -1,31 +1,27 @@
 name: Continious Integration
-
-on:
-  pull_request
-
+on: pull_request
 jobs:
   black:
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v4
+      - uses: actions/checkout@v6
       - name: Run black
-        uses: actions/setup-python@v5
+        uses: actions/setup-python@v6
         with:
           python-version: 3.8
       - name: install black
         run: pip install "black<23"
       - name: run black
         run: black --check pymzml
-
   build:
     runs-on: ubuntu-latest
     strategy:
       matrix:
-        python: ['3.8', '3.9', '3.10']
+        python: ['3.9', '3.10', '3.11']
     steps:
-      - uses: actions/checkout@v4
+      - uses: actions/checkout@v6
       - name: Setup Python
-        uses: actions/setup-python@v5
+        uses: actions/setup-python@v6
         with:
           python-version: ${{ matrix.python }}
       - name: install tox

.pre-commit-config.yaml

@@ -1,14 +1,14 @@
 repos:
--   repo: https://github.com/pre-commit/pre-commit-hooks
+  - repo: https://github.com/pre-commit/pre-commit-hooks
     rev: v4.0.1
     hooks:
-    -   id: trailing-whitespace
-    -   id: end-of-file-fixer
-    -   id: check-yaml
-    -   id: debug-statements
--   repo: https://github.com/ambv/black
+      - id: trailing-whitespace
+      - id: end-of-file-fixer
+      - id: check-yaml
+      - id: debug-statements
+  - repo: https://github.com/ambv/black
     rev: 18.9b0
     hooks:
-    - id: black
-      language_version: python
-      exclude: ^docs/, ^tests/
+      - id: black
+        language_version: python
+        exclude: ^docs/, ^tests/

.readthedocs.yml

@@ -3,7 +3,6 @@
 
 # Required
 version: 2
-
 # Set the OS, Python version and other tools you might need
 build:
   os: ubuntu-22.04
@@ -13,15 +12,13 @@ build:
     # nodejs: "20"
     # rust: "1.70"
     # golang: "1.20"
-
 # Build documentation in the "docs/" directory with Sphinx
 sphinx:
   configuration: docs/source/conf.py
   # You can configure Sphinx to use a different builder, for instance use the dirhtml builder for simpler URLs
   # builder: "dirhtml"
   # Fail on all warnings to avoid broken references
   # fail_on_warning: true
-
 # Optionally build your docs in additional formats such as PDF and ePub
 # formats:
 #    - pdf
@@ -31,5 +28,5 @@ sphinx:
 # to build your documentation
 # See https://docs.readthedocs.io/en/stable/guides/reproducible-builds.html
 python:
-   install:
-   - requirements: docs/requirements.txt
+  install:
+    - requirements: docs/requirements.txt

README.rst

@@ -29,7 +29,7 @@ General information
 
 Module to parse mzML data in Python based on cElementTree
 
-Copyright 2010-2021 by:
+Copyright 2010-2024 by:
 
     | M. Kösters,
     | J. Leufken,
@@ -88,8 +88,8 @@ Download
 Get the latest version via github
     | https://github.com/pymzml/pymzML
 
-The complete Documentation can be found as pdf
-    | https://pymzml.readthedocs.io/_/downloads/en/latest/pdf/
+The complete Documentation can be found here
+    | https://pymzml.readthedocs.io/en/latest/
 
 
 ********

codecov.yml

@@ -5,12 +5,10 @@ coverage:
   precision: 2
   round: down
   range: "70...100"
-
   status:
     project: yes
     patch: yes
     changes: no
-
 parsers:
   gcov:
     branch_detection:
@@ -19,9 +17,7 @@ parsers:
       method: False
       changes: False
       macro: False
-
   comment:
     layout: "head, diff"
     behaviour: default
     require_change: no
-

docs/parse_example_scripts.py

@@ -1,45 +1,43 @@
 #!/usr/bin/env python3
 # encoding: utf-8
 
-'''
+"""
 
 Originally created for Ursgal ( https://github.com/ursgal/ursgal )
 
 
-'''
+"""
 
 import glob
 import os
 
-if __name__ == '__main__':
-    print('''
+if __name__ == "__main__":
+    print(
+        """
         Formatting example scripts into rst files for the docs
-''')
+"""
+    )
     # input()
     example_script_path = os.path.join(
         os.path.dirname(__file__),
         os.pardir,
-        'example_scripts',
-        '*.py',
+        "example_scripts",
+        "*.py",
     )
     print(example_script_path)
     for example_script in glob.glob(example_script_path):
         if os.path.exists(example_script) is False:
             continue
         basename = os.path.basename(example_script)
-        print(
-            'Reading: {0}'.format(example_script)
-        )
+        print("Reading: {0}".format(example_script))
         file_path = os.path.join(
             os.path.dirname(__file__),
-            'source',
-            'code_inc',
-            '{0}',
+            "source",
+            "code_inc",
+            "{0}",
         )
-        with open( file_path.format( basename.replace('.py', '.inc')), 'w') as o:
-            print('''.. code-block:: python\n''', file=o)
-            with open( example_script ) as infile:
+        with open(file_path.format(basename.replace(".py", ".inc")), "w") as o:
+            print(""".. code-block:: python\n""", file=o)
+            with open(example_script) as infile:
                 for line in infile:
-                    print('\t{0}'.format( line.rstrip()), file=o)
-
-
+                    print("\t{0}".format(line.rstrip()), file=o)