[repo-helper] Configuration Update

.github/workflows/flake8.yml

@@ -16,7 +16,7 @@ permissions:
 jobs:
   Run:
     name: "Flake8"
-    runs-on: "ubuntu-20.04"
+    runs-on: "ubuntu-22.04"
 
     steps:
       - name: Checkout 🛎️

.github/workflows/mypy.yml

@@ -20,7 +20,7 @@ jobs:
 
     strategy:
       matrix:
-        os: ['ubuntu-20.04', 'windows-2019']
+        os: ['ubuntu-22.04', 'windows-2019']
       fail-fast: false
 
     steps:
@@ -43,7 +43,7 @@ jobs:
           python-version: "3.8"
 
       - name: Install dependencies (Linux) 🔧
-        if: ${{ matrix.os == 'ubuntu-20.04' && steps.changes.outputs.code == 'true' }}
+        if: ${{ matrix.os == 'ubuntu-22.04' && steps.changes.outputs.code == 'true' }}
         run: |
           python -VV
           python -m site
@@ -54,7 +54,7 @@ jobs:
           sudo apt install libhdf5-dev netcdf-bin libnetcdf-dev
 
       - name: Install dependencies (Windows) 🔧
-        if: ${{ matrix.os != 'ubuntu-20.04' && steps.changes.outputs.code == 'true' }}
+        if: ${{ matrix.os != 'ubuntu-22.04' && steps.changes.outputs.code == 'true' }}
         run: |
           python -VV
           python -m site

.github/workflows/python_ci.yml

@@ -76,3 +76,4 @@ jobs:
         with:
           name: "coverage-${{ matrix.config.python-version }}"
           path: .coverage
+          include-hidden-files: true

.github/workflows/python_ci_linux.yml

@@ -19,8 +19,8 @@ permissions:
 
 jobs:
   tests:
-    name: "ubuntu-20.04 / Python ${{ matrix.config.python-version }}"
-    runs-on: "ubuntu-20.04"
+    name: "ubuntu-22.04 / Python ${{ matrix.config.python-version }}"
+    runs-on: "ubuntu-22.04"
     continue-on-error: ${{ matrix.config.experimental }}
     env:
       USING_COVERAGE: '3.7,3.8,3.9,3.10,3.11,3.12,3.13'
@@ -80,11 +80,12 @@ jobs:
         with:
           name: "coverage-${{ matrix.config.python-version }}"
           path: .coverage
+          include-hidden-files: true
 
 
   Coverage:
     needs: tests
-    runs-on: "ubuntu-20.04"
+    runs-on: "ubuntu-22.04"
     steps:
       - name: Checkout 🛎️
         uses: "actions/checkout@v4"
@@ -122,6 +123,7 @@ jobs:
         with:
           name: "combined-coverage"
           path: .coverage
+          include-hidden-files: true
 
       - name: "Upload Combined Coverage to Coveralls"
         if: ${{ steps.show.outcome != 'failure' }}
@@ -133,7 +135,7 @@ jobs:
   Deploy:
     needs: tests
 
-    runs-on: "ubuntu-20.04"
+    runs-on: "ubuntu-22.04"
     steps:
       - name: Checkout 🛎️
         uses: "actions/checkout@v4"
@@ -207,6 +209,7 @@ jobs:
           $CONDA/bin/conda config --set always_yes yes --set changeps1 no
           $CONDA/bin/conda update -n base conda
           $CONDA/bin/conda info -a
+          $CONDA/bin/conda install conda-forge::py-lief=0.14.1
           $CONDA/bin/conda config --add channels bioconda
           $CONDA/bin/conda config --add channels conda-forge
           $CONDA/bin/conda config --add channels domdfcoding

.github/workflows/python_ci_macos.yml

@@ -18,8 +18,8 @@ permissions:
 
 jobs:
   tests:
-    name: "macos-13 / Python ${{ matrix.config.python-version }}"
-    runs-on: "macos-13"
+    name: "macos-${{ matrix.config.os-ver }} / Python ${{ matrix.config.python-version }}"
+    runs-on: "macos-${{ matrix.config.os-ver }}"
     continue-on-error: ${{ matrix.config.experimental }}
     env:
       USING_COVERAGE: '3.7,3.8,3.9,3.10,3.11,3.12,3.13'
@@ -28,13 +28,13 @@ jobs:
       fail-fast: False
       matrix:
         config:
-          - {python-version: "3.7", testenvs: "py37,build", experimental: False}
-          - {python-version: "3.8", testenvs: "py38,build", experimental: False}
-          - {python-version: "3.9", testenvs: "py39,build", experimental: False}
-          - {python-version: "3.10", testenvs: "py310,build", experimental: False}
-          - {python-version: "3.11", testenvs: "py311,build", experimental: False}
-          - {python-version: "3.12", testenvs: "py312,build", experimental: False}
-          - {python-version: "3.13", testenvs: "py313,build", experimental: False}
+          - {python-version: "3.7", os-ver: "13", testenvs: "py37,build", experimental: False}
+          - {python-version: "3.8", os-ver: "14", testenvs: "py38,build", experimental: False}
+          - {python-version: "3.9", os-ver: "14", testenvs: "py39,build", experimental: False}
+          - {python-version: "3.10", os-ver: "14", testenvs: "py310,build", experimental: False}
+          - {python-version: "3.11", os-ver: "14", testenvs: "py311,build", experimental: False}
+          - {python-version: "3.12", os-ver: "14", testenvs: "py312,build", experimental: False}
+          - {python-version: "3.13", os-ver: "14", testenvs: "py313,build", experimental: False}
 
     steps:
       - name: Checkout 🛎️
@@ -76,3 +76,4 @@ jobs:
         with:
           name: "coverage-${{ matrix.config.python-version }}"
           path: .coverage
+          include-hidden-files: true

.pre-commit-config.yaml

@@ -8,7 +8,7 @@ ci:
 
 repos:
  - repo: https://github.com/repo-helper/pyproject-parser
-   rev: v0.11.1
+   rev: v0.13.0
    hooks:
     - id: reformat-pyproject
 
@@ -81,7 +81,7 @@ repos:
     - id: snippet-fmt
 
  - repo: https://github.com/python-formate/formate
-   rev: v0.7.0
+   rev: v0.8.0
    hooks:
     - id: formate
       exclude: ^(doc-source/conf|__pkginfo__|setup)\.(_)?py$

.readthedocs.yml

@@ -13,7 +13,7 @@ python:
    - requirements: requirements.txt
    - requirements: doc-source/requirements.txt
 build:
-  os: ubuntu-20.04
+  os: ubuntu-22.04
   tools:
     python: '3.9'
   jobs:

README.rst

@@ -109,7 +109,7 @@ PyMassSpec-Plot
 	:target: https://github.com/PyMassSpec/PyMassSpec-Plot/commit/master
 	:alt: GitHub last commit
 
-.. |maintained| image:: https://img.shields.io/maintenance/yes/2024
+.. |maintained| image:: https://img.shields.io/maintenance/yes/2025
 	:alt: Maintenance
 
 .. |pypi-downloads| image:: https://img.shields.io/pypi/dm/PyMassSpec-Plot

doc-source/index.rst

@@ -114,7 +114,7 @@ PyMassSpec-Plot
 		:last-commit:
 		:alt: GitHub last commit
 
-	.. |maintained| maintained-shield:: 2024
+	.. |maintained| maintained-shield:: 2025
 		:alt: Maintenance
 
 	.. |pypi-downloads| pypi-shield::