Merge branch 'master' into dependabot/pip/master/sphinx-gallery-0.18.0

.flake8

@@ -0,0 +1,11 @@
+[flake8]
+max-line-length = 300
+exclude =
+    .git
+    docs/build
+    docs/source/gallery
+    development
+
+count = true
+per-file-ignores =
+    __init__.py: F403, F401

.github/workflows/deploy_PyPi.yml

@@ -0,0 +1,20 @@
+name: Deploy to PyPi
+
+on:
+  push:
+    branches: [ "master" ]
+    tags:
+      - '*'
+  pull_request:
+    branches: [ "master" ]
+
+permissions:
+    contents: write
+
+jobs:
+  ManyLinux_x86_64:
+    uses: MartinPdeS/MPSActions/.github/workflows/publish_compiled_package_to_PyPi.yml@master
+    with:
+      python-version: "3.11"
+    secrets:
+      PYPI_API_TOKEN: ${{ secrets.PYPI_API_TOKEN }}

.github/workflows/deploy_anaconda.yml

@@ -0,0 +1,21 @@
+name: Deploy Conda Packages
+
+on:
+  push:
+    branches: [ "master" ]
+    tags:
+      - '*'
+  pull_request:
+    branches: [ "master" ]
+
+permissions:
+    contents: write
+
+jobs:
+  ManyLinux_x86_64:
+    uses: MartinPdeS/MPSActions/.github/workflows/publish_compiled_package_to_anaconda.yml@master
+    with:
+      python-versions: '["3.11", "3.12"]'
+    secrets:
+      ANACONDA_API_TOKEN: ${{ secrets.ANACONDA_API_TOKEN }}
+

.github/workflows/deploy_coverage.yml

@@ -1,5 +1,5 @@
-# .github/workflows/coverage.yml
-name: Coverage
+# Simple workflow for deploying static content to GitHub Pages
+name: Deploy coverage
 
 on:
   push:
@@ -9,44 +9,17 @@ on:
   pull_request:
     branches: [ "master" ]
 
-jobs:
-  coverage:
-    name: Run test and generate coverage data
-    runs-on: ubuntu-latest
-    permissions:
-      pull-requests: write
-      contents: write
-
-    steps:
-      - name: "Set-up: Python ${{ env.cp_python_version }}"
-        uses: actions/setup-python@v4
-        id: cp310
-        with:
-            python-version: "3.10"
-
 
-      - name: "Install: Dependencies for headless server"
-        shell: bash
-        run: |
-            sudo apt-get update
-            sudo apt-get install libgl1-mesa-glx xvfb
+# Sets permissions of the  GITHUB_TOKEN to allow deployment to GitHub Pages
+permissions:
+  contents: write
+  pages: write
+  id-token: write
 
-      - name: "Checkout requirements and files for testing"
-        uses: actions/checkout@v4
-        with:
-          fetch-depth: 0
-          submodules: true
-
-      - name: Install everything, run the tests, produce the .coverage file
-        run: |
-          python -m pip install wheel build
-          python -m build --wheel
-          python -m pip install .[testing]
-          pytest
-
-      - name: Coverage comment
-        uses: py-cov-action/python-coverage-comment-action@v3
-        with:
-          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
-          MINIMUM_GREEN: 90
-          MINIMUM_ORANGE: 50
+jobs:
+  ManyLinux_x86_64:
+    uses: MartinPdeS/MPSActions/.github/workflows/publish_coverage.yml@master
+    with:
+      python-version: "3.11"
+    secrets:
+      _GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}

.github/workflows/deploy_documentation.yml

@@ -1,5 +1,5 @@
-# .github/workflows/deploy_documentation.yml
-name: Documentation
+# Simple workflow for deploying static content to GitHub Pages
+name: Deploy documentation to github page
 
 on:
   push:
@@ -9,52 +9,15 @@ on:
   pull_request:
     branches: [ "master" ]
 
-jobs:
-  documentation:
-    name: Run the documentation building tools
-    runs-on: ubuntu-latest
-    permissions:
-      pull-requests: write
-      contents: write
-
-    steps:
-      - name: "Set-up: Python 3.10"
-        uses: actions/setup-python@v4
-        id: cp310
-        with:
-            python-version: "3.10"
-
-      - name: "Install: Dependencies for headless server"
-        shell: bash
-        run: |
-            sudo apt-get update
-            sudo apt-get install libgl1-mesa-glx xvfb
-
-      - name: "Checkout requirements and files for testing"
-        uses: actions/checkout@v4
-        with:
-          fetch-depth: 0
-          submodules: true
 
-      - name: Install everything, run the tests, produce the .coverage file
-        run: |
-          python -m pip install wheel build
-          python -m build --wheel
-          python -m pip install .[documentation]
+# Sets permissions of the GITHUB_TOKEN to allow deployment to GitHub Pages
+permissions:
+  contents: write
+  pages: write
+  id-token: write
 
-      - name: Install dependencies
-        run: |
-          pip install sphinx sphinx_rtd_theme myst_parser
-
-      - name: Sphinx build
-        run: |
-          sphinx-build docs/source _build
-
-      - name: Deploy to GitHub Pages
-        uses: peaceiris/actions-gh-pages@v3
-        if: github.event_name == 'push' && startsWith(github.ref, 'refs/tags/')
-        with:
-          publish_branch: gh-pages
-          github_token: ${{ secrets.GITHUB_TOKEN }}
-          publish_dir: _build/
-          force_orphan: true
+jobs:
+  ManyLinux_x86_64:
+    uses: MartinPdeS/MPSActions/.github/workflows/publish_documentation.yml@master
+    with:
+      python-version: "3.11"

.gitignore

@@ -1,32 +1,32 @@
+# General patterns
 *.DS_store
 *.ipynb_checkpoints*
 *__pycache__*
 *.so
 *.a
-*.pdf
-*.pickle
-
-
-.tox
-.coverage.*
-coverage.json
-htmlcov
+.coverage*
 *.pytest_cache
-SuPyMode/user_data/*
-!SuPyMode/user_data/__init__.py
-
+htmlcov
 dist
 build
 *.egg*
 *.whl
-.pdf
-perso/
-
-docs/source/gallery
-docs/source/api
-
 CMakeCache.txt
 CMakeFiles
 install_manifest.txt
 cmake_install.cmake
-.coverage
+wheelhouse
+
+# Docs-specific patterns
+docs/source/gallery/*
+!docs/source/gallery/index.rst
+PyOptik/data/**/test*
+PyOptik/data/**/example*
+
+# Override for documentation_build
+!documentation_build
+!documentation_build/**
+
+
+# Package specifics
+SuPyMode/user_data/*

.gitmodules

@@ -1,6 +1,6 @@
 [submodule "extern/eigen"]
 	path = extern/eigen
-	url = https://github.com/libigl/eigen.git
+	url = https://gitlab.com/libeigen/eigen.git
 	ignore = dirty
 [submodule "extern/spectra"]
 	path = extern/spectra

CMakeLists.txt

@@ -22,8 +22,6 @@ include_directories("${CMAKE_SOURCE_DIR}/SuPyMode/cpp/headers")
 include_directories("${CMAKE_SOURCE_DIR}/extern/eigen/Eigen")
 include_directories("${CMAKE_SOURCE_DIR}/extern/spectra")
 
-add_compile_options("-w" "-Wdeprecated-declarations")
-
 # Platform-specific settings for static linking
 if (WIN32)
     message("Windows OS detected")
@@ -42,7 +40,7 @@ message(STATUS "Binary will be installed in location: " ${SUPYMODE_BIN_DIR})
 #Building EigenSolver----------------------------------------------
 pybind11_add_module(EigenSolver MODULE "${SUPYMODE_CXX_DIR}/eigensolver_interface.cpp")
 set_target_properties(EigenSolver PROPERTIES OUTPUT_NAME "CppSolver")
-target_link_libraries(EigenSolver PRIVATE "${Eigen_LIBRARIES}")
+target_include_directories(EigenSolver PRIVATE "${CMAKE_CURRENT_SOURCE_DIR}/extern/eigen")
 target_link_options(EigenSolver PUBLIC ${STATIC_LINK_OPTIONS})
 target_include_directories(EigenSolver PRIVATE "${CMAKE_CURRENT_SOURCE_DIR}/extern/eigen")
 target_include_directories(EigenSolver PRIVATE "${CMAKE_CURRENT_SOURCE_DIR}/extern/spectra/include")

README.rst

@@ -119,4 +119,4 @@ Email:`[email protected] <mailto:martin.poinsinet-de-sivry@po
    :target: https://pypistats.org/packages/supymode
 
 .. |colab| image:: https://colab.research.google.com/assets/colab-badge.svg
-   :target: https://colab.research.google.com/github/MartinPdeS/SuPyMode/blob/master/SuPyModes.ipynb
+   :target: https://colab.research.google.com/github/MartinPdeS/SuPyMode/blob/master/notebook.ipynb

SuPyMode/_version.py

@@ -12,5 +12,5 @@
 __version_tuple__: VERSION_TUPLE
 version_tuple: VERSION_TUPLE
 
-__version__ = version = '2.0.0.post2'
-__version_tuple__ = version_tuple = (2, 0, 0)
+__version__ = version = '2.0.3.0'
+__version_tuple__ = version_tuple = (2, 0, 3, 0)

SuPyMode/directories.py

@@ -9,7 +9,6 @@
     'root_path',
     'project_path',
     'test_path',
-    'instance_directory',
     'version_path',
     'validation_data_path',
     'doc_path',