Initial commit.

.coveragerc

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+# .coveragerc to control coverage.py
+[run]
+branch = False
+concurrency = multiprocessing
+parallel = True
+omit = */site-packages/*,*/tests/*,*/.eggs/*
+
+[report]
+show_missing = True
+
+# Regexes for lines to exclude from consideration
+exclude_lines =
+    # Have to re-enable the standard pragma
+    pragma: no cover
+
+    # Don't complain if tests don't hit defensive assertion code:
+    raise AssertionError
+    raise NotImplementedError
+
+    # Don't complain if non-runnable code isn't run:
+    if 0:
+    if __name__ == .__main__.:
+
+ignore_errors = True
+
+[html]
+directory = htmlcov

.editorconfig

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+# http://editorconfig.org
+
+root = true
+
+[*]
+indent_style = space
+indent_size = 4
+trim_trailing_whitespace = true
+insert_final_newline = true
+charset = utf-8
+end_of_line = lf
+
+[*.bat]
+indent_style = tab
+end_of_line = crlf
+
+[LICENSE]
+insert_final_newline = false
+
+[Makefile]
+indent_style = tab

.gitattributes

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+# *.h5 filter=lfs diff=lfs merge=lfs -text
+# *.png filter=lfs diff=lfs merge=lfs -text

.github/workflows/ci.yml

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+name: CI
+
+on:
+  push:
+    branches:
+      - main
+      - githubci
+
+env:
+    SKIP: true
+
+jobs:
+  before_script:
+    runs-on: self-hosted
+
+    strategy:
+      matrix:
+        node-version: [ 20.x ]
+
+    steps:
+      - name: Checkout code
+        uses: actions/checkout@v4
+
+      - name: Set up Python
+        uses: actions/setup-python@v5
+        with:
+          python-version: '3.x'
+
+      - name: Install dependencies
+        run: |
+          conda init bash
+          source ~/.bashrc
+          conda info
+          source activate ci_env
+        shell: bash
+
+  test_sarvey:
+    runs-on: self-hosted
+    needs: before_script
+    steps:
+      - name: Checkout code
+        uses: actions/checkout@v4
+
+      - name: Set up Python
+        uses: actions/setup-python@v5
+        with:
+          python-version: '3.x'
+
+      - name: Run tests
+        if: env.SKIP == 'false'
+        run: |
+          conda init bash
+          source ~/.bashrc
+          source activate ci_env
+          rm -rf tests/testdata
+          wget -c https://seafile.projekt.uni-hannover.de/f/4b3be399dffa488e98db/?dl=1 -P tests/
+          unzip tests/testdata.zip
+          ls tests/testdata
+          make pytest
+        shell: bash
+
+      - name: create docs
+        run: |
+          conda init bash
+          source ~/.bashrc
+          source activate ci_env
+          make docs
+        shell: bash
+
+      - name: Upload coverage report
+        uses: actions/upload-artifact@v4
+        with:
+          name: coverage-report
+          path: htmlcov/
+
+      - name: Upload report.html
+        uses: actions/upload-artifact@v4
+        with:
+          name: test-report
+          path: report.html
+
+      - name: Upload docs
+        uses: actions/upload-artifact@v4
+        with:
+          name: docs
+          path: docs/_build/html/
+
+      - name: Upload cobertura coverage report
+        uses: actions/upload-artifact@v4
+        with:
+          name: cobertura-coverage
+          path: coverage.xml
+
+      - name: Upload junit report
+        uses: actions/upload-artifact@v4
+        with:
+          name: junit-report
+          path: report.xml
+
+  test_styles:
+    runs-on: self-hosted
+    needs: before_script
+    steps:
+      - name: Checkout code
+        uses: actions/checkout@v4
+
+      - name: Set up Python
+        uses: actions/setup-python@v5
+        with:
+          python-version: '3.x'
+
+      - name: Install dependencies
+        run: |
+          conda init bash
+          source ~/.bashrc
+          conda info
+          source activate ci_env
+          make lint
+        shell: bash
+
+      - name: Upload flake8 log
+        uses: actions/upload-artifact@v4
+        with:
+          name: flake8-log
+          path: tests/linting/flake8.log
+
+      - name: Upload pycodestyle log
+        uses: actions/upload-artifact@v4
+        with:
+          name: pycodestyle-log
+          path: tests/linting/pycodestyle.log
+
+      - name: Upload pydocstyle log
+        uses: actions/upload-artifact@v4
+        with:
+          name: pydocstyle-log
+          path: tests/linting/pydocstyle.log
+
+  test_urls:
+    runs-on: self-hosted
+    needs: before_script
+    steps:
+      - name: Checkout code
+        uses: actions/checkout@v4
+
+      - name: Set up Python
+        uses: actions/setup-python@v5
+        with:
+          python-version: '3.x'
+
+      - name: Install dependencies
+        run: |
+          conda init bash
+          source ~/.bashrc
+          conda info
+          source activate ci_env
+          make urlcheck
+        shell: bash
+
+  test_sarvey_install:
+    runs-on: self-hosted
+    steps:
+      - name: Checkout code
+        uses: actions/checkout@v4
+
+      - name: Set up Python
+        uses: actions/setup-python@v5
+        with:
+          python-version: '3.x'
+
+      - name: Install dependencies
+        run: |
+          conda init bash
+          source ~/.bashrc
+          mamba update -n base mamba conda
+          mamba info
+          mamba env remove --name sarvey_testinstall --yes || echo "Environment sarvey_testinstall does not exist"
+          pip install conda-merge
+          wget https://raw.githubusercontent.com/insarlab/MiaplPy/main/conda-env.yml
+          conda-merge conda-env.yml tests/CI_docker/context/environment_sarvey.yml > env.yml
+          mamba env create --name sarvey_testinstall -f env.yml
+          source activate sarvey_testinstall
+          pip install git+https://github.com/insarlab/MiaplPy.git
+          pip install .
+          pip check
+          cd ..
+          python -c "import sarvey; print(sarvey)"
+        shell: bash
+
+  deploy_pages:
+    runs-on: self-hosted
+
+    needs: test_sarvey
+    steps:
+      - name: Checkout code
+        uses: actions/checkout@v4
+
+      - name: Set up Python
+        uses: actions/setup-python@v5
+        with:
+          python-version: '3.x'
+
+      - name: Deploy to GitHub Pages
+        if: env.SKIP == 'false'
+        run: |
+          rm -rf public
+          mkdir -p public/doc
+          mkdir -p public/images/
+          mkdir -p public/coverage
+          mkdir -p public/test_reports
+          cp -r docs/_build/html/* public/doc/
+          cp -r htmlcov/* public/coverage/
+          cp report.html public/test_reports/
+          ls -al public
+          ls -al public/doc
+          ls -al public/coverage
+          ls -al public/test_reports
+        shell: bash
+
+      - name: Upload to GitHub Pages
+        if: env.SKIP == 'false'
+        uses: peaceiris/actions-gh-pages@v4
+        with:
+          github_token: ${{ secrets.GITHUB_TOKEN }}
+          publish_dir: ./public

.gitignore

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+# Byte-compiled / optimized / DLL files
+__pycache__/
+*.py[cod]
+*$py.class
+
+# C extensions
+*.so
+
+# Distribution / packaging
+.Python
+env/
+build/
+develop-eggs/
+dist/
+downloads/
+eggs/
+.eggs/
+lib/
+lib64/
+parts/
+sdist/
+var/
+wheels/
+*.egg-info/
+.installed.cfg
+*.egg
+
+# PyInstaller
+#  Usually these files are written by a python script from a template
+#  before PyInstaller builds the exe, so as to inject date/other infos into it.
+*.manifest
+*.spec
+
+# Installer logs
+pip-log.txt
+pip-delete-this-directory.txt
+
+# Unit test / coverage reports
+htmlcov/
+.tox/
+.coverage
+.coverage.*
+.cache
+nosetests.xml
+coverage.xml
+*.cover
+.hypothesis/
+.pytest_cache/
+report.xml
+report.html
+
+# Translations
+*.mo
+*.pot
+
+# Django stuff:
+*.log
+local_settings.py
+
+# Flask stuff:
+instance/
+.webassets-cache
+
+# Scrapy stuff:
+.scrapy
+
+# Sphinx documentation
+docs/_build/
+
+# PyBuilder
+target/
+
+# Jupyter Notebook
+.ipynb_checkpoints
+
+# pyenv
+.python-version
+
+# celery beat schedule file
+celerybeat-schedule
+
+# SageMath parsed files
+*.sage.py
+
+# dotenv
+.env
+
+# virtualenv
+.venv
+venv/
+ENV/
+
+# Spyder project settings
+.spyderproject
+.spyproject
+
+# Rope project settings
+.ropeproject
+
+# mkdocs documentation
+/site
+
+# mypy
+.mypy_cache/
+
+# IDE settings
+.vscode/
+
+# IntelliJ Idea family of suites
+.idea
+*.iml
+## File-based project format:
+*.ipr
+*.iws
+## mpeltonen/sbt-idea plugin
+.idea_modules/