spotmax 1.0.3__tar.gz

spotmax-1.0.3/.github/ISSUE_TEMPLATE/bug_report.yml

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+name: Report a bug
+description: Report an error, problem or unexpected behavior in spotMAX.
+title: "<Comprehensive title summarizing the bug>"
+labels: [":bug: Bug"]
+
+body:
+  - type: markdown
+    attributes:
+      value: >
+        Thank you for reporting an issue!
+        Please, **remember to upload the log file**. You can find the log file from the 
+        menu `Help --> Show log files...`
+
+  - type: textarea
+    validations:
+      required: true
+    attributes:
+      label: "Description:"
+      description: >
+        Describe your issue with all necessary detail.
+        What kind of behavior are you experiencing?
+        What would you expect instead?
+        Upload the log file here too. You can find the log file from the 
+        menu on the top menubar called `Help --> Show log files...`
+      placeholder: |
+        Your description...
+
+  - type: textarea
+    attributes:
+      label: "Way to reproduce:"
+      description: >
+        Provide a as many details as possible about the process required to 
+        reproduce the error.
+
+  - type: textarea
+    attributes:
+      label: "(Optional) Link to data to reproduce error:"
+      description: >
+        Many issues are specifically related to the data you are using. If possible, 
+        consider providing a link to download the data that I can test with. 
+        You could use Google Drive and share it with me at elpado6872@gmail.com
+
+  - type: textarea
+    attributes:
+      label: "Terminal output:"
+      description: >
+        Paste here the entire terminal session.
+      placeholder: |
+        Full error or terminal output..
+      render: Shell
+
+  - type: textarea
+    attributes:
+      label: "Version information:"
+      description: |
+        After activating the environment where you have spotMAX installed, 
+        run the following command and paste the output
+        ```shell
+        python -c "import sys; print(sys.version); import platform; print(platform.platform()); import cellacdc; print(f'Cell-ACDC version: {cellacdc.__version__}'); import spotmax; print(f'spotMAX version: {spotmax.__version__}')"
+        ```
+      placeholder: |
+        Version information...
+      render: Shell

spotmax-1.0.3/.github/ISSUE_TEMPLATE/enhanchement_request.yml

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+name: Suggest an improvement
+description: Suggest an idea on how to improve existing features.
+title: "<Title of the enhancement>"
+labels: [":balloon: Enhancement"]
+
+body:
+  - type: markdown
+    attributes:
+      value: >
+        Thank you for your suggestion! You can also discuss the enhancement on our 
+        [discussion forum](https://github.com/SchmollerLab/Cell_ACDC/discussions)
+
+  - type: textarea
+    validations:
+      required: true
+    attributes:
+      label: "Description:"
+      description: >
+        Describe your suggestion with all necessary detail.
+        What is the current feature you would like to see improved?
+        Does the feature have a problem?
+        Great! Please let us know.
+      placeholder: |
+        Your suggestion...

spotmax-1.0.3/.github/ISSUE_TEMPLATE/feature_request.yml

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+name: Feature request
+description: Suggest an idea for a new feature for spotMAX.
+title: "<Title of the new feature>"
+labels: [":rocket: New feature"]
+
+body:
+  - type: markdown
+    attributes:
+      value: >
+        Thank you for your suggestion! You can also discuss the new feature on our 
+        [discussion forum](https://github.com/SchmollerLab/Cell_ACDC/discussions)
+
+  - type: textarea
+    validations:
+      required: true
+    attributes:
+      label: "Description:"
+      description: >
+        Describe your suggestion with all necessary detail.
+        What kind of behavior would you like to see?
+        Is your feature request related to a problem?
+        Great! Please let us know.
+      placeholder: |
+        Your suggestion...

spotmax-1.0.3/.github/ISSUE_TEMPLATE/informal-request.yml

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+name: Informal request/question
+description: Ask a question or post a comment about spotMAX.
+title: "<Title of your question/comment>"
+labels: [":question: Help/question"]
+
+body:
+  - type: markdown
+    attributes:
+      value: >
+        Thank you for your question! You can also discuss your question/comment on our 
+        [discussion forum](https://github.com/SchmollerLab/Cell_ACDC/discussions)
+
+  - type: textarea
+    validations:
+      required: true
+    attributes:
+      label: "Description:"
+      description: >
+        Ask any question or write any comment about spotMAX. Thanks!
+        If you had an error, please upload the log file here too. 
+        You can find the log file from the menu on the top menubar 
+        called `Help --> Show log files...`
+      placeholder: |
+        Your question...
+

spotmax-1.0.3/.github/workflows/build-macos_pyqt5.yml

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+# This workflow will install Python dependencies, run tests and lint with a variety of Python versions
+# For more information see: https://help.github.com/actions/language-and-framework-guides/using-python-with-github-actions
+
+name: macOS build, lint and test (PyQt5)
+
+on:
+  push:
+    branches: [ main ]
+  pull_request:
+    branches: [ main ]
+
+jobs:
+  build:
+
+    runs-on: macos-latest
+    strategy:
+      fail-fast: false
+      matrix:
+        python-version: ["3.9", "3.10", "3.11"]
+
+    steps:
+    - uses: actions/checkout@v4
+    - name: Set up Python ${{ matrix.python-version }}
+      uses: actions/setup-python@v5
+      with:
+        python-version: ${{ matrix.python-version }}
+    - name: Install dependencies
+      run: |
+        python -m pip install --upgrade pip
+        python -m pip install flake8 pytest
+        if [ -f requirements.txt ]; then pip install -r requirements.txt; fi
+        python -m pip install -e .
+        python -m pip install "git+https://github.com/SchmollerLab/Cell_ACDC.git"
+        python -m pip install -r requirements_gui_pyqt5.txt
+    - name: Lint with flake8
+      run: |
+        # stop the build if there are Python syntax errors or undefined names
+        flake8 . --count --select=E9,F63,F7,F82 --show-source --statistics
+        # exit-zero treats all errors as warnings. The GitHub editor is 127 chars wide
+        flake8 . --count --exit-zero --max-complexity=10 --max-line-length=127 --statistics
+    - name: Test with pytest
+      run: |
+        pytest

spotmax-1.0.3/.github/workflows/build-macos_pyqt6.yml

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+# This workflow will install Python dependencies, run tests and lint with a variety of Python versions
+# For more information see: https://help.github.com/actions/language-and-framework-guides/using-python-with-github-actions
+
+name: macOS build, lint and test (PyQt6)
+
+on:
+  push:
+    branches: [ main ]
+  pull_request:
+    branches: [ main ]
+
+jobs:
+  build:
+
+    runs-on: macos-latest
+    strategy:
+      fail-fast: false
+      matrix:
+        python-version: ["3.9", "3.10", "3.11"]
+
+    steps:
+    - uses: actions/checkout@v4
+    - name: Set up Python ${{ matrix.python-version }}
+      uses: actions/setup-python@v5
+      with:
+        python-version: ${{ matrix.python-version }}
+    - name: Install dependencies
+      run: |
+        python -m pip install --upgrade pip
+        python -m pip install flake8 pytest
+        if [ -f requirements.txt ]; then pip install -r requirements.txt; fi
+        python -m pip install -e .
+        python -m pip install "git+https://github.com/SchmollerLab/Cell_ACDC.git"
+        python -m pip install -r requirements_gui_pyqt6.txt
+    - name: Lint with flake8
+      run: |
+        # stop the build if there are Python syntax errors or undefined names
+        flake8 . --count --select=E9,F63,F7,F82 --show-source --statistics
+        # exit-zero treats all errors as warnings. The GitHub editor is 127 chars wide
+        flake8 . --count --exit-zero --max-complexity=10 --max-line-length=127 --statistics
+    - name: Test with pytest
+      run: |
+        pytest

spotmax-1.0.3/.github/workflows/build-ubuntu_pyqt5.yml

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+# This workflow will install Python dependencies, run tests and lint with a variety of Python versions
+# For more information see: https://help.github.com/actions/language-and-framework-guides/using-python-with-github-actions
+
+name: Ubuntu build, lint and test (PyQt5)
+
+on:
+  push:
+    branches: [ main ]
+  pull_request:
+    branches: [ main ]
+
+jobs:
+  build:
+
+    runs-on: ubuntu-latest
+    strategy:
+      fail-fast: false
+      matrix:
+        python-version: ["3.9", "3.10", "3.11"]
+    env:
+      DISPLAY: ':99.0'
+
+    steps:
+    - uses: actions/checkout@v4
+    - name: Set up Python ${{ matrix.python-version }}
+      uses: actions/setup-python@v5
+      with:
+        python-version: ${{ matrix.python-version }}
+    - name: setup ubuntu-latest
+      run: |
+        sudo apt install libxkbcommon-x11-0 libxcb-icccm4 libxcb-image0 libxcb-keysyms1 libxcb-randr0 libxcb-render-util0 libxcb-xinerama0 libxcb-xfixes0 x11-utils
+        /sbin/start-stop-daemon --start --quiet --pidfile /tmp/custom_xvfb_99.pid --make-pidfile --background --exec /usr/bin/Xvfb -- :99 -screen 0 1920x1200x24 -ac +extension GLX
+    - name: Install dependencies
+      run: |
+        python -m pip install --upgrade pip
+        python -m pip install flake8 pytest
+        if [ -f requirements.txt ]; then pip install -r requirements.txt; fi
+        python -m pip install -e .
+        python -m pip install "git+https://github.com/SchmollerLab/Cell_ACDC.git"
+        python -m pip install -r requirements_gui_pyqt5.txt
+    - name: Lint with flake8
+      run: |
+        # stop the build if there are Python syntax errors or undefined names
+        flake8 . --count --select=E9,F63,F7,F82 --show-source --statistics
+        # exit-zero treats all errors as warnings. The GitHub editor is 127 chars wide
+        flake8 . --count --exit-zero --max-complexity=10 --max-line-length=127 --statistics
+    - name: Test with pytest
+      run: |
+        pytest

spotmax-1.0.3/.github/workflows/build-windows_pyqt5.yml

@@ -0,0 +1,42 @@
+# This workflow will install Python dependencies, run tests and lint with a variety of Python versions
+# For more information see: https://help.github.com/actions/language-and-framework-guides/using-python-with-github-actions
+
+name: Windows build, lint and test (PyQt5)
+
+on:
+  push:
+    branches: [ main ]
+  pull_request:
+    branches: [ main ]
+
+jobs:
+  build:
+
+    runs-on: windows-latest
+    strategy:
+      fail-fast: false
+      matrix:
+        python-version: ["3.9", "3.10", "3.11"]
+
+    steps:
+    - uses: actions/checkout@v4
+    - name: Set up Python ${{ matrix.python-version }}
+      uses: actions/setup-python@v5
+      with:
+        python-version: ${{ matrix.python-version }}
+    - name: Install dependencies
+      run: |
+        python -m pip install --upgrade pip
+        python -m pip install flake8 pytest
+        python -m pip install -e .
+        python -m pip install "git+https://github.com/SchmollerLab/Cell_ACDC.git"
+        python -m pip install -r requirements_gui_pyqt5.txt
+    - name: Lint with flake8
+      run: |
+        # stop the build if there are Python syntax errors or undefined names
+        flake8 . --count --select=E9,F63,F7,F82 --show-source --statistics
+        # exit-zero treats all errors as warnings. The GitHub editor is 127 chars wide
+        flake8 . --count --exit-zero --max-complexity=10 --max-line-length=127 --statistics
+    - name: Test with pytest
+      run: |
+        pytest

spotmax-1.0.3/.github/workflows/build-windows_pyqt6.yml

@@ -0,0 +1,42 @@
+# This workflow will install Python dependencies, run tests and lint with a variety of Python versions
+# For more information see: https://help.github.com/actions/language-and-framework-guides/using-python-with-github-actions
+
+name: Windows build, lint and test (PyQt6)
+
+on:
+  push:
+    branches: [ main ]
+  pull_request:
+    branches: [ main ]
+
+jobs:
+  build:
+
+    runs-on: windows-latest
+    strategy:
+      fail-fast: false
+      matrix:
+        python-version: ["3.9", "3.10", "3.11"]
+
+    steps:
+    - uses: actions/checkout@v4
+    - name: Set up Python ${{ matrix.python-version }}
+      uses: actions/setup-python@v5
+      with:
+        python-version: ${{ matrix.python-version }}
+    - name: Install dependencies
+      run: |
+        python -m pip install --upgrade pip
+        python -m pip install flake8 pytest
+        python -m pip install -e .
+        python -m pip install "git+https://github.com/SchmollerLab/Cell_ACDC.git"
+        python -m pip install -r requirements_gui_pyqt6.txt
+    - name: Lint with flake8
+      run: |
+        # stop the build if there are Python syntax errors or undefined names
+        flake8 . --count --select=E9,F63,F7,F82 --show-source --statistics
+        # exit-zero treats all errors as warnings. The GitHub editor is 127 chars wide
+        flake8 . --count --exit-zero --max-complexity=10 --max-line-length=127 --statistics
+    - name: Test with pytest
+      run: |
+        pytest

spotmax-1.0.3/.github/workflows/inactive-issues.yml

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+# Mark issues and pull requests without activity as dormant
+# See https://github.com/actions/stale for documentation and configuration
+
+name: Mark inactive issues
+on:
+  schedule:
+    - cron: "15 2 * * *" # trigger every day at 2:15
+  workflow_dispatch: # or run manually
+permissions:
+  issues: write
+  pull-requests: write
+jobs:
+  stale:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/stale@v9.0.0
+        with:
+          days-before-stale: 180
+          days-before-close: -1 # never close
+          stale-issue-label: ":sleeping: Inactive"
+          stale-pr-label: ":sleeping: Inactive"
+          remove-stale-when-updated: true
+          stale-issue-message: >
+            Hi there, I'm the spotMAX bot :wave:. 
+            This issue had no activity for more than 180 days. 
+            For now, we have marked it as "inactive" until there is some
+            new activity. If this issue was not solved yet, unfortunately 
+            we haven't had the time to implement it or it requires more discussion. 
+            Note that it doesn't mean it has been ignored, but a little reminder 
+            from your side would help :D. 
+            Feel free to reach out to us here or on our
+            [forum](https://github.com/SchmollerLab/Cell_ACDC/discussions).
+            If you think that this issue is no longer relevant, 
+            you may close it by yourself.
+            In any case, we apologise for the inconvenience and we thank you 
+            for your patience and contributions so far!
+          stale-pr-message: >
+            Hi there, I'm the Cell-ACDC bot :wave:. 
+            This pull request had no activity for more than 180 days. 
+            For now, we have marked it as "inactive" until there is some
+            new activity. If this PR was not implemented yet, unfortunately 
+            we haven't had the time to implement it or it requires more discussion. 
+            Note that it doesn't mean it has been ignored, but a little reminder 
+            from your side would help :D. 
+            Feel free to reach out to us here or on our
+            [forum](https://github.com/SchmollerLab/Cell_ACDC/discussions).
+            If you think that this issue is no longer relevant, 
+            you may close it by yourself.
+            In any case, we apologise for the inconvenience and we thank you 
+            for your patience and contributions so far!

spotmax-1.0.3/.gitignore

@@ -0,0 +1,170 @@
+# Custom ignores
+.vscode
+**/.DS_Store
+data/*
+mytests
+notebooks/test.ipynb
+notebooks/Untitled-1.ipynb
+spotmax/qtest.py
+spotmax/test.py
+spotmax/test1.py
+spotmax/deprecated.py
+spotmax/docs/deprecated.py
+spotmax/_version.py
+spotmax/_tests
+spotmax/docs/_build
+spotmax/_nnet
+spotmax/_deprecated
+spotmax/_old_gui.py
+spotmax/mytests/*
+spotmax/_deprecated_qrc_resources_spotmax.py
+spotmax/spotmax_v1_paramWin.png
+spotmax/spotmax_v2_parameters.png
+spotmax/nnet/models/deprecated_pytorch3dunet
+spotmax/docs/source/tutorials/data
+spotmax/docs/source/images/home_carousel/svgs
+spotmax/resources/_deprecated_icons
+examples/notebooks/bioimageio_models
+deprecated
+cuda-keyring_1.1-1_all.deb
+**/checkpoints
+_tests
+.setup.cfg
+setup.cfg
+*.deb
+
+spotmax/logs/*
+!spotmax/logs/dummy.txt
+
+spotmax/settings/*
+!spotmax/settings/dummy.txt
+
+# Byte-compiled / optimized / DLL files
+__pycache__/
+*.py[cod]
+*$py.class
+
+# C extensions
+*.so
+
+# Distribution / packaging
+.Python
+build/
+develop-eggs/
+dist/
+downloads/
+eggs/
+.eggs/
+lib/
+lib64/
+parts/
+sdist/
+var/
+wheels/
+pip-wheel-metadata/
+share/python-wheels/
+*.egg-info/
+.installed.cfg
+*.egg
+MANIFEST
+
+# 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/
+.nox/
+.coverage
+.coverage.*
+.cache
+nosetests.xml
+coverage.xml
+*.cover
+*.py,cover
+.hypothesis/
+.pytest_cache/
+
+# Translations
+*.mo
+*.pot
+
+# Django stuff:
+*.log
+local_settings.py
+db.sqlite3
+db.sqlite3-journal
+
+# Flask stuff:
+instance/
+.webassets-cache
+
+# Scrapy stuff:
+.scrapy
+
+# Sphinx documentation
+docs/_build/
+
+# PyBuilder
+target/
+
+# Jupyter Notebook
+.ipynb_checkpoints
+
+# IPython
+profile_default/
+ipython_config.py
+
+# pyenv
+.python-version
+
+# pipenv
+#   According to pypa/pipenv#598, it is recommended to include Pipfile.lock in version control.
+#   However, in case of collaboration, if having platform-specific dependencies or dependencies
+#   having no cross-platform support, pipenv may install dependencies that don't work, or not
+#   install all needed dependencies.
+#Pipfile.lock
+
+# PEP 582; used by e.g. github.com/David-OConnor/pyflow
+__pypackages__/
+
+# Celery stuff
+celerybeat-schedule
+celerybeat.pid
+
+# SageMath parsed files
+*.sage.py
+
+# Environments
+.env
+.venv
+env/
+venv/
+ENV/
+env.bak/
+venv.bak/
+
+# Spyder project settings
+.spyderproject
+.spyproject
+
+# Rope project settings
+.ropeproject
+
+# mkdocs documentation
+/site
+
+# mypy
+.mypy_cache/
+.dmypy.json
+dmypy.json
+
+# Pyre type checker
+.pyre/

spotmax-1.0.3/.readthedocs.yaml

@@ -0,0 +1,19 @@
+version: "2"
+
+build:
+  os: "ubuntu-22.04"
+  tools:
+    python: "3.11"
+
+python:
+  install:
+    - requirements: spotmax/docs/requirements.txt
+    # Install our python package before building the docs
+    - method: pip
+      path: .
+
+sphinx:
+  configuration: spotmax/docs/source/conf.py
+
+formats:
+  - pdf