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Commit e358d4ab authored by florez_j's avatar florez_j
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    .gitignore
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    *.pyc *.pyc
    __pycache__/ __pycache__/
    *.h5 *.h5
    tmp_files/ tmp_files/
    *.ipynb *.ipynb
    logs/ logs/
    envs/ envs/
    hidden.py hidden.py
    output_files/ output_files/
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    .gitlab-ci.yml
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    pages: pages:
    stage: deploy stage: deploy
    script: script:
    - echo "Deploying pre-built HTML..." - echo "Deploying pre-built HTML..."
    - cp -r docs/build/html public # Copy the pre-built HTML to the public directory - cp -r docs/build/html public # Copy the pre-built HTML to the public directory
    artifacts: artifacts:
    paths: paths:
    - public - public
    only: only:
    changes: changes:
    - docs/source/** # Run only if files in docs/source/ change - docs/source/** # Run only if files in docs/source/ change
    - docs/Makefile - docs/Makefile
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    README.md
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    TODO.md
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    ## TODO ## TODO
    * Improve file reader for rga txt files (Talk to Thorsten). Example folder contains incosistent rga txt files, there is no unique column separator (, or ). * Improve file reader for rga txt files (Talk to Thorsten). Example folder contains incosistent rga txt files, there is no unique column separator (, or ).
    * Improve documentation of file reader extensions. Specify PY file reader template with expect input and output and file naming convention. * Improve documentation of file reader extensions. Specify PY file reader template with expect input and output and file naming convention.
    docs/Makefile
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    # Minimal makefile for Sphinx documentation # Minimal makefile for Sphinx documentation
    # #
    # You can set these variables from the command line, and also # You can set these variables from the command line, and also
    # from the environment for the first two. # from the environment for the first two.
    SPHINXOPTS ?= SPHINXOPTS ?=
    SPHINXBUILD ?= sphinx-build SPHINXBUILD ?= sphinx-build
    SOURCEDIR = source SOURCEDIR = source
    BUILDDIR = build BUILDDIR = build
    # Put it first so that "make" without argument is like "make help". # Put it first so that "make" without argument is like "make help".
    help: help:
    @$(SPHINXBUILD) -M help "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O) @$(SPHINXBUILD) -M help "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)
    .PHONY: help Makefile .PHONY: help Makefile
    # Catch-all target: route all unknown targets to Sphinx using the new # Catch-all target: route all unknown targets to Sphinx using the new
    # "make mode" option. $(O) is meant as a shortcut for $(SPHINXOPTS). # "make mode" option. $(O) is meant as a shortcut for $(SPHINXOPTS).
    %: Makefile %: Makefile
    @$(SPHINXBUILD) -M $@ "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O) @$(SPHINXBUILD) -M $@ "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)
    docs/build/html/.buildinfo
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    # Sphinx build info version 1 # Sphinx build info version 1
    # This file hashes the configuration used when building these files. When it is not found, a full rebuild will be done. # This file hashes the configuration used when building these files. When it is not found, a full rebuild will be done.
    config: 19124d911d3357bfa2d9f6131966b4c9 config: 19124d911d3357bfa2d9f6131966b4c9
    tags: 645f666f9bcd5a90fca523b33c5a78b7 tags: 645f666f9bcd5a90fca523b33c5a78b7
    docs/build/html/_modules/index.html
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    <!DOCTYPE html> <!DOCTYPE html>
    <html class="writer-html5" lang="en" data-content_root="../"> <html class="writer-html5" lang="en" data-content_root="../">
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    <meta name="viewport" content="width=device-width, initial-scale=1.0" /> <meta name="viewport" content="width=device-width, initial-scale=1.0" />
    <title>Overview: module code &mdash; DIMA 1.0.0 documentation</title> <title>Overview: module code &mdash; DIMA 1.0.0 documentation</title>
    <link rel="stylesheet" type="text/css" href="../_static/pygments.css?v=80d5e7a1" /> <link rel="stylesheet" type="text/css" href="../_static/pygments.css?v=80d5e7a1" />
    <link rel="stylesheet" type="text/css" href="../_static/css/theme.css?v=19f00094" /> <link rel="stylesheet" type="text/css" href="../_static/css/theme.css?v=19f00094" />
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    <script src="../_static/documentation_options.js?v=8d563738"></script> <script src="../_static/documentation_options.js?v=8d563738"></script>
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    <script src="../_static/sphinx_highlight.js?v=dc90522c"></script> <script src="../_static/sphinx_highlight.js?v=dc90522c"></script>
    <script crossorigin="anonymous" integrity="sha256-Ae2Vz/4ePdIu6ZyI/5ZGsYnb+m0JlOmKPjt6XZ9JJkA=" src="https://cdnjs.cloudflare.com/ajax/libs/require.js/2.3.4/require.min.js"></script> <script crossorigin="anonymous" integrity="sha256-Ae2Vz/4ePdIu6ZyI/5ZGsYnb+m0JlOmKPjt6XZ9JJkA=" src="https://cdnjs.cloudflare.com/ajax/libs/require.js/2.3.4/require.min.js"></script>
    <script src="../_static/js/theme.js"></script> <script src="../_static/js/theme.js"></script>
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    <p class="caption" role="heading"><span class="caption-text">Contents:</span></p> <p class="caption" role="heading"><span class="caption-text">Contents:</span></p>
    <ul> <ul>
    <li class="toctree-l1"><a class="reference internal" href="../modules/src.html">HDF5 Data Operations</a></li> <li class="toctree-l1"><a class="reference internal" href="../modules/src.html">HDF5 Data Operations</a></li>
    <li class="toctree-l1"><a class="reference internal" href="../modules/src.html#module-src.hdf5_writer">HDF5 Writer</a></li> <li class="toctree-l1"><a class="reference internal" href="../modules/src.html#module-src.hdf5_writer">HDF5 Writer</a></li>
    <li class="toctree-l1"><a class="reference internal" href="../modules/pipelines.html">Pipelines and workflows</a></li> <li class="toctree-l1"><a class="reference internal" href="../modules/pipelines.html">Pipelines and workflows</a></li>
    <li class="toctree-l1"><a class="reference internal" href="../modules/vis.html">Data Visualization</a></li> <li class="toctree-l1"><a class="reference internal" href="../modules/vis.html">Data Visualization</a></li>
    <li class="toctree-l1"><a class="reference internal" href="../modules/utils.html">Data Structure Conversion</a></li> <li class="toctree-l1"><a class="reference internal" href="../modules/utils.html">Data Structure Conversion</a></li>
    <li class="toctree-l1"><a class="reference internal" href="../modules/notebooks.html">Notebooks</a></li> <li class="toctree-l1"><a class="reference internal" href="../modules/notebooks.html">Notebooks</a></li>
    </ul> </ul>
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    <li class="breadcrumb-item active">Overview: module code</li> <li class="breadcrumb-item active">Overview: module code</li>
    <li class="wy-breadcrumbs-aside"> <li class="wy-breadcrumbs-aside">
    </li> </li>
    </ul> </ul>
    <hr/> <hr/>
    </div> </div>
    <div role="main" class="document" itemscope="itemscope" itemtype="http://schema.org/Article"> <div role="main" class="document" itemscope="itemscope" itemtype="http://schema.org/Article">
    <div itemprop="articleBody"> <div itemprop="articleBody">
    <h1>All modules for which code is available</h1> <h1>All modules for which code is available</h1>
    <ul><li><a href="pipelines/data_integration.html">pipelines.data_integration</a></li> <ul><li><a href="pipelines/data_integration.html">pipelines.data_integration</a></li>
    <li><a href="pipelines/metadata_revision.html">pipelines.metadata_revision</a></li> <li><a href="pipelines/metadata_revision.html">pipelines.metadata_revision</a></li>
    <li><a href="src/hdf5_ops.html">src.hdf5_ops</a></li> <li><a href="src/hdf5_ops.html">src.hdf5_ops</a></li>
    <li><a href="src/hdf5_writer.html">src.hdf5_writer</a></li> <li><a href="src/hdf5_writer.html">src.hdf5_writer</a></li>
    <li><a href="utils/g5505_utils.html">utils.g5505_utils</a></li> <li><a href="utils/g5505_utils.html">utils.g5505_utils</a></li>
    <li><a href="visualization/hdf5_vis.html">visualization.hdf5_vis</a></li> <li><a href="visualization/hdf5_vis.html">visualization.hdf5_vis</a></li>
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    docs/build/html/_sources/index.rst.txt
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    .. DIMA documentation master file, created by .. DIMA documentation master file, created by
    sphinx-quickstart on Wed Jul 10 15:50:06 2024. sphinx-quickstart on Wed Jul 10 15:50:06 2024.
    You can adapt this file completely to your liking, but it should at least You can adapt this file completely to your liking, but it should at least
    contain the root `toctree` directive. contain the root `toctree` directive.
    Welcome to DIMA's documentation! Welcome to DIMA's documentation!
    ================================ ================================
    .. toctree:: .. toctree::
    :maxdepth: 2 :maxdepth: 2
    :caption: Contents: :caption: Contents:
    modules/src modules/src
    modules/pipelines modules/pipelines
    modules/vis modules/vis
    modules/utils modules/utils
    modules/notebooks modules/notebooks
    Indices and tables Indices and tables
    ================== ==================
    * :ref:`genindex` * :ref:`genindex`
    * :ref:`modindex` * :ref:`modindex`
    * :ref:`search` * :ref:`search`
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