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diff --git a/.buildinfo b/.buildinfo
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+# Sphinx build info version 1
+# This file records the configuration used when building these files. When it is not found, a full rebuild will be done.
+config: e2c36d49dfbfe6a435adb30b39dee074
+tags: 645f666f9bcd5a90fca523b33c5a78b7
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diff --git a/_modules/probinet/evaluation/covariate_prediction.html b/_modules/probinet/evaluation/covariate_prediction.html
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diff --git a/_modules/probinet/evaluation/likelihood.html b/_modules/probinet/evaluation/likelihood.html
diff --git a/_modules/probinet/evaluation/link_prediction.html b/_modules/probinet/evaluation/link_prediction.html
diff --git a/_modules/probinet/input/loader.html b/_modules/probinet/input/loader.html
diff --git a/_modules/probinet/input/preprocessing.html b/_modules/probinet/input/preprocessing.html
diff --git a/_modules/probinet/input/stats.html b/_modules/probinet/input/stats.html
diff --git a/_modules/probinet/main.html b/_modules/probinet/main.html
diff --git a/_modules/probinet/model_selection/acd_cross_validation.html b/_modules/probinet/model_selection/acd_cross_validation.html
diff --git a/_modules/probinet/model_selection/crep_cross_validation.html b/_modules/probinet/model_selection/crep_cross_validation.html
diff --git a/_modules/probinet/model_selection/cross_validation.html b/_modules/probinet/model_selection/cross_validation.html
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diff --git a/_modules/probinet/model_selection/jointcrep_cross_validation.html b/_modules/probinet/model_selection/jointcrep_cross_validation.html
diff --git a/_modules/probinet/model_selection/main.html b/_modules/probinet/model_selection/main.html
diff --git a/_modules/probinet/model_selection/masking.html b/_modules/probinet/model_selection/masking.html
diff --git a/_modules/probinet/model_selection/mtcov_cross_validation.html b/_modules/probinet/model_selection/mtcov_cross_validation.html
diff --git a/_modules/probinet/model_selection/parameter_search.html b/_modules/probinet/model_selection/parameter_search.html
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diff --git a/_modules/probinet/models/base.html b/_modules/probinet/models/base.html
diff --git a/_modules/probinet/models/crep.html b/_modules/probinet/models/crep.html
diff --git a/_modules/probinet/models/dyncrep.html b/_modules/probinet/models/dyncrep.html
diff --git a/_modules/probinet/models/jointcrep.html b/_modules/probinet/models/jointcrep.html
diff --git a/_modules/probinet/models/mtcov.html b/_modules/probinet/models/mtcov.html
diff --git a/_modules/probinet/synthetic/anomaly.html b/_modules/probinet/synthetic/anomaly.html
diff --git a/_modules/probinet/synthetic/base.html b/_modules/probinet/synthetic/base.html
diff --git a/_modules/probinet/synthetic/dynamic.html b/_modules/probinet/synthetic/dynamic.html
diff --git a/_modules/probinet/synthetic/multilayer.html b/_modules/probinet/synthetic/multilayer.html
diff --git a/_modules/probinet/synthetic/reciprocity.html b/_modules/probinet/synthetic/reciprocity.html
diff --git a/_modules/probinet/utils/matrix_operations.html b/_modules/probinet/utils/matrix_operations.html
diff --git a/_modules/probinet/utils/tools.html b/_modules/probinet/utils/tools.html
diff --git a/_modules/probinet/visualization/plot.html b/_modules/probinet/visualization/plot.html
diff --git a/_sources/api.rst b/_sources/api.rst
@@ -0,0 +1,49 @@
+API
+---
+
+.. autosummary::
+   :toctree: generated
+
+    probinet.evaluation
+    probinet.evaluation.community_detection
+    probinet.evaluation.covariate_prediction
+    probinet.evaluation.expectation_computation
+    probinet.evaluation.likelihood
+    probinet.evaluation.link_prediction
+    probinet.input
+    probinet.input.loader
+    probinet.input.preprocessing
+    probinet.input.stats
+    probinet.main
+    probinet.model_selection
+    probinet.model_selection.acd_cross_validation
+    probinet.model_selection.crep_cross_validation
+    probinet.model_selection.cross_validation
+    probinet.model_selection.dyncrep_cross_validation
+    probinet.model_selection.jointcrep_cross_validation
+    probinet.model_selection.main
+    probinet.model_selection.masking
+    probinet.model_selection.mtcov_cross_validation
+    probinet.model_selection.parameter_search
+    probinet.models
+    probinet.models.acd
+    probinet.models.base
+    probinet.models.classes
+    probinet.models.constants
+    probinet.models.crep
+    probinet.models.dyncrep
+    probinet.models.jointcrep
+    probinet.models.mtcov
+    probinet.synthetic
+    probinet.synthetic.anomaly
+    probinet.synthetic.base
+    probinet.synthetic.dynamic
+    probinet.synthetic.multilayer
+    probinet.synthetic.reciprocity
+    probinet.utils
+    probinet.utils.matrix_operations
+    probinet.utils.tools
+    probinet.version
+    probinet.visualization
+    probinet.visualization.plot
+
diff --git a/_sources/contributing.rst b/_sources/contributing.rst
@@ -0,0 +1,123 @@
+Contributing
+============
+
+Thank you for your interest in contributing to **ProbINet**! Your contributions help improve the
+package and make it more useful for everyone. Please follow the steps below to get started.
+
+Getting Started
+---------------
+
+- Fork this repository to your GitHub account: `https://github.com/MPI-IS/probinet <https://github.com/MPI-IS/probinet>`_. You can fork it by clicking the "Fork" button in the top-right corner of the page.
+- Clone the forked repository to your local machine:
+
+  .. code-block:: bash
+
+     git clone https://github.com/<your-username>/probinet.git
+
+- Navigate to the project directory:
+
+  .. code-block:: bash
+
+     cd probinet
+
+- Add the original repository as a remote named ``upstream`` to keep your fork updated:
+
+  .. code-block:: bash
+
+     git remote add upstream https://github.com/MPI-IS/probinet.git
+
+Setting Up the Development Environment
+--------------------------------------
+
+This project uses ``pyproject.toml`` for dependency management. To set up a development environment:
+
+- Install the package with the ``.dev`` flag:
+
+  .. code-block:: bash
+
+     pip install ".[dev]"
+
+- Verify the installation by running the following command:
+
+  .. code-block:: bash
+
+     pip show probinet
+
+If the package is installed, this will display details about it, such as the version and installation location.
+
+Syncing Your Fork
+-----------------
+
+Before starting work on a new feature or bug fix, ensure your fork is up to date with the original repository:
+
+- Fetch the latest changes from the ``upstream`` repository:
+
+  .. code-block:: bash
+
+     git fetch upstream
+
+- Update your local ``main`` branch:
+
+  .. code-block:: bash
+
+     git checkout main
+     git merge upstream/main
+
+Making Changes
+--------------
+
+- Create a new branch for your contribution:
+
+  .. code-block:: bash
+
+     git checkout -b feature/your-feature-name
+
+- Make your changes in this branch. Ensure the code is:
+
+  - Well-documented.
+  - Aligned with the existing code style.
+
+- Add or update unit tests for your changes. You can see the existing tests in the ``tests`` directory.
+
+Running Tests
+-------------
+
+Tests are written using Python's built-in ``unittest`` framework.
+
+- Run all tests to verify your changes:
+
+  .. code-block:: bash
+
+     python -W ignore -m unittest discover
+
+Submitting Your Contribution
+----------------------------
+
+- Commit your changes with a clear and concise message:
+
+  .. code-block:: bash
+
+     git commit -m "Add description of your changes"
+
+- Push your changes to your fork:
+
+  .. code-block:: bash
+
+     git push origin feature/your-feature-name
+
+- Open a Pull Request (PR) to the **original repository**. Include:
+
+  - A detailed explanation of your changes.
+  - The issue number your PR addresses (if applicable).
+  - Any additional context or screenshots.
+
+  You can view all open and merged Pull Requests `here <https://github.com/MPI-IS/probinet/pulls>`_.
+
+
+Code of Conduct
+---------------
+
+By contributing to this repository, you agree to follow our `Code of Conduct
+<https://policies.python.org/python.org/code-of-conduct/>`_.
+
+We appreciate your contributions and will review your Pull Request promptly!
diff --git a/_sources/generated/probinet.evaluation.community_detection.rst b/_sources/generated/probinet.evaluation.community_detection.rst
@@ -0,0 +1,15 @@
+probinet.evaluation.community\_detection
+========================================
+
+.. automodule:: probinet.evaluation.community_detection
+
+
+   .. rubric:: Functions
+
+   .. autosummary::
+
+      calculate_metric
+      compute_community_detection_metric
+      compute_permutation_matrix
+      cosine_similarity
+
diff --git a/_sources/generated/probinet.evaluation.covariate_prediction.rst b/_sources/generated/probinet.evaluation.covariate_prediction.rst
@@ -0,0 +1,14 @@
+probinet.evaluation.covariate\_prediction
+=========================================
+
+.. automodule:: probinet.evaluation.covariate_prediction
+
+
+   .. rubric:: Functions
+
+   .. autosummary::
+
+      compute_covariate_prediction_accuracy
+      extract_true_label
+      predict_label
+
diff --git a/_sources/generated/probinet.evaluation.expectation_computation.rst b/_sources/generated/probinet.evaluation.expectation_computation.rst
@@ -0,0 +1,27 @@
+probinet.evaluation.expectation\_computation
+============================================
+
+.. automodule:: probinet.evaluation.expectation_computation
+
+
+   .. rubric:: Functions
+
+   .. autosummary::
+
+      calculate_Q_dense
+      calculate_Z
+      calculate_conditional_expectation
+      calculate_conditional_expectation_dyncrep
+      calculate_expectation
+      calculate_expectation_acd
+      compute_L1loss
+      compute_M_joint
+      compute_expected_adjacency_tensor
+      compute_expected_adjacency_tensor_multilayer
+      compute_lagrange_multiplier
+      compute_marginal_and_conditional_expectation
+      compute_mean_lambda0
+      compute_mean_lambda0_dyncrep
+      compute_mean_lambda0_nonzero
+      u_with_lagrange_multiplier
+
diff --git a/_sources/generated/probinet.evaluation.likelihood.rst b/_sources/generated/probinet.evaluation.likelihood.rst
@@ -0,0 +1,18 @@
+probinet.evaluation.likelihood
+==============================
+
+.. automodule:: probinet.evaluation.likelihood
+
+
+   .. rubric:: Functions
+
+   .. autosummary::
+
+      PSloglikelihood
+      calculate_opt_func
+      likelihood_conditional
+      log_likelihood_given_model
+      loglikelihood
+      loglikelihood_attributes
+      loglikelihood_network
+
diff --git a/_sources/generated/probinet.evaluation.link_prediction.rst b/_sources/generated/probinet.evaluation.link_prediction.rst
@@ -0,0 +1,16 @@
+probinet.evaluation.link\_prediction
+====================================
+
+.. automodule:: probinet.evaluation.link_prediction
+
+
+   .. rubric:: Functions
+
+   .. autosummary::
+
+      calculate_f1_score
+      compute_AUC_from_ranked_predictions
+      compute_link_prediction_AUC
+      compute_multilayer_link_prediction_AUC
+      mask_or_flatten_array
+
diff --git a/_sources/generated/probinet.evaluation.rst b/_sources/generated/probinet.evaluation.rst
@@ -0,0 +1,6 @@
+probinet.evaluation
+===================
+
+.. automodule:: probinet.evaluation
+
+
diff --git a/_sources/generated/probinet.input.loader.rst b/_sources/generated/probinet.input.loader.rst
@@ -0,0 +1,17 @@
+probinet.input.loader
+=====================
+
+.. automodule:: probinet.input.loader
+
+
+   .. rubric:: Functions
+
+   .. autosummary::
+
+      build_adjacency_and_design_from_file
+      build_adjacency_from_file
+      build_adjacency_from_networkx
+      read_and_process_design_matrix
+      read_design_matrix
+      read_graph
+
diff --git a/_sources/generated/probinet.input.preprocessing.rst b/_sources/generated/probinet.input.preprocessing.rst
@@ -0,0 +1,15 @@
+probinet.input.preprocessing
+============================
+
+.. automodule:: probinet.input.preprocessing
+
+
+   .. rubric:: Functions
+
+   .. autosummary::
+
+      create_adjacency_tensor_from_graph_list
+      create_sparse_adjacency_tensor_from_graph_list
+      preprocess_adjacency_tensor
+      preprocess_data_matrix
+
diff --git a/_sources/generated/probinet.input.rst b/_sources/generated/probinet.input.rst
@@ -0,0 +1,6 @@
+probinet.input
+==============
+
+.. automodule:: probinet.input
+
+
diff --git a/_sources/generated/probinet.input.stats.rst b/_sources/generated/probinet.input.stats.rst
@@ -0,0 +1,14 @@
+probinet.input.stats
+====================
+
+.. automodule:: probinet.input.stats
+
+
+   .. rubric:: Functions
+
+   .. autosummary::
+
+      print_graph_stats
+      print_graph_stats_MTCOV
+      reciprocal_edges
+
diff --git a/_sources/generated/probinet.main.rst b/_sources/generated/probinet.main.rst
@@ -0,0 +1,13 @@
+probinet.main
+=============
+
+.. automodule:: probinet.main
+
+
+   .. rubric:: Functions
+
+   .. autosummary::
+
+      main
+      parse_args
+
diff --git a/_sources/generated/probinet.model_selection.acd_cross_validation.rst b/_sources/generated/probinet.model_selection.acd_cross_validation.rst
@@ -0,0 +1,12 @@
+probinet.model\_selection.acd\_cross\_validation
+================================================
+
+.. automodule:: probinet.model_selection.acd_cross_validation
+
+
+   .. rubric:: Classes
+
+   .. autosummary::
+
+      ACDCrossValidation
+
diff --git a/_sources/generated/probinet.model_selection.crep_cross_validation.rst b/_sources/generated/probinet.model_selection.crep_cross_validation.rst
@@ -0,0 +1,12 @@
+probinet.model\_selection.crep\_cross\_validation
+=================================================
+
+.. automodule:: probinet.model_selection.crep_cross_validation
+
+
+   .. rubric:: Classes
+
+   .. autosummary::
+
+      CRepCrossValidation
+