Merge branch 'develop' of https://github.com/snaeimi/pelicun into dev…

…elop

.github/workflows/build_docs.yaml

@@ -2,7 +2,7 @@ name: Build and deploy documentation
 on:
   push:
     branches:
-      - docs
+      - master
 jobs:
   build-docs:
     runs-on: ${{ matrix.os }}

.github/workflows/deploy_to_pypi.yaml

@@ -5,6 +5,8 @@ on:
 jobs:
   deploy:
     runs-on: ubuntu-latest
+    permissions:
+      id-token: write
     steps:
       - name: Check out code
         uses: actions/checkout@v4
@@ -24,5 +26,4 @@ jobs:
       - name: Publish package to PyPI
         uses: pypa/gh-action-pypi-publish@release/v1
         with:
-          user: zsarnoczay
-          password: ${{ secrets.PELICUN_GITHUB_TOKEN }}
+          # use trusted publisher, no password needed

.github/workflows/docs_check.yaml

@@ -12,8 +12,8 @@ jobs:
     steps:
     - name: Check out the repository
       uses: actions/checkout@v4
-        with:
-          submodules: true
+      with:
+        submodules: true
     - name: Set up Python
       uses: actions/setup-python@v4
       with:

.github/workflows/spell_check.yml

@@ -6,7 +6,7 @@ jobs:
     steps:
     - name: Checkout code
       uses: actions/checkout@v4
-        with:
-          submodules: true
+      with:
+        submodules: true
     - name: Run codespell
       uses: codespell-project/actions-codespell@v2

doc/source/_static/hide_empty_pre.js

@@ -0,0 +1,13 @@
+document.addEventListener("DOMContentLoaded", function() {
+    document.querySelectorAll('div.nboutput.docutils.container').forEach(function(div) {
+        // Our objective is to hide all `div` elements of which all
+        // children elements only contain whitespace.
+        // This remedies the nbsphinx issue where an extra newline was
+        // added to each line in the code block output.
+        let isEmpty = Array.from(div.children).every(child => !child.textContent.trim());
+
+        if (isEmpty) {
+            div.style.display = 'none';
+        }
+    });
+});

doc/source/conf.py

@@ -60,6 +60,7 @@
 html_static_path = ['_static']
 
 html_css_files = ['css/custom.css']
+html_js_files = ['hide_empty_pre.js']
 
 # List of patterns, relative to source directory, that match files and
 # directories to ignore when looking for source files.

doc/source/developer_guide/development_environment.rst

@@ -8,6 +8,18 @@ Setting up a development environment
    We recommend creating a dedicated `virtual environment <https://docs.python.org/3/library/venv.html>`_ for your pelicun development environment.
    See also `conda <https://docs.conda.io/en/latest/>`_ and `mamba <https://mamba.readthedocs.io/en/latest/>`_, two widely used programs featuring environment management.
 
+Clone the repository::
+
+  git clone --recurse-submodules https://github.com/NHERI-SimCenter/pelicun
+
+Pelicun uses the SimCenter `DamageAndLossModelLibrary <https://github.com/NHERI-SimCenter/DamageAndLossModelLibrary>`_ as a submodule.
+In the above, ``recurse-submodules`` ensures that all files of that repository are also obtained.
+
+.. tip::
+
+   If you are planning to contribute code, please `fork the repository <https://github.com/NHERI-SimCenter/pelicun/fork>`_ and clone your own fork.
+
+
 Install pelicun in editable mode with the following command issued from the package's root directory::
 
   python -m pip install -e .[development]

doc/source/examples/index.rst

@@ -14,59 +14,29 @@ Pelicun examples are listed in the following index.
    Increasing the set of examples is a very high priority.
    Please come back soon!
 
-Complete list
--------------
-
 +-----------+---------------------------------------------------------+
 |Example    |Description                                              |
 +===========+=========================================================+
-|`E1`_      |This example demonstrates the seismic performance        |
-|           |assessment of a steel moment frame structure using the   |
-|           |FEMA P-58 methodology.                                   |
+|`E1`_      |Example of a simple assessment involving a single loss   |
+|           |function. The example and associated input files can be  |
+|           |easily extended to include more loss functions and input |
+|           |demands.                                                 |
++-----------+---------------------------------------------------------+
+|`E2`_      |Example validating the estimated damage state            |
+|           |probabilities of a single component.                     |
++-----------+---------------------------------------------------------+
+|`E3`_      |A loss assessment combining fragility-based damage       |
+|           |consequences and loss functions.                         |
 +-----------+---------------------------------------------------------+
-
-Grouped by feature
-------------------
-
-The following sections group the examples above based on the specific features they illustrate, helping you pick the ones most relevant to what you are looking for.
-
-.. dropdown:: Asset type
-
-   +------------------------------------------------------+---------------------------------------------------------+
-   |Feature                                               |Examples                                                 |
-   +======================================================+=========================================================+
-   |Building                                              |`E1`_                                                    |
-   +------------------------------------------------------+---------------------------------------------------------+
-
-.. dropdown:: Demand Simulation
-
-   +------------------------------------------------------+---------------------------------------------------------+
-   |Feature                                               |Examples                                                 |
-   +======================================================+=========================================================+
-   |:ref:`Model calibration <fo_calibration>`             |`E1`_                                                    |
-   +------------------------------------------------------+---------------------------------------------------------+
-   |:ref:`RID|PID inference <fo_pidrid>`                  |`E1`_                                                    |
-   +------------------------------------------------------+---------------------------------------------------------+
-   |:ref:`Sample expansion <fo_sample_expansion>`         |`E1`_                                                    |
-   +------------------------------------------------------+---------------------------------------------------------+
-
-
-.. dropdown:: Loss estimation
-
-   +------------------------------------------------------+---------------------------------------------------------+
-   |Feature                                               |Examples                                                 |
-   +======================================================+=========================================================+
-   |:ref:`Loss maps <fo_loss_maps>`                       |`E1`_                                                    |
-   +------------------------------------------------------+---------------------------------------------------------+
-   |:ref:`Active decision variables <fo_active_dvs>`      |`E1`_                                                    |
-   +------------------------------------------------------+---------------------------------------------------------+
-   |:ref:`Loss aggregation <fo_loss_aggregation>`         |`E1`_                                                    |
-   +------------------------------------------------------+---------------------------------------------------------+
 
 .. toctree::
    :maxdepth: 1
    :hidden:
 
    notebooks/example_1.pct.py
+   notebooks/example_2.pct.py
+   notebooks/example_3.pct.py
 
 .. _E1: notebooks/example_1.pct.py
+.. _E2: notebooks/example_2.pct.py
+.. _E3: notebooks/example_3.pct.py