Merge pull request #94 from NHERI-SimCenter/develop

Merging develop into master as we are preparing for the v3.5 release

.github/workflows/build_docs.yaml

@@ -12,8 +12,9 @@ jobs:
         os: [ubuntu-latest]
         python-version: ['3.10']
     steps:
-      - uses: actions/checkout@v3
-      - name: Set up Python ${{ matrix.python-version }}
+      - uses: actions/checkout@v4
+        with:
+          submodules: true
         uses: actions/setup-python@v3
         with:
           python-version: ${{ matrix.python-version }}

.github/workflows/deploy_to_pypi.yaml

@@ -1,32 +1,29 @@
 name: Deploy to PyPI
-
 on:
   release:
     types: [created]
-
 jobs:
   deploy:
     runs-on: ubuntu-latest
+    permissions:
+      id-token: write
     steps:
       - name: Check out code
-        uses: actions/checkout@v3
-
+        uses: actions/checkout@v4
+        with:
+          submodules: true
       - name: Set up Python
         uses: actions/setup-python@v3
         with:
           python-version: '3.10'
-
       - name: Install dependencies
         run: |
           python -m pip install --upgrade pip
           python -m pip install setuptools wheel twine
-
       - name: Build package
         run: |
           python setup.py sdist bdist_wheel
-
       - 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

@@ -1,32 +1,28 @@
 name: Check for Sphinx Warnings
-
 on:
   pull_request:
     paths:
       - "doc/**"
       - "**/*.rst"
       - ".github/workflows/docs_check.yaml"
       - "setup.py"
-
 jobs:
   build:
     runs-on: ubuntu-latest
-
     steps:
     - name: Check out the repository
-      uses: actions/checkout@v3
-
+      uses: actions/checkout@v4
+      with:
+        submodules: true
     - name: Set up Python
       uses: actions/setup-python@v4
       with:
         python-version: '3.x'
-
     - name: Install dependencies
       run: |
           sudo apt-get update
           sudo apt-get install -y pandoc
           python -m pip install -e .[development]
-
     - name: Check for Sphinx warnings
       run: |
         sphinx-build -M html ./doc/source ./doc/_build --fail-on-warning

.github/workflows/format_check.yml

@@ -5,6 +5,8 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - uses: actions/checkout@v4
+        with:
+          submodules: true
       - uses: chartboost/ruff-action@v1
         with:
           args: 'format --check'

.github/workflows/lint.yml

@@ -5,6 +5,8 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - uses: actions/checkout@v4
+        with:
+          submodules: true
       - uses: chartboost/ruff-action@v1
         with:
           version: 0.7.0

.github/workflows/spell_check.yml

@@ -1,15 +1,12 @@
 name: Spell Check
-
 on: [push, pull_request]
-
 jobs:
   spell-check:
     runs-on: ubuntu-latest
-
     steps:
     - name: Checkout code
-      uses: actions/checkout@v2
-
+      uses: actions/checkout@v4
+      with:
+        submodules: true
     - name: Run codespell
       uses: codespell-project/actions-codespell@v2
-

.github/workflows/tests.yml

@@ -1,9 +1,7 @@
 name: Tests
-
 on:
   - push
   - pull_request
-
 jobs:
   test:
     runs-on: ${{ matrix.os }}
@@ -12,7 +10,9 @@ jobs:
         os: [ubuntu-latest, windows-latest, macos-latest]
         python-version: ['3.9', '3.10', '3.11','3.12']
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v4
+        with:
+          submodules: true
       - name: Set up Python ${{ matrix.python-version }}
         uses: actions/setup-python@v2
         with:

pelicun/assessment.py

@@ -63,14 +63,18 @@
         'Hazus Earthquake - Stories': 'damage_DB_Hazus_EQ_story.csv',
         'Hazus Earthquake - Transportation': 'damage_DB_Hazus_EQ_trnsp.csv',
         'Hazus Earthquake - Water': 'damage_DB_Hazus_EQ_water.csv',
+        'Hazus Earthquake - Power': 'damage_DB_Hazus_EQ_power.csv',
         'Hazus Hurricane': 'damage_DB_SimCenter_Hazus_HU_bldg.csv',
     },
     'repair': {
         'FEMA P-58': 'loss_repair_DB_FEMA_P58_2nd.csv',
         'Hazus Earthquake - Buildings': 'loss_repair_DB_Hazus_EQ_bldg.csv',
         'Hazus Earthquake - Stories': 'loss_repair_DB_Hazus_EQ_story.csv',
         'Hazus Earthquake - Transportation': 'loss_repair_DB_Hazus_EQ_trnsp.csv',
-        'Hazus Hurricane': 'loss_repair_DB_SimCenter_Hazus_HU_bldg.csv',
+        'Hazus Hurricane': (
+            'loss_repair_DB_SimCenter_Hazus_HU_bldg.csv,'
+            'loss_repair_DB_Hazus_FL_bldg.csv'
+        ),
     },
 }
 
@@ -218,7 +222,10 @@ def get_default_data(self, data_name: str) -> pd.DataFrame:
                 'Please use `loss_repair_DB` instead.'
             )
 
-        data_path = f'{base.pelicun_path}/resources/SimCenterDBDL/{data_name}.csv'
+        data_path = file_io.substitute_default_path(
+            [f'PelicunDefault/{data_name}.csv']
+        )[0]
+        assert isinstance(data_path, str)
 
         data = file_io.load_data(
             data_path, None, orientation=1, reindex=False, log=self.log
@@ -249,7 +256,10 @@ def get_default_metadata(self, data_name: str) -> dict:
                 '`fragility_DB` is deprecated and will be dropped in '
                 'future versions of pelicun. Please use `damage_DB` instead.'
             )
-        data_path = f'{base.pelicun_path}/resources/SimCenterDBDL/{data_name}.json'
+        data_path = file_io.substitute_default_path(
+            [f'PelicunDefault/{data_name}.json']
+        )[0]
+        assert isinstance(data_path, str)
 
         with Path(data_path).open(encoding='utf-8') as f:
             data = json.load(f)
@@ -963,7 +973,10 @@ def calculate_damage(  # noqa: C901
         # load the fragility information
         if component_database in default_dbs['fragility']:
             component_db = [
-                'PelicunDefault/' + default_dbs['fragility'][component_database],
+                'PelicunDefault/' + filename
+                for filename in default_dbs['fragility'][component_database].split(
+                    ','
+                )
             ]
         else:
             component_db = []
@@ -1253,6 +1266,10 @@ def calculate_loss(
         replacement_energy_parameters: dict[str, float | str] | None = None,
         loss_map_path: str | None = None,
         decision_variables: tuple[str, ...] | None = None,
+        replacement_configuration: (
+            tuple[uq.RandomVariableRegistry, dict[str, float]] | None
+        ) = None,
+        loss_combination_method: str | None = None,
     ) -> tuple[pd.DataFrame, pd.DataFrame]:
         """
         Calculate losses.
@@ -1284,6 +1301,11 @@ def calculate_loss(
             Optional path to a loss map file.
         decision_variables: tuple[str] or None
             Optional decision variables for the assessment.
+        replacement_configuration: tuple or None
+            Loss thresholds of replacement consequences.
+        loss_combination_method: str, optional
+            String defining the method to use for combining losses for
+            components that represent different demands.
 
         Returns
         -------
@@ -1389,7 +1411,40 @@ def calculate_loss(
 
         self.loss.calculate()
 
-        df_agg, exceedance_bool_df = self.loss.aggregate_losses(future=True)
+        if loss_combination_method is None:
+            loss_combination = None
+
+        elif loss_combination_method == 'Hazus Hurricane':
+            # assemble the combination dict for wind and storm surge
+            # open the base combination matrix
+            file_path = file_io.substitute_default_path(
+                ['PelicunDefault/Wind_Flood_Hazus_HU_bldg.csv']
+            )[0]
+            assert isinstance(file_path, str)
+            combination_array = pd.read_csv(
+                file_path,
+                index_col=None,
+                header=None,
+            ).to_numpy()
+
+            # get the component names
+            # assume that the first and second component in the loss map
+            # are the wind and flood components, respectively
+            wind_comp, flood_comp = loss_map.index.to_numpy()[[0, 1]]
+
+            loss_combination = {
+                'Cost': {
+                    (wind_comp, flood_comp): combination_array,
+                },
+            }
+
+        else:
+            msg = f'Invalid loss combination method: `{loss_combination_method}`.'
+            raise ValueError(msg)
+
+        df_agg, exceedance_bool_df = self.loss.aggregate_losses(
+            replacement_configuration, loss_combination, future=True
+        )
         assert isinstance(df_agg, pd.DataFrame)
         assert isinstance(exceedance_bool_df, pd.DataFrame)
         return df_agg, exceedance_bool_df
@@ -1426,12 +1481,19 @@ def load_consequence_info(
 
         """
         if consequence_database in default_dbs['repair']:
+            default_consequence_dbs = default_dbs['repair'][
+                consequence_database
+            ].split(',')
+
             consequence_db = [
-                'PelicunDefault/' + default_dbs['repair'][consequence_database],
+                'PelicunDefault/' + filename for filename in default_consequence_dbs
             ]
 
-            conseq_df = self.get_default_data(
-                default_dbs['repair'][consequence_database][:-4]
+            conseq_df = pd.concat(
+                [
+                    self.get_default_data(filename[:-4])
+                    for filename in default_consequence_dbs
+                ]
             )
         else:
             consequence_db = []
@@ -1902,11 +1964,13 @@ def _loss__map_auto(
     """
     # get the damage sample
     dmg_sample = assessment.damage.save_sample()
+    asset_sample = assessment.asset.save_cmp_sample()
     assert isinstance(dmg_sample, pd.DataFrame)
+    assert isinstance(asset_sample, pd.DataFrame)
 
     # create a mapping for all components that are also in
     # the prescribed consequence database
-    dmg_cmps = dmg_sample.columns.unique(level='cmp')
+    asset_cmps = asset_sample.columns.unique(level='cmp')
     loss_cmps = conseq_df.index.unique(level=0)
 
     drivers = []
@@ -1916,32 +1980,32 @@ def _loss__map_auto(
         # with these methods, we assume fragility and consequence data
         # have the same IDs
 
-        for dmg_cmp in dmg_cmps:
-            if dmg_cmp == 'collapse':
+        for asset_cmp in asset_cmps:
+            if asset_cmp == 'collapse':
                 continue
 
-            if dmg_cmp in loss_cmps:
-                drivers.append(dmg_cmp)
-                loss_models.append(dmg_cmp)
+            if asset_cmp in loss_cmps:
+                drivers.append(asset_cmp)
+                loss_models.append(asset_cmp)
 
     elif dl_method in {
         'Hazus Earthquake',
         'Hazus Earthquake Transportation',
     }:
         # with Hazus Earthquake we assume that consequence
         # archetypes are only differentiated by occupancy type
-        for dmg_cmp in dmg_cmps:
-            if dmg_cmp == 'collapse':
+        for asset_cmp in asset_cmps:
+            if asset_cmp == 'collapse':
                 continue
 
-            cmp_class = dmg_cmp.split('.')[0]
+            cmp_class = asset_cmp.split('.')[0]
             if occupancy_type is not None:
                 loss_cmp = f'{cmp_class}.{occupancy_type}'
             else:
                 loss_cmp = cmp_class
 
             if loss_cmp in loss_cmps:
-                drivers.append(dmg_cmp)
+                drivers.append(asset_cmp)
                 loss_models.append(loss_cmp)
 
     return pd.DataFrame(loss_models, columns=['Repair'], index=drivers)