merge and close CoV_xml branch (#79)

[NicoleA-GA]

• including cov.csv

• merge master into CoV_xml branch (merge master into CoV_xml branch #78)

• Version 1.1 release

• Fix failing tests

• rc1.1 (rc1.1 #52)

• Add categorisation and tabulation (pivot table)

• TCRM-47: Implemented S3 download and upload functionality.

• WIP: Asset count in defined damage states for aggregated output

• Calculate percentages in damage state table

• NHIRS-15: Add NRML schema from https://github.com/gem/oq-nrmllib/tree/master/openquake/nrmllib/schema (NHIRS-15: Add NRML schema from https://github.com/gem/oq-nrmllib/tree… #29)

• NHIRS-14: Add XML schema validation, validate vulnerability curves against NRLM schema; update vulnerability curves to match NRML schema; update unit tests; update create_vuln_xml.py to generate XML conforming to NRML schema

• NHIRS-9: Add unit tests for creation of choropleth aggregation

• NHIRS-9: Default output format for spatial aggregation

• NHIRS-10: Add support for configuring choropleth aggregation fields (NHIRS-10: Add support for configuring choropleth aggregation fields #32)

• Move PEP8 conformance test into tests module, and fix E501 failures

• Add aggregation functions to provenance statement

• add domesitc eq vulnerability curves in MMI (add domesitc eq vulnerability curves in MMI  #35)

• NHIRS-22: Increase unit test coverage (NHIRS-22: Increase unit test coverage #36)

• Update to NRML 0.5 (Update to NRML 0.5 #38)

• NHIRS-18 - Initial Earthquake template with example (NHIRS-18 - Initial Earthquake template with example #39)

• NHIRS-18: Split templates into new module separated by hazard type

• NHIRS-8 - Improve memory usage for large raster input (NHIRS-8 - Improve memory usage for large raster input #41)

• NHIRS-54: Change default aggregate output format to GeoJSON (NHIRS-54: Change default aggregate output format to GeoJSON #42)

• NHIRS-58: Add domestic_wind_vul_curves_2021.xml to resources folder

• NHIRS-92: Support multiple aggregate output formats

• Update hazimp-tests.yml to test with range of python versions

• Categorise aggregated features (Categorise aggregated features #49)

• NHIRS-48: Add and test categorisation of aggregated fields

• NHIRS-48: Update unit tests

• NHIRS-48: Improve Shapefile labelling of categorised damage state

• Update provenance connections between activities

• Calculate "worst-case" loss by permution of exposure

• Documentation updates

• Update config requirements

• Add requirements.txt

• Example config includes count of damage states

• Add time info to log messages

• Add image for cov of vulnerability

• Add lower quantile for permutations (Add lower quantile for permutations #56)

• Update docs to reflect range of percentiles in permutation

• Version 1.2 (Version 1.2 #58)

• NHIRS-15: Add NRML schema from https://github.com/gem/oq-nrmllib/tree/master/openquake/nrmllib/schema (NHIRS-15: Add NRML schema from https://github.com/gem/oq-nrmllib/tree… #29)

• NHIRS-14: Add XML schema validation, validate vulnerability curves against NRLM schema; update vulnerability curves to match NRML schema; update unit tests; update create_vuln_xml.py to generate XML conforming to NRML schema (NHIRS-14: Validate xml-format vulnerability files prior to execution #30)

• Conda versions, tests module, default aggregate output (Conda versions, tests module, default aggregate output #31)

• NHIRS-10: Add support for configuring choropleth aggregation fields (NHIRS-10: Add support for configuring choropleth aggregation fields #32)

• NHIRS-11 - Update flood templates to use generic raster reader (NHIRS-11 - Update flood templates to use generic raster reader #33)

• NHIRS-11: Add support for generic 'hazard_raster' to wind templates

• Switched template instantiation to use config dictionary, removed use of config list

• Update find_attributes to use config dictionary for locating attributes, and support lookup via a ordered list of keys to ease deprecation

• Update to NRML 0.5 schema

• NHIRS-18 - Initial Earthquake template with example (NHIRS-18 - Initial Earthquake template with example #39)

• NHIRS-8 - Improve memory usage for large raster input (NHIRS-8 - Improve memory usage for large raster input #41)- No longer reads the entire raster into memory, reads only the cells defined in the exposure data

• Added a 'ThreadPoolExecutor' for some performance improvement when reading hazard data for large exposure datasets

• NHIRS-48: Add and test categorisation of aggregated fields

• Update provenance connections between activities

• Calculate "worst-case" loss by permution of exposure

• Add git remote URL to provenance

• Update hazimp-tests.yml

• Update to a new configuration structure where vulnerability information is a node in the yaml, rather than separate keys for each piece of information (file name, vulnerability set, etc.)

• Fixes an issue when creating a mock s3 bucket with no region specified raised IllegalLocationConstraintException

• Replace a large number of deprecated scipy array calls with numpy equivalents

• Update gdal import to from osgeo import gdal and equivalent for other gdal functions (required to get gdal correctly installed for Python 3.8)

• Update xml creation test for actual coefficient of variation values (previously ignored)

• Remove Python 3.6 from github actions

• Add time info to log messages

• Add image for cov of vulnerability

• Add lower quantile for permutations (Add lower quantile for permutations #56)

• Update docs to reflect range of percentiles in permutation

• rc1.2 (rc1.2 #59)

• Update create_vuln_xml.py

• Revert change to zero cov values

• Add 2022 vulnerability curves

• v1.2.1 release (v1.2.1 release #60)

• AH-1763 Add 2022 vulnerability curves

• Merge install notes

• Squashed commit of the following:

commit 3fc8465
Merge: be42197 8e5d551
Author: Craig Arthur [email protected]
Date: Thu Jul 13 15:01:25 2023 +1000

Merge to v1.2.1

commit be42197
Author: Craig Arthur [email protected]
Date: Thu Jul 13 14:49:20 2023 +1000

Merge install notes

commit 8e5d551
Author: Craig Arthur [email protected]
Date: Thu Jul 13 14:47:05 2023 +1000

v1.2.1 release (#60)

* AH-1763 Add 2022 vulnerability curves

• Underscores inserted in aggregation field names #61 Fix insertion of underscores (#61 Fix insertion of underscores #62)

• v1.2.1 release (v1.2.1 release #60)

• AH-1763 Add 2022 vulnerability curves

• BUGFIX for aggregate.py (Underscores inserted in aggregation field names #61)

• AH-1801 Make aggregation field types consistent (AH-1801 Make aggregation field types consistent #65)

• AH-1801 Change key dtypes to match

• AH-1801 update workflow file - Trying fixes from Sporadic failures using mamba-version: "*" conda-incubator/setup-miniconda#274

• AH-1801 fix pylint errors

• Make aggregation field types consistent (Make aggregation field types consistent #66)

• AH-1801 Change key dtypes to match

• AH-1801 update workflow file - Trying fixes from Sporadic failures using mamba-version: "*" conda-incubator/setup-miniconda#274

• AH-1801 fix pylint errors

• HOTFIX: Update readthedocs configuration

• HOTFIX: Further readthedocs changes

• AH-1902 HOTFIX: Use gitdb to fix SHA error (AH-1902 HOTFIX: Use gitdb to fix SHA error #67)

Solution based on gitpython-developers/GitPython#1180 (comment)

• NHIRS-209 bugfix for inexplicable pd.merge errors (NHIRS-209 bugfix for inexplicable pd.merge errors #68)

• NHIRS-209 bugfix for inexplicable pd.merge errors

pd.merge in aggregate.py started throwing InvalidIndexError when merging the aggregate and pivot_table outputs. The fix renames the first column with itself, which seems to repair the indexing and allows the merge to be done without error.

• Version 1.3 release (Version 1.3 release #70)

• AH-2003 Surge templates (AH-2003 Surge templates #69)

• Remove wind templates on which the surge template is based

• Update flood.py - PEP8 conformance (line > 80 characters)

• RC1.3 Update docs and version numbers

• Remove deprecated wind_reader_v3

• rc1.3 (rc1.3 #71)

• AH-2003 Surge templates (AH-2003 Surge templates #69)

• AH-2003 Add surge template test

• Remove wind templates on which the surge template is based

• RC1.3 Update docs and version numbers

• RC1.3 - PEP8 fixes

• Version 1.4

  • Handle absence of CoV coefficients in create_vuln_xml.py: some vulnerability functions may not include the requuired fields to calculate coefficient of variation around the mean value. This raised a ValueError when attempting to convert to a float.
  • Add updated flood vulnerability functions: these were provided by VRMS in 2024, but were dated 2019. Changed the IMT to match the required NRML schema definition
  • Update test_misc for older versions of Python that don't use moto v5.0 or above
  • Update upload-artifact to v4
  • Add surge vulnerability models for example case
  • Use gitdb to fix SHA error: dolution based on Cannot get commits in code, but it works in REPL? gitpython-developers/GitPython#1180 (comment)

• HOTFIX: create_vuln_xml.py converted IMLs to ints before looking up values

• Remove numpy.NAN alias, fix mambaforge deprecation in actions

• Flood impact fixes and hazard raster scaling (Flood impact fixes and hazard raster scaling #73)

• Minor flood impact fixes

• Add option to apply scaling factor to hazard raster

• edits to user guide to include scaling_factor and aggregate (edits to user guide to include scaling_factor and aggregate #74)

• update flood vuln curves to reach 0 (update flood vuln curves to reach 0 #76)

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