edits to user guide to include scaling_factor and aggregate #74
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NicoleA-GA
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* Version 1.1 release * Fix failing tests * 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 (#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 (#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 (#35) * NHIRS-22: Increase unit test coverage (#36) * Update to NRML 0.5 (#38) * 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 (#41) * 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 (#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 Co-authored-by: MahmudulHasanGA <[email protected]> Co-authored-by: mahmudulhasanGA <[email protected]> Co-authored-by: Callum <[email protected]> Co-authored-by: Callum McKenna <[email protected]> Co-authored-by: Hyeuk Ryu <[email protected]> * Add time info to log messages * Add image for cov of vulnerability * Add lower quantile for permutations (#56) * Update docs to reflect range of percentiles in permutation * Version 1.2 (#58) * NHIRS-15: Add NRML schema from https://github.com/gem/oq-nrmllib/tree/master/openquake/nrmllib/schema (#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 (#30) * Conda versions, tests module, default aggregate output (#31) * NHIRS-10: Add support for configuring choropleth aggregation fields (#32) * 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 (#39) * 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 (#56) * Update docs to reflect range of percentiles in permutation Co-authored-by: MahmudulHasanGA <[email protected]> Co-authored-by: mahmudulhasanGA <[email protected]> Co-authored-by: Callum <[email protected]> Co-authored-by: Callum McKenna <[email protected]> Co-authored-by: Hyeuk Ryu <[email protected]> Co-authored-by: NicoleA-GA <[email protected]> * rc1.2 (#59) * Update create_vuln_xml.py * Revert change to zero cov values * Add 2022 vulnerability curves * 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 * #61 Fix insertion of underscores (#62) * v1.2.1 release (#60) * AH-1763 Add 2022 vulnerability curves * BUGFIX for aggregate.py (#61) * AH-1801 Make aggregation field types consistent (#65) * AH-1801 Change key dtypes to match * AH-1801 update workflow file - Trying fixes from conda-incubator/setup-miniconda#274 * AH-1801 fix pylint errors * Make aggregation field types consistent (#66) * AH-1801 Change key dtypes to match * AH-1801 update workflow file - Trying fixes from 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 (#67) Solution based on gitpython-developers/GitPython#1180 (comment) * 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 (#70) * 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 (#71) * 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 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 (#73) * Minor flood impact fixes * Add option to apply scaling factor to hazard raster * edits to user guide to include scaling_factor and aggregate (#74) * update flood vuln curves to reach 0 (#76) --------- Co-authored-by: Craig Arthur <[email protected]> Co-authored-by: MahmudulHasanGA <[email protected]> Co-authored-by: mahmudulhasanGA <[email protected]> Co-authored-by: Callum <[email protected]> Co-authored-by: Callum McKenna <[email protected]> Co-authored-by: Hyeuk Ryu <[email protected]> Co-authored-by: Craig Arthur <[email protected]>
NicoleA-GA
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Jan 29, 2025
* including cov.csv * merge master into CoV_xml branch (#78) * Version 1.1 release * Fix failing tests * 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 (#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 (#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 (#35) * NHIRS-22: Increase unit test coverage (#36) * Update to NRML 0.5 (#38) * 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 (#41) * 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 (#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 Co-authored-by: MahmudulHasanGA <[email protected]> Co-authored-by: mahmudulhasanGA <[email protected]> Co-authored-by: Callum <[email protected]> Co-authored-by: Callum McKenna <[email protected]> Co-authored-by: Hyeuk Ryu <[email protected]> * Add time info to log messages * Add image for cov of vulnerability * Add lower quantile for permutations (#56) * Update docs to reflect range of percentiles in permutation * Version 1.2 (#58) * NHIRS-15: Add NRML schema from https://github.com/gem/oq-nrmllib/tree/master/openquake/nrmllib/schema (#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 (#30) * Conda versions, tests module, default aggregate output (#31) * NHIRS-10: Add support for configuring choropleth aggregation fields (#32) * 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 (#39) * 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 (#56) * Update docs to reflect range of percentiles in permutation Co-authored-by: MahmudulHasanGA <[email protected]> Co-authored-by: mahmudulhasanGA <[email protected]> Co-authored-by: Callum <[email protected]> Co-authored-by: Callum McKenna <[email protected]> Co-authored-by: Hyeuk Ryu <[email protected]> Co-authored-by: NicoleA-GA <[email protected]> * rc1.2 (#59) * Update create_vuln_xml.py * Revert change to zero cov values * Add 2022 vulnerability curves * 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 * #61 Fix insertion of underscores (#62) * v1.2.1 release (#60) * AH-1763 Add 2022 vulnerability curves * BUGFIX for aggregate.py (#61) * AH-1801 Make aggregation field types consistent (#65) * AH-1801 Change key dtypes to match * AH-1801 update workflow file - Trying fixes from conda-incubator/setup-miniconda#274 * AH-1801 fix pylint errors * Make aggregation field types consistent (#66) * AH-1801 Change key dtypes to match * AH-1801 update workflow file - Trying fixes from 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 (#67) Solution based on gitpython-developers/GitPython#1180 (comment) * 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 (#70) * 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 (#71) * 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 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 (#73) * Minor flood impact fixes * Add option to apply scaling factor to hazard raster * edits to user guide to include scaling_factor and aggregate (#74) * update flood vuln curves to reach 0 (#76) --------- Co-authored-by: Craig Arthur <[email protected]> Co-authored-by: MahmudulHasanGA <[email protected]> Co-authored-by: mahmudulhasanGA <[email protected]> Co-authored-by: Callum <[email protected]> Co-authored-by: Callum McKenna <[email protected]> Co-authored-by: Hyeuk Ryu <[email protected]> Co-authored-by: Craig Arthur <[email protected]> --------- Co-authored-by: Craig Arthur <[email protected]> Co-authored-by: MahmudulHasanGA <[email protected]> Co-authored-by: mahmudulhasanGA <[email protected]> Co-authored-by: Callum <[email protected]> Co-authored-by: Callum McKenna <[email protected]> Co-authored-by: Hyeuk Ryu <[email protected]> Co-authored-by: Craig Arthur <[email protected]>
NicoleA-GA
added a commit
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Jan 29, 2025
* including cov.csv * merge master into CoV_xml branch (#78) * Version 1.1 release * Fix failing tests * 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 (#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 (#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 (#35) * NHIRS-22: Increase unit test coverage (#36) * Update to NRML 0.5 (#38) * 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 (#41) * 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 (#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 (#56) * Update docs to reflect range of percentiles in permutation * Version 1.2 (#58) * NHIRS-15: Add NRML schema from https://github.com/gem/oq-nrmllib/tree/master/openquake/nrmllib/schema (#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 (#30) * Conda versions, tests module, default aggregate output (#31) * NHIRS-10: Add support for configuring choropleth aggregation fields (#32) * 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 (#39) * 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 (#56) * Update docs to reflect range of percentiles in permutation * rc1.2 (#59) * Update create_vuln_xml.py * Revert change to zero cov values * Add 2022 vulnerability curves * 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 * #61 Fix insertion of underscores (#62) * v1.2.1 release (#60) * AH-1763 Add 2022 vulnerability curves * BUGFIX for aggregate.py (#61) * AH-1801 Make aggregation field types consistent (#65) * AH-1801 Change key dtypes to match * AH-1801 update workflow file - Trying fixes from conda-incubator/setup-miniconda#274 * AH-1801 fix pylint errors * Make aggregation field types consistent (#66) * AH-1801 Change key dtypes to match * AH-1801 update workflow file - Trying fixes from 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 (#67) Solution based on gitpython-developers/GitPython#1180 (comment) * 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 (#70) * 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 (#71) * 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 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 (#73) * Minor flood impact fixes * Add option to apply scaling factor to hazard raster * edits to user guide to include scaling_factor and aggregate (#74) * update flood vuln curves to reach 0 (#76) --------- --------- Co-authored-by: Craig Arthur <[email protected]> Co-authored-by: MahmudulHasanGA <[email protected]> Co-authored-by: mahmudulhasanGA <[email protected]> Co-authored-by: Callum <[email protected]> Co-authored-by: Callum McKenna <[email protected]> Co-authored-by: Hyeuk Ryu <[email protected]> Co-authored-by: Craig Arthur <[email protected]>
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