Remove Zarr version pin because bug is fixed - #569

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fix-zarr-dep
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Remove Zarr version pin because bug is fixed#569
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fix-zarr-dep

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@tasansaltasansal commented Jul 7, 2025

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@tasansaltasansal self-assigned this Jul 7, 2025
@tasansaltasansal added dependencies Pull requests that update a dependency file v1 labels Jul 7, 2025
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tasansal merged commit 4062a77 into v1Jul 7, 2025
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tasansal deleted the fix-zarr-dep branch July 7, 2025 14:12
tasansal added a commit that referenced this pull request Sep 8, 2025
@tasansal@dmitriyrepin
@BrianMichellDmitriy Repin
MDIO v1 beta release (#641)
65d8263
* update project metadata and deps
* update project metadata and deps
* add schemas
* Relocate quickstart notebook to tutorials directory
* update docs dependencies
* add new docs
* remove incorrect exclude
* remove duplicate doc directive
* fix creation notebook
* Add basic unit test for v1 dataset schema validation
* update lockfile
* fix broken creation nb
* update lockfile
* lint v1 files
* update lock file
* schema_v1-dataset_builder-add_dimension
* V1 schema review (#553)
* Update from list to discrete values for coordinate metadata
* Add docs to help users understand difference
* Update docs and fix case sensitivity.
* Linting
* Add CoordianteMetadata to docs
* First take on add_dimension(), add_coordinate(), add_variable()
* Finished add_dimension, add_coordinate, add_variable
* Work on build
* Generalize _to_dictionary()
* build
* [v1] Update dependencies to latest (#567)
* Update dependencies to latest versions
* Update linter type-checking code to 'TC' in pyproject.toml
https://astral.sh/blog/ruff-v0.8.0#new-error-codes-for-flake8-type-checking-rules
* Refactor: Move Zarr codec imports to top-level
* disable safety in CI (temporary)
* Refactor: Replace Zarr codec imports with numcodecs equivalents
* Refactor: Remove unused numcodecs imports and related methods
* pin zarr due to zarr 3.0.9 bug
* Dataset Build - pass one
* unpin zarr because breaking bug fixed (#569)
* Revert .container changes
* PR review: remove DEVELOPER_NOTES.md
* PR Review: add_coordinate() should accept only data_type: ScalarType
* PR review: add_variable() data_type remove default
* RE review: do not add dimension variable
* PR Review: get api version from the package version
* PR Review: remove add_dimension_coordinate
* PR Review: add_coordinate() remove data_type default value
* PR Review: improve unit tests by extracting common functionality in validate* functions
* Remove the Dockerfile changes. They are not supposed to be a part of this PR
* PR Review: run ruff
* PR Review: fix pre-commit errors
* remove some noqa overrides
* Implement MDIO Dataset builder to create in-memory instance of schemas.v1.dataset.Dataset (#568)
* schema_v1-dataset_builder-add_dimension
* First take on add_dimension(), add_coordinate(), add_variable()
* Finished add_dimension, add_coordinate, add_variable
* Work on build
* Generalize _to_dictionary()
* build
* Dataset Build - pass one
* Revert .container changes
* PR review: remove DEVELOPER_NOTES.md
* PR Review: add_coordinate() should accept only data_type: ScalarType
* PR review: add_variable() data_type remove default
* RE review: do not add dimension variable
* PR Review: get api version from the package version
* PR Review: remove add_dimension_coordinate
* PR Review: add_coordinate() remove data_type default value
* PR Review: improve unit tests by extracting common functionality in validate* functions
* Remove the Dockerfile changes. They are not supposed to be a part of this PR
* PR Review: run ruff
* PR Review: fix pre-commit errors
* remove some noqa overrides
---------
Co-authored-by: Altay Sansal <tasansal@users.noreply.github.com>
* Writing XArray / Zarr
* gitignore
* to_zarr() fix compression
* Fix precommit issues
* Use only make_campos_3d_acceptance_dataset
* PR Review: address the review comments
* Update _get_fill_value for StructuredType
* Fix fill type issue for the Structured Types
* Improve code coverage
* Fix spelling
* Revert "Fix spelling"
This reverts commit 0447659.
* extend per-file ignores for PLR2004 and remove noqa overrides in specific tests
* Refactor tests: clarify Zarr-related test names, fix type hints, and clean unused `# noqa` comments.
* MDIO v1 Templates and Template Registry (#573)
* Templates and TemplateRegistry
* Fix pre-commit issues
* Rever dev container changes
* PR Review: address issues
* PR Review: register default templates at registry initialization
* update deps
* address issues with VS Code dev containers (see issue 559) (#576)
* Templates and TemplateRegistry
* Fix pre-commit issues
* Rever dev container changes
* PR Review: address issues
* PR Review: register default templates at registry initialization
* Dockerfile.dev
---------
Co-authored-by: Altay Sansal <tasansal@users.noreply.github.com>
* segy_to_mdio_v1 (#577)
* Templates and TemplateRegistry
* Fix pre-commit issues
* Rever dev container changes
* PR Review: address issues
* PR Review: register default templates at registry initialization
* Dockerfile.dev
* segy_to_mdio_v1
* Clean up
* Prototype review notes
* Add dev comment
* Add notes that will be deleted later
* segy_to_mdio_v1 pass 1
* indexing_v1 and blocked_io_v1
* Remove DEV notes
* Clean up
* Document bug location
* Work around IndexError
* Clean temporary code
* More clean up
* Remove *_1 infrastructure files
* Restore accidently removed dask.array
* Created an issue reproducer
* Make the required template properties public
* Simplify type converter
* Improve templates
* Move test_type_converter.py
* Move test_type_converter.py
* Revert to use the original grid
* Integrate segy_to_mdio_v1_customized, fix indexing
* Add dimension coordinates in tem,plates
* Write statistics to Zarr
* Delete factory_v1.py
* Complete integrationtest. Fix coordinates
* Fir pre-commit errors
* PR review: fix trace_worker docstring
* Review: address some of the issue
* Fix bug
* dding todo for sum squares calculation
* Refactor ChunkIterator
* Refactor ChunkIterator into ChunkIteratorV1
* Remove segy_to_mdio_v1_customized, dataset_serializer.to_zarr
* Add support for trace headers without using _FillValue
* Use StorageLocation in trace_worker_v1
* Fix statistics attribute name
* PR review changes
* PR Improvements: do a single write
* TODO: chunked write for non-dimensional coordinates and trace_mask
* Update StorageLocation to use fsspec
* Reformat with pre-commit
* Use domain name in get_grid_plan
* Fix non-dim coords and chunk_samples=False
* Convert test_3d_import_v1 to V1
* Fix test_meta_dataset_read
* remove whitespace
* clean up comments
* update deps in lockfile
* simplify dim and non-dim coordinate handling after scan
* remove compatibility tests
* add filtering capability to header worker
* accept subset filter to pass to workers
* make v1 grid planner awesome
* double to single underscores in test names
* fix broken test harnesses due to incorrect Sequence import
* clean up dev comment
* clean up whitespace
* use new module name
* clean up segy_to_mdio_v1
* fix whitespace and remove unnecessary list call
* these are defined as float64 in template
Previous check was passing due to an error in assignment during creation of coordinate variables
* fix missing dimension coordinate for vertical axis
* fix incorrect dtype comparison for time variable
* simplify and fix critical bugs
* rename v1 out of things and get rid of old code
* remove fixed todo
* remove more v1 from names
* rename chunk iterator
* fix dimensionality in tests due to new (missing) vertical dimension coordinate
* add todo for numpy ingestion
* fix references to non-v1 naming
* extract grid operations to its own function
* fix typo
Co-authored-by: Brian Michell <brianm314@comcast.net>
* add todo for simplifying storage location
* Remove no_fill_var_names, add domain var to Seismic3DPreStackShotTemplate
* Part 2 of the previous commit
* pre-commit formatting
* remove dev mount
---------
Co-authored-by: Dmitriy Repin <dmitriy_repin@epam.com>
Co-authored-by: Altay Sansal <tasansal@users.noreply.github.com>
Co-authored-by: Brian Michell <brianm314@comcast.net>
* Make some integration tests for work with new `segy_to_mdio` (#599)
* Fix integration import tests
* Fix integration import tests
* mask_and_scale=False
* PR Review
* pre-commit
* PR Review issues
* add todo for headers
* update line length limit to 120 in pyproject.toml
* compact nested code for improved readability in validation tests
* compact coordinate and dimension name definitions in 2D/3D prestack shot templates
* refactor names in header validation in SEG-Y export tests
* remove v1 suffix
* compact code by merging multi-line blocks into single lines where possible
* bump prettier to v3.1.0 and remove prettier-plugin-toml
* update lock file
---------
Co-authored-by: Altay Sansal <tasansal@users.noreply.github.com>
* remove developer tests
* Serialize text and binary headers (#600)
* Fix integration import tests
* mask_and_scale=False
* pre-commit
* PR Review issues
* serialize-text-and-binary-headers
* remove dev test data
* add back whitespace
* revert import changes
* fix attribute initialization in `_add_text_binary_headers`
* Add tests
* refactor: improve type annotations and docstrings in test utilities
* fix formatting
* remove redundant `str()` casting in `xr.open_dataset` calls
---------
Co-authored-by: Altay Sansal <tasansal@users.noreply.github.com>
* shot_point (#602)
* Add template: Offset + Azimuth binned CDP gathers (COCA) (#605)
* update helper to support structured types in variable validation
* add Seismic3DPreStackCocaTemplate and corresponding unit tests
* register Seismic3DPreStackCocaTemplate in template registry
* reorganize template registrations in template_registry and remove depth ones from shots.
* use registered templates instead of listing them all by hand.
* simplify template instantiation in unit tests
* fix default templates and add missing ones
* refactor default template assertions using shared constant
* Eager memory allocation fix (#609)
* Implement fixes to ensure lazy allocation of data arrays on serialization
* Avoid unnecessary copies of data in memory
* Linting
* Eliminate immediate overwrite of `data` bug
* Remove unused import
* Set appropriate fill value for lazy arrays
* Clean up header value handler
* Resolve data serialization issues
* Ensure all encodings are captured
* Simplify dataset coordinate population logic by removing unused imports and redundant variable handling
* Refactor `_workers.py` to streamline variable handling, replace manual Variable creation with direct assignment, and resolve redundant imports.
* make better use of grid
* fix type hint
* make better use of grid
* fix(regression): make dataset serialization less eager
* update zarr
* remove comment
---------
Co-authored-by: Altay Sansal <tasansal@users.noreply.github.com>
* Fix memory and core utilization regressions
* Export functionality for MDIO v1 ingested files (#611)
* Export part 1
* Enable header value validation
* Revert the test names back
* Remove Endianness, new_chunks API args and traceDomain,
* PR review
* lint
* create/use new api location and lint
* allow configuring opener chunks
* clarify xarray open parameters
* fix regression of not-opening with native dask re-chunking
* fix regression of not-opening with native dask re-chunking
* make export rechunker work with named dimension sizes and chunks
* make StorageLocation available at library level and update mdio to segy example
* pre-open with zarr backend and simplify dataset slicing after lazy loading
* better opener docs
* more explicit xarray selection
* rename trace variable name to default variable name
* remove the guard for setting storage options to empty dictionary. new zarr is ok with None.
* update lockfile
* fix broken tests and inconsistent type hints
* clean up comments
* clarify binary header scaling
* make test names clearer
* fix broken unit tests due to storage_options handling
---------
Co-authored-by: Altay Sansal <tasansal@users.noreply.github.com>
* v1 implementation of AutoChannelWrap grid override (#632)
* AutoChannelWrap over updated-v1
* Fix test
* rename function for new behaviour and improve type hint for grid_overrides
* simplify metadata handling
* lint
* gridOverride is not required
* remove unnecessary byte order change, handled upstream.
* remove rtol adds, tests pass.
* remove expected behaviour comment
* clean up tests
* use grouped assignments to fix PLR915
* add comments to clarify
---------
Co-authored-by: Altay Sansal <tasansal@users.noreply.github.com>
* Move to Zarr v3 as default for on disk storage format (#630)
* remove all zarr v2 refs and fix fill_value attributes
* fix codec initialization for zarr3
* use correct kwargs for compressor definition
* fix fill value for structs
* fix numpy imports
* fix creation logic
* make numpy import namespace
* ensure fill value is correct for structured arrays
* fill value all fields
* remove legacy test for bug in v2
* fix codec related issues and warning spamming
* use UPath instead of StorageLocation and remove all v0 stuff
* undo warning suppression for now
* remove v0 dataset schema
* make immutable metadata tuples, performance optimizations. consistent code styling as well
- remove old zarr APIs
- Ensure grid attrs (map and live) get compressed properly.
- move grid_map slicing to worker from main process
-
* fix cloud i/o issue (#637)
* snake-case to camelCase (#638)
* Fix output URI handling for remote stores (#639)
* fix output uri handling for remote stores
* switch from `as_uri` to `as_posix` for compatibility with xarray
* allow legacy v2 support (#640)
* Reorganize code and simplify schemas and logic everywhere (#642)
* reorg and simplify
* fix comparison of stats
* fix regression in dataset attribute serialization
* ensure histogram alias is compared correctly
* update docs references
* fix broken refs
* remove top level metadata ref
* remove blosc config refs (we now get from zarr)
* delete removed stats metadata wrapper
* update deps and remove safety
- reason for removal: pyupio/safety#673
* fix numpy rng lint errors
* exclude lower level members
* remove singleton from template registry title
* make template registry api ref with autodoc
* First pass review and alignment of templates (#643)
* rename things to be more sensible and add angle gathers configuration to PreStackCdp templates.
- add missing 2d test
* align shot data template with prod
* fix tests for 3d pre-stack shot
* remove deleted attribute (processingStage)
* rename gatherType for coca
* lint and fix 1 bug
* rename gather -> ensemble or raw field data
* add missing 2d shot
* fix docstrings
* fix wrong validation namings
* Fix ingestion of coordinates without full dimensions (#644)
* fix correct ingestion for coordinates that don't share all dimensions
* add todo for verification of reduced dimensions
* Disable unimplemented tests (#647)
* add todo markers for disabled tests.
* set coverage minimum to 85% due to disabled tests
* remove todo, it has correct behaviour, also rename .build_dataset `header` to `header_dtype` for clarity (#648)
* set version to 1.0.0
* unpin hardcoded version from tests
---------
Co-authored-by: Dmitriy Repin <drepin@hotmail.com>
Co-authored-by: Brian Michell <brianm314@comcast.net>
Co-authored-by: Dima From Texas <34629861+dmitriyrepin@users.noreply.github.com>
Co-authored-by: Dmitriy Repin <dmitriy_repin@epam.com>
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Remove Zarr version pin because bug is fixed - #569
Merged
tasansal merged 1 commit into
v1from 
fix-zarr-dep
Jul 7, 2025
Merged
Remove Zarr version pin because bug is fixed#569
tasansal merged 1 commit into
v1from 
fix-zarr-dep
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fix-zarr-dep

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July 7, 2025 14:12
tasansal added a commit
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this pull request
Sep 8, 2025
@tasansal@dmitriyrepin
@BrianMichellDmitriy Repin
MDIO v1 beta release (#641)
65d8263
* update project metadata and deps
* update project metadata and deps
* add schemas
* Relocate quickstart notebook to tutorials directory
* update docs dependencies
* add new docs
* remove incorrect exclude
* remove duplicate doc directive
* fix creation notebook
* Add basic unit test for v1 dataset schema validation
* update lockfile
* fix broken creation nb
* update lockfile
* lint v1 files
* update lock file
* schema_v1-dataset_builder-add_dimension
* V1 schema review (#553)
* Update from list to discrete values for coordinate metadata
* Add docs to help users understand difference
* Update docs and fix case sensitivity.
* Linting
* Add CoordianteMetadata to docs
* First take on add_dimension(), add_coordinate(), add_variable()
* Finished add_dimension, add_coordinate, add_variable
* Work on build
* Generalize _to_dictionary()
* build
* [v1] Update dependencies to latest (#567)
* Update dependencies to latest versions
* Update linter type-checking code to 'TC' in pyproject.toml
https://astral.sh/blog/ruff-v0.8.0#new-error-codes-for-flake8-type-checking-rules
* Refactor: Move Zarr codec imports to top-level
* disable safety in CI (temporary)
* Refactor: Replace Zarr codec imports with numcodecs equivalents
* Refactor: Remove unused numcodecs imports and related methods
* pin zarr due to zarr 3.0.9 bug
* Dataset Build - pass one
* unpin zarr because breaking bug fixed (#569)
* Revert .container changes
* PR review: remove DEVELOPER_NOTES.md
* PR Review: add_coordinate() should accept only data_type: ScalarType
* PR review: add_variable() data_type remove default
* RE review: do not add dimension variable
* PR Review: get api version from the package version
* PR Review: remove add_dimension_coordinate
* PR Review: add_coordinate() remove data_type default value
* PR Review: improve unit tests by extracting common functionality in validate* functions
* Remove the Dockerfile changes. They are not supposed to be a part of this PR
* PR Review: run ruff
* PR Review: fix pre-commit errors
* remove some noqa overrides
* Implement MDIO Dataset builder to create in-memory instance of schemas.v1.dataset.Dataset (#568)
* schema_v1-dataset_builder-add_dimension
* First take on add_dimension(), add_coordinate(), add_variable()
* Finished add_dimension, add_coordinate, add_variable
* Work on build
* Generalize _to_dictionary()
* build
* Dataset Build - pass one
* Revert .container changes
* PR review: remove DEVELOPER_NOTES.md
* PR Review: add_coordinate() should accept only data_type: ScalarType
* PR review: add_variable() data_type remove default
* RE review: do not add dimension variable
* PR Review: get api version from the package version
* PR Review: remove add_dimension_coordinate
* PR Review: add_coordinate() remove data_type default value
* PR Review: improve unit tests by extracting common functionality in validate* functions
* Remove the Dockerfile changes. They are not supposed to be a part of this PR
* PR Review: run ruff
* PR Review: fix pre-commit errors
* remove some noqa overrides
---------
Co-authored-by: Altay Sansal <tasansal@users.noreply.github.com>
* Writing XArray / Zarr
* gitignore
* to_zarr() fix compression
* Fix precommit issues
* Use only make_campos_3d_acceptance_dataset
* PR Review: address the review comments
* Update _get_fill_value for StructuredType
* Fix fill type issue for the Structured Types
* Improve code coverage
* Fix spelling
* Revert "Fix spelling"
This reverts commit 0447659.
* extend per-file ignores for PLR2004 and remove noqa overrides in specific tests
* Refactor tests: clarify Zarr-related test names, fix type hints, and clean unused `# noqa` comments.
* MDIO v1 Templates and Template Registry (#573)
* Templates and TemplateRegistry
* Fix pre-commit issues
* Rever dev container changes
* PR Review: address issues
* PR Review: register default templates at registry initialization
* update deps
* address issues with VS Code dev containers (see issue 559) (#576)
* Templates and TemplateRegistry
* Fix pre-commit issues
* Rever dev container changes
* PR Review: address issues
* PR Review: register default templates at registry initialization
* Dockerfile.dev
---------
Co-authored-by: Altay Sansal <tasansal@users.noreply.github.com>
* segy_to_mdio_v1 (#577)
* Templates and TemplateRegistry
* Fix pre-commit issues
* Rever dev container changes
* PR Review: address issues
* PR Review: register default templates at registry initialization
* Dockerfile.dev
* segy_to_mdio_v1
* Clean up
* Prototype review notes
* Add dev comment
* Add notes that will be deleted later
* segy_to_mdio_v1 pass 1
* indexing_v1 and blocked_io_v1
* Remove DEV notes
* Clean up
* Document bug location
* Work around IndexError
* Clean temporary code
* More clean up
* Remove *_1 infrastructure files
* Restore accidently removed dask.array
* Created an issue reproducer
* Make the required template properties public
* Simplify type converter
* Improve templates
* Move test_type_converter.py
* Move test_type_converter.py
* Revert to use the original grid
* Integrate segy_to_mdio_v1_customized, fix indexing
* Add dimension coordinates in tem,plates
* Write statistics to Zarr
* Delete factory_v1.py
* Complete integrationtest. Fix coordinates
* Fir pre-commit errors
* PR review: fix trace_worker docstring
* Review: address some of the issue
* Fix bug
* dding todo for sum squares calculation
* Refactor ChunkIterator
* Refactor ChunkIterator into ChunkIteratorV1
* Remove segy_to_mdio_v1_customized, dataset_serializer.to_zarr
* Add support for trace headers without using _FillValue
* Use StorageLocation in trace_worker_v1
* Fix statistics attribute name
* PR review changes
* PR Improvements: do a single write
* TODO: chunked write for non-dimensional coordinates and trace_mask
* Update StorageLocation to use fsspec
* Reformat with pre-commit
* Use domain name in get_grid_plan
* Fix non-dim coords and chunk_samples=False
* Convert test_3d_import_v1 to V1
* Fix test_meta_dataset_read
* remove whitespace
* clean up comments
* update deps in lockfile
* simplify dim and non-dim coordinate handling after scan
* remove compatibility tests
* add filtering capability to header worker
* accept subset filter to pass to workers
* make v1 grid planner awesome
* double to single underscores in test names
* fix broken test harnesses due to incorrect Sequence import
* clean up dev comment
* clean up whitespace
* use new module name
* clean up segy_to_mdio_v1
* fix whitespace and remove unnecessary list call
* these are defined as float64 in template
Previous check was passing due to an error in assignment during creation of coordinate variables
* fix missing dimension coordinate for vertical axis
* fix incorrect dtype comparison for time variable
* simplify and fix critical bugs
* rename v1 out of things and get rid of old code
* remove fixed todo
* remove more v1 from names
* rename chunk iterator
* fix dimensionality in tests due to new (missing) vertical dimension coordinate
* add todo for numpy ingestion
* fix references to non-v1 naming
* extract grid operations to its own function
* fix typo
Co-authored-by: Brian Michell <brianm314@comcast.net>
* add todo for simplifying storage location
* Remove no_fill_var_names, add domain var to Seismic3DPreStackShotTemplate
* Part 2 of the previous commit
* pre-commit formatting
* remove dev mount
---------
Co-authored-by: Dmitriy Repin <dmitriy_repin@epam.com>
Co-authored-by: Altay Sansal <tasansal@users.noreply.github.com>
Co-authored-by: Brian Michell <brianm314@comcast.net>
* Make some integration tests for work with new `segy_to_mdio` (#599)
* Fix integration import tests
* Fix integration import tests
* mask_and_scale=False
* PR Review
* pre-commit
* PR Review issues
* add todo for headers
* update line length limit to 120 in pyproject.toml
* compact nested code for improved readability in validation tests
* compact coordinate and dimension name definitions in 2D/3D prestack shot templates
* refactor names in header validation in SEG-Y export tests
* remove v1 suffix
* compact code by merging multi-line blocks into single lines where possible
* bump prettier to v3.1.0 and remove prettier-plugin-toml
* update lock file
---------
Co-authored-by: Altay Sansal <tasansal@users.noreply.github.com>
* remove developer tests
* Serialize text and binary headers (#600)
* Fix integration import tests
* mask_and_scale=False
* pre-commit
* PR Review issues
* serialize-text-and-binary-headers
* remove dev test data
* add back whitespace
* revert import changes
* fix attribute initialization in `_add_text_binary_headers`
* Add tests
* refactor: improve type annotations and docstrings in test utilities
* fix formatting
* remove redundant `str()` casting in `xr.open_dataset` calls
---------
Co-authored-by: Altay Sansal <tasansal@users.noreply.github.com>
* shot_point (#602)
* Add template: Offset + Azimuth binned CDP gathers (COCA) (#605)
* update helper to support structured types in variable validation
* add Seismic3DPreStackCocaTemplate and corresponding unit tests
* register Seismic3DPreStackCocaTemplate in template registry
* reorganize template registrations in template_registry and remove depth ones from shots.
* use registered templates instead of listing them all by hand.
* simplify template instantiation in unit tests
* fix default templates and add missing ones
* refactor default template assertions using shared constant
* Eager memory allocation fix (#609)
* Implement fixes to ensure lazy allocation of data arrays on serialization
* Avoid unnecessary copies of data in memory
* Linting
* Eliminate immediate overwrite of `data` bug
* Remove unused import
* Set appropriate fill value for lazy arrays
* Clean up header value handler
* Resolve data serialization issues
* Ensure all encodings are captured
* Simplify dataset coordinate population logic by removing unused imports and redundant variable handling
* Refactor `_workers.py` to streamline variable handling, replace manual Variable creation with direct assignment, and resolve redundant imports.
* make better use of grid
* fix type hint
* make better use of grid
* fix(regression): make dataset serialization less eager
* update zarr
* remove comment
---------
Co-authored-by: Altay Sansal <tasansal@users.noreply.github.com>
* Fix memory and core utilization regressions
* Export functionality for MDIO v1 ingested files (#611)
* Export part 1
* Enable header value validation
* Revert the test names back
* Remove Endianness, new_chunks API args and traceDomain,
* PR review
* lint
* create/use new api location and lint
* allow configuring opener chunks
* clarify xarray open parameters
* fix regression of not-opening with native dask re-chunking
* fix regression of not-opening with native dask re-chunking
* make export rechunker work with named dimension sizes and chunks
* make StorageLocation available at library level and update mdio to segy example
* pre-open with zarr backend and simplify dataset slicing after lazy loading
* better opener docs
* more explicit xarray selection
* rename trace variable name to default variable name
* remove the guard for setting storage options to empty dictionary. new zarr is ok with None.
* update lockfile
* fix broken tests and inconsistent type hints
* clean up comments
* clarify binary header scaling
* make test names clearer
* fix broken unit tests due to storage_options handling
---------
Co-authored-by: Altay Sansal <tasansal@users.noreply.github.com>
* v1 implementation of AutoChannelWrap grid override (#632)
* AutoChannelWrap over updated-v1
* Fix test
* rename function for new behaviour and improve type hint for grid_overrides
* simplify metadata handling
* lint
* gridOverride is not required
* remove unnecessary byte order change, handled upstream.
* remove rtol adds, tests pass.
* remove expected behaviour comment
* clean up tests
* use grouped assignments to fix PLR915
* add comments to clarify
---------
Co-authored-by: Altay Sansal <tasansal@users.noreply.github.com>
* Move to Zarr v3 as default for on disk storage format (#630)
* remove all zarr v2 refs and fix fill_value attributes
* fix codec initialization for zarr3
* use correct kwargs for compressor definition
* fix fill value for structs
* fix numpy imports
* fix creation logic
* make numpy import namespace
* ensure fill value is correct for structured arrays
* fill value all fields
* remove legacy test for bug in v2
* fix codec related issues and warning spamming
* use UPath instead of StorageLocation and remove all v0 stuff
* undo warning suppression for now
* remove v0 dataset schema
* make immutable metadata tuples, performance optimizations. consistent code styling as well
- remove old zarr APIs
- Ensure grid attrs (map and live) get compressed properly.
- move grid_map slicing to worker from main process
-
* fix cloud i/o issue (#637)
* snake-case to camelCase (#638)
* Fix output URI handling for remote stores (#639)
* fix output uri handling for remote stores
* switch from `as_uri` to `as_posix` for compatibility with xarray
* allow legacy v2 support (#640)
* Reorganize code and simplify schemas and logic everywhere (#642)
* reorg and simplify
* fix comparison of stats
* fix regression in dataset attribute serialization
* ensure histogram alias is compared correctly
* update docs references
* fix broken refs
* remove top level metadata ref
* remove blosc config refs (we now get from zarr)
* delete removed stats metadata wrapper
* update deps and remove safety
- reason for removal: pyupio/safety#673
* fix numpy rng lint errors
* exclude lower level members
* remove singleton from template registry title
* make template registry api ref with autodoc
* First pass review and alignment of templates (#643)
* rename things to be more sensible and add angle gathers configuration to PreStackCdp templates.
- add missing 2d test
* align shot data template with prod
* fix tests for 3d pre-stack shot
* remove deleted attribute (processingStage)
* rename gatherType for coca
* lint and fix 1 bug
* rename gather -> ensemble or raw field data
* add missing 2d shot
* fix docstrings
* fix wrong validation namings
* Fix ingestion of coordinates without full dimensions (#644)
* fix correct ingestion for coordinates that don't share all dimensions
* add todo for verification of reduced dimensions
* Disable unimplemented tests (#647)
* add todo markers for disabled tests.
* set coverage minimum to 85% due to disabled tests
* remove todo, it has correct behaviour, also rename .build_dataset `header` to `header_dtype` for clarity (#648)
* set version to 1.0.0
* unpin hardcoded version from tests
---------
Co-authored-by: Dmitriy Repin <drepin@hotmail.com>
Co-authored-by: Brian Michell <brianm314@comcast.net>
Co-authored-by: Dima From Texas <34629861+dmitriyrepin@users.noreply.github.com>
Co-authored-by: Dmitriy Repin <dmitriy_repin@epam.com>
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, 'i');
if (__m === '*' || __re.test(location.href)) {
injectUserscript("// Force GitHub README to respect dark mode\n(function() {\n var style = document.createElement('style');\n style.textContent = '\n .markdown-body {\n color-scheme: dark light;\n }\n .markdown-body pre { background: #161b22 !important; }\n .markdown-body code { background: rgba(110, 118, 129, 0.4) !important; }\n .markdown-body table th, .markdown-body table td { border-color: #30363d !important; }\n .markdown-body img { background: #0d1117; }\n .markdown-body blockquote { border-left-color: #8b949e; }\n .markdown-body hr { border-color: #30363d; }\n ';\n document.head.appendChild(style);\n})();", "GitHub Dark Mode README Fix");
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try {
var __m = "*";
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Remove Zarr version pin because bug is fixed - #569
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tasansal merged 1 commit into
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Remove Zarr version pin because bug is fixed#569
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@tasansal@dmitriyrepin
@BrianMichellDmitriy Repin
MDIO v1 beta release (#641)
65d8263
* update project metadata and deps
* update project metadata and deps
* add schemas
* Relocate quickstart notebook to tutorials directory
* update docs dependencies
* add new docs
* remove incorrect exclude
* remove duplicate doc directive
* fix creation notebook
* Add basic unit test for v1 dataset schema validation
* update lockfile
* fix broken creation nb
* update lockfile
* lint v1 files
* update lock file
* schema_v1-dataset_builder-add_dimension
* V1 schema review (#553)
* Update from list to discrete values for coordinate metadata
* Add docs to help users understand difference
* Update docs and fix case sensitivity.
* Linting
* Add CoordianteMetadata to docs
* First take on add_dimension(), add_coordinate(), add_variable()
* Finished add_dimension, add_coordinate, add_variable
* Work on build
* Generalize _to_dictionary()
* build
* [v1] Update dependencies to latest (#567)
* Update dependencies to latest versions
* Update linter type-checking code to 'TC' in pyproject.toml
https://astral.sh/blog/ruff-v0.8.0#new-error-codes-for-flake8-type-checking-rules
* Refactor: Move Zarr codec imports to top-level
* disable safety in CI (temporary)
* Refactor: Replace Zarr codec imports with numcodecs equivalents
* Refactor: Remove unused numcodecs imports and related methods
* pin zarr due to zarr 3.0.9 bug
* Dataset Build - pass one
* unpin zarr because breaking bug fixed (#569)
* Revert .container changes
* PR review: remove DEVELOPER_NOTES.md
* PR Review: add_coordinate() should accept only data_type: ScalarType
* PR review: add_variable() data_type remove default
* RE review: do not add dimension variable
* PR Review: get api version from the package version
* PR Review: remove add_dimension_coordinate
* PR Review: add_coordinate() remove data_type default value
* PR Review: improve unit tests by extracting common functionality in validate* functions
* Remove the Dockerfile changes. They are not supposed to be a part of this PR
* PR Review: run ruff
* PR Review: fix pre-commit errors
* remove some noqa overrides
* Implement MDIO Dataset builder to create in-memory instance of schemas.v1.dataset.Dataset (#568)
* schema_v1-dataset_builder-add_dimension
* First take on add_dimension(), add_coordinate(), add_variable()
* Finished add_dimension, add_coordinate, add_variable
* Work on build
* Generalize _to_dictionary()
* build
* Dataset Build - pass one
* Revert .container changes
* PR review: remove DEVELOPER_NOTES.md
* PR Review: add_coordinate() should accept only data_type: ScalarType
* PR review: add_variable() data_type remove default
* RE review: do not add dimension variable
* PR Review: get api version from the package version
* PR Review: remove add_dimension_coordinate
* PR Review: add_coordinate() remove data_type default value
* PR Review: improve unit tests by extracting common functionality in validate* functions
* Remove the Dockerfile changes. They are not supposed to be a part of this PR
* PR Review: run ruff
* PR Review: fix pre-commit errors
* remove some noqa overrides
---------
Co-authored-by: Altay Sansal <tasansal@users.noreply.github.com>
* Writing XArray / Zarr
* gitignore
* to_zarr() fix compression
* Fix precommit issues
* Use only make_campos_3d_acceptance_dataset
* PR Review: address the review comments
* Update _get_fill_value for StructuredType
* Fix fill type issue for the Structured Types
* Improve code coverage
* Fix spelling
* Revert "Fix spelling"
This reverts commit 0447659.
* extend per-file ignores for PLR2004 and remove noqa overrides in specific tests
* Refactor tests: clarify Zarr-related test names, fix type hints, and clean unused `# noqa` comments.
* MDIO v1 Templates and Template Registry (#573)
* Templates and TemplateRegistry
* Fix pre-commit issues
* Rever dev container changes
* PR Review: address issues
* PR Review: register default templates at registry initialization
* update deps
* address issues with VS Code dev containers (see issue 559) (#576)
* Templates and TemplateRegistry
* Fix pre-commit issues
* Rever dev container changes
* PR Review: address issues
* PR Review: register default templates at registry initialization
* Dockerfile.dev
---------
Co-authored-by: Altay Sansal <tasansal@users.noreply.github.com>
* segy_to_mdio_v1 (#577)
* Templates and TemplateRegistry
* Fix pre-commit issues
* Rever dev container changes
* PR Review: address issues
* PR Review: register default templates at registry initialization
* Dockerfile.dev
* segy_to_mdio_v1
* Clean up
* Prototype review notes
* Add dev comment
* Add notes that will be deleted later
* segy_to_mdio_v1 pass 1
* indexing_v1 and blocked_io_v1
* Remove DEV notes
* Clean up
* Document bug location
* Work around IndexError
* Clean temporary code
* More clean up
* Remove *_1 infrastructure files
* Restore accidently removed dask.array
* Created an issue reproducer
* Make the required template properties public
* Simplify type converter
* Improve templates
* Move test_type_converter.py
* Move test_type_converter.py
* Revert to use the original grid
* Integrate segy_to_mdio_v1_customized, fix indexing
* Add dimension coordinates in tem,plates
* Write statistics to Zarr
* Delete factory_v1.py
* Complete integrationtest. Fix coordinates
* Fir pre-commit errors
* PR review: fix trace_worker docstring
* Review: address some of the issue
* Fix bug
* dding todo for sum squares calculation
* Refactor ChunkIterator
* Refactor ChunkIterator into ChunkIteratorV1
* Remove segy_to_mdio_v1_customized, dataset_serializer.to_zarr
* Add support for trace headers without using _FillValue
* Use StorageLocation in trace_worker_v1
* Fix statistics attribute name
* PR review changes
* PR Improvements: do a single write
* TODO: chunked write for non-dimensional coordinates and trace_mask
* Update StorageLocation to use fsspec
* Reformat with pre-commit
* Use domain name in get_grid_plan
* Fix non-dim coords and chunk_samples=False
* Convert test_3d_import_v1 to V1
* Fix test_meta_dataset_read
* remove whitespace
* clean up comments
* update deps in lockfile
* simplify dim and non-dim coordinate handling after scan
* remove compatibility tests
* add filtering capability to header worker
* accept subset filter to pass to workers
* make v1 grid planner awesome
* double to single underscores in test names
* fix broken test harnesses due to incorrect Sequence import
* clean up dev comment
* clean up whitespace
* use new module name
* clean up segy_to_mdio_v1
* fix whitespace and remove unnecessary list call
* these are defined as float64 in template
Previous check was passing due to an error in assignment during creation of coordinate variables
* fix missing dimension coordinate for vertical axis
* fix incorrect dtype comparison for time variable
* simplify and fix critical bugs
* rename v1 out of things and get rid of old code
* remove fixed todo
* remove more v1 from names
* rename chunk iterator
* fix dimensionality in tests due to new (missing) vertical dimension coordinate
* add todo for numpy ingestion
* fix references to non-v1 naming
* extract grid operations to its own function
* fix typo
Co-authored-by: Brian Michell <brianm314@comcast.net>
* add todo for simplifying storage location
* Remove no_fill_var_names, add domain var to Seismic3DPreStackShotTemplate
* Part 2 of the previous commit
* pre-commit formatting
* remove dev mount
---------
Co-authored-by: Dmitriy Repin <dmitriy_repin@epam.com>
Co-authored-by: Altay Sansal <tasansal@users.noreply.github.com>
Co-authored-by: Brian Michell <brianm314@comcast.net>
* Make some integration tests for work with new `segy_to_mdio` (#599)
* Fix integration import tests
* Fix integration import tests
* mask_and_scale=False
* PR Review
* pre-commit
* PR Review issues
* add todo for headers
* update line length limit to 120 in pyproject.toml
* compact nested code for improved readability in validation tests
* compact coordinate and dimension name definitions in 2D/3D prestack shot templates
* refactor names in header validation in SEG-Y export tests
* remove v1 suffix
* compact code by merging multi-line blocks into single lines where possible
* bump prettier to v3.1.0 and remove prettier-plugin-toml
* update lock file
---------
Co-authored-by: Altay Sansal <tasansal@users.noreply.github.com>
* remove developer tests
* Serialize text and binary headers (#600)
* Fix integration import tests
* mask_and_scale=False
* pre-commit
* PR Review issues
* serialize-text-and-binary-headers
* remove dev test data
* add back whitespace
* revert import changes
* fix attribute initialization in `_add_text_binary_headers`
* Add tests
* refactor: improve type annotations and docstrings in test utilities
* fix formatting
* remove redundant `str()` casting in `xr.open_dataset` calls
---------
Co-authored-by: Altay Sansal <tasansal@users.noreply.github.com>
* shot_point (#602)
* Add template: Offset + Azimuth binned CDP gathers (COCA) (#605)
* update helper to support structured types in variable validation
* add Seismic3DPreStackCocaTemplate and corresponding unit tests
* register Seismic3DPreStackCocaTemplate in template registry
* reorganize template registrations in template_registry and remove depth ones from shots.
* use registered templates instead of listing them all by hand.
* simplify template instantiation in unit tests
* fix default templates and add missing ones
* refactor default template assertions using shared constant
* Eager memory allocation fix (#609)
* Implement fixes to ensure lazy allocation of data arrays on serialization
* Avoid unnecessary copies of data in memory
* Linting
* Eliminate immediate overwrite of `data` bug
* Remove unused import
* Set appropriate fill value for lazy arrays
* Clean up header value handler
* Resolve data serialization issues
* Ensure all encodings are captured
* Simplify dataset coordinate population logic by removing unused imports and redundant variable handling
* Refactor `_workers.py` to streamline variable handling, replace manual Variable creation with direct assignment, and resolve redundant imports.
* make better use of grid
* fix type hint
* make better use of grid
* fix(regression): make dataset serialization less eager
* update zarr
* remove comment
---------
Co-authored-by: Altay Sansal <tasansal@users.noreply.github.com>
* Fix memory and core utilization regressions
* Export functionality for MDIO v1 ingested files (#611)
* Export part 1
* Enable header value validation
* Revert the test names back
* Remove Endianness, new_chunks API args and traceDomain,
* PR review
* lint
* create/use new api location and lint
* allow configuring opener chunks
* clarify xarray open parameters
* fix regression of not-opening with native dask re-chunking
* fix regression of not-opening with native dask re-chunking
* make export rechunker work with named dimension sizes and chunks
* make StorageLocation available at library level and update mdio to segy example
* pre-open with zarr backend and simplify dataset slicing after lazy loading
* better opener docs
* more explicit xarray selection
* rename trace variable name to default variable name
* remove the guard for setting storage options to empty dictionary. new zarr is ok with None.
* update lockfile
* fix broken tests and inconsistent type hints
* clean up comments
* clarify binary header scaling
* make test names clearer
* fix broken unit tests due to storage_options handling
---------
Co-authored-by: Altay Sansal <tasansal@users.noreply.github.com>
* v1 implementation of AutoChannelWrap grid override (#632)
* AutoChannelWrap over updated-v1
* Fix test
* rename function for new behaviour and improve type hint for grid_overrides
* simplify metadata handling
* lint
* gridOverride is not required
* remove unnecessary byte order change, handled upstream.
* remove rtol adds, tests pass.
* remove expected behaviour comment
* clean up tests
* use grouped assignments to fix PLR915
* add comments to clarify
---------
Co-authored-by: Altay Sansal <tasansal@users.noreply.github.com>
* Move to Zarr v3 as default for on disk storage format (#630)
* remove all zarr v2 refs and fix fill_value attributes
* fix codec initialization for zarr3
* use correct kwargs for compressor definition
* fix fill value for structs
* fix numpy imports
* fix creation logic
* make numpy import namespace
* ensure fill value is correct for structured arrays
* fill value all fields
* remove legacy test for bug in v2
* fix codec related issues and warning spamming
* use UPath instead of StorageLocation and remove all v0 stuff
* undo warning suppression for now
* remove v0 dataset schema
* make immutable metadata tuples, performance optimizations. consistent code styling as well
- remove old zarr APIs
- Ensure grid attrs (map and live) get compressed properly.
- move grid_map slicing to worker from main process
-
* fix cloud i/o issue (#637)
* snake-case to camelCase (#638)
* Fix output URI handling for remote stores (#639)
* fix output uri handling for remote stores
* switch from `as_uri` to `as_posix` for compatibility with xarray
* allow legacy v2 support (#640)
* Reorganize code and simplify schemas and logic everywhere (#642)
* reorg and simplify
* fix comparison of stats
* fix regression in dataset attribute serialization
* ensure histogram alias is compared correctly
* update docs references
* fix broken refs
* remove top level metadata ref
* remove blosc config refs (we now get from zarr)
* delete removed stats metadata wrapper
* update deps and remove safety
- reason for removal: pyupio/safety#673
* fix numpy rng lint errors
* exclude lower level members
* remove singleton from template registry title
* make template registry api ref with autodoc
* First pass review and alignment of templates (#643)
* rename things to be more sensible and add angle gathers configuration to PreStackCdp templates.
- add missing 2d test
* align shot data template with prod
* fix tests for 3d pre-stack shot
* remove deleted attribute (processingStage)
* rename gatherType for coca
* lint and fix 1 bug
* rename gather -> ensemble or raw field data
* add missing 2d shot
* fix docstrings
* fix wrong validation namings
* Fix ingestion of coordinates without full dimensions (#644)
* fix correct ingestion for coordinates that don't share all dimensions
* add todo for verification of reduced dimensions
* Disable unimplemented tests (#647)
* add todo markers for disabled tests.
* set coverage minimum to 85% due to disabled tests
* remove todo, it has correct behaviour, also rename .build_dataset `header` to `header_dtype` for clarity (#648)
* set version to 1.0.0
* unpin hardcoded version from tests
---------
Co-authored-by: Dmitriy Repin <drepin@hotmail.com>
Co-authored-by: Brian Michell <brianm314@comcast.net>
Co-authored-by: Dima From Texas <34629861+dmitriyrepin@users.noreply.github.com>
Co-authored-by: Dmitriy Repin <dmitriy_repin@epam.com>
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, 'i');
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Skip to content
Remove Zarr version pin because bug is fixed - #569
Merged
tasansal merged 1 commit into
v1from 
fix-zarr-dep
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Merged
Remove Zarr version pin because bug is fixed#569
tasansal merged 1 commit into
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fix-zarr-dep
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@tasansal
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tasansal added a commit
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@tasansal@dmitriyrepin
@BrianMichellDmitriy Repin
MDIO v1 beta release (#641)
65d8263
* update project metadata and deps
* update project metadata and deps
* add schemas
* Relocate quickstart notebook to tutorials directory
* update docs dependencies
* add new docs
* remove incorrect exclude
* remove duplicate doc directive
* fix creation notebook
* Add basic unit test for v1 dataset schema validation
* update lockfile
* fix broken creation nb
* update lockfile
* lint v1 files
* update lock file
* schema_v1-dataset_builder-add_dimension
* V1 schema review (#553)
* Update from list to discrete values for coordinate metadata
* Add docs to help users understand difference
* Update docs and fix case sensitivity.
* Linting
* Add CoordianteMetadata to docs
* First take on add_dimension(), add_coordinate(), add_variable()
* Finished add_dimension, add_coordinate, add_variable
* Work on build
* Generalize _to_dictionary()
* build
* [v1] Update dependencies to latest (#567)
* Update dependencies to latest versions
* Update linter type-checking code to 'TC' in pyproject.toml
https://astral.sh/blog/ruff-v0.8.0#new-error-codes-for-flake8-type-checking-rules
* Refactor: Move Zarr codec imports to top-level
* disable safety in CI (temporary)
* Refactor: Replace Zarr codec imports with numcodecs equivalents
* Refactor: Remove unused numcodecs imports and related methods
* pin zarr due to zarr 3.0.9 bug
* Dataset Build - pass one
* unpin zarr because breaking bug fixed (#569)
* Revert .container changes
* PR review: remove DEVELOPER_NOTES.md
* PR Review: add_coordinate() should accept only data_type: ScalarType
* PR review: add_variable() data_type remove default
* RE review: do not add dimension variable
* PR Review: get api version from the package version
* PR Review: remove add_dimension_coordinate
* PR Review: add_coordinate() remove data_type default value
* PR Review: improve unit tests by extracting common functionality in validate* functions
* Remove the Dockerfile changes. They are not supposed to be a part of this PR
* PR Review: run ruff
* PR Review: fix pre-commit errors
* remove some noqa overrides
* Implement MDIO Dataset builder to create in-memory instance of schemas.v1.dataset.Dataset (#568)
* schema_v1-dataset_builder-add_dimension
* First take on add_dimension(), add_coordinate(), add_variable()
* Finished add_dimension, add_coordinate, add_variable
* Work on build
* Generalize _to_dictionary()
* build
* Dataset Build - pass one
* Revert .container changes
* PR review: remove DEVELOPER_NOTES.md
* PR Review: add_coordinate() should accept only data_type: ScalarType
* PR review: add_variable() data_type remove default
* RE review: do not add dimension variable
* PR Review: get api version from the package version
* PR Review: remove add_dimension_coordinate
* PR Review: add_coordinate() remove data_type default value
* PR Review: improve unit tests by extracting common functionality in validate* functions
* Remove the Dockerfile changes. They are not supposed to be a part of this PR
* PR Review: run ruff
* PR Review: fix pre-commit errors
* remove some noqa overrides
---------
Co-authored-by: Altay Sansal <tasansal@users.noreply.github.com>
* Writing XArray / Zarr
* gitignore
* to_zarr() fix compression
* Fix precommit issues
* Use only make_campos_3d_acceptance_dataset
* PR Review: address the review comments
* Update _get_fill_value for StructuredType
* Fix fill type issue for the Structured Types
* Improve code coverage
* Fix spelling
* Revert "Fix spelling"
This reverts commit 0447659.
* extend per-file ignores for PLR2004 and remove noqa overrides in specific tests
* Refactor tests: clarify Zarr-related test names, fix type hints, and clean unused `# noqa` comments.
* MDIO v1 Templates and Template Registry (#573)
* Templates and TemplateRegistry
* Fix pre-commit issues
* Rever dev container changes
* PR Review: address issues
* PR Review: register default templates at registry initialization
* update deps
* address issues with VS Code dev containers (see issue 559) (#576)
* Templates and TemplateRegistry
* Fix pre-commit issues
* Rever dev container changes
* PR Review: address issues
* PR Review: register default templates at registry initialization
* Dockerfile.dev
---------
Co-authored-by: Altay Sansal <tasansal@users.noreply.github.com>
* segy_to_mdio_v1 (#577)
* Templates and TemplateRegistry
* Fix pre-commit issues
* Rever dev container changes
* PR Review: address issues
* PR Review: register default templates at registry initialization
* Dockerfile.dev
* segy_to_mdio_v1
* Clean up
* Prototype review notes
* Add dev comment
* Add notes that will be deleted later
* segy_to_mdio_v1 pass 1
* indexing_v1 and blocked_io_v1
* Remove DEV notes
* Clean up
* Document bug location
* Work around IndexError
* Clean temporary code
* More clean up
* Remove *_1 infrastructure files
* Restore accidently removed dask.array
* Created an issue reproducer
* Make the required template properties public
* Simplify type converter
* Improve templates
* Move test_type_converter.py
* Move test_type_converter.py
* Revert to use the original grid
* Integrate segy_to_mdio_v1_customized, fix indexing
* Add dimension coordinates in tem,plates
* Write statistics to Zarr
* Delete factory_v1.py
* Complete integrationtest. Fix coordinates
* Fir pre-commit errors
* PR review: fix trace_worker docstring
* Review: address some of the issue
* Fix bug
* dding todo for sum squares calculation
* Refactor ChunkIterator
* Refactor ChunkIterator into ChunkIteratorV1
* Remove segy_to_mdio_v1_customized, dataset_serializer.to_zarr
* Add support for trace headers without using _FillValue
* Use StorageLocation in trace_worker_v1
* Fix statistics attribute name
* PR review changes
* PR Improvements: do a single write
* TODO: chunked write for non-dimensional coordinates and trace_mask
* Update StorageLocation to use fsspec
* Reformat with pre-commit
* Use domain name in get_grid_plan
* Fix non-dim coords and chunk_samples=False
* Convert test_3d_import_v1 to V1
* Fix test_meta_dataset_read
* remove whitespace
* clean up comments
* update deps in lockfile
* simplify dim and non-dim coordinate handling after scan
* remove compatibility tests
* add filtering capability to header worker
* accept subset filter to pass to workers
* make v1 grid planner awesome
* double to single underscores in test names
* fix broken test harnesses due to incorrect Sequence import
* clean up dev comment
* clean up whitespace
* use new module name
* clean up segy_to_mdio_v1
* fix whitespace and remove unnecessary list call
* these are defined as float64 in template
Previous check was passing due to an error in assignment during creation of coordinate variables
* fix missing dimension coordinate for vertical axis
* fix incorrect dtype comparison for time variable
* simplify and fix critical bugs
* rename v1 out of things and get rid of old code
* remove fixed todo
* remove more v1 from names
* rename chunk iterator
* fix dimensionality in tests due to new (missing) vertical dimension coordinate
* add todo for numpy ingestion
* fix references to non-v1 naming
* extract grid operations to its own function
* fix typo
Co-authored-by: Brian Michell <brianm314@comcast.net>
* add todo for simplifying storage location
* Remove no_fill_var_names, add domain var to Seismic3DPreStackShotTemplate
* Part 2 of the previous commit
* pre-commit formatting
* remove dev mount
---------
Co-authored-by: Dmitriy Repin <dmitriy_repin@epam.com>
Co-authored-by: Altay Sansal <tasansal@users.noreply.github.com>
Co-authored-by: Brian Michell <brianm314@comcast.net>
* Make some integration tests for work with new `segy_to_mdio` (#599)
* Fix integration import tests
* Fix integration import tests
* mask_and_scale=False
* PR Review
* pre-commit
* PR Review issues
* add todo for headers
* update line length limit to 120 in pyproject.toml
* compact nested code for improved readability in validation tests
* compact coordinate and dimension name definitions in 2D/3D prestack shot templates
* refactor names in header validation in SEG-Y export tests
* remove v1 suffix
* compact code by merging multi-line blocks into single lines where possible
* bump prettier to v3.1.0 and remove prettier-plugin-toml
* update lock file
---------
Co-authored-by: Altay Sansal <tasansal@users.noreply.github.com>
* remove developer tests
* Serialize text and binary headers (#600)
* Fix integration import tests
* mask_and_scale=False
* pre-commit
* PR Review issues
* serialize-text-and-binary-headers
* remove dev test data
* add back whitespace
* revert import changes
* fix attribute initialization in `_add_text_binary_headers`
* Add tests
* refactor: improve type annotations and docstrings in test utilities
* fix formatting
* remove redundant `str()` casting in `xr.open_dataset` calls
---------
Co-authored-by: Altay Sansal <tasansal@users.noreply.github.com>
* shot_point (#602)
* Add template: Offset + Azimuth binned CDP gathers (COCA) (#605)
* update helper to support structured types in variable validation
* add Seismic3DPreStackCocaTemplate and corresponding unit tests
* register Seismic3DPreStackCocaTemplate in template registry
* reorganize template registrations in template_registry and remove depth ones from shots.
* use registered templates instead of listing them all by hand.
* simplify template instantiation in unit tests
* fix default templates and add missing ones
* refactor default template assertions using shared constant
* Eager memory allocation fix (#609)
* Implement fixes to ensure lazy allocation of data arrays on serialization
* Avoid unnecessary copies of data in memory
* Linting
* Eliminate immediate overwrite of `data` bug
* Remove unused import
* Set appropriate fill value for lazy arrays
* Clean up header value handler
* Resolve data serialization issues
* Ensure all encodings are captured
* Simplify dataset coordinate population logic by removing unused imports and redundant variable handling
* Refactor `_workers.py` to streamline variable handling, replace manual Variable creation with direct assignment, and resolve redundant imports.
* make better use of grid
* fix type hint
* make better use of grid
* fix(regression): make dataset serialization less eager
* update zarr
* remove comment
---------
Co-authored-by: Altay Sansal <tasansal@users.noreply.github.com>
* Fix memory and core utilization regressions
* Export functionality for MDIO v1 ingested files (#611)
* Export part 1
* Enable header value validation
* Revert the test names back
* Remove Endianness, new_chunks API args and traceDomain,
* PR review
* lint
* create/use new api location and lint
* allow configuring opener chunks
* clarify xarray open parameters
* fix regression of not-opening with native dask re-chunking
* fix regression of not-opening with native dask re-chunking
* make export rechunker work with named dimension sizes and chunks
* make StorageLocation available at library level and update mdio to segy example
* pre-open with zarr backend and simplify dataset slicing after lazy loading
* better opener docs
* more explicit xarray selection
* rename trace variable name to default variable name
* remove the guard for setting storage options to empty dictionary. new zarr is ok with None.
* update lockfile
* fix broken tests and inconsistent type hints
* clean up comments
* clarify binary header scaling
* make test names clearer
* fix broken unit tests due to storage_options handling
---------
Co-authored-by: Altay Sansal <tasansal@users.noreply.github.com>
* v1 implementation of AutoChannelWrap grid override (#632)
* AutoChannelWrap over updated-v1
* Fix test
* rename function for new behaviour and improve type hint for grid_overrides
* simplify metadata handling
* lint
* gridOverride is not required
* remove unnecessary byte order change, handled upstream.
* remove rtol adds, tests pass.
* remove expected behaviour comment
* clean up tests
* use grouped assignments to fix PLR915
* add comments to clarify
---------
Co-authored-by: Altay Sansal <tasansal@users.noreply.github.com>
* Move to Zarr v3 as default for on disk storage format (#630)
* remove all zarr v2 refs and fix fill_value attributes
* fix codec initialization for zarr3
* use correct kwargs for compressor definition
* fix fill value for structs
* fix numpy imports
* fix creation logic
* make numpy import namespace
* ensure fill value is correct for structured arrays
* fill value all fields
* remove legacy test for bug in v2
* fix codec related issues and warning spamming
* use UPath instead of StorageLocation and remove all v0 stuff
* undo warning suppression for now
* remove v0 dataset schema
* make immutable metadata tuples, performance optimizations. consistent code styling as well
- remove old zarr APIs
- Ensure grid attrs (map and live) get compressed properly.
- move grid_map slicing to worker from main process
-
* fix cloud i/o issue (#637)
* snake-case to camelCase (#638)
* Fix output URI handling for remote stores (#639)
* fix output uri handling for remote stores
* switch from `as_uri` to `as_posix` for compatibility with xarray
* allow legacy v2 support (#640)
* Reorganize code and simplify schemas and logic everywhere (#642)
* reorg and simplify
* fix comparison of stats
* fix regression in dataset attribute serialization
* ensure histogram alias is compared correctly
* update docs references
* fix broken refs
* remove top level metadata ref
* remove blosc config refs (we now get from zarr)
* delete removed stats metadata wrapper
* update deps and remove safety
- reason for removal: pyupio/safety#673
* fix numpy rng lint errors
* exclude lower level members
* remove singleton from template registry title
* make template registry api ref with autodoc
* First pass review and alignment of templates (#643)
* rename things to be more sensible and add angle gathers configuration to PreStackCdp templates.
- add missing 2d test
* align shot data template with prod
* fix tests for 3d pre-stack shot
* remove deleted attribute (processingStage)
* rename gatherType for coca
* lint and fix 1 bug
* rename gather -> ensemble or raw field data
* add missing 2d shot
* fix docstrings
* fix wrong validation namings
* Fix ingestion of coordinates without full dimensions (#644)
* fix correct ingestion for coordinates that don't share all dimensions
* add todo for verification of reduced dimensions
* Disable unimplemented tests (#647)
* add todo markers for disabled tests.
* set coverage minimum to 85% due to disabled tests
* remove todo, it has correct behaviour, also rename .build_dataset `header` to `header_dtype` for clarity (#648)
* set version to 1.0.0
* unpin hardcoded version from tests
---------
Co-authored-by: Dmitriy Repin <drepin@hotmail.com>
Co-authored-by: Brian Michell <brianm314@comcast.net>
Co-authored-by: Dima From Texas <34629861+dmitriyrepin@users.noreply.github.com>
Co-authored-by: Dmitriy Repin <dmitriy_repin@epam.com>
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, 'i');
if (__m === '*' || __re.test(location.href)) {
injectUserscript("// Strip utm_, fbclid, gclid, etc. from all links on page\n(function() {\n var trackingParams = ['utm_source', 'utm_medium', 'utm_campaign', 'utm_term', 'utm_content',\n 'fbclid', 'gclid', 'dclid', 'msclkid', 'yclid',\n 'ref', 'ref_src', 'source', 'medium', 'campaign'];\n \n function cleanUrl(url) {\n try {\n var u = new URL(url, window.location.origin);\n var changed = false;\n trackingParams.forEach(function(p) {\n if (u.searchParams.has(p)) {\n u.searchParams.delete(p);\n changed = true;\n }\n });\n return changed ? u.toString() : url;\n } catch (e) {\n return url;\n }\n }\n \n function cleanLinks() {\n document.querySelectorAll('a[href]').forEach(function(a) {\n var clean = cleanUrl(a.href);\n if (clean !== a.href) a.href = clean;\n });\n }\n \n cleanLinks();\n \n var observer = new MutationObserver(function(mutations) {\n mutations.forEach(function(m) {\n m.addedNodes.forEach(function(node) {\n if (node.nodeType === 1) {\n if (node.tagName === 'A') cleanLinks();\n node.querySelectorAll('a[href]').forEach(function(a) {\n var clean = cleanUrl(a.href);\n if (clean !== a.href) a.href = clean;\n });\n }\n });\n });\n });\n observer.observe(document.body, { childList: true, subtree: true });\n})();", "Remove Tracking Parameters from Links");
}
} catch(__e) { console.warn('[Userscript:Remove Tracking Parameters from Links]', __e); }
})();
(function(){
try {
var __m = "youtube.com";
var __re = new RegExp('^' + "youtube\\.com" + '

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Remove Zarr version pin because bug is fixed - #569
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fix-zarr-dep
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Remove Zarr version pin because bug is fixed#569
tasansal merged 1 commit into
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@tasansal@dmitriyrepin
@BrianMichellDmitriy Repin
MDIO v1 beta release (#641)
65d8263
* update project metadata and deps
* update project metadata and deps
* add schemas
* Relocate quickstart notebook to tutorials directory
* update docs dependencies
* add new docs
* remove incorrect exclude
* remove duplicate doc directive
* fix creation notebook
* Add basic unit test for v1 dataset schema validation
* update lockfile
* fix broken creation nb
* update lockfile
* lint v1 files
* update lock file
* schema_v1-dataset_builder-add_dimension
* V1 schema review (#553)
* Update from list to discrete values for coordinate metadata
* Add docs to help users understand difference
* Update docs and fix case sensitivity.
* Linting
* Add CoordianteMetadata to docs
* First take on add_dimension(), add_coordinate(), add_variable()
* Finished add_dimension, add_coordinate, add_variable
* Work on build
* Generalize _to_dictionary()
* build
* [v1] Update dependencies to latest (#567)
* Update dependencies to latest versions
* Update linter type-checking code to 'TC' in pyproject.toml
https://astral.sh/blog/ruff-v0.8.0#new-error-codes-for-flake8-type-checking-rules
* Refactor: Move Zarr codec imports to top-level
* disable safety in CI (temporary)
* Refactor: Replace Zarr codec imports with numcodecs equivalents
* Refactor: Remove unused numcodecs imports and related methods
* pin zarr due to zarr 3.0.9 bug
* Dataset Build - pass one
* unpin zarr because breaking bug fixed (#569)
* Revert .container changes
* PR review: remove DEVELOPER_NOTES.md
* PR Review: add_coordinate() should accept only data_type: ScalarType
* PR review: add_variable() data_type remove default
* RE review: do not add dimension variable
* PR Review: get api version from the package version
* PR Review: remove add_dimension_coordinate
* PR Review: add_coordinate() remove data_type default value
* PR Review: improve unit tests by extracting common functionality in validate* functions
* Remove the Dockerfile changes. They are not supposed to be a part of this PR
* PR Review: run ruff
* PR Review: fix pre-commit errors
* remove some noqa overrides
* Implement MDIO Dataset builder to create in-memory instance of schemas.v1.dataset.Dataset (#568)
* schema_v1-dataset_builder-add_dimension
* First take on add_dimension(), add_coordinate(), add_variable()
* Finished add_dimension, add_coordinate, add_variable
* Work on build
* Generalize _to_dictionary()
* build
* Dataset Build - pass one
* Revert .container changes
* PR review: remove DEVELOPER_NOTES.md
* PR Review: add_coordinate() should accept only data_type: ScalarType
* PR review: add_variable() data_type remove default
* RE review: do not add dimension variable
* PR Review: get api version from the package version
* PR Review: remove add_dimension_coordinate
* PR Review: add_coordinate() remove data_type default value
* PR Review: improve unit tests by extracting common functionality in validate* functions
* Remove the Dockerfile changes. They are not supposed to be a part of this PR
* PR Review: run ruff
* PR Review: fix pre-commit errors
* remove some noqa overrides
---------
Co-authored-by: Altay Sansal <tasansal@users.noreply.github.com>
* Writing XArray / Zarr
* gitignore
* to_zarr() fix compression
* Fix precommit issues
* Use only make_campos_3d_acceptance_dataset
* PR Review: address the review comments
* Update _get_fill_value for StructuredType
* Fix fill type issue for the Structured Types
* Improve code coverage
* Fix spelling
* Revert "Fix spelling"
This reverts commit 0447659.
* extend per-file ignores for PLR2004 and remove noqa overrides in specific tests
* Refactor tests: clarify Zarr-related test names, fix type hints, and clean unused `# noqa` comments.
* MDIO v1 Templates and Template Registry (#573)
* Templates and TemplateRegistry
* Fix pre-commit issues
* Rever dev container changes
* PR Review: address issues
* PR Review: register default templates at registry initialization
* update deps
* address issues with VS Code dev containers (see issue 559) (#576)
* Templates and TemplateRegistry
* Fix pre-commit issues
* Rever dev container changes
* PR Review: address issues
* PR Review: register default templates at registry initialization
* Dockerfile.dev
---------
Co-authored-by: Altay Sansal <tasansal@users.noreply.github.com>
* segy_to_mdio_v1 (#577)
* Templates and TemplateRegistry
* Fix pre-commit issues
* Rever dev container changes
* PR Review: address issues
* PR Review: register default templates at registry initialization
* Dockerfile.dev
* segy_to_mdio_v1
* Clean up
* Prototype review notes
* Add dev comment
* Add notes that will be deleted later
* segy_to_mdio_v1 pass 1
* indexing_v1 and blocked_io_v1
* Remove DEV notes
* Clean up
* Document bug location
* Work around IndexError
* Clean temporary code
* More clean up
* Remove *_1 infrastructure files
* Restore accidently removed dask.array
* Created an issue reproducer
* Make the required template properties public
* Simplify type converter
* Improve templates
* Move test_type_converter.py
* Move test_type_converter.py
* Revert to use the original grid
* Integrate segy_to_mdio_v1_customized, fix indexing
* Add dimension coordinates in tem,plates
* Write statistics to Zarr
* Delete factory_v1.py
* Complete integrationtest. Fix coordinates
* Fir pre-commit errors
* PR review: fix trace_worker docstring
* Review: address some of the issue
* Fix bug
* dding todo for sum squares calculation
* Refactor ChunkIterator
* Refactor ChunkIterator into ChunkIteratorV1
* Remove segy_to_mdio_v1_customized, dataset_serializer.to_zarr
* Add support for trace headers without using _FillValue
* Use StorageLocation in trace_worker_v1
* Fix statistics attribute name
* PR review changes
* PR Improvements: do a single write
* TODO: chunked write for non-dimensional coordinates and trace_mask
* Update StorageLocation to use fsspec
* Reformat with pre-commit
* Use domain name in get_grid_plan
* Fix non-dim coords and chunk_samples=False
* Convert test_3d_import_v1 to V1
* Fix test_meta_dataset_read
* remove whitespace
* clean up comments
* update deps in lockfile
* simplify dim and non-dim coordinate handling after scan
* remove compatibility tests
* add filtering capability to header worker
* accept subset filter to pass to workers
* make v1 grid planner awesome
* double to single underscores in test names
* fix broken test harnesses due to incorrect Sequence import
* clean up dev comment
* clean up whitespace
* use new module name
* clean up segy_to_mdio_v1
* fix whitespace and remove unnecessary list call
* these are defined as float64 in template
Previous check was passing due to an error in assignment during creation of coordinate variables
* fix missing dimension coordinate for vertical axis
* fix incorrect dtype comparison for time variable
* simplify and fix critical bugs
* rename v1 out of things and get rid of old code
* remove fixed todo
* remove more v1 from names
* rename chunk iterator
* fix dimensionality in tests due to new (missing) vertical dimension coordinate
* add todo for numpy ingestion
* fix references to non-v1 naming
* extract grid operations to its own function
* fix typo
Co-authored-by: Brian Michell <brianm314@comcast.net>
* add todo for simplifying storage location
* Remove no_fill_var_names, add domain var to Seismic3DPreStackShotTemplate
* Part 2 of the previous commit
* pre-commit formatting
* remove dev mount
---------
Co-authored-by: Dmitriy Repin <dmitriy_repin@epam.com>
Co-authored-by: Altay Sansal <tasansal@users.noreply.github.com>
Co-authored-by: Brian Michell <brianm314@comcast.net>
* Make some integration tests for work with new `segy_to_mdio` (#599)
* Fix integration import tests
* Fix integration import tests
* mask_and_scale=False
* PR Review
* pre-commit
* PR Review issues
* add todo for headers
* update line length limit to 120 in pyproject.toml
* compact nested code for improved readability in validation tests
* compact coordinate and dimension name definitions in 2D/3D prestack shot templates
* refactor names in header validation in SEG-Y export tests
* remove v1 suffix
* compact code by merging multi-line blocks into single lines where possible
* bump prettier to v3.1.0 and remove prettier-plugin-toml
* update lock file
---------
Co-authored-by: Altay Sansal <tasansal@users.noreply.github.com>
* remove developer tests
* Serialize text and binary headers (#600)
* Fix integration import tests
* mask_and_scale=False
* pre-commit
* PR Review issues
* serialize-text-and-binary-headers
* remove dev test data
* add back whitespace
* revert import changes
* fix attribute initialization in `_add_text_binary_headers`
* Add tests
* refactor: improve type annotations and docstrings in test utilities
* fix formatting
* remove redundant `str()` casting in `xr.open_dataset` calls
---------
Co-authored-by: Altay Sansal <tasansal@users.noreply.github.com>
* shot_point (#602)
* Add template: Offset + Azimuth binned CDP gathers (COCA) (#605)
* update helper to support structured types in variable validation
* add Seismic3DPreStackCocaTemplate and corresponding unit tests
* register Seismic3DPreStackCocaTemplate in template registry
* reorganize template registrations in template_registry and remove depth ones from shots.
* use registered templates instead of listing them all by hand.
* simplify template instantiation in unit tests
* fix default templates and add missing ones
* refactor default template assertions using shared constant
* Eager memory allocation fix (#609)
* Implement fixes to ensure lazy allocation of data arrays on serialization
* Avoid unnecessary copies of data in memory
* Linting
* Eliminate immediate overwrite of `data` bug
* Remove unused import
* Set appropriate fill value for lazy arrays
* Clean up header value handler
* Resolve data serialization issues
* Ensure all encodings are captured
* Simplify dataset coordinate population logic by removing unused imports and redundant variable handling
* Refactor `_workers.py` to streamline variable handling, replace manual Variable creation with direct assignment, and resolve redundant imports.
* make better use of grid
* fix type hint
* make better use of grid
* fix(regression): make dataset serialization less eager
* update zarr
* remove comment
---------
Co-authored-by: Altay Sansal <tasansal@users.noreply.github.com>
* Fix memory and core utilization regressions
* Export functionality for MDIO v1 ingested files (#611)
* Export part 1
* Enable header value validation
* Revert the test names back
* Remove Endianness, new_chunks API args and traceDomain,
* PR review
* lint
* create/use new api location and lint
* allow configuring opener chunks
* clarify xarray open parameters
* fix regression of not-opening with native dask re-chunking
* fix regression of not-opening with native dask re-chunking
* make export rechunker work with named dimension sizes and chunks
* make StorageLocation available at library level and update mdio to segy example
* pre-open with zarr backend and simplify dataset slicing after lazy loading
* better opener docs
* more explicit xarray selection
* rename trace variable name to default variable name
* remove the guard for setting storage options to empty dictionary. new zarr is ok with None.
* update lockfile
* fix broken tests and inconsistent type hints
* clean up comments
* clarify binary header scaling
* make test names clearer
* fix broken unit tests due to storage_options handling
---------
Co-authored-by: Altay Sansal <tasansal@users.noreply.github.com>
* v1 implementation of AutoChannelWrap grid override (#632)
* AutoChannelWrap over updated-v1
* Fix test
* rename function for new behaviour and improve type hint for grid_overrides
* simplify metadata handling
* lint
* gridOverride is not required
* remove unnecessary byte order change, handled upstream.
* remove rtol adds, tests pass.
* remove expected behaviour comment
* clean up tests
* use grouped assignments to fix PLR915
* add comments to clarify
---------
Co-authored-by: Altay Sansal <tasansal@users.noreply.github.com>
* Move to Zarr v3 as default for on disk storage format (#630)
* remove all zarr v2 refs and fix fill_value attributes
* fix codec initialization for zarr3
* use correct kwargs for compressor definition
* fix fill value for structs
* fix numpy imports
* fix creation logic
* make numpy import namespace
* ensure fill value is correct for structured arrays
* fill value all fields
* remove legacy test for bug in v2
* fix codec related issues and warning spamming
* use UPath instead of StorageLocation and remove all v0 stuff
* undo warning suppression for now
* remove v0 dataset schema
* make immutable metadata tuples, performance optimizations. consistent code styling as well
- remove old zarr APIs
- Ensure grid attrs (map and live) get compressed properly.
- move grid_map slicing to worker from main process
-
* fix cloud i/o issue (#637)
* snake-case to camelCase (#638)
* Fix output URI handling for remote stores (#639)
* fix output uri handling for remote stores
* switch from `as_uri` to `as_posix` for compatibility with xarray
* allow legacy v2 support (#640)
* Reorganize code and simplify schemas and logic everywhere (#642)
* reorg and simplify
* fix comparison of stats
* fix regression in dataset attribute serialization
* ensure histogram alias is compared correctly
* update docs references
* fix broken refs
* remove top level metadata ref
* remove blosc config refs (we now get from zarr)
* delete removed stats metadata wrapper
* update deps and remove safety
- reason for removal: pyupio/safety#673
* fix numpy rng lint errors
* exclude lower level members
* remove singleton from template registry title
* make template registry api ref with autodoc
* First pass review and alignment of templates (#643)
* rename things to be more sensible and add angle gathers configuration to PreStackCdp templates.
- add missing 2d test
* align shot data template with prod
* fix tests for 3d pre-stack shot
* remove deleted attribute (processingStage)
* rename gatherType for coca
* lint and fix 1 bug
* rename gather -> ensemble or raw field data
* add missing 2d shot
* fix docstrings
* fix wrong validation namings
* Fix ingestion of coordinates without full dimensions (#644)
* fix correct ingestion for coordinates that don't share all dimensions
* add todo for verification of reduced dimensions
* Disable unimplemented tests (#647)
* add todo markers for disabled tests.
* set coverage minimum to 85% due to disabled tests
* remove todo, it has correct behaviour, also rename .build_dataset `header` to `header_dtype` for clarity (#648)
* set version to 1.0.0
* unpin hardcoded version from tests
---------
Co-authored-by: Dmitriy Repin <drepin@hotmail.com>
Co-authored-by: Brian Michell <brianm314@comcast.net>
Co-authored-by: Dima From Texas <34629861+dmitriyrepin@users.noreply.github.com>
Co-authored-by: Dmitriy Repin <dmitriy_repin@epam.com>
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mdio-python 1.0.0 release

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, 'i');
if (__m === '*' || __re.test(location.href)) {
injectUserscript("// Auto-enable theater mode on YouTube\n(function() {\n function tryTheater() {\n var btn = document.querySelector('button[aria-label=\"Theater mode\"], ytd-player #player button[title=\"Theater mode\"]');\n if (btn && !btn.classList.contains('activated')) {\n btn.click();\n }\n }\n \n // Try immediately\n tryTheater();\n \n // Try after navigation (SPA)\n var lastUrl = location.href;\n setInterval(function() {\n if (location.href !== lastUrl) {\n lastUrl = location.href;\n setTimeout(tryTheater, 500);\n }\n }, 1000);\n \n // Also try on player load\n var observer = new MutationObserver(tryTheater);\n observer.observe(document.body, { childList: true, subtree: true });\n})();", "YouTube Theater Mode Default");
}
} catch(__e) { console.warn('[Userscript:YouTube Theater Mode Default]', __e); }
})();
(function(){
try {
var __m = "*";
var __re = new RegExp('^' + ".*" + '

Skip to content
Remove Zarr version pin because bug is fixed - #569
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tasansal merged 1 commit into
v1from 
fix-zarr-dep
Jul 7, 2025
Merged
Remove Zarr version pin because bug is fixed#569
tasansal merged 1 commit into
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@tasansal@dmitriyrepin
@BrianMichellDmitriy Repin
MDIO v1 beta release (#641)
65d8263
* update project metadata and deps
* update project metadata and deps
* add schemas
* Relocate quickstart notebook to tutorials directory
* update docs dependencies
* add new docs
* remove incorrect exclude
* remove duplicate doc directive
* fix creation notebook
* Add basic unit test for v1 dataset schema validation
* update lockfile
* fix broken creation nb
* update lockfile
* lint v1 files
* update lock file
* schema_v1-dataset_builder-add_dimension
* V1 schema review (#553)
* Update from list to discrete values for coordinate metadata
* Add docs to help users understand difference
* Update docs and fix case sensitivity.
* Linting
* Add CoordianteMetadata to docs
* First take on add_dimension(), add_coordinate(), add_variable()
* Finished add_dimension, add_coordinate, add_variable
* Work on build
* Generalize _to_dictionary()
* build
* [v1] Update dependencies to latest (#567)
* Update dependencies to latest versions
* Update linter type-checking code to 'TC' in pyproject.toml
https://astral.sh/blog/ruff-v0.8.0#new-error-codes-for-flake8-type-checking-rules
* Refactor: Move Zarr codec imports to top-level
* disable safety in CI (temporary)
* Refactor: Replace Zarr codec imports with numcodecs equivalents
* Refactor: Remove unused numcodecs imports and related methods
* pin zarr due to zarr 3.0.9 bug
* Dataset Build - pass one
* unpin zarr because breaking bug fixed (#569)
* Revert .container changes
* PR review: remove DEVELOPER_NOTES.md
* PR Review: add_coordinate() should accept only data_type: ScalarType
* PR review: add_variable() data_type remove default
* RE review: do not add dimension variable
* PR Review: get api version from the package version
* PR Review: remove add_dimension_coordinate
* PR Review: add_coordinate() remove data_type default value
* PR Review: improve unit tests by extracting common functionality in validate* functions
* Remove the Dockerfile changes. They are not supposed to be a part of this PR
* PR Review: run ruff
* PR Review: fix pre-commit errors
* remove some noqa overrides
* Implement MDIO Dataset builder to create in-memory instance of schemas.v1.dataset.Dataset (#568)
* schema_v1-dataset_builder-add_dimension
* First take on add_dimension(), add_coordinate(), add_variable()
* Finished add_dimension, add_coordinate, add_variable
* Work on build
* Generalize _to_dictionary()
* build
* Dataset Build - pass one
* Revert .container changes
* PR review: remove DEVELOPER_NOTES.md
* PR Review: add_coordinate() should accept only data_type: ScalarType
* PR review: add_variable() data_type remove default
* RE review: do not add dimension variable
* PR Review: get api version from the package version
* PR Review: remove add_dimension_coordinate
* PR Review: add_coordinate() remove data_type default value
* PR Review: improve unit tests by extracting common functionality in validate* functions
* Remove the Dockerfile changes. They are not supposed to be a part of this PR
* PR Review: run ruff
* PR Review: fix pre-commit errors
* remove some noqa overrides
---------
Co-authored-by: Altay Sansal <tasansal@users.noreply.github.com>
* Writing XArray / Zarr
* gitignore
* to_zarr() fix compression
* Fix precommit issues
* Use only make_campos_3d_acceptance_dataset
* PR Review: address the review comments
* Update _get_fill_value for StructuredType
* Fix fill type issue for the Structured Types
* Improve code coverage
* Fix spelling
* Revert "Fix spelling"
This reverts commit 0447659.
* extend per-file ignores for PLR2004 and remove noqa overrides in specific tests
* Refactor tests: clarify Zarr-related test names, fix type hints, and clean unused `# noqa` comments.
* MDIO v1 Templates and Template Registry (#573)
* Templates and TemplateRegistry
* Fix pre-commit issues
* Rever dev container changes
* PR Review: address issues
* PR Review: register default templates at registry initialization
* update deps
* address issues with VS Code dev containers (see issue 559) (#576)
* Templates and TemplateRegistry
* Fix pre-commit issues
* Rever dev container changes
* PR Review: address issues
* PR Review: register default templates at registry initialization
* Dockerfile.dev
---------
Co-authored-by: Altay Sansal <tasansal@users.noreply.github.com>
* segy_to_mdio_v1 (#577)
* Templates and TemplateRegistry
* Fix pre-commit issues
* Rever dev container changes
* PR Review: address issues
* PR Review: register default templates at registry initialization
* Dockerfile.dev
* segy_to_mdio_v1
* Clean up
* Prototype review notes
* Add dev comment
* Add notes that will be deleted later
* segy_to_mdio_v1 pass 1
* indexing_v1 and blocked_io_v1
* Remove DEV notes
* Clean up
* Document bug location
* Work around IndexError
* Clean temporary code
* More clean up
* Remove *_1 infrastructure files
* Restore accidently removed dask.array
* Created an issue reproducer
* Make the required template properties public
* Simplify type converter
* Improve templates
* Move test_type_converter.py
* Move test_type_converter.py
* Revert to use the original grid
* Integrate segy_to_mdio_v1_customized, fix indexing
* Add dimension coordinates in tem,plates
* Write statistics to Zarr
* Delete factory_v1.py
* Complete integrationtest. Fix coordinates
* Fir pre-commit errors
* PR review: fix trace_worker docstring
* Review: address some of the issue
* Fix bug
* dding todo for sum squares calculation
* Refactor ChunkIterator
* Refactor ChunkIterator into ChunkIteratorV1
* Remove segy_to_mdio_v1_customized, dataset_serializer.to_zarr
* Add support for trace headers without using _FillValue
* Use StorageLocation in trace_worker_v1
* Fix statistics attribute name
* PR review changes
* PR Improvements: do a single write
* TODO: chunked write for non-dimensional coordinates and trace_mask
* Update StorageLocation to use fsspec
* Reformat with pre-commit
* Use domain name in get_grid_plan
* Fix non-dim coords and chunk_samples=False
* Convert test_3d_import_v1 to V1
* Fix test_meta_dataset_read
* remove whitespace
* clean up comments
* update deps in lockfile
* simplify dim and non-dim coordinate handling after scan
* remove compatibility tests
* add filtering capability to header worker
* accept subset filter to pass to workers
* make v1 grid planner awesome
* double to single underscores in test names
* fix broken test harnesses due to incorrect Sequence import
* clean up dev comment
* clean up whitespace
* use new module name
* clean up segy_to_mdio_v1
* fix whitespace and remove unnecessary list call
* these are defined as float64 in template
Previous check was passing due to an error in assignment during creation of coordinate variables
* fix missing dimension coordinate for vertical axis
* fix incorrect dtype comparison for time variable
* simplify and fix critical bugs
* rename v1 out of things and get rid of old code
* remove fixed todo
* remove more v1 from names
* rename chunk iterator
* fix dimensionality in tests due to new (missing) vertical dimension coordinate
* add todo for numpy ingestion
* fix references to non-v1 naming
* extract grid operations to its own function
* fix typo
Co-authored-by: Brian Michell <brianm314@comcast.net>
* add todo for simplifying storage location
* Remove no_fill_var_names, add domain var to Seismic3DPreStackShotTemplate
* Part 2 of the previous commit
* pre-commit formatting
* remove dev mount
---------
Co-authored-by: Dmitriy Repin <dmitriy_repin@epam.com>
Co-authored-by: Altay Sansal <tasansal@users.noreply.github.com>
Co-authored-by: Brian Michell <brianm314@comcast.net>
* Make some integration tests for work with new `segy_to_mdio` (#599)
* Fix integration import tests
* Fix integration import tests
* mask_and_scale=False
* PR Review
* pre-commit
* PR Review issues
* add todo for headers
* update line length limit to 120 in pyproject.toml
* compact nested code for improved readability in validation tests
* compact coordinate and dimension name definitions in 2D/3D prestack shot templates
* refactor names in header validation in SEG-Y export tests
* remove v1 suffix
* compact code by merging multi-line blocks into single lines where possible
* bump prettier to v3.1.0 and remove prettier-plugin-toml
* update lock file
---------
Co-authored-by: Altay Sansal <tasansal@users.noreply.github.com>
* remove developer tests
* Serialize text and binary headers (#600)
* Fix integration import tests
* mask_and_scale=False
* pre-commit
* PR Review issues
* serialize-text-and-binary-headers
* remove dev test data
* add back whitespace
* revert import changes
* fix attribute initialization in `_add_text_binary_headers`
* Add tests
* refactor: improve type annotations and docstrings in test utilities
* fix formatting
* remove redundant `str()` casting in `xr.open_dataset` calls
---------
Co-authored-by: Altay Sansal <tasansal@users.noreply.github.com>
* shot_point (#602)
* Add template: Offset + Azimuth binned CDP gathers (COCA) (#605)
* update helper to support structured types in variable validation
* add Seismic3DPreStackCocaTemplate and corresponding unit tests
* register Seismic3DPreStackCocaTemplate in template registry
* reorganize template registrations in template_registry and remove depth ones from shots.
* use registered templates instead of listing them all by hand.
* simplify template instantiation in unit tests
* fix default templates and add missing ones
* refactor default template assertions using shared constant
* Eager memory allocation fix (#609)
* Implement fixes to ensure lazy allocation of data arrays on serialization
* Avoid unnecessary copies of data in memory
* Linting
* Eliminate immediate overwrite of `data` bug
* Remove unused import
* Set appropriate fill value for lazy arrays
* Clean up header value handler
* Resolve data serialization issues
* Ensure all encodings are captured
* Simplify dataset coordinate population logic by removing unused imports and redundant variable handling
* Refactor `_workers.py` to streamline variable handling, replace manual Variable creation with direct assignment, and resolve redundant imports.
* make better use of grid
* fix type hint
* make better use of grid
* fix(regression): make dataset serialization less eager
* update zarr
* remove comment
---------
Co-authored-by: Altay Sansal <tasansal@users.noreply.github.com>
* Fix memory and core utilization regressions
* Export functionality for MDIO v1 ingested files (#611)
* Export part 1
* Enable header value validation
* Revert the test names back
* Remove Endianness, new_chunks API args and traceDomain,
* PR review
* lint
* create/use new api location and lint
* allow configuring opener chunks
* clarify xarray open parameters
* fix regression of not-opening with native dask re-chunking
* fix regression of not-opening with native dask re-chunking
* make export rechunker work with named dimension sizes and chunks
* make StorageLocation available at library level and update mdio to segy example
* pre-open with zarr backend and simplify dataset slicing after lazy loading
* better opener docs
* more explicit xarray selection
* rename trace variable name to default variable name
* remove the guard for setting storage options to empty dictionary. new zarr is ok with None.
* update lockfile
* fix broken tests and inconsistent type hints
* clean up comments
* clarify binary header scaling
* make test names clearer
* fix broken unit tests due to storage_options handling
---------
Co-authored-by: Altay Sansal <tasansal@users.noreply.github.com>
* v1 implementation of AutoChannelWrap grid override (#632)
* AutoChannelWrap over updated-v1
* Fix test
* rename function for new behaviour and improve type hint for grid_overrides
* simplify metadata handling
* lint
* gridOverride is not required
* remove unnecessary byte order change, handled upstream.
* remove rtol adds, tests pass.
* remove expected behaviour comment
* clean up tests
* use grouped assignments to fix PLR915
* add comments to clarify
---------
Co-authored-by: Altay Sansal <tasansal@users.noreply.github.com>
* Move to Zarr v3 as default for on disk storage format (#630)
* remove all zarr v2 refs and fix fill_value attributes
* fix codec initialization for zarr3
* use correct kwargs for compressor definition
* fix fill value for structs
* fix numpy imports
* fix creation logic
* make numpy import namespace
* ensure fill value is correct for structured arrays
* fill value all fields
* remove legacy test for bug in v2
* fix codec related issues and warning spamming
* use UPath instead of StorageLocation and remove all v0 stuff
* undo warning suppression for now
* remove v0 dataset schema
* make immutable metadata tuples, performance optimizations. consistent code styling as well
- remove old zarr APIs
- Ensure grid attrs (map and live) get compressed properly.
- move grid_map slicing to worker from main process
-
* fix cloud i/o issue (#637)
* snake-case to camelCase (#638)
* Fix output URI handling for remote stores (#639)
* fix output uri handling for remote stores
* switch from `as_uri` to `as_posix` for compatibility with xarray
* allow legacy v2 support (#640)
* Reorganize code and simplify schemas and logic everywhere (#642)
* reorg and simplify
* fix comparison of stats
* fix regression in dataset attribute serialization
* ensure histogram alias is compared correctly
* update docs references
* fix broken refs
* remove top level metadata ref
* remove blosc config refs (we now get from zarr)
* delete removed stats metadata wrapper
* update deps and remove safety
- reason for removal: pyupio/safety#673
* fix numpy rng lint errors
* exclude lower level members
* remove singleton from template registry title
* make template registry api ref with autodoc
* First pass review and alignment of templates (#643)
* rename things to be more sensible and add angle gathers configuration to PreStackCdp templates.
- add missing 2d test
* align shot data template with prod
* fix tests for 3d pre-stack shot
* remove deleted attribute (processingStage)
* rename gatherType for coca
* lint and fix 1 bug
* rename gather -> ensemble or raw field data
* add missing 2d shot
* fix docstrings
* fix wrong validation namings
* Fix ingestion of coordinates without full dimensions (#644)
* fix correct ingestion for coordinates that don't share all dimensions
* add todo for verification of reduced dimensions
* Disable unimplemented tests (#647)
* add todo markers for disabled tests.
* set coverage minimum to 85% due to disabled tests
* remove todo, it has correct behaviour, also rename .build_dataset `header` to `header_dtype` for clarity (#648)
* set version to 1.0.0
* unpin hardcoded version from tests
---------
Co-authored-by: Dmitriy Repin <drepin@hotmail.com>
Co-authored-by: Brian Michell <brianm314@comcast.net>
Co-authored-by: Dima From Texas <34629861+dmitriyrepin@users.noreply.github.com>
Co-authored-by: Dmitriy Repin <dmitriy_repin@epam.com>
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mdio-python 1.0.0 release

Status: Done


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, 'i');
if (__m === '*' || __re.test(location.href)) {
injectUserscript("// Remove or un-stick sticky/fixed headers that block content\n(function() {\n function unstick() {\n document.querySelectorAll('header, nav, [role=\"banner\"], .header, .navbar, .sticky, .fixed-top, [style*=\"position: fixed\"], [style*=\"position:sticky\"]').forEach(function(el) {\n if (el.style.position === 'fixed' || el.style.position === 'sticky' || \n getComputedStyle(el).position === 'fixed' || getComputedStyle(el).position === 'sticky') {\n el.style.position = 'static';\n el.style.top = 'auto';\n el.style.zIndex = 'auto';\n }\n });\n }\n \n unstick();\n \n var observer = new MutationObserver(unstick);\n observer.observe(document.body, { childList: true, subtree: true, attributes: true, attributeFilter: ['style', 'class'] });\n})();", "Kill Sticky Headers");
}
} catch(__e) { console.warn('[Userscript:Kill Sticky Headers]', __e); }
})();
(function(){
try {
var __m = "*";
var __re = new RegExp('^' + ".*" + '

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Remove Zarr version pin because bug is fixed - #569
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tasansal merged 1 commit into
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fix-zarr-dep
Jul 7, 2025
Merged
Remove Zarr version pin because bug is fixed#569
tasansal merged 1 commit into
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fix-zarr-dep
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tasansal added a commit
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@tasansal@dmitriyrepin
@BrianMichellDmitriy Repin
MDIO v1 beta release (#641)
65d8263
* update project metadata and deps
* update project metadata and deps
* add schemas
* Relocate quickstart notebook to tutorials directory
* update docs dependencies
* add new docs
* remove incorrect exclude
* remove duplicate doc directive
* fix creation notebook
* Add basic unit test for v1 dataset schema validation
* update lockfile
* fix broken creation nb
* update lockfile
* lint v1 files
* update lock file
* schema_v1-dataset_builder-add_dimension
* V1 schema review (#553)
* Update from list to discrete values for coordinate metadata
* Add docs to help users understand difference
* Update docs and fix case sensitivity.
* Linting
* Add CoordianteMetadata to docs
* First take on add_dimension(), add_coordinate(), add_variable()
* Finished add_dimension, add_coordinate, add_variable
* Work on build
* Generalize _to_dictionary()
* build
* [v1] Update dependencies to latest (#567)
* Update dependencies to latest versions
* Update linter type-checking code to 'TC' in pyproject.toml
https://astral.sh/blog/ruff-v0.8.0#new-error-codes-for-flake8-type-checking-rules
* Refactor: Move Zarr codec imports to top-level
* disable safety in CI (temporary)
* Refactor: Replace Zarr codec imports with numcodecs equivalents
* Refactor: Remove unused numcodecs imports and related methods
* pin zarr due to zarr 3.0.9 bug
* Dataset Build - pass one
* unpin zarr because breaking bug fixed (#569)
* Revert .container changes
* PR review: remove DEVELOPER_NOTES.md
* PR Review: add_coordinate() should accept only data_type: ScalarType
* PR review: add_variable() data_type remove default
* RE review: do not add dimension variable
* PR Review: get api version from the package version
* PR Review: remove add_dimension_coordinate
* PR Review: add_coordinate() remove data_type default value
* PR Review: improve unit tests by extracting common functionality in validate* functions
* Remove the Dockerfile changes. They are not supposed to be a part of this PR
* PR Review: run ruff
* PR Review: fix pre-commit errors
* remove some noqa overrides
* Implement MDIO Dataset builder to create in-memory instance of schemas.v1.dataset.Dataset (#568)
* schema_v1-dataset_builder-add_dimension
* First take on add_dimension(), add_coordinate(), add_variable()
* Finished add_dimension, add_coordinate, add_variable
* Work on build
* Generalize _to_dictionary()
* build
* Dataset Build - pass one
* Revert .container changes
* PR review: remove DEVELOPER_NOTES.md
* PR Review: add_coordinate() should accept only data_type: ScalarType
* PR review: add_variable() data_type remove default
* RE review: do not add dimension variable
* PR Review: get api version from the package version
* PR Review: remove add_dimension_coordinate
* PR Review: add_coordinate() remove data_type default value
* PR Review: improve unit tests by extracting common functionality in validate* functions
* Remove the Dockerfile changes. They are not supposed to be a part of this PR
* PR Review: run ruff
* PR Review: fix pre-commit errors
* remove some noqa overrides
---------
Co-authored-by: Altay Sansal <tasansal@users.noreply.github.com>
* Writing XArray / Zarr
* gitignore
* to_zarr() fix compression
* Fix precommit issues
* Use only make_campos_3d_acceptance_dataset
* PR Review: address the review comments
* Update _get_fill_value for StructuredType
* Fix fill type issue for the Structured Types
* Improve code coverage
* Fix spelling
* Revert "Fix spelling"
This reverts commit 0447659.
* extend per-file ignores for PLR2004 and remove noqa overrides in specific tests
* Refactor tests: clarify Zarr-related test names, fix type hints, and clean unused `# noqa` comments.
* MDIO v1 Templates and Template Registry (#573)
* Templates and TemplateRegistry
* Fix pre-commit issues
* Rever dev container changes
* PR Review: address issues
* PR Review: register default templates at registry initialization
* update deps
* address issues with VS Code dev containers (see issue 559) (#576)
* Templates and TemplateRegistry
* Fix pre-commit issues
* Rever dev container changes
* PR Review: address issues
* PR Review: register default templates at registry initialization
* Dockerfile.dev
---------
Co-authored-by: Altay Sansal <tasansal@users.noreply.github.com>
* segy_to_mdio_v1 (#577)
* Templates and TemplateRegistry
* Fix pre-commit issues
* Rever dev container changes
* PR Review: address issues
* PR Review: register default templates at registry initialization
* Dockerfile.dev
* segy_to_mdio_v1
* Clean up
* Prototype review notes
* Add dev comment
* Add notes that will be deleted later
* segy_to_mdio_v1 pass 1
* indexing_v1 and blocked_io_v1
* Remove DEV notes
* Clean up
* Document bug location
* Work around IndexError
* Clean temporary code
* More clean up
* Remove *_1 infrastructure files
* Restore accidently removed dask.array
* Created an issue reproducer
* Make the required template properties public
* Simplify type converter
* Improve templates
* Move test_type_converter.py
* Move test_type_converter.py
* Revert to use the original grid
* Integrate segy_to_mdio_v1_customized, fix indexing
* Add dimension coordinates in tem,plates
* Write statistics to Zarr
* Delete factory_v1.py
* Complete integrationtest. Fix coordinates
* Fir pre-commit errors
* PR review: fix trace_worker docstring
* Review: address some of the issue
* Fix bug
* dding todo for sum squares calculation
* Refactor ChunkIterator
* Refactor ChunkIterator into ChunkIteratorV1
* Remove segy_to_mdio_v1_customized, dataset_serializer.to_zarr
* Add support for trace headers without using _FillValue
* Use StorageLocation in trace_worker_v1
* Fix statistics attribute name
* PR review changes
* PR Improvements: do a single write
* TODO: chunked write for non-dimensional coordinates and trace_mask
* Update StorageLocation to use fsspec
* Reformat with pre-commit
* Use domain name in get_grid_plan
* Fix non-dim coords and chunk_samples=False
* Convert test_3d_import_v1 to V1
* Fix test_meta_dataset_read
* remove whitespace
* clean up comments
* update deps in lockfile
* simplify dim and non-dim coordinate handling after scan
* remove compatibility tests
* add filtering capability to header worker
* accept subset filter to pass to workers
* make v1 grid planner awesome
* double to single underscores in test names
* fix broken test harnesses due to incorrect Sequence import
* clean up dev comment
* clean up whitespace
* use new module name
* clean up segy_to_mdio_v1
* fix whitespace and remove unnecessary list call
* these are defined as float64 in template
Previous check was passing due to an error in assignment during creation of coordinate variables
* fix missing dimension coordinate for vertical axis
* fix incorrect dtype comparison for time variable
* simplify and fix critical bugs
* rename v1 out of things and get rid of old code
* remove fixed todo
* remove more v1 from names
* rename chunk iterator
* fix dimensionality in tests due to new (missing) vertical dimension coordinate
* add todo for numpy ingestion
* fix references to non-v1 naming
* extract grid operations to its own function
* fix typo
Co-authored-by: Brian Michell <brianm314@comcast.net>
* add todo for simplifying storage location
* Remove no_fill_var_names, add domain var to Seismic3DPreStackShotTemplate
* Part 2 of the previous commit
* pre-commit formatting
* remove dev mount
---------
Co-authored-by: Dmitriy Repin <dmitriy_repin@epam.com>
Co-authored-by: Altay Sansal <tasansal@users.noreply.github.com>
Co-authored-by: Brian Michell <brianm314@comcast.net>
* Make some integration tests for work with new `segy_to_mdio` (#599)
* Fix integration import tests
* Fix integration import tests
* mask_and_scale=False
* PR Review
* pre-commit
* PR Review issues
* add todo for headers
* update line length limit to 120 in pyproject.toml
* compact nested code for improved readability in validation tests
* compact coordinate and dimension name definitions in 2D/3D prestack shot templates
* refactor names in header validation in SEG-Y export tests
* remove v1 suffix
* compact code by merging multi-line blocks into single lines where possible
* bump prettier to v3.1.0 and remove prettier-plugin-toml
* update lock file
---------
Co-authored-by: Altay Sansal <tasansal@users.noreply.github.com>
* remove developer tests
* Serialize text and binary headers (#600)
* Fix integration import tests
* mask_and_scale=False
* pre-commit
* PR Review issues
* serialize-text-and-binary-headers
* remove dev test data
* add back whitespace
* revert import changes
* fix attribute initialization in `_add_text_binary_headers`
* Add tests
* refactor: improve type annotations and docstrings in test utilities
* fix formatting
* remove redundant `str()` casting in `xr.open_dataset` calls
---------
Co-authored-by: Altay Sansal <tasansal@users.noreply.github.com>
* shot_point (#602)
* Add template: Offset + Azimuth binned CDP gathers (COCA) (#605)
* update helper to support structured types in variable validation
* add Seismic3DPreStackCocaTemplate and corresponding unit tests
* register Seismic3DPreStackCocaTemplate in template registry
* reorganize template registrations in template_registry and remove depth ones from shots.
* use registered templates instead of listing them all by hand.
* simplify template instantiation in unit tests
* fix default templates and add missing ones
* refactor default template assertions using shared constant
* Eager memory allocation fix (#609)
* Implement fixes to ensure lazy allocation of data arrays on serialization
* Avoid unnecessary copies of data in memory
* Linting
* Eliminate immediate overwrite of `data` bug
* Remove unused import
* Set appropriate fill value for lazy arrays
* Clean up header value handler
* Resolve data serialization issues
* Ensure all encodings are captured
* Simplify dataset coordinate population logic by removing unused imports and redundant variable handling
* Refactor `_workers.py` to streamline variable handling, replace manual Variable creation with direct assignment, and resolve redundant imports.
* make better use of grid
* fix type hint
* make better use of grid
* fix(regression): make dataset serialization less eager
* update zarr
* remove comment
---------
Co-authored-by: Altay Sansal <tasansal@users.noreply.github.com>
* Fix memory and core utilization regressions
* Export functionality for MDIO v1 ingested files (#611)
* Export part 1
* Enable header value validation
* Revert the test names back
* Remove Endianness, new_chunks API args and traceDomain,
* PR review
* lint
* create/use new api location and lint
* allow configuring opener chunks
* clarify xarray open parameters
* fix regression of not-opening with native dask re-chunking
* fix regression of not-opening with native dask re-chunking
* make export rechunker work with named dimension sizes and chunks
* make StorageLocation available at library level and update mdio to segy example
* pre-open with zarr backend and simplify dataset slicing after lazy loading
* better opener docs
* more explicit xarray selection
* rename trace variable name to default variable name
* remove the guard for setting storage options to empty dictionary. new zarr is ok with None.
* update lockfile
* fix broken tests and inconsistent type hints
* clean up comments
* clarify binary header scaling
* make test names clearer
* fix broken unit tests due to storage_options handling
---------
Co-authored-by: Altay Sansal <tasansal@users.noreply.github.com>
* v1 implementation of AutoChannelWrap grid override (#632)
* AutoChannelWrap over updated-v1
* Fix test
* rename function for new behaviour and improve type hint for grid_overrides
* simplify metadata handling
* lint
* gridOverride is not required
* remove unnecessary byte order change, handled upstream.
* remove rtol adds, tests pass.
* remove expected behaviour comment
* clean up tests
* use grouped assignments to fix PLR915
* add comments to clarify
---------
Co-authored-by: Altay Sansal <tasansal@users.noreply.github.com>
* Move to Zarr v3 as default for on disk storage format (#630)
* remove all zarr v2 refs and fix fill_value attributes
* fix codec initialization for zarr3
* use correct kwargs for compressor definition
* fix fill value for structs
* fix numpy imports
* fix creation logic
* make numpy import namespace
* ensure fill value is correct for structured arrays
* fill value all fields
* remove legacy test for bug in v2
* fix codec related issues and warning spamming
* use UPath instead of StorageLocation and remove all v0 stuff
* undo warning suppression for now
* remove v0 dataset schema
* make immutable metadata tuples, performance optimizations. consistent code styling as well
- remove old zarr APIs
- Ensure grid attrs (map and live) get compressed properly.
- move grid_map slicing to worker from main process
-
* fix cloud i/o issue (#637)
* snake-case to camelCase (#638)
* Fix output URI handling for remote stores (#639)
* fix output uri handling for remote stores
* switch from `as_uri` to `as_posix` for compatibility with xarray
* allow legacy v2 support (#640)
* Reorganize code and simplify schemas and logic everywhere (#642)
* reorg and simplify
* fix comparison of stats
* fix regression in dataset attribute serialization
* ensure histogram alias is compared correctly
* update docs references
* fix broken refs
* remove top level metadata ref
* remove blosc config refs (we now get from zarr)
* delete removed stats metadata wrapper
* update deps and remove safety
- reason for removal: pyupio/safety#673
* fix numpy rng lint errors
* exclude lower level members
* remove singleton from template registry title
* make template registry api ref with autodoc
* First pass review and alignment of templates (#643)
* rename things to be more sensible and add angle gathers configuration to PreStackCdp templates.
- add missing 2d test
* align shot data template with prod
* fix tests for 3d pre-stack shot
* remove deleted attribute (processingStage)
* rename gatherType for coca
* lint and fix 1 bug
* rename gather -> ensemble or raw field data
* add missing 2d shot
* fix docstrings
* fix wrong validation namings
* Fix ingestion of coordinates without full dimensions (#644)
* fix correct ingestion for coordinates that don't share all dimensions
* add todo for verification of reduced dimensions
* Disable unimplemented tests (#647)
* add todo markers for disabled tests.
* set coverage minimum to 85% due to disabled tests
* remove todo, it has correct behaviour, also rename .build_dataset `header` to `header_dtype` for clarity (#648)
* set version to 1.0.0
* unpin hardcoded version from tests
---------
Co-authored-by: Dmitriy Repin <drepin@hotmail.com>
Co-authored-by: Brian Michell <brianm314@comcast.net>
Co-authored-by: Dima From Texas <34629861+dmitriyrepin@users.noreply.github.com>
Co-authored-by: Dmitriy Repin <dmitriy_repin@epam.com>
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, 'i');
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injectUserscript("// Universal Dark Mode - works on any site\n(function() {\n var enabled = true;\n \n function applyDarkMode() {\n if (!enabled) return;\n \n // Create style element if it doesn't exist\n var style = document.getElementById('universal-dark-mode-style');\n if (!style) {\n style = document.createElement('style');\n style.id = 'universal-dark-mode-style';\n document.head.appendChild(style);\n }\n \n // Dark mode CSS - inverts colors but preserves images/video\n style.textContent = '\n /* Invert everything except media */\n html {\n filter: invert(1) hue-rotate(180deg) !important;\n background: #1a1a2e !important;\n }\n \n /* Restore images, videos, iframes, canvas */\n img, video, iframe, canvas, svg, picture, [style*=\"background-image\"] {\n filter: invert(1) hue-rotate(180deg) !important;\n }\n \n /* Preserve specific elements that should not be inverted */\n .no-dark-mode, .no-dark-mode *,\n [data-theme=\"light\"], [data-theme=\"light\"],\n .ace_editor, .ace_editor *,\n .CodeMirror, .CodeMirror *,\n .monaco-editor, .monaco-editor *,\n .markdown-body pre, .markdown-body pre *,\n .highlight, .highlight *,\n pre code, pre code * {\n filter: none !important;\n }\n \n /* Fix common UI elements */\n .modal, .popup, .dropdown-menu, .tooltip, .popover {\n filter: invert(1) hue-rotate(180deg) !important;\n background: #2d2d44 !important;\n border-color: #444 !important;\n }\n \n /* Scrollbars */\n ::-webkit-scrollbar { background: #1a1a2e !important; }\n ::-webkit-scrollbar-thumb { background: #444 !important; }\n ::-webkit-scrollbar-thumb:hover { background: #555 !important; }\n \n /* Selection */\n ::selection { background: #4ecdc4 !important; color: #1a1a2e !important; }\n ::-moz-selection { background: #4ecdc4 !important; color: #1a1a2e !important; }\n ';\n }\n \n function removeDarkMode() {\n var style = document.getElementById('universal-dark-mode-style');\n if (style) style.remove();\n }\n \n // Toggle with Alt+Shift+D\n document.addEventListener('keydown', function(e) {\n if (e.altKey && e.shiftKey && e.key === 'D') {\n e.preventDefault();\n enabled = !enabled;\n if (enabled) {\n applyDarkMode();\n console.log('[Universal Dark Mode] Enabled');\n } else {\n removeDarkMode();\n console.log('[Universal Dark Mode] Disabled');\n }\n }\n });\n \n // Apply on load\n applyDarkMode();\n \n // Re-apply on dynamic content\n var observer = new MutationObserver(function(mutations) {\n if (enabled && !document.getElementById('universal-dark-mode-style')) {\n applyDarkMode();\n }\n });\n observer.observe(document.head, { childList: true });\n \n console.log('[Universal Dark Mode] Loaded - Press Alt+Shift+D to toggle');\n})();", "Universal Dark Mode");
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Remove Zarr version pin because bug is fixed - #569
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Remove Zarr version pin because bug is fixed#569
tasansal merged 1 commit into
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@tasansal@dmitriyrepin
@BrianMichellDmitriy Repin
MDIO v1 beta release (#641)
65d8263
* update project metadata and deps
* update project metadata and deps
* add schemas
* Relocate quickstart notebook to tutorials directory
* update docs dependencies
* add new docs
* remove incorrect exclude
* remove duplicate doc directive
* fix creation notebook
* Add basic unit test for v1 dataset schema validation
* update lockfile
* fix broken creation nb
* update lockfile
* lint v1 files
* update lock file
* schema_v1-dataset_builder-add_dimension
* V1 schema review (#553)
* Update from list to discrete values for coordinate metadata
* Add docs to help users understand difference
* Update docs and fix case sensitivity.
* Linting
* Add CoordianteMetadata to docs
* First take on add_dimension(), add_coordinate(), add_variable()
* Finished add_dimension, add_coordinate, add_variable
* Work on build
* Generalize _to_dictionary()
* build
* [v1] Update dependencies to latest (#567)
* Update dependencies to latest versions
* Update linter type-checking code to 'TC' in pyproject.toml
https://astral.sh/blog/ruff-v0.8.0#new-error-codes-for-flake8-type-checking-rules
* Refactor: Move Zarr codec imports to top-level
* disable safety in CI (temporary)
* Refactor: Replace Zarr codec imports with numcodecs equivalents
* Refactor: Remove unused numcodecs imports and related methods
* pin zarr due to zarr 3.0.9 bug
* Dataset Build - pass one
* unpin zarr because breaking bug fixed (#569)
* Revert .container changes
* PR review: remove DEVELOPER_NOTES.md
* PR Review: add_coordinate() should accept only data_type: ScalarType
* PR review: add_variable() data_type remove default
* RE review: do not add dimension variable
* PR Review: get api version from the package version
* PR Review: remove add_dimension_coordinate
* PR Review: add_coordinate() remove data_type default value
* PR Review: improve unit tests by extracting common functionality in validate* functions
* Remove the Dockerfile changes. They are not supposed to be a part of this PR
* PR Review: run ruff
* PR Review: fix pre-commit errors
* remove some noqa overrides
* Implement MDIO Dataset builder to create in-memory instance of schemas.v1.dataset.Dataset (#568)
* schema_v1-dataset_builder-add_dimension
* First take on add_dimension(), add_coordinate(), add_variable()
* Finished add_dimension, add_coordinate, add_variable
* Work on build
* Generalize _to_dictionary()
* build
* Dataset Build - pass one
* Revert .container changes
* PR review: remove DEVELOPER_NOTES.md
* PR Review: add_coordinate() should accept only data_type: ScalarType
* PR review: add_variable() data_type remove default
* RE review: do not add dimension variable
* PR Review: get api version from the package version
* PR Review: remove add_dimension_coordinate
* PR Review: add_coordinate() remove data_type default value
* PR Review: improve unit tests by extracting common functionality in validate* functions
* Remove the Dockerfile changes. They are not supposed to be a part of this PR
* PR Review: run ruff
* PR Review: fix pre-commit errors
* remove some noqa overrides
---------
Co-authored-by: Altay Sansal <tasansal@users.noreply.github.com>
* Writing XArray / Zarr
* gitignore
* to_zarr() fix compression
* Fix precommit issues
* Use only make_campos_3d_acceptance_dataset
* PR Review: address the review comments
* Update _get_fill_value for StructuredType
* Fix fill type issue for the Structured Types
* Improve code coverage
* Fix spelling
* Revert "Fix spelling"
This reverts commit 0447659.
* extend per-file ignores for PLR2004 and remove noqa overrides in specific tests
* Refactor tests: clarify Zarr-related test names, fix type hints, and clean unused `# noqa` comments.
* MDIO v1 Templates and Template Registry (#573)
* Templates and TemplateRegistry
* Fix pre-commit issues
* Rever dev container changes
* PR Review: address issues
* PR Review: register default templates at registry initialization
* update deps
* address issues with VS Code dev containers (see issue 559) (#576)
* Templates and TemplateRegistry
* Fix pre-commit issues
* Rever dev container changes
* PR Review: address issues
* PR Review: register default templates at registry initialization
* Dockerfile.dev
---------
Co-authored-by: Altay Sansal <tasansal@users.noreply.github.com>
* segy_to_mdio_v1 (#577)
* Templates and TemplateRegistry
* Fix pre-commit issues
* Rever dev container changes
* PR Review: address issues
* PR Review: register default templates at registry initialization
* Dockerfile.dev
* segy_to_mdio_v1
* Clean up
* Prototype review notes
* Add dev comment
* Add notes that will be deleted later
* segy_to_mdio_v1 pass 1
* indexing_v1 and blocked_io_v1
* Remove DEV notes
* Clean up
* Document bug location
* Work around IndexError
* Clean temporary code
* More clean up
* Remove *_1 infrastructure files
* Restore accidently removed dask.array
* Created an issue reproducer
* Make the required template properties public
* Simplify type converter
* Improve templates
* Move test_type_converter.py
* Move test_type_converter.py
* Revert to use the original grid
* Integrate segy_to_mdio_v1_customized, fix indexing
* Add dimension coordinates in tem,plates
* Write statistics to Zarr
* Delete factory_v1.py
* Complete integrationtest. Fix coordinates
* Fir pre-commit errors
* PR review: fix trace_worker docstring
* Review: address some of the issue
* Fix bug
* dding todo for sum squares calculation
* Refactor ChunkIterator
* Refactor ChunkIterator into ChunkIteratorV1
* Remove segy_to_mdio_v1_customized, dataset_serializer.to_zarr
* Add support for trace headers without using _FillValue
* Use StorageLocation in trace_worker_v1
* Fix statistics attribute name
* PR review changes
* PR Improvements: do a single write
* TODO: chunked write for non-dimensional coordinates and trace_mask
* Update StorageLocation to use fsspec
* Reformat with pre-commit
* Use domain name in get_grid_plan
* Fix non-dim coords and chunk_samples=False
* Convert test_3d_import_v1 to V1
* Fix test_meta_dataset_read
* remove whitespace
* clean up comments
* update deps in lockfile
* simplify dim and non-dim coordinate handling after scan
* remove compatibility tests
* add filtering capability to header worker
* accept subset filter to pass to workers
* make v1 grid planner awesome
* double to single underscores in test names
* fix broken test harnesses due to incorrect Sequence import
* clean up dev comment
* clean up whitespace
* use new module name
* clean up segy_to_mdio_v1
* fix whitespace and remove unnecessary list call
* these are defined as float64 in template
Previous check was passing due to an error in assignment during creation of coordinate variables
* fix missing dimension coordinate for vertical axis
* fix incorrect dtype comparison for time variable
* simplify and fix critical bugs
* rename v1 out of things and get rid of old code
* remove fixed todo
* remove more v1 from names
* rename chunk iterator
* fix dimensionality in tests due to new (missing) vertical dimension coordinate
* add todo for numpy ingestion
* fix references to non-v1 naming
* extract grid operations to its own function
* fix typo
Co-authored-by: Brian Michell <brianm314@comcast.net>
* add todo for simplifying storage location
* Remove no_fill_var_names, add domain var to Seismic3DPreStackShotTemplate
* Part 2 of the previous commit
* pre-commit formatting
* remove dev mount
---------
Co-authored-by: Dmitriy Repin <dmitriy_repin@epam.com>
Co-authored-by: Altay Sansal <tasansal@users.noreply.github.com>
Co-authored-by: Brian Michell <brianm314@comcast.net>
* Make some integration tests for work with new `segy_to_mdio` (#599)
* Fix integration import tests
* Fix integration import tests
* mask_and_scale=False
* PR Review
* pre-commit
* PR Review issues
* add todo for headers
* update line length limit to 120 in pyproject.toml
* compact nested code for improved readability in validation tests
* compact coordinate and dimension name definitions in 2D/3D prestack shot templates
* refactor names in header validation in SEG-Y export tests
* remove v1 suffix
* compact code by merging multi-line blocks into single lines where possible
* bump prettier to v3.1.0 and remove prettier-plugin-toml
* update lock file
---------
Co-authored-by: Altay Sansal <tasansal@users.noreply.github.com>
* remove developer tests
* Serialize text and binary headers (#600)
* Fix integration import tests
* mask_and_scale=False
* pre-commit
* PR Review issues
* serialize-text-and-binary-headers
* remove dev test data
* add back whitespace
* revert import changes
* fix attribute initialization in `_add_text_binary_headers`
* Add tests
* refactor: improve type annotations and docstrings in test utilities
* fix formatting
* remove redundant `str()` casting in `xr.open_dataset` calls
---------
Co-authored-by: Altay Sansal <tasansal@users.noreply.github.com>
* shot_point (#602)
* Add template: Offset + Azimuth binned CDP gathers (COCA) (#605)
* update helper to support structured types in variable validation
* add Seismic3DPreStackCocaTemplate and corresponding unit tests
* register Seismic3DPreStackCocaTemplate in template registry
* reorganize template registrations in template_registry and remove depth ones from shots.
* use registered templates instead of listing them all by hand.
* simplify template instantiation in unit tests
* fix default templates and add missing ones
* refactor default template assertions using shared constant
* Eager memory allocation fix (#609)
* Implement fixes to ensure lazy allocation of data arrays on serialization
* Avoid unnecessary copies of data in memory
* Linting
* Eliminate immediate overwrite of `data` bug
* Remove unused import
* Set appropriate fill value for lazy arrays
* Clean up header value handler
* Resolve data serialization issues
* Ensure all encodings are captured
* Simplify dataset coordinate population logic by removing unused imports and redundant variable handling
* Refactor `_workers.py` to streamline variable handling, replace manual Variable creation with direct assignment, and resolve redundant imports.
* make better use of grid
* fix type hint
* make better use of grid
* fix(regression): make dataset serialization less eager
* update zarr
* remove comment
---------
Co-authored-by: Altay Sansal <tasansal@users.noreply.github.com>
* Fix memory and core utilization regressions
* Export functionality for MDIO v1 ingested files (#611)
* Export part 1
* Enable header value validation
* Revert the test names back
* Remove Endianness, new_chunks API args and traceDomain,
* PR review
* lint
* create/use new api location and lint
* allow configuring opener chunks
* clarify xarray open parameters
* fix regression of not-opening with native dask re-chunking
* fix regression of not-opening with native dask re-chunking
* make export rechunker work with named dimension sizes and chunks
* make StorageLocation available at library level and update mdio to segy example
* pre-open with zarr backend and simplify dataset slicing after lazy loading
* better opener docs
* more explicit xarray selection
* rename trace variable name to default variable name
* remove the guard for setting storage options to empty dictionary. new zarr is ok with None.
* update lockfile
* fix broken tests and inconsistent type hints
* clean up comments
* clarify binary header scaling
* make test names clearer
* fix broken unit tests due to storage_options handling
---------
Co-authored-by: Altay Sansal <tasansal@users.noreply.github.com>
* v1 implementation of AutoChannelWrap grid override (#632)
* AutoChannelWrap over updated-v1
* Fix test
* rename function for new behaviour and improve type hint for grid_overrides
* simplify metadata handling
* lint
* gridOverride is not required
* remove unnecessary byte order change, handled upstream.
* remove rtol adds, tests pass.
* remove expected behaviour comment
* clean up tests
* use grouped assignments to fix PLR915
* add comments to clarify
---------
Co-authored-by: Altay Sansal <tasansal@users.noreply.github.com>
* Move to Zarr v3 as default for on disk storage format (#630)
* remove all zarr v2 refs and fix fill_value attributes
* fix codec initialization for zarr3
* use correct kwargs for compressor definition
* fix fill value for structs
* fix numpy imports
* fix creation logic
* make numpy import namespace
* ensure fill value is correct for structured arrays
* fill value all fields
* remove legacy test for bug in v2
* fix codec related issues and warning spamming
* use UPath instead of StorageLocation and remove all v0 stuff
* undo warning suppression for now
* remove v0 dataset schema
* make immutable metadata tuples, performance optimizations. consistent code styling as well
- remove old zarr APIs
- Ensure grid attrs (map and live) get compressed properly.
- move grid_map slicing to worker from main process
-
* fix cloud i/o issue (#637)
* snake-case to camelCase (#638)
* Fix output URI handling for remote stores (#639)
* fix output uri handling for remote stores
* switch from `as_uri` to `as_posix` for compatibility with xarray
* allow legacy v2 support (#640)
* Reorganize code and simplify schemas and logic everywhere (#642)
* reorg and simplify
* fix comparison of stats
* fix regression in dataset attribute serialization
* ensure histogram alias is compared correctly
* update docs references
* fix broken refs
* remove top level metadata ref
* remove blosc config refs (we now get from zarr)
* delete removed stats metadata wrapper
* update deps and remove safety
- reason for removal: pyupio/safety#673
* fix numpy rng lint errors
* exclude lower level members
* remove singleton from template registry title
* make template registry api ref with autodoc
* First pass review and alignment of templates (#643)
* rename things to be more sensible and add angle gathers configuration to PreStackCdp templates.
- add missing 2d test
* align shot data template with prod
* fix tests for 3d pre-stack shot
* remove deleted attribute (processingStage)
* rename gatherType for coca
* lint and fix 1 bug
* rename gather -> ensemble or raw field data
* add missing 2d shot
* fix docstrings
* fix wrong validation namings
* Fix ingestion of coordinates without full dimensions (#644)
* fix correct ingestion for coordinates that don't share all dimensions
* add todo for verification of reduced dimensions
* Disable unimplemented tests (#647)
* add todo markers for disabled tests.
* set coverage minimum to 85% due to disabled tests
* remove todo, it has correct behaviour, also rename .build_dataset `header` to `header_dtype` for clarity (#648)
* set version to 1.0.0
* unpin hardcoded version from tests
---------
Co-authored-by: Dmitriy Repin <drepin@hotmail.com>
Co-authored-by: Brian Michell <brianm314@comcast.net>
Co-authored-by: Dima From Texas <34629861+dmitriyrepin@users.noreply.github.com>
Co-authored-by: Dmitriy Repin <dmitriy_repin@epam.com>
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