From e98430c261a9f188c15da60e030e10f58338908b Mon Sep 17 00:00:00 2001 From: Chris Chamberlain Date: Mon, 27 May 2024 17:00:32 +1200 Subject: [PATCH] doc improvements; docs layout; theme switcher; update mkdocs libs; --- CHANGELOG.md | 3 + README.md | 14 +- docs/domain_model/demo_thp_stategies.md | 59 -- .../arrow_sanity_testing.md | 4 +- .../hazard_import_processing-may-2024.md | 0 .../revision_4_disagg_testing.md | 0 .../revision_4_migration_testing.md | 0 mkdocs.yml | 69 +- poetry.lock | 782 ++++++++---------- pyproject.toml | 2 +- 10 files changed, 408 insertions(+), 525 deletions(-) delete mode 100644 docs/domain_model/demo_thp_stategies.md rename docs/{domain_model => migration}/arrow_sanity_testing.md (99%) rename docs/{domain_model => migration}/hazard_import_processing-may-2024.md (100%) rename docs/{domain_model => migration}/revision_4_disagg_testing.md (100%) rename docs/{domain_model => migration}/revision_4_migration_testing.md (100%) diff --git a/CHANGELOG.md b/CHANGELOG.md index 5d65e8a..1649be5 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -12,10 +12,13 @@ - ths_r4_query - migration/ths_r4_sanity - extract datasets directly from hdf5 + - more documtention ### Changed - switch to nzshm-common#pre-release branch - switch to nzshm-model#pre-release branch + - move outdated scripts to scripts/legacy + - new documentation theme ## [0.8.0] - 2024-02 ### Added diff --git a/README.md b/README.md index f428691..ae72151 100644 --- a/README.md +++ b/README.md @@ -12,12 +12,18 @@ * PyPI: * Free software: GPL-3.0-only + +This library provides different hazard storage options used withon NSHM hazard pipelines. Third parties may wish to +process models based on, or similar in scale to the NZSHM 22. + ## Features -* Manage Openquake hazard results in AWS DynamodDB tables defined herein. -* Option for caching using sqlite, See NZSHM22_HAZARD_STORE_LOCAL_CACHE environment variable. -* Option to use a local sqlite store instead of DynamoDB, see THS_USE_SQLITE_ADAPTER and THS_SQLITE_FOLDER variables. -* cli tools for end users +* Extract realisations from PSHA (openquake) hazard calcs and store these in Parquet dataset. +* Manage Openquake hazard results in AWS DynamodDB tables defined herein (used by NSHM project). +* CLI tools for end users +* **Legacy features:** + * Option for caching using sqlite, See NZSHM22_HAZARD_STORE_LOCAL_CACHE environment variable. + * Option to use a local sqlite store instead of DynamoDB, see THS_USE_SQLITE_ADAPTER and THS_SQLITE_FOLDER variables. ## Credits diff --git a/docs/domain_model/demo_thp_stategies.md b/docs/domain_model/demo_thp_stategies.md deleted file mode 100644 index fb8a1ed..0000000 --- a/docs/domain_model/demo_thp_stategies.md +++ /dev/null @@ -1,59 +0,0 @@ -demo_thp_stategies.md - -# try to use arrow more effectively - - -## baseline_thp_first_cut - -``` -chrisbc@tryharder-ubuntu:/GNSDATA/LIB/toshi-hazard-store$ time poetry run python scripts/migration/demo_thp_arrow_strategies.py -/GNSDATA/LIB/toshi-hazard-store/WORKING/ARROW/pq-CDC4 -load ds: 0.007607, table_pandas:2.718801: filt_1: 0.484222 iter_filt_2: 0.376349 -baseline_thp_first_cut took 3.7193017520476133 seconds - -real 0m4.763s -``` - - -### two more ... - -this is an extremely good example , but still .... - - - -``` -/GNSDATA/LIB/toshi-hazard-store/WORKING/ARROW/pq-CDC4 -load ds: 0.007536, table_pandas:1.385321: filt_1: 0.388817 iter_filt_2: 0.35966 -RSS: 703MB -baseline_thp_first_cut took 2.209011 seconds - -load ds: 0.000603, table_flt:0.099626: to_pandas: 0.00149 iter_filt_2: 0.37484 -RSS: 0MB -more_arrow took 0.478658 seconds - -(912, 3) -load ds: 0.000608, scanner:0.000164 duck_sql:0.013131: to_arrow 0.081936 -RSS: 0MB -duckdb_attempt_two took 0.099231 seconds - -real 0m3.839s -``` - -and one of the worst .... - -``` -chrisbc@tryharder-ubuntu:/GNSDATA/LIB/toshi-hazard-store$ time poetry run python scripts/migration/demo_thp_arrow_strategies.py -/GNSDATA/LIB/toshi-hazard-store/WORKING/ARROW/pq-CDC4 -load ds: 0.007613, table_pandas:1.295651: filt_1: 0.40045 iter_filt_2: 0.376122 -RSS: 559MB -baseline_thp_first_cut took 2.132328 seconds - -load ds: 0.000621, table_flt:0.671431: to_pandas: 0.006025 iter_filt_2: 0.531729 -RSS: 0MB -more_arrow took 1.211358 seconds - -(912, 3) -load ds: 0.000573, scanner:0.000166 duck_sql:0.026913: to_arrow 0.942266 -RSS: 0MB -duckdb_attempt_two took 0.978871 seconds -``` \ No newline at end of file diff --git a/docs/domain_model/arrow_sanity_testing.md b/docs/migration/arrow_sanity_testing.md similarity index 99% rename from docs/domain_model/arrow_sanity_testing.md rename to docs/migration/arrow_sanity_testing.md index aa76ea9..167de06 100644 --- a/docs/domain_model/arrow_sanity_testing.md +++ b/docs/migration/arrow_sanity_testing.md @@ -1,9 +1,10 @@ -# Newest first: +These are outputs from the [ths_r4_sanity script](../cli/ths_r4_sanity.md) ## ARROW_DIRECT May 10 first test pass +``` INFO:pynamodb.settings:Override settings for pynamo available /etc/pynamodb/global_default_settings.py querying arrow/parquet dataset DIRECT_CLASSIC calculation_id, uniq_rlzs, uniq_locs, uniq_imts, uniq_gmms, uniq_srcs, uniq_vs30, consistent @@ -58,6 +59,7 @@ T3BlbnF1YWtlSGF6YXJkVGFzazoxMzI4NTEw, 2262897, 3991, 27, 21, 1, 1, True T3BlbnF1YWtlSGF6YXJkVGFzazoxMzI4NTEy, 2262897, 3991, 27, 21, 1, 1, True Grand total: 96981300 +``` ## NLOC IMT defragged diff --git a/docs/domain_model/hazard_import_processing-may-2024.md b/docs/migration/hazard_import_processing-may-2024.md similarity index 100% rename from docs/domain_model/hazard_import_processing-may-2024.md rename to docs/migration/hazard_import_processing-may-2024.md diff --git a/docs/domain_model/revision_4_disagg_testing.md b/docs/migration/revision_4_disagg_testing.md similarity index 100% rename from docs/domain_model/revision_4_disagg_testing.md rename to docs/migration/revision_4_disagg_testing.md diff --git a/docs/domain_model/revision_4_migration_testing.md b/docs/migration/revision_4_migration_testing.md similarity index 100% rename from docs/domain_model/revision_4_migration_testing.md rename to docs/migration/revision_4_migration_testing.md diff --git a/mkdocs.yml b/mkdocs.yml index c7c42ec..fb0394a 100644 --- a/mkdocs.yml +++ b/mkdocs.yml @@ -7,11 +7,14 @@ watch: - toshi_hazard_store - scripts nav: - - Home: index.md - - Installation: installation.md - - Configuration: configuration.md - - Usage: usage.md - # - Local configuration: sqlite_adapter_usage.md + - Home: + - README: index.md + - Installation: installation.md + - Configuration: configuration.md + - Usage: + - Vanilla (DynamodDB): usage.md + - LOCAL (sqlite): sqlite_adapter_usage.md + # - Parquet: TODO.md - CLI tools: - store_hazard_v4: cli/store_hazard_v4.md - ths_r4_import: cli/ths_r4_import.md @@ -21,36 +24,48 @@ nav: - ths_r4_filter_dataset: cli/ths_r4_filter_dataset.md - ths_r4_query: cli/ths_r4_query.md - Legacy scripts: cli/legacy.md + - Migrations: + # - Overview: migration_overview.md + - Hazard dataset May-2024: migration/hazard_import_processing-may-2024.md + - Arrow sanity tests: migration/arrow_sanity_testing.md + - Rev4 migration testing: migration/revision_4_migration_testing.md + - Rev4 disagg testing: migration/revision_4_disagg_testing.md - Query API: - Hazard: hazard_query_api.md - Gridded Hazard: gridded_hazard_query_api.md - Hazard Disaggregation: hazard_disagg_query_api.md - Database Models: + - New Hazard: domain_model/proposed_hazard_models.md - Hazard: domain_model/openquake_models.md - Gridded Hazard: domain_model/gridded_hazard_models.md - Hazard Disaggregation: domain_model/disaggregation_models.md - - PROPOSED: - - Hazard: domain_model/proposed_hazard_models.md - - Migration Tests: domain_model/revision_4_migration_testing.md - Contributing: contributing.md - Changelog: changelog.md + theme: name: material language: en #logo: assets/logo.png palette: - scheme: preference - primary: indigo - accent: indigo + # Palette toggle for light mode + - scheme: default + toggle: + icon: material/brightness-7 + name: Switch to dark mode + + # Palette toggle for dark mode + - scheme: slate + toggle: + icon: material/brightness-4 + name: Switch to light mode features: - navigation.indexes - navigation.instant - - navigation.tabs.sticky + - navigation.tabs + # - navigation.tabs.sticky + markdown_extensions: - mkdocs-click - - pymdownx.emoji: - emoji_index: !!python/name:materialx.emoji.twemoji - emoji_generator: !!python/name:materialx.emoji.to_svg - pymdownx.critic - pymdownx.caret - pymdownx.mark @@ -65,9 +80,8 @@ markdown_extensions: - pymdownx.details - admonition - toc: - baselevel: 2 + baselevel: 1 permalink: true - slugify: !!python/name:pymdownx.slugs.uslugify - meta - pymdownx.superfences: custom_fences: @@ -80,9 +94,6 @@ plugins: - search: lang: en - mkdocstrings: - watch: - - toshi_hazard_store - - scripts handlers: python: options: @@ -90,19 +101,19 @@ plugins: extra: social: - - icon: fontawesome/brands/twitter - # replace with your own tweet link below - link: https://github.com/waynerv/cookiecutter-pypackage - name: Tweet - - icon: fontawesome/brands/facebook - # replace with your own facebook link below - link: https://github.com/waynerv/cookiecutter-pypackage - name: Facebook + # - icon: fontawesome/brands/twitter + # # replace with your own tweet link below + # link: https://github.com/waynerv/cookiecutter-pypackage + # name: Tweet + # - icon: fontawesome/brands/facebook + # # replace with your own facebook link below + # link: https://github.com/waynerv/cookiecutter-pypackage + # name: Facebook - icon: fontawesome/brands/github link: https://github.com/GNS-Science/toshi-hazard-store name: Github - icon: material/email - link: "mailto:chrisbc@artisan.co.nz" + link: "mailto:nshm@gns.cri.nz" # to enable disqus, uncomment the following and put your disqus id below # disqus: disqus_id # uncomment the following and put your google tracking id below to enable GA diff --git a/poetry.lock b/poetry.lock index 4c70563..43f02ba 100644 --- a/poetry.lock +++ b/poetry.lock @@ -128,13 +128,13 @@ shapely = "*" [[package]] name = "anyio" -version = "4.3.0" +version = "4.4.0" description = "High level compatibility layer for multiple asynchronous event loop implementations" optional = false python-versions = ">=3.8" files = [ - {file = "anyio-4.3.0-py3-none-any.whl", hash = "sha256:048e05d0f6caeed70d731f3db756d35dcc1f35747c8c403364a8332c630441b8"}, - {file = "anyio-4.3.0.tar.gz", hash = "sha256:f75253795a87df48568485fd18cdd2a3fa5c4f7c5be8e5e36637733fce06fed6"}, + {file = "anyio-4.4.0-py3-none-any.whl", 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a/pyproject.toml b/pyproject.toml index c808288..29c2e7d 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -78,7 +78,7 @@ mkdocstrings-python = "^1.3.0" moto = "^3.1.10" mypy = "^1.5.0" pre-commit = "^3.0.4" -pymdown-extensions = {version = "^9.4"} +# pymdown-extensions = {version = "^9.4"} pytest = { version = "^6.2.4"} pytest-cov = { version = "^2.12.0"} pytest-lazy-fixture = "^0.6.3"