From 29b0423ae750c9021d8cc06060912271af5cf893 Mon Sep 17 00:00:00 2001 From: "github-actions[bot]" <41898282+github-actions[bot]@users.noreply.github.com> Date: Wed, 8 May 2024 13:47:08 +0000 Subject: [PATCH] chore(346-release-concept): release 0.1.0 --- .release-please-manifest.json | 2 +- CHANGELOG.md | 195 ++++++++++++++++++++++++++++++++++ version.txt | 2 +- 3 files changed, 197 insertions(+), 2 deletions(-) create mode 100644 CHANGELOG.md diff --git a/.release-please-manifest.json b/.release-please-manifest.json index b7888c913..96d9691c1 100644 --- a/.release-please-manifest.json +++ b/.release-please-manifest.json @@ -1,3 +1,3 @@ { - ".": "0.0.1" + ".": "0.1.0" } diff --git a/CHANGELOG.md b/CHANGELOG.md new file mode 100644 index 000000000..cf4475538 --- /dev/null +++ b/CHANGELOG.md @@ -0,0 +1,195 @@ +# Changelog + +## [0.1.0](https://github.com/GenSpectrum/LAPIS-SILO/compare/v0.0.1...v0.1.0) (2024-05-08) + + +### ⚠ BREAKING CHANGES + +* return data as NDJSON instead of JSON + +### Features + +* AAMutations with multiple sequences ([0def8b2](https://github.com/GenSpectrum/LAPIS-SILO/commit/0def8b21e27cbc25973fb64ac9e56670c09cc023)) +* Action for amino acid distribution ([a0a4cf1](https://github.com/GenSpectrum/LAPIS-SILO/commit/a0a4cf1e7422ef536c6e40863f27fdd85151cc65)) +* add limit orderBy and offset to all query actions ([13b7e01](https://github.com/GenSpectrum/LAPIS-SILO/commit/13b7e01cbd4396e8e4cbb6357baec4514ad2eb6c)) +* add log statements to loadDatabaseState ([46a0421](https://github.com/GenSpectrum/LAPIS-SILO/commit/46a04214244ba4ff799bcb2b9bf4c2cd1ad4e006)) +* add more tests, make less flaky and viable with large dataset ([7772ae3](https://github.com/GenSpectrum/LAPIS-SILO/commit/7772ae345d44a2feb32126f87026f011e7e49a59)) +* add unit test for findIllegalNucleotideChar, unique test case name for insertion contains invalid pattern tests ([99c9c4b](https://github.com/GenSpectrum/LAPIS-SILO/commit/99c9c4b3cd8935c2b2ba9998cf2e0847107edd4f)) +* added amino acid insertion search, added many test cases and fixed various bugs ([d1e4b2b](https://github.com/GenSpectrum/LAPIS-SILO/commit/d1e4b2b757a23f81effe3e8c1be4a112f073d590)) +* allow default preprocessing config along with user defined preprocessing config ([ee9f20e](https://github.com/GenSpectrum/LAPIS-SILO/commit/ee9f20edc58b55f6afd168888ed88f0faa486109)) +* allow reading fasta files with missing segments and genes [#220](https://github.com/GenSpectrum/LAPIS-SILO/issues/220) ([8ea9893](https://github.com/GenSpectrum/LAPIS-SILO/commit/8ea9893b5f0fcc0135864eae69057118ff5375dd)) +* allow reading segments and genes that are null from ndjson file [#220](https://github.com/GenSpectrum/LAPIS-SILO/issues/220) ([d0a3a7e](https://github.com/GenSpectrum/LAPIS-SILO/commit/d0a3a7e0f6eb2c8d45e400bee183889d4cd41e4e)) +* also get Runtime Config options from environment variables ([33bdd65](https://github.com/GenSpectrum/LAPIS-SILO/commit/33bdd65b826f97d682aed9f4f98c18870220e60a)) +* also log to stdout ([54b8a47](https://github.com/GenSpectrum/LAPIS-SILO/commit/54b8a472316ad5230bcec14e0e0abfab2b7caba2)) +* also return mutation destructed that does not need to be reparsed ([a93abbf](https://github.com/GenSpectrum/LAPIS-SILO/commit/a93abbf3b294a61f5858b34a140a3e6b9b228657)) +* Alternative templating of symbol classes ([6b61985](https://github.com/GenSpectrum/LAPIS-SILO/commit/6b619858b8651914098a850a9bbed877921a4cd7)) +* automatically detect file endings for fasta files ([75bd14e](https://github.com/GenSpectrum/LAPIS-SILO/commit/75bd14e87531e3f3d6c08d7bc3dea8158a4311e1)) +* be more lenient on input data, ignore superfluous sequences and fill missing sequences with Ns ([ee12186](https://github.com/GenSpectrum/LAPIS-SILO/commit/ee1218670d4cea5c4599c5c42b0c913d9eb8b864)) +* Better test coverage for SymbolEquals filter ([42c685c](https://github.com/GenSpectrum/LAPIS-SILO/commit/42c685cf4c8ce068072fbf35ac8b6a0e263234f9)) +* **boolean columns, resolves #384:** const declaration ([685db9f](https://github.com/GenSpectrum/LAPIS-SILO/commit/685db9fea3562076e2dbcb9dbf426154fbd60eb7)) +* **boolean columns:** actions/tuple: update assignTupleField() ([b020109](https://github.com/GenSpectrum/LAPIS-SILO/commit/b020109a7c25908b2ef647c94eb240d9a92ba8c1)) +* **boolean columns:** add and use JsonValueType ([2ad1268](https://github.com/GenSpectrum/LAPIS-SILO/commit/2ad1268c36fd6c4dbd926db0adbeef0a5cf28127)) +* **boolean columns:** add bool to JsonValueType, update tuple ([3c990e2](https://github.com/GenSpectrum/LAPIS-SILO/commit/3c990e25f4e42c802d9552e19342edfc6fc2f378)) +* **boolean columns:** add expression_type "BooleanEquals" ([b82ec69](https://github.com/GenSpectrum/LAPIS-SILO/commit/b82ec69e5d7aef6b75dc68de6290e1d962b0edf5)) +* **boolean columns:** add filter_expressions/bool_equals ([ff2a138](https://github.com/GenSpectrum/LAPIS-SILO/commit/ff2a138a82670ba3035c7432c0c558d520d79268)) +* **boolean columns:** add optional_bool ([a2e47f8](https://github.com/GenSpectrum/LAPIS-SILO/commit/a2e47f8d1895e852d487be0ed3a88fa5a928f4f4)) +* **boolean columns:** add storage/column/bool_column ([5eb3430](https://github.com/GenSpectrum/LAPIS-SILO/commit/5eb3430e3eafe5ab28dbf90632f1bb85663d66e8)) +* **boolean columns:** column_group: update ColumnPartitionGroup ([d7adecf](https://github.com/GenSpectrum/LAPIS-SILO/commit/d7adecf4e9c51bb9e3e6b1aad8e3f7b43e0692b0)) +* **boolean columns:** column_group.h: add {ColumnPartitionGroup,ColumnGroup}::bool_columns fields ([af44f1a](https://github.com/GenSpectrum/LAPIS-SILO/commit/af44f1a8cf552d8ab6625d9fd440d83b2e10c36f)) +* **boolean columns:** database ([c555a68](https://github.com/GenSpectrum/LAPIS-SILO/commit/c555a68801db08d089be8d337f40a8793ac54b48)) +* **boolean columns:** database_config: add "bool" case to DatabaseConfigReader::readConfig() ([12fc7b8](https://github.com/GenSpectrum/LAPIS-SILO/commit/12fc7b8c95decfd58692332a9496e7046ca12242)) +* **boolean columns:** database_config: add "boolean" case to de/serialisation ([e6d5363](https://github.com/GenSpectrum/LAPIS-SILO/commit/e6d536330fb4ac162db34f5c5233ae495211da3e)) +* **boolean columns:** database_config: add BOOL to ValueType ([0b47b82](https://github.com/GenSpectrum/LAPIS-SILO/commit/0b47b828915b293a1ed6c1210b3574045a6fcf67)) +* **boolean columns:** database_config: update DatabaseMetadata::getColumnType() ([30febdd](https://github.com/GenSpectrum/LAPIS-SILO/commit/30febddb8914d1e909b10d7f31a0803b4a485ba7)) +* **boolean columns:** database_partition ([0aef8f0](https://github.com/GenSpectrum/LAPIS-SILO/commit/0aef8f0c4e28fa8bdeec9f6638388e62d9b7b9cc)) +* **boolean columns:** optional_bool: add `==` ([f0aa3e8](https://github.com/GenSpectrum/LAPIS-SILO/commit/f0aa3e8c1ac5b43d9414a84587bfb13ed818323e)) +* **boolean columns:** selection ([e52f2dc](https://github.com/GenSpectrum/LAPIS-SILO/commit/e52f2dc5623929395d40aff3264c48099f6a246a)) +* build metadata in parallel to sequences. Do not create unaligned sequence tables in preprocessing, rather hive-partition them directly to disk. Better (debug-)logging ([c1cdfeb](https://github.com/GenSpectrum/LAPIS-SILO/commit/c1cdfeb3cb25e8bcbd5e095e5dbc0f78ae35492f)) +* bulk Tuple allocations now possible ([902ec04](https://github.com/GenSpectrum/LAPIS-SILO/commit/902ec0461544fc0cbc0e8e0ba07b18600b29126d)) +* clearer Operator::negate and Expression::toString, logical Equivalents for debug printing/logging for the Leaf Operators IndexScan and BitmapSelection ([026b639](https://github.com/GenSpectrum/LAPIS-SILO/commit/026b639af5d45690c42c70b13b926ce72fdcc837)) +* consistent behavior of configs when starting SILO with both --preprocessing and --api ([847ec7e](https://github.com/GenSpectrum/LAPIS-SILO/commit/847ec7e8af6eda73c95076c9b4428ed3fd5c3f9f)) +* declutter README.md from linting option, which is now disabled by default and enforced in the CI for the Linter ([9220435](https://github.com/GenSpectrum/LAPIS-SILO/commit/922043538a39992b2322c02434826dab070d1538)) +* details no longer shows insertions ([#354](https://github.com/GenSpectrum/LAPIS-SILO/issues/354)) ([473cd98](https://github.com/GenSpectrum/LAPIS-SILO/commit/473cd980f6aee5267e8d4d0cd65671e5722dc26b)) +* display database info after loading new database state ([0249416](https://github.com/GenSpectrum/LAPIS-SILO/commit/02494165930eefbafb0f74e069962a94f830d3e8)) +* display preprocessing duration in logs in human-readable format (not in microseconds) [#296](https://github.com/GenSpectrum/LAPIS-SILO/issues/296) ([a2499af](https://github.com/GenSpectrum/LAPIS-SILO/commit/a2499af5cf3c5f46c695f019fda632c28939c62c)) +* do not enforce building with clang-tidy by default. Linter will still be enforced ([7134e45](https://github.com/GenSpectrum/LAPIS-SILO/commit/7134e45ae2c66acb0e53ac433a187cdc4e2ccefa)) +* FastaAligned action ([50776c8](https://github.com/GenSpectrum/LAPIS-SILO/commit/50776c83d8cb4409e4f01c6b49a189647f5140de)) +* faster builds by copying [@corneliusroemer](https://github.com/corneliusroemer) image caching for our dependency images, which rarely change ([#374](https://github.com/GenSpectrum/LAPIS-SILO/issues/374)) ([7867bc7](https://github.com/GenSpectrum/LAPIS-SILO/commit/7867bc744648f5410793eef8d52df24b23c3c918)) +* filter for amino acids ([b52aabd](https://github.com/GenSpectrum/LAPIS-SILO/commit/b52aabde38ef4e1fb976a37c89fe1869f03ace57)) +* fix sorting ([1ed18ae](https://github.com/GenSpectrum/LAPIS-SILO/commit/1ed18ae4ab38fb4822b075e5c3deeac90b2bfb37)) +* flipped bitmap can now be set before insertion ([f61c803](https://github.com/GenSpectrum/LAPIS-SILO/commit/f61c803f74d135e75865aa09a9b373aa3603f19d)) +* format DatabaseConfig ([4fb8f1b](https://github.com/GenSpectrum/LAPIS-SILO/commit/4fb8f1b90486abc84d7d9e941fb8d31fa3cc3e5d)) +* format PreprocessingConfig ([ee35207](https://github.com/GenSpectrum/LAPIS-SILO/commit/ee35207e29888d52cbbfba0ae4f4fe0dda80be1d)) +* generalize mutations action to have consistent behavior for different symbols ([9834aea](https://github.com/GenSpectrum/LAPIS-SILO/commit/9834aea8413fe34efb5414178de8a93f4fbf076f)) +* generalizing symbol and mutation filters. Clear handling of ambiguous symbols ([aa9ad4d](https://github.com/GenSpectrum/LAPIS-SILO/commit/aa9ad4df935eed84f482cb9d81bafaca6f3374a3)) +* Generalizing the config for multiple nucleotide sequences and multiple genes ([9a80204](https://github.com/GenSpectrum/LAPIS-SILO/commit/9a802049ea95fb30955f12d9696ac672bd14ce21)) +* have structured and destructured insertion in insertions response ([0a7e46a](https://github.com/GenSpectrum/LAPIS-SILO/commit/0a7e46ad0e7740919059773c327dcda2cb1ae09e)) +* hide intermediate results of the preprocessing - don't put it in the output ([44327b0](https://github.com/GenSpectrum/LAPIS-SILO/commit/44327b0b30203c526fe7a3e40e1701645808940e)) +* implement basic request id to trace requests [#303](https://github.com/GenSpectrum/LAPIS-SILO/issues/303) ([4defb59](https://github.com/GenSpectrum/LAPIS-SILO/commit/4defb59cfe9d48635592ae0a4cd572d6caa94895)) +* implement data updates at runtime. More resilient to superfluous or missing directory separators ([dc5dfaa](https://github.com/GenSpectrum/LAPIS-SILO/commit/dc5dfaa50d13512dc39c665aeab20630fa94415c)) +* implement insertion columns and search ([9167236](https://github.com/GenSpectrum/LAPIS-SILO/commit/91672365f8cfdfbecd71804e3064134f93adc1cb)) +* improve loadDB speeds ([2b7cd7d](https://github.com/GenSpectrum/LAPIS-SILO/commit/2b7cd7dacadb5e3887225aa84b57da8f7ca84394)) +* improve validation error message of some actions on orderByFields ([a0da5b5](https://github.com/GenSpectrum/LAPIS-SILO/commit/a0da5b54a1ca2e9eff9c718028bea56fc8cd2661)) +* insertion action targets all insertion columns by default ([6b70241](https://github.com/GenSpectrum/LAPIS-SILO/commit/6b70241db3577480078e51e7bc861579013dd4e6)) +* insertion columns for amino acids and multiple sequence names ([3cc8fee](https://github.com/GenSpectrum/LAPIS-SILO/commit/3cc8fee9153ec1b23a819c4331b3f9dce3e16b37)) +* insertions action ([e067062](https://github.com/GenSpectrum/LAPIS-SILO/commit/e0670629b1a40dc0e56a31e15eaa42e51a350d66)) +* insertions contains action now targets all columns if the column name is missing ([32a6951](https://github.com/GenSpectrum/LAPIS-SILO/commit/32a69514b654a737478f0aafe9cdca9c41cc0691)) +* introduce new storage type for Sequence Positions, where the most numerous symbol is deleted ([6e15204](https://github.com/GenSpectrum/LAPIS-SILO/commit/6e15204a9265e65e26562c227f5ccaf5cfba8c65)) +* introduce storage of unaligned sequences from either ndjson file or fasta file and make them queryable via the Fasta action ([44df849](https://github.com/GenSpectrum/LAPIS-SILO/commit/44df849d6f84eba3321285bdaf6f22509c0c5f17)) +* load table lazily. Unaligned Sequences do not need to load the table ([c2a8439](https://github.com/GenSpectrum/LAPIS-SILO/commit/c2a8439fc724452c4184f8c49b3db65c6a99b731)) +* log databaseConfig and preprocessingConfig ([d2dc58c](https://github.com/GenSpectrum/LAPIS-SILO/commit/d2dc58cdbed9cea1e9e3028324eaeef32d82dbba)) +* logging for partition ([e75a925](https://github.com/GenSpectrum/LAPIS-SILO/commit/e75a925d8b4ac7bd66229437d244089d26cb10de)) +* logging improvements ([4c12a88](https://github.com/GenSpectrum/LAPIS-SILO/commit/4c12a882aa75025fac99e65ba3a491f72a2b78ec)) +* make database serializable again ([2523e67](https://github.com/GenSpectrum/LAPIS-SILO/commit/2523e67d08cc59c297bc4ad0a9134f1b96d2cb0a)) +* make pangoLineageDefinitionFilename in preprocessing config optional, linter errors ([0f3dc53](https://github.com/GenSpectrum/LAPIS-SILO/commit/0f3dc534891f4d6553385e85de8ad77565f2a9f9)) +* make partition_by field in config optional ([3942418](https://github.com/GenSpectrum/LAPIS-SILO/commit/394241812df369a908c5d4495e503eca3abdf3db)) +* make SILO Docker image by default read data from /data ([e83b910](https://github.com/GenSpectrum/LAPIS-SILO/commit/e83b910d8f9c7e38fa7c80ee4571b85601f99ab4)) +* make threads and max queued http connections available through optional parameter ([3ecde68](https://github.com/GenSpectrum/LAPIS-SILO/commit/3ecde686b4c6979d07b8dce73b2ccb8fda6b48ee)) +* migration to duckdb 0.10.1 ([c1426ef](https://github.com/GenSpectrum/LAPIS-SILO/commit/c1426ef906da8d8914718eaa5173a1e7750d407b)) +* mine data version at beginning of preprocessing ([362fe0f](https://github.com/GenSpectrum/LAPIS-SILO/commit/362fe0f988e9901ba5b48a5b0c1a81d480093eb8)) +* More robust InputStreamWrapper ([305dd36](https://github.com/GenSpectrum/LAPIS-SILO/commit/305dd366422131d6ecfbb4ef97f3cb3edb712211)) +* multiple performance improvements for details endpoint ([28f41d0](https://github.com/GenSpectrum/LAPIS-SILO/commit/28f41d01933a53095bf69888beef1ee5ebbc6208)) +* optimize bitmaps before finishing partition ([5b06d58](https://github.com/GenSpectrum/LAPIS-SILO/commit/5b06d582859ec9dd1bb0c63ff5c52b21fa08b9fe)) +* order all actions by default ([a2f5c04](https://github.com/GenSpectrum/LAPIS-SILO/commit/a2f5c04b64e9b175ea023cd82d7fe8f1bacf2f95)) +* preparation of insertion columns ([c14a370](https://github.com/GenSpectrum/LAPIS-SILO/commit/c14a370ebf19800e9ad0b6eeb9e4957dafd77cba)) +* put output and logs to gitignore ([789e489](https://github.com/GenSpectrum/LAPIS-SILO/commit/789e489980be9f65c618822c6460588c9ed7aff7)) +* reenable bitmap inversion ([75ac20f](https://github.com/GenSpectrum/LAPIS-SILO/commit/75ac20f679c433f7b439ec4e9935f7ea005d9ca8)) +* reenable pushdown of And expressions through selections ([802bec0](https://github.com/GenSpectrum/LAPIS-SILO/commit/802bec0cf1ba876138641b9c0702dde77ea01683)) +* refactor saving and loading database to not require preprocessing structs anymore ([45bf7ed](https://github.com/GenSpectrum/LAPIS-SILO/commit/45bf7ede2130ec9d2cfc3c8d1c48d32a921e6e83)) +* reintroduce randomize for all query actions ([166045c](https://github.com/GenSpectrum/LAPIS-SILO/commit/166045cad4953dfd1eb8c3ff2b72b2d903d2193b)) +* reserve space in columns when bulk inserting rows ([e3c9620](https://github.com/GenSpectrum/LAPIS-SILO/commit/e3c962095152cdb427bd5ee2f6a748bb4788ef73)) +* return data as NDJSON instead of JSON ([c236ba4](https://github.com/GenSpectrum/LAPIS-SILO/commit/c236ba43af666758a0c59083c3bd97396a6e4fec)), closes [#126](https://github.com/GenSpectrum/LAPIS-SILO/issues/126) +* return data version on each query ([be5c886](https://github.com/GenSpectrum/LAPIS-SILO/commit/be5c886e4dcdf8d1094ee28a08738f62a4ededb4)) +* return only aliased pango lineages ([abf0844](https://github.com/GenSpectrum/LAPIS-SILO/commit/abf08444677ebd796dc2fad6107051c571a221ff)) +* reveal some more details when reading YAML fails ([1f8d9db](https://github.com/GenSpectrum/LAPIS-SILO/commit/1f8d9db929add1120169b73c80b11700c88d4cfc)) +* run preprocessing in github ci ([f53eddb](https://github.com/GenSpectrum/LAPIS-SILO/commit/f53eddbbbc6e24d1ee371cac4c752bae19ebaeb0)) +* save database state into folder with name <data version> ([41923eb](https://github.com/GenSpectrum/LAPIS-SILO/commit/41923eb1c99ab1373d448a9fbdaa8219ddd4df92)) +* separate preprocessing and starting silo ([9808e2d](https://github.com/GenSpectrum/LAPIS-SILO/commit/9808e2d91cece622121e6d47734b1901b76cdeef)) +* serialization of partition descriptor to json ([472c1da](https://github.com/GenSpectrum/LAPIS-SILO/commit/472c1da51d66b79ea8e20aaa59d1e2856f333756)) +* some suggestions for the insertion search ([ae900da](https://github.com/GenSpectrum/LAPIS-SILO/commit/ae900da3672e30d6c04ad4edf56e9b8d3195d13b)) +* Specifiable nucSequence query target ([7cc609f](https://github.com/GenSpectrum/LAPIS-SILO/commit/7cc609fe716116ab0a77443eaa2dce73482b6116)) +* statically disable deleted symbol optimisations because of performance penalty ([4e522f4](https://github.com/GenSpectrum/LAPIS-SILO/commit/4e522f41fbc5bccb14a505f38af83c96e17634fc)) +* stick to the default of having config value keys in camel case ([a1cae40](https://github.com/GenSpectrum/LAPIS-SILO/commit/a1cae40d7e5163289bbf68f6398a036a59eb0cae)) +* storing amino acids ([f11a330](https://github.com/GenSpectrum/LAPIS-SILO/commit/f11a330302d61eff2dfa2354c0d565faae89b400)) +* support for nullable columns ([6f78e3a](https://github.com/GenSpectrum/LAPIS-SILO/commit/6f78e3ad61af29e20b98bda72d4edc34951e7c1b)) +* support recombinant lineages ([3e848a5](https://github.com/GenSpectrum/LAPIS-SILO/commit/3e848a539f2b4970b071028f347e654c9b745149)) +* template class for sequence store ([cef4d48](https://github.com/GenSpectrum/LAPIS-SILO/commit/cef4d487db0ef57b2aab5ffa339a5abec05f65cd)) +* templatized Symbol classes ([6b9d734](https://github.com/GenSpectrum/LAPIS-SILO/commit/6b9d734d49fe2ae0ca47065361f6d6465166177c)) +* test set with amino acid insertions ([de2c4f8](https://github.com/GenSpectrum/LAPIS-SILO/commit/de2c4f83d8b5d45cd9d0944f496b7a2f5b7d763f)) +* throw an error when there is not initialized database loaded yet [#295](https://github.com/GenSpectrum/LAPIS-SILO/issues/295) ([b17f72a](https://github.com/GenSpectrum/LAPIS-SILO/commit/b17f72a55c7835ef5c07409ce7f0d742661a859c)) +* tidying up CLI and file configuration for runtime config. Added option for specifying the port ([c3a88a0](https://github.com/GenSpectrum/LAPIS-SILO/commit/c3a88a0f44e6d1eaaf715ade8389f13e7a87fb40)) +* Unit tests for Tuple ([4fc06e8](https://github.com/GenSpectrum/LAPIS-SILO/commit/4fc06e81de653dac470c02fd258eaf4532f876ae)) +* update conan version ([5540a67](https://github.com/GenSpectrum/LAPIS-SILO/commit/5540a67f4054f5f985791b283593f2bdd6885232)) +* use 'pragma once' as include guards instead of 'ifndef...' ([bc49aa5](https://github.com/GenSpectrum/LAPIS-SILO/commit/bc49aa5530c97ca7cc10f7da4c27e29cb6ee16c9)) +* use own scope for preprocessing ([2a93846](https://github.com/GenSpectrum/LAPIS-SILO/commit/2a9384651ba545265a5c8ccc6feccc1249b44ffd)) +* use same default min proportions for mutations actions as the old LAPIS ([f42f830](https://github.com/GenSpectrum/LAPIS-SILO/commit/f42f83088e2302cf604d8846b69ea7e58659570a)) + + +### Bug Fixes + +* adapt randomize query results to target architecture. x86 and ARM have possibly different std::hash results ([#355](https://github.com/GenSpectrum/LAPIS-SILO/issues/355)) ([600000d](https://github.com/GenSpectrum/LAPIS-SILO/commit/600000d80616bb1688eb4fc8a7855b361a1eae1d)) +* add bash dependency which is required by conan build of pkgconf and is not installed on alpine by default ([1b3f51c](https://github.com/GenSpectrum/LAPIS-SILO/commit/1b3f51c5e7e6a88c5b7500f3fd832eead62fff3b)) +* add insertion to database_config test ([aec40d0](https://github.com/GenSpectrum/LAPIS-SILO/commit/aec40d0f8366c8f15906c6edbed35439b5a794a0)) +* add missing file for test ([262bedc](https://github.com/GenSpectrum/LAPIS-SILO/commit/262bedc35fc3704854b2f321c8cab49e08d803a3)) +* add missing sequenceName field to mutation action "orderBy" ([06c8c86](https://github.com/GenSpectrum/LAPIS-SILO/commit/06c8c86ebeb822d03f46342faafcf1f7d29a7d51)) +* add sleep statement before row call ([8fa8efb](https://github.com/GenSpectrum/LAPIS-SILO/commit/8fa8efb5f7634e9eb91ad71d0d5d3af47c0fcf30)) +* add workaround so insertions are read correctly ([8a2bfa8](https://github.com/GenSpectrum/LAPIS-SILO/commit/8a2bfa8ee211a8e8ec6c2e83671eab8abe69fc87)) +* allow sql keywords for metadata field names [#259](https://github.com/GenSpectrum/LAPIS-SILO/issues/259) ([6fbeee5](https://github.com/GenSpectrum/LAPIS-SILO/commit/6fbeee56732d2d3934ff5769cc07ded2cbf2caa4)) +* also consider 'missing' symbols in the mutation action. Bugfix where Position invariant was broken because of 'missing' symbols ([fab72a6](https://github.com/GenSpectrum/LAPIS-SILO/commit/fab72a60795568d0d1dddc25bf4a8e594f77477b)) +* alternative non-exhaustive three mer index ([467086f](https://github.com/GenSpectrum/LAPIS-SILO/commit/467086f52d75ecee39a2fcb7937554869a7d03e1)) +* always build dependency image for amd64 platform ([4f73cb0](https://github.com/GenSpectrum/LAPIS-SILO/commit/4f73cb04687ec57df32878e310139671a110ed5a)) +* bug when filtering for indexedStringColumns which are not present in some partitions ([62d4e08](https://github.com/GenSpectrum/LAPIS-SILO/commit/62d4e08d3718a4b4b20e283602b558ad26c23a13)) +* bug where sequence reconstruction is false when the flipped bitmap is different from the reference sequence symbol ([edac58c](https://github.com/GenSpectrum/LAPIS-SILO/commit/edac58cb340c409f3db96f5e6d6c325c8fb9ecb7)) +* change random ordering for gcc hashing ([78055ff](https://github.com/GenSpectrum/LAPIS-SILO/commit/78055ff25fef2541b260285552e416433c4b6ca2)) +* change test to reflect new optimisations ([cb63010](https://github.com/GenSpectrum/LAPIS-SILO/commit/cb630104c81e1846d8d87de0704a90216fbe5986)) +* compiling And: append selection_child->predicates to predicates - not vice versa ([bdebca5](https://github.com/GenSpectrum/LAPIS-SILO/commit/bdebca5caab90ce4f37c7cf7c7844fc7808b2ba6)) +* deterministic order for e2e test ([02427a2](https://github.com/GenSpectrum/LAPIS-SILO/commit/02427a25d291f3aba8fcaa95e577bb32c9c32179)) +* divergence between mac and linux info test results, fix memory leaks in Threshold.cpp ([ffcefd0](https://github.com/GenSpectrum/LAPIS-SILO/commit/ffcefd0fb82345dddce170c0254fb20a167e18ba)) +* do not exclude zstd filter from boost installation ([c974230](https://github.com/GenSpectrum/LAPIS-SILO/commit/c97423091d073a501499e30d0ee3a6782da4ba3c)) +* do not use std::filesystem::path::relative_path() to also support absolute paths ([b9ff422](https://github.com/GenSpectrum/LAPIS-SILO/commit/b9ff422b76e63a673b8869725dc3a3fec677979a)) +* endToEndResults ([c807a33](https://github.com/GenSpectrum/LAPIS-SILO/commit/c807a33b11ceb3e2db81f14613cc7601e81ea689)) +* error when the Mutations action looked for sequences but the filter was empty ([91e5d52](https://github.com/GenSpectrum/LAPIS-SILO/commit/91e5d52e0dc6d11522c8ea2cc0be237d332d967c)) +* fix memory leaks in indexed_string_column.cpp and insertion_contains.cpp ([c2eeac8](https://github.com/GenSpectrum/LAPIS-SILO/commit/c2eeac88ec688f25e65409490dcf68b954e53789)) +* floatEquals and floatBetween with null values ([47b436e](https://github.com/GenSpectrum/LAPIS-SILO/commit/47b436e611e2266226c3070d11dcbc3366de2c7c)) +* hide nucleotide sequence for default sequence ([584715c](https://github.com/GenSpectrum/LAPIS-SILO/commit/584715cd210f51c4e24a2b301145a1bdf4a91ac5)) +* insertion column, remove reference ([d940c52](https://github.com/GenSpectrum/LAPIS-SILO/commit/d940c52a206ab9884f707baa491c4b12c59dfe50)) +* insertion search e2e and insertion column tests, dont allow non-empty value for insertion search ([19af04d](https://github.com/GenSpectrum/LAPIS-SILO/commit/19af04dd7fbcafa6004ddc4c2894967d427a8308)) +* linking error on linux ([ad9076c](https://github.com/GenSpectrum/LAPIS-SILO/commit/ad9076c8f385c5d56f20219422ee1d1d49602966)) +* linter ([54d3c34](https://github.com/GenSpectrum/LAPIS-SILO/commit/54d3c3435a38dbfa0ddbfaf5af01b03f2dbbfaa1)) +* linter ([e6b6ab7](https://github.com/GenSpectrum/LAPIS-SILO/commit/e6b6ab70b89ce7065185d2a19c0017d93d40801b)) +* linter ([b31851c](https://github.com/GenSpectrum/LAPIS-SILO/commit/b31851c44d2473560ef486659bd3f3aad1f40709)) +* linter ([34830ab](https://github.com/GenSpectrum/LAPIS-SILO/commit/34830ab0f0818c07f19ad28f8aa12b4229018fca)) +* linter errors ([e9e1bbf](https://github.com/GenSpectrum/LAPIS-SILO/commit/e9e1bbfea06510b2dbb1c1097daadab90ade3ab1)) +* Linter throws again and added clang-format option ([87cb4a5](https://github.com/GenSpectrum/LAPIS-SILO/commit/87cb4a57422773c5117edc8cba9afdea5754f1b6)) +* Make C++ flags in CMake compatible for MacOS ([38cae69](https://github.com/GenSpectrum/LAPIS-SILO/commit/38cae694f86abad05b650756091e2238c02baf72)) +* metadata info test accessing getMetadataFields output no longer directly but over the address of a const ([0dcdee1](https://github.com/GenSpectrum/LAPIS-SILO/commit/0dcdee1f8b0f788d850dd9576e6d9f770969d440)) +* missing include ([0773999](https://github.com/GenSpectrum/LAPIS-SILO/commit/0773999ae2178dc2b5e221cf74b5ffd7e523f06a)) +* new linter errors ([ea6934c](https://github.com/GenSpectrum/LAPIS-SILO/commit/ea6934cb3daf6b8cdbcb707a113ed3866f87e6cd)) +* no longer have regression when no bitmap flipped is most efficient ([b653753](https://github.com/GenSpectrum/LAPIS-SILO/commit/b65375320612625fd1a7325878174a1e2d621eda)) +* nodiscard (silence warnings) ([69421c1](https://github.com/GenSpectrum/LAPIS-SILO/commit/69421c158424dd75fba9c3804ebf6d0d89262aea)), closes [#390](https://github.com/GenSpectrum/LAPIS-SILO/issues/390) +* non default unaligned nucleotide sequence prefix ([93b4829](https://github.com/GenSpectrum/LAPIS-SILO/commit/93b4829d834269cfbbc86fb1eb53a29bb0659190)) +* nucleotide symbol equals with dot ([6ad623e](https://github.com/GenSpectrum/LAPIS-SILO/commit/6ad623eeaf9089808bdfc29c9b30d1486f2f9782)) +* only apply order-by if the field is set, validate orderBy fields for all operations ([405a7f1](https://github.com/GenSpectrum/LAPIS-SILO/commit/405a7f1657c94c327fc667eabcef14e07e858779)) +* pango lineage filter with null values ([b7238a8](https://github.com/GenSpectrum/LAPIS-SILO/commit/b7238a8ddced5c2661d8778b838c3a5aa0bd860c)) +* parse error messages for mutation filter expressions ([9e4612d](https://github.com/GenSpectrum/LAPIS-SILO/commit/9e4612d34b3e4b50909d3759b1dfc5050783fa6d)) +* put compressors into sql function to avoid static variables ([c1a11c8](https://github.com/GenSpectrum/LAPIS-SILO/commit/c1a11c88676d597d4ed66f7611a42a8b726c3753)) +* quoting {} in "x.{}" SQL struct accesses, as a string starting with a number leads to parser errors ([#409](https://github.com/GenSpectrum/LAPIS-SILO/issues/409)) ([f3ba6db](https://github.com/GenSpectrum/LAPIS-SILO/commit/f3ba6dbfbaf276ee7161d79751bdb68533e2c19a)) +* random (but deterministic for a version) result can depend on internal state, which was changed with duckdb update ([9d9351b](https://github.com/GenSpectrum/LAPIS-SILO/commit/9d9351b27353a8bc8630f9498f8e390bb5b4ca56)) +* recursive file reading for nodejs<20 ([9ac0ffe](https://github.com/GenSpectrum/LAPIS-SILO/commit/9ac0ffebc5fd7d831fc4b37bb54a0493be31b822)) +* remove caching for linter. Docker image to large on github actions. ([8eaeee6](https://github.com/GenSpectrum/LAPIS-SILO/commit/8eaeee6a1395ef10006f2a8ff3044ffef1b6007c)) +* response format ([bca4961](https://github.com/GenSpectrum/LAPIS-SILO/commit/bca49612e55245ceff20e26ca37e0e1260912dd0)) +* revert duckdb migration due to it being unable to build the new version on the GitHub runner ([2a62c54](https://github.com/GenSpectrum/LAPIS-SILO/commit/2a62c54d8de3aebabf20394c3b58c15c43773f08)) +* revert test numbers to pre-optimization ([99b600a](https://github.com/GenSpectrum/LAPIS-SILO/commit/99b600abda10d4d204ebc2f69cae1d2aa5ebeb4e)) +* Roaring from 1.3.0 -> 1.0.0 because of broken CI ([ce82c77](https://github.com/GenSpectrum/LAPIS-SILO/commit/ce82c779c453882c2fa0491778c5df2163d1ce48)) +* seralization for insertion_index and insertion_column ([ee99f8d](https://github.com/GenSpectrum/LAPIS-SILO/commit/ee99f8d2dd0631b20ff78026f716c6c8a40411ae)) +* single partition build fix ([a8af1c9](https://github.com/GenSpectrum/LAPIS-SILO/commit/a8af1c9792b9d95fc9d146e4a12daec72cc7a4fb)) +* specify namespace fmt in calls to format_to ([#353](https://github.com/GenSpectrum/LAPIS-SILO/issues/353)) ([62ffa3b](https://github.com/GenSpectrum/LAPIS-SILO/commit/62ffa3b9b3cf9b14a50cfafd87ce10adae2b7294)) +* specifying apk versions ([2c2354e](https://github.com/GenSpectrum/LAPIS-SILO/commit/2c2354edea80063b941a5e84f264401bff4a9b1b)) +* test cases verifying that the positions index for mutation distribution are now 1-indexed ([fdf972a](https://github.com/GenSpectrum/LAPIS-SILO/commit/fdf972a631ec49e8186a00b089e5b96be1f0617a)) +* test with deterministic results, remove 2 unused variables ([96a424b](https://github.com/GenSpectrum/LAPIS-SILO/commit/96a424b2610865203eae460baac7dc2a388f91db)) +* unit test info number updates for new pango-lineages in test data ([39d07c2](https://github.com/GenSpectrum/LAPIS-SILO/commit/39d07c2e5e3970a1ad819751834cdb859a9c591c)) +* unit tests and mock fixtures ([db506a1](https://github.com/GenSpectrum/LAPIS-SILO/commit/db506a1ff2eb03249f5ba58eb3faa42255a0a27a)) +* update cmake version on ubuntu ([227a2dd](https://github.com/GenSpectrum/LAPIS-SILO/commit/227a2dde0f0d8fa3dfeaf4f4fe48c900f54561f2)) +* Upper and lower bound should be inclusive in DateBetween filter ([53c6c05](https://github.com/GenSpectrum/LAPIS-SILO/commit/53c6c05f8c7a66b6dbb67d9a9535831d7f0fa21e)) +* Wrong compare function used in multi-threaded case, which displayed wrong tuples in the details endpoint when a limit was used ([650bf36](https://github.com/GenSpectrum/LAPIS-SILO/commit/650bf367427e2d92a6e29be4c01438dffa7358f6)) +* zstd dependency ([c145722](https://github.com/GenSpectrum/LAPIS-SILO/commit/c1457228bdca3996a58ea4b785aa330caf96802d)) diff --git a/version.txt b/version.txt index 8a9ecc2ea..6e8bf73aa 100644 --- a/version.txt +++ b/version.txt @@ -1 +1 @@ -0.0.1 \ No newline at end of file +0.1.0