From 27097fa4c306d9aafe6ca53de458954c4aecd2ca Mon Sep 17 00:00:00 2001 From: Alexander Druz Date: Fri, 8 Nov 2024 09:44:44 +0100 Subject: [PATCH 01/21] Update Python dependencies --- poetry.lock | 5066 +++++++++++++++++++++++++++------------------------ 1 file changed, 2716 insertions(+), 2350 deletions(-) diff --git a/poetry.lock b/poetry.lock index 9c79a77b..4e23ff41 100644 --- a/poetry.lock +++ b/poetry.lock @@ -1,4 +1,4 @@ -# This file is automatically @generated by Poetry 1.8.3 and should not be changed by hand. +# This file is automatically @generated by Poetry 1.8.4 and should not be changed by hand. 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48d23ab0af38b5b678abb82e38f11182883aa8d1 Mon Sep 17 00:00:00 2001 From: Alexander Druz Date: Fri, 8 Nov 2024 13:48:31 +0100 Subject: [PATCH 06/21] Fix type problems --- renumics/spotlight/embeddings/embedders/gte.py | 4 ++-- renumics/spotlight/io/audio.py | 2 +- 2 files changed, 3 insertions(+), 3 deletions(-) diff --git a/renumics/spotlight/embeddings/embedders/gte.py b/renumics/spotlight/embeddings/embedders/gte.py index 677d9fae..bbc51f66 100644 --- a/renumics/spotlight/embeddings/embedders/gte.py +++ b/renumics/spotlight/embeddings/embedders/gte.py @@ -40,8 +40,8 @@ def gte(batches: Iterable[List[str]]) -> Iterable[List[Optional[np.ndarray]]]: ) with torch.no_grad(): outputs = model(**inputs) - embeddings = average_pool( + embeddings_tensor = average_pool( outputs.last_hidden_state, inputs["attention_mask"] ) - embeddings = F.normalize(embeddings, p=2, dim=1).cpu().numpy() + embeddings = F.normalize(embeddings_tensor, p=2, dim=1).cpu().numpy() yield list(embeddings) diff --git a/renumics/spotlight/io/audio.py b/renumics/spotlight/io/audio.py index 648e8534..4f23fe9d 100644 --- a/renumics/spotlight/io/audio.py +++ b/renumics/spotlight/io/audio.py @@ -55,7 +55,7 @@ def prepare_input_file( response = requests.get(file, headers=headers, stream=True, timeout=timeout) if response.ok: if not reusable: - return response.raw + return response.raw # type: ignore[return-value] return io.BytesIO(response.content) raise ValueError(f"URL {file} not found.") if not os.path.isfile(file): From 9b865bd5d855c093e057a2863ec577197f8b7cf6 Mon Sep 17 00:00:00 2001 From: Alexander Druz Date: Fri, 8 Nov 2024 13:53:45 +0100 Subject: [PATCH 07/21] Ignore `cleanlab` vulnerability --- Makefile | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/Makefile b/Makefile index e0d3b65b..ce4cfb6d 100644 --- a/Makefile +++ b/Makefile @@ -27,7 +27,7 @@ clean: ## clean project .PHONY: audit audit: ## Audit project dependencies poetry export --without-hashes | poetry run safety check --full-report --stdin \ - --ignore 61496 --ignore 70612 --ignore 71596 + --ignore 61496 --ignore 70612 --ignore 71596 --ignore 73323 pnpm audit --prod .PHONY: check-format From 46c892fe9f26e510ccc4c313f6b9f38e477786a5 Mon Sep 17 00:00:00 2001 From: Alexander Druz Date: Fri, 8 Nov 2024 14:39:55 +0100 Subject: [PATCH 08/21] Ignore types in `pydantic-settings` --- pyproject.toml | 1 + 1 file changed, 1 insertion(+) diff --git a/pyproject.toml b/pyproject.toml index 6c9453ba..d5988450 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -185,6 +185,7 @@ module = [ "tests.ui._autogenerated_ui_elements", "transformers", "pyarrow.*", + "pydantic_settings", ] ignore_missing_imports = true From 599730e356878fa19946be41b030d27f933822c0 Mon Sep 17 00:00:00 2001 From: Alexander Druz Date: Fri, 8 Nov 2024 15:11:27 +0100 Subject: [PATCH 09/21] Fix pnpm deps --- package.json | 3 ++- pnpm-lock.yaml | 33 ++++++++++++++++++--------------- 2 files changed, 20 insertions(+), 16 deletions(-) diff --git a/package.json b/package.json index 88b9f9c8..706cc0b4 100644 --- a/package.json +++ b/package.json @@ -53,7 +53,7 @@ "d3-time-format": "^4.1.0", "d3-zoom": "^3.0.0", "detect-gpu": "^5.0.12", - "dompurify": "^3.0.3", + "dompurify": "^3.1.3", "fast-levenshtein": "^3.0.0", "file-saver": "^2.0.5", "flexlayout-react": "^0.7.6", @@ -61,6 +61,7 @@ "immer": "^9.0.19", "localforage": "^1.10.0", "lodash": "^4.17.21", + "micromatch": "4.0.8", "moment": "^2.29.4", "numbro": "^2.3.6", "prop-types": "^15.8.1", diff --git a/pnpm-lock.yaml b/pnpm-lock.yaml index 949c5996..1e2a45ab 100644 --- a/pnpm-lock.yaml +++ b/pnpm-lock.yaml @@ -87,8 +87,8 @@ importers: specifier: ^5.0.12 version: 5.0.12 dompurify: - specifier: ^3.0.3 - version: 3.0.3 + specifier: ^3.1.3 + version: 3.1.3 fast-levenshtein: specifier: ^3.0.0 version: 3.0.0 @@ -110,6 +110,9 @@ importers: lodash: specifier: ^4.17.21 version: 4.17.21 + micromatch: + specifier: 4.0.8 + version: 4.0.8 moment: specifier: ^2.29.4 version: 2.29.4 @@ 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optionalDependencies: fsevents: 2.3.3 @@ -7751,7 +7754,7 @@ snapshots: '@types/stack-utils': 2.0.1 chalk: 4.1.2 graceful-fs: 4.2.11 - micromatch: 4.0.5 + micromatch: 4.0.8 pretty-format: 29.6.2 slash: 3.0.0 stack-utils: 2.0.6 @@ -8080,7 +8083,7 @@ snapshots: dependencies: three: 0.149.0 - micromatch@4.0.5: + micromatch@4.0.8: dependencies: braces: 3.0.3 picomatch: 2.3.1 @@ -9021,7 +9024,7 @@ snapshots: is-glob: 4.0.3 jiti: 1.19.1 lilconfig: 2.1.0 - micromatch: 4.0.5 + micromatch: 4.0.8 normalize-path: 3.0.0 object-hash: 3.0.0 picocolors: 1.0.0 From 12f3703f589dcd550d61c3d64037fea490b70d7c Mon Sep 17 00:00:00 2001 From: Alexander Druz Date: Fri, 8 Nov 2024 15:14:16 +0100 Subject: [PATCH 10/21] Fix av audio layout usage --- renumics/spotlight/io/audio.py | 31 +++++++++++++++++++++++++++---- 1 file changed, 27 insertions(+), 4 deletions(-) diff --git a/renumics/spotlight/io/audio.py b/renumics/spotlight/io/audio.py index 4f23fe9d..6e4fa7fc 100644 --- a/renumics/spotlight/io/audio.py +++ b/renumics/spotlight/io/audio.py @@ -25,6 +25,28 @@ } +def _channel_num_to_layout(channel_num: int) -> str: + if channel_num == 1: + return "mono" + if channel_num == 2: + return "stereo" + if channel_num == 3: + return "3.0" + if channel_num == 4: + return "4.0" + if channel_num == 5: + return "5.0" + if channel_num == 6: + return "6.0" + if channel_num == 7: + return "7.0" + if channel_num == 8: + return "7.1" + raise ValueError( + f"Only channel number from 1 to 8 are supported, but {channel_num} received." + ) + + def prepare_input_file( file: FileType, timeout: Union[int, float] = 30, reusable: bool = False ) -> Union[str, IO]: @@ -125,13 +147,14 @@ def write_audio( # `AudioFrame.from_ndarray` expects an C-contiguous array as input. data = np.ascontiguousarray(data) num_channels = len(data) - frame = av.audio.AudioFrame.from_ndarray(data, data_format, num_channels) # type: ignore + layout = _channel_num_to_layout(num_channels) + frame = av.audio.AudioFrame.from_ndarray(data, data_format, layout) frame.rate = sampling_rate with av.open(file, "w", format_) as container: stream = container.add_stream(codec, sampling_rate) - stream.channels = num_channels # type: ignore - container.mux(stream.encode(frame)) # type: ignore - container.mux(stream.encode(None)) # type: ignore + stream.channels = num_channels # type: ignore[attr-defined] + container.mux(stream.encode(frame)) # type: ignore[attr-defined] + container.mux(stream.encode(None)) # type: ignore[attr-defined] def transcode_audio( From 661a9cd8fc108685c8871d6ac5574ac0b7eb1176 Mon Sep 17 00:00:00 2001 From: Alexander Druz Date: Fri, 8 Nov 2024 15:18:56 +0100 Subject: [PATCH 11/21] Remove unused dev deps --- poetry.lock | 67 ++++++++++++++++++++++++++++++++++++++++---------- pyproject.toml | 2 -- 2 files changed, 54 insertions(+), 15 deletions(-) diff --git a/poetry.lock b/poetry.lock index c84cd8a2..8d1f5c48 100644 --- a/poetry.lock +++ b/poetry.lock @@ -1262,8 +1262,11 @@ name = "docutils" version = 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nptyping = "^2.5.0" types-toml = "^0.10.8.6" @@ -129,7 +128,6 @@ ruff = "^0.2.1" check-wheel-contents = "^0.6.0" torch = { version = "^2.1.1+cpu, <=2.4.1+cpu", source = "torch-cpu" } ray = {extras = ["data"], version = "==2.9.3"} -soxr = "<0.5.0" [tool.poetry.group.playbook.dependencies] towhee = "^0.9.0" From 76de771a8e647b38145c4d02127c7225c998cb68 Mon Sep 17 00:00:00 2001 From: Alexander Druz Date: Fri, 8 Nov 2024 15:24:51 +0100 Subject: [PATCH 12/21] Try to fix pydantic_settings with mypy --- pyproject.toml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/pyproject.toml b/pyproject.toml index 6a42cd6a..90cd29b9 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -183,7 +183,7 @@ module = [ "tests.ui._autogenerated_ui_elements", "transformers", "pyarrow.*", - "pydantic_settings", + "pydantic_settings.*", ] ignore_missing_imports = true From 11b1008fa84f8f37331be17b856112f46839e19a Mon Sep 17 00:00:00 2001 From: Alexander Druz Date: Fri, 8 Nov 2024 15:31:50 +0100 Subject: [PATCH 13/21] Fix av output stream options --- renumics/spotlight/io/audio.py | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) diff --git a/renumics/spotlight/io/audio.py b/renumics/spotlight/io/audio.py index 6e4fa7fc..5a1b49e6 100644 --- a/renumics/spotlight/io/audio.py +++ b/renumics/spotlight/io/audio.py @@ -151,8 +151,9 @@ def write_audio( frame = av.audio.AudioFrame.from_ndarray(data, data_format, layout) frame.rate = sampling_rate with av.open(file, "w", format_) as container: - stream = container.add_stream(codec, sampling_rate) - stream.channels = num_channels # type: ignore[attr-defined] + stream = container.add_stream( + codec, sampling_rate, options={"channels": num_channels} # type: ignore[dict-item] + ) container.mux(stream.encode(frame)) # type: ignore[attr-defined] container.mux(stream.encode(None)) # type: ignore[attr-defined] From 366773e2d98e40d88982f1d8e84676c21dffda75 Mon Sep 17 00:00:00 2001 From: Alexander Druz Date: Fri, 8 Nov 2024 15:36:26 +0100 Subject: [PATCH 14/21] Ignore Spotlight settings file in mypy --- pyproject.toml | 1 - renumics/spotlight/settings.py | 3 +++ 2 files changed, 3 insertions(+), 1 deletion(-) diff --git a/pyproject.toml b/pyproject.toml index 90cd29b9..c1f0b5ec 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -183,7 +183,6 @@ module = [ "tests.ui._autogenerated_ui_elements", "transformers", "pyarrow.*", - "pydantic_settings.*", ] ignore_missing_imports = true diff --git a/renumics/spotlight/settings.py b/renumics/spotlight/settings.py index e6aee746..410725b4 100644 --- a/renumics/spotlight/settings.py +++ b/renumics/spotlight/settings.py @@ -2,6 +2,9 @@ global settings (read from env) """ +# Currently, mypy doesn't work with pydantic_settings. +# type: ignore + from typing import Optional from pydantic_settings import BaseSettings, SettingsConfigDict From 4727dac700bdc9115b004367d45807b04b3c561e Mon Sep 17 00:00:00 2001 From: Alexander Druz Date: Fri, 8 Nov 2024 15:47:46 +0100 Subject: [PATCH 15/21] Set output stream channels as kwargs --- renumics/spotlight/io/audio.py | 4 +--- 1 file changed, 1 insertion(+), 3 deletions(-) diff --git a/renumics/spotlight/io/audio.py b/renumics/spotlight/io/audio.py index 5a1b49e6..644e35be 100644 --- a/renumics/spotlight/io/audio.py +++ b/renumics/spotlight/io/audio.py @@ -151,9 +151,7 @@ def write_audio( frame = av.audio.AudioFrame.from_ndarray(data, data_format, layout) frame.rate = sampling_rate with av.open(file, "w", format_) as container: - stream = container.add_stream( - codec, sampling_rate, options={"channels": num_channels} # type: ignore[dict-item] - ) + stream = container.add_stream(codec, sampling_rate, channels=num_channels) # type: ignore[call-arg] container.mux(stream.encode(frame)) # type: ignore[attr-defined] container.mux(stream.encode(None)) # type: ignore[attr-defined] From 50833bee9e6a00fd9f2c6b562f9c8967ce437e09 Mon Sep 17 00:00:00 2001 From: Alexander Druz Date: Fri, 8 Nov 2024 16:02:58 +0100 Subject: [PATCH 16/21] Use Python 3.10 in CI by default --- .github/actions/setup-poetry/action.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/actions/setup-poetry/action.yml b/.github/actions/setup-poetry/action.yml index bdd60d6b..df83267b 100644 --- a/.github/actions/setup-poetry/action.yml +++ b/.github/actions/setup-poetry/action.yml @@ -5,7 +5,7 @@ description: | inputs: python-version: description: Python version to use - default: '3.8' + default: '3.10' install-dependencies: description: Whether to install and cache/restore dependencies default: 'true' From 0a6c16a1f6cb1590c764e4da3f7d80f351d1fd68 Mon Sep 17 00:00:00 2001 From: Alexander Druz Date: Fri, 8 Nov 2024 16:19:15 +0100 Subject: [PATCH 17/21] Do not ignore Spotlight settings file for mypy --- renumics/spotlight/settings.py | 3 --- 1 file changed, 3 deletions(-) diff --git a/renumics/spotlight/settings.py b/renumics/spotlight/settings.py index 410725b4..e6aee746 100644 --- a/renumics/spotlight/settings.py +++ b/renumics/spotlight/settings.py @@ -2,9 +2,6 @@ global settings (read from env) """ -# Currently, mypy doesn't work with pydantic_settings. -# type: ignore - from typing import Optional from pydantic_settings import BaseSettings, SettingsConfigDict From 5eebb2e5df7b0f11e6b4e2d3ee41851d1ed8f66b Mon Sep 17 00:00:00 2001 From: Alexander Druz Date: Fri, 8 Nov 2024 16:19:48 +0100 Subject: [PATCH 18/21] Pin av<=13.0.0 --- poetry.lock | 2 +- pyproject.toml | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/poetry.lock b/poetry.lock index 8d1f5c48..517e2833 100644 --- a/poetry.lock +++ b/poetry.lock @@ -7675,4 +7675,4 @@ descriptors = ["pycatch22"] [metadata] lock-version = "2.0" python-versions = ">=3.8, <3.12" -content-hash = "59c9f8c8aa6e1ead372514a79418646139154be4112ec3ae65a26125cfa7b855" +content-hash = "b740513d1985c7d7b4ea1b706fc4aabf31604d34e4c8cd8475f638ddc9338f79" diff --git a/pyproject.toml b/pyproject.toml index c1f0b5ec..bea0cffe 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -74,7 +74,7 @@ pandas = "*" importlib_resources = "<5.8.0" scikit-image = "*" imagecodecs = [{ version = "*", markers = 'platform_machine != "arm64"' }] -av = "*" +av = "<=13.0.0" validators = "*" ipywidgets = "*" jinja2 = "*" From 3b585252d2e5203e6db775e42202bb957ca09c5f Mon Sep 17 00:00:00 2001 From: Alexander Druz Date: Fri, 8 Nov 2024 17:51:27 +0100 Subject: [PATCH 19/21] Update Python deps --- Makefile | 2 +- poetry.lock | 101 ++++++++++++++++++++++--------------------------- pyproject.toml | 3 +- 3 files changed, 49 insertions(+), 57 deletions(-) diff --git a/Makefile b/Makefile index ce4cfb6d..10f9b603 100644 --- a/Makefile +++ b/Makefile @@ -27,7 +27,7 @@ clean: ## clean project .PHONY: audit audit: ## Audit project dependencies poetry export --without-hashes | poetry run safety check --full-report --stdin \ - --ignore 61496 --ignore 70612 --ignore 71596 --ignore 73323 + --ignore 61496 --ignore 65477 --ignore 70612 --ignore 71596 --ignore 73323 pnpm audit --prod .PHONY: check-format diff --git a/poetry.lock b/poetry.lock index 517e2833..916c2cdb 100644 --- a/poetry.lock +++ b/poetry.lock @@ -1089,49 +1089,47 @@ typing-inspect = ">=0.4.0,<1" [[package]] name = "datasets" -version = "2.20.0" +version = "2.14.4" description = "HuggingFace community-driven open-source library of datasets" optional = false python-versions = ">=3.8.0" files = [ - {file = "datasets-2.20.0-py3-none-any.whl", hash = "sha256:76ac02e3bdfff824492e20678f0b6b1b6d080515957fe834b00c2ba8d6b18e5e"}, - {file = "datasets-2.20.0.tar.gz", hash = "sha256:3c4dbcd27e0f642b9d41d20ff2efa721a5e04b32b2ca4009e0fc9139e324553f"}, + {file = "datasets-2.14.4-py3-none-any.whl", hash = "sha256:29336bd316a7d827ccd4da2236596279b20ca2ac78f64c04c9483da7cbc2459b"}, + {file = "datasets-2.14.4.tar.gz", hash = "sha256:ef29c2b5841de488cd343cfc26ab979bff77efa4d2285af51f1ad7db5c46a83b"}, ] [package.dependencies] aiohttp = "*" -dill = ">=0.3.0,<0.3.9" -filelock = "*" -fsspec = {version = 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source = "torch-cpu" } ray = {extras = ["data"], version = "==2.9.3"} +soxr = "*" [tool.poetry.group.playbook.dependencies] towhee = "^0.9.0" From 30d8982d94cccf84d5031cd3368033daafd76f72 Mon Sep 17 00:00:00 2001 From: Alexander Druz Date: Fri, 8 Nov 2024 22:29:04 +0100 Subject: [PATCH 20/21] Only audit production Python packages --- Makefile | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) diff --git a/Makefile b/Makefile index 10f9b603..abe081fc 100644 --- a/Makefile +++ b/Makefile @@ -26,8 +26,9 @@ clean: ## clean project .PHONY: audit audit: ## Audit project dependencies - poetry export --without-hashes | poetry run safety check --full-report --stdin \ - --ignore 61496 --ignore 65477 --ignore 70612 --ignore 71596 --ignore 73323 + poetry export --without-hashes --all-extras --without dev --without playbook \ + | poetry run safety check --full-report --stdin \ + --ignore 61496 --ignore 70612 --ignore 71596 --ignore 73323 pnpm audit --prod .PHONY: check-format From 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[[package]] name = "typed-ast" version = "1.5.5" @@ -7666,4 +7196,4 @@ descriptors = ["pycatch22"] [metadata] lock-version = "2.0" python-versions = ">=3.8, <3.12" -content-hash = "74a0bdf05ef1c8f3f1e7d4452d80bb7228803b6a1db54937e91b19cc16c475e2" +content-hash = "37e00037e3a770b4d1bcfab0695e01a58cb5ee4afb4bd52f2b8b27500f4e0ab4" diff --git a/pyproject.toml b/pyproject.toml index 9fc5cde6..942ac091 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -131,7 +131,6 @@ ray = {extras = ["data"], version = "==2.9.3"} soxr = "*" [tool.poetry.group.playbook.dependencies] -towhee = "^0.9.0" annoy = "^1.17.2" cleanlab = "^2.4.0" torch = { version = "^2.1.1+cpu", source = "torch-cpu" }