ssec-jhu / dplutils

Distributed(Data) Pipeline Uitilities
BSD 3-Clause "New" or "Revised" License
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Bump the all-minor-and-patch-dependency-updates group with 13 updates #83

Closed dependabot[bot] closed 3 months ago

dependabot[bot] commented 3 months ago

Bumps the all-minor-and-patch-dependency-updates group with 13 updates:

Package From To
bandit 1.7.7 1.7.8
aim 3.17.5 3.19.3
mlflow 2.11.3 2.12.1
tox 4.14.2 4.15.0
ray[default] 2.10.0 2.12.0
networkx 3.2.1 3.3
sphinx 7.2.6 7.3.7
sphinx-automodapi 0.16.0 0.17.0
sphinx-issues 4.0.0 4.1.0
sphinx-book-theme 1.1.0 1.1.2
build 1.1.1 1.2.1
pytest 8.1.1 8.2.0
ruff 0.1.15 0.4.2

Updates bandit from 1.7.7 to 1.7.8

Release notes

Sourced from bandit's releases.

1.7.8

What's Changed

New Contributors

Full Changelog: https://github.com/PyCQA/bandit/compare/1.7.7...1.7.8

Commits


Updates aim from 3.17.5 to 3.19.3

Release notes

Sourced from aim's releases.

🚀 v3.19.3 - Fixes in Remote tracking with multiple runs and base path handling when opening Explorer in new tab

What's Changed

Full Changelog: https://github.com/aimhubio/aim/compare/v3.19.2...v3.19.3

🚀 v3.19.2 - Tracking server connection protocol probing fix, Fix in query results live update functionality

What's Changed

Full Changelog: https://github.com/aimhubio/aim/compare/v3.19.1...v3.19.2

🚀 v3.19.1 - Tracking server redirects fix for endpoints without trailing slashes

What's Changed

Full Changelog: https://github.com/aimhubio/aim/compare/v3.19.0...v3.19.1

🚀 v3.19.0 New HTTP-based tracking server, Support of Artifacts logging, Fixes in lightning and huggingface integrations

What's Changed

New Contributors

Full Changelog: https://github.com/aimhubio/aim/compare/v3.18.1...v3.19.0

Changelog

Sourced from aim's changelog.

3.19.3 Apr 17, 2024

  • Resolve issue with new runs after tracking queue shutdown (mihran113)
  • Reset base path when opening new tabs (mihran113)

3.19.2 Mar 22, 2024

  • Resolve live update failing issue (mihran113)
  • Resolve issue with remote tracking protocol probe fail (mihran113)

3.19.1 Mar 14, 2024

  • Accept calls on tracking server without trailing slashes (mihran113)

3.19.0 Mar 13, 2024

Enhancements:

  • Replace grpc with http/ws as transport for aim tracking server (mihran113)
  • Remove aim storage upgrade 2to3 command (mihran113)
  • Allow HF callback to initialize run at on_init_end for tracking custom metrics with callback (dushyantbehl)
  • Support artifacts logging and storage in AWS S3 (alberttorosyan)
  • Always set run name when initializing Run in lightning callback (martenlienen)

Fixes

  • Allow the web UI to serve assets symlinked into the static files directory (martenlienen)

3.18.1 Feb 7, 2024

Enhancements:

  • Add support for sqlalchemy 2.0 (mihran113)
  • Add min/max/first values tracking and visualization for metrics (mihran113, KaroMourad)

Fixes

  • Fix pytorch_lightning aliases issue (popfido)
  • Fix typos in stat.py to collect gpu memory and power correctly (ChanderG)
  • Fix bug in pytorch lightning raising lock timeout (inc0)
  • Fix compatibility with sqlalchemy < 2.0 versions (mihran113)
  • Switch to patched version of official pynvml (mihran113)
  • Remove telemetry tracking (mihran113)
Commits
  • 17cdf0b Bump up Aim to v3.19.3
  • 56b915a [fix] Resolve issue with new runs after tracking queue shutdown (#3134)
  • b172492 [fix] Base path is ignored on new tab open (#3131)
  • 3cdc97e [fix] Resolve issue with multiple token refreshes (#3130)
  • d1426d9 Bump up Aim to v3.19.2
  • ed8ac3e [fix] Resolve live update failing issue (#3126)
  • 7dd290b [fix] Resolve issue with remote tracking protocol probe fail (#3127)
  • 555ac20 Bump up Aim to v3.19.1
  • 09c0f93 [fix] Accept calls on tracking server without trailing slashes (#3119)
  • 9899aea Bump up Aim to v3.19.0
  • Additional commits viewable in compare view


Updates mlflow from 2.11.3 to 2.12.1

Release notes

Sourced from mlflow's releases.

MLflow 2.12.1 includes several major features and improvements

With this release, we're pleased to introduce several major new features that are focused on enhanced GenAI support, Deep Learning workflows involving images, expanded table logging functionality, and general usability enhancements within the UI and external integrations.

Major Features and Improvements:

  • PromptFlow: Introducing the new PromptFlow flavor, designed to enrich the GenAI landscape within MLflow. This feature simplifies the creation and management of dynamic prompts, enhancing user interaction with AI models and streamlining prompt engineering processes. (#11311, #11385 @​brynn-code)

  • Enhanced Metadata Sharing for Unity Catalog: MLflow now supports the ability to share metadata (and not model weights) within Databricks Unity Catalog. When logging a model, this functionality enables the automatic duplication of metadata into a dedicated subdirectory, distinct from the model’s actual storage location, allowing for different sharing permissions and access control limits. (#11357, #11720 @​WeichenXu123)

  • Code Paths Unification and Standardization: We have unified and standardized the code_paths parameter across all MLflow flavors to ensure a cohesive and streamlined user experience. This change promotes consistency and reduces complexity in the model deployment lifecycle. (#11688, @​BenWilson2)

  • ChatOpenAI and AzureChatOpenAI Support: Support for the ChatOpenAI and AzureChatOpenAI interfaces has been integrated into the LangChain flavor, facilitating seamless deployment of conversational AI models. This development opens new doors for building sophisticated and responsive chat applications leveraging cutting-edge language models. (#11644, @​B-Step62)

  • Custom Models in Sentence-Transformers: The sentence-transformers flavor now supports custom models, allowing for a greater flexibility in deploying tailored NLP solutions. (#11635, @​B-Step62)

  • Native MLflow Image support in the log_image API: Added support for optimized image logging, including step-based iterative logging for images generated as part of a training run. This feature enables the ability to track your image generation, classification, segmentation, enhancement and object detection deep learning models effortlessly. (#11243, #11404, @​jessechancy)

  • Image Support for Log Table: With the addition of image support in log_table, MLflow enhances its capabilities in handling rich media. This functionality allows for direct logging and visualization of images within the platform, improving the interpretability and analysis of visual data. (#11535, @​jessechancy)

  • Streaming Support for LangChain: The newly introduced predict_stream API for LangChain models supports streaming outputs, enabling real-time output for chain invocation via pyfunc. This feature is pivotal for applications requiring continuous data processing and instant feedback. (#11490, #11580 @​WeichenXu123)

Security Fixes:

  • Security Patch: Addressed a critical Local File Read/Path Traversal vulnerability within the Model Registry, ensuring robust protection against unauthorized access and securing user data integrity. (#11376, @​WeichenXu123)

Features:

  • [Models] Add the PromptFlow flavor (#11311, #11385 @​brynn-code)
  • [Models] Add a new predict_stream API for streamable output for Langchain models and the DatabricksDeploymentClient (#11490, #11580 @​WeichenXu123)
  • [Models] Deprecate and add code_paths alias for code_path in pyfunc to be standardized to other flavor implementations (#11688, @​BenWilson2)
  • [Models] Add support for custom models within the sentence-transformers flavor (#11635, @​B-Step62)
  • [Models] Enable Spark MapType support within model signatures when used with Spark udf inference (#11265, @​WeichenXu123)
  • [Models] Add support for metadata-only sharing within Unity Catalog through the use of a subdirectory (#11357, #11720 @​WeichenXu123)
  • [Models] Add Support for the ChatOpenAI and AzureChatOpenAI LLM interfaces within the LangChain flavor (#11644, @​B-Step62)
  • [Artifacts] Add support for utilizing presigned URLs when uploading and downloading files when using Unity Catalog (#11534, @​artjen)
  • [Artifacts] Add a new Image object for handling the logging and optimized compression of images (#11404, @​jessechancy)
  • [Artifacts] Add time and step-based metadata to the logging of images (#11243, @​jessechancy)
  • [Artifacts] Add the ability to log a dataset to Unity Catalog by means of UCVolumeDatasetSource (#11301, @​chenmoneygithub)
  • [Tracking] Remove the restrictions for logging a table in Delta format to no longer require running within a Databricks environment (#11521, @​chenmoneygithub)
  • [Tracking] Add support for logging mlflow.Image files within tables (#11535, @​jessechancy)
  • [Server-infra] Introduce override configurations for controlling how http retries are handled (#11590, @​BenWilson2)
  • [Deployments] Implement chat & chat streaming for Anthropic within the MLflow deployments server (#11195, @​gabrielfu)

Security fixes:

Bug fixes:

... (truncated)

Changelog

Sourced from mlflow's changelog.

2.12.1 (2024-04-17)

MLflow 2.12.1 includes several major features and improvements

With this release, we're pleased to introduce several major new features that are focused on enhanced GenAI support, Deep Learning workflows involving images, expanded table logging functionality, and general usability enhancements within the UI and external integrations.

Major Features and Improvements:

  • PromptFlow: Introducing the new PromptFlow flavor, designed to enrich the GenAI landscape within MLflow. This feature simplifies the creation and management of dynamic prompts, enhancing user interaction with AI models and streamlining prompt engineering processes. (#11311, #11385 @​brynn-code)

  • Enhanced Metadata Sharing for Unity Catalog: MLflow now supports the ability to share metadata (and not model weights) within Databricks Unity Catalog. When logging a model, this functionality enables the automatic duplication of metadata into a dedicated subdirectory, distinct from the model’s actual storage location, allowing for different sharing permissions and access control limits. (#11357, #11720 @​WeichenXu123)

  • Code Paths Unification and Standardization: We have unified and standardized the code_paths parameter across all MLflow flavors to ensure a cohesive and streamlined user experience. This change promotes consistency and reduces complexity in the model deployment lifecycle. (#11688, @​BenWilson2)

  • ChatOpenAI and AzureChatOpenAI Support: Support for the ChatOpenAI and AzureChatOpenAI interfaces has been integrated into the LangChain flavor, facilitating seamless deployment of conversational AI models. This development opens new doors for building sophisticated and responsive chat applications leveraging cutting-edge language models. (#11644, @​B-Step62)

  • Custom Models in Sentence-Transformers: The sentence-transformers flavor now supports custom models, allowing for a greater flexibility in deploying tailored NLP solutions. (#11635, @​B-Step62)

  • Image Support for Log Table: With the addition of image support in log_table, MLflow enhances its capabilities in handling rich media. This functionality allows for direct logging and visualization of images within the platform, improving the interpretability and analysis of visual data. (#11535, @​jessechancy)

  • Streaming Support for LangChain: The newly introduced predict_stream API for LangChain models supports streaming outputs, enabling real-time output for chain invocation via pyfunc. This feature is pivotal for applications requiring continuous data processing and instant feedback. (#11490, #11580 @​WeichenXu123)

Security Fixes:

  • Security Patch: Addressed a critical Local File Read/Path Traversal vulnerability within the Model Registry, ensuring robust protection against unauthorized access and securing user data integrity. (#11376, @​WeichenXu123)

Features:

  • [Models] Add the PromptFlow flavor (#11311, #11385 @​brynn-code)
  • [Models] Add a new predict_stream API for streamable output for Langchain models and the DatabricksDeploymentClient (#11490, #11580 @​WeichenXu123)
  • [Models] Deprecate and add code_paths alias for code_path in pyfunc to be standardized to other flavor implementations (#11688, @​BenWilson2)
  • [Models] Add support for custom models within the sentence-transformers flavor (#11635, @​B-Step62)
  • [Models] Enable Spark MapType support within model signatures when used with Spark udf inference (#11265, @​WeichenXu123)
  • [Models] Add support for metadata-only sharing within Unity Catalog through the use of a subdirectory (#11357, #11720 @​WeichenXu123)
  • [Models] Add Support for the ChatOpenAI and AzureChatOpenAI LLM interfaces within the LangChain flavor (#11644, @​B-Step62)
  • [Artifacts] Add support for utilizing presigned URLs when uploading and downloading files when using Unity Catalog (#11534, @​artjen)
  • [Artifacts] Add a new Image object for handling the logging and optimized compression of images (#11404, @​jessechancy)
  • [Artifacts] Add time and step-based metadata to the logging of images (#11243, @​jessechancy)
  • [Artifacts] Add the ability to log a dataset to Unity Catalog by means of UCVolumeDatasetSource (#11301, @​chenmoneygithub)
  • [Tracking] Remove the restrictions for logging a table in Delta format to no longer require running within a Databricks environment (#11521, @​chenmoneygithub)
  • [Tracking] Add support for logging mlflow.Image files within tables (#11535, @​jessechancy)
  • [Server-infra] Introduce override configurations for controlling how http retries are handled (#11590, @​BenWilson2)
  • [Deployments] Implement chat & chat streaming for Anthropic within the MLflow deployments server (#11195, @​gabrielfu)

Security fixes:

Bug fixes:

... (truncated)

Commits


Updates tox from 4.14.2 to 4.15.0

Release notes

Sourced from tox's releases.

4.15.0

What's Changed

New Contributors

Full Changelog: https://github.com/tox-dev/tox/compare/4.14.2...4.15.0

Changelog

Sourced from tox's changelog.

v4.15.0 (2024-04-26)

Features - 4.15.0

- Add support for multiple appending override options (-x, --override) on command line - by :user:`amitschang`. (:issue:`3261`)
- Add support for inverting exit code success criteria using bang (!) (:issue:`3271`)

Bugfixes - 4.15.0

  • Fix issue that the leading character c was dropped from packages in constraints files - by :user:jugmac00. (:issue:3247)
  • Allow appending to deps with --override testenv.deps+=foo - by :user:stefanor. (:issue:3256)
  • Fix non-existing branch rewrite in the documentation to main. (:issue:3257)
  • Update test typing for build 1.2.0, which has an explicit Distribution type - by :user:stefanor. (:issue:3260)
  • Fix broken input parsing for --discover flag. - by :user:mimre25 (:issue:3272)

Improved Documentation - 4.15.0

- Rephrase ``--discover`` flag's description to avoid confusion between paths and executables. - by :user:`mimre25` (:issue:`3274`)
Commits


Updates ray[default] from 2.10.0 to 2.12.0

Release notes

Sourced from ray[default]'s releases.

Ray-2.12.0

Ray Libraries

Ray Data

🎉 New Features:

  • Store Ray Data logs in special subdirectory (#44743)

💫 Enhancements:

  • Add in local_read option to from_torch (#44752)

🔨 Fixes:

  • Fix the config to disable progress bar (#44342)

📖 Documentation:

  • Clarify deprecated Datasource docstrings (#44790)

Ray Train

🔨 Fixes:

  • Disable gathering the full state dict in RayFSDPStrategy for lightning>2.1 (#44569)

Ray Tune

💫 Enhancements:

  • Remove spammy log for "new output engine" (#44824)
  • Enable isort (#44693)

Ray Serve

🔨 Fixes:

  • [Serve] fix getting attributes on stdout during Serve logging redirect (#44787)

RLlib

🎉 New Features:

  • Support of images and video logging in WandB (env rendering example script for the new API stack coming up). (#43356)

💫 Enhancements:

  • Better support and separation-of-concerns for model_config_dict in new API stack. (#44263)
  • Added example script to pre-train an RLModule in single-agent fashion, then bring checkpoint into multi-agent setup and continue training. (#44674)
  • More examples scripts got translated from the old- to the new API stack: Curriculum learning, custom-gym-env, etc..: (#44706, #44707, #44735, #44841)

Ray Core and Ray Clusters

🔨 Fixes:

... (truncated)

Commits
  • 549c4b7 [release] change version to 2.12.0
  • 7c9209f [ci][bisect/1] initial version of macos test bisect (#44618)
  • fe4dd5d [ci][bisect/0] add a function to run a single macos tests (#44848)
  • 9587ef3 [serve] fix documentation typo (#44855)
  • 05232b5 [Tune] Remove spammy log for "new output engine" (#44824)
  • 7e315fe [serve] add num replicas auto telemetry (#44609)
  • a2b2663 [release] add 2.11.0 performance metrics (#44847)
  • 650aa79 [GCS] Fixed GCS pub-sub channel-types to be explicitly mapped to either cappe...
  • 2185fa9 [spark] Fix Ray-on-Spark ray child process shebang issue (#44827)
  • 1e936e3 [jobs] Fix Job submission issue on Windows platform (#44632)
  • Additional commits viewable in compare view


Updates networkx from 3.2.1 to 3.3

Release notes

Sourced from networkx's releases.

NetworkX 3.3

networkx 3.3

We're happy to announce the release of networkx 3.3!

API Changes

  • Disallow negative number of nodes in complete_multipartite_graph (#7057).
  • DEP: Deprecate the all_triplets one-liner (#7060).
  • [A-star] Added expansion pruning via cutoff if cutoff is provided (#7073).
  • Make HITS raise exceptions consistent with power iterations (#7084).
  • DEP: Deprecate random_triad (#7061).
  • Added feature modular graph product (#7227).
  • ENH: Speed up common/non_neighbors by using _adj dict operations (#7244).
  • Deprecate the create argument of nonisomorphic_trees (#7316).
  • Improve total_spanning_tree_weight (#7100).
  • Update init.py (#7320).
  • add **kwargs to traveling_salesman_problem (#7371).

Enhancements

  • Add Tadpole graph (#6999).
  • [A-star] Added expansion pruning via cutoff if cutoff is provided (#7073).
  • Implementation of $S^1$ model (#6858).
  • [Feat] Random expanders utilities (#6761).
  • Compare graphs for generator functions when running tests with backend (#7066).
  • Add Kirchhoff index / Effective graph resistance (#6926).
  • Changed return types of shortest path methods to improve consistency (#6584).
  • New PR for Fixes minimal d-separator function failing to handle cases where no d-separators exist (#7019).
  • ENH : Provide non-normalized and normalized directed laplacian matrix calculation (#7199).
  • feat: drop the use of node attribute "first_nbr" in PlanarEmbedding (#7202).
  • Add functions to compute Schultz and Gutman Index (#3709).
  • Divisive community algorithms (#5830).
  • Added feature modular graph product (#7227).
  • ENH : added sort_neighbors to all functions in depth_first_search.py (#7196).
  • New graph generator for the Kneser graph (#7146).
  • Draw MultiDiGraph edges and labels qa7008 (#7010).
  • Use github actions to run a comparison benchmark (#7268).
  • BFS layout implementation (#5179).
  • Add max_level= argument to louvain_communities to limit macro-iterations (#6909).
  • Review and update @nx._dispatchable usage since 3.2.1 (#7302).
  • Transmogrify _dispatchable objects into functions (#7298).
  • fix: make PlanarEmbedding.copy() use add_edges_from() from parent (closes #7223) (#7224).
  • Allow seed of np.random instance to exactly produce arbitrarily large integers (#6869).
  • Improve total_spanning_tree_weight (#7100).
  • add seed to nx.generate_random_paths (#7332).
  • Allow backends to implement should_run (#7257).
  • Adding tree broadcasting algorithm in a new module (#6928).
  • Option to include initial labels in weisfeiler_lehman_subgraph_hashes (#6601).
  • Add better error message when trying to get edge that is not present (#7245).

... (truncated)

Commits
  • 7fdddfa Designate 3.3 release
  • 7fe09dd Bump the GH actions with 3 updates (#7310)
  • 83d2cf4 Move the backend docs and connect the config docs. Both in a single sidebar e...
  • 754173b Fix exception for del config[key] (#7391)
  • 26d218b Rm deprecated np.row_stack in favor of vstack. (#7390)
  • 0d878d8 Update test suite to handle when scipy is not installed (#7388)
  • fbb2d82 Add dispatching to broadcasting.py (#7386)
  • 76c3e9b Fix pygraphviz tests causing segmentation faults in backend test (#7380)
  • c8c838f add **kwargs to traveling_salesman_problem (#7371)
  • 6e84e1e ENH: Cache graphs objects when converting to a backend (#7345)
  • Additional commits viewable in compare view


Updates sphinx from 7.2.6 to 7.3.7

Release notes

Sourced from sphinx's releases.

Sphinx 7.3.7

Changelog: https://www.sphinx-doc.org/en/master/changes.html

Sphinx 7.3.6

Changelog: https://www.sphinx-doc.org/en/master/changes.html

Sphinx 7.3.5

Changelog: https://www.sphinx-doc.org/en/master/changes.html

Sphinx 7.3.4

Changelog: https://www.sphinx-doc.org/en/master/changes.html

Sphinx 7.3.3

Changelog: https://www.sphinx-doc.org/en/master/changes.html

Sphinx 7.3.2

Changelog: https://www.sphinx-doc.org/en/master/changes.html

Sphinx 7.3.1

Changelog: https://www.sphinx-doc.org/en/master/changes.html

Sphinx 7.3.0

Changelog: https://www.sphinx-doc.org/en/master/changes.html

Changelog

Sourced from sphinx's changelog.

Release 7.3.7 (released Apr 19, 2024)

Bugs fixed

  • #12299: Defer loading themes defined via entry points until their explicit use by the user or a child theme. Patch by Adam Turner.
  • #12305: Return the default value for theme.get_config() with an unsupported theme configuration section. Patch by Adam Turner.

Release 7.3.6 (released Apr 17, 2024)

Bugs fixed

  • #12295: Re-export all AST types in the C and C++ domains. Patch by Adam Turner.
  • #12295: Re-export various objects from sphinx.domains.python._annotations in sphinx.domains.python. Patch by Jacob Chesslo and Adam Turner.

Release 7.3.5 (released Apr 17, 2024)

Bugs fixed

  • #12295: Re-export various objects from sphinx.domains.python._object in sphinx.domains.python. Patch by Jacob Chesslo and Adam Turner.

Release 7.3.4 (released Apr 17, 2024)

Bugs fixed

  • Handle cases when Any is not an instance of type. Patch by Adam Turner.

Release 7.3.3 (released Apr 17, 2024)

Bugs fixed

... (truncated)

Commits
  • de4ac2f Bump to 7.3.7 final
  • 4a0c9dd Return the default value for unsupported theme configuration sections
  • 62c3bad Re-export py_sig_re from the Python domain
  • 3bcc669 Defer loading entry-point themes until needed
  • fa4563f Bump version
  • 630b4fb Bump to 7.3.6 final
  • 740b964 fixup! Elaborate a little more in the warning message for config.cache
  • 141f3ec Elaborate a little more in the warning message for config.cache
  • af27188 Add config.cache to the list of warning types
  • be2b083 Re-export more names in sphinx.domains.python (#12297)
  • Additional commits viewable in compare view


Updates sphinx-automodapi from 0.16.0 to 0.17.0

Release notes

Sourced from sphinx-automodapi's releases.

v0.17.0 Release Notes

Also see CHANGES.rst.

What's Changed