sl-shared-assets 1.0.0rc20__tar.gz → 1.0.0rc21__tar.gz

{sl_shared_assets-1.0.0rc20 → sl_shared_assets-1.0.0rc21}/PKG-INFO

@@ -1,10 +1,10 @@
 Metadata-Version: 2.4
 Name: sl-shared-assets
-Version: 1.0.0rc20
+Version: 1.0.0rc21
 Summary: Stores assets shared between multiple Sun (NeuroAI) lab data pipelines.
 Project-URL: Homepage, https://github.com/Sun-Lab-NBB/sl-shared-assets
 Project-URL: Documentation, https://sl-shared-assets-api-docs.netlify.app/
-Author: Ivan Kondratyev, Kushaan Gupta, Yuantao Deng
+Author: Ivan Kondratyev, Kushaan Gupta, Yuantao Deng, Natalie Yeung
 Maintainer-email: Ivan Kondratyev <ik278@cornell.edu>
 License:                     GNU GENERAL PUBLIC LICENSE
                                Version 3, 29 June 2007
@@ -695,8 +695,10 @@ Requires-Dist: ataraxis-base-utilities<4,>=3
 Requires-Dist: ataraxis-data-structures<4,>=3.1.1
 Requires-Dist: ataraxis-time<4,>=3
 Requires-Dist: click<9,>=8
-Requires-Dist: dacite<2,>=1
+Requires-Dist: natsort<9,>=8
 Requires-Dist: paramiko<4,>=3.5.1
+Requires-Dist: polars<2,>=1
+Requires-Dist: pyarrow<21,>=20
 Requires-Dist: simple-slurm<1,>=0
 Requires-Dist: tqdm<5,>=4
 Requires-Dist: xxhash<4,>=3
@@ -717,8 +719,10 @@ Requires-Dist: types-tqdm<5,>=4; extra == 'conda'
 Provides-Extra: condarun
 Requires-Dist: appdirs<2,>=1; extra == 'condarun'
 Requires-Dist: click<9,>=8; extra == 'condarun'
-Requires-Dist: dacite<2,>=1; extra == 'condarun'
+Requires-Dist: natsort<9,>=8; extra == 'condarun'
 Requires-Dist: paramiko<4,>=3.5.1; extra == 'condarun'
+Requires-Dist: polars<2,>=1; extra == 'condarun'
+Requires-Dist: pyarrow<21,>=20; extra == 'condarun'
 Requires-Dist: tqdm<5,>=4; extra == 'condarun'
 Provides-Extra: dev
 Requires-Dist: ataraxis-automation<5,>=4; extra == 'dev'
@@ -781,6 +785,7 @@ acquisition and processing and provides the API for accessing the lab’s main c
 
 - [Dependencies](#dependencies)
 - [Installation](#installation)
+- [Usage](#usage)
 - [API Documentation](#api-documentation)
 - [Versioning](#versioning)
 - [Authors](#authors)
@@ -811,11 +816,22 @@ Use the following command to install the library using pip: ```pip install sl-sh
 
 ---
 
+## Usage
+
+All library components are intended to be used via other Sun lab libraries. Developers should study the API and CLI 
+documentation below to learn how to use library components in other Sun lab libraries.
+
+---
+
 ## API Documentation
 
 See the [API documentation](https://sl-shared-assets-api-docs.netlify.app/) for the
 detailed description of the methods and classes exposed by components of this library.
 
+**Note!** The API documentation includes important information about Command-Line-Interfaces (CLIs) exposed by this 
+library as part of installation into a Python environment. All users are highly encouraged to study the CLI 
+documentation to learn how to use library components via the terminal.
+
 ___
 
 ## Versioning
@@ -830,6 +846,7 @@ We use [semantic versioning](https://semver.org/) for this project. For the vers
 - Ivan Kondratyev ([Inkaros](https://github.com/Inkaros))
 - Kushaan Gupta ([kushaangupta](https://github.com/kushaangupta))
 - Yuantao Deng ([YuantaoDeng](https://github.com/YuantaoDeng))
+- Natalie Yeung
 
 ___
 

{sl_shared_assets-1.0.0rc20 → sl_shared_assets-1.0.0rc21}/README.md

@@ -30,6 +30,7 @@ acquisition and processing and provides the API for accessing the lab’s main c
 
 - [Dependencies](#dependencies)
 - [Installation](#installation)
+- [Usage](#usage)
 - [API Documentation](#api-documentation)
 - [Versioning](#versioning)
 - [Authors](#authors)
@@ -60,11 +61,22 @@ Use the following command to install the library using pip: ```pip install sl-sh
 
 ---
 
+## Usage
+
+All library components are intended to be used via other Sun lab libraries. Developers should study the API and CLI 
+documentation below to learn how to use library components in other Sun lab libraries.
+
+---
+
 ## API Documentation
 
 See the [API documentation](https://sl-shared-assets-api-docs.netlify.app/) for the
 detailed description of the methods and classes exposed by components of this library.
 
+**Note!** The API documentation includes important information about Command-Line-Interfaces (CLIs) exposed by this 
+library as part of installation into a Python environment. All users are highly encouraged to study the CLI 
+documentation to learn how to use library components via the terminal.
+
 ___
 
 ## Versioning
@@ -79,6 +91,7 @@ We use [semantic versioning](https://semver.org/) for this project. For the vers
 - Ivan Kondratyev ([Inkaros](https://github.com/Inkaros))
 - Kushaan Gupta ([kushaangupta](https://github.com/kushaangupta))
 - Yuantao Deng ([YuantaoDeng](https://github.com/YuantaoDeng))
+- Natalie Yeung
 
 ___
 

{sl_shared_assets-1.0.0rc20 → sl_shared_assets-1.0.0rc21}/docs/source/api.rst

@@ -9,16 +9,32 @@ Command Line Interfaces
    :undoc-members:
    :show-inheritance:
 
-.. click:: sl_shared_assets.cli:replace_local_root_directory
-   :prog: sl-replace-root
+.. click:: sl_shared_assets.cli:verify_session_integrity
+   :prog: sl-verify-session
+   :nested: full
+
+.. click:: sl_shared_assets.cli:generate_project_manifest_file
+   :prog: sl-project-manifest
+   :nested: full
+
+.. click:: sl_shared_assets.cli:generate_system_configuration_file
+   :prog: sl-create-system-config
    :nested: full
 
 .. click:: sl_shared_assets.cli:generate_server_credentials_file
-   :prog: sl-generate-credentials
+   :prog: sl-create-server-credentials
+   :nested: full
+
+.. click:: sl_shared_assets.cli:generate_project_configuration_file
+   :prog: sl-create-project
+   :nested: full
+
+.. click:: sl_shared_assets.cli:generate_experiment_configuration_file
+   :prog: sl-create-experiment
    :nested: full
 
 .. click:: sl_shared_assets.cli:ascend_tyche_directory
-   :prog: sl-ascend
+   :prog: sl-ascend-tyche
    :nested: full
 
 Tools
@@ -28,22 +44,15 @@ Tools
    :undoc-members:
    :show-inheritance:
 
-Suite2P Configuration
-=====================
-.. automodule:: sl_shared_assets.suite2p
-   :members:
-   :undoc-members:
-   :show-inheritance:
-
-General Data and Configuration Classes
-======================================
+Data and Configuration Classes
+==============================
 .. automodule:: sl_shared_assets.data_classes
    :members:
    :undoc-members:
    :show-inheritance:
 
-Compute Server Tools
-====================
+Server
+======
 .. automodule:: sl_shared_assets.server
    :members:
    :undoc-members:

{sl_shared_assets-1.0.0rc20 → sl_shared_assets-1.0.0rc21}/docs/source/conf.py

@@ -4,8 +4,8 @@ import importlib_metadata
 # -- Project information -----------------------------------------------------
 project = 'sl-shared-assets'
 # noinspection PyShadowingBuiltins
-copyright = '2025, Ivan Kondratyev & Sun Lab'
-authors = ['Ivan Kondratyev (Inkaros)', 'Kushaan Gupta', 'Yuantao Deng']
+copyright = '2025, Sun (NeuroAI) lab'
+authors = ['Ivan Kondratyev (Inkaros)', 'Kushaan Gupta', 'Yuantao Deng', 'Natalie Yeung']
 # Extracts the project version from the .toml file.
 release = importlib_metadata.version("sl-shared-assets")
 
@@ -26,8 +26,8 @@ exclude_patterns = []
 napoleon_google_docstring = True
 napoleon_numpy_docstring = False
 napoleon_include_init_with_doc = False
-napoleon_include_private_with_doc = True
-napoleon_include_special_with_doc = True
+napoleon_include_private_with_doc = False
+napoleon_include_special_with_doc = False
 napoleon_use_admonition_for_examples = False
 napoleon_use_admonition_for_notes = False
 napoleon_use_admonition_for_references = False

{sl_shared_assets-1.0.0rc20 → sl_shared_assets-1.0.0rc21}/docs/source/welcome.rst

@@ -4,8 +4,8 @@ Welcome to sl-shared-assets API documentation page
 sl-shared-assets is a Python library that stores assets shared between multiple Sun (NeuroAI) lab data pipelines.
 
 This library is developed in the `Sun lab <https://neuroai.github.io/sunlab/>`_ at Cornell University. The main purpose
-of this library is to provide the tools used by multiple other data acquisition nd processing libraries in the lab
-to configure their runtime and store experiment data.
+of this library is to provide the tools used by multiple other data acquisition and processing libraries in the lab to
+avoid circular or hierarchical cross-dependencies.
 
 This website only contains the API documentation for the classes and methods offered by this library. See the project
 GitHub repository for installation instructions and library usage examples:

{sl_shared_assets-1.0.0rc20 → sl_shared_assets-1.0.0rc21}/envs/slsa_dev_lin.yml

@@ -7,41 +7,62 @@ dependencies:
   - _python_abi3_support=1.0=hd8ed1ab_2
   - alabaster=1.0.0=pyhd8ed1ab_1
   - appdirs=1.4.4=pyhd8ed1ab_1
+  - aws-c-auth=0.9.0=h59ae206_7
+  - aws-c-cal=0.9.0=h5e3027f_1
+  - aws-c-common=0.12.3=hb9d3cd8_0
+  - aws-c-compression=0.3.1=hafb2847_5
+  - aws-c-event-stream=0.5.4=h2dcaabb_9
+  - aws-c-http=0.10.1=hb50fa74_1
+  - aws-c-io=0.19.0=h7962f60_2
+  - aws-c-mqtt=0.13.0=h35de22e_3
+  - aws-c-s3=0.7.17=h50d7d24_2
+  - aws-c-sdkutils=0.2.3=hafb2847_5
+  - aws-checksums=0.2.7=hafb2847_1
+  - aws-crt-cpp=0.32.5=h2811929_3
+  - aws-sdk-cpp=1.11.510=hffe9a0f_8
+  - azure-core-cpp=1.14.0=h5cfcd09_0
+  - azure-identity-cpp=1.10.0=h113e628_0
+  - azure-storage-blobs-cpp=12.13.0=h3cf044e_1
+  - azure-storage-common-cpp=12.8.0=h736e048_1
+  - azure-storage-files-datalake-cpp=12.12.0=ha633028_1
   - babel=2.17.0=pyhd8ed1ab_0
   - backports=1.0=pyhd8ed1ab_5
   - backports.tarfile=1.2.0=pyhd8ed1ab_1
   - bcrypt=4.3.0=py313h920b4c0_0
-  - beautifulsoup4=4.13.3=pyha770c72_0
+  - beautifulsoup4=4.13.4=pyha770c72_0
   - brotli-python=1.1.0=py313h46c70d0_2
   - bzip2=1.0.8=h4bc722e_7
-  - ca-certificates=2025.1.31=hbcca054_0
+  - c-ares=1.34.5=hb9d3cd8_0
+  - ca-certificates=2025.4.26=hbd8a1cb_0
   - cachetools=5.5.2=pyhd8ed1ab_0
-  - certifi=2025.1.31=pyhd8ed1ab_0
+  - certifi=2025.4.26=pyhd8ed1ab_0
   - cffi=1.17.1=py313hfab6e84_0
   - chardet=5.2.0=pyhd8ed1ab_3
-  - charset-normalizer=3.4.1=pyhd8ed1ab_0
-  - click=8.1.8=pyh707e725_0
+  - charset-normalizer=3.4.2=pyhd8ed1ab_0
+  - click=8.2.1=pyh707e725_0
   - cmarkgfm=2024.11.20=py313h536fd9c_0
   - colorama=0.4.6=pyhd8ed1ab_1
   - conda-souschef=2.2.3=pyhd8ed1ab_0
   - cpython=3.13.3=py313hd8ed1ab_101
-  - cryptography=44.0.2=py313h6556f6e_0
-  - dbus=1.13.6=h5008d03_3
+  - cryptography=45.0.2=py313h6556f6e_0
+  - dbus=1.16.2=h3c4dab8_0
   - distlib=0.3.9=pyhd8ed1ab_1
   - docutils=0.21.2=pyhd8ed1ab_1
   - editables=0.5=pyhd8ed1ab_1
-  - expat=2.7.0=h5888daf_0
   - filelock=3.18.0=pyhd8ed1ab_0
+  - gflags=2.2.2=h5888daf_1005
+  - glog=0.7.1=hbabe93e_0
   - grayskull=2.9.1=pyhd8ed1ab_0
   - h2=4.2.0=pyhd8ed1ab_0
   - hatchling=1.27.0=pypyhd8ed1ab_0
   - hpack=4.1.0=pyhd8ed1ab_0
   - hyperframe=6.1.0=pyhd8ed1ab_0
+  - icu=75.1=he02047a_0
   - id=1.5.0=pyh29332c3_0
   - idna=3.10=pyhd8ed1ab_1
   - imagesize=1.4.1=pyhd8ed1ab_0
-  - importlib-metadata=8.6.1=pyha770c72_0
-  - importlib_metadata=8.6.1=hd8ed1ab_0
+  - importlib-metadata=8.7.0=pyhe01879c_0
+  - importlib_metadata=8.7.0=he374078_0
   - importlib_resources=6.5.2=pyhd8ed1ab_0
   - jaraco.classes=3.4.0=pyhd8ed1ab_2
   - jaraco.context=6.0.1=pyhd8ed1ab_0
@@ -49,58 +70,95 @@ dependencies:
   - jeepney=0.9.0=pyhd8ed1ab_0
   - jinja2=3.1.6=pyhd8ed1ab_0
   - keyring=25.6.0=pyha804496_0
+  - keyutils=1.6.1=h166bdaf_0
+  - krb5=1.21.3=h659f571_0
   - ld_impl_linux-64=2.43=h712a8e2_4
+  - libabseil=20250127.1=cxx17_hbbce691_0
+  - libarrow=20.0.0=hebdba27_3_cpu
+  - libarrow-acero=20.0.0=hcb10f89_3_cpu
+  - libarrow-dataset=20.0.0=hcb10f89_3_cpu
+  - libarrow-substrait=20.0.0=h1bed206_3_cpu
   - libblas=3.9.0=31_h59b9bed_openblas
+  - libbrotlicommon=1.1.0=hb9d3cd8_2
+  - libbrotlidec=1.1.0=hb9d3cd8_2
+  - libbrotlienc=1.1.0=hb9d3cd8_2
   - libcblas=3.9.0=31_he106b2a_openblas
+  - libcrc32c=1.1.2=h9c3ff4c_0
+  - libcurl=8.13.0=h332b0f4_0
+  - libedit=3.1.20250104=pl5321h7949ede_0
+  - libev=4.33=hd590300_2
+  - libevent=2.1.12=hf998b51_1
   - libexpat=2.7.0=h5888daf_0
   - libffi=3.4.6=h2dba641_1
-  - libgcc=14.2.0=h767d61c_2
-  - libgcc-ng=14.2.0=h69a702a_2
-  - libgfortran=14.2.0=h69a702a_2
-  - libgfortran5=14.2.0=hf1ad2bd_2
-  - libglib=2.84.1=h2ff4ddf_0
-  - libgomp=14.2.0=h767d61c_2
+  - libgcc=15.1.0=h767d61c_2
+  - libgcc-ng=15.1.0=h69a702a_2
+  - libgfortran=15.1.0=h69a702a_2
+  - libgfortran5=15.1.0=hcea5267_2
+  - libglib=2.84.2=h3618099_0
+  - libgomp=15.1.0=h767d61c_2
+  - libgoogle-cloud=2.36.0=hc4361e1_1
+  - libgoogle-cloud-storage=2.36.0=h0121fbd_1
+  - libgrpc=1.71.0=h8e591d7_1
   - libiconv=1.18=h4ce23a2_1
   - liblapack=3.9.0=31_h7ac8fdf_openblas
-  - liblzma=5.8.1=hb9d3cd8_0
+  - liblzma=5.8.1=hb9d3cd8_1
   - libmpdec=4.0.0=h4bc722e_0
+  - libnghttp2=1.64.0=h161d5f1_0
   - libopenblas=0.3.29=pthreads_h94d23a6_0
+  - libopentelemetry-cpp=1.20.0=hd1b1c89_0
+  - libopentelemetry-cpp-headers=1.20.0=ha770c72_0
+  - libparquet=20.0.0=h081d1f1_3_cpu
+  - libprotobuf=5.29.3=h501fc15_1
+  - libre2-11=2024.07.02=hba17884_3
   - libsodium=1.0.20=h4ab18f5_0
-  - libsqlite=3.49.1=hee588c1_2
-  - libstdcxx=14.2.0=h8f9b012_2
+  - libsqlite=3.49.2=hee588c1_0
+  - libssh2=1.11.1=hcf80075_0
+  - libstdcxx=15.1.0=h8f9b012_2
+  - libstdcxx-ng=15.1.0=h4852527_2
+  - libthrift=0.21.0=h0e7cc3e_0
+  - libutf8proc=2.10.0=h4c51ac1_0
   - libuuid=2.38.1=h0b41bf4_0
+  - libxml2=2.13.8=h4bc477f_0
   - libzlib=1.3.1=hb9d3cd8_2
+  - lz4-c=1.10.0=h5888daf_1
   - markdown-it-py=3.0.0=pyhd8ed1ab_1
   - markupsafe=3.0.2=py313h8060acc_1
   - mdurl=0.1.2=pyhd8ed1ab_1
-  - more-itertools=10.6.0=pyhd8ed1ab_0
+  - more-itertools=10.7.0=pyhd8ed1ab_0
   - mypy=1.15.0=py313h536fd9c_0
-  - mypy_extensions=1.0.0=pyha770c72_1
+  - mypy_extensions=1.1.0=pyha770c72_0
+  - natsort=8.4.0=pyh29332c3_1
   - ncurses=6.5=h2d0b736_3
   - nh3=0.2.21=py39h77e2912_1
-  - numpy=2.2.4=py313h17eae1a_0
-  - openssl=3.5.0=h7b32b05_0
-  - packaging=24.2=pyhd8ed1ab_2
+  - nlohmann_json=3.12.0=h3f2d84a_0
+  - numpy=2.2.6=py313h17eae1a_0
+  - openssl=3.5.0=h7b32b05_1
+  - orc=2.1.2=h17f744e_0
+  - packaging=25.0=pyh29332c3_1
   - paramiko=3.5.1=pyhd8ed1ab_0
   - pathspec=0.12.1=pyhd8ed1ab_1
-  - pcre2=10.44=hba22ea6_2
-  - pip=25.0.1=pyh145f28c_0
+  - pcre2=10.45=hc749103_0
+  - pip=25.1.1=pyh145f28c_0
   - pkginfo=1.12.1.2=pyhd8ed1ab_0
-  - platformdirs=4.3.7=pyh29332c3_0
-  - pluggy=1.5.0=pyhd8ed1ab_1
+  - platformdirs=4.3.8=pyhe01879c_0
+  - pluggy=1.6.0=pyhd8ed1ab_0
+  - polars-default=1.30.0=py39hfac2b71_0
   - progressbar2=4.5.0=pyhd8ed1ab_1
+  - prometheus-cpp=1.3.0=ha5d0236_0
   - psutil=7.0.0=py313h536fd9c_0
+  - pyarrow-core=20.0.0=py313he5f92c8_0_cpu
   - pycparser=2.22=pyh29332c3_1
   - pygments=2.19.1=pyhd8ed1ab_0
   - pynacl=1.5.0=py313h536fd9c_4
-  - pyproject-api=1.9.0=pyh29332c3_0
+  - pyproject-api=1.9.1=pyhe01879c_0
   - pysocks=1.7.1=pyha55dd90_7
   - python=3.13.3=hf636f53_101_cp313
   - python-gil=3.13.3=h4df99d1_101
   - python-utils=3.9.1=pyhff2d567_1
-  - python_abi=3.13=6_cp313
+  - python_abi=3.13=7_cp313
   - pytz=2025.2=pyhd8ed1ab_0
   - rapidfuzz=3.13.0=py313h46c70d0_0
+  - re2=2024.07.02=h9925aae_3
   - readline=8.2=h8c095d6_2
   - readme_renderer=44.0=pyhd8ed1ab_1
   - requests=2.32.3=pyhd8ed1ab_1
@@ -111,14 +169,16 @@ dependencies:
   - ruamel.yaml=0.18.10=py313h536fd9c_0
   - ruamel.yaml.clib=0.2.8=py313h536fd9c_1
   - ruamel.yaml.jinja2=0.2.7=pyhd8ed1ab_1
-  - ruff=0.11.5=py313h22842b3_0
+  - ruff=0.11.10=py313h67f39b2_1
+  - s2n=1.5.18=h763c568_1
   - secretstorage=3.3.3=py313h78bf25f_3
-  - setuptools=78.1.0=pyhff2d567_0
+  - setuptools=80.8.0=pyhff2d567_0
   - six=1.17.0=pyhd8ed1ab_0
-  - snowballstemmer=2.2.0=pyhd8ed1ab_0
-  - soupsieve=2.5=pyhd8ed1ab_1
+  - snappy=1.2.1=h8bd8927_1
+  - snowballstemmer=3.0.1=pyhd8ed1ab_0
+  - soupsieve=2.7=pyhd8ed1ab_0
   - sphinx=8.2.3=pyhd8ed1ab_0
-  - sphinx-autodoc-typehints=3.1.0=pyhd8ed1ab_0
+  - sphinx-autodoc-typehints=3.2.0=pyhd8ed1ab_0
   - sphinx-click=6.0.0=pyhd8ed1ab_1
   - sphinx-rtd-theme=3.0.1=hd8ed1ab_0
   - sphinx_rtd_theme=3.0.1=pyha770c72_0
@@ -133,21 +193,23 @@ dependencies:
   - tk=8.6.13=noxft_h4845f30_101
   - tomli=2.2.1=pyhd8ed1ab_1
   - tomli-w=1.2.0=pyhd8ed1ab_0
-  - tox=4.25.0=pyh29332c3_1
+  - tox=4.26.0=pyhe01879c_0
   - tqdm=4.67.1=pyhd8ed1ab_1
-  - trove-classifiers=2025.4.11.15=pyhd8ed1ab_0
+  - trove-classifiers=2025.5.9.12=pyhd8ed1ab_0
   - twine=6.1.0=pyh29332c3_0
   - types-appdirs=1.4.3.5=pyhd8ed1ab_1
-  - types-paramiko=3.5.0.20240928=pyhd8ed1ab_1
-  - types-requests=2.32.0.20250306=pyhd8ed1ab_0
-  - types-tqdm=4.67.0.20250319=pyhd8ed1ab_0
+  - types-paramiko=3.5.0.20250516=pyhd8ed1ab_0
+  - types-requests=2.32.0.20250515=pyhd8ed1ab_0
+  - types-tqdm=4.67.0.20250516=pyhd8ed1ab_0
   - typing-extensions=4.13.2=h0e9735f_0
   - typing_extensions=4.13.2=pyh29332c3_0
   - tzdata=2025b=h78e105d_0
   - urllib3=2.4.0=pyhd8ed1ab_0
-  - virtualenv=20.30.0=pyhd8ed1ab_0
+  - virtualenv=20.31.2=pyhd8ed1ab_0
   - zipp=3.21.0=pyhd8ed1ab_1
-  - zstandard=0.23.0=py313h536fd9c_1
+  - zlib=1.3.1=hb9d3cd8_2
+  - zstandard=0.23.0=py313h536fd9c_2
+  - zstd=1.5.7=hb8e6e7a_2
   - pip:
       - ataraxis-automation==4.0.1
       - ataraxis-base-utilities==3.0.1
@@ -156,6 +218,8 @@ dependencies:
       - build==1.2.2.post1
       - dacite==1.9.2
       - loguru==0.7.3
+      - polars==1.29.0
+      - pyarrow==20.0.0
       - pyproject-hooks==1.2.0
       - pyyaml==6.0.2
       - simple-slurm==0.3.5