PyPI - sl-shared-assets - Versions diffs - 1.0.0rc27__tar.gz → 1.0.1__tar.gz - Mend

sl-shared-assets 1.0.0rc27tar.gz → 1.0.1tar.gz

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{sl_shared_assets-1.0.0rc27 → sl_shared_assets-1.0.1}/PKG-INFO RENAMED Viewed

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: sl-shared-assets
-Version: 1.0.0rc27
+Version: 1.0.1
 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/
@@ -768,16 +768,16 @@ ___
 ## Detailed Description
-Primarily, this library is designed to make the two main Sun lab libraries used in data acquisition
+Primarily, this library is designed to make the two main Sun lab libraries used for data acquisition
 ([sl-experiment](https://github.com/Sun-Lab-NBB/sl-experiment)) and processing
 ([sl-forgery](https://github.com/Sun-Lab-NBB/sl-forgery)) independent of each other. This is beneficial, as both
-libraries feature an extensive and potentially incompatible set of runtime dependencies. Moreover, having a shared
+libraries feature an extensive and largely incompatible set of runtime dependencies. Moreover, having a shared
 repository of classes and tools reused across Sun lab pipelines streamlines the maintenance of these tools.
 The library broadly stores two types of assets. First, it stores various dataclasses used to save the data acquired
-during experiments in the lab. Moreover, it also stores the dataclasses used to configure data acquisition and
-processing runtimes. Secondly, it stores the tools used to safely move the data between the computers used in the data
-acquisition and processing and provides the API for accessing the lab’s main computation server.
+during experiments in the lab and the dataclasses used to configure data acquisition and processing runtimes. Secondly,
+it stores the tools used to safely move the data between the machines (computers) used in the data acquisition and
+processing, and provides the API for running various data processing jobs on remote compute servers.
 ---
@@ -819,7 +819,10 @@ 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.
+documentation below to learn how to use library components in other Sun lab libraries. For notes on using shared
+assets for data acquisition, see the [sl-experiment](https://github.com/Sun-Lab-NBB/sl-experiment) library ReadMe.
+For notes on using shared assets for data processing, see the [sl-forgery](https://github.com/Sun-Lab-NBB/sl-forgery)
+library ReadMe.
 ---

{sl_shared_assets-1.0.0rc27 → sl_shared_assets-1.0.1}/README.md RENAMED Viewed

@@ -13,16 +13,16 @@ ___
 ## Detailed Description
-Primarily, this library is designed to make the two main Sun lab libraries used in data acquisition
+Primarily, this library is designed to make the two main Sun lab libraries used for data acquisition
 ([sl-experiment](https://github.com/Sun-Lab-NBB/sl-experiment)) and processing
 ([sl-forgery](https://github.com/Sun-Lab-NBB/sl-forgery)) independent of each other. This is beneficial, as both
-libraries feature an extensive and potentially incompatible set of runtime dependencies. Moreover, having a shared
+libraries feature an extensive and largely incompatible set of runtime dependencies. Moreover, having a shared
 repository of classes and tools reused across Sun lab pipelines streamlines the maintenance of these tools.
 The library broadly stores two types of assets. First, it stores various dataclasses used to save the data acquired
-during experiments in the lab. Moreover, it also stores the dataclasses used to configure data acquisition and
-processing runtimes. Secondly, it stores the tools used to safely move the data between the computers used in the data
-acquisition and processing and provides the API for accessing the lab’s main computation server.
+during experiments in the lab and the dataclasses used to configure data acquisition and processing runtimes. Secondly,
+it stores the tools used to safely move the data between the machines (computers) used in the data acquisition and
+processing, and provides the API for running various data processing jobs on remote compute servers.
 ---
@@ -64,7 +64,10 @@ 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.
+documentation below to learn how to use library components in other Sun lab libraries. For notes on using shared
+assets for data acquisition, see the [sl-experiment](https://github.com/Sun-Lab-NBB/sl-experiment) library ReadMe.
+For notes on using shared assets for data processing, see the [sl-forgery](https://github.com/Sun-Lab-NBB/sl-forgery)
+library ReadMe.
 ---

{sl_shared_assets-1.0.0rc27 → sl_shared_assets-1.0.1}/docs/source/welcome.rst RENAMED Viewed

@@ -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 and processing libraries in the lab to
-avoid circular or hierarchical cross-dependencies.
+of this library is to provide the tools adn assets used by multiple other data acquisition and processing libraries in
+the lab to avoid cross-dependency issues.
 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-1.0.0rc27 → sl_shared_assets-1.0.1}/envs/slsa_dev_lin.yml RENAMED Viewed

@@ -7,19 +7,19 @@ 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-auth=0.9.0=h3318fae_10
+  - aws-c-cal=0.9.1=h5e3027f_0
   - 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-c-event-stream=0.5.4=haaa725d_10
+  - aws-c-http=0.10.1=hd7992d4_3
+  - aws-c-io=0.19.1=h93b6419_1
+  - aws-c-mqtt=0.13.0=h7b3935a_4
+  - aws-c-s3=0.8.0=h365f71b_1
+  - aws-c-sdkutils=0.2.4=hafb2847_0
   - aws-checksums=0.2.7=hafb2847_1
-  - aws-crt-cpp=0.32.5=h2811929_3
-  - aws-sdk-cpp=1.11.510=hffe9a0f_8
+  - aws-crt-cpp=0.32.6=h96107e3_3
+  - aws-sdk-cpp=1.11.510=hf282fd2_9
   - 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
@@ -34,7 +34,7 @@ dependencies:
   - bzip2=1.0.8=h4bc722e_7
   - c-ares=1.34.5=hb9d3cd8_0
   - ca-certificates=2025.4.26=hbd8a1cb_0
-  - cachetools=5.5.2=pyhd8ed1ab_0
+  - cachetools=6.0.0=pyhd8ed1ab_0
   - certifi=2025.4.26=pyhd8ed1ab_0
   - cffi=1.17.1=py313hfab6e84_0
   - chardet=5.2.0=pyhd8ed1ab_3
@@ -44,7 +44,7 @@ dependencies:
   - colorama=0.4.6=pyhd8ed1ab_1
   - conda-souschef=2.2.3=pyhd8ed1ab_0
   - cpython=3.13.3=py313hd8ed1ab_101
-  - cryptography=45.0.2=py313h6556f6e_0
+  - cryptography=45.0.3=py313h6556f6e_0
   - dbus=1.16.2=h3c4dab8_0
   - distlib=0.3.9=pyhd8ed1ab_1
   - docutils=0.21.2=pyhd8ed1ab_1
@@ -61,8 +61,8 @@ dependencies:
   - id=1.5.0=pyh29332c3_0
   - idna=3.10=pyhd8ed1ab_1
   - imagesize=1.4.1=pyhd8ed1ab_0
-  - importlib-metadata=8.7.0=pyhe01879c_0
-  - importlib_metadata=8.7.0=he374078_0
+  - importlib-metadata=8.7.0=pyhe01879c_1
+  - importlib_metadata=8.7.0=h40b2b14_1
   - importlib_resources=6.5.2=pyhd8ed1ab_0
   - jaraco.classes=3.4.0=pyhd8ed1ab_2
   - jaraco.context=6.0.1=pyhd8ed1ab_0
@@ -74,17 +74,17 @@ dependencies:
   - 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
+  - libarrow=20.0.0=h9b1bdb9_4_cpu
+  - libarrow-acero=20.0.0=hcb10f89_4_cpu
+  - libarrow-dataset=20.0.0=hcb10f89_4_cpu
+  - libarrow-substrait=20.0.0=h1bed206_4_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
+  - libcurl=8.14.0=h332b0f4_0
   - libedit=3.1.20250104=pl5321h7949ede_0
   - libev=4.33=hd590300_2
   - libevent=2.1.12=hf998b51_1
@@ -102,21 +102,21 @@ dependencies:
   - libiconv=1.18=h4ce23a2_1
   - liblapack=3.9.0=31_h7ac8fdf_openblas
   - liblzma=5.8.1=hb9d3cd8_1
-  - libmpdec=4.0.0=h4bc722e_0
+  - libmpdec=4.0.0=hb9d3cd8_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
+  - libparquet=20.0.0=h081d1f1_4_cpu
   - libprotobuf=5.29.3=h501fc15_1
   - libre2-11=2024.07.02=hba17884_3
   - libsodium=1.0.20=h4ab18f5_0
-  - libsqlite=3.49.2=hee588c1_0
+  - libsqlite=3.50.0=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
+  - libutf8proc=2.10.0=h202a827_0
   - libuuid=2.38.1=h0b41bf4_0
   - libxml2=2.13.8=h4bc477f_0
   - libzlib=1.3.1=hb9d3cd8_2
@@ -125,7 +125,7 @@ dependencies:
   - markupsafe=3.0.2=py313h8060acc_1
   - mdurl=0.1.2=pyhd8ed1ab_1
   - more-itertools=10.7.0=pyhd8ed1ab_0
-  - mypy=1.15.0=py313h536fd9c_0
+  - mypy=1.16.0=py313h536fd9c_0
   - mypy_extensions=1.1.0=pyha770c72_0
   - natsort=8.4.0=pyh29332c3_1
   - ncurses=6.5=h2d0b736_3
@@ -142,6 +142,7 @@ dependencies:
   - pkginfo=1.12.1.2=pyhd8ed1ab_0
   - platformdirs=4.3.8=pyhe01879c_0
   - pluggy=1.6.0=pyhd8ed1ab_0
+  - polars=1.30.0=default_h1443d73_0
   - polars-default=1.30.0=py39hfac2b71_0
   - progressbar2=4.5.0=pyhd8ed1ab_1
   - prometheus-cpp=1.3.0=ha5d0236_0
@@ -166,11 +167,11 @@ dependencies:
   - rfc3986=2.0.0=pyhd8ed1ab_1
   - rich=14.0.0=pyh29332c3_0
   - roman-numerals-py=3.1.0=pyhd8ed1ab_0
-  - ruamel.yaml=0.18.10=py313h536fd9c_0
+  - ruamel.yaml=0.18.11=py313h536fd9c_0
   - ruamel.yaml.clib=0.2.8=py313h536fd9c_1
   - ruamel.yaml.jinja2=0.2.7=pyhd8ed1ab_1
-  - ruff=0.11.10=py313h67f39b2_1
-  - s2n=1.5.18=h763c568_1
+  - ruff=0.11.12=py313h67f39b2_0
+  - s2n=1.5.19=h763c568_0
   - secretstorage=3.3.3=py313h78bf25f_3
   - setuptools=80.8.0=pyhff2d567_0
   - six=1.17.0=pyhd8ed1ab_0
@@ -190,7 +191,7 @@ dependencies:
   - sphinxcontrib-qthelp=2.0.0=pyhd8ed1ab_1
   - sphinxcontrib-serializinghtml=1.1.10=pyhd8ed1ab_1
   - stdlib-list=0.11.1=pyhd8ed1ab_0
-  - tk=8.6.13=noxft_h4845f30_101
+  - tk=8.6.13=noxft_hd72426e_102
   - tomli=2.2.1=pyhd8ed1ab_1
   - tomli-w=1.2.0=pyhd8ed1ab_0
   - tox=4.26.0=pyhe01879c_0
@@ -206,7 +207,7 @@ dependencies:
   - tzdata=2025b=h78e105d_0
   - urllib3=2.4.0=pyhd8ed1ab_0
   - virtualenv=20.31.2=pyhd8ed1ab_0
-  - zipp=3.21.0=pyhd8ed1ab_1
+  - zipp=3.22.0=pyhd8ed1ab_0
   - zlib=1.3.1=hb9d3cd8_2
   - zstandard=0.23.0=py313h536fd9c_2
   - zstd=1.5.7=hb8e6e7a_2
@@ -218,12 +219,11 @@ 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
-      - sl-shared-assets==1.0.0
+      - sl-shared-assets==1.0.0rc28
       - sphinx-rtd-dark-mode==1.3.0
       - tox-uv==1.25.0
       - uv==0.6.14

{sl_shared_assets-1.0.0rc27 → sl_shared_assets-1.0.1}/envs/slsa_dev_lin_spec.txt RENAMED Viewed

@@ -1381,3 +1381,431 @@
     +zstandard-0.23.0 (conda-forge/linux-64)
     +zstd-1.5.7 (conda-forge/linux-64)
+2025-05-30 12:58:07  (rev 14)
+    -_libgcc_mutex-0.1 (conda-forge/linux-64)
+    -_openmp_mutex-4.5 (conda-forge/linux-64)
+    -_python_abi3_support-1.0 (conda-forge/noarch)
+    -alabaster-1.0.0 (conda-forge/noarch)
+    -appdirs-1.4.4 (conda-forge/noarch)
+    -aws-c-auth-0.9.0 (conda-forge/linux-64)
+    -aws-c-cal-0.9.0 (conda-forge/linux-64)
+    -aws-c-common-0.12.3 (conda-forge/linux-64)
+    -aws-c-compression-0.3.1 (conda-forge/linux-64)
+    -aws-c-event-stream-0.5.4 (conda-forge/linux-64)
+    -aws-c-http-0.10.1 (conda-forge/linux-64)
+    -aws-c-io-0.19.0 (conda-forge/linux-64)
+    -aws-c-mqtt-0.13.0 (conda-forge/linux-64)
+    -aws-c-s3-0.7.17 (conda-forge/linux-64)
+    -aws-c-sdkutils-0.2.3 (conda-forge/linux-64)
+    -aws-checksums-0.2.7 (conda-forge/linux-64)
+    -aws-crt-cpp-0.32.5 (conda-forge/linux-64)
+    -aws-sdk-cpp-1.11.510 (conda-forge/linux-64)
+    -azure-core-cpp-1.14.0 (conda-forge/linux-64)
+    -azure-identity-cpp-1.10.0 (conda-forge/linux-64)
+    -azure-storage-blobs-cpp-12.13.0 (conda-forge/linux-64)
+    -azure-storage-common-cpp-12.8.0 (conda-forge/linux-64)
+    -azure-storage-files-datalake-cpp-12.12.0 (conda-forge/linux-64)
+    -babel-2.17.0 (conda-forge/noarch)
+    -backports-1.0 (conda-forge/noarch)
+    -backports.tarfile-1.2.0 (conda-forge/noarch)
+    -bcrypt-4.3.0 (conda-forge/linux-64)
+    -beautifulsoup4-4.13.4 (conda-forge/noarch)
+    -brotli-python-1.1.0 (conda-forge/linux-64)
+    -bzip2-1.0.8 (conda-forge/linux-64)
+    -c-ares-1.34.5 (conda-forge/linux-64)
+    -ca-certificates-2025.4.26 (conda-forge/noarch)
+    -cachetools-5.5.2 (conda-forge/noarch)
+    -certifi-2025.4.26 (conda-forge/noarch)
+    -cffi-1.17.1 (conda-forge/linux-64)
+    -chardet-5.2.0 (conda-forge/noarch)
+    -charset-normalizer-3.4.2 (conda-forge/noarch)
+    -click-8.2.1 (conda-forge/noarch)
+    -cmarkgfm-2024.11.20 (conda-forge/linux-64)
+    -colorama-0.4.6 (conda-forge/noarch)
+    -conda-souschef-2.2.3 (conda-forge/noarch)
+    -cpython-3.13.3 (conda-forge/noarch)
+    -cryptography-45.0.2 (conda-forge/linux-64)
+    -dbus-1.16.2 (conda-forge/linux-64)
+    -distlib-0.3.9 (conda-forge/noarch)
+    -docutils-0.21.2 (conda-forge/noarch)
+    -editables-0.5 (conda-forge/noarch)
+    -filelock-3.18.0 (conda-forge/noarch)
+    -gflags-2.2.2 (conda-forge/linux-64)
+    -glog-0.7.1 (conda-forge/linux-64)
+    -grayskull-2.9.1 (conda-forge/noarch)
+    -h2-4.2.0 (conda-forge/noarch)
+    -hatchling-1.27.0 (conda-forge/noarch)
+    -hpack-4.1.0 (conda-forge/noarch)
+    -hyperframe-6.1.0 (conda-forge/noarch)
+    -icu-75.1 (conda-forge/linux-64)
+    -id-1.5.0 (conda-forge/noarch)
+    -idna-3.10 (conda-forge/noarch)
+    -imagesize-1.4.1 (conda-forge/noarch)
+    -importlib-metadata-8.7.0 (conda-forge/noarch)
+    -importlib_metadata-8.7.0 (conda-forge/noarch)
+    -importlib_resources-6.5.2 (conda-forge/noarch)
+    -jaraco.classes-3.4.0 (conda-forge/noarch)
+    -jaraco.context-6.0.1 (conda-forge/noarch)
+    -jaraco.functools-4.1.0 (conda-forge/noarch)
+    -jeepney-0.9.0 (conda-forge/noarch)
+    -jinja2-3.1.6 (conda-forge/noarch)
+    -keyring-25.6.0 (conda-forge/noarch)
+    -keyutils-1.6.1 (conda-forge/linux-64)
+    -krb5-1.21.3 (conda-forge/linux-64)
+    -ld_impl_linux-64-2.43 (conda-forge/linux-64)
+    -libabseil-20250127.1 (conda-forge/linux-64)
+    -libarrow-20.0.0 (conda-forge/linux-64)
+    -libarrow-acero-20.0.0 (conda-forge/linux-64)
+    -libarrow-dataset-20.0.0 (conda-forge/linux-64)
+    -libarrow-substrait-20.0.0 (conda-forge/linux-64)
+    -libblas-3.9.0 (conda-forge/linux-64)
+    -libbrotlicommon-1.1.0 (conda-forge/linux-64)
+    -libbrotlidec-1.1.0 (conda-forge/linux-64)
+    -libbrotlienc-1.1.0 (conda-forge/linux-64)
+    -libcblas-3.9.0 (conda-forge/linux-64)
+    -libcrc32c-1.1.2 (conda-forge/linux-64)
+    -libcurl-8.13.0 (conda-forge/linux-64)
+    -libedit-3.1.20250104 (conda-forge/linux-64)
+    -libev-4.33 (conda-forge/linux-64)
+    -libevent-2.1.12 (conda-forge/linux-64)
+    -libexpat-2.7.0 (conda-forge/linux-64)
+    -libffi-3.4.6 (conda-forge/linux-64)
+    -libgcc-15.1.0 (conda-forge/linux-64)
+    -libgcc-ng-15.1.0 (conda-forge/linux-64)
+    -libgfortran-15.1.0 (conda-forge/linux-64)
+    -libgfortran5-15.1.0 (conda-forge/linux-64)
+    -libglib-2.84.2 (conda-forge/linux-64)
+    -libgomp-15.1.0 (conda-forge/linux-64)
+    -libgoogle-cloud-2.36.0 (conda-forge/linux-64)
+    -libgoogle-cloud-storage-2.36.0 (conda-forge/linux-64)
+    -libgrpc-1.71.0 (conda-forge/linux-64)
+    -libiconv-1.18 (conda-forge/linux-64)
+    -liblapack-3.9.0 (conda-forge/linux-64)
+    -liblzma-5.8.1 (conda-forge/linux-64)
+    -libmpdec-4.0.0 (conda-forge/linux-64)
+    -libnghttp2-1.64.0 (conda-forge/linux-64)
+    -libopenblas-0.3.29 (conda-forge/linux-64)
+    -libopentelemetry-cpp-1.20.0 (conda-forge/linux-64)
+    -libopentelemetry-cpp-headers-1.20.0 (conda-forge/linux-64)
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+    +tomli-w-1.2.0 (conda-forge/noarch)
+    +tqdm-4.67.1 (conda-forge/noarch)
+    +trove-classifiers-2025.5.9.12 (conda-forge/noarch)
+    +twine-6.1.0 (conda-forge/noarch)
+    +types-appdirs-1.4.3.5 (conda-forge/noarch)
+    +types-paramiko-3.5.0.20250516 (conda-forge/noarch)
+    +types-requests-2.32.0.20250515 (conda-forge/noarch)
+    +types-tqdm-4.67.0.20250516 (conda-forge/noarch)
+    +typing-extensions-4.13.2 (conda-forge/noarch)
+    +urllib3-2.4.0 (conda-forge/noarch)
+    +zipp-3.22.0 (conda-forge/noarch)
+    +zlib-1.3.1 (conda-forge/linux-64)
+    +zstandard-0.23.0 (conda-forge/linux-64)
+    +zstd-1.5.7 (conda-forge/linux-64)

{sl_shared_assets-1.0.0rc27 → sl_shared_assets-1.0.1}/pyproject.toml RENAMED Viewed

@@ -8,7 +8,7 @@ build-backend = "hatchling.build"
 # Project metdata section. Provides the genral ID information about the project.
 [project]
 name = "sl-shared-assets"
-version = "1.0.0rc27"
+version = "1.0.1"
 description = "Stores assets shared between multiple Sun (NeuroAI) lab data pipelines."
 readme = "README.md"
 license = { file = "LICENSE" }

{sl_shared_assets-1.0.0rc27 → sl_shared_assets-1.0.1}/src/sl_shared_assets/cli.py RENAMED Viewed

@@ -8,6 +8,7 @@ from ataraxis_base_utilities import LogLevel, console, ensure_directory_exists
 from .tools import ascend_tyche_data, verify_session_checksum, generate_project_manifest
 from .server import generate_server_credentials
 from .data_classes import (
+    SessionData,
     ExperimentState,
     ProjectConfiguration,
     MesoscopeSystemConfiguration,
@@ -57,18 +58,25 @@ def verify_session_integrity(session_path: str, create_processed_directories: bo
     that stores the data checksum generated before transferring the data to long-term storage destination. This function
     always verified the integrity of the 'raw_data' directory. It does not work with 'processed_data' or any other
     directories. If the session data was corrupted, the command removes the 'telomere.bin' file, marking the session as
-    'incomplete' and automatically excluding it from all further automated processing runtimes.
+    'incomplete' and automatically excluding it from all further automated processing runtimes. if the session data
+    is intact, generates a 'verified.bin' marker file inside the session's raw_data folder.
     The command is also used by Sun lab data acquisition systems to generate the processed data hierarchy for each
     processed session. This use case is fully automated and should not be triggered manually by the user.
     """
     session = Path(session_path)
-    if verify_session_checksum(
+    # Runs the verification process
+    verify_session_checksum(
         session, create_processed_data_directory=create_processed_directories, processed_data_root=processed_data_root
-    ):
-        console.echo(message=f"Session {session.stem} raw data integrity: verified.", level=LogLevel.SUCCESS)
+    )
+    # Checks the outcome of the verification process
+    session_data = SessionData.load(session_path=session)
+    if session_data.raw_data.verified_bin_path.exists():
+        console.echo(message=f"Session {session.stem} raw data integrity: Verified.", level=LogLevel.SUCCESS)
     else:
-        console.echo(message=f"Session {session.stem} raw data integrity: compromised!", level=LogLevel.ERROR)
+        console.echo(message=f"Session {session.stem} raw data integrity: Compromised!", level=LogLevel.ERROR)
 @click.command()

{sl_shared_assets-1.0.0rc27 → sl_shared_assets-1.0.1}/src/sl_shared_assets/cli.pyi RENAMED Viewed

@@ -7,6 +7,7 @@ from .tools import (
 )
 from .server import generate_server_credentials as generate_server_credentials
 from .data_classes import (
+    SessionData as SessionData,
     ExperimentState as ExperimentState,
     ProjectConfiguration as ProjectConfiguration,
     MesoscopeSystemConfiguration as MesoscopeSystemConfiguration,
@@ -22,7 +23,8 @@ def verify_session_integrity(session_path: str, create_processed_directories: bo
     that stores the data checksum generated before transferring the data to long-term storage destination. This function
     always verified the integrity of the 'raw_data' directory. It does not work with 'processed_data' or any other
     directories. If the session data was corrupted, the command removes the 'telomere.bin' file, marking the session as
-    'incomplete' and automatically excluding it from all further automated processing runtimes.
+    'incomplete' and automatically excluding it from all further automated processing runtimes. if the session data
+    is intact, generates a 'verified.bin' marker file inside the session's raw_data folder.
     The command is also used by Sun lab data acquisition systems to generate the processed data hierarchy for each
     processed session. This use case is fully automated and should not be triggered manually by the user.

{sl_shared_assets-1.0.0rc27 → sl_shared_assets-1.0.1}/src/sl_shared_assets/data_classes/configuration_data.py RENAMED Viewed

@@ -207,7 +207,7 @@ class MesoscopeMicroControllers:
     PC, conserving communication bandwidth."""
     torque_averaging_pool_size: int = 10
     """The number of torque sensor readouts to average together to produce the final torque sensor readout value."""
-    wheel_encoder_ppr = 8192
+    wheel_encoder_ppr: int = 8192
     """The resolution of the managed quadrature encoder, in Pulses Per Revolution (PPR). This is the number of
     quadrature pulses the encoder emits per full 360-degree rotation."""
     wheel_encoder_report_cw: bool = False
@@ -219,9 +219,9 @@ class MesoscopeMicroControllers:
     wheel_encoder_delta_threshold_pulse: int = 15
     """The minimum difference, in encoder pulse counts, between two encoder readouts for the change to be reported to
     the PC. This is used to prevent reporting idle readouts and filter out sub-threshold noise."""
-    wheel_encoder_polling_delay_us = 500
+    wheel_encoder_polling_delay_us: int = 500
     """The delay, in microseconds, between any two successive encoder state readouts."""
-    cm_per_unity_unit = 10.0
+    cm_per_unity_unit: float = 10.0
     """The length of each Unity 'unit' in real-world centimeters recorded by the running wheel encoder."""
     screen_trigger_pulse_duration_ms: int = 500
     """The duration of the HIGH phase of the TTL pulse used to toggle the VR screens between ON and OFF states."""

{sl_shared_assets-1.0.0rc27 → sl_shared_assets-1.0.1}/src/sl_shared_assets/data_classes/configuration_data.pyi RENAMED Viewed

@@ -97,12 +97,12 @@ class MesoscopeMicroControllers:
     torque_signal_threshold_adc: int = ...
     torque_delta_threshold_adc: int = ...
     torque_averaging_pool_size: int = ...
-    wheel_encoder_ppr = ...
+    wheel_encoder_ppr: int = ...
     wheel_encoder_report_cw: bool = ...
     wheel_encoder_report_ccw: bool = ...
     wheel_encoder_delta_threshold_pulse: int = ...
-    wheel_encoder_polling_delay_us = ...
-    cm_per_unity_unit = ...
+    wheel_encoder_polling_delay_us: int = ...
+    cm_per_unity_unit: float = ...
     screen_trigger_pulse_duration_ms: int = ...
     auditory_tone_duration_ms: int = ...
     valve_calibration_pulse_count: int = ...

{sl_shared_assets-1.0.0rc27 → sl_shared_assets-1.0.1}/src/sl_shared_assets/data_classes/session_data.py RENAMED Viewed

@@ -217,6 +217,11 @@ class RawData:
     the long-term storage destinations (NAS and Server) and the integrity of the moved data is verified on at least one
     destination. During 'purge' sl-experiment runtimes, the library discovers and removes all session data marked with
     'ubiquitin.bin' files from the machine that runs the code."""
+    verified_bin_path: Path = Path()
+    """Stores the path to the verified.bin file. This marker file is created (or removed) by the sl-shared-assets
+    'verify-session' CLI command to indicate whether the session data inside the folder marked by the file has been
+    verified for integrity. Primarily, this is used when the data is moved to the long-term storage destination (BioHPC
+    server) to ensure it is safe to remove any local copies of the data stored on the acquisition system machine(s)."""
     def resolve_paths(self, root_directory_path: Path) -> None:
         """Resolves all paths managed by the class instance based on the input root directory path.
@@ -248,6 +253,7 @@ class RawData:
         self.system_configuration_path = self.raw_data_path.joinpath("system_configuration.yaml")
         self.telomere_path = self.raw_data_path.joinpath("telomere.bin")
         self.ubiquitin_path = self.raw_data_path.joinpath("ubiquitin.bin")
+        self.verified_bin_path = self.raw_data_path.joinpath("verified.bin")
     def make_directories(self) -> None:
         """Ensures that all major subdirectories and the root directory exist, creating any missing directories."""

{sl_shared_assets-1.0.0rc27 → sl_shared_assets-1.0.1}/src/sl_shared_assets/data_classes/session_data.pyi RENAMED Viewed

@@ -96,6 +96,7 @@ class RawData:
     checksum_path: Path = ...
     telomere_path: Path = ...
     ubiquitin_path: Path = ...
+    verified_bin_path: Path = ...
     def resolve_paths(self, root_directory_path: Path) -> None:
         """Resolves all paths managed by the class instance based on the input root directory path.

{sl_shared_assets-1.0.0rc27 → sl_shared_assets-1.0.1}/src/sl_shared_assets/server/server.py RENAMED Viewed

@@ -75,7 +75,7 @@ class Server:
     """
     def __init__(self, credentials_path: Path) -> None:
-        # Tracker used to prevent __del__ from classing stop() for a partially initialized class.
+        # Tracker used to prevent __del__ from calling stop() for a partially initialized class.
         self._open: bool = False
         # Loads the credentials from the provided .yaml file
@@ -95,6 +95,7 @@ class Server:
                     self._credentials.host, username=self._credentials.username, password=self._credentials.password
                 )
                 console.echo(f"Connected to {self._credentials.host}", level=LogLevel.SUCCESS)
+                self._open = True
                 break
             except paramiko.AuthenticationException:
                 message = (
@@ -131,7 +132,7 @@ class Server:
             job: The Job object that contains all job data.
         Returns:
-            The job object whose 'job_id' attribute had been modified with the job ID, if the job was successfully
+            The job object whose 'job_id' attribute had been modified with the job ID if the job was successfully
             submitted.
         Raises:

{sl_shared_assets-1.0.0rc27 → sl_shared_assets-1.0.1}/src/sl_shared_assets/server/server.pyi RENAMED Viewed

@@ -69,7 +69,7 @@ class Server:
             job: The Job object that contains all job data.
         Returns:
-            The job object whose 'job_id' attribute had been modified with the job ID, if the job was successfully
+            The job object whose 'job_id' attribute had been modified with the job ID if the job was successfully
             submitted.
         Raises:

{sl_shared_assets-1.0.0rc27 → sl_shared_assets-1.0.1}/src/sl_shared_assets/tools/packaging_tools.py RENAMED Viewed

@@ -21,6 +21,7 @@ _excluded_files = {
     "multi_day_suite2p.bin",
     "behavior.bin",
     "dlc.bin",
+    "verified.bin",
 }

{sl_shared_assets-1.0.0rc27 → sl_shared_assets-1.0.1}/src/sl_shared_assets/tools/project_management_tools.py RENAMED Viewed

@@ -61,6 +61,7 @@ def generate_project_manifest(
         "raw_data": [],  # Server-side raw_data folder path.
         "processed_data": [],  # Server-side processed_data folder path.
         "complete": [],  # Determines if the session data is complete. Incomplete sessions are excluded from processing.
+        "verified": [],  # Determines if the session data integrity has been verified upon transfer to storage machine.
         "single_day_suite2p": [],  # Determines whether the session has been processed with the single-day s2p pipeline.
         "multi_day_suite2p": [],  # Determines whether the session has been processed with the multi-day s2p pipeline.
         "behavior": [],  # Determines whether the session has been processed with the behavior extraction pipeline.
@@ -87,9 +88,13 @@ def generate_project_manifest(
         # If the session raw_data folder contains the telomere.bin file, marks the session as complete.
         manifest["complete"].append(session_data.raw_data.telomere_path.exists())
-        # If the session is incomplete, marks all processing steps as FALSE, as automatic processing is disabled for
-        # incomplete sessions.
-        if not manifest["complete"][-1]:
+        # If the session raw_data folder contains the verified.bin file, marks the session as verified.
+        manifest["verified"].append(session_data.raw_data.verified_bin_path.exists())
+        # If the session is incomplete or unverified, marks all processing steps as FALSE, as automatic processing is
+        # disabled for incomplete sessions. If the session unverified, the case is even more severe, as its data may be
+        # corrupted.
+        if not manifest["complete"][-1] or not not manifest["verified"][-1]:
             manifest["single_day_suite2p"].append(False)
             manifest["multi_day_suite2p"].append(False)
             manifest["behavior"].append(False)
@@ -120,6 +125,7 @@ def generate_project_manifest(
         "processed_data": pl.String,
         "type": pl.String,
         "complete": pl.Boolean,
+        "verified": pl.Boolean,
         "single_day_suite2p": pl.Boolean,
         "multi_day_suite2p": pl.Boolean,
         "behavior": pl.Boolean,
@@ -139,13 +145,13 @@ def generate_project_manifest(
 def verify_session_checksum(
     session_path: Path, create_processed_data_directory: bool = True, processed_data_root: None | Path = None
-) -> bool:
+) -> None:
     """Verifies the integrity of the session's raw data by generating the checksum of the raw_data directory and
     comparing it against the checksum stored in the ax_checksum.txt file.
     Primarily, this function is used to verify data integrity after transferring it from a local PC to the remote
-    server for long-term storage. This function is designed to do nothing if the checksum matches and to remove the
-    'telomere.bin' marker file if it does not.
+    server for long-term storage. This function is designed to create the 'verified.bin' marker file if the checksum
+    matches and to remove the 'telomere.bin' and 'verified.bin' marker files if it does not.
     Notes:
         Removing the telomere.bin marker file from session's raw_data folder marks the session as incomplete, excluding
@@ -161,9 +167,6 @@ def verify_session_checksum(
         processed_data_root: The root directory where to store the processed data hierarchy. This path has to point to
             the root directory where to store the processed data from all projects, and it will be automatically
             modified to include the project name, the animal name, and the session ID.
-    Returns:
-        True if the checksum matches, False otherwise.
     """
     # Loads session data layout. If configured to do so, also creates the processed data hierarchy
@@ -173,6 +176,11 @@ def verify_session_checksum(
         make_processed_data_directory=create_processed_data_directory,
     )
+    # Unlinks the verified.bin marker if it exists. The presence or absence of the marker is used as the
+    # primary heuristic for determining if the session data passed verification. Unlinking it early helps in the case
+    # the verification procedure aborts unexpectedly for any reason.
+    session_data.raw_data.verified_bin_path.unlink(missing_ok=True)
     # Re-calculates the checksum for the raw_data directory
     calculated_checksum = calculate_directory_checksum(
         directory=session_data.raw_data.raw_data_path, batch=False, save_checksum=False
@@ -185,10 +193,9 @@ def verify_session_checksum(
     # If the two checksums do not match, this likely indicates data corruption.
     if stored_checksum != calculated_checksum:
         # If the telomere.bin file exists, removes this file. This automatically marks the session as incomplete for
-        # all other Sun lab runtimes. The presence of the telomere.bin file after integrity verification is used as a
-        # heuristic for determining whether the session has passed the verification process.
-        if session_data.raw_data.telomere_path.exists():
-            session_data.raw_data.telomere_path.unlink()
-        return False
+        # all other Sun lab runtimes.
+        session_data.raw_data.telomere_path.unlink(missing_ok=True)
-    return True
+    # Otherwise, ensures that the session is marked with the verified.bin marker file.
+    else:
+        session_data.raw_data.verified_bin_path.touch(exist_ok=True)

{sl_shared_assets-1.0.0rc27 → sl_shared_assets-1.0.1}/src/sl_shared_assets/tools/project_management_tools.pyi RENAMED Viewed

@@ -29,13 +29,13 @@ def generate_project_manifest(
 def verify_session_checksum(
     session_path: Path, create_processed_data_directory: bool = True, processed_data_root: None | Path = None
-) -> bool:
+) -> None:
     """Verifies the integrity of the session's raw data by generating the checksum of the raw_data directory and
     comparing it against the checksum stored in the ax_checksum.txt file.
     Primarily, this function is used to verify data integrity after transferring it from a local PC to the remote
-    server for long-term storage. This function is designed to do nothing if the checksum matches and to remove the
-    'telomere.bin' marker file if it does not.
+    server for long-term storage. This function is designed to create the 'verified.bin' marker file if the checksum
+    matches and to remove the 'telomere.bin' and 'verified.bin' marker files if it does not.
     Notes:
         Removing the telomere.bin marker file from session's raw_data folder marks the session as incomplete, excluding
@@ -51,7 +51,4 @@ def verify_session_checksum(
         processed_data_root: The root directory where to store the processed data hierarchy. This path has to point to
             the root directory where to store the processed data from all projects, and it will be automatically
             modified to include the project name, the animal name, and the session ID.
-    Returns:
-        True if the checksum matches, False otherwise.
     """