.gitignore

@@ -99,5 +99,4 @@ cython_debug/
 *.sigmf-meta
 *.blue
 *.wav
-/images/
+images/
-!docs/source/images/**

CHANGELOG.md

@@ -1,24 +1,5 @@
 # Changelog
 
-## [0.1.7] - 2026-05-26
-
-### Added
-
-- **Human-readable agent names** — `ria-agent register` now generates a default `adjective-colour-animal` name (e.g. `swift-teal-falcon`) via the new `namegen` module when `--name` is omitted, instead of registering with an empty string.
-- **Structured registration error messages** — `ria-agent register` translates hub responses into actionable English for the known failure reasons (`invalid_key`, `expired`, `revoked`, `already_consumed`) and rate-limit (`HTTP 429`) responses, instead of surfacing raw `HTTP 4xx` text.
-
-### Changed
-
-- **`ria-agent register` `--api-key` help** — now describes the personal `ria_reg_*` registration key flow (minted from **Settings → RIA Agents** on the hub, shown once at mint time). The legacy shared `[wac] API_KEY` is still accepted by the hub for back-compat, but the CLI documents the per-user flow as preferred.
-- **`ria-agent register` success output** — now prints both the hub-assigned agent ID and the chosen name: `Registered agent: <id> (<name>)`.
-
-### Fixed
-
-- **`ria-agent register` blocked by Cloudflare on hubs behind it** — set an explicit `User-Agent` (`ria-agent/<package-version> (+https://riahub.ai/qoherent/ria-toolkit-oss)`) so the request isn't rejected as `Python-urllib/<ver>` (Cloudflare Browser Integrity Check returns HTTP 403, edge error code 1010). Version is read from package metadata so it tracks releases automatically.
-- **`ria-agent register` could hang indefinitely** — added a 15-second timeout to the hub request; previously `urllib`'s default of no timeout meant a stuck hub would block the CLI forever.
-
----
-
 ## [0.1.0] - 2026-02-20
 
 ### Added

README.md

@@ -185,7 +185,7 @@ RIA Toolkit OSS is developed and maintained by [Qoherent](https://qoherent.ai/),
 If you are doing research with RIA Toolkit OSS, please cite the project:
 
 ```
-[1] Qoherent Inc., "Radio Intelligence Apps Toolkit OSS," 2026. [Online]. Available: https://riahub.ai/qoherent/ria-toolkit-oss
+[1] Qoherent Inc., "Radio Intelligence Apps Toolkit OSS," 2025. [Online]. Available: https://riahub.ai/qoherent/ria-toolkit-oss
 ```
 
 If you like what we're doing, don't forget to give the project a star! ⭐

docs/_build/html/_sources/intro/getting_started.rst.txt

@@ -6,10 +6,10 @@ This is a practical reference for the ``ria`` CLI from ``ria-toolkit-oss``.
 
 **Scope of this guide:**
 
-* **Installation and SDR driver prerequisites** — how to install RIA Toolkit OSS and configure the system drivers your hardware requires
+* Installation and setup
-* **End-to-end CLI workflow** — a step-by-step walkthrough from hardware discovery through capture, annotation, and processing
+* End-to-end CLI workflows
-* **Full command reference** — options, flags, and examples for every ``ria`` command
+* Full command reference for CLI features
-* **Python scripting preview** — using the toolkit API directly without the CLI
+* Brief scripting section
 
 **Official resources:**
 
@@ -18,15 +18,76 @@ This is a practical reference for the ``ria`` CLI from ``ria-toolkit-oss``.
 * `PyPI package <https://pypi.org/project/ria-toolkit-oss/>`_
 * `RIA Hub Conda package <https://riahub.ai/qoherent/-/packages/conda/ria-toolkit-oss>`_
 
+.. contents:: Contents
+   :local:
+   :depth: 2
+   :backlinks: none
+
 
 1) Installation and Setup
 ==========================
 
-Before using the ``ria`` CLI, follow the :doc:`Installation <installation>` guide to
+1.1 Installation with Conda
-install RIA Toolkit OSS and any SDR drivers required for your hardware.
+----------------------------
+
+RIA Toolkit OSS is available as a Conda package on RIA Hub. This is typically the easiest
+path when using SDR tooling that depends on native/system libraries.
+
+.. code-block:: bash
+
+   conda update --force conda
+   conda config --add channels https://riahub.ai/api/packages/qoherent/conda
+   conda activate base
+   conda install ria-toolkit-oss
+
+Verify:
+
+.. code-block:: bash
+
+   conda list | grep ria-toolkit-oss
 
 
-1.1 SDR driver prerequisites
+1.2 Installation with pip
+--------------------------
+
+Use pip unless you specifically need to edit toolkit source.
+
+.. code-block:: bash
+
+   python3 -m venv .venv
+   source .venv/bin/activate
+   pip install --upgrade pip
+   pip install ria-toolkit-oss
+
+Verify CLI entrypoint:
+
+.. code-block:: bash
+
+   ria --help
+
+``pyproject.toml`` defines two script entry points:
+
+* ``ria``
+* ``ria-tools``
+
+Both point to the same CLI module (``ria_toolkit_oss_cli.cli:cli``).
+
+
+1.3 Optional install from source
+----------------------------------
+
+Use this for local development or testing unreleased changes.
+
+.. code-block:: bash
+
+   git clone https://riahub.ai/qoherent/ria-toolkit-oss.git
+   cd ria-toolkit-oss
+   python3 -m venv .venv
+   source .venv/bin/activate
+   pip install -e .
+
+
+1.4 SDR driver prerequisites
 -----------------------------
 
 Toolkit package install does not install all system SDR drivers. Install vendor/runtime
@@ -34,22 +95,11 @@ dependencies for the hardware you use.
 
 Examples (depends on device and OS):
 
-.. list-table::
+* USRP: UHD drivers
-   :widths: 25 75
+* Pluto: libiio / IIO utilities
-   :header-rows: 1
+* BladeRF: libbladeRF
-
+* HackRF: libhackrf
-   * - Device
+* RTL-SDR: librtlsdr
-     - Driver Package
-   * - USRP
-     - UHD drivers
-   * - Pluto
-     - libiio / IIO utilities
-   * - BladeRF
-     - libbladeRF
-   * - HackRF
-     - libhackrf
-   * - RTL-SDR
-     - librtlsdr
 
 See repo docs under ``docs/source/sdr_guides/*`` and your OS package instructions.
 
@@ -69,34 +119,18 @@ Top-level CLI follows this model:
 
 **Top-level commands:**
 
-.. list-table::
+* ``discover``
-   :widths: 25 75
+* ``init``
-   :header-rows: 1
+* ``capture``
-
+* ``view``
-   * - Command
+* ``annotate`` (group)
-     - Purpose
+* ``convert``
-   * - :ref:`discover <cmd-discover>`
+* ``split``
-     - Probe SDR drivers and enumerate attached hardware
+* ``combine``
-   * - :ref:`init <cmd-init>`
+* ``generate`` (group)
-     - Create and manage user metadata defaults
+* ``transform`` (group)
-   * - :ref:`capture <cmd-capture>`
+* ``transmit``
-     - Record IQ samples from a connected SDR
+* ``synth`` (alias of ``generate`` in command bindings)
-   * - :ref:`view <cmd-view>`
-     - Generate visualizations from IQ files
-   * - :ref:`annotate <cmd-annotate>`
-     - Label signal regions manually or with auto-detection (group)
-   * - :ref:`convert <cmd-convert>`
-     - Convert between IQ file formats
-   * - :ref:`split <cmd-split>`
-     - Split, trim, or extract recordings
-   * - :ref:`combine <cmd-combine>`
-     - Merge multiple recordings by concatenation or addition
-   * - :ref:`generate / synth <cmd-generate>`
-     - Generate synthetic IQ signals (group; ``synth`` is an alias)
-   * - :ref:`transform <cmd-transform>`
-     - Apply augmentations or impairments to recordings (group)
-   * - :ref:`transmit <cmd-transmit>`
-     - Transmit IQ through a TX-capable SDR
 
 
 3) Quick End-to-End Workflow
@@ -124,8 +158,10 @@ provenance fields.
 .. code-block:: bash
 
    ria init
-   ria init --author "Jane Doe" --project "rf-campaign-1" --location "Lab-A"  # non-interactive
+   # or non-interactive
-   ria init --show  # show config
+   ria init --author "Jane Doe" --project "rf-campaign-1" --location "Lab-A"
+   # show config
+   ria init --show
 
 
 3.3 Capture IQ
@@ -191,14 +227,13 @@ Replay recorded or synthesized IQ through a transmit-capable SDR.
 .. code-block:: bash
 
    ria transmit -d hackrf -f 2.44G -s 2e6 --input capture.sigmf-data
-   ria transmit -d hackrf --generate lfm --continuous  # generated waveform
+   # or generated waveform
+   ria transmit -d hackrf --generate lfm --continuous
 
 
 4) Command Reference
 =====================
 
-.. _cmd-discover:
-
 4.1 ``discover``
 -----------------
 
@@ -228,8 +263,6 @@ Replay recorded or synthesized IQ through a transmit-capable SDR.
   hidden in default output.
 
 
-.. _cmd-init:
-
 4.2 ``init``
 -------------
 
@@ -276,8 +309,6 @@ Replay recorded or synthesized IQ through a transmit-capable SDR.
    generate metadata, and YAML config loading paths).
 
 
-.. _cmd-capture:
-
 4.3 ``capture``
 ----------------
 
@@ -351,8 +382,6 @@ Device selection (``--device``) is optional if only one device is detected. Exac
    ria capture -c capture_config.yaml
 
 
-.. _cmd-view:
-
 4.4 ``view``
 -------------
 
@@ -413,21 +442,7 @@ Device selection (``--device``) is optional if only one device is detected. Exac
    ria view capture.npy --type full --title "Test Capture" --format pdf
    ria view capture.npy --show --no-save
    ria view old.npy --legacy --type simple
-   ria view recordings\qam64_35.npy --type simple
-   ria view recordings\qam64_35.npy --type full
 
-.. figure:: ../images/recordings/qam64_35.png
-   :alt: Example output of ria view recordings\qam64_35.npy --type simple
-
-   Output of ``ria view recordings\qam64_35.npy --type simple``
-
-.. figure:: ../images/recordings/qam64_35-full.png
-   :alt: Example output of ria view recordings\qam64_35.npy --type full
-
-   Output of ``ria view recordings\qam64_35.npy --type full``
-
-
-.. _cmd-annotate:
 
 4.5 ``annotate`` group
 -----------------------
@@ -444,30 +459,8 @@ Device selection (``--device``) is optional if only one device is detected. Exac
 
    ria annotate <subcommand> ...
 
-**Subcommands:**
+**Subcommands:** ``list``, ``add``, ``remove``, ``clear``, ``energy``, ``cusum``,
-
+``threshold``, ``separate``
-.. list-table::
-   :widths: 25 75
-   :header-rows: 1
-
-   * - Subcommand
-     - Purpose
-   * - ``list``
-     - Inspect all annotations on a recording
-   * - ``add``
-     - Add one annotation with explicit sample-domain bounds
-   * - ``remove``
-     - Remove one annotation by index
-   * - ``clear``
-     - Remove all annotations from a recording
-   * - ``energy``
-     - Auto-detect regions above the estimated noise floor
-   * - ``cusum``
-     - Auto-detect regime changes using change-point detection
-   * - ``threshold``
-     - Auto-detect regions using normalized magnitude thresholding
-   * - ``separate``
-     - Decompose annotations into narrower spectral components
 
 **General behavior:**
 
@@ -594,16 +587,8 @@ annotations.
    ria annotate add capture.sigmf-data --start 10000 --count 5000 --label burst
    ria annotate energy capture.sigmf-data --label signal --threshold 1.3
    ria annotate cusum capture.sigmf-data --min-duration 5
-   ria annotate threshold recordings/sample_recording3.npy --threshold 0.7 --label 70%
    ria annotate separate capture.sigmf-data --indices 0,1 --verbose
 
-.. figure:: ../images/recordings/sample_recording3_annotated.png
-   :alt: Example output of ria annotate threshold recordings/sample_recording3.npy --threshold 0.7 --label 70%
-
-   Output of ``ria annotate threshold recordings/sample_recording3.npy --threshold 0.7 --label 70%``
-
-
-.. _cmd-convert:
 
 4.6 ``convert``
 ----------------
@@ -644,8 +629,6 @@ inferred from the output file extension.
    ria convert old.npy --format sigmf --legacy --overwrite
 
 
-.. _cmd-split:
-
 4.7 ``split``
 --------------
 
@@ -687,8 +670,6 @@ Choose exactly one operation per invocation:
    ria split annotated.sigmf-data --extract-annotations --annotation-label payload
 
 
-.. _cmd-combine:
-
 4.8 ``combine``
 ----------------
 
@@ -736,8 +717,6 @@ Choose exactly one operation per invocation:
    ria combine signal.npy pattern.npy out.npy --mode add --align-mode repeat-spaced --repeat-spacing 10000
 
 
-.. _cmd-generate:
-
 4.9 ``generate`` group (and ``synth`` alias)
 ---------------------------------------------
 
@@ -749,34 +728,15 @@ Choose exactly one operation per invocation:
 
 ``ria synth ...`` is an alias for ``ria generate ...``.
 
-**Usage:**
+**Shape:**
 
 .. code-block:: bash
 
    ria generate <subcommand> [subcommand options] [common options]
 
 **Available subcommands:**
-
+``tone``, ``noise``, ``chirp``, ``square``, ``sawtooth``, ``qam``, ``apsk``, ``pam``,
-.. list-table::
+``fsk``, ``ook``, ``oqpsk``, ``gmsk``, ``psk``
-   :widths: 30 70
-   :header-rows: 1
-
-   * - Subcommand(s)
-     - Description
-   * - ``tone``
-     - Clean sinusoidal calibration/reference source
-   * - ``noise``
-     - Baseline noise floor data or controlled additive-noise synthesis
-   * - ``chirp``
-     - Sweep-based radar/sonar-style signals and bandwidth occupancy tests
-   * - ``square``, ``sawtooth``
-     - Periodic waveform primitives
-   * - ``qam``, ``apsk``, ``pam``, ``psk``
-     - Digital modulation families with pulse-shaping filter support
-   * - ``fsk``
-     - Frequency-shift keying with configurable tone spacing
-   * - ``ook``, ``oqpsk``, ``gmsk``
-     - On-off keying and continuous-phase modulation schemes
 
 **Common options shared across all generators:**
 
@@ -800,16 +760,22 @@ Multipath and IQ imbalance flags apply impairment-style post-processing during g
 
 Options: ``--frequency``, ``--amplitude``, ``--phase``
 
+Clean sinusoidal calibration/reference source.
+
 ``noise``
 ~~~~~~~~~~
 
 Options: ``--noise-type {gaussian,uniform}``, ``--power``
 
+Baseline noise floor data or controlled additive-noise synthesis.
+
 ``chirp``
 ~~~~~~~~~~
 
 Options: ``--bandwidth`` (required), ``--period`` (required), ``--type {up,down,up_down}``
 
+Sweep-based radar/sonar-style signals and bandwidth occupancy tests.
+
 ``square``
 ~~~~~~~~~~~
 
@@ -860,8 +826,6 @@ symbol transition sharpness).
    ria synth psk -s 2e6 -r 100e3 -M 8 -N 8000 -o psk8.npy
 
 
-.. _cmd-transform:
-
 4.10 ``transform`` group
 -------------------------
 
@@ -870,7 +834,7 @@ symbol transition sharpness).
 * Apply algorithmic transforms to existing recordings.
 * Run reusable augmentations/impairments for dataset diversity and robustness testing.
 
-**Usage:**
+**Shape:**
 
 .. code-block:: bash
 
@@ -931,8 +895,6 @@ inspect parameter hints. ``--view`` writes a PNG preview alongside transform out
    ria transform custom my_filter in.npy out.npy --transform-dir ./my_transforms --params cutoff=0.2
 
 
-.. _cmd-transmit:
-
 4.11 ``transmit``
 ------------------
 
@@ -1031,7 +993,17 @@ experiment-specific fields on the CLI.
    ria generate noise --config generate.yaml
 
 
-6) Version Notes
+6) Practical Tips and Safety
+=============================
+
+* Use ``ria discover`` before capture/transmit sessions.
+* Keep TX gain conservative first; validate with attenuators/dummy loads when needed.
+* Prefer SigMF for interoperable metadata and annotations.
+* For long workflows, keep outputs organized by campaign directories and consistent prefixes.
+* Use ``--verbose`` when debugging device init or driver issues.
+
+
+7) Version Notes
 =================
 
 These notes are based on the current implementation and should be re-validated against future
@@ -1044,19 +1016,18 @@ releases.
 3. Multiple non-CLI modules still import ``utils.*``, which can create runtime dependency
    coupling when using only ``ria-toolkit-oss`` in isolation.
 
-.. tip::
+If you observe unexpected import errors after install, check the package version and
-   If you observe unexpected import errors after install, check the package version and
+changelog, then test ``ria --help`` in a clean virtual environment.
-   changelog, then test ``ria --help`` in a clean virtual environment.
 
 
-7) Brief Scripting (Python) Preview
+8) Brief Scripting (Python) Preview
 =====================================
 
 For quick non-CLI use:
 
 .. code-block:: python
 
-   from ria_toolkit_oss.data import Recording
+   from ria_toolkit_oss.datatypes import Recording
    from ria_toolkit_oss.io import load_recording, to_sigmf
    from ria_toolkit_oss.transforms import iq_augmentations, iq_impairments
 
@@ -1066,3 +1037,47 @@ For quick non-CLI use:
    to_sigmf(imp, filename="capture_awgn", path=".")
 
 You can also call annotation algorithms and block-generator primitives from Python directly.
+
+
+9) Cheat Sheet
+===============
+
+.. code-block:: bash
+
+   # Install
+   pip install ria-toolkit-oss
+
+   # Discover
+   ria discover -v
+
+   # Init defaults
+   ria init --author "Jane" --project "rf1" --location "Lab-A"
+
+   # Capture
+   ria capture -d pluto -f 2.44G -s 2e6 -n 1000000 -o cap.sigmf-data
+
+   # View
+   ria view cap.sigmf-data --type simple
+
+   # Annotate
+   ria annotate energy cap.sigmf-data --threshold 1.2
+   ria annotate list cap.sigmf-data --verbose
+
+   # Convert
+   ria convert cap.sigmf-data cap.npy
+
+   # Split
+   ria split cap.sigmf-data --split-every 100000 --output-dir chunks
+
+   # Combine
+   ria combine chunks/a.npy chunks/b.npy merged.npy
+
+   # Generate
+   ria generate qam -s 2e6 -r 100e3 -M 16 -N 5000 -o qam16.npy
+
+   # Transform
+   ria transform augment channel_swap cap.npy
+   ria transform impair add_awgn_to_signal cap.npy --params snr=10
+
+   # Transmit
+   ria transmit -d hackrf --input cap.sigmf-data -f 2.44G -s 2e6

docs/source/_static/custom.css

@@ -1,7 +1,6 @@
 /* Change the hex values below to customize heading colours */
 
-.rst-content { color: #e0e0e0; }
+.rst-content h1 { color: #2c3e50; }
-.rst-content h1 { color: #ffffff; }
 .rst-content h2,
 .rst-content h2 a { color: #ffffff !important; font-size: 22px !important; }
 
@@ -23,20 +22,8 @@
 .rst-content .admonition.warning p {
     color: #ffffff !important;
 }
-.rst-content h4 { color: #cccccc; }
+.rst-content h4 { color: #404040; }
 
 .highlight * { color: #ffffff !important; }
 
 .ria-cmd { color: #2980b9 !important; }
-
-
-/* Table header text */
-.rst-content table.docutils th {
-    color: #ffffff !important;
-}
-
-/* Remove alternating row background colors from tables */
-.rst-content table.docutils td,
-.rst-content table.docutils tr:nth-child(2n-1) td {
-    background-color: transparent !important;
-}

docs/source/conf.py

@@ -12,9 +12,9 @@ sys.path.insert(0, os.path.abspath(os.path.join('..', '..')))
 # https://www.sphinx-doc.org/en/master/usage/configuration.html#project-information
 
 project = 'ria-toolkit-oss'
-copyright = '2026, Qoherent Inc'
+copyright = '2025, Qoherent Inc'
 author = 'Qoherent Inc.'
-release = '0.1.7'
+release = '0.1.5'
 
 # -- General configuration ---------------------------------------------------
 # https://www.sphinx-doc.org/en/master/usage/configuration.html#general-configuration

docs/source/examples/sdr/index.rst

@@ -1,4 +1,4 @@
-.. _sdr_examples:
+.. _examples:
 
 ############
 SDR Examples

docs/source/intro/installation.rst

@@ -4,26 +4,7 @@ Installation
 RIA Hub Toolkit OSS can be installed either as a Conda package or as a standard Python package.
 
 Please note that SDR drivers must be installed separately. Refer to the relevant guide in the
-:ref:`SDR Guides <sdr_guides>` section of the documentation for additional setup instructions.
+:ref:`SDR Guides <sdr_guides>` section of the documentation for addition setup instructions.
-
-Common driver packages by device (exact package names depend on your OS):
-
-.. list-table::
-   :widths: 25 75
-   :header-rows: 1
-
-   * - Device
-     - Driver Package
-   * - USRP
-     - UHD drivers
-   * - Pluto
-     - libiio / IIO utilities
-   * - BladeRF
-     - libbladeRF
-   * - HackRF
-     - libhackrf
-   * - RTL-SDR
-     - librtlsdr
 
 We want your experience with RIA Toolkit OSS to be as smooth and frictionless as possible. If you run into any 
 issues during installation, please reach out to our support team: ``support@qoherent.ai``.
@@ -103,22 +84,12 @@ Please follow the steps below to install RIA Toolkit OSS using pip:
       python -m venv venv
       venv\Scripts\activate
 
-2. Upgrade pip and install RIA Toolkit OSS:
+2. Install RIA Toolkit OSS from PyPI with pip:
 
    .. code-block:: bash
 
-      pip install --upgrade pip
       pip install ria-toolkit-oss
 
-3. Verify the CLI is available:
-
-   .. code-block:: bash
-
-      ria --help
-
-   A successful install prints the top-level help text. ``pyproject.toml`` registers two
-   entrypoints — ``ria`` and ``ria-tools`` — that both point to the same CLI module.
-
 RIA Toolkit OSS can also be installed from RIA Hub. However, RIA Hub does not yet support a proxy or cache for public packages. 
 We intend to add this missing functionality soon. In the meantime, please use the ``--no-deps`` option with pip to skip automatic
 dependency installation, and then manually install each dependency afterward.
@@ -148,6 +119,3 @@ Follow the steps below to install RIA Toolkit OSS from source:
    .. code-block:: bash
 
       pip install .
-
-   For local development, use ``pip install -e .`` instead to install in editable mode
-   so local changes take effect immediately without reinstalling.

docs/source/ria_toolkit_oss/datatypes/ria_toolkit_oss.datatypes.rst

@@ -1,5 +1,5 @@
-Data Package (ria_toolkit_oss.data)
+Datatypes Package (ria_toolkit_oss.data)
-=======================================
+=============================================
 
 .. |br| raw:: html
 

docs/source/sdr_guides/blade.rst

@@ -40,44 +40,34 @@ Limitations
 - USB 3.0 connectivity is required for optimal performance; using USB 2.0 will significantly limit data
   transfer rates.
 
-Set up instructions (Linux)
+Set up instructions (Linux, Radioconda)
----------------------------
+---------------------------------------
 
-No additional Python packages are required for BladeRF beyond the base RIA Toolkit OSS installation.
+1. Activate your Radioconda environment.
-
-1. Install the system library:
 
   .. code-block:: bash
 
-    sudo apt install libbladerf-dev
+     conda activate <your-env-name>
 
-  For a more complete installation including CLI tools and FPGA images, use the Nuand PPA:
+2. Install the base dependencies and drivers (*Easy method*):
 
   .. code-block:: bash
 
     sudo add-apt-repository ppa:nuandllc/bladerf
     sudo apt-get update
-    sudo apt-get install bladerf libbladerf-dev
+    sudo apt-get install bladerf
-    sudo apt-get install bladerf-fpga-hostedxa4  # Necessary for BladeRF 2.0 Micro xA4
+    sudo apt-get install libbladerf-dev
+    sudo apt-get install bladerf-fpga-hostedxa4  # Necessary for installation of bladeRF 2.0 Micro A4.
 
-2. Install udev rules:
+3. Install a ``udev`` rule by creating a link into your Radioconda installation:
-
-  For most users:
 
   .. code-block:: bash
 
-    sudo udevadm control --reload
+     sudo ln -s $CONDA_PREFIX/lib/udev/rules.d/88-nuand-bladerf1.rules /etc/udev/rules.d/88-radioconda-nuand-bladerf1.rules
-    sudo udevadm trigger
+     sudo ln -s $CONDA_PREFIX/lib/udev/rules.d/88-nuand-bladerf2.rules /etc/udev/rules.d/88-radioconda-nuand-bladerf2.rules
-
+     sudo ln -s $CONDA_PREFIX/lib/udev/rules.d/88-nuand-bootloader.rules /etc/udev/rules.d/88-radioconda-nuand-bootloader.rules
-  For **Radioconda** users, create symlinks from your conda environment instead:
+     sudo udevadm control --reload
-
+     sudo udevadm trigger
-  .. code-block:: bash
-
-    sudo ln -s $CONDA_PREFIX/lib/udev/rules.d/88-nuand-bladerf1.rules /etc/udev/rules.d/88-radioconda-nuand-bladerf1.rules
-    sudo ln -s $CONDA_PREFIX/lib/udev/rules.d/88-nuand-bladerf2.rules /etc/udev/rules.d/88-radioconda-nuand-bladerf2.rules
-    sudo ln -s $CONDA_PREFIX/lib/udev/rules.d/88-nuand-bootloader.rules /etc/udev/rules.d/88-radioconda-nuand-bootloader.rules
-    sudo udevadm control --reload
-    sudo udevadm trigger
 
 Further Information
 -------------------

docs/source/sdr_guides/hackrf.rst

@@ -39,44 +39,39 @@ Limitations
 - Bandwidth is limited to 20 MHz.
 - USB 2.0 connectivity might limit data transfer rates compared to USB 3.0 or Ethernet-based SDRs.
 
-Set up instructions (Linux)
+Set up instructions (Linux, Radioconda)
----------------------------
+---------------------------------------
 
-HackRF is supported out of the box after installing RIA Toolkit OSS.
+1. Activate your Radioconda environment:
-
-1. Ensure ``libhackrf`` is installed at the system level. On most Ubuntu installations this is already
-   present. If not:
 
   .. code-block:: bash
 
-    sudo apt install libhackrf-dev
+     conda activate <your-env-name>
 
-2. Install udev rules to allow non-root device access:
+2. Install the System Package (Ubuntu / Debian):
-
-  For most users:
 
   .. code-block:: bash
 
-    sudo udevadm control --reload
+     sudo apt-get update
-    sudo udevadm trigger
+     sudo apt-get install hackrf
 
-  For **Radioconda** users, create a symlink from your conda environment instead:
+3. Install a ``udev`` rule by creating a link into your Radioconda installation:
 
   .. code-block:: bash
 
-    sudo ln -s $CONDA_PREFIX/lib/udev/rules.d/53-hackrf.rules /etc/udev/rules.d/53-radioconda-hackrf.rules
+     sudo ln -s $CONDA_PREFIX/lib/udev/rules.d/53-hackrf.rules /etc/udev/rules.d/53-radioconda-hackrf.rules
-    sudo udevadm control --reload
+     sudo udevadm control --reload
-    sudo udevadm trigger
+     sudo udevadm trigger
 
-  Make sure your user account belongs to the ``plugdev`` group in order to access your device:
+  Make sure your user account belongs to the plugdev group in order to access your device:
 
   .. code-block:: bash
 
-    sudo usermod -a -G plugdev <user>
+     sudo usermod -a -G plugdev <user>
 
 .. note::
 
-   You may have to restart your system for group membership changes to take effect.
+   You may have to restart your system for changes to take effect.
 
 Further information
 -------------------

docs/source/sdr_guides/pluto.rst

@@ -43,34 +43,34 @@ Limitations
   affect stability.
 - USB 2.0 connectivity might limit data transfer rates compared to USB 3.0 or Ethernet-based SDRs.
 
-Set up instructions (Linux)
+Set up instructions (Linux, Radioconda)
----------------------------
+---------------------------------------
 
-The PlutoSDR is supported out of the box after installing RIA Toolkit OSS. The required Python package
+1. Activate your Radioconda environment:
-(``pyadi-iio``) is included in the toolkit's dependencies.
-
-1. Ensure ``libiio`` is installed at the system level. On most Ubuntu installations this is already present.
-   If not:
 
   .. code-block:: bash
 
-    sudo apt install libiio-dev libiio-utils libiio0
+    conda activate <your-env-name>
 
-.. note::
+2. Install system dependencies:
-
-   PlutoSDR devices are discoverable over both USB and network (mDNS). Network discovery uses Avahi — if
-   ``avahi-daemon`` is not running, network discovery will be skipped but USB discovery still works.
-
-2. Install a ``udev`` rule to allow non-root device access:
-
-  For most users:
 
   .. code-block:: bash
 
-    sudo udevadm control --reload
+    sudo apt-get update
-    sudo udevadm trigger
+    sudo apt-get install -y \
+          build-essential \
+          git \
+          libxml2-dev \
+          bison \
+          flex \
+          libcdk5-dev \
+          cmake \
+          libusb-1.0-0-dev \
+          libavahi-client-dev \
+          libavahi-common-dev \
+          libaio-dev
 
-  For **Radioconda** users, create a symlink from your conda environment instead:
+3. Install a ``udev`` rule by creating a link into your Radioconda installation:
 
   .. code-block:: bash
 
@@ -78,18 +78,11 @@ The PlutoSDR is supported out of the box after installing RIA Toolkit OSS. The r
     sudo udevadm control --reload
     sudo udevadm trigger
 
-  Once you can communicate with the hardware, you may want to perform the post-install steps detailed on
+  Once you can talk to the hardware, you may want to perform the post-install steps detailed on the `PlutoSDR Documentation <https://wiki.analog.com/university/tools/pluto>`_.
-  the `PlutoSDR Documentation <https://wiki.analog.com/university/tools/pluto>`_.
 
-3. (Optional) Building ``libiio`` or ``libad9361-iio`` from source:
+4. (Optional) Building ``libiio`` or ``libad9361-iio`` from source:
 
-  This step is only required if you need a version not available via ``apt``. First install build
+  This step is only required if you want the latest version of these libraries not provided in Radioconda.
-  dependencies:
-
-  .. code-block:: bash
-
-    sudo apt-get install -y build-essential git libxml2-dev bison flex libcdk5-dev cmake \
-      libusb-1.0-0-dev libavahi-client-dev libavahi-common-dev libaio-dev
 
   .. code-block:: bash
 

docs/source/sdr_guides/rtlsdr.rst

@@ -30,10 +30,18 @@ Limitations
     - Sensitivity and performance can vary depending on the specific model and components.
     - Requires external software for signal processing and analysis.
 
-Set up instructions (Linux)
+Set up instructions (Linux, Radioconda)
----------------------------
+---------------------------------------
 
-1. If you previously had RTL-SDR drivers installed, purge them first:
+1. Activate your Radioconda environment:
+
+  .. code-block:: bash
+
+    conda activate <your-env-name>
+
+2. Purge drivers:
+
+If you already have other drivers installed, purge them from your system.
 
   .. code-block:: bash
 
@@ -45,95 +53,47 @@ Set up instructions (Linux)
     sudo rm -rvf /usr/local/include/rtl_* 
     sudo rm -rvf /usr/local/bin/rtl_*
 
-2. Install build dependencies:
+3. Install RTL-SDR Blog drivers:
 
   .. code-block:: bash
 
-    sudo apt install libusb-1.0-0-dev git cmake pkg-config build-essential
+    sudo apt-get install libusb-1.0-0-dev git cmake pkg-config build-essential
-
+    git clone https://github.com/osmocom/rtl-sdr 
-3. Build ``librtlsdr`` from source:
+    cd rtl-sdr
-
+    mkdir build
-  The standard ``librtlsdr`` package available via ``apt`` is missing symbols required by the Python
+    cd build
-  bindings. Build from the **rtl-sdr-blog fork**:
+    cmake ../ -DINSTALL_UDEV_RULES=ON
-
-  .. code-block:: bash
-
-    git clone https://github.com/rtlsdrblog/rtl-sdr-blog.git
-    cd rtl-sdr-blog
-    mkdir build && cd build
-    cmake .. -DINSTALL_UDEV_RULES=ON
     make
     sudo make install
     sudo cp ../rtl-sdr.rules /etc/udev/rules.d/
     sudo ldconfig
 
-  .. important::
+4. Blacklist the DVB-T modules that would otherwise claim the device:
-
-     Do not use the osmocom ``rtl-sdr`` repository or the Ubuntu ``librtlsdr-dev`` apt package. Neither
-     provides the ``rtlsdr_set_dithering`` symbol that the Python bindings require.
-
-4. Blacklist the kernel DVB driver:
-
-  The kernel DVB-T driver (``dvb_usb_rtl28xxu``) claims the RTL-SDR device and prevents ``librtlsdr``
-  from accessing it.
-
-  For most users:
 
   .. code-block:: bash
-
-    echo 'blacklist dvb_usb_rtl28xxu' | sudo tee /etc/modprobe.d/blacklist-rtlsdr.conf
-    sudo modprobe -r dvb_usb_rtl28xxu
-
-  For **Radioconda** users, a blacklist configuration is already provided in your conda environment:
-
-  .. code-block:: bash
-
     sudo ln -s $CONDA_PREFIX/etc/modprobe.d/rtl-sdr-blacklist.conf /etc/modprobe.d/radioconda-rtl-sdr-blacklist.conf
     sudo modprobe -r $(cat $CONDA_PREFIX/etc/modprobe.d/rtl-sdr-blacklist.conf | sed -n -e 's/^blacklist //p')
 
-  If ``modprobe -r`` fails with "Module is in use", unplug the RTL-SDR dongle, run the command again,
+.. note::
-  then plug it back in. Alternatively, reboot — the blacklist takes effect on next boot.
 
-  .. note::
+   In addition to the Radioconda blacklist file, some systems also require
+   manually blacklisting the following DVB-T modules to prevent them from
+   claiming the device:
 
-     Some systems also require blacklisting additional DVB-T modules. Add these entries to your
+     - ``dvb_usb_rtl28xxu``
-     blacklist configuration if needed:
+     - ``rtl2832``
+     - ``rtl2830``
 
-       - ``rtl2832``
+   Add these entries to ``rtlsdr.conf`` (or create the file at
-       - ``rtl2830``
+   ``/etc/modprobe.d/rtlsdr.conf``) if they are not already present.
 
-5. Reload udev rules:
+5. Install a udev rule by creating a link into your radioconda installation:
-
-  For most users (rules are installed by the build step above):
 
   .. code-block:: bash
-
-    sudo udevadm control --reload
-    sudo udevadm trigger
-
-  For **Radioconda** users, create a symlink from your conda environment instead:
-
-  .. code-block:: bash
-
     sudo ln -s $CONDA_PREFIX/lib/udev/rules.d/rtl-sdr.rules /etc/udev/rules.d/radioconda-rtl-sdr.rules
     sudo udevadm control --reload
     sudo udevadm trigger
 
-6. Install Python packages:
-
-  .. code-block:: bash
-
-    pip install pyrtlsdr==0.3.0
-    pip install setuptools==69.5.1
-
-  .. note::
-
-     ``pyrtlsdr`` 0.4.0 references a ``rtlsdr_set_dithering`` symbol not present in standard
-     ``librtlsdr`` builds. Version 0.3.0 works correctly.
-
-     ``pyrtlsdr`` 0.3.0 depends on ``pkg_resources``, which was removed in ``setuptools`` >= 82.
-     Pinning to 69.5.1 ensures ``pkg_resources`` is available.
-
 Further Information
 -------------------
     - `RTL-SDR Official Website <https://www.rtl-sdr.com/>`_

docs/source/sdr_guides/thinkrf.rst

@@ -39,48 +39,18 @@ Limitations
 Set up instructions (Linux)
 ---------------------------------
 
-ThinkRF devices require the ``pyrf`` package, which is written in Python 2 syntax and must be patched
+Install PyRF
-after installation to work with Python 3.
-
-.. note::
-
-   ``lib2to3`` was fully removed in Python 3.13. ThinkRF support is currently limited to
-   **Python 3.12 and below**.
-
-1. Install ``lib2to3``:
-
-  On some distributions (including Ubuntu 24.04+), ``lib2to3`` is not included by default:
 
   .. code-block:: bash
 
-    sudo apt install python3-lib2to3
+    pip install 'pyrf>=2.8.0'
 
-2. Install ``pyrf``:
+Convert PyRF scripts to Python 3
 
   .. code-block:: bash
 
-    pip install pyrf
+    cd ../scripts
-
+    ./convert_pyrf_to_python3.sh
-3. Patch ``pyrf`` for Python 3:
-
-  The ``pyrf`` package contains Python 2 syntax throughout (e.g., ``dict.iteritems()``, ``print``
-  statements). Run the following to automatically convert the entire package to Python 3:
-
-  .. code-block:: bash
-
-    python -c "
-    from lib2to3.refactor import RefactoringTool, get_fixers_from_package
-    import pyrf, os
-    pyrf_path = os.path.dirname(pyrf.__file__)
-    fixers = get_fixers_from_package('lib2to3.fixes')
-    tool = RefactoringTool(fixers)
-    tool.refactor_dir(pyrf_path, write=True)
-    print('Done')
-    "
-
-  .. note::
-
-     This patches the entire ``pyrf`` package in place, which is required for the driver to fully load.
 
 Further Information
 -------------------

docs/source/sdr_guides/usrp.rst

@@ -41,111 +41,48 @@ Limitations
 - Compatibility with certain software tools may vary depending on the version of the UHD.
 - Price range can be a consideration, especially for high-end models.
 
-Set up instructions (Linux)
+Set up instructions (Linux, Radioconda)
----------------------------
+---------------------------------------
 
-USRP devices require the UHD (USRP Hardware Driver) library with Python bindings. There is no pip-installable
+1. Activate your Radioconda environment:
-UHD package — it must either be installed via conda or built from source.
-
-**Option A: Install via conda (recommended for conda environments)**
 
   .. code-block:: bash
 
-    conda install conda-forge::uhd
+     conda activate <your-env-name>
 
-**Option B: Build from source (required for pip/venv environments)**
+2. Install UHD and Python bindings:
 
-  The Python bindings must target the same Python version used in your virtual environment.
+  .. code-block:: bash
 
-  1. Install build dependencies:
+     conda install conda-forge::uhd    
 
-    .. code-block:: bash
+3. Download UHD images:
-
-      sudo apt install cmake build-essential libboost-all-dev libusb-1.0-0-dev \
-        python3-dev python3-numpy libncurses-dev
-
-  2. Install the Mako template library into your virtual environment (used by UHD's build system):
-
-    .. code-block:: bash
-
-      pip install mako
-
-  3. Clone and build UHD with your virtual environment activated:
-
-    .. code-block:: bash
-
-      git clone https://github.com/EttusResearch/uhd.git
-      cd uhd
-      git checkout v4.7.0.0
-      cd host
-      mkdir build && cd build
-      cmake -DENABLE_PYTHON_API=ON -DPYTHON_EXECUTABLE=$(which python3) ..
-      make -j$(nproc)
-      sudo make install
-      sudo ldconfig
-
-    .. important::
-
-       Run the ``cmake`` command with your virtual environment activated so ``$(which python3)`` points
-       to the correct interpreter. Before running ``make``, verify the cmake output includes::
-
-         --   * LibUHD - Python API          → must say "Enabling"
-         -- Python interpreter: .../your-venv/bin/python3
-
-       If "LibUHD - Python API" is not listed under enabled components, the Python bindings will not be
-       built. The build typically takes 10–30 minutes.
-
-  4. Copy the Python bindings into your virtual environment if ``import uhd`` fails after installation:
-
-    .. code-block:: bash
-
-      cp -r ~/uhd/host/build/python/uhd ~/.venv/lib/python3.XX/site-packages/
-
-    Replace ``python3.XX`` with your Python version (e.g., ``python3.12``).
-
-    .. note::
-
-       If you have a pre-existing UHD installation built against a different Python version, you will see
-       a circular import error. The bindings must match the Python version in your virtual environment exactly.
-
-**After either installation method:**
-
-1. Download UHD FPGA/firmware images:
 
   .. code-block:: bash
 
     uhd_images_downloader
 
-2. Verify device access:
+4. Verify access to your device:
 
-  .. code-block:: bash
+   .. code-block:: bash
 
-    uhd_find_devices
+      uhd_find_devices
 
-  For USB devices (e.g. B-series), install a ``udev`` rule.
+   For USB devices only (e.g. B series), install a ``udev`` rule by creating a link into your Radioconda installation.
 
-  For most users:
+   .. code-block:: bash
 
-  .. code-block:: bash
+      sudo ln -s $CONDA_PREFIX/lib/uhd/utils/uhd-usrp.rules /etc/udev/rules.d/radioconda-uhd-usrp.rules
+      sudo udevadm control --reload
+      sudo udevadm trigger
 
-    sudo udevadm control --reload
+5. (Optional) Update firmware/FPGA images:
-    sudo udevadm trigger
 
-  For **Radioconda** users, create a symlink from your conda environment instead:
+   .. code-block:: bash
 
-  .. code-block:: bash
+      uhd_usrp_probe
 
-    sudo ln -s $CONDA_PREFIX/lib/uhd/utils/uhd-usrp.rules /etc/udev/rules.d/radioconda-uhd-usrp.rules
+   This will ensure your device is running the latest firmware and FPGA versions.
-    sudo udevadm control --reload
-    sudo udevadm trigger
-
-3. (Optional) Update firmware/FPGA images:
-
-  .. code-block:: bash
-
-    uhd_usrp_probe
-
-  This will ensure your device is running the latest firmware and FPGA versions.
 
 Further information
 -------------------

pyproject.toml

@@ -1,6 +1,6 @@
 [project]
 name = "ria-toolkit-oss"
-version = "0.1.7"
+version = "0.1.5"
 description = "An open-source version of the RIA Toolkit, including the fundamental tools to get started developing, testing, and deploying radio intelligence applications"
 license = { text = "AGPL-3.0-only" }
 readme = "README.md"

src/ria_toolkit_oss/agent/cli.py

@@ -5,11 +5,8 @@ Subcommands:
 - ``ria-agent run [legacy args]`` — legacy long-poll NodeAgent (unchanged).
 - ``ria-agent stream`` — new WebSocket-based IQ streamer.
 - ``ria-agent detect`` — print SDR drivers whose modules import cleanly.
-- ``ria-agent register --hub URL --api-key KEY`` — register with the hub
+- ``ria-agent register --hub URL --api-key KEY`` — register with the hub and
-  using a personal registration key (minted from **Settings → RIA Agents**
+  save credentials (and optional TX interlocks) to ``~/.ria/agent.json``.
-  on the hub, shown once at mint time) and save credentials (and optional
-  TX interlocks) to ``~/.ria/agent.json``. The hub also accepts the legacy
-  shared ``[wac] API_KEY`` for back-compat, but that path is deprecated.
 
 Invoking ``ria-agent`` with no subcommand falls through to the legacy
 long-poll behavior for back-compatibility with existing deployments.
@@ -28,75 +25,9 @@ from .hardware import available_devices
 from .legacy_executor import main as _legacy_main
 from .namegen import generate_agent_name
 
-DEFAULT_HUB_URL = "https://riahub.ai"
-
 _LEGACY_ALIASES = {"--hub", "--key", "--name", "--device", "--insecure", "--log-level", "--config"}
 
 
-def _user_agent() -> str:
-    """Build the User-Agent header for hub requests.
-
-    Set explicitly so we don't fall back to Python's default `Python-urllib/<ver>`,
-    which is blocked by Cloudflare's Browser Integrity Check on `riahub.ai`
-    (HTTP 403 edge code 1010). Version is read from package metadata so it
-    tracks releases instead of going stale.
-    """
-    from importlib.metadata import PackageNotFoundError, version
-
-    try:
-        pkg_version = version("ria-toolkit-oss")
-    except PackageNotFoundError:
-        pkg_version = "unknown"
-    return f"ria-agent/{pkg_version} (+https://riahub.ai/qoherent/ria-toolkit-oss)"
-
-
-# How long to wait on the hub before giving up. The register endpoint is a
-# small DB lookup + insert; anything past this is a stuck hub, not a slow one.
-_REGISTER_TIMEOUT_S = 15
-
-
-REGISTRATION_REASON_MESSAGES = {
-    "invalid_key": ("Registration key not recognized. Generate a fresh key from " "Settings → RIA Agents on the hub."),
-    "expired": ("This registration key has expired. Generate a new one from " "Settings → RIA Agents on the hub."),
-    "revoked": ("This registration key was revoked. Generate a new one from " "Settings → RIA Agents on the hub."),
-    "already_consumed": (
-        "This single-use registration key has already been used. "
-        "Generate a new one, or mint a reusable key instead."
-    ),
-}
-
-
-def _explain_registration_failure(status: int, body: bytes) -> str:
-    """Return a human-readable explanation for a failed register call."""
-    try:
-        parsed = json.loads(body) if body else None
-    except ValueError:
-        parsed = None
-
-    if status == 429:
-        # 429 carries a plain string detail, never a reason code.
-        if isinstance(parsed, dict) and parsed.get("detail"):
-            detail = parsed["detail"]
-        else:
-            detail = body.decode("utf-8", "replace") or "rate limited"
-        return f"Registration rate-limited by the hub: {detail}"
-
-    if not isinstance(parsed, dict):
-        text = body.decode("utf-8", "replace")
-        return f"HTTP {status}: {text or 'no body'}"
-
-    detail = parsed.get("detail")
-    if isinstance(detail, dict):
-        reason = detail.get("reason")
-        if reason in REGISTRATION_REASON_MESSAGES:
-            return REGISTRATION_REASON_MESSAGES[reason]
-        if reason:
-            return f"Registration rejected ({reason})"
-    if isinstance(detail, str) and detail:
-        return f"Registration rejected: {detail}"
-    return f"HTTP {status}: {parsed}"
-
-
 def _cmd_detect(_args: argparse.Namespace) -> int:
     devices = available_devices()
     if not devices:
@@ -108,7 +39,6 @@ def _cmd_detect(_args: argparse.Namespace) -> int:
 
 
 def _cmd_register(args: argparse.Namespace) -> int:
-    import urllib.error
     import urllib.request
 
     hub_url = args.hub.rstrip("/")
@@ -121,20 +51,11 @@ def _cmd_register(args: argparse.Namespace) -> int:
         headers={
             "Content-Type": "application/json",
             "X-API-Key": args.api_key,
-            "User-Agent": _user_agent(),
         },
     )
     try:
-        with urllib.request.urlopen(req, timeout=_REGISTER_TIMEOUT_S) as resp:
+        with urllib.request.urlopen(req) as resp:
             data = json.loads(resp.read())
-    except urllib.error.HTTPError as e:
-        try:
-            err_body = e.read()
-        except Exception:
-            err_body = b""
-        msg = _explain_registration_failure(e.code, err_body)
-        print(f"error: registration failed: {msg}", file=sys.stderr)
-        return 1
     except Exception as e:
         print(f"error: registration failed: {e}", file=sys.stderr)
         return 1
@@ -159,7 +80,7 @@ def _cmd_register(args: argparse.Namespace) -> int:
         cfg.tx_allowed_freq_ranges = [[float(lo), float(hi)] for lo, hi in freq_ranges]
     path = _config.save(cfg)
 
-    print(f"Registered agent: {agent_id} ({name})")
+    print(f"Registered agent: {agent_id}")
     if cfg.tx_enabled:
         caps: list[str] = []
         if cfg.tx_max_gain_db is not None:
@@ -219,17 +140,8 @@ def main() -> None:
     sub.add_parser("detect", help="List available SDR drivers")
 
     p_reg = sub.add_parser("register", help="Register agent with RIA Hub and save credentials")
-    p_reg.add_argument("--hub", default=DEFAULT_HUB_URL, help=f"RIA Hub URL (default: {DEFAULT_HUB_URL})")
+    p_reg.add_argument("--hub", required=True, help="RIA Hub URL (e.g. http://whitehorse:3005)")
-    p_reg.add_argument(
+    p_reg.add_argument("--api-key", dest="api_key", required=True, help="Hub API key")
-        "--api-key",
-        dest="api_key",
-        required=True,
-        help=(
-            "Personal registration key from the RIA Agents page on the hub "
-            "(format: ria_reg_...). Shown once when generated; save it then. "
-            "The legacy shared API key is also accepted but deprecated."
-        ),
-    )
     p_reg.add_argument("--name", default=None, help="Human-friendly agent name")
     p_reg.add_argument("--insecure", action="store_true", help="Skip TLS verification")
     p_reg.add_argument(

src/ria_toolkit_oss/annotations/annotation_transforms.py

@@ -45,14 +45,7 @@ def is_annotation_contained(inner: Annotation, outer: Annotation) -> bool:
     outer_sample_stop = outer.sample_start + outer.sample_count
 
     if inner.sample_start > outer.sample_start and inner_sample_stop < outer_sample_stop:
-        if (
+        if inner.freq_lower_edge > outer.freq_lower_edge and inner.freq_upper_edge < outer.freq_upper_edge:
-            inner.freq_lower_edge is not None
-            and inner.freq_upper_edge is not None
-            and outer.freq_lower_edge is not None
-            and outer.freq_upper_edge is not None
-            and inner.freq_lower_edge > outer.freq_lower_edge
-            and inner.freq_upper_edge < outer.freq_upper_edge
-        ):
             return True
 
     return False

src/ria_toolkit_oss/annotations/cusum_annotator.py

@@ -38,13 +38,7 @@ def annotate_with_cusum(
     :type annotation_type: str
     """
 
-    sample_rate = recording.metadata.get("sample_rate")
+    sample_rate = recording.metadata["sample_rate"]
-    if sample_rate is None:
-        raise ValueError(
-            "Recording metadata does not contain 'sample_rate'. "
-            "Supply it with --sample-rate when using the CLI, or set "
-            "recording.sample_rate before calling this function."
-        )
     center_frequency = recording.metadata.get("center_frequency", 0)
 
     # Create an object of the time segmenter

src/ria_toolkit_oss/annotations/energy_detector.py

@@ -6,7 +6,6 @@ and occupied bandwidth calculation following ITU-R SM.328 standard.
 """
 
 import json
-import warnings
 from typing import Tuple
 
 import numpy as np
@@ -120,17 +119,6 @@ def detect_signals_energy(
     if active:
         boundaries.append((start, len(smoothed_power) - start))
 
-    if not boundaries and noise_floor > 0:
-        peak = float(np.max(smoothed_power))
-        dynamic_range = peak / noise_floor
-        if dynamic_range < threshold_factor:
-            warnings.warn(
-                f"detect_signals_energy: no signal boundaries found — dynamic range {dynamic_range:.2f}x is below "
-                f"the threshold factor {threshold_factor}x. The signal may be constant-envelope (e.g. CW or chirp). "
-                "If the entire recording is signal, use 'ria annotate cusum' to segment it as a single region.",
-                stacklevel=2,
-            )
-
     # Merge boundaries that are closer than min_distance
     merged_boundaries = []
     if boundaries:
@@ -147,13 +135,7 @@ def detect_signals_energy(
         merged_boundaries.append((start, length))
 
     # Create annotations from detected boundaries
-    sample_rate = recording.metadata.get("sample_rate")
+    sample_rate = recording.metadata["sample_rate"]
-    if sample_rate is None:
-        raise ValueError(
-            "Recording metadata does not contain 'sample_rate'. "
-            "Supply it with --sample-rate when using the CLI, or set "
-            "recording.sample_rate before calling this function."
-        )
     center_frequency = recording.metadata.get("center_frequency", 0)
 
     # Validate frequency method
@@ -369,12 +351,7 @@ def annotate_with_obw(
         >>> annotated = annotate_with_obw(recording, label="signal_obw")
     """
     signal = recording.data[0]
-    sample_rate = recording.metadata.get("sample_rate")
+    sample_rate = recording.metadata["sample_rate"]
-    if sample_rate is None:
-        raise ValueError(
-            "Recording metadata does not contain 'sample_rate'. "
-            "Set recording.sample_rate before calling this function."
-        )
     center_freq = recording.metadata.get("center_frequency", 0)
 
     # Calculate OBW

src/ria_toolkit_oss/annotations/parallel_signal_separator.py

@@ -49,7 +49,6 @@ allowing splitting of overlapping signals into separate training samples.
 """
 
 import json
-import warnings
 from typing import List, Optional, Tuple
 
 import numpy as np
@@ -402,13 +401,7 @@ def split_recording_annotations(
         return recording
 
     signal = recording.data[0]
-    sample_rate = recording.metadata.get("sample_rate")
+    sample_rate = recording.metadata["sample_rate"]
-    if sample_rate is None:
-        raise ValueError(
-            "Recording metadata does not contain 'sample_rate'. "
-            "Supply it with --sample-rate when using the CLI, or set "
-            "recording.sample_rate before calling this function."
-        )
     center_frequency = recording.metadata.get("center_frequency", 0.0)
 
     # Build new annotation list
@@ -432,11 +425,8 @@ def split_recording_annotations(
                 else:
                     # No components found, keep original
                     new_annotations.append(anno)
-            except Exception as e:
+            except Exception:
-                warnings.warn(
+                # Split failed for any reason, keep original
-                    f"split_recording_annotations: failed to split annotation at index {i} ({e}); keeping original.",
-                    stacklevel=2,
-                )
                 new_annotations.append(anno)
         else:
             # Not in split list, keep as-is

src/ria_toolkit_oss/annotations/qualify_slice.py

@@ -24,7 +24,7 @@ def qualify_slice_from_annotations(recording: Recording, slice_length: int):
 
     output_recordings = []
 
-    for i in range(len(recording.data[0]) // slice_length):
+    for i in range((len(recording.data[0]) // slice_length) - 1):
         start_index = slice_length * i
         end_index = slice_length * (i + 1)
 

src/ria_toolkit_oss/annotations/signal_isolation.py

@@ -35,24 +35,17 @@ def isolate_signal(recording: Recording, annotation: Annotation) -> Recording:
 
     isolation_bw = anno_bw
 
-    sample_rate = recording.metadata.get("sample_rate")
-    if sample_rate is None:
-        raise ValueError(
-            "Recording metadata does not contain 'sample_rate'. "
-            "Set recording.sample_rate before calling isolate_signal."
-        )
-
     # frequency shift the center of the box about zero
     shifted_signal_slice = frequency_shift_iq_samples(
         iq_samples=signal_slice,
-        sample_rate=sample_rate,
+        sample_rate=recording.metadata["sample_rate"],
         shift_frequency=-1 * anno_base_center_freq,
     )
 
     # filter
-    if isolation_bw < sample_rate - 1:
+    if isolation_bw < recording.metadata["sample_rate"] - 1:
         filtered_signal = apply_complex_lowpass_filter(
-            signal=shifted_signal_slice, cutoff_frequency=isolation_bw, sample_rate=sample_rate
+            signal=shifted_signal_slice, cutoff_frequency=isolation_bw, sample_rate=recording.metadata["sample_rate"]
         )
 
     else:

src/ria_toolkit_oss/annotations/threshold_qualifier.py

@@ -42,7 +42,6 @@ classification or demodulation stages.
 """
 
 import json
-import warnings
 from typing import Optional
 
 import numpy as np
@@ -217,22 +216,11 @@ def threshold_qualifier(
     """
     # Extract signal and metadata
     sample_data = recording.data[channel]
-    sample_rate = recording.metadata.get("sample_rate")
+    sample_rate = recording.metadata["sample_rate"]
-    if sample_rate is None:
-        raise ValueError(
-            "Recording metadata does not contain 'sample_rate'. "
-            "Supply it with --sample-rate when using the CLI, or set "
-            "recording.sample_rate before calling this function."
-        )
     center_frequency = recording.metadata.get("center_frequency", 0)
 
-    n_samples = len(sample_data)
-
     if window_size is None:
         window_size = max(64, int(sample_rate * 0.001))
-    # Cap at 1% of signal length so short recordings aren't over-smoothed into
-    # a flat envelope that collapses the dynamic range below the early-exit guard.
-    window_size = min(window_size, max(64, n_samples // 100))
 
     # --- 1. SIGNAL CONDITIONING ---
     # Convert to power (Magnitude squared)
@@ -249,12 +237,6 @@ def threshold_qualifier(
     # Soft early exit: keep a guard for low-contrast noise, but compute it from
     # the quieter tail of the envelope so burst-heavy captures are not rejected.
     if dynamic_range_ratio < 1.5:
-        warnings.warn(
-            f"threshold_qualifier: dynamic range ratio {dynamic_range_ratio:.2f} is below 1.5 — "
-            "the signal appears to be constant-envelope or pure noise, so no burst boundaries can be found. "
-            "If the entire recording is signal, use 'ria annotate cusum' to segment it as a single region.",
-            stacklevel=2,
-        )
         return Recording(data=recording.data, metadata=recording.metadata, annotations=recording.annotations)
 
     trigger_val = noise_floor + threshold * (max_power - noise_floor)
@@ -314,7 +296,7 @@ def threshold_qualifier(
     # burst energy does not bleed through the long window into adjacent regions,
     # which would inflate macro_residual_max and push the trigger above the
     # faint burst's average power.
-    macro_window_size = min(max(window_size * 16, int(sample_rate * 0.02)), max(window_size * 2, n_samples // 4))
+    macro_window_size = max(window_size * 16, int(sample_rate * 0.02))
     macro_kernel = np.ones(macro_window_size, dtype=np.float64) / macro_window_size
     # Expand each annotated range by half the macro window on both sides so that
     # the long convolution cannot "see" the leading/trailing edges of already-

src/ria_toolkit_oss/data/annotation.py

@@ -17,10 +17,10 @@ class Annotation:
     :type sample_start: int
     :param sample_count: The index of the ending sample of the annotation, inclusive.
     :type sample_count: int
-    :param freq_lower_edge: The lower frequency of the annotation. Optional; None if not specified in source.
+    :param freq_lower_edge: The lower frequency of the annotation.
-    :type freq_lower_edge: float, optional
+    :type freq_lower_edge: float
-    :param freq_upper_edge: The upper frequency of the annotation. Optional; None if not specified in source.
+    :param freq_upper_edge: The upper frequency of the annotation.
-    :type freq_upper_edge: float, optional
+    :type freq_upper_edge: float
     :param label: The label that will be displayed with the bounding box in compatible viewers including IQEngine.
      Defaults to an emtpy string.
     :type label: str, optional
@@ -34,8 +34,8 @@ class Annotation:
         self,
         sample_start: int,
         sample_count: int,
-        freq_lower_edge: Optional[float] = None,
+        freq_lower_edge: float,
-        freq_upper_edge: Optional[float] = None,
+        freq_upper_edge: float,
         label: Optional[str] = "",
         comment: Optional[str] = "",
         detail: Optional[dict] = None,
@@ -43,8 +43,8 @@ class Annotation:
         """Initialize a new Annotation instance."""
         self.sample_start = int(sample_start)
         self.sample_count = int(sample_count)
-        self.freq_lower_edge = float(freq_lower_edge) if freq_lower_edge is not None else None
+        self.freq_lower_edge = float(freq_lower_edge)
-        self.freq_upper_edge = float(freq_upper_edge) if freq_upper_edge is not None else None
+        self.freq_upper_edge = float(freq_upper_edge)
         self.label = str(label)
         self.comment = str(comment)
 
@@ -62,8 +62,6 @@ class Annotation:
         :returns: True if valid, False if not.
         """
 
-        if self.freq_lower_edge is None or self.freq_upper_edge is None:
-            return self.sample_count > 0
         return self.sample_count > 0 and self.freq_lower_edge < self.freq_upper_edge
 
     def overlap(self, other):
@@ -75,14 +73,6 @@ class Annotation:
 
         :returns: The area of the overlap in samples*frequency, or 0 if they do not overlap."""
 
-        if (
-            self.freq_lower_edge is None
-            or self.freq_upper_edge is None
-            or other.freq_lower_edge is None
-            or other.freq_upper_edge is None
-        ):
-            return 0
-
         sample_overlap_start = max(self.sample_start, other.sample_start)
         sample_overlap_end = min(self.sample_start + self.sample_count, other.sample_start + other.sample_count)
 
@@ -101,8 +91,6 @@ class Annotation:
 
         :returns: sample length multiplied by bandwidth."""
 
-        if self.freq_lower_edge is None or self.freq_upper_edge is None:
-            return 0
         return self.sample_count * (self.freq_upper_edge - self.freq_lower_edge)
 
     def __eq__(self, other: Annotation) -> bool:
@@ -115,16 +103,13 @@ class Annotation:
 
         annotation_dict = {SigMFFile.START_INDEX_KEY: self.sample_start, SigMFFile.LENGTH_INDEX_KEY: self.sample_count}
 
-        metadata = {
+        annotation_dict["metadata"] = {
             SigMFFile.LABEL_KEY: self.label,
             SigMFFile.COMMENT_KEY: self.comment,
+            SigMFFile.FHI_KEY: self.freq_upper_edge,
+            SigMFFile.FLO_KEY: self.freq_lower_edge,
             "ria:detail": self.detail,
         }
-        if self.freq_upper_edge is not None:
-            metadata[SigMFFile.FHI_KEY] = self.freq_upper_edge
-        if self.freq_lower_edge is not None:
-            metadata[SigMFFile.FLO_KEY] = self.freq_lower_edge
-        annotation_dict["metadata"] = metadata
 
         if _is_jsonable(annotation_dict):
             return annotation_dict

src/ria_toolkit_oss/io/recording.py

@@ -175,15 +175,6 @@ def from_npy(file: os.PathLike | str, legacy: bool = False) -> Recording:
             )
             data = first  # already loaded without pickle (numeric array)
             metadata = np.load(f, allow_pickle=True).tolist()
-            # Normalize namespaced keys (e.g. "BlockGenerator:Foo:sample_rate") to
-            # their bare equivalents so downstream code can find them reliably.
-            _STANDARD_KEYS = {"sample_rate", "center_frequency", "bandwidth"}
-            if isinstance(metadata, dict):
-                for k in list(metadata):
-                    if ":" in k:
-                        bare = k.rsplit(":", 1)[-1]
-                        if bare in _STANDARD_KEYS and bare not in metadata:
-                            metadata[bare] = metadata[k]
             try:
                 annotations = list(np.load(f, allow_pickle=True))
             except EOFError:

src/ria_toolkit_oss/sdr/hackrf.py

@@ -58,7 +58,7 @@ class HackRF(SDR):
         :param channel: The channel the HackRF is set to. (Not actually used)
         :type channel: int
         :param gain_mode: 'absolute' passes gain directly to the sdr,
-            'relative' means that gain should be a negative value, and it will be subtracted from the max gain (40).
+        'relative' means that gain should be a negative value, and it will be subtracted from the max gain (40).
         :type gain_mode: str
         """
         print("Initializing RX")

src/ria_toolkit_oss/sdr/usrp.py

@@ -54,7 +54,7 @@ class USRP(SDR):
         :param channel: The channel the USRP is set to.
         :type channel: int
         :param gain_mode: 'absolute' passes gain directly to the sdr,
-            'relative' means that gain should be a negative value, and it will be subtracted from the max gain.
+        'relative' means that gain should be a negative value, and it will be subtracted from the max gain.
         :type gain_mode: str
         :param rx_buffer_size: Internal buffer size for receiving samples. Defaults to 960000.
         :type rx_buffer_size: int
@@ -285,7 +285,7 @@ class USRP(SDR):
         :param channel: The channel the USRP is set to.
         :type channel: int
         :param gain_mode: 'absolute' passes gain directly to the sdr,
-            'relative' means that gain should be a negative value, and it will be subtracted from the max gain.
+        'relative' means that gain should be a negative value, and it will be subtracted from the max gain.
         :type gain_mode: str
         """
 

src/ria_toolkit_oss/view/tools.py

@@ -32,15 +32,16 @@ def extract_metadata_fields(metadata):
 
 
 def set_path(output_path):
-    path = pathlib.Path(output_path)
+    split_path = output_path.split("/")
 
-    # If only filename provided (no directory), use default 'images' folder
+    if len(split_path) == 1:
-    if len(path.parts) == 1:
+        folder = "images"
-        folder = pathlib.Path("images")
+        file = split_path[0]
-        file = path.name
+    elif len(split_path) > 2:
+        file = split_path[-1]
+        folder = "/".join(split_path[:-1])
     else:
-        folder = path.parent
+        folder, file = split_path
-        file = path.name
 
     split_file = file.split(".")
     if len(split_file) == 2:
@@ -52,5 +53,5 @@ def set_path(output_path):
         extension = "png"
         file = file + ".png"
 
-    folder.mkdir(parents=True, exist_ok=True)
+    pathlib.Path(folder).mkdir(parents=True, exist_ok=True)
-    return str(folder / file), extension
+    return "/".join([folder, file]), extension

src/ria_toolkit_oss/view/view_signal.py

@@ -3,12 +3,11 @@ import os
 import textwrap
 from typing import Optional
 
-import matplotlib
 import matplotlib.pyplot as plt
 import numpy as np
-from matplotlib import gridspec, ticker
+from matplotlib import gridspec
 from matplotlib.patches import Patch
-from PIL import Image, UnidentifiedImageError
+from PIL import Image
 from scipy.fft import fft, fftshift
 from scipy.signal import spectrogram
 from scipy.signal.windows import hann
@@ -81,8 +80,6 @@ def view_annotations(
             return 0
 
     for annotation in sorted(annotations, key=_threshold_sort_key, reverse=True):
-        if annotation.freq_lower_edge is None or annotation.freq_upper_edge is None:
-            continue
         t_start = annotation.sample_start / sample_rate
         t_width = annotation.sample_count / sample_rate
         f_start = annotation.freq_lower_edge
@@ -188,7 +185,7 @@ def view_sig(
     logo: Optional[bool] = True,
     dark: Optional[bool] = True,
     spines: Optional[bool] = False,
-    title_fontsize: Optional[int] = 25,
+    title_fontsize: Optional[int] = 35,
     subtitle_fontsize: Optional[int] = 15,
 ) -> None:
     """
@@ -233,26 +230,11 @@ def view_sig(
     complex_signal = recording.data[0]
     sample_rate, center_frequency, _ = extract_metadata_fields(recording.metadata)
 
-    subplot_height = 3 * (plot_spectrogram) + 2 * (iq + frequency) + 3 * (constellation or metadata or logo)
+    subplot_height = 2 * (plot_spectrogram + iq + frequency) + 3 * (constellation or metadata or logo)
     subplot_width = max((constellation + metadata or 1), logo * 3)
 
     if dark:
         plt.style.use("dark_background")
-        matplotlib.rcParams.update(
-            {
-                "figure.facecolor": "#161616",
-                "axes.facecolor": "#161616",
-                "savefig.facecolor": "#161616",
-                "savefig.edgecolor": "#161616",
-                "font.size": 10,
-                "axes.titlesize": 15,
-                "axes.labelsize": 10,
-                "xtick.labelsize": 10,
-                "ytick.labelsize": 10,
-                "legend.frameon": False,
-                "legend.facecolor": "none",
-            }
-        )
         logo_path = os.path.dirname(__file__) + "/graphics/Qoherent-logo-white-transparent.png"
     else:
         plt.style.use("default")
@@ -270,8 +252,8 @@ def view_sig(
     plot_x_indx = 0
 
     if plot_spectrogram:
-        spec_ax = plt.subplot(gs[plot_y_indx : plot_y_indx + 3, :])
+        spec_ax = plt.subplot(gs[plot_y_indx : plot_y_indx + 2, :])
-        plot_y_indx = plot_y_indx + 3
+        plot_y_indx = plot_y_indx + 2
         fft_size = get_fft_size(plot_length=plot_length)
 
         _, t_spec, Sxx = spectrogram(
@@ -298,10 +280,7 @@ def view_sig(
         )
 
         set_spines(spec_ax, spines)
-        spec_ax.set_title("Spectrogram", loc="left", fontsize=subtitle_fontsize)
+        spec_ax.set_title("Spectrogram", loc="center", fontsize=subtitle_fontsize)
-        spec_ax.set_xlabel("Time (s)")
-        spec_ax.set_ylabel("Frequency (MHz)")
-        spec_ax.yaxis.set_major_formatter(ticker.FuncFormatter(lambda x, _: f"{x / 1e6:.1f}"))
 
     if iq:
         iq_ax = plt.subplot(gs[plot_y_indx : plot_y_indx + 2, :])
@@ -312,13 +291,12 @@ def view_sig(
 
         iq_ax.plot(t, plot_iq.real, color=COLORS["purple"], linewidth=0.6, alpha=0.8, label="I")
         iq_ax.plot(t, plot_iq.imag, color=COLORS["magenta"], linewidth=0.6, alpha=0.8, label="Q")
-        iq_ax.grid(True, alpha=0.2, linewidth=0.5)
+        iq_ax.grid(False)
 
         iq_ax.set_ylabel("Amplitude")
         iq_ax.set_xlim([min(t), max(t)])
         iq_ax.set_xlabel("Time (s)")
-        iq_ax.set_title("IQ Sample Plot", loc="left", fontsize=subtitle_fontsize)
+        iq_ax.set_title("IQ Sample Plot", fontsize=subtitle_fontsize)
-        iq_ax.legend(loc="upper right", fontsize=10)
         set_spines(iq_ax, spines)
 
     if frequency:
@@ -332,14 +310,10 @@ def view_sig(
         # Convert to dB
         spectrum_db = 20 * np.log10(spectrum + 1e-12)  # 20*log for magnitude
 
-        freqs = (
+        freqs = np.linspace(-sample_rate / 2, sample_rate / 2, len(complex_signal[:plot_length])) + center_frequency
-            np.linspace(-sample_rate / 2, sample_rate / 2, len(complex_signal[:plot_length])) + center_frequency
-        ) / 1e6
         freq_ax.plot(freqs, spectrum_db, color=COLORS["accent"], linewidth=0.8)
-        freq_ax.set_xlabel("Frequency (MHz)")
         freq_ax.set_ylabel("Magnitude (dB)")
-        freq_ax.grid(True, alpha=0.2, linewidth=0.5)
+        freq_ax.set_title("Frequency Spectrum (Windowed FFT)", fontsize=subtitle_fontsize)
-        freq_ax.set_title("Frequency Spectrum (Windowed FFT)", loc="left", fontsize=subtitle_fontsize)
         set_spines(freq_ax, spines)
 
     if constellation:
@@ -352,7 +326,7 @@ def view_sig(
         const_ax.set_ylim([-1 * dimension, dimension])
         const_ax.set_xlabel("In-phase (I)")
         const_ax.set_ylabel("Quadrature (Q)")
-        const_ax.set_title("Constellation", loc="left", fontsize=subtitle_fontsize)
+        const_ax.set_title("Constellation", fontsize=subtitle_fontsize)
         const_ax.set_aspect("equal")
 
         if not spines:
@@ -401,8 +375,8 @@ def view_sig(
             image = Image.open(logo_path)  # Open the PNG image using PIL
             logo_ax.imshow(image)
 
-        except (FileNotFoundError, UnidentifiedImageError, OSError) as exc:
+        except FileNotFoundError:
-            print(f"Warning, could not load logo image: {logo_path}. Reason: {exc}")
+            print(f"Warning, {logo_path} not found.")
 
     fig.subplots_adjust(
         left=0.1,  # Left margin

src/ria_toolkit_oss/view/view_signal_simple.py

@@ -119,19 +119,24 @@ def setup_style(*, labels_mode: bool = False, compact_mode: bool = False) -> Non
         label_font = 14
     else:
         base_font = 10
-        title_font = 15
+        title_font = 12
         label_font = 10
 
     matplotlib.rcParams.update(
         {
-            "figure.facecolor": "#161616",
+            "figure.facecolor": "#0f172a",
-            "axes.facecolor": "#161616",
+            "axes.facecolor": "#1e293b",
-            "savefig.facecolor": "#161616",
+            "axes.edgecolor": COLORS["muted"],
-            "savefig.edgecolor": "#161616",
+            "axes.labelcolor": COLORS["light"],
+            "text.color": COLORS["light"],
+            "xtick.color": COLORS["muted"],
+            "ytick.color": COLORS["muted"],
+            "grid.color": COLORS["muted"],
+            "grid.alpha": 0.3,
             "font.size": base_font,
             "axes.titlesize": title_font,
             "axes.labelsize": label_font,
-            "figure.titlesize": title_font + 4,
+            "figure.titlesize": title_font + 2,
             "legend.frameon": False,
             "legend.facecolor": "none",
             "xtick.labelsize": base_font,
@@ -189,7 +194,7 @@ def view_simple_sig(
     constellation_mode: Optional[bool] = False,
     labels_mode: Optional[bool] = False,
     slice: Optional[tuple] = None,
-    title: Optional[str] = "Signal Plot",
+    title: Optional[str] = "Signal",
 ):
     """
     Create a simple plot of various signal visualizations as a png or svg image.
@@ -232,7 +237,7 @@ def view_simple_sig(
     spec_signal = signal
 
     if compact_mode:
-        fig, (ax2, ax1) = plt.subplots(2, 1, figsize=(12, 6), gridspec_kw={"height_ratios": [5, 1]})
+        fig, (ax1, ax2) = plt.subplots(2, 1, figsize=(12, 6), gridspec_kw={"height_ratios": [1, 5]})
         show_title = False
         show_labels = False
         ax_constellation = ax_psd = None
@@ -248,24 +253,25 @@ def view_simple_sig(
         ax_psd = None
     else:
         if constellation_mode:
-            fig, ((ax2, ax1), (ax3, ax4)) = plt.subplots(2, 2, figsize=(16, 12))
+            fig, ((ax1, ax2), (ax3, ax4)) = plt.subplots(2, 2, figsize=(16, 12))
             ax_constellation, ax_psd = ax3, ax4
         else:
-            fig, (ax2, ax1) = plt.subplots(2, 1, figsize=(14, 10))
+            fig, (ax1, ax2) = plt.subplots(2, 1, figsize=(14, 10))
             ax_constellation = ax_psd = None
         show_title = True
         show_labels = labels_mode
 
     if show_title:
-        fig.suptitle(title, fontsize=25)
+        fig.suptitle(title, fontsize=16, color=COLORS["light"], y=0.96)
-    fig.patch.set_facecolor(matplotlib.rcParams["figure.facecolor"])
+    fig.patch.set_facecolor("#0f172a")
 
     total_duration_s = len(signal) / sample_rate_hz if sample_rate_hz else 0.0
     t_s = np.linspace(0, total_duration_s, len(display_signal)) if len(display_signal) else np.array([])
 
-    ax1.plot(t_s, display_signal.real, color=COLORS["purple"], linewidth=0.6, alpha=0.8, label="I")
+    ax1.plot(t_s, display_signal.real, color=COLORS["purple"], linewidth=0.8, alpha=0.8, label="I")
-    ax1.plot(t_s, display_signal.imag, color=COLORS["magenta"], linewidth=0.6, alpha=0.8, label="Q")
+    ax1.plot(t_s, display_signal.imag, color=COLORS["magenta"], linewidth=0.8, alpha=0.8, label="Q")
-    ax1.grid(True, alpha=0.2, linewidth=0.5)
+    ax1.set_xlim(0, total_duration_s)
+    ax1.grid(True, alpha=0.3)
 
     nfft, overlap = _get_nfft_size(signal=signal, fast_mode=fast_mode)
 
@@ -279,7 +285,7 @@ def view_simple_sig(
     )
 
     ax2.set_ylim(center_freq_hz - sample_rate_hz / 2, center_freq_hz + sample_rate_hz / 2)
-    ax1.set_xlim(ax2.get_xlim())
+    ax2.set_xlim(0, total_duration_s)
 
     if show_labels:
         if horizontal_mode:
@@ -288,25 +294,20 @@ def view_simple_sig(
             ax2.set_xlabel("Time (s)")
 
         ax1.set_ylabel("Amplitude")
-        ax1.set_title(f"IQ Sample Plot - {sdr} SDR", loc="left", pad=10, fontsize=15)
+        ax1.set_title(f"Time Series - {sdr} SDR", loc="left", pad=10)
-        ax1.legend(loc="upper right", fontsize=10)
+        ax1.legend(loc="upper right")
 
-        ax2.set_ylabel("Frequency (MHz)")
+        ax2.set_ylabel("Frequency (Hz)")
         ax2.set_title(
-            f"Spectrogram - {center_freq_hz / 1e6:.1f} MHz ± {sample_rate_hz / 2e6:.1f} MHz",
+            f"Spectrogram - {center_freq_hz / 1e6:.1f} MHz ± {sample_rate_hz / 2e6:.1f} MHz", loc="left", pad=10
-            loc="left",
-            pad=10,
-            fontsize=15,
         )
-        ax2.yaxis.set_major_formatter(matplotlib.ticker.FuncFormatter(lambda x, _: f"{x / 1e6:.1f}"))
+        yticks = ax2.get_yticks()
+        ax2.set_yticklabels([f"{y / 1e6:.1f}" for y in yticks])
     elif not compact_mode:
-        ax1.set_title("IQ Sample Plot", loc="left", pad=10, fontsize=15)
+        ax1.set_title("Time Series", loc="left", pad=10)
-        ax1.legend(loc="upper right", fontsize=10)
+        ax1.legend(loc="upper right", fontsize=8)
 
-        ax2.set_xlabel("Time (s)")
+        ax2.set_title("Spectrogram", loc="left", pad=10)
-        ax2.set_ylabel("Frequency (MHz)")
-        ax2.set_title("Spectrogram", loc="left", pad=10, fontsize=15)
-        ax2.yaxis.set_major_formatter(matplotlib.ticker.FuncFormatter(lambda x, _: f"{x / 1e6:.1f}"))
 
     _add_annotations(
         annotations=annotations,
@@ -338,8 +339,8 @@ def view_simple_sig(
         )
         ax_constellation.set_xlabel("In-phase (I)")
         ax_constellation.set_ylabel("Quadrature (Q)")
-        ax_constellation.set_title("Constellation", loc="left", fontsize=15)
+        ax_constellation.set_title("Constellation")
-        ax_constellation.grid(True, alpha=0.2, linewidth=0.5)
+        ax_constellation.grid(True, alpha=0.3)
         ax_constellation.set_aspect("equal")
 
     if ax_psd is not None:
@@ -350,11 +351,11 @@ def view_simple_sig(
         freqs = freqs + center_freq_hz
         spectrum_db = 10 * np.log10(spectrum + 1e-12)
 
-        ax_psd.plot(freqs / 1e6, spectrum_db, color=COLORS["accent"], linewidth=0.8)
+        ax_psd.plot(freqs / 1e6, spectrum_db, color=COLORS["accent"], linewidth=1.0)
         ax_psd.set_xlabel("Frequency (MHz)")
         ax_psd.set_ylabel("Power (dB)")
-        ax_psd.set_title("Power Spectral Density", loc="left", fontsize=15)
+        ax_psd.set_title("Power Spectral Density")
-        ax_psd.grid(True, alpha=0.2, linewidth=0.5)
+        ax_psd.grid(True, alpha=0.3)
 
     if compact_mode:
         ax1.set_xticks([])
@@ -366,20 +367,13 @@ def view_simple_sig(
     else:
         plt.tight_layout()
         if show_title:
-            plt.subplots_adjust(top=0.9)
+            plt.subplots_adjust(top=0.92)
 
     if saveplot:
         output_path, extension = set_path(output_path=output_path)
         dpi_value = _set_dpi(fast_mode=fast_mode, labels_mode=labels_mode, extension=extension)
 
-        plt.savefig(
+        plt.savefig(output_path, dpi=dpi_value, bbox_inches="tight", facecolor="#0f172a", edgecolor="none")
-            output_path,
-            dpi=dpi_value,
-            bbox_inches="tight",
-            pad_inches=0.3,
-            facecolor=matplotlib.rcParams["savefig.facecolor"],
-            edgecolor=matplotlib.rcParams["savefig.edgecolor"],
-        )
         print(f"Saved signal plot to {output_path}")
         return output_path
 

src/ria_toolkit_oss_cli/cli.py

@@ -2,57 +2,15 @@
 This module contains the main group for the ria toolkit oss CLI.
 """
 
-import subprocess
+import click
-import sys
-import warnings
 
-warnings.filterwarnings(
+from ria_toolkit_oss_cli.ria_toolkit_oss import commands
-    "ignore",
-    message="Unable to import Axes3D",
-    category=UserWarning,
-    module="matplotlib",
-)
-
-import click  # noqa: E402
-
-from ria_toolkit_oss_cli.ria_toolkit_oss import commands  # noqa: E402
 
 
-def _git_lfs_installed() -> bool:
+@click.group()
-    """Return True if git-lfs is available on PATH."""
-    try:
-        return (
-            subprocess.run(
-                ["git", "lfs", "version"],
-                capture_output=True,
-            ).returncode
-            == 0
-        )
-    except FileNotFoundError:
-        return False
-
-
-@click.group(invoke_without_command=True)
 @click.option("-v", "--verbose", is_flag=True, type=bool, help="Increase verbosity, especially useful for debugging.")
-@click.pass_context
+def cli(verbose):
-def cli(ctx, verbose):
+    pass
-    lfs_missing = not _git_lfs_installed()
-    if lfs_missing:
-        click.echo(
-            "Warning: git-lfs is not installed. RIA Hub projects require git-lfs to\n"
-            "track large binary files (models, recordings, datasets).\n"
-            "\n"
-            "  Linux:           sudo apt-get install git-lfs\n"
-            "  macOS:           brew install git-lfs\n"
-            "  Other platforms: https://git-lfs.com\n"
-            "\n"
-            "After installing, run: git lfs install",
-            err=True,
-        )
-    if ctx.invoked_subcommand is None:
-        if lfs_missing and sys.stdin.isatty():
-            click.pause(info="\nPress Enter to continue...", err=True)
-        click.echo(ctx.get_help())
 
 
 # Loop through project commands, binding them all to the CLI.

src/ria_toolkit_oss_cli/ria_toolkit_oss/_hub_auth.py

@@ -1,97 +0,0 @@
-"""Shared authentication and security helpers for RIA Hub API calls."""
-
-import base64
-import subprocess
-import urllib.error
-import urllib.parse
-import urllib.request
-
-import click
-
-DEFAULT_HUB = "https://riahub.ai"
-
-
-class _NoRedirectHandler(urllib.request.HTTPRedirectHandler):
-    """Block redirects on authenticated requests to prevent credential exfiltration.
-
-    urllib re-sends the Authorization header on same-host redirects by default.
-    A malicious server could redirect a POST to a different host to harvest
-    credentials. We refuse all redirects — API clients should not encounter them
-    in normal operation.
-    """
-
-    def redirect_request(self, req, fp, code, msg, headers, newurl):
-        raise urllib.error.URLError(f"Unexpected redirect ({code}) to {newurl} — aborting to protect credentials")
-
-
-def hub_opener() -> urllib.request.OpenerDirector:
-    """Return a urllib opener that blocks redirects."""
-    return urllib.request.build_opener(_NoRedirectHandler)
-
-
-def warn_if_insecure(hub: str) -> None:
-    """Warn when credentials would be sent over plain HTTP to a non-localhost host."""
-    parsed = urllib.parse.urlparse(hub)
-    if parsed.scheme == "http":
-        host = parsed.hostname or ""
-        if host not in ("localhost", "127.0.0.1", "::1"):
-            click.echo(
-                f"Warning: sending credentials over plain HTTP to {host}. " "Use HTTPS in production.",
-                err=True,
-            )
-
-
-def basic_auth(username: str, password: str) -> str:
-    return "Basic " + base64.b64encode(f"{username}:{password}".encode()).decode()
-
-
-def get_stored_credentials(hub_url: str) -> tuple[str | None, str | None]:
-    """Ask git credential fill for stored creds. Returns (username, password) or (None, None)."""
-    parsed = urllib.parse.urlparse(hub_url)
-    payload = f"protocol={parsed.scheme}\nhost={parsed.netloc}\n\n"
-    try:
-        result = subprocess.run(
-            ["git", "credential", "fill"],
-            input=payload,
-            capture_output=True,
-            text=True,
-            timeout=5,
-        )
-        creds = {}
-        for line in result.stdout.splitlines():
-            # Partition on the FIRST '=' only so passwords containing '=' are preserved.
-            k, sep, v = line.partition("=")
-            if sep:
-                creds[k.strip()] = v  # keep value verbatim
-        return creds.get("username"), creds.get("password")
-    except Exception:
-        return None, None
-
-
-def store_credentials(hub_url: str, username: str, password: str) -> None:
-    """Cache credentials via git credential approve (uses the system keychain/store)."""
-    parsed = urllib.parse.urlparse(hub_url)
-    payload = (
-        f"protocol={parsed.scheme}\n" f"host={parsed.netloc}\n" f"username={username}\n" f"password={password}\n\n"
-    )
-    try:
-        subprocess.run(
-            ["git", "credential", "approve"],
-            input=payload,
-            capture_output=True,
-            text=True,
-            timeout=5,
-        )
-    except Exception:
-        pass  # non-fatal — next push just prompts again
-
-
-def resolve_credentials(hub: str) -> tuple[str, str]:
-    """Return (username, password), prompting interactively if not cached."""
-    username, password = get_stored_credentials(hub)
-    if username and password:
-        return username, password
-    click.echo(f"No stored credentials found for {hub}.")
-    username = click.prompt("RIA Hub username")
-    password = click.prompt("Password / personal access token", hide_input=True)
-    return username, password

src/ria_toolkit_oss_cli/ria_toolkit_oss/annotate.py

@@ -51,7 +51,7 @@ def detect_input_format(filepath):
         raise click.ClickException(f"Unknown format for '{filepath}'. Supported: .sigmf, .npy, .wav, .blue")
 
 
-def determine_output_path(input_path, output_path, fmt, overwrite):
+def determine_output_path(input_path, output_path, fmt, quiet, overwrite):
     input_path = Path(input_path)
     input_is_annotated = input_path.stem.endswith("_annotated")
 
@@ -63,20 +63,24 @@ def determine_output_path(input_path, output_path, fmt, overwrite):
     else:
         target = input_path.with_name(f"{input_path.stem}_annotated{input_path.suffix}")
 
-    final_path = normalize_sigmf_path(target) if fmt == "sigmf" else target
+    if fmt == "sigmf":
+        final_path = normalize_sigmf_path(target)
+        if not quiet:
+            click.echo(f"Saving SigMF metadata to: {final_path}")
+    else:
+        final_path = target
+        if not quiet:
+            click.echo(f"Saving to: {final_path}")
 
-    if final_path.exists() and not overwrite:
+    # Always allow writing to _annotated files; guard against overwriting originals
-        raise click.ClickException(f"{final_path} already exists. Use --overwrite to replace it.")
+    target_is_annotated = final_path.stem.endswith("_annotated")
+    if final_path.exists() and not target_is_annotated and final_path != input_path:
+        click.echo(f"Error: {final_path} is not an annotated file and cannot be overwritten.", err=True)
+        return None
 
     return final_path
 
 
-def check_output_available(input_path, output_path, overwrite):
-    """Raise ClickException before any work begins if the output file already exists."""
-    fmt = detect_input_format(Path(input_path))
-    determine_output_path(input_path=input_path, output_path=output_path, fmt=fmt, overwrite=overwrite)
-
-
 def save_recording_auto(recording, output_path, input_path, quiet=False, overwrite=False):
     """Save recording, auto-detecting format from extension.
 
@@ -86,13 +90,10 @@ def save_recording_auto(recording, output_path, input_path, quiet=False, overwri
     input_path = Path(input_path)
     fmt = detect_input_format(input_path)
 
-    output_path = determine_output_path(input_path=input_path, output_path=output_path, fmt=fmt, overwrite=overwrite)
+    # Determine output path
-
+    output_path = determine_output_path(
-    if not quiet:
+        input_path=input_path, output_path=output_path, fmt=fmt, quiet=quiet, overwrite=overwrite
-        if fmt == "sigmf":
+    )
-            click.echo(f"Saving SigMF metadata to: {output_path}")
-        else:
-            click.echo(f"Saving to: {output_path}")
 
     if fmt == "sigmf":
         # Normalize path for SigMF
@@ -256,11 +257,7 @@ def list(input, verbose):
             user_comment = ann.comment or ""
 
         # Basic info
-        freq_range = (
+        freq_range = f"{format_frequency(ann.freq_lower_edge)} - {format_frequency(ann.freq_upper_edge)}"
-            f"{format_frequency(ann.freq_lower_edge)} - {format_frequency(ann.freq_upper_edge)}"
-            if ann.freq_lower_edge is not None and ann.freq_upper_edge is not None
-            else "N/A"
-        )
         click.echo(
             f"  [{i}] Samples {format_sample_count(ann.sample_start)}-"
             f"{format_sample_count(ann.sample_start + ann.sample_count)}: {ann.label}"
@@ -315,8 +312,6 @@ def add(input, start, count, label, freq_lower, freq_upper, comment, annotation_
     except Exception as e:
         raise click.ClickException(f"Failed to load recording: {e}")
 
-    check_output_available(input, output, overwrite)
-
     # Validate sample range
     n_samples = len(recording.data[0])
     if start < 0:
@@ -368,9 +363,12 @@ def add(input, start, count, label, freq_lower, freq_upper, comment, annotation_
         if comment:
             click.echo(f"  Comment: {comment}")
 
-    save_recording_auto(recording, output, input, quiet, overwrite)
+    try:
-    if not quiet:
+        save_recording_auto(recording, output, input, quiet, overwrite)
-        click.echo("  ✓ Saved")
+        if not quiet:
+            click.echo("  ✓ Saved")
+    except Exception as e:
+        raise click.ClickException(f"Failed to save: {e}")
 
 
 # ============================================================================
@@ -468,6 +466,8 @@ def clear(input, output, overwrite, force, quiet):
     if not quiet:
         click.echo(f"\nCleared {count_before} annotation(s)")
 
+    recording._annotations = []
+
     try:
         save_recording_auto(recording, output_path=input, input_path=input, quiet=quiet, overwrite=True)
         if not quiet:
@@ -503,9 +503,6 @@ def clear(input, output, overwrite, force, quiet):
     default="standalone",
     help="Annotation type",
 )
-@click.option(
-    "--sample-rate", type=float, default=None, help="Sample rate in Hz (overrides metadata; required if not in file)"
-)
 @click.option("--output", "-o", type=click.Path(), help="Output file path")
 @click.option("--overwrite", is_flag=True, help="Overwrite input file (non-SigMF only)")
 @click.option("--quiet", is_flag=True, help="Quiet mode")
@@ -520,7 +517,6 @@ def energy(
     nfft,
     obw_power,
     annotation_type,
-    sample_rate,
     output,
     overwrite,
     quiet,
@@ -543,11 +539,8 @@ def energy(
       ria annotate energy signal.npy --threshold 1.5 --min-distance 10000
       ria annotate energy signal.sigmf-data --freq-method obw
       ria annotate energy signal.sigmf-data --freq-method full-detected
-      ria annotate energy signal.npy --sample-rate 1e6
 
     """
-    check_output_available(input, output, overwrite)
-
     try:
         recording = load_recording(input)
         if not quiet:
@@ -555,15 +548,6 @@ def energy(
     except Exception as e:
         raise click.ClickException(f"Failed to load recording: {e}")
 
-    if sample_rate is not None:
-        recording.sample_rate = sample_rate
-
-    if recording.sample_rate is None:
-        raise click.ClickException(
-            "Recording metadata does not contain a sample rate. "
-            "Provide it with --sample-rate (e.g. --sample-rate 1e6)."
-        )
-
     if not quiet:
         click.echo("\nDetecting signals using energy-based method...")
         click.echo("  Time detection:")
@@ -591,13 +575,13 @@ def energy(
 
         if not quiet:
             click.echo(f"  ✓ Added {added} annotation(s)")
+
+        save_recording_auto(recording, output, input, quiet, overwrite)
+        if not quiet:
+            click.echo("  ✓ Saved")
     except Exception as e:
         raise click.ClickException(f"Energy detection failed: {e}")
 
-    save_recording_auto(recording, output, input, quiet, overwrite)
-    if not quiet:
-        click.echo("  ✓ Saved")
-
 
 # ============================================================================
 # CUSUM detection subcommand
@@ -617,13 +601,10 @@ def energy(
     default="standalone",
     help="Annotation type",
 )
-@click.option(
-    "--sample-rate", type=float, default=None, help="Sample rate in Hz (overrides metadata; required if not in file)"
-)
 @click.option("--output", "-o", type=click.Path(), help="Output file path")
 @click.option("--overwrite", is_flag=True, help="Overwrite input file (non-SigMF only)")
 @click.option("--quiet", is_flag=True, help="Quiet mode")
-def cusum(input, label, min_duration, window_size, tolerance, annotation_type, sample_rate, output, overwrite, quiet):
+def cusum(input, label, min_duration, window_size, tolerance, annotation_type, output, overwrite, quiet):
     """Auto-detect segments using CUSUM method.
 
     Detects signal state changes (on/off, amplitude transitions). Best for
@@ -635,10 +616,7 @@ def cusum(input, label, min_duration, window_size, tolerance, annotation_type, s
     Examples:
       ria annotate cusum signal.sigmf-data --min-duration 5.0
       ria annotate cusum data.npy --min-duration 10.0 --label state
-      ria annotate cusum data.npy --sample-rate 1e6
     """
-    check_output_available(input, output, overwrite)
-
     try:
         recording = load_recording(input)
         if not quiet:
@@ -646,15 +624,6 @@ def cusum(input, label, min_duration, window_size, tolerance, annotation_type, s
     except Exception as e:
         raise click.ClickException(f"Failed to load recording: {e}")
 
-    if sample_rate is not None:
-        recording.sample_rate = sample_rate
-
-    if recording.sample_rate is None:
-        raise click.ClickException(
-            "Recording metadata does not contain a sample rate. "
-            "Provide it with --sample-rate (e.g. --sample-rate 1e6)."
-        )
-
     if not quiet:
         click.echo("\nDetecting segments using CUSUM...")
         click.echo(f"  Min duration: {min_duration} ms")
@@ -675,13 +644,13 @@ def cusum(input, label, min_duration, window_size, tolerance, annotation_type, s
 
         if not quiet:
             click.echo(f"  ✓ Added {added} annotation(s)")
+
+        save_recording_auto(recording, output, input, quiet, overwrite)
+        if not quiet:
+            click.echo("  ✓ Saved")
     except Exception as e:
         raise click.ClickException(f"CUSUM detection failed: {e}")
 
-    save_recording_auto(recording, output, input, quiet, overwrite)
-    if not quiet:
-        click.echo("  ✓ Saved")
-
 
 # ============================================================================
 # Threshold detection subcommand
@@ -706,13 +675,10 @@ def cusum(input, label, min_duration, window_size, tolerance, annotation_type, s
     help="Annotation type",
 )
 @click.option("--channel", type=int, default=0, help="Channel index to annotate (default: 0)")
-@click.option(
-    "--sample-rate", type=float, default=None, help="Sample rate in Hz (overrides metadata; required if not in file)"
-)
 @click.option("--output", "-o", type=click.Path(), help="Output file path")
 @click.option("--overwrite", is_flag=True, help="Overwrite input file (non-SigMF only)")
 @click.option("--quiet", is_flag=True, help="Quiet mode")
-def threshold(input, threshold, label, window_size, annotation_type, channel, sample_rate, output, overwrite, quiet):
+def threshold(input, threshold, label, window_size, annotation_type, channel, output, overwrite, quiet):
     """Auto-detect signals using threshold method.
 
     Detects samples above a percentage of maximum magnitude. Best for simple
@@ -722,13 +688,10 @@ def threshold(input, threshold, label, window_size, annotation_type, channel, sa
     Examples:
       ria annotate threshold signal.sigmf-data --threshold 0.7 --label wifi
       ria annotate threshold data.npy --threshold 0.5 --window-size 2048
-      ria annotate threshold data.npy --threshold 0.4 --sample-rate 1e6
     """
     if not (0.0 <= threshold <= 1.0):
         raise click.ClickException(f"--threshold must be between 0.0 and 1.0, got {threshold}")
 
-    check_output_available(input, output, overwrite)
-
     try:
         recording = load_recording(input)
         if not quiet:
@@ -736,21 +699,11 @@ def threshold(input, threshold, label, window_size, annotation_type, channel, sa
     except Exception as e:
         raise click.ClickException(f"Failed to load recording: {e}")
 
-    if sample_rate is not None:
-        recording.sample_rate = sample_rate
-
-    if recording.sample_rate is None:
-        raise click.ClickException(
-            "Recording metadata does not contain a sample rate. "
-            "Provide it with --sample-rate (e.g. --sample-rate 1e6)."
-        )
-
     if not quiet:
         click.echo("\nDetecting signals using threshold qualifier...")
         click.echo(f"  Threshold: {threshold * 100:.1f}% of max magnitude")
         click.echo(f"  Window size: {'auto (1ms)' if window_size is None else f'{window_size} samples'}")
         click.echo(f"  Channel: {channel}")
-        click.echo(f"  Sample rate: {recording.sample_rate:.0f} Hz")
 
     try:
         initial_count = len(recording.annotations)
@@ -766,13 +719,13 @@ def threshold(input, threshold, label, window_size, annotation_type, channel, sa
 
         if not quiet:
             click.echo(f"  ✓ Added {added} annotation(s)")
+
+        save_recording_auto(recording, output, input, quiet, overwrite)
+        if not quiet:
+            click.echo("  ✓ Saved")
     except Exception as e:
         raise click.ClickException(f"Threshold detection failed: {e}")
 
-    save_recording_auto(recording, output, input, quiet, overwrite)
-    if not quiet:
-        click.echo("  ✓ Saved")
-
 
 # ============================================================================
 # Separate subcommand (Phase 2: Parallel signal separation)
@@ -785,30 +738,11 @@ def threshold(input, threshold, label, window_size, annotation_type, channel, sa
 @click.option("--nfft", type=int, default=65536, help="FFT size for spectral analysis")
 @click.option("--noise-threshold-db", type=float, help="Noise floor threshold in dB (auto-estimated if not specified)")
 @click.option("--min-component-bw", type=float, default=50e3, help="Min component bandwidth in Hz")
-@click.option(
-    "--sample-rate", type=float, default=None, help="Sample rate in Hz (overrides metadata; required if not in file)"
-)
 @click.option("--output", "-o", type=click.Path(), help="Output file path")
 @click.option("--overwrite", is_flag=True, help="Overwrite input file (non-SigMF only)")
 @click.option("--quiet", is_flag=True, help="Quiet mode")
 @click.option("--verbose", is_flag=True, help="Verbose output (show detected components)")
-def _log_separate_start(quiet, recording, indices_list, nfft, noise_threshold_db, min_component_bw):
+def separate(input, indices, nfft, noise_threshold_db, min_component_bw, output, overwrite, quiet, verbose):
-    if not quiet:
-        click.echo("\nSplitting annotations by frequency components...")
-        click.echo(f"  Input annotations: {len(recording.annotations)}")
-        if indices_list:
-            click.echo(f"  Splitting indices: {indices_list}")
-        click.echo(f"  FFT size: {nfft}")
-        if noise_threshold_db is not None:
-            click.echo(f"  Noise threshold: {noise_threshold_db} dB")
-        else:
-            click.echo("  Noise threshold: auto-estimated")
-        click.echo(f"  Min component BW: {format_frequency(min_component_bw)}")
-
-
-def separate(
-    input, indices, nfft, noise_threshold_db, min_component_bw, sample_rate, output, overwrite, quiet, verbose
-):
     """
     Auto-detect parallel frequency-offset signals and split into sub-bands.
 
@@ -834,8 +768,6 @@ def separate(
       ria annotate separate signal.npy --min-component-bw 100000
 
     """
-    check_output_available(input, output, overwrite)
-
     try:
         recording = load_recording(input)
         if not quiet:
@@ -843,15 +775,6 @@ def separate(
     except Exception as e:
         raise click.ClickException(f"Failed to load recording: {e}")
 
-    if sample_rate is not None:
-        recording.sample_rate = sample_rate
-
-    if recording.sample_rate is None:
-        raise click.ClickException(
-            "Recording metadata does not contain a sample rate. "
-            "Provide it with --sample-rate (e.g. --sample-rate 1e6)."
-        )
-
     # Parse indices if specified
     indices_list = get_indices_list(indices=indices, recording=recording)
 
@@ -860,7 +783,17 @@ def separate(
             click.echo("No annotations to split")
         return
 
-    _log_separate_start(quiet, recording, indices_list, nfft, noise_threshold_db, min_component_bw)
+    if not quiet:
+        click.echo("\nSplitting annotations by frequency components...")
+        click.echo(f"  Input annotations: {len(recording.annotations)}")
+        if indices_list:
+            click.echo(f"  Splitting indices: {indices_list}")
+        click.echo(f"  FFT size: {nfft}")
+        if noise_threshold_db is not None:
+            click.echo(f"  Noise threshold: {noise_threshold_db} dB")
+        else:
+            click.echo("  Noise threshold: auto-estimated")
+        click.echo(f"  Min component BW: {format_frequency(min_component_bw)}")
 
     try:
         initial_count = len(recording.annotations)
@@ -882,19 +815,14 @@ def separate(
                 click.echo("\n  Details:")
                 for i in range(initial_count, final_count):
                     ann = recording.annotations[i]
-                    freq_range = (
+                    freq_range = f"{format_frequency(ann.freq_lower_edge)} - {format_frequency(ann.freq_upper_edge)}"
-                        f"{format_frequency(ann.freq_lower_edge)} - {format_frequency(ann.freq_upper_edge)}"
-                        if ann.freq_lower_edge is not None and ann.freq_upper_edge is not None
-                        else "N/A"
-                    )
                     click.echo(
                         f"    [{i}] samples {format_sample_count(ann.sample_start)}-"
                         f"{format_sample_count(ann.sample_start + ann.sample_count)}: {freq_range}"
                     )
 
+        save_recording_auto(recording, output, input, quiet, overwrite)
+        if not quiet:
+            click.echo("  ✓ Saved")
     except Exception as e:
         raise click.ClickException(f"Spectral separation failed: {e}")
-
-    save_recording_auto(recording, output, input, quiet, overwrite)
-    if not quiet:
-        click.echo("  ✓ Saved")

src/ria_toolkit_oss_cli/ria_toolkit_oss/commands.py

@@ -16,11 +16,9 @@ from .generate import generate
 # from .generate import generate
 from .init import init
 from .serve import serve
-from .setup_repo import setup_repo
 from .split import split
 from .transform import transform
 from .transmit import transmit
-from .upload import upload
 from .view import view
 
 # Aliases

src/ria_toolkit_oss_cli/ria_toolkit_oss/setup_repo.py

@@ -1,401 +0,0 @@
-"""ria setup_repo — create and configure a RIA Hub Project repo."""
-
-import json
-import os
-import re
-import subprocess
-import sys
-import urllib.error
-import urllib.parse
-import urllib.request
-
-import click
-
-from ._hub_auth import (
-    DEFAULT_HUB,
-    _NoRedirectHandler,
-    basic_auth,
-    resolve_credentials,
-    store_credentials,
-    warn_if_insecure,
-)
-
-RIA_LFS_RULES = [
-    ("*.pt", "filter=lfs diff=lfs merge=lfs -text"),
-    ("*.pth", "filter=lfs diff=lfs merge=lfs -text"),
-    ("*.onnx", "filter=lfs diff=lfs merge=lfs -text"),
-    ("*.sigmf", "filter=lfs diff=lfs merge=lfs -text"),
-    ("*.sigmf-data", "filter=lfs diff=lfs merge=lfs -text"),
-    ("*.sigmf-meta", "filter=lfs diff=lfs merge=lfs -text"),
-    ("*.npy", "filter=lfs diff=lfs merge=lfs -text"),
-    ("*.npz", "filter=lfs diff=lfs merge=lfs -text"),
-    ("*.h5", "filter=lfs diff=lfs merge=lfs -text"),
-    ("*.hdf5", "filter=lfs diff=lfs merge=lfs -text"),
-    ("*.bin", "filter=lfs diff=lfs merge=lfs -text"),
-    ("*.pkl", "filter=lfs diff=lfs merge=lfs -text"),
-]
-
-# Repo names must be safe directory names and valid git remote path components.
-_SAFE_NAME_RE = re.compile(r"^[A-Za-z0-9._-]{1,100}$")
-
-
-# ---------------------------------------------------------------------------
-# API helpers
-# ---------------------------------------------------------------------------
-
-
-def _api_request(
-    hub: str,
-    path: str,
-    method: str,
-    username: str,
-    password: str,
-    body: dict | None = None,
-) -> tuple[dict, int]:
-    """
-    Make an authenticated request to the RIA Hub API.
-    Returns (parsed_response_body, http_status_code).
-    Status 0 means a network/connection error.
-    Credentials are sent as HTTP Basic auth — safe over HTTPS and localhost HTTP.
-    Redirects are blocked to prevent credential exfiltration.
-    """
-    url = f"{hub.rstrip('/')}/api/v1{path}"
-    data = json.dumps(body).encode() if body is not None else None
-    req = urllib.request.Request(url, data=data, method=method)
-    req.add_header("Content-Type", "application/json")
-    req.add_header("Authorization", basic_auth(username, password))
-
-    opener = urllib.request.build_opener(_NoRedirectHandler)
-    try:
-        with opener.open(req, timeout=15) as resp:
-            return json.loads(resp.read() or b"{}"), resp.status
-    except urllib.error.HTTPError as e:
-        try:
-            resp_body = json.loads(e.read() or b"{}")
-        except Exception:
-            resp_body = {}
-        return resp_body, e.code
-    except urllib.error.URLError as e:
-        return {"message": str(e.reason)}, 0
-
-
-def _get_authenticated_username(hub: str, username: str, password: str) -> str | None:
-    """Return the login name of the authenticated user from GET /api/v1/user.
-
-    This is the canonical username for URL construction — it may differ from
-    git config user.name which is a display name, not a login.
-    """
-    body, status = _api_request(hub, "/user", "GET", username, password)
-    if status == 200:
-        return body.get("login")
-    return None
-
-
-def _repo_exists(hub: str, owner: str, name: str, username: str, password: str) -> bool:
-    body, status = _api_request(
-        hub,
-        f"/repos/{urllib.parse.quote(owner, safe='')}/{urllib.parse.quote(name, safe='')}",
-        "GET",
-        username,
-        password,
-    )
-    return status == 200
-
-
-def _create_repo_on_hub(hub: str, name: str, username: str, password: str, private: bool) -> bool:
-    """Create an RIA Hub Project repo via API.
-
-    Returns True if the repo was freshly created (server seeded README.md and
-    .gitattributes via auto_init + is_ria), False if the hub was unreachable
-    (local fallback needed). Exits on fatal errors (auth, quota, name taken).
-    """
-    body, status = _api_request(
-        hub,
-        "/user/repos",
-        "POST",
-        username,
-        password,
-        {
-            "name": name,
-            "auto_init": True,
-            "is_ria": True,
-            "private": private,
-            "default_branch": "main",
-        },
-    )
-
-    if status == 201:
-        click.echo(f"Repository '{name}' created on RIA Hub.")
-        return True
-
-    if status == 0:
-        click.echo(
-            f"Warning: could not reach RIA Hub at {hub}: {body.get('message', 'connection failed')}",
-            err=True,
-        )
-        click.echo("Continuing with local setup only — create the repo manually on RIA Hub.", err=True)
-        return False
-
-    msg = body.get("message", "")
-
-    if status == 401:
-        click.echo("Error: authentication failed — check your username/password.", err=True)
-        sys.exit(1)
-
-    if status in (403, 413) or "quota" in msg.lower() or "limit" in msg.lower():
-        click.echo("Error: cannot create repository — storage quota or account limit reached.", err=True)
-        if msg:
-            click.echo(f"  Server message: {msg}", err=True)
-        sys.exit(1)
-
-    if status == 422 or "already exist" in msg.lower():
-        click.echo(f"Repository '{name}' already exists on RIA Hub.")
-        return False
-
-    click.echo(f"Error creating repository (HTTP {status}): {msg}", err=True)
-    sys.exit(1)
-
-
-# ---------------------------------------------------------------------------
-# Local git helpers
-# ---------------------------------------------------------------------------
-
-
-def _tracked_patterns(ga_path: str) -> set:
-    if not os.path.exists(ga_path):
-        return set()
-    patterns = set()
-    with open(ga_path, encoding="utf-8") as f:
-        for line in f:
-            line = line.strip()
-            if not line or line.startswith("#"):
-                continue
-            m = re.match(r"^(\S+)\s+", line)
-            if m:
-                patterns.add(m.group(1))
-    return patterns
-
-
-def _write_local_ria_files(repo_path: str, repo_name: str) -> None:
-    """Seed README.md and .gitattributes locally (used when hub is unreachable or --no-remote)."""
-    # README
-    for candidate in ("README.md", "README.rst", "README.txt", "README"):
-        if os.path.exists(os.path.join(repo_path, candidate)):
-            click.echo(f"README: {candidate} already exists, skipping")
-            break
-    else:
-        with open(os.path.join(repo_path, "README.md"), "w", encoding="utf-8") as f:
-            f.write(
-                f"# {repo_name}\n"
-                "\n"
-                "A RIA Hub project.\n"
-                "\n"
-                "## Description\n"
-                "\n"
-                "<!-- Add your project description here -->\n"
-                "\n"
-                "## Contents\n"
-                "\n"
-                "<!-- Describe the signals, models, or datasets in this repository -->\n"
-            )
-        click.echo("README.md: created")
-
-    # .gitattributes
-    ga_path = os.path.join(repo_path, ".gitattributes")
-    existing = _tracked_patterns(ga_path)
-    new_rules = [(p, a) for p, a in RIA_LFS_RULES if p not in existing]
-
-    if new_rules:
-        existing_content = ""
-        if os.path.exists(ga_path):
-            with open(ga_path, encoding="utf-8") as f:
-                existing_content = f.read()
-
-        separator = "" if (not existing_content or existing_content.endswith("\n")) else "\n"
-        addition = separator + "".join(f"{pattern} {attrs}\n" for pattern, attrs in new_rules)
-
-        with open(ga_path, "a", encoding="utf-8") as f:
-            f.write(addition)
-        click.echo(f".gitattributes: {len(new_rules)} rule(s) added")
-    else:
-        click.echo(".gitattributes: all RIA Hub rules are already present")
-
-
-def _git(repo_path: str, *args: str, check: bool = True) -> subprocess.CompletedProcess:
-    return subprocess.run(
-        ["git", "-C", repo_path, *args],
-        capture_output=True,
-        text=True,
-        check=check,
-    )
-
-
-def _resolve_path_and_name(name: str | None, local_path: str | None) -> tuple[str, str]:
-    if local_path:
-        repo_path = os.path.abspath(local_path)
-        repo_name = name or os.path.basename(repo_path)
-    elif name:
-        repo_path = os.path.abspath(name)
-        repo_name = name
-    else:
-        repo_path = os.path.abspath(".")
-        repo_name = os.path.basename(repo_path)
-    return repo_path, repo_name
-
-
-def _resolve_owner(hub: str, username: str | None, password: str | None, owner: str | None) -> str:
-    if not owner and username and password:
-        api_login = _get_authenticated_username(hub, username, password)
-        owner = api_login or username
-    return owner or "unknown"
-
-
-def _git_init(repo_path: str) -> None:
-    if os.path.isdir(os.path.join(repo_path, ".git")):
-        return
-    result = _git(repo_path, "init", "-b", "main", check=False)
-    if result.returncode != 0:
-        # Older git (< 2.28) doesn't support -b; fall back and rename.
-        _git(repo_path, "init")
-        _git(repo_path, "symbolic-ref", "HEAD", "refs/heads/main")
-    click.echo("git init: done (branch: main)")
-
-
-def _configure_remote(
-    repo_path: str, hub: str, resolved_owner: str, repo_name: str, username: str | None, no_remote: bool
-) -> None:
-    if no_remote or not username:
-        click.echo(
-            f"Skipped remote setup. Add it manually:\n"
-            f"  git -C {repo_path} remote add origin "
-            f"{hub.rstrip('/')}/{resolved_owner}/{repo_name}.git"
-        )
-        return
-    remote_url = f"{hub.rstrip('/')}/{resolved_owner}/{repo_name}.git"
-    existing = _git(repo_path, "remote", "get-url", "origin", check=False)
-    if existing.returncode == 0:
-        existing_url = existing.stdout.strip()
-        if existing_url == remote_url:
-            click.echo(f"remote origin: {remote_url} (already set)")
-        else:
-            click.echo(
-                f"remote 'origin' already points to {existing_url}.\n"
-                f"  To update: git remote set-url origin {remote_url}"
-            )
-    else:
-        _git(repo_path, "remote", "add", "origin", remote_url)
-        click.echo(f"remote origin: {remote_url}")
-
-
-# ---------------------------------------------------------------------------
-# Command
-# ---------------------------------------------------------------------------
-
-
-@click.command("setup_repo")
-@click.argument("name", required=False)
-@click.option(
-    "--path", "local_path", default=None, help="Local directory (default: current dir, or created from NAME)."
-)
-@click.option("--hub", default=DEFAULT_HUB, show_default=True, metavar="URL", help="RIA Hub base URL.")
-@click.option(
-    "--owner",
-    default=None,
-    metavar="USER",
-    help="RIA Hub login username (default: looked up from the API using your credentials).",
-)
-@click.option("--private", is_flag=True, default=False, help="Create the repository as private.")
-@click.option(
-    "--no-remote", is_flag=True, default=False, help="Skip creating the repository on RIA Hub (local setup only)."
-)
-def setup_repo(
-    name: str | None,
-    local_path: str | None,
-    hub: str,
-    owner: str | None,
-    private: bool,
-    no_remote: bool,
-) -> None:
-    """Create and configure a RIA Hub Project repo.
-
-    NAME is the repository name. If the local directory does not exist or is
-    not a git repo, it will be initialised automatically. Credentials are
-    retrieved from git's credential store — no token setup required if you
-    have used RIA Hub with git before.
-
-    \b
-    Examples:
-      ria setup_repo my-dataset
-      ria setup_repo my-dataset --hub https://riahub.example.com
-      ria setup_repo --path ./existing-dir
-      ria setup_repo my-dataset --private
-    """
-    repo_path, repo_name = _resolve_path_and_name(name, local_path)
-
-    if not _SAFE_NAME_RE.match(repo_name):
-        click.echo(
-            f"Error: '{repo_name}' is not a valid repository name.\n"
-            "Use only letters, numbers, hyphens, underscores, and dots (max 100 chars).",
-            err=True,
-        )
-        sys.exit(1)
-
-    if not no_remote:
-        warn_if_insecure(hub)
-
-    username, password = (None, None) if no_remote else resolve_credentials(hub)
-    resolved_owner = _resolve_owner(hub, username, password, owner)
-
-    # newly_created=True means the server ran auto_init+is_ria and seeded
-    # README.md + .gitattributes in the initial commit; local setup pulls
-    # those files via fetch rather than writing them from scratch.
-    newly_created = False
-    if not no_remote and username and password:
-        if _repo_exists(hub, resolved_owner, repo_name, username, password):
-            click.echo(f"Repository '{resolved_owner}/{repo_name}' already exists on RIA Hub.")
-        else:
-            newly_created = _create_repo_on_hub(hub, repo_name, username, password, private)
-        store_credentials(hub, username, password)
-
-    if not os.path.exists(repo_path):
-        os.makedirs(repo_path)
-        click.echo(f"Created directory: {repo_path}")
-
-    _git_init(repo_path)
-
-    if subprocess.run(["git", "lfs", "version"], capture_output=True).returncode != 0:
-        click.echo(
-            "Error: git-lfs is not installed.\n"
-            "  Linux:           sudo apt-get install git-lfs\n"
-            "  macOS:           brew install git-lfs\n"
-            "  Other platforms: https://git-lfs.com",
-            err=True,
-        )
-        sys.exit(1)
-
-    _git(repo_path, "lfs", "install", "--local")
-    click.echo("git lfs install --local: done")
-
-    _configure_remote(repo_path, hub, resolved_owner, repo_name, username, no_remote)
-
-    if newly_created:
-        fetch = _git(repo_path, "fetch", "origin", check=False)
-        if fetch.returncode == 0:
-            _git(repo_path, "reset", "--hard", "origin/main")
-            click.echo("Pulled initial commit from RIA Hub (README.md + .gitattributes)")
-        else:
-            click.echo("Warning: fetch failed — falling back to local file setup.", err=True)
-            _write_local_ria_files(repo_path, repo_name)
-    else:
-        _write_local_ria_files(repo_path, repo_name)
-
-    if newly_created:
-        click.echo(f"\nRepo is ready. Push your work:\n  cd {repo_path}\n  git push -u origin main")
-    else:
-        click.echo(
-            f"\nRepo is ready. Commit and push:\n"
-            f"  cd {repo_path}\n"
-            f"  git add README.md .gitattributes\n"
-            f"  git commit -m 'chore: initialise RIA Hub project'\n"
-            f"  git push -u origin main"
-        )

src/ria_toolkit_oss_cli/ria_toolkit_oss/upload.py

@@ -1,392 +0,0 @@
-"""ria upload — stream large files to a RIA Hub Project via the LFS API.
-
-How it works
-------------
-1. The file is hashed locally (SHA-256 + size) — this is the LFS object ID.
-2. A single POST to the repo's LFS batch endpoint returns an upload URL
-   (and headers) for any object the server does not already have.
-3. The file is streamed to that URL in fixed-size chunks — nothing is ever
-   fully loaded into memory, so files of any size work.
-4. A commit is created via the Gitea contents API that records the LFS
-   pointer (a small text file) so the file appears in the repo tree.
-
-No server-side changes are required — this uses the same authenticated LFS
-protocol that `git lfs push` uses internally.
-"""
-
-import base64
-import hashlib
-import http.client
-import json
-import math
-import os
-import sys
-import urllib.error
-import urllib.parse
-import urllib.request
-
-import click
-
-from ._hub_auth import (
-    DEFAULT_HUB,
-    basic_auth,
-    hub_opener,
-    resolve_credentials,
-    warn_if_insecure,
-)
-
-# Read buffer for hashing and streaming — 8 MB keeps memory use flat
-# for arbitrarily large files.
-_CHUNK = 8 * 1024 * 1024
-
-LFS_MEDIA_TYPE = "application/vnd.git-lfs+json"
-
-
-# ---------------------------------------------------------------------------
-# File helpers
-# ---------------------------------------------------------------------------
-
-
-def _hash_file(path: str) -> tuple[str, int]:
-    """Return (sha256_hex, byte_size) by streaming the file."""
-    h = hashlib.sha256()
-    size = 0
-    with open(path, "rb") as f:
-        while True:
-            chunk = f.read(_CHUNK)
-            if not chunk:
-                break
-            h.update(chunk)
-            size += len(chunk)
-    return h.hexdigest(), size
-
-
-def _lfs_pointer_text(oid: str, size: int) -> str:
-    return f"version https://git-lfs.github.com/spec/v1\noid sha256:{oid}\nsize {size}\n"
-
-
-# ---------------------------------------------------------------------------
-# LFS batch API
-# ---------------------------------------------------------------------------
-
-
-def _lfs_batch(
-    hub: str,
-    owner: str,
-    repo: str,
-    objects: list[dict],
-    username: str,
-    password: str,
-) -> dict:
-    """
-    POST to /{owner}/{repo}.git/info/lfs/objects/batch.
-    Returns the parsed JSON response.
-    Raises on HTTP error or JSON decode failure.
-    """
-    url = (
-        f"{hub.rstrip('/')}"
-        f"/{urllib.parse.quote(owner, safe='')}"
-        f"/{urllib.parse.quote(repo, safe='')}"
-        f".git/info/lfs/objects/batch"
-    )
-    body = json.dumps(
-        {
-            "operation": "upload",
-            "transfers": ["basic"],
-            "objects": objects,
-        }
-    ).encode()
-
-    req = urllib.request.Request(url, data=body, method="POST")
-    req.add_header("Content-Type", LFS_MEDIA_TYPE)
-    req.add_header("Accept", LFS_MEDIA_TYPE)
-    req.add_header("Authorization", basic_auth(username, password))
-
-    opener = hub_opener()
-    try:
-        with opener.open(req, timeout=30) as resp:
-            return json.loads(resp.read())
-    except urllib.error.HTTPError as e:
-        body_text = e.read().decode(errors="replace")
-        raise RuntimeError(f"LFS batch request failed (HTTP {e.code}): {body_text}") from e
-
-
-# ---------------------------------------------------------------------------
-# Gitea contents API — create / update a file to record the LFS pointer
-# ---------------------------------------------------------------------------
-
-
-def _get_file_sha(
-    hub: str,
-    owner: str,
-    repo: str,
-    path: str,
-    branch: str,
-    username: str,
-    password: str,
-) -> str | None:
-    """Return the blob SHA of an existing file, or None if it doesn't exist."""
-    url = (
-        f"{hub.rstrip('/')}/api/v1"
-        f"/repos/{urllib.parse.quote(owner, safe='')}/{urllib.parse.quote(repo, safe='')}"
-        f"/contents/{urllib.parse.quote(path)}"
-        f"?ref={urllib.parse.quote(branch)}"
-    )
-    req = urllib.request.Request(url)
-    req.add_header("Authorization", basic_auth(username, password))
-    try:
-        with hub_opener().open(req, timeout=15) as resp:
-            return json.loads(resp.read()).get("sha")
-    except urllib.error.HTTPError as e:
-        if e.code == 404:
-            return None
-        raise
-
-
-def _commit_lfs_pointer(
-    hub: str,
-    owner: str,
-    repo: str,
-    remote_path: str,
-    pointer_text: str,
-    branch: str,
-    message: str,
-    username: str,
-    password: str,
-) -> None:
-    """Create or update a file in the repo containing the LFS pointer."""
-    url = (
-        f"{hub.rstrip('/')}/api/v1"
-        f"/repos/{urllib.parse.quote(owner, safe='')}/{urllib.parse.quote(repo, safe='')}"
-        f"/contents/{urllib.parse.quote(remote_path)}"
-    )
-
-    existing_sha = _get_file_sha(hub, owner, repo, remote_path, branch, username, password)
-
-    body: dict = {
-        "message": message,
-        "content": base64.b64encode(pointer_text.encode()).decode(),
-        "branch": branch,
-    }
-    if existing_sha:
-        body["sha"] = existing_sha
-
-    method = "PUT" if existing_sha else "POST"
-    req = urllib.request.Request(url, data=json.dumps(body).encode(), method=method)
-    req.add_header("Content-Type", "application/json")
-    req.add_header("Authorization", basic_auth(username, password))
-
-    try:
-        with hub_opener().open(req, timeout=30) as resp:
-            resp.read()
-    except urllib.error.HTTPError as e:
-        body_text = e.read().decode(errors="replace")
-        raise RuntimeError(f"Failed to commit LFS pointer for '{remote_path}' (HTTP {e.code}): {body_text}") from e
-
-
-# ---------------------------------------------------------------------------
-# Per-file upload logic
-# ---------------------------------------------------------------------------
-
-
-def _upload_single_file(
-    hub: str,
-    owner: str,
-    repo_name: str,
-    username: str,
-    password: str,
-    file_path: str,
-    remote_dir: str,
-    message: str | None,
-    branch: str,
-) -> None:
-    """Hash, upload (if needed), and commit the LFS pointer for one file."""
-    filename = os.path.basename(file_path)
-    file_size = os.path.getsize(file_path)
-    size_mb = file_size / (1024 * 1024)
-
-    click.echo(f"\n  {filename} ({size_mb:.1f} MB)")
-
-    click.echo("    Hashing...", nl=False)
-    oid, size = _hash_file(file_path)
-    click.echo(f" sha256:{oid[:12]}...")
-
-    try:
-        batch = _lfs_batch(hub, owner, repo_name, [{"oid": oid, "size": size}], username, password)
-    except RuntimeError as e:
-        click.echo(f"\n    Error: {e}", err=True)
-        sys.exit(1)
-
-    objects = batch.get("objects", [])
-    if not objects:
-        click.echo("    Already in LFS — skipping upload.")
-    else:
-        obj = objects[0]
-        if "error" in obj:
-            err_msg = obj["error"].get("message", "unknown error")
-            err_code = obj["error"].get("code", 0)
-            if err_code == 413 or "quota" in err_msg.lower() or "limit" in err_msg.lower():
-                click.echo(
-                    f"\n    Error: storage quota exceeded for this repo.\n    Server: {err_msg}",
-                    err=True,
-                )
-            else:
-                click.echo(f"\n    Error from server: {err_msg}", err=True)
-            sys.exit(1)
-
-        upload_action = obj.get("actions", {}).get("upload")
-        if not upload_action:
-            click.echo("    Already in LFS — skipping upload.")
-        else:
-            href = upload_action["href"]
-            up_headers = upload_action.get("header", {})
-            chunks = math.ceil(size / _CHUNK)
-            click.echo(f"    Uploading ({size_mb:.1f} MB, {chunks} chunk{'s' if chunks != 1 else ''})...")
-            try:
-                _stream_upload_progress(href, up_headers, file_path, size)
-            except RuntimeError as e:
-                click.echo(f"\n    Upload failed: {e}", err=True)
-                sys.exit(1)
-            click.echo("    Upload complete.")
-
-            verify_action = obj.get("actions", {}).get("verify")
-            if verify_action:
-                try:
-                    vreq = urllib.request.Request(
-                        verify_action["href"],
-                        data=json.dumps({"oid": oid, "size": size}).encode(),
-                        method="POST",
-                    )
-                    vreq.add_header("Content-Type", LFS_MEDIA_TYPE)
-                    vreq.add_header("Accept", LFS_MEDIA_TYPE)
-                    for k, v in verify_action.get("header", {}).items():
-                        vreq.add_header(k, v)
-                    with urllib.request.urlopen(vreq, timeout=15):
-                        pass
-                except Exception:
-                    pass  # verify is optional; non-fatal on failure
-
-    pointer = _lfs_pointer_text(oid, size)
-    remote_path = (f"{remote_dir.rstrip('/')}/{filename}").lstrip("/") if remote_dir else filename
-    commit_msg = message or f"chore: upload {filename} via ria"
-
-    click.echo(f"    Committing pointer → {remote_path}...", nl=False)
-    try:
-        _commit_lfs_pointer(hub, owner, repo_name, remote_path, pointer, branch, commit_msg, username, password)
-        click.echo(" done.")
-    except RuntimeError as e:
-        click.echo(f"\n    Error: {e}", err=True)
-        sys.exit(1)
-
-
-def _stream_upload_progress(href: str, headers: dict, file_path: str, size: int) -> None:
-    """Stream file_path to href with a click progress bar."""
-    parsed = urllib.parse.urlparse(href)
-    host = parsed.netloc
-    path_q = parsed.path + (f"?{parsed.query}" if parsed.query else "")
-
-    if parsed.scheme == "https":
-        conn = http.client.HTTPSConnection(host, timeout=300)
-    else:
-        conn = http.client.HTTPConnection(host, timeout=300)
-
-    all_headers = dict(headers)
-    all_headers.setdefault("Content-Type", "application/octet-stream")
-    all_headers["Content-Length"] = str(size)
-
-    try:
-        conn.connect()
-        conn.putrequest("PUT", path_q)
-        for k, v in all_headers.items():
-            conn.putheader(k, v)
-        conn.endheaders()
-
-        with click.progressbar(
-            length=size,
-            label="    ",
-            width=40,
-            show_eta=True,
-            show_percent=True,
-            fill_char="█",
-            empty_char="░",
-        ) as bar:
-            with open(file_path, "rb") as f:
-                while True:
-                    chunk = f.read(_CHUNK)
-                    if not chunk:
-                        break
-                    conn.send(chunk)
-                    bar.update(len(chunk))
-
-        resp = conn.getresponse()
-        resp.read()
-        if resp.status not in (200, 201):
-            raise RuntimeError(f"HTTP {resp.status}")
-    finally:
-        conn.close()
-
-
-# ---------------------------------------------------------------------------
-# Command
-# ---------------------------------------------------------------------------
-
-
-@click.command("upload")
-@click.argument("files", nargs=-1, required=True)
-@click.option(
-    "--repo", required=True, metavar="OWNER/NAME", help="Target repository on RIA Hub (e.g. benchinnery/my-dataset)."
-)
-@click.option("--hub", default=DEFAULT_HUB, show_default=True, metavar="URL", help="RIA Hub base URL.")
-@click.option("--branch", default="main", show_default=True, help="Branch to commit the files to.")
-@click.option(
-    "--path",
-    "remote_dir",
-    default="",
-    metavar="DIR",
-    help="Remote directory path inside the repo (default: repo root).",
-)
-@click.option("--message", "-m", default=None, help="Commit message (default: 'chore: upload <filename> via ria').")
-def upload(
-    files: tuple[str],
-    repo: str,
-    hub: str,
-    branch: str,
-    remote_dir: str,
-    message: str | None,
-) -> None:
-    """Upload large files to a RIA Hub Project via Git LFS.
-
-    Files are streamed directly to the repo's LFS object store — nothing is
-    buffered into memory, so files of any size work. Each file creates one
-    commit recording the LFS pointer.
-
-    \b
-    Examples:
-      ria upload recording.sigmf-data --repo benchinnery/my-recordings
-      ria upload *.npy --repo benchinnery/my-recordings --branch main
-      ria upload big.pt --repo benchinnery/models --path weights/
-    """
-    # Validate repo argument
-    if "/" not in repo:
-        click.echo("Error: --repo must be in the form OWNER/NAME.", err=True)
-        sys.exit(1)
-    owner, repo_name = repo.split("/", 1)
-
-    # Expand and validate files
-    resolved = []
-    for pattern in files:
-        if not os.path.isfile(pattern):
-            click.echo(f"Error: '{pattern}' is not a file or does not exist.", err=True)
-            sys.exit(1)
-        resolved.append(os.path.abspath(pattern))
-
-    hub = hub.rstrip("/")
-    warn_if_insecure(hub)
-    username, password = resolve_credentials(hub)
-
-    click.echo(f"Uploading {len(resolved)} file(s) to {owner}/{repo_name} on {hub}...")
-
-    for file_path in resolved:
-        _upload_single_file(hub, owner, repo_name, username, password, file_path, remote_dir, message, branch)
-
-    click.echo(f"\nAll done. {len(resolved)} file(s) uploaded to {owner}/{repo_name}.")

tests/agent/test_cli_register_errors.py

@@ -1,145 +0,0 @@
-"""Structured error reporting for `ria-agent register` (T2)."""
-
-from __future__ import annotations
-
-import json
-import sys
-import urllib.error
-from io import BytesIO
-from unittest.mock import patch
-
-import pytest
-
-from ria_toolkit_oss.agent import cli as agent_cli
-
-
-def _structured(reason: str) -> bytes:
-    return json.dumps({"detail": {"reason": reason}}).encode()
-
-
-@pytest.mark.parametrize(
-    "reason",
-    ["invalid_key", "expired", "revoked", "already_consumed"],
-)
-def test_explain_maps_known_reasons(reason):
-    msg = agent_cli._explain_registration_failure(403, _structured(reason))
-    assert msg == agent_cli.REGISTRATION_REASON_MESSAGES[reason]
-
-
-def test_explain_unknown_reason_falls_through_with_code():
-    msg = agent_cli._explain_registration_failure(403, _structured("brand_new_thing"))
-    assert "brand_new_thing" in msg
-    assert "rejected" in msg.lower()
-
-
-def test_explain_string_detail():
-    body = json.dumps({"detail": "Forbidden"}).encode()
-    msg = agent_cli._explain_registration_failure(403, body)
-    assert msg == "Registration rejected: Forbidden"
-
-
-def test_explain_429_with_string_detail():
-    body = json.dumps({"detail": "Too many attempts; try again shortly"}).encode()
-    msg = agent_cli._explain_registration_failure(429, body)
-    assert "rate-limited" in msg
-    assert "Too many attempts" in msg
-
-
-def test_explain_429_with_no_body():
-    msg = agent_cli._explain_registration_failure(429, b"")
-    assert "rate-limited" in msg
-
-
-def test_explain_malformed_json():
-    msg = agent_cli._explain_registration_failure(500, b"<html>boom</html>")
-    assert msg.startswith("HTTP 500")
-    assert "boom" in msg
-
-
-def test_explain_empty_body():
-    msg = agent_cli._explain_registration_failure(502, b"")
-    assert msg == "HTTP 502: no body"
-
-
-def _http_error(status: int, body: bytes) -> urllib.error.HTTPError:
-    return urllib.error.HTTPError(
-        url="http://hub/screens/agents/register",
-        code=status,
-        msg="",
-        hdrs=None,  # type: ignore[arg-type]
-        fp=BytesIO(body),
-    )
-
-
-def test_user_agent_is_set_and_not_python_default():
-    """Cloudflare on `riahub.ai` returns 403 code 1010 to `Python-urllib/*`.
-
-    Guarding the UA explicitly is the entire point of the register-flow fix;
-    if this test ever breaks, the production bug is back.
-    """
-    ua = agent_cli._user_agent()
-    assert ua, "User-Agent must not be empty"
-    assert not ua.lower().startswith(
-        "python-urllib"
-    ), f"User-Agent must not be Python's default (got {ua!r}) — Cloudflare blocks it"
-    assert ua.startswith("ria-agent/")
-
-
-def test_register_request_carries_explicit_user_agent(tmp_path):
-    """Capture the outbound urllib Request and verify the UA header is set."""
-    cfg_path = tmp_path / "agent.json"
-    captured: dict = {}
-
-    def _fake_urlopen(req, *args, **kwargs):
-        # urllib normalizes header names; get_header takes the title-cased form.
-        captured["ua"] = req.get_header("User-agent")
-        captured["api_key"] = req.get_header("X-api-key")
-        captured["timeout"] = kwargs.get("timeout")
-        raise urllib.error.HTTPError(
-            url=req.full_url,
-            code=403,
-            msg="",
-            hdrs=None,  # type: ignore[arg-type]
-            fp=BytesIO(_structured("invalid_key")),
-        )
-
-    with (
-        patch.dict("os.environ", {"RIA_AGENT_CONFIG": str(cfg_path)}, clear=False),
-        patch("urllib.request.urlopen", side_effect=_fake_urlopen),
-        patch.object(
-            sys,
-            "argv",
-            ["ria-agent", "register", "--hub", "http://hub:3005", "--api-key", "ria_reg_x"],
-        ),
-    ):
-        with pytest.raises(SystemExit):
-            agent_cli.main()
-
-    assert captured["ua"], "User-Agent header was not sent"
-    assert not captured["ua"].lower().startswith("python-urllib")
-    assert captured["api_key"] == "ria_reg_x"
-    assert captured["timeout"] is not None, "register must pass a timeout to urlopen"
-
-
-def test_register_surfaces_reason_on_http_error(tmp_path, capsys):
-    cfg_path = tmp_path / "agent.json"
-    err = _http_error(403, _structured("revoked"))
-
-    with (
-        patch.dict("os.environ", {"RIA_AGENT_CONFIG": str(cfg_path)}, clear=False),
-        patch("urllib.request.urlopen", side_effect=err),
-        patch.object(
-            sys,
-            "argv",
-            ["ria-agent", "register", "--hub", "http://hub:3005", "--api-key", "ria_reg_x"],
-        ),
-    ):
-        with pytest.raises(SystemExit) as exc:
-            agent_cli.main()
-
-    assert exc.value.code == 1
-    captured = capsys.readouterr()
-    assert "revoked" in captured.err.lower()
-    assert "Settings → RIA Agents" in captured.err
-    # Config must NOT be written on failure.
-    assert not cfg_path.exists()

tests/datatypes/test_annotation.py

@@ -199,44 +199,3 @@ def test_annotation_to_sigmf_format_values():
     values = list(result.values())
     assert 50 in values or ann.sample_start in values
     assert 100 in values or ann.sample_count in values
-
-
-# ---------------------------------------------------------------------------
-# None freq-edge regression tests (SigMF optional fields)
-# ---------------------------------------------------------------------------
-
-
-def test_annotation_no_freq_edges():
-    ann = Annotation(sample_start=0, sample_count=10, label="burst")
-    assert ann.freq_lower_edge is None
-    assert ann.freq_upper_edge is None
-
-
-def test_annotation_is_valid_no_freq_edges():
-    ann = Annotation(sample_start=0, sample_count=10, label="burst")
-    assert ann.is_valid() is True
-
-    ann_zero = Annotation(sample_start=0, sample_count=0, label="burst")
-    assert ann_zero.is_valid() is False
-
-
-def test_annotation_overlap_none_edges_returns_zero():
-    ann1 = Annotation(sample_start=0, sample_count=10)
-    ann2 = Annotation(sample_start=0, sample_count=10, freq_lower_edge=0, freq_upper_edge=100)
-    assert ann1.overlap(ann2) == 0
-    assert ann2.overlap(ann1) == 0
-
-
-def test_annotation_area_none_edges_returns_zero():
-    ann = Annotation(sample_start=0, sample_count=10, label="burst")
-    assert ann.area() == 0
-
-
-def test_annotation_to_sigmf_omits_freq_keys_when_none():
-    from sigmf import SigMFFile
-
-    ann = Annotation(sample_start=0, sample_count=10, label="burst")
-    result = ann.to_sigmf_format()
-    metadata = result["metadata"]
-    assert SigMFFile.FLO_KEY not in metadata
-    assert SigMFFile.FHI_KEY not in metadata

tests/io/test_recording_io.py

@@ -189,21 +189,3 @@ def test_sigmf_3(tmp_path):
         to_sigmf(recording=recording1, path=tmp_path, filename=filename.name)
     except IOError as e:
         assert str(e) == "File already exists"
-
-
-def test_sigmf_annotation_without_freq_edges(tmp_path):
-    # Regression: annotations that omit the optional SigMF freq edge fields must
-    # load without error; edges should be None and the annotation still valid.
-    ann = Annotation(sample_start=0, sample_count=5, label="burst")
-    recording1 = Recording(data=complex_data_1, metadata=sample_metadata, annotations=[ann])
-
-    filename = tmp_path / "test"
-    to_sigmf(recording=recording1, path=tmp_path, filename=filename.name, overwrite=True)
-    recording2 = from_sigmf(filename)
-
-    assert len(recording2.annotations) == 1
-    loaded = recording2.annotations[0]
-    assert loaded.freq_lower_edge is None
-    assert loaded.freq_upper_edge is None
-    assert loaded.is_valid() is True
-    assert loaded.label == "burst"