From d4496a35f73ee5a355b372e3083d5ee8f27faa7e Mon Sep 17 00:00:00 2001 From: P S Kesavan Date: Wed, 17 Jun 2026 04:13:42 +0530 Subject: [PATCH 1/2] fix: bump __version__ to 0.22.0 to match release gently/__init__.py still carried 0.22.0.dev0 while pyproject.toml and the README were bumped to 0.22.0. Align it with the release version. Co-Authored-By: Claude Opus 4.8 (1M context) --- gently/__init__.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/gently/__init__.py b/gently/__init__.py index 29b0b3b4..25c8c925 100644 --- a/gently/__init__.py +++ b/gently/__init__.py @@ -81,7 +81,7 @@ except ImportError: _VISUALIZATION_AVAILABLE = False -__version__ = "0.22.0.dev0" +__version__ = "0.22.0" __all__ = [ # Main entry point "Gently", From 87a52c52c2a2e0390b1fc49687afb9b85411ea92 Mon Sep 17 00:00:00 2001 From: Magdalena Schneider Date: Wed, 17 Jun 2026 13:03:53 -0400 Subject: [PATCH 2/2] Move hardware-control stack into default-on device dependency group --- README.md | 16 ++- pyproject.toml | 48 ++++--- uv.lock | 377 +++++++++++++++++++++++++++++++++++++++++++++---- 3 files changed, 389 insertions(+), 52 deletions(-) diff --git a/README.md b/README.md index 78039e70..7bf25135 100644 --- a/README.md +++ b/README.md @@ -116,15 +116,23 @@ You get a `.venv` in the project directory with the runtime + dev dependencies pinned in `uv.lock`. Activate it with `source .venv/bin/activate`, or prefix commands with `uv run` (e.g. `uv run python ...`) to use it without activating. -#### Optional extras +#### The `device` group and optional extras + +The hardware-control stack (`pymmcore`, `bluesky`, `ophyd`) plus the accessory +transports (BLE/serial/MQTT — SwitchBot room light, ACUITYnano thermal +controller) live in the `device` dependency group, which is **installed by +default**. None of it is imported by the agent or by `--offline` launch — only +by the device layer — so a machine with no microscope can drop the whole stack: + +```bash +# Laptop / review / CI — no microscope, skip the hardware-control stack +uv sync --no-group device +``` PyTorch is **not** in the base install — the CUDA build is machine-specific, so it lives in mutually-exclusive extras wired to the right PyTorch index: ```bash -# Device-layer accessories (microscope computer): BLE/serial/MQTT transports -uv sync --extra device - # PyTorch (needed for SAM detection and the ML pipeline) # NOTE: the GPU and CPU builds are mutually exclusive, so they can't be combined. uv sync --extra torch-gpu # CUDA 11.8 build (GPU box, e.g. the microscope PC) diff --git a/pyproject.toml b/pyproject.toml index 561326b8..3e6fdd86 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -43,13 +43,11 @@ dependencies = [ # Perception harness — installed as an editable sibling clone (see # [tool.uv.sources]); clone gently-project/gently-perception next to this repo. "gently-perception", - # Device control. - # pymmcore pinned exactly: its MMCore must match the device-interface version - # (70) of the Micro-Manager device adapters installed on the microscope PC. - # Bumping this requires upgrading the MM adapter install in lockstep. - "pymmcore==10.1.1.70.6", - "bluesky>=1.11.0", - "ophyd>=1.9.0", + # NOTE: the hardware-control stack (pymmcore / bluesky / ophyd) is NOT a base + # dep — it lives in the default-on `device` group below so a machine with no + # microscope can drop it via `uv sync --no-group device`. It is imported only + # by the device-layer process and gently.hardware.dispim, never by the agent + # or `--offline` launch. # NOTE: torch / torchvision / nvidia-ml-py are NOT base deps — CUDA build is # machine-specific. Install via an extra: `uv sync --extra torch-gpu` (CUDA # 11.8) or `uv sync --extra torch-cpu`. All torch imports are lazy/guarded. @@ -76,19 +74,12 @@ torch-cpu = [ "torch>=2.0.0", "torchvision>=0.15.0", ] -# Device-layer accessories for the microscope computer. Core hardware-control -# deps (pymmcore, bluesky, ophyd) are already in [project.dependencies]; these -# are the extras the device layer needs: BLE (SwitchBot room light), serial and -# MQTT transports (ACUITYnano thermal controller). Install: uv sync --extra device -device = [ - "bleak>=0.21.0", - "pyserial>=3.5", - "paho-mqtt>=1.6.0", -] -# Test/dev tooling — installed by `uv sync` (uv enables the `dev` group by -# default) but excluded from gently's published runtime requirements. +# Dependency groups are installed by `uv sync` (per [tool.uv] default-groups +# below) but excluded from gently's published runtime requirements. Exclude any +# group on a given machine with `uv sync --no-group `. [dependency-groups] +# Test/dev tooling. dev = [ "pytest>=7.0.0", "pytest-asyncio>=0.21.0", @@ -99,6 +90,23 @@ dev = [ # and the install step in .github/workflows/lint.yml. "mypy==2.1.0", ] +# Everything the microscope computer needs to drive hardware. Default-on (see +# [tool.uv] default-groups); drop on a machine with no microscope via +# `uv sync --no-group device`. None of these is imported by the agent or by +# `--offline` launch — only by the device-layer process and gently.hardware.dispim. +device = [ + # pymmcore pinned exactly: its MMCore must match the device-interface version + # (70) of the Micro-Manager device adapters installed on the microscope PC. + # Bumping this requires upgrading the MM adapter install in lockstep. + "pymmcore==10.1.1.70.6", + "bluesky>=1.11.0", + "ophyd>=1.9.0", + # Accessory transports: BLE (SwitchBot room light), serial and MQTT + # (ACUITYnano thermal controller). + "bleak>=0.21.0", + "pyserial>=3.5", + "paho-mqtt>=1.6.0", +] [project.scripts] gently = "launch_gently:cli_main" @@ -106,6 +114,10 @@ gently = "launch_gently:cli_main" # torch-gpu and torch-cpu extras are mutually exclusive — they pull torch/ # torchvision from different indexes, so they can't be installed together. [tool.uv] +# Groups installed by default. `dev` is uv's implicit default; listing it here +# keeps it on while also defaulting `device` (the microscope computer's +# accessory transports) on. 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