np-workflows 1.6.85__tar.gz → 1.6.90__tar.gz

{np_workflows-1.6.85 → np_workflows-1.6.90}/PKG-INFO

@@ -1,17 +1,18 @@
-Metadata-Version: 2.1
+Metadata-Version: 2.4
 Name: np-workflows
-Version: 1.6.85
+Version: 1.6.90
 Summary: Ecephys and behavior workflows for the Mindscope Neuropixels team.
-Author-Email: Ben Hardcastle <ben.hardcastle@alleninstitute.org>
+Author-email: Ben Hardcastle <ben.hardcastle@alleninstitute.org>
 License: MIT
+Project-URL: Repository, https://github.com/AllenInstitute/np_workflows
+Project-URL: Issues, https://github.com/AllenInstitute/np_workflows/issues
 Classifier: Programming Language :: Python :: 3
 Classifier: Programming Language :: Python :: 3.11
 Classifier: License :: OSI Approved :: MIT License
 Classifier: Operating System :: Microsoft :: Windows
 Classifier: Operating System :: POSIX :: Linux
-Project-URL: Repository, https://github.com/AllenInstitute/np_workflows
-Project-URL: Issues, https://github.com/AllenInstitute/np_workflows/issues
 Requires-Python: ==3.11.*
+Description-Content-Type: text/markdown
 Requires-Dist: np-services>=0.1.69
 Requires-Dist: np-session>=0.6.48
 Requires-Dist: np-config>=0.4.33
@@ -29,16 +30,6 @@ Requires-Dist: np-codeocean[dynamic-routing-metadata]>=0.2.1
 Requires-Dist: panel>=1.4.5
 Requires-Dist: aind-session>=0.1.20
 Requires-Dist: jupyter-bokeh>=4.0.5
-Provides-Extra: dev
-Requires-Dist: blue>=0.9.1; extra == "dev"
-Requires-Dist: pytest>=7.2.2; extra == "dev"
-Requires-Dist: mypy>=1.1.1; extra == "dev"
-Requires-Dist: coverage[toml]>=7.2.2; extra == "dev"
-Requires-Dist: pytest-cov>=4.0.0; extra == "dev"
-Requires-Dist: bump>=1.3.2; extra == "dev"
-Requires-Dist: types-backports>=0.1.3; extra == "dev"
-Requires-Dist: ruff>=0.0.260; extra == "dev"
-Description-Content-Type: text/markdown
 
 # np_workflows
 

np_workflows-1.6.90/pyproject.toml

@@ -0,0 +1,199 @@
+[project]
+name = "np-workflows"
+version = "1.6.90"
+description = "Ecephys and behavior workflows for the Mindscope Neuropixels team."
+authors = [
+    { name = "Ben Hardcastle", email = "ben.hardcastle@alleninstitute.org" },
+]
+readme = "README.md"
+requires-python = "==3.11.*"
+dependencies = [
+    "np-services>=0.1.69",
+    "np-session>=0.6.48",
+    "np-config>=0.4.33",
+    "ipywidgets>=7",
+    "pydantic>=2",
+    "jupyterlab >= 3.6",
+    "ipylab >= 0.6.0",
+    "np-tools>=0.1.24",
+    "np-jobs>=0.0.3",
+    "universal-pathlib>=0.1.0",
+    "s3fs>=2023.6.0",
+    "npc-shields>=0.1.10",
+    "npc-sessions>=0.0.225",
+    "np-codeocean[dynamic-routing-metadata]>=0.2.1",
+    "panel>=1.4.5",
+    "aind-session>=0.1.20",
+    "jupyter-bokeh>=4.0.5",
+]
+classifiers = [
+    "Programming Language :: Python :: 3",
+    "Programming Language :: Python :: 3.11",
+    "License :: OSI Approved :: MIT License",
+    "Operating System :: Microsoft :: Windows",
+    "Operating System :: POSIX :: Linux",
+]
+
+[project.license]
+text = "MIT"
+
+[project.urls]
+Repository = "https://github.com/AllenInstitute/np_workflows"
+Issues = "https://github.com/AllenInstitute/np_workflows/issues"
+
+
+[build-system]
+requires = ["setuptools>=61", "wheel"]
+build-backend = "setuptools.build_meta"
+
+[project.scripts]
+task = "poethepoet:main"
+
+[dependency-groups]
+task_runner = ["poethepoet>=0.33.1"]
+linting = ["black>=25.1.0", "isort>=6.0.1", "ruff>=0.11.2"]
+testing = ["pytest>=7.4.0", "mypy>=1.4.1", "pytest-cov>=4.1.0"]
+bump = [
+    "bump-my-version>=1.1.1",
+    "git-changelog>=2.5.3",
+]
+pynwb = [
+    "hdmf-zarr==0.11.0",
+    "pynwb==3.0.0",
+]
+
+[tool.uv]
+package = true
+default-groups = "all"
+
+[tool.bumpversion]
+tag = true
+allow_dirty = true
+commit = true
+commit_args = "-a"
+message = "Bump version: {current_version} → {new_version} [skip actions]"
+pre_commit_hooks = [
+    "uv lock --upgrade-package np_workflows",
+    "git-changelog -o CHANGELOG.md",
+    "uv build",
+    "uv publish",
+]
+post_commit_hooks = [
+    "git push origin main",
+    "git push --tags",
+]
+
+[tool.poe.tasks]
+mypy = "mypy src --install-types --non-interactive"
+pytest = "pytest --cov-report term-missing:skip-covered --cov-report=html"
+test = ["pytest"]
+ruff = "ruff check src --fix-only"
+black = "black src"
+format = ["ruff", "black"]
+bump_pub_tag = "bump-my-version bump patch"
+release = ["format", "bump_pub_tag"]
+
+[tool.setuptools.packages.find]
+where = ["src"]
+
+[tool.setuptools.package-data]
+np_workflows = ["py.typed"]
+
+[tool.setuptools]
+license-files = ["LICENSE"]
+
+[tool.black]
+# line-length = 100
+target-version = ["py39", "py310", "py311"]
+
+[tool.ruff]
+line-length = 100
+select = [
+    "B",      # flake8-bugbear
+    "C4",     # flake8-comprehensions
+    "E",      # pycodestyle
+    "F",      # pyflakes
+    "PGH",    # pygrep-hooks
+    "RUF",    # ruff
+    "W",      # pycodestyle
+    "YTT",    # flake8-2020
+    "ANN",
+    "C",
+    "I",
+    "RUF100",
+    "N",
+    "UP",
+]
+# extend-ignore = ["B018", "B019"]
+src = ["src"]
+extend-exclude = ["tests/fixtures"]
+target-version = "py39"
+
+[tool.ruff.flake8-tidy-imports]
+ban-relative-imports = "all"
+
+[tool.ruff.mccabe]
+max-complexity = 10
+
+[tool.ruff.isort]
+known-first-party = ["np_workflows"]
+
+[tool.coverage.paths]
+source = ["src"]
+
+[tool.coverage.run]
+branch = true
+source = ["src"]
+
+[tool.coverage.report]
+skip_covered = true
+show_missing = true
+skip_empty = true
+exclude_also = [
+    "raise AssertionError",
+    "raise NotImplementedError",
+    "if __name__ == .__main__.:",
+    "@(abc.)?abstractmethod",
+    "@typing.runtime_checkable",
+]
+
+[tool.pytest.ini_options]
+addopts = [
+    "--import-mode=importlib",
+    # "--doctest-modules",
+    "--ignore-glob=*scripts*,*examples*,*docs*",
+    "--cov",
+    "--cov-report=html",
+    "--cov-config=pyproject.toml",
+    "--doctest-glob=*README.md",
+    "-x",
+    # "-n=auto", for use with pytest-xdist
+]
+doctest_optionflags = [
+    "NORMALIZE_WHITESPACE",
+    "IGNORE_EXCEPTION_DETAIL",
+    "ELLIPSIS",
+]
+testpaths = ["src", "tests"]
+
+[tool.mypy]
+check_untyped_defs = false
+disallow_untyped_defs = false
+disallow_incomplete_defs = false
+disallow_untyped_decorators = false
+disallow_any_unimported = false
+warn_return_any = false
+warn_unused_ignores = true
+no_implicit_optional = true
+show_error_codes = true
+ignore_missing_imports = true
+implicit_reexport = false
+exclude = ["src/np_workflows/scripts"]
+
+[tool.isort]
+profile = "black"
+atomic = true
+skip_glob = ["*/setup.py"]
+filter_files = true
+known_first_party = ["np_workflows"]
+

np_workflows-1.6.90/setup.cfg

@@ -0,0 +1,4 @@
+[egg_info]
+tag_build = 
+tag_date = 0
+

{np_workflows-1.6.85 → np_workflows-1.6.90}/src/np_workflows/__init__.py

@@ -1,7 +1,5 @@
+import np_workflows.experiments as experiments
+import np_workflows.shared.base_experiments as base_experiments
 import np_workflows.shared.npxc as npxc
 import np_workflows.shared.widgets as widgets
-import np_workflows.shared.base_experiments as base_experiments
-
-import np_workflows.experiments as experiments
-
-from np_workflows.shared import *
+from np_workflows.shared import *

{np_workflows-1.6.85 → np_workflows-1.6.90}/src/np_workflows/experiments/dynamic_routing/main.py

@@ -1,48 +1,21 @@
 from __future__ import annotations
 
-import configparser
-import contextlib
-import copy
-import dataclasses
-import datetime
-import enum
-import functools
-import pathlib
-import platform
-import shutil
-import threading
-import time
-import zlib
-from typing import ClassVar, Literal, NamedTuple, NoReturn, Optional, Type, TypedDict
-
-import IPython
-import IPython.display
-import ipywidgets as ipw
-import np_config
 import np_logging
-import np_services
 import np_session
-import np_workflows
-import fabric
-import PIL.Image
-import pydantic
-from pyparsing import Any
 from np_services import (
-    Service,
-    Finalizable,
-    ScriptCamstim,
+    MouseDirector,
+    NewScaleCoordinateRecorder,
     OpenEphys,
+    ScriptCamstim,
     Sync,
-    ImageMVR,
     VideoMVR,
-    NewScaleCoordinateRecorder,
-    MouseDirector,
 )
 
 from np_workflows.shared import base_experiments
 
 logger = np_logging.getLogger(__name__)
 
+
 def new_experiment(
     mouse: int | str | np_session.Mouse,
     user: str | np_session.User,
@@ -50,29 +23,33 @@ def new_experiment(
 ) -> DRTask:
     """Create a new experiment for the given mouse and user."""
     experiment: DRTask
-    if any(tag in workflow.name for tag in ('EPHYS', 'PRETEST')):
+    if any(tag in workflow.name for tag in ("EPHYS", "PRETEST")):
         experiment = Ephys(mouse, user)
-    elif 'HAB' in workflow.name:
+    elif "HAB" in workflow.name:
         experiment = Hab(mouse, user)
-    elif 'OPTO' in workflow.name:
+    elif "OPTO" in workflow.name:
         experiment = Opto(mouse, user)
-    elif 'TRAINING' in workflow.name:
+    elif "TRAINING" in workflow.name:
         experiment = Training(mouse, user)
     else:
-        raise ValueError(f"Unknown {workflow = }. Create an experiment with e.g.\n\n\texperiment = Ephys(mouse, user)\nexperiment.session.npexp_path.mkdir()")
+        raise ValueError(
+            f"Unknown {workflow = }. Create an experiment with e.g.\n\n\texperiment = Ephys(mouse, user)\nexperiment.session.npexp_path.mkdir()"
+        )
     experiment.workflow = workflow
     experiment.log(f"{experiment} created")
-    experiment.session.npexp_path.mkdir(parents=True, exist_ok=True) 
+    experiment.session.npexp_path.mkdir(parents=True, exist_ok=True)
     return experiment
 
+
 class DRTask(base_experiments.DynamicRoutingExperiment):
     """Provides project-specific methods and attributes, mainly related to camstim scripts."""
-    
+
     default_session_subclass = np_session.DRPilotSession
-    
+
     workflow: base_experiments.DynamicRoutingExperiment.Workflow
     """Enum for workflow type, e.g. PRETEST, HAB_AUD, HAB_VIS, EPHYS_ etc."""
 
+
 class Hab(DRTask):
     def __init__(self, *args, **kwargs):
         self.services = (
@@ -82,7 +59,8 @@ class Hab(DRTask):
             ScriptCamstim,
         )
         super().__init__(*args, **kwargs)
-        
+
+
 class Opto(DRTask):
     def __init__(self, *args, **kwargs):
         self.services = (
@@ -106,6 +84,7 @@ class Ephys(DRTask):
         )
         super().__init__(*args, **kwargs)
 
+
 class Training(DRTask):
     def __init__(self, *args, **kwargs):
         self.services = (
@@ -114,4 +93,4 @@ class Training(DRTask):
             VideoMVR,
             ScriptCamstim,
         )
-        super().__init__(*args, **kwargs)
+        super().__init__(*args, **kwargs)

{np_workflows-1.6.85 → np_workflows-1.6.90}/src/np_workflows/experiments/dynamic_routing/widgets.py

@@ -1,29 +1,22 @@
-import configparser
-import contextlib
-import copy
-import enum
-import functools
-from typing import ClassVar, Literal, NamedTuple, NoReturn, Optional, TypedDict
-
 import IPython.display
 import ipywidgets as ipw
-import np_config
-import np_logging
 import np_session
-import np_workflows
-from pyparsing import Any
 
-from np_workflows.experiments.dynamic_routing.main import Ephys, Hab, DRTask
 from np_workflows.shared.base_experiments import DynamicRoutingExperiment
 
-
 # for widget, before creating a experiment --------------------------------------------- #
 
 
 class SelectedWorkflow:
-    def __init__(self, workflow: str | DynamicRoutingExperiment.Workflow, mouse: str | int | np_session.Mouse):
+    def __init__(
+        self,
+        workflow: str | DynamicRoutingExperiment.Workflow,
+        mouse: str | int | np_session.Mouse,
+    ):
         if isinstance(workflow, str):
-            workflow = DynamicRoutingExperiment.Workflow[workflow] # uses enum name (not value)
+            workflow = DynamicRoutingExperiment.Workflow[
+                workflow
+            ]  # uses enum name (not value)
         self.workflow = workflow
         self.mouse = str(mouse)
 
@@ -55,8 +48,12 @@ def workflow_select_widget(
     )
     console = ipw.Output()
     with console:
-        if last_workflow := np_session.Mouse(selection.mouse).state.get('last_workflow'):
-            print(f"{mouse} last workflow: {last_workflow}\t({np_session.Mouse(selection.mouse).state.get('last_session')})")
+        if last_workflow := np_session.Mouse(selection.mouse).state.get(
+            "last_workflow"
+        ):
+            print(
+                f"{mouse} last workflow: {last_workflow}\t({np_session.Mouse(selection.mouse).state.get('last_session')})"
+            )
         print(f"Selected: {selection.workflow.name}")
 
     def update(change):
@@ -68,15 +65,23 @@ def workflow_select_widget(
             return
         if change["new"] == change["old"]:
             return
-        selection.__init__(str(workflow_dropdown.value), mouse.id if isinstance(mouse, np_session.Mouse) else str(mouse))
+        selection.__init__(
+            str(workflow_dropdown.value),
+            mouse.id if isinstance(mouse, np_session.Mouse) else str(mouse),
+        )
         with console:
             print(f"Selected: {selection.workflow}")
-    workflow_dropdown.observe(update, names='value')
 
-    IPython.display.display(ipw.VBox([ipw.HBox([workflow_dropdown, workflow_descriptions]), console]))
+    workflow_dropdown.observe(update, names="value")
+
+    IPython.display.display(
+        ipw.VBox([ipw.HBox([workflow_dropdown, workflow_descriptions]), console])
+    )
 
     return selection
-    
-    
-def photodoc_widget(session: np_session.Session, reminder: str) -> None: 
-    print(f'Take an image in Vimba Viewer and save as:\n{session.npexp_path.name}_{reminder}.png')
+
+
+def photodoc_widget(session: np_session.Session, reminder: str) -> None:
+    print(
+        f"Take an image in Vimba Viewer and save as:\n{session.npexp_path.name}_{reminder}.png"
+    )

np_workflows-1.6.90/src/np_workflows/experiments/openscope_P3/P3_workflow_widget.py

@@ -0,0 +1,75 @@
+import IPython.display
+import ipywidgets as ipw
+import np_session
+
+from np_workflows.experiments.openscope_P3.main_P3_pilot import P3Session
+
+global_state = {}
+"""Global variable for persisting widget states."""
+
+# for widget, before creating a experiment --------------------------------------------- #
+
+
+class SelectedSession:
+    def __init__(self, session: str | P3Session, mouse: str | int | np_session.Mouse):
+        if isinstance(session, str):
+            session = P3Session(session)
+        self.session = session
+        self.mouse = str(mouse)
+
+    def __repr__(self) -> str:
+        return f"{self.__class__.__name__}({self.session}, {self.mouse})"
+
+
+def P3_workflow_widget(
+    mouse: str | int | np_session.Mouse,
+) -> SelectedSession:
+    """Select a stimulus session (hab, pretest, ephys) to run.
+
+    An object with mutable attributes is returned, so the selected session can be
+    updated along with the GUI selection. (Preference would be to return an enum
+    directly, and change it's value, but that doesn't seem possible.)
+
+    """
+
+    selection = SelectedSession(P3Session.PRETEST, mouse)
+
+    session_dropdown = ipw.Select(
+        options=tuple(_.value for _ in P3Session),
+        description="Session",
+    )
+
+    def update_selection():
+        selection.__init__(str(session_dropdown.value), str(mouse))
+
+    if previously_selected_value := global_state.get("selected_session"):
+        session_dropdown.value = previously_selected_value
+        update_selection()
+
+    console = ipw.Output()
+    with console:
+        if last_session := np_session.Mouse(selection.mouse).state.get(
+            "last_P3_session"
+        ):
+            print(f"{mouse} last session: {last_session}")
+        print(f"Selected: {selection.session}")
+
+    def update(change):
+        if change["name"] != "value":
+            return
+        if (options := getattr(change["owner"], "options", None)) and change[
+            "new"
+        ] not in options:
+            return
+        if change["new"] == change["old"]:
+            return
+        update_selection()
+        with console:
+            print(f"Selected: {selection.session}")
+        global_state["selected_session"] = selection.session.value
+
+    session_dropdown.observe(update, names="value")
+
+    IPython.display.display(ipw.VBox([session_dropdown, console]))
+
+    return selection

np_workflows-1.6.90/src/np_workflows/experiments/openscope_P3/__init__.py

@@ -0,0 +1,2 @@
+from .main_P3_pilot import Ephys, Hab, new_experiment, validate_selected_workflow
+from .P3_workflow_widget import P3_workflow_widget