mesofield 0.3.2b0__tar.gz

mesofield-0.3.2b0/.github/release.yml

@@ -0,0 +1,8 @@
+changelog:
+  categories:
+    - title: "New Features"
+      labels: [enhancement, feat, Feat, Enhancement]
+    - title: "Bug Fixes"
+      labels: [bug, fix, Fix, Bug]
+    - title: "Other Changes"
+      labels: ["*"]

mesofield-0.3.2b0/.github/workflows/docs.yml

@@ -0,0 +1,44 @@
+name: Docs
+
+on:
+  push:
+    branches: [main]
+  workflow_dispatch:
+
+permissions:
+  contents: write
+
+concurrency:
+  group: docs-${{ github.ref }}
+  cancel-in-progress: true
+
+jobs:
+  build-and-deploy:
+    runs-on: ubuntu-latest
+    steps:
+      - name: Checkout
+        uses: actions/checkout@v4
+        with:
+          fetch-depth: 0
+
+      - name: Set up Python
+        uses: actions/setup-python@v5
+        with:
+          python-version: "3.12"
+          cache: pip
+
+      - name: Install docs dependencies
+        run: |
+          python -m pip install --upgrade pip
+          pip install -e ".[docs]"
+
+      - name: Build Sphinx site
+        run: |
+          sphinx-build -b html --keep-going docs docs/_build/html
+
+      - name: Deploy to gh-pages
+        uses: peaceiris/actions-gh-pages@v4
+        with:
+          github_token: ${{ secrets.GITHUB_TOKEN }}
+          publish_dir: docs/_build/html
+          force_orphan: true

mesofield-0.3.2b0/.github/workflows/publish.yml

@@ -0,0 +1,64 @@
+name: Publish
+
+on:
+  release:
+    types: [published]   # -> publish to real PyPI
+  workflow_dispatch: {}  # -> manual run publishes to TestPyPI
+
+jobs:
+  build:
+    name: Build distributions
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+        with:
+          fetch-depth: 0   # setuptools_scm needs full history + tags
+
+      - uses: actions/setup-python@v5
+        with:
+          python-version: "3.12"
+
+      - name: Build sdist and wheel
+        run: |
+          python -m pip install --upgrade pip build twine
+          python -m build
+          python -m twine check dist/*
+
+      - uses: actions/upload-artifact@v4
+        with:
+          name: dist
+          path: dist/
+
+  publish-testpypi:
+    name: Publish to TestPyPI
+    needs: build
+    if: github.event_name == 'workflow_dispatch'
+    runs-on: ubuntu-latest
+    environment: testpypi
+    permissions:
+      id-token: write   # OIDC for Trusted Publishing
+    steps:
+      - uses: actions/download-artifact@v4
+        with:
+          name: dist
+          path: dist/
+
+      - uses: pypa/gh-action-pypi-publish@release/v1
+        with:
+          repository-url: https://test.pypi.org/legacy/
+
+  publish-pypi:
+    name: Publish to PyPI
+    needs: build
+    if: github.event_name == 'release'
+    runs-on: ubuntu-latest
+    environment: pypi
+    permissions:
+      id-token: write   # OIDC for Trusted Publishing
+    steps:
+      - uses: actions/download-artifact@v4
+        with:
+          name: dist
+          path: dist/
+
+      - uses: pypa/gh-action-pypi-publish@release/v1

mesofield-0.3.2b0/.github/workflows/release.yml

@@ -0,0 +1,25 @@
+name: Release
+on:
+  push:
+    tags:
+      - 'v*'
+
+permissions:
+  contents: write
+
+jobs:
+  release:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+        with:
+          fetch-depth: 0
+      - uses: actions/setup-python@v5
+        with:
+          python-version: '3.11'
+      - run: pip install build
+      - run: python -m build
+      - uses: softprops/action-gh-release@v2
+        with:
+          files: dist/*
+          generate_release_notes: true

mesofield-0.3.2b0/.gitignore

@@ -0,0 +1,191 @@
+#mesofield
+mesofield/_version.py
+/data/
+/logs/
+**/*.log.*
+/mesofield/logs/
+mesofield/external/drivers
+/experiments
+# Ignore hardware.yaml everywhere except the one in mesofield/tests and mesofield/sample_experiments
+*/hardware.yaml
+!/mesofield/tests/sample_experiment/hardware.yaml
+!/mesofield/sample_experiments/hardware.yaml
+# Byte-compiled / optimized / DLL files
+__pycache__/
+*.py[cod]
+*$py.class
+
+# C extensions
+*.so
+
+# Distribution / packaging
+.conda/
+.Python
+build/
+develop-eggs/
+dist/
+downloads/
+eggs/
+.eggs/
+lib/
+lib64/
+parts/
+sdist/
+var/
+wheels/
+share/python-wheels/
+*.egg-info/
+.installed.cfg
+*.egg
+MANIFEST
+
+# PyInstaller
+#  Usually these files are written by a python script from a template
+#  before PyInstaller builds the exe, so as to inject date/other infos into it.
+*.manifest
+*.spec
+
+# Installer logs
+pip-log.txt
+pip-delete-this-directory.txt
+
+# Unit test / coverage reports
+htmlcov/
+.tox/
+.nox/
+.coverage
+.coverage.*
+.cache
+nosetests.xml
+coverage.xml
+*.cover
+*.py,cover
+.hypothesis/
+.pytest_cache/
+cover/
+
+# Translations
+*.mo
+*.pot
+
+# Django stuff:
+*.log
+local_settings.py
+db.sqlite3
+db.sqlite3-journal
+
+# Flask stuff:
+instance/
+.webassets-cache
+
+# Scrapy stuff:
+.scrapy
+
+# Sphinx documentation
+docs/_build/
+
+# PyBuilder
+.pybuilder/
+target/
+
+# Jupyter Notebook
+.ipynb_checkpoints
+
+# IPython
+profile_default/
+ipython_config.py
+
+# pyenv
+#   For a library or package, you might want to ignore these files since the code is
+#   intended to run in multiple environments; otherwise, check them in:
+# .python-version
+
+# pipenv
+#   According to pypa/pipenv#598, it is recommended to include Pipfile.lock in version control.
+#   However, in case of collaboration, if having platform-specific dependencies or dependencies
+#   having no cross-platform support, pipenv may install dependencies that don't work, or not
+#   install all needed dependencies.
+#Pipfile.lock
+
+# UV
+#   Similar to Pipfile.lock, it is generally recommended to include uv.lock in version control.
+#   This is especially recommended for binary packages to ensure reproducibility, and is more
+#   commonly ignored for libraries.
+#uv.lock
+
+# poetry
+#   Similar to Pipfile.lock, it is generally recommended to include poetry.lock in version control.
+#   This is especially recommended for binary packages to ensure reproducibility, and is more
+#   commonly ignored for libraries.
+#   https://python-poetry.org/docs/basic-usage/#commit-your-poetrylock-file-to-version-control
+#poetry.lock
+
+# pdm
+#   Similar to Pipfile.lock, it is generally recommended to include pdm.lock in version control.
+#pdm.lock
+#   pdm stores project-wide configurations in .pdm.toml, but it is recommended to not include it
+#   in version control.
+#   https://pdm.fming.dev/latest/usage/project/#working-with-version-control
+.pdm.toml
+.pdm-python
+.pdm-build/
+
+# PEP 582; used by e.g. github.com/David-OConnor/pyflow and github.com/pdm-project/pdm
+__pypackages__/
+
+# Celery stuff
+celerybeat-schedule
+celerybeat.pid
+
+# SageMath parsed files
+*.sage.py
+
+# Environments
+.env
+.venv
+env/
+venv/
+ENV/
+env.bak/
+venv.bak/
+
+# Spyder project settings
+.spyderproject
+.spyproject
+
+# Rope project settings
+.ropeproject
+
+# mkdocs documentation
+/site
+
+# mypy
+.mypy_cache/
+.dmypy.json
+dmypy.json
+
+# Pyre type checker
+.pyre/
+
+# pytype static type analyzer
+.pytype/
+
+# Cython debug symbols
+cython_debug/
+
+# PyCharm
+#  JetBrains specific template is maintained in a separate JetBrains.gitignore that can
+#  be found at https://github.com/github/gitignore/blob/main/Global/JetBrains.gitignore
+#  and can be added to the global gitignore or merged into this file.  For a more nuclear
+#  option (not recommended) you can uncomment the following to ignore the entire idea folder.
+#.idea/
+
+# PyPI configuration file
+.pypirc
+Dhyana 400BSI_PIDe408.xml
+.vscode/launch.json
+
+
+# Sphinx-apidoc generated stubs (rebuilt every docs build)
+docs/api/mesofield*.rst
+docs/_build/

mesofield-0.3.2b0/LICENSE

@@ -0,0 +1,21 @@
+MIT License
+
+Copyright (c) 2024 Gronemeyer
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.

mesofield-0.3.2b0/Makefile

@@ -0,0 +1,5 @@
+release:
+	@test -n "$(V)" || (echo "usage: make release V=1.3.0"; exit 1)
+	python -m build
+	git tag v$(V)
+	git push --tags

mesofield-0.3.2b0/PKG-INFO

@@ -0,0 +1,178 @@
+Metadata-Version: 2.4
+Name: mesofield
+Version: 0.3.2b0
+Summary: Mesofield is an open-source image acquisition Python software package build for the Sipe Laboratory at Pennsylvania State University.
+Author: Jacob Gronemeyer
+License: MIT License
+        
+        Copyright (c) 2024 Gronemeyer
+        
+        Permission is hereby granted, free of charge, to any person obtaining a copy
+        of this software and associated documentation files (the "Software"), to deal
+        in the Software without restriction, including without limitation the rights
+        to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+        copies of the Software, and to permit persons to whom the Software is
+        furnished to do so, subject to the following conditions:
+        
+        The above copyright notice and this permission notice shall be included in all
+        copies or substantial portions of the Software.
+        
+        THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+        IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+        FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+        AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+        LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+        OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+        SOFTWARE.
+        
+Project-URL: Homepage, https://github.com/Gronemeyer/mesofield/
+Project-URL: Repository, https://github.com/Gronemeyer/mesofield/
+Project-URL: Issues, https://github.com/Gronemeyer/mesofield/issues
+Project-URL: Documentation, https://gronemeyer.github.io/mesofield/
+Keywords: imaging,microscopy,acquisition,neuroscience
+Classifier: Development Status :: 4 - Beta
+Classifier: Intended Audience :: Science/Research
+Classifier: License :: OSI Approved :: MIT License
+Classifier: Operating System :: OS Independent
+Classifier: Programming Language :: Python :: 3.10
+Classifier: Programming Language :: Python :: 3.11
+Classifier: Programming Language :: Python :: 3.12
+Classifier: Topic :: Scientific/Engineering
+Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
+Requires-Python: >=3.10
+Description-Content-Type: text/markdown
+License-File: LICENSE
+Requires-Dist: annotated-types
+Requires-Dist: click
+Requires-Dist: ipykernel
+Requires-Dist: ipython
+Requires-Dist: jupyter_client
+Requires-Dist: jupyter_core
+Requires-Dist: loguru
+Requires-Dist: markdown-it-py
+Requires-Dist: matplotlib
+Requires-Dist: mesokit-schema
+Requires-Dist: nidaqmx
+Requires-Dist: numpy
+Requires-Dist: packaging
+Requires-Dist: pandas
+Requires-Dist: parso
+Requires-Dist: pillow
+Requires-Dist: platformdirs
+Requires-Dist: psygnal
+Requires-Dist: pyaml
+Requires-Dist: opencv-python
+Requires-Dist: pymmcore
+Requires-Dist: pymmcore-plus
+Requires-Dist: pymmcore-widgets
+Requires-Dist: PyQt6
+Requires-Dist: PyQt6-Qt6
+Requires-Dist: PyQt6_sip
+Requires-Dist: pyqtgraph
+Requires-Dist: pyserial
+Requires-Dist: python-dateutil
+Requires-Dist: pytz
+Requires-Dist: pywin32; sys_platform == "win32"
+Requires-Dist: pyzmq
+Requires-Dist: qtconsole
+Requires-Dist: rich
+Requires-Dist: setuptools
+Requires-Dist: tifffile
+Requires-Dist: typer
+Requires-Dist: typer-slim
+Requires-Dist: typing_extensions
+Requires-Dist: useq-schema
+Requires-Dist: wheel
+Provides-Extra: test
+Requires-Dist: pytest; extra == "test"
+Requires-Dist: coverage; extra == "test"
+Requires-Dist: flake8; extra == "test"
+Requires-Dist: black; extra == "test"
+Requires-Dist: isort; extra == "test"
+Requires-Dist: pytest-cov; extra == "test"
+Requires-Dist: mypy; extra == "test"
+Requires-Dist: gitchangelog; extra == "test"
+Provides-Extra: docs
+Requires-Dist: sphinx>=7; extra == "docs"
+Requires-Dist: pydata-sphinx-theme; extra == "docs"
+Requires-Dist: myst-parser; extra == "docs"
+Requires-Dist: sphinx-copybutton; extra == "docs"
+Requires-Dist: sphinx-design; extra == "docs"
+Dynamic: license-file
+
+```
+ __    __     ______     ______     ______     ______   __     ______     __         _____
+/\ "-./  \   /\  ___\   /\  ___\   /\  __ \   /\  ___\ /\ \   /\  ___\   /\ \       /\  __-.
+\ \ \-./\ \  \ \  __\   \ \___  \  \ \ \/\ \  \ \  __\ \ \ \  \ \  __\   \ \ \____  \ \ \/\ \
+ \ \_\ \ \_\  \ \_____\  \/\_____\  \ \_____\  \ \_\    \ \_\  \ \_____\  \ \_____\  \ \____-
+  \/_/  \/_/   \/_____/   \/_____/   \/_____/   \/_/     \/_/   \/_____/   \/_____/   \/____/
+```
+
+Mesofield is a PyQt6-based framework for running real-time, multi-camera
+neuroscience experiments. It coordinates hardware via serial connections
+and MicroManager (through [pymmcore-plus](https://pymmcore-plus.github.io/pymmcore-plus/)
+custom `MDAEngine`s and multi-`CMMCorePlus` instancing) and manages
+experiment configuration, acquisition orchestration, and data logging.
+The project is aimed at laboratory use and is not a full production
+package; some specialised knowledge of device hardware and
+MicroManager device configuration is necessary to get started.
+
+<img width="2454" height="1592" alt="Mesofield acquisition window" src="https://github.com/user-attachments/assets/151196ab-2d74-4644-85b7-c4facf3b779a" />
+
+---
+
+## Documentation
+
+Documentation lives at **[gronemeyer.github.io/mesofield](https://gronemeyer.github.io/mesofield/)**
+and is split by audience:
+
+- **[Tutorial](https://gronemeyer.github.io/mesofield/tutorial.html)** —
+  the fastest path from a fresh conda env to a working acquisition on
+  your hardware.
+- **[User Guide](https://gronemeyer.github.io/mesofield/user_guide.html)** —
+  for experimenters running acquisitions: launching the GUI, writing
+  `experiment.json`, interpreting the on-disk output.
+- **[Developer Guide](https://gronemeyer.github.io/mesofield/developer_guide.html)** —
+  for developers extending mesofield: custom devices, `Procedure`
+  subclasses, frame processors, threading models.
+- **[API Reference](https://gronemeyer.github.io/mesofield/api/index.html)** —
+  auto-generated from docstrings.
+
+---
+
+## Quick start
+
+```bash
+conda create -n mesofield python=3.12 -y
+conda activate mesofield
+pip install -e .
+```
+
+Launch an acquisition:
+
+```bash
+mesofield launch path/to/experiment.json
+```
+
+Scaffold a new experiment:
+
+```bash
+mesofield new my-experiment
+```
+
+For end-to-end setup, follow the
+[Tutorial](https://gronemeyer.github.io/mesofield/tutorial.html).
+
+---
+
+## System requirements
+
+Tested on Windows 10/11. For multi-camera acquisition with large files
+we recommend ≥ 32 GB RAM, a 12th-gen Intel i7 or equivalent, and fast
+local NVMe storage for the experiment directory.
+
+---
+
+## License
+
+MIT — see `LICENSE`.

mesofield-0.3.2b0/README.md

@@ -0,0 +1,76 @@
+```
+ __    __     ______     ______     ______     ______   __     ______     __         _____
+/\ "-./  \   /\  ___\   /\  ___\   /\  __ \   /\  ___\ /\ \   /\  ___\   /\ \       /\  __-.
+\ \ \-./\ \  \ \  __\   \ \___  \  \ \ \/\ \  \ \  __\ \ \ \  \ \  __\   \ \ \____  \ \ \/\ \
+ \ \_\ \ \_\  \ \_____\  \/\_____\  \ \_____\  \ \_\    \ \_\  \ \_____\  \ \_____\  \ \____-
+  \/_/  \/_/   \/_____/   \/_____/   \/_____/   \/_/     \/_/   \/_____/   \/_____/   \/____/
+```
+
+Mesofield is a PyQt6-based framework for running real-time, multi-camera
+neuroscience experiments. It coordinates hardware via serial connections
+and MicroManager (through [pymmcore-plus](https://pymmcore-plus.github.io/pymmcore-plus/)
+custom `MDAEngine`s and multi-`CMMCorePlus` instancing) and manages
+experiment configuration, acquisition orchestration, and data logging.
+The project is aimed at laboratory use and is not a full production
+package; some specialised knowledge of device hardware and
+MicroManager device configuration is necessary to get started.
+
+<img width="2454" height="1592" alt="Mesofield acquisition window" src="https://github.com/user-attachments/assets/151196ab-2d74-4644-85b7-c4facf3b779a" />
+
+---
+
+## Documentation
+
+Documentation lives at **[gronemeyer.github.io/mesofield](https://gronemeyer.github.io/mesofield/)**
+and is split by audience:
+
+- **[Tutorial](https://gronemeyer.github.io/mesofield/tutorial.html)** —
+  the fastest path from a fresh conda env to a working acquisition on
+  your hardware.
+- **[User Guide](https://gronemeyer.github.io/mesofield/user_guide.html)** —
+  for experimenters running acquisitions: launching the GUI, writing
+  `experiment.json`, interpreting the on-disk output.
+- **[Developer Guide](https://gronemeyer.github.io/mesofield/developer_guide.html)** —
+  for developers extending mesofield: custom devices, `Procedure`
+  subclasses, frame processors, threading models.
+- **[API Reference](https://gronemeyer.github.io/mesofield/api/index.html)** —
+  auto-generated from docstrings.
+
+---
+
+## Quick start
+
+```bash
+conda create -n mesofield python=3.12 -y
+conda activate mesofield
+pip install -e .
+```
+
+Launch an acquisition:
+
+```bash
+mesofield launch path/to/experiment.json
+```
+
+Scaffold a new experiment:
+
+```bash
+mesofield new my-experiment
+```
+
+For end-to-end setup, follow the
+[Tutorial](https://gronemeyer.github.io/mesofield/tutorial.html).
+
+---
+
+## System requirements
+
+Tested on Windows 10/11. For multi-camera acquisition with large files
+we recommend ≥ 32 GB RAM, a 12th-gen Intel i7 or equivalent, and fast
+local NVMe storage for the experiment directory.
+
+---
+
+## License
+
+MIT — see `LICENSE`.