Merge pull request #692 from int-brain-lab/iblrigv8dev

8.21.0

.github/workflows/main.yaml

@@ -35,39 +35,30 @@ jobs:
  uses: actions/checkout@v4
  with:
  fetch-depth: 0
-
- - name: Setup Python
- uses: actions/setup-python@v5
+ - name: Set up PDM
+ uses: pdm-project/setup-pdm@v4
  with:
  python-version: ${{ matrix.python-version }}
- cache: 'pip'
- cache-dependency-path: 'pyproject.toml'
-
- - name: install requirements
- shell: bash -l {0}
- run: |
- pip install --editable .[DEV]
-
+ cache: true
+ - name: Install requirements
+ run: pdm sync -dG test
  - name: Install audio library (Ubuntu only)
  if: matrix.os == 'ubuntu-latest'
  run: sudo apt-get install -y libportaudio2
-
  - name: iblrig unit tests
- run: pytest
-
+ run: pdm run pytest
  - name: coveralls.io
  uses: coverallsapp/github-action@v2
  with:
  flag-name: ${{ matrix.python-version }}, ${{ matrix.os }}
  parallel: true
  file: coverage.xml
  compare-ref: iblrigv8
-
  - name: Generate requirements_frozen.txt
- run: pip freeze > requirements_frozen.txt
-
+ run: pdm export -o requirements_frozen.txt --no-hashes
  - name: Store frozen requirements as artifacts
- uses: actions/upload-artifact@v3
+ if: matrix.os == 'ubuntu-latest'
+ uses: actions/upload-artifact@v4
  with:
  name: requirements_frozen
  path: requirements_frozen.txt

.gitignore

@@ -43,3 +43,6 @@ coverage.xml
 
 devices/camera_setup/*.layout
 devices/camera_recordings/*.layout
+.pdm-python
+/dist
+*~

.pre-commit-config.yaml

@@ -1,30 +1,22 @@
 repos:
 
 - repo: https://github.com/pre-commit/pre-commit-hooks
- rev: v4.5.0
+ rev: v4.6.0
  hooks:
  - id: end-of-file-fixer
  types_or: [python, yaml, json, toml]
  - id: trailing-whitespace
  types_or: [python, yaml, json, toml]
- - id: check-case-conflict
- - id: check-ast
  - id: check-yaml
  - id: check-json
  - id: check-toml
  - id: check-xml
- - id: check-vcs-permalinks
- - id: detect-private-key
-
-- repo: https://github.com/pre-commit/pygrep-hooks
- rev: v1.10.0
- hooks:
- - id: python-use-type-annotations
- - id: python-no-log-warn
- - id: text-unicode-replacement-char
 
 - repo: https://github.com/astral-sh/ruff-pre-commit
- rev: v0.3.5
+ rev: v0.5.1
  hooks:
  - id: ruff
+ types_or: [ python, pyi ]
+ args: [ --fix ]
  - id: ruff-format
+ types_or: [ python, pyi ]

CHANGELOG.md

@@ -2,6 +2,18 @@ Changelog
 =========
 
 
+8.21.0
+------
+* display values of automatically inferred task parameters
+* store pause durations to trial info
+* add backend for UDP communication between rig computers
+* use PDM for managing dependencies
+* log session call / commandline parameters to disk
+* fix: potential deadlock with SerialSingleton
+* fix: "galloping" valve during valve calibration
+* fix: values computed by "Get Training Phase" in "Tools" menu
+* fix: incorrect parsing of adaptive gain value in trainingChoiceWorld
+
 8.20.0
 ------
 * tab for displaying local sessions and their respective status
@@ -317,5 +329,6 @@ Changelog
 8.9.0
 -----
 * major rework of the GUI
+* allow pausing between trials
 * task-specific settings
 * new dialogs for weight & droppings

docs/source/installation.rst

@@ -237,6 +237,12 @@ To update the additional tasks and extractors (see :ref:`Installing iblrigv8`, p
  git pull
 
 
+.. tip::
+
+ While usually quite snappy, upgrading the virtual environment in some instances can take longer than expected.
+ Please be patient during the upgrade procedure.
+
+
 Switch to specific iblrig version
 ---------------------------------
 .. warning:: Downgrading is not recommended and may not work as some releases break compatibility with earlier versions.

docs/source/reference_developer_guide.rst

@@ -35,54 +35,61 @@ Here,
 Both of these fields are inferred by means of git describe and do not require manual interaction from the developer.
 
 
+PDM
+---
+
+We use `PDM <https://pdm-project.org/en/latest/>`_ to manage dependencies of IBLRIG.
+See `PDM's documentation <https://pdm-project.org/en/latest/#installation>` for help with installing PDM.
+
+
 Installing Developer Dependencies
 ---------------------------------
 
-To install additional dependencies needed for working on IBLRIG's code-base, run the following within the venv:
+To install additional dependencies needed for working on IBLRIG's code-base, run:
 
 .. code-block:: console
 
- pip install -U -e .[DEV]
+ pdm sync -d
 
 
 Running Unit Tests Locally
 --------------------------
 
-To run unit tests locally, run the following within IBLRIG's venv:
+To run unit tests locally, run:
 
 .. code-block:: console
 
- pytest
+ pdm run pytest
 
 This will also generate a coverage report which can be found in the ``htmlcov`` directory.
 
 
 Linting & Formatting
 --------------------
 
-To lint your code, run the following within IBLRIG's venv:
+To lint your code, run the:
 
 .. code-block:: console
 
- ruff check .
+ pdm run ruff check
 
 Adding the commandline flag ``--fix`` will automatically fix issues that are deemed safe to handle:
 
 .. code-block:: console
 
- ruff check . --fix
+ pdm run ruff check --fix
 
 To *check* if your code conforms to the `Black code style <https://black.readthedocs.io/en/stable/the_black_code_style/current_style.html>`_, run:
 
 .. code-block:: console
 
- ruff format . --check
+ pdm run ruff format --check
 
 To reformat your code according to the `Black code style <https://black.readthedocs.io/en/stable/the_black_code_style/current_style.html>`_, run:
 
 .. code-block:: console
 
- ruff format .
+ pdm run ruff format
 
 Refer to `Ruff Formater's documentation <https://docs.astral.sh/ruff/formatter/>`_ for further details.
 
@@ -103,17 +110,8 @@ Building the documentation
 
 .. code-block:: console
 
- # make sure pre-requisites are installed
- pip install --upgrade -e .[DEV]
- # create the static directory
- rm -rf ./docs/build
- mkdir -p ./docs/build/html/_static
- # unit tests generate task diagrams
- python -m unittest discover ./iblrig/test
- # generate class diagrams
- pyreverse -o png -m y --ignore iblrig.test -A --output-directory ./docs/build/html/_static ./iblrig_tasks
- # build and serve the docs locally
- sphinx-autobuild ./docs/source ./docs/build/html/
+ pdm run sphinx-autobuild ./docs/source ./docs/build
+
 
 Contribute to the documentation
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

iblrig/__init__.py

@@ -6,7 +6,7 @@
 # 5) git tag the release in accordance to the version number below (after merge!)
 # >>> git tag 8.15.6
 # >>> git push origin --tags
-__version__ = '8.20.0'
+__version__ = '8.21.0'
 
 
 from iblrig.version_management import get_detailed_version_string