Merge pull request #830 from int-brain-lab/iblrigv8dev

8.29.0

Author: bimac

.editorconfig

@@ -0,0 +1,28 @@
+# EditorConfig is awesome: https://editorconfig.org
+
+# top-most EditorConfig file
+root = true
+
+# General settings
+[*]
+end_of_line = lf
+insert_final_newline = true
+trim_trailing_whitespace = true
+max_line_length = 80
+charset = utf-8
+
+# 4 space indentation
+[*.py]
+max_line_length = 130
+indent_style = space
+indent_size = 4
+
+# Indentation override for rst files
+[*.rst]
+indent_style = space
+indent_size = 3
+
+# Indentation override for rst and yaml files
+[*.{toml,yaml,qrc}]
+indent_style = space
+indent_size = 2

.github/workflows/documentation.yaml

@@ -18,17 +18,14 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - uses: actions/checkout@v4
-      - name: Set up PDM
-        uses: pdm-project/setup-pdm@v4
-        with:
-          cache: true
-          python-version-file: pyproject.toml
-      - name: Install requirements
-        run: pdm sync -dG doc
+      - name: Install uv
+        uses: astral-sh/setup-uv@v6
+      - name: Install dependencies
+        run: uv sync --no-default-groups --group doc
       - name: Install PortAudio and GraphViz
         run: sudo apt-get install -y libportaudio2 graphviz
       - name: Sphinx build
-        run: pdm run sphinx-build docs/source docs/build/html
+        run: uv run --frozen sphinx-build docs/source docs/build/html
       - name: Deploy
         uses: peaceiris/actions-gh-pages@v3
         with:

.github/workflows/main.yaml

@@ -20,6 +20,7 @@ jobs:
           version-file: 'pyproject.toml'
           args: 'check --output-format=github'
       - run: 'ruff format --check --diff'
+        
   tests:
     name: build (${{ matrix.python-version }}, ${{ matrix.os }})
     needs: ruff
@@ -33,37 +34,28 @@ jobs:
         uses: actions/checkout@v4
         with:
           fetch-depth: 0
-      - name: Set up PDM
-        uses: pdm-project/setup-pdm@v4
+      - name: Install uv
+        uses: astral-sh/setup-uv@v6
         with:
-          python-version: ${{ matrix.python-version }}
-          cache: true
-      - name: Install requirements
-        run: pdm sync -G project-extraction -dG test -dG ci
-      - name: Install audio library (Ubuntu only)
+          activate-environment: true
+      - name: Install dependencies
+        run: uv sync --no-default-groups --group test --group ci --extra project-extraction
+      - name: Install required libraries (Ubuntu only)
         if: matrix.os == 'ubuntu-latest'
-        run: sudo apt-get install -y libportaudio2
-      - uses: pyvista/setup-headless-display-action@v3
-        with:
-          qt: true
-          pyvista: false
+        run: sudo apt-get install -y libportaudio2 libegl1 libxkbcommon-x11-0
       - name: iblrig unit tests
-        run: pdm run pytest
+        run: pytest
+        env:
+          QT_QPA_PLATFORM: offscreen
+          QT_QUICK_BACKEND: software
+          QT_OPENGL: software
       - 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: pdm export -o requirements_frozen.txt --no-hashes
-      - name: Store frozen requirements as artifacts
-        if: matrix.os == 'ubuntu-latest'
-        uses: actions/upload-artifact@v4
-        with:
-          name: requirements_frozen
-          path: requirements_frozen.txt
 
   finish:
     needs: [ruff, tests]

.github/workflows/release.yaml

@@ -11,15 +11,14 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - uses: actions/checkout@v4
-      - name: Set up PDM
-        uses: pdm-project/setup-pdm@v4
-        with:
-          cache: true
-          python-version-file: pyproject.toml
-      - name: Install requirements
-        run: pdm sync -dG doc
+      - name: Install uv
+        uses: astral-sh/setup-uv@v6
+      - name: Install dependencies
+        run: uv sync --no-default-groups --group doc
+      - name: Sphinx build
+        run: uv run --frozen sphinx-build docs/source docs/build/html
       - name: Build PDF
-        run: pdm run make -C docs/ simplepdf
+        run: uv run --frozen make -C docs/ simplepdf
       - name: Upload artifact
         uses: actions/upload-artifact@v4
         with:

CHANGELOG.md

@@ -1,6 +1,12 @@
 Changelog
 =========
 
+8.29.0
+------
+* added: GUI settings for changing MAIN_SYNC
+* fixed: Stop/Pause button not always working for UDP sessions
+* changed: use UV for packaging
+
 8.28.2
 ------
 * fixed: ensure that reward amount shown in online plots stays visible at all times
@@ -26,7 +32,7 @@ Changelog
 * fixed: online plots included timeout trials
 * fixed: online plots showed wrong reward amount for adaptive rewards
 * fixed: online plots did not take into account initial delay
-* fixed: data tab did not show correct session copy status 
+* fixed: data tab did not show correct session copy status
 
 -------------------------------
 
@@ -36,7 +42,7 @@ Changelog
 
 8.27.6
 ------
-* fixed: detection of LED control ability broken for Bpods with old firmware  
+* fixed: detection of LED control ability broken for Bpods with old firmware
 
 8.27.5
 ------
@@ -52,7 +58,7 @@ Changelog
 * changed: reset camera(s) prior to starting task when inconsistencies have been detected
 * changed: include stock subjects if user is stock manager
 * changed: skip validation of Ambient Module if device_bpod.USE_AMBIENT_MODULE is false
-* added: `remove_bonsai_layouts` command for troubleshooting BONSAI GUIs not appearing 
+* added: `remove_bonsai_layouts` command for troubleshooting BONSAI GUIs not appearing
 
 8.27.2
 ------
@@ -84,7 +90,7 @@ Changelog
 8.25.0
 ------
 * feature: fiber photometry loader
-* feature: dataframe converter for Bpod session data 
+* feature: dataframe converter for Bpod session data
 * removed: remaining tkinter dialogs
 
 -------------------------------
@@ -128,7 +134,7 @@ Changelog
 * feature: validate values in `trials_table` using Pydantic
 * feature: add auto-generated API reference to documentation
 * changed: `show_trial_log()` now accepts a dict for including additional log items
-* fix: `_ephysChoiceWorld` - values from the pre-generated sessions were not actually used 
+* fix: `_ephysChoiceWorld` - values from the pre-generated sessions were not actually used
 * fix: `_ephysChoiceWorld` - trial fixtures contained inverted values for `probability_left`
 * fix: GUI - Subjects and Projects are not being cached
 * add script for validating audio output of Bpod HiFi Module (in `scripts/` folder)
@@ -271,7 +277,7 @@ Changelog
 
 8.15.4
 ------
-* hotfix: disable prompt for deleting "duds" for appended sessions 
+* hotfix: disable prompt for deleting "duds" for appended sessions
 
 8.15.3
 ------

docs/source/conf.py

@@ -26,6 +26,8 @@
     'sphinx.ext.autosummary',
     'sphinx.ext.inheritance_diagram',
     'sphinx.ext.viewcode',
+    'sphinx_design',
+    'sphinx_copybutton',
 ]
 autosectionlabel_prefix_document = True
 source_suffix = ['.rst', '.md']

docs/source/developer_guide.rst

@@ -36,23 +36,38 @@ Both of these fields are automatically inferred (by means of ``git describe``) a
 developer.
 
 
-Package Management and Development Workflows with PDM
------------------------------------------------------
+Package Management and Development Workflows with UV
+----------------------------------------------------
 
-We use `PDM <https://pdm-project.org/en/latest/>`_ to manage dependencies of IBLRIG.
-PDM can also be used to run various commands with relevance to the development process without having to activate a virtual
-environment first.
-Please refer to `PDM's documentation <https://pdm-project.org/en/latest/#installation>`_ for help with installing PDM.
+This project is utilizing `UV <https://github.com/astral-sh/uv>`_ as its package
+manager for managing dependencies and ensuring consistent and reproducible environments.
+To install UV:
+
+.. tab-set::
+
+   .. tab-item:: Linux and macOS
+
+      .. code-block:: console
+
+         $ curl -LsSf https://astral.sh/uv/install.sh | sh
+
+   .. tab-item:: Windows
+
+      .. code-block:: pwsh-session
+
+         PS> powershell -ExecutionPolicy ByPass -c "irm https://astral.sh/uv/install.ps1 | iex"
+
+See `UV's documentation <https://docs.astral.sh/uv/>`_ for details.
 
 
 Installing Developer Dependencies
 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
 
-To install additional dependencies needed for working on IBLRIG's code-base, run:
+To install IBLRIG as an editable package including all developer dependencies:
 
-.. code-block:: console
+.. code-block:: pwsh-session
 
-   pdm sync -d
+   PS> uv sync
 
 
 Running Unit Tests
@@ -62,7 +77,7 @@ To run unit tests locally, run:
 
 .. code-block:: console
 
-   pdm run pytest
+   uv run --frozen pytest
 
 This will also generate a HTML based coverage report which can be found in the ``htmlcov`` directory.
 
@@ -77,15 +92,15 @@ To lint your code, run:
 
 .. code-block:: console
 
-   pdm run ruff check
+   uv run --frozen ruff check
 
 Appending the flag ``--fix`` to the above command will automatically fix issues that are deemed safe to handle.
 
 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
 
-   pdm run ruff format
+   uv run --frozen uff format
 
 Appending the flag ``--check`` to the above command will check your code for formatting issues without applying any changes.
 Refer to `Ruff Formater's documentation <https://docs.astral.sh/ruff/formatter/>`_ for further details.
@@ -116,13 +131,13 @@ To build the documentation, run:
 
 .. code-block:: console
 
-   pdm run sphinx-autobuild ./docs/source ./docs/build
+   uv run --frozen sphinx-autobuild ./docs/source ./docs/build
 
 You can also export the documentation to a PDF file:
 
 .. code-block:: console
 
-   pdm run make -C docs/ simplepdf
+   uv run --frozen make -C docs/ simplepdf
 
 Find the exported PDF file in ``docs/build/simplepdf``.
 

iblrig/__init__.py

@@ -6,4 +6,4 @@
 # 5) git tag the release in accordance to the version number below (after merge!)
 # >>> git tag 8.15.6
 # >>> git push origin --tags
-__version__ = '8.28.2'
+__version__ = '8.29.0'

iblrig/base_choice_world.py

@@ -295,24 +295,21 @@ def _run(self) -> None:
             time_last_trial_end = time.time()
 
             # handle pause event
-            flag_pause = self.paths.SESSION_FOLDER.joinpath('.pause')
-            flag_stop = self.paths.SESSION_FOLDER.joinpath('.stop')
-            if flag_pause.exists() and trial_number < (self.task_params.NTRIALS - 1):
+            if self.paused and trial_number < (self.task_params.NTRIALS - 1):
                 log.info(f'Pausing session inbetween trials {trial_number} and {trial_number + 1}')
-                while flag_pause.exists() and not flag_stop.exists():
+                while self.paused and not self.stopped:
                     time.sleep(1)
                 self.trials_table.at[self.trial_num, 'pause_duration'] = time.time() - time_last_trial_end
-                if not flag_stop.exists():
+                if not self.stopped:
                     log.info('Resuming session')
 
             # save trial and update log
             self.trial_completed(self.bpod.session.current_trial.export())
             self.show_trial_log()
 
             # handle stop event
-            if flag_stop.exists():
+            if self.stopped:
                 log.info('Stopping session after trial %d', trial_number)
-                flag_stop.unlink()
                 break
 
     def mock(self, file_jsonable_fixture=None):
@@ -605,8 +602,6 @@ def trial_completed(self, bpod_data: dict[str, Any]) -> None:
             with self.paths['AMBIENT_FILE_PATH'].open('ab') as f:
                 binary.write_array(f, [self.trial_num, *sensor_reading], DTYPE_AMBIENT_SENSOR_BIN)
 
-        # this is a flag for the online plots. If online plots were in pyqt5, there is a file watcher functionality
-        Path(self.paths['DATA_FILE_PATH']).parent.joinpath('new_trial.flag').touch()
         self.paths.SESSION_FOLDER.joinpath('transfer_me.flag').touch()
         self.check_sync_pulses(bpod_data=bpod_data)
 
@@ -823,7 +818,7 @@ def _run(self):
             )
         super()._run()
 
-    def __del__(self):
+    def _finalize(self):
         if isinstance(self.plot_subprocess, subprocess.Popen) and self.plot_subprocess.poll() is None:
             log.info('Terminating subprocess: online plots')
             self.plot_subprocess.terminate()