Merge pull request #211 from auto-pi-lot/fix-dtoverlay-location

update location of /boot/firmware/config.txt and bugfixing enough to get the thing running

.github/workflows/tests.yml

@@ -0,0 +1,64 @@
+name: Tests
+
+on:
+  push:
+  pull_request:
+    branches:
+      - main
+      - dev
+
+jobs:
+  test:
+    env:
+      # https://pytest-qt.readthedocs.io/en/latest/troubleshooting.html?highlight=travis#xvfb-assertionerror-timeouterror-when-using-waituntil-waitexposed-and-ui-events
+      DISPLAY: ":99.0"
+      QT_DEBUG_PLUGINS: 1
+    strategy:
+      fail-fast: false
+      matrix:
+        python-version: ["3.9", "3.10", "3.11"]
+
+    runs-on: ubuntu-latest
+
+    steps:
+      - uses: actions/checkout@v2
+      - name: Set up python
+        uses: actions/setup-python@v4
+        with:
+          python-version: ${{ matrix.python-version }}
+          cache: 'pip'
+
+      # see:
+      # - https://pytest-qt.readthedocs.io/en/latest/troubleshooting.html#github-actions
+      # - https://pytest-qt.readthedocs.io/en/latest/troubleshooting.html#xvfb-assertionerror-timeouterror-when-using-waituntil-waitexposed-and-ui-events
+      - name: Install system dependencies
+        uses: awalsh128/cache-apt-pkgs-action@latest
+        with:
+          packages: x11-utils libxkbcommon-x11-0 xvfb herbstluftwm qt5-default qttools5-dev-tools libxcb-icccm4 libxcb-image0 libxcb-keysyms1 libxcb-randr0 libxcb-render-util0 libxcb-xinerama0 libxcb-xfixes0
+          version: "0.5.1"
+
+      - name: Install package dependencies
+        run: pip install -e ".[tests]"
+
+      - name: Run Tests
+        run: |
+          herbstluftwm &
+          sleep 1
+          mkdir -p $HOME/autopilot
+          mkdir -p $HOME/autopilot/logs
+          pytest --cov=autopilot --cov-config=.coveragerc --cov-report term-missing tests
+
+      - name: Coveralls
+        uses: coverallsapp/github-action@v2
+        with:
+          flag-name: run-${{ join(matrix.*, '-') }}
+          parallel: true
+
+  coverage:
+    needs: test
+    runs-on: ubuntu-latest
+    steps:
+      - name: Coveralls Finished
+        uses: coverallsapp/github-action@v2
+        with:
+          parallel-finished: true

.readthedocs.yml

@@ -9,17 +9,17 @@ version: 2
 sphinx:
   configuration: docs/conf.py
 
-# Build documentation with MkDocs
-#mkdocs:
-#  configuration: mkdocs.yml
+build:
+  os: ubuntu-22.04
+  tools:
+    python: "3.9"
 
 # Optionally build your docs in additional formats such as PDF
 formats:
   - pdf
 
 # Optionally set the version of Python and requirements required to build your docs
 python:
-  version: 3.8
   install:
     - method: pip
       path: .

autopilot/data/interfaces/datajoint.py

@@ -1,7 +1,9 @@
 """
 Prototype interface to datajoint models using ``datajoint-babel``
+
+This module was not completed and is left as a reference :)
+
 """
-raise NotImplementedError('The datajoint interface is not complete, it is left here for reference')
 
 # import typing
 # from typing import Optional

autopilot/setup/scripts.py

@@ -94,8 +94,8 @@
         'text': 'Setup Hifiberry DAC/AMP?',
         'commands': [
             {'command': 'sudo adduser pi i2c', 'optional': True},
-            'sudo sed -i \'s/^dtparam=audio=on/#dtparam=audio=on/g\' /boot/config.txt',
-            'sudo sed -i \'$s/$/\\ndtoverlay=hifiberry-dacplus\\ndtoverlay=i2s-mmap\\ndtoverlay=i2c-mmap\\ndtparam=i2c1=on\\ndtparam=i2c_arm=on/\' /boot/config.txt',
+            'sudo sed -i \'s/^dtparam=audio=on/#dtparam=audio=on/g\' /boot/firmware/config.txt',
+            'sudo sed -i \'$s/$/\\ndtoverlay=hifiberry-dacplus\\ndtoverlay=i2s-mmap\\ndtoverlay=i2c-mmap\\ndtparam=i2c1=on\\ndtparam=i2c_arm=on/\' /boot/firmware/config.txt',
             'echo -e \'pcm.!default {\\n type hw card 0\\n}\\nctl.!default {\\n type hw card 0\\n}\' | sudo tee /etc/asound.conf'
         ]
     },
@@ -107,7 +107,7 @@
         'type': 'bool',
         'text': 'Disable Bluetooth? (recommended unless you\'re using it <3',
         'commands': [
-            'sudo sed - i \'$s/$/\ndtoverlay=pi3-disable-bt/\' /boot/config.txt',
+            'sudo sed - i \'$s/$/\ndtoverlay=pi3-disable-bt/\' /boot/firmware/config.txt',
             'sudo systemctl disable hciuart.service',
             'sudo systemctl disable bluealsa.service',
             'sudo systemctl disable bluetooth.service'
@@ -223,8 +223,8 @@
         'type': 'bool',
         'text': 'Enable i2c and set baudrate to 100kHz',
         'commands': [
-            'sudo sed -i \'s/^#dtparam=i2c_arm=on/dtparam=i2c_arm=on/g\' /boot/config.txt',
-            'sudo sed -i \'$s/$/\ni2c_arm_baudrate=100000/\' /boot/config.txt',
+            'sudo sed -i \'s/^#dtparam=i2c_arm=on/dtparam=i2c_arm=on/g\' /boot/firmware/config.txt',
+            'sudo sed -i \'$s/$/\ni2c_arm_baudrate=100000/\' /boot/firmware/config.txt',
             'sudo sed -i \'$s/$/\ni2c-dev/\' /etc/modules',
             'sudo dtparam i2c_arm=on',
             'sudo modprobe i2c-dev'

autopilot/setup/setup_mlx90640.sh

@@ -4,10 +4,10 @@ sudo apt-get update
 sudo apt-get install -y libi2c-dev swig
 
 # enable i2c module
-sudo sed -i 's/^#dtparam=i2c_arm=on/dtparam=i2c_arm=on/g' /boot/config.txt
+sudo sed -i 's/^#dtparam=i2c_arm=on/dtparam=i2c_arm=on/g' /boot/firmware/config.txt
 
 # increase baudrate
-sudo sed -i '$s/$/\ndtparam=i2c_arm_baudrate=1000000/' /boot/config.txt
+sudo sed -i '$s/$/\ndtparam=i2c_arm_baudrate=1000000/' /boot/firmware/config.txt
 
 #cd ~/git
 # clone submodules if we haven't already

autopilot/transform/geometry.py

@@ -737,8 +737,8 @@ def _maxlinedev(self, x, y):
         # all credit to http://ieeexplore.ieee.org/document/6166585/
         # adapted from MATLAB scripts here: https://docs.google.com/open?id=0B10RxHxW3I92dG9SU0pNMV84alk
 
-        x = x.astype(np.float)
-        y = y.astype(np.float)
+        x = x.astype(float)
+        y = y.astype(float)
 
         results = {}
 

autopilot/utils/wiki.py

@@ -1,7 +1,7 @@
 """
 Utility functions for dealing with the wiki (https://wiki.auto-pi-lot.com).
 
-See the docstrings of the :func:`.ask` function, as well as the :ref:`guide_wiki_plugins` section
+See the docstrings of the :func:`.ask` function, as well as the :ref:`guide_plugins_wiki` section
 in the user guide for use.
 """
 from typing import Union, Optional, List

conftest.py

@@ -0,0 +1,22 @@
+import pytest
+import os
+import sys
+
+def on_gh_actions() -> bool:
+    return "CI" in os.environ or os.environ["CI"] or "GITHUB_RUN_ID" in os.environ
+
+# patch cpuinfo which doesn't work on github actions
+# (and actually isn't needed by blosc2 or pytables, but they
+# call it at the module level so their imports fail and we need
+# to monkeypatch in this janky way
+module = type(sys)('cpuinfo')
+module.get_cpu_info = lambda: {}
+sys.modules['cpuinfo'] = module
+
+def pytest_collection_modifyitems(config, items):
+
+    skip_gui = pytest.mark.skip('GUI is not working with pyside6 atm')
+    for item in items:
+        if item.get_closest_marker('gui'):
+            item.add_marker(skip_gui)
+

docs/conf.py

@@ -110,6 +110,7 @@
 autodoc_member_order = "bysource"
 #autodoc_default_flags = ['members']
 #autodoc_mock_imports = ['tables', 'PySide', 'pyo', 'jack', 'pyqtgraph']
+autodoc_mock_imports = ['pytestqt']
 autodata_content = "both"
 
 autodoc_default_options = {
@@ -142,6 +143,7 @@
 # pydantic_autodoc
 # --------------------------------------------------
 autodoc_pydantic_field_doc_policy = "both"
+autodoc_pydantic_model_show_json_error_strategy = 'coerce'
 
 
 
@@ -163,7 +165,7 @@
 #
 # This is also used if you do content translation via gettext catalogs.
 # Usually you set "language" from the command line for these cases.
-language = None
+language = 'en'
 
 # List of patterns, relative to source directory, that match files and
 # directories to ignore when looking for source files.

docs/examples/index.md

@@ -8,7 +8,7 @@ Also see the ``examples`` folder in the repository for jupyter notebooks we have
 ```{toctree}
 :maxdepth: 1
 :caption: Tasks
------------------
+
 blink
 gonogo
 ```

docs/gui/widgets/protocol.rst

@@ -2,7 +2,7 @@
 protocol
 ---------
 
-.. automodule:: autopilot.gui.widgets.model
+.. automodule:: autopilot.gui.widgets.protocol
     :members:
     :undoc-members:
     :show-inheritance:

docs/guide/configuration.md

@@ -110,7 +110,7 @@ After configuration, all the files you'll interact with will be in the user dire
 
 An example user directory might look like this:
 
-```
+```text
 ./autopilot
 ├── calibration
 ├── data

docs/guide/plugins.rst

@@ -43,7 +43,9 @@ Using plugins is simple! Anything inside of the directory indicated by ``prefs.g
 provide objects that inherit from Autopilot classes supported by an entry in :data:`.registry.REGISTRIES` .
 
 For example, we want to write a task that uses some special hardware that we need. We could start by making a directory
-within ``'PLUGINDIR'`` like this::
+within ``'PLUGINDIR'`` like this:
+
+.. code-block:: text
 
     plugins
     ├── my-autopilot-plugin

docs/tests/test_transforms.rst

@@ -2,5 +2,5 @@ Transforms
 ===========
 
 
-.. automodule:: tests.test_transform_geometry
+.. automodule:: tests.test_transforms_geometry
     :members: