Refactor codebase into installable "reprostim" Python module (+ reprostim-videocapture) package

.autorc

@@ -0,0 +1,16 @@
+{
+    "onlyPublishWithReleaseLabel": true,
+    "baseBranch": "master",
+    "author": "DANDI Bot <[email protected]>",
+    "noVersionPrefix": true,
+    "plugins": [
+        "git-tag",
+        [
+            "exec",
+            {
+                  "afterRelease": "python -m build && twine upload dist/*"
+            }
+        ],
+        "released"
+    ]
+}

.codespell-ignore

@@ -0,0 +1 @@
+acend

.codespellrc

@@ -0,0 +1,3 @@
+[codespell]
+ignore-words = .codespell-ignore
+skip = venv,reprostim-capture,build,cmake-build-debug

.github/workflows/ccpp.yml

@@ -28,21 +28,21 @@ jobs:
         cd build
         cmake ..
         make
-      working-directory: Capture
+      working-directory: src/reprostim-capture
 
     - name: Test "reprostim-videocapture -h"
       run: |
         ./reprostim-videocapture -V
         ./reprostim-videocapture -h
-      working-directory: Capture/build/videocapture
+      working-directory: src/reprostim-capture/build/videocapture
 
     - name: Test "reprostim-screencapture -h"
       run: |
         ./reprostim-screencapture -V
         ./reprostim-screencapture -h
-      working-directory: Capture/build/screencapture
+      working-directory: src/reprostim-capture/build/screencapture
 
     - name: Run tests with CTest
       run: |
         ctest --output-on-failure
-      working-directory: Capture/build
+      working-directory: src/reprostim-capture/build

.github/workflows/codespell.yml

@@ -0,0 +1,22 @@
+---
+name: Codespell
+
+on:
+  push:
+    branches: [main]
+  pull_request:
+    branches: [main]
+
+permissions:
+  contents: read
+
+jobs:
+  codespell:
+    name: Check for spelling errors
+    runs-on: ubuntu-latest
+
+    steps:
+      - name: Checkout
+        uses: actions/checkout@v3
+      - name: Codespell
+        uses: codespell-project/actions-codespell@v2

.github/workflows/pytest.yml

@@ -0,0 +1,57 @@
+---
+name: Test with pytest and hatch
+
+on:
+  push:
+    branches: [main]
+  pull_request:
+    branches: [main]
+
+permissions:
+  contents: read
+
+jobs:
+  pytest:
+    name: Test with pytest
+    runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        python:
+          - '3.10'
+    steps:
+    - name: Configure environment
+      run: |
+        git config --global user.name "reprostim-test"
+        git config --global user.email "[email protected]"
+        uname -a
+        date -Is
+        date -u
+
+    - name: Checkout source code
+      uses: actions/checkout@v4
+      with:
+        fetch-depth: 0
+
+    - name: Setup Python
+      uses: actions/setup-python@v4
+      with:
+        python-version: ${{ matrix.python }}
+
+    - name: Install hatch and virtual environment
+      run: |
+        pwd
+        ls -l
+        pip install --upgrade pip
+        pip install hatch
+        hatch env create
+      shell: bash
+
+    - name: Run pytest
+      run: |
+        hatch run pytest --cov=. --cov-report=xml
+      shell: bash
+
+    - name: Upload coverage reports to Codecov
+      uses: codecov/codecov-action@v3
+      env:
+        CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN }}

.github/workflows/release.yml

@@ -0,0 +1,40 @@
+name: Auto-release on PR merge
+
+on:
+  # ATM, this is the closest trigger to a PR merging
+  push:
+    branches:
+      - master
+
+jobs:
+  auto-release:
+    runs-on: ubuntu-latest
+    if: "!contains(github.event.head_commit.message, 'ci skip') && !contains(github.event.head_commit.message, 'skip ci')"
+    steps:
+      - name: Checkout source
+        uses: actions/checkout@v4
+        with:
+          fetch-depth: 0
+
+      - name: Download latest auto
+        run: |
+          auto_download_url="$(curl -fsSL https://api.github.com/repos/intuit/auto/releases/latest | jq -r '.assets[] | select(.name == "auto-linux.gz") | .browser_download_url')"
+          wget -O- "$auto_download_url" | gunzip > ~/auto
+          chmod a+x ~/auto
+
+      - name: Set up Python
+        uses: actions/setup-python@v5
+        with:
+          python-version: 3.9
+
+      - name: Install build & twine
+        run: python -m pip install build twine
+
+      - name: Create release
+        run: ~/auto shipit -vv
+        env:
+          GH_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+          TWINE_USERNAME: __token__
+          TWINE_PASSWORD: ${{ secrets.PYPI_TOKEN }}
+
+# vim:set sts=2:

.gitignore

@@ -8,3 +8,17 @@ Videos/
 *.pyc
 Capture/C++/VideoCapture
 venvs
+build/
+.coverage*
+.dir-locals.el
+dist/
+*.egg-info
+.env.*
+!.env.local
+.flake8
+.idea/
+.mypy_cache/
+*.pid
+*.pyc
+.python-version
+

.pre-commit-config.yaml

@@ -0,0 +1,37 @@
+repos:
+  - repo: https://github.com/pre-commit/pre-commit-hooks
+    rev: v4.6.0
+    hooks:
+      - id: check-added-large-files
+      - id: check-json
+      - id: check-toml
+      - id: check-yaml
+      - id: end-of-file-fixer
+      - id: trailing-whitespace
+
+  - repo: https://github.com/PyCQA/isort
+    rev: 5.13.2
+    hooks:
+      - id: isort
+
+  - repo: https://github.com/psf/black
+    rev: 24.4.2
+    hooks:
+      - id: black
+
+  - repo: https://github.com/pycqa/flake8
+    rev: 7.0.0
+    hooks:
+      - id: flake8
+        # B008 Do not perform function calls in argument defaults.
+        # A003 class attribute "id" is shadowing a python builtin
+        args: ["-j8", "--ignore=B008,A003", "--max-line-length=89"]
+        additional_dependencies:
+          - flake8-bugbear
+          - flake8-builtins
+          - flake8-unused-arguments
+
+exclude: '^src/reprostim-capture/.*|.codespellrc'
+
+default_language_version:
+    python: python3.10

Events/listeners.py

@@ -10,7 +10,7 @@ def listen(command, pyb):
 	Notes
 	-----
 	* This could be set up as a global listener, though that might be overkill just for conveying stimulus events.
-	* Using `-1` polling to disable timouts, we could use ipoll instead:
+	* Using `-1` polling to disable timeouts, we could use ipoll instead:
 		https://docs.micropython.org/en/latest/library/select.html?highlight=poll#select.poll.ipoll
 	"""
 

LICENSE.txt

@@ -0,0 +1,21 @@
+The MIT License (MIT)
+
+Copyright (c) 2020-2024 TBD
+
+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.

README.md

@@ -84,7 +84,7 @@ The A/V out connections from SC can be any standard as long as you have the
 appropriate adapters, dongles, etc. However, if your Video out does not
 support embedded audio (e.g. VGA), then you will need a separate audio out
 set of splitters and cables. The Magewell device has standard audio ports to
-accomodate this eventuality.
+accommodate this eventuality.
 
 Note: Missing from Schematics A and B, is any connection back to SC that
 records subject response information. That's because ReproStim is not
@@ -123,26 +123,30 @@ subjects.
 
 On Debian
 
+```shell
     apt-get install -y ffmpeg libudev-dev libasound-dev libv4l-dev libyaml-cpp-dev libspdlog-dev catch2 v4l-utils libopencv-dev libcurl4-openssl-dev nlohmann-json3-dev cmake g++
+```
 
 "Parsing/parse_wQR.py" script requires in zbar to be installed as well:
 
+```shell
     apt-get install -y libzbar0
-
+````
 
 ## Build
 
-    cd Capture
+```shell
+    cd src/reprostim-capture
 
     mkdir build
     cd build
     cmake ..
     make
-
+```
 
 ## Subdirectories Structure
 
-### Capture
+### src/reprostim-capture
 
 Contains all code needed for setting up video capture. This includes C++
 code for interfacing with the video capture device, and scheme for setting
@@ -188,7 +192,9 @@ it can accidentally produce the same error message ERROR[003].
 
 This is optional step, only for information purposes:
 
+```shell
     lsusb
+```
 
 And locate line with device, e.g.:
 
@@ -198,8 +204,9 @@ In this sample, 2935 is the "Vendor ID", and 0008 is the "Product ID".
 
 Optionally Magewell device name and serial number can be quickly checked with this command:
 
+```shell
     lsusb -d 2935: -v | grep -E 'iSerial|iProduct'
-
+```
 
 ### 2) Create "udev" rules
 Create text file under "/etc/udev/rules.d/189-reprostim.rules" location with
@@ -217,18 +224,24 @@ Note: we can see that "ATTR{idVendor}" value 2935 is equal to one we got in
 step 1) from lsusb utility.
 
 Also sample udev rules configuration added to project under 
-"Capture/etc/udev/189-reprostim.rules" location.
+"src/reprostim-capture/etc/udev/189-reprostim.rules" location.
 
 Note: make sure the file has owner "root", group "root" and 644 permissions:
 
+```shell
     ls -l /etc/udev/rules.d/189*
+````
+```
     -rw-r--r-- 1 root root 72 ... /etc/udev/rules.d/189-reprostim.rules
+```    
 
 ### 3) Add user to "plugdev" group
 Make sure the user running VideoCapture utility is a member of the 
 "plugdev" group, e.g.:
 
+```shell
     sudo usermod -aG plugdev TODO_user
+```    
 
 ### 4) Restart computer
 Restart computer to make changes effect.

docs/design/rf-library.md

@@ -0,0 +1,38 @@
+# ReproStim Python library/CLI
+
+## Current status
+
+This repository collects various sub-projects 
+
+- Magewell SDK
+- C++ code of ReproStim `reprostim-videocapture` (and `reprostim-screencapture`)
+- ReproEvents for MicroPython board
+- ReproStim videograbber
+- ReproStim stimuli for calibration
+
+## The Goal
+
+Refactor stuff here into cleanly separated and documented libraries etc.
+
+## Approach/Layout
+
+- `src/`
+  - `reprostim/` - Python library and CLIs for working with ReproStim
+    - `audio/` - Audio fingerprinting/processing
+    - `cli/` - CLI entrypoints (for `reprostim CMD`, could be hierarchical like `reprostim qr parse`)
+      - `base.py` - common base commands for CLI
+      - `cmd_timesync_stimuli.py` - CLI to replace `tools/reprostim-timesync-stimuli`
+    - `qr/` - QR code utilities
+    - `__init__.py` - sets up the library
+  - `reprostim-capture/` - C++ code(s) relating to capturing
+    - `3rdparty/` - Magewell MWCapture SDK
+  - `reproevents/` - move MicroPython ReproEvents here (do not strive to make it work)
+- `test/` - some global tests possibly for integration testing etc
+
+## Refactor log
+
+| Old           | New                     |
+|---------------|-------------------------|
+| [x] `Capture` | `src/reprostim-capture` |
+| [ ] `Events`  | `src/reproevents`       |
+| [ ] `TBD`     | `TODO`                  |