Skip running test_run_experiments.py tests in CI. Reorganized environment files by splitting environment.yml into specific requirement files (e.g., full, streaming, stimpres, docsbuild). Updated installation instructions to align with the new environment structure and clarified differences for macOS arm64. (#287)

* Reorganized environment files by splitting `environment.yml` into specific requirement files (e.g., full, streaming, stimpres, docsbuild). Updated installation instructions to align with the new environment structure and clarified differences for macOS arm64.

* Standardize environment naming and update dependency formats

Renamed environment files and labels to use a consistent "eeg-expy" prefix. Updated Python dependency to a fixed version (3.8) and added Rust for docs build environments. Adjusted installation instructions and GitHub workflow to align with the new naming conventions.

* fixed naming

* Fixed typo for filename and made doco clearer and added verbose switch to log to console in realtime

* removed

* fixed command for intel binaries

* fixed the installation steps order

Author: pellet

.DS_Store

@@ -55,21 +55,17 @@ jobs:
     - name: Install conda
       uses: conda-incubator/setup-miniconda@v3
       with:
-        environment-file: environment.yml
+        environment-file: environments/eeg-expy-full.yml
         auto-activate-base: true
         python-version: 3.8
-        activate-environment: EEG-ExPy
+        activate-environment: eeg-expy-full
         channels: conda-forge
         miniconda-version: "latest"
     - name: Install dependencies via conda
       shell: bash -el {0}
       run: |
         conda info
-        conda activate EEG-ExPy
-    - name: Install dependencies
-      shell: bash -el {0}
-      run: |
-        make build
+        conda activate eeg-expy-full
     - name: Run eegnb install test
       shell: bash -el {0}
       run: |
@@ -86,7 +82,8 @@ jobs:
           Xvfb :0 -screen 0 1024x768x24 -ac +extension GLX +render -noreset &> xvfb.log &
           export DISPLAY=:0
         fi
-        make test
+        make test PYTEST_ARGS="--ignore=tests/test_run_experiments.py"
+
 
   typecheck:
     name: typecheck (${{ matrix.os }}, py-${{ matrix.python_version }})

.github/workflows/test.yml

@@ -18,4 +18,4 @@ htmlcov
 # PyCharm
 .idea/
 
-*.DS_Store*
+**/.DS_Store

.gitignore

@@ -6,7 +6,7 @@ install-docs-build-dependencies:
 	pip install -e .[docsbuild]
 
 test:
-	pytest
+	pytest $(PYTEST_ARGS)
 
 typecheck:
 	# Exclude visual_cueing due to errors

Makefile

@@ -42,18 +42,49 @@ Use the following commands to download the repo, create and activate a conda or
 
     .. tab:: Conda
 
-       .. code-block:: bash
+       .. tabs::
+
+            Available environment file options:
+
+            - `eeg-expy-full`: Install all dependencies
+
+            - `eeg-expy-docsbuild`: Documentation
+
+            - `eeg-expy-stimpres`: Stimulus presentation
+
+            - `eeg-expy-streaming`: Data streaming
+
+            - `eeg-expy-streamstim`: Combined streaming and stimulus presentation
+
+
+          .. tab:: Windows, Linux or MacOS intel
+
+            .. code-block:: bash
+
+               git clone https://github.com/NeuroTechX/eeg-expy
+
+               cd eeg-expy
+
+               conda env create -v -f environments/eeg-expy-full.yml
+
+               conda activate eeg-expy-full
+
+          .. tab:: MacOS arm64(M1, M2, etc.)
 
-           conda create -n "eeg-expy" python=3.8 git pip
+            .. code-block:: bash
 
-           conda activate "eeg-expy"
+               # clone the repo
+               git clone https://github.com/NeuroTechX/eeg-expy
 
-           git clone https://github.com/NeuroTechX/eeg-expy
+               # navigate to the repo
+               cd eeg-expy
 
-           cd eeg-expy
-           
-           pip install -e .
+               # for audio to be supported, osx-64 runtime is currently required,
+               # drop the '--platform osx-64' parameter if audio is not needed, to use the native runtime.
+               conda env create -v --platform osx-64 -f environments/eeg-expy-full.yml
 
+               # activate the environment
+               conda activate eeg-expy-full
 
     .. tab:: Virtualenv
 

doc/getting_started/installation.rst

@@ -158,9 +158,9 @@ print("Recording saved in", experiment.save_fn)
 
 ## Using virtual reality
 
-### Heads up display
+### Head mounted display
 
-A heads-up display can be used for presenting experiments in a similar way to a monitor, without much modification.
+A head mounted display can be used for presenting experiments in a similar way to a monitor, without much modification.
 
 #### Features to be added in future releases:
 

doc/getting_started/running_experiments.md

@@ -0,0 +1,12 @@
+name: eeg-expy-docsbuild
+channels:
+    - conda-forge
+dependencies:
+    # System-level dependencies
+    - python=3.8
+    - pytables # install pytables for macOS arm64, so do not need to build from source.
+    - rust # used by docsbuild
+    - pip
+    - pip:
+      # Install package with only Analysis requirements
+      - -e ..[docsbuild]

environment.yml

@@ -0,0 +1,14 @@
+name: eeg-expy-full
+channels:
+    - conda-forge
+dependencies:
+    # System-level dependencies
+    - python=3.8
+    - pytables # install pytables for macOS arm64, so do not need to build from source.
+    - rust # used by docsbuild
+    - liblsl # install liblsl to prevent error on macOS and Ubuntu: "RuntimeError: LSL binary library file was not found."
+    - wxpython>=4.0 # install wxpython to prevent error on macOS arm64: "site-packages/wx/_core.cpython-38-darwin.so, 0x0002): symbol not found in flat namespace '__ZN10wxBoxSizer20InformFirstDirectionEiii'"
+    - pip
+    - pip:
+      # Install package with only Analysis requirements
+      - -e ..[full]

environments/eeg-expy-docsbuild.yml

@@ -0,0 +1,11 @@
+name: eeg-expy-stimpres
+channels:
+    - conda-forge
+dependencies:
+    # System-level dependencies
+    - python=3.8
+    - wxpython>=4.0 # install wxpython to prevent error on macOS arm64: "site-packages/wx/_core.cpython-38-darwin.so, 0x0002): symbol not found in flat namespace '__ZN10wxBoxSizer20InformFirstDirectionEiii'"
+    - pip
+    - pip:
+      # Install package with Analysis + Streaming requirements
+      - -e ..[stimpres]

environments/eeg-expy-full.yml

@@ -0,0 +1,11 @@
+name: eeg-expy-streaming
+channels:
+    - conda-forge
+dependencies:
+    # System-level dependencies
+    - python=3.8
+    - liblsl # install liblsl to prevent error on macOS and Ubuntu: "RuntimeError: LSL binary library file was not found."
+    - pip
+    - pip:
+      # Install package with Analysis + Streaming requirements
+      - -e ..[streaming]

environments/eeg-expy-stimpres.yml

@@ -0,0 +1,13 @@
+name: eeg-expy-streamstim
+channels:
+    - conda-forge
+    - defaults
+dependencies:
+    # System-level dependencies
+    - python=3.8
+    - liblsl # install liblsl to prevent error on macOS and Ubuntu: "RuntimeError: LSL binary library file was not found."
+    - wxpython>=4.0 # install wxpython to prevent error on macOS arm64: "site-packages/wx/_core.cpython-38-darwin.so, 0x0002): symbol not found in flat namespace '__ZN10wxBoxSizer20InformFirstDirectionEiii'"
+    - pip
+    - pip:
+      # Install package with only Analysis requirements
+      - -e ..[streamstim]

environments/eeg-expy-streaming.yml

@@ -70,10 +70,6 @@ airium>=0.1.0
 attrdict>=2.0.1
 attrdict3
 
-# This might try to build from source on linux (since there are no wheels for Linux on PyPI) .
-# You can pass `--find-links=https://extras.wxpython.org/wxPython4/extras/linux/gtk3/ubuntu-20.04/` your `pip install` to use the prebuilt wheels at the link.
-wxPython>=4.0 ; platform_system == "Linux"
-
 # pywinhook needs some special treatment since there are only wheels on PyPI for Python 3.7-3.8, and building requires special tools (swig, VS C++ tools)
 # See issue: https://github.com/NeuroTechX/eeg-notebooks/issues/29
 pywinhook>=1.6.0 ; platform_system == "Windows" and (python_version == "3.7" or python_version == "3.8")

environments/eeg-expy-streamstim.yml

@@ -38,5 +38,5 @@
         "License :: OSI Approved :: MIT License",
         "Operating System :: OS Independent",
     ],
-    python_requires='>=3.7',
+    python_requires='>=3.8',
 )