Refactor environment configuration and switch CI to Conda

.github/workflows/docs.yml

@@ -9,24 +9,24 @@ on:
 jobs:
   build:
     runs-on: ubuntu-22.04
+    defaults:
+      run:
+        shell: bash -l {0}
     steps:
     - name: Checkout repo
       uses: actions/checkout@v3
       with:
         fetch-depth: 0   
 
-    - name: Set up Python
-      uses: actions/setup-python@v4
+    - name: Install conda
+      uses: conda-incubator/setup-miniconda@v3
       with:
+        environment-file: environments/eeg-expy-docsbuild.yml
+        auto-activate-base: false
         python-version: 3.8
-
-    - name: Install dependencies
-      run: |
-        make install-deps-apt
-        python -m pip install --upgrade pip wheel
-        python -m pip install attrdict
-
-        make install-deps-wxpython
+        activate-environment: eeg-expy-full
+        channels: conda-forge
+        miniconda-version: "latest"
 
     - name: Build project
       run: |

environments/eeg-expy-docsbuild.yml

@@ -1,9 +1,11 @@
-name: eeg-expy-docsbuild
 channels:
     - conda-forge
 dependencies:
     # System-level dependencies
-    - python>=3.8,<=3.13
+
+    # conda overrides current environment python version when not using --freeze-installed, and installs a random version of python...
+    # - python>=3.8,<=3.13
+
     - pytables # install pytables for macOS arm64, so do not need to build from source.
     - rust # used by docsbuild
     - pip

environments/eeg-expy-full.yml

@@ -1,9 +1,11 @@
-name: eeg-expy-full
 channels:
     - conda-forge
 dependencies:
     # System-level dependencies
-    - python>=3.8,<=3.10 # psychopy <= 3.10
+
+    # conda overrides current environment python version when not using --freeze-installed, and installs a random version of python...
+    # - python>=3.8,<=3.10 # psychopy <= 3.10
+
     - dukpy==0.2.3 # psychopy dependency, avoid failing due to building wheel on win 3.9.
     - numpy # fix PsychXR numpy dependency DLL issues on Windows
     - pytables # install pytables for macOS arm64, so do not need to build from source.

environments/eeg-expy-stimpres.yml

@@ -1,9 +1,11 @@
-name: eeg-expy-stimpres
 channels:
     - conda-forge
 dependencies:
     # System-level dependencies
-    - python>=3.8,<=3.10 # psychopy <= 3.10
+
+    # conda overrides current environment python version when not using --freeze-installed, and installs a random version of python...
+    #- python>=3.8,<=3.10 # psychopy <= 3.10
+
     - dukpy==0.2.3 # psychopy dependency, avoid failing due to building wheel on win 3.9.
     - 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'"
     - cffi # Fix sound ffi.callback() issue with sounddevice on macOS: https://github.com/spatialaudio/python-sounddevice/issues/397

environments/eeg-expy-streaming.yml

@@ -1,9 +1,11 @@
-name: eeg-expy-streaming
 channels:
     - conda-forge
 dependencies:
     # System-level dependencies
-    - python>=3.8,<=3.13
+
+    # conda overrides current environment python version when not using --freeze-installed, and installs a random version of python...
+    #- python>=3.8,<=3.13
+
     - liblsl # install liblsl to prevent error on macOS and Ubuntu: "RuntimeError: LSL binary library file was not found."
     - pip
     - pip:

environments/eeg-expy-streamstim.yml

@@ -1,10 +1,12 @@
-name: eeg-expy-streamstim
 channels:
     - conda-forge
     - defaults
 dependencies:
     # System-level dependencies
-    - python>=3.8,<=3.10 # psychopy <= 3.10
+
+    # conda overrides current environment python version when not using --freeze-installed, and installs a random version of python...
+    #- python>=3.8,<=3.10 # psychopy <= 3.10
+
     - dukpy==0.2.3 # psychopy dependency, avoid failing due to building wheel on win 3.9.
     - 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'"

requirements.txt

@@ -3,7 +3,8 @@
 
 scikit-learn>=0.23.2
 pandas>=1.1.4
-numpy>=1.26.0;  python_version >= "3.9"
+# psychxr build pinned to this version of numpy.
+numpy>=1.26,<1.27;  python_version >= "3.9"
 numpy<=1.24.4; python_version == "3.8"
 mne>=0.20.8
 seaborn>=0.11.0
@@ -60,7 +61,8 @@ ffpyplayer==4.5.2 # 4.5.3 fails to build as wheel.
 psychtoolbox
 scikit-learn>=0.23.2
 pandas>=1.1.4
-numpy>=1.26.0;  python_version >= "3.9"
+# psychxr build pinned to this version of numpy.
+numpy>=1.26,<1.27;  python_version >= "3.9"
 numpy==1.24.4; python_version == "3.8"
 mne>=0.20.8
 seaborn>=0.11.0
@@ -87,7 +89,8 @@ pyglet==1.4.11 ; platform_system == "Windows"
 psychxr>=0.2.4rc2; platform_system == "Windows" and python_version <= "3.9"
 
 
-
+# Used for generating checkerboard in pattern reversal experiment
+stimupy
 
 ## ~~ Docsbuild Requirements ~~ 
 recommonmark