From 0ce831cf538f12100a87085364d45b86671374d5 Mon Sep 17 00:00:00 2001 From: Ben Pettit Date: Sun, 23 Oct 2022 23:23:24 +1000 Subject: [PATCH 1/3] fixes to get docs building by github action --- .github/workflows/docs.yml | 15 ++++++++------- .gitignore | 3 +++ .../01r__cueing_singlesub_analysis.py | 4 ++-- .../visual_cueing/02r__cueing_group_analysis.py | 4 ++-- .../04r__cueing_group_analysis_winter2019.py | 4 ++-- examples/visual_cueing/CueingAnalysis_Colab.ipynb | 4 ++-- .../visual_cueing/CueingGroupAnalysis_Colab.ipynb | 4 ++-- .../CueingGroupAnalysis_Colab_Winter2019.ipynb | 4 ++-- examples/visual_cueing/cueing.ipynb | 4 ++-- .../visual_cueing/cueing_group_analysis.ipynb | 4 ++-- examples/visual_cueing/cueing_loop.ipynb | 4 ++-- examples/visual_ssvep/01r__ssvep_viz.py | 5 +++-- 12 files changed, 32 insertions(+), 27 deletions(-) diff --git a/.github/workflows/docs.yml b/.github/workflows/docs.yml index f1f23d9d..b74b87cf 100644 --- a/.github/workflows/docs.yml +++ b/.github/workflows/docs.yml @@ -2,26 +2,27 @@ name: Docs on: push: - branches: [ master, develop, 'dev/*' ] + branches: [ '**' ] pull_request: - branches: [ master, develop ] + branches: [ '**' ] jobs: build: - runs-on: ubuntu-18.04 + runs-on: ubuntu-20.04 steps: - - uses: actions/checkout@v2 + - uses: actions/checkout@v3 - name: Set up Python - uses: actions/setup-python@v1 + uses: actions/setup-python@v4 with: - python-version: 3.7 + python-version: 3.8 - name: Install dependencies run: | python -m pip install --upgrade pip wheel + python -m pip install attrdict # Install wxPython wheels since they are distribution-specific and therefore not on PyPI # See: https://wxpython.org/pages/downloads/index.html - pip install -U -f https://extras.wxpython.org/wxPython4/extras/linux/gtk3/ubuntu-18.04 wxPython + pip install -f https://extras.wxpython.org/wxPython4/extras/linux/gtk3/ubuntu-20.04 wxPython pip install . - name: Build docs diff --git a/.gitignore b/.gitignore index 7d84d133..d6bf9a8f 100644 --- a/.gitignore +++ b/.gitignore @@ -14,3 +14,6 @@ examples/visual_cueing/*.csv .coverage coverage.xml htmlcov + +# PyCharm +.idea/ \ No newline at end of file diff --git a/examples/visual_cueing/01r__cueing_singlesub_analysis.py b/examples/visual_cueing/01r__cueing_singlesub_analysis.py index fcee0f83..9ba11022 100644 --- a/examples/visual_cueing/01r__cueing_singlesub_analysis.py +++ b/examples/visual_cueing/01r__cueing_singlesub_analysis.py @@ -132,7 +132,7 @@ # Left Cue tfr, itc = tfr_morlet(epochs['LeftCue'], freqs=frequencies, n_cycles=wave_cycles, return_itc=True) -tfr = tfr.apply_baseline([-1,-.5],mode='mean') +tfr = tfr.apply_baseline((-1,-.5),mode='mean') tfr.plot(picks=[0], mode='logratio', title='TP9 - Ipsi'); tfr.plot(picks=[1], mode='logratio', @@ -143,7 +143,7 @@ # Right Cue tfr, itc = tfr_morlet(epochs['RightCue'], freqs=frequencies, n_cycles=wave_cycles, return_itc=True) -tfr = tfr.apply_baseline([-1,-.5],mode='mean') +tfr = tfr.apply_baseline((-1,-.5),mode='mean') tfr.plot(picks=[0], mode='logratio', title='TP9 - Contra'); tfr.plot(picks=[1], mode='logratio', diff --git a/examples/visual_cueing/02r__cueing_group_analysis.py b/examples/visual_cueing/02r__cueing_group_analysis.py index 9053412a..535d8db3 100644 --- a/examples/visual_cueing/02r__cueing_group_analysis.py +++ b/examples/visual_cueing/02r__cueing_group_analysis.py @@ -123,7 +123,7 @@ # Left Cue tfr, itc = tfr_morlet(epochs['LeftCue'], freqs=frequencies, n_cycles=wave_cycles, return_itc=True) - tfr = tfr.apply_baseline([-1,-.5],mode='mean') + tfr = tfr.apply_baseline((-1,-.5),mode='mean') #tfr.plot(picks=[0], mode='logratio', # title='TP9 - Ipsi'); #tfr.plot(picks=[3], mode='logratio', @@ -134,7 +134,7 @@ # Right Cue tfr, itc = tfr_morlet(epochs['RightCue'], freqs=frequencies, n_cycles=wave_cycles, return_itc=True) - tfr = tfr.apply_baseline([-1,-.5],mode='mean') + tfr = tfr.apply_baseline((-1,-.5),mode='mean') #tfr.plot(picks=[0], mode='logratio', # title='TP9 - Contra'); #tfr.plot(picks=[3], mode='logratio', diff --git a/examples/visual_cueing/04r__cueing_group_analysis_winter2019.py b/examples/visual_cueing/04r__cueing_group_analysis_winter2019.py index 8c2fb9cc..50c382c8 100644 --- a/examples/visual_cueing/04r__cueing_group_analysis_winter2019.py +++ b/examples/visual_cueing/04r__cueing_group_analysis_winter2019.py @@ -136,14 +136,14 @@ # Left Cue tfr, itc = tfr_morlet(epochs['LeftCue'], freqs=frequencies, n_cycles=wave_cycles, return_itc=True) - tfr = tfr.apply_baseline([-1,-.5],mode='mean') + tfr = tfr.apply_baseline((-1,-.5),mode='mean') power_Ipsi_TP9 = tfr.data[0,:,:] power_Contra_TP10 = tfr.data[1,:,:] # Right Cue tfr, itc = tfr_morlet(epochs['RightCue'], freqs=frequencies, n_cycles=wave_cycles, return_itc=True) - tfr = tfr.apply_baseline([-1,-.5],mode='mean') + tfr = tfr.apply_baseline((-1,-.5),mode='mean') power_Contra_TP9 = tfr.data[0,:,:] power_Ipsi_TP10 = tfr.data[1,:,:] diff --git a/examples/visual_cueing/CueingAnalysis_Colab.ipynb b/examples/visual_cueing/CueingAnalysis_Colab.ipynb index 47bfd1b2..5a5712c1 100644 --- a/examples/visual_cueing/CueingAnalysis_Colab.ipynb +++ b/examples/visual_cueing/CueingAnalysis_Colab.ipynb @@ -434,7 +434,7 @@ "# Left Cue\n", "tfr, itc = tfr_morlet(epochs['LeftCue'], freqs=frequencies, \n", " n_cycles=wave_cycles, return_itc=True)\n", - "tfr = tfr.apply_baseline([-1,-.5],mode='mean')\n", + "tfr = tfr.apply_baseline((-1,-.5),mode='mean')\n", "tfr.plot(picks=[0], mode='logratio', \n", " title='TP9 - Ipsi');\n", "tfr.plot(picks=[1], mode='logratio', \n", @@ -445,7 +445,7 @@ "# Right Cue\n", "tfr, itc = tfr_morlet(epochs['RightCue'], freqs=frequencies, \n", " n_cycles=wave_cycles, return_itc=True)\n", - "tfr = tfr.apply_baseline([-1,-.5],mode='mean')\n", + "tfr = tfr.apply_baseline((-1,-.5),mode='mean')\n", "tfr.plot(picks=[0], mode='logratio', \n", " title='TP9 - Contra');\n", "tfr.plot(picks=[1], mode='logratio', \n", diff --git a/examples/visual_cueing/CueingGroupAnalysis_Colab.ipynb b/examples/visual_cueing/CueingGroupAnalysis_Colab.ipynb index 1b7c9172..1d3d25dc 100644 --- a/examples/visual_cueing/CueingGroupAnalysis_Colab.ipynb +++ b/examples/visual_cueing/CueingGroupAnalysis_Colab.ipynb @@ -215,7 +215,7 @@ " # Left Cue\n", " tfr, itc = tfr_morlet(epochs['LeftCue'], freqs=frequencies, \n", " n_cycles=wave_cycles, return_itc=True)\n", - " tfr = tfr.apply_baseline([-1,-.5],mode='mean')\n", + " tfr = tfr.apply_baseline((-1,-.5),mode='mean')\n", " #tfr.plot(picks=[0], mode='logratio', \n", " # title='TP9 - Ipsi');\n", " #tfr.plot(picks=[3], mode='logratio', \n", @@ -226,7 +226,7 @@ " # Right Cue\n", " tfr, itc = tfr_morlet(epochs['RightCue'], freqs=frequencies, \n", " n_cycles=wave_cycles, return_itc=True)\n", - " tfr = tfr.apply_baseline([-1,-.5],mode='mean')\n", + " tfr = tfr.apply_baseline((-1,-.5),mode='mean')\n", " #tfr.plot(picks=[0], mode='logratio', \n", " # title='TP9 - Contra');\n", " #tfr.plot(picks=[3], mode='logratio', \n", diff --git a/examples/visual_cueing/CueingGroupAnalysis_Colab_Winter2019.ipynb b/examples/visual_cueing/CueingGroupAnalysis_Colab_Winter2019.ipynb index 390ec855..30f8af16 100644 --- a/examples/visual_cueing/CueingGroupAnalysis_Colab_Winter2019.ipynb +++ b/examples/visual_cueing/CueingGroupAnalysis_Colab_Winter2019.ipynb @@ -215,14 +215,14 @@ " # Left Cue\n", " tfr, itc = tfr_morlet(epochs['LeftCue'], freqs=frequencies, \n", " n_cycles=wave_cycles, return_itc=True)\n", - " tfr = tfr.apply_baseline([-1,-.5],mode='mean')\n", + " tfr = tfr.apply_baseline((-1,-.5),mode='mean')\n", " power_Ipsi_TP9 = tfr.data[0,:,:]\n", " power_Contra_TP10 = tfr.data[1,:,:]\n", "\n", " # Right Cue\n", " tfr, itc = tfr_morlet(epochs['RightCue'], freqs=frequencies, \n", " n_cycles=wave_cycles, return_itc=True)\n", - " tfr = tfr.apply_baseline([-1,-.5],mode='mean')\n", + " tfr = tfr.apply_baseline((-1,-.5),mode='mean')\n", " power_Contra_TP9 = tfr.data[0,:,:]\n", " power_Ipsi_TP10 = tfr.data[1,:,:]\n", "\n", diff --git a/examples/visual_cueing/cueing.ipynb b/examples/visual_cueing/cueing.ipynb index 0406e41e..ad9f3fb6 100644 --- a/examples/visual_cueing/cueing.ipynb +++ b/examples/visual_cueing/cueing.ipynb @@ -529,7 +529,7 @@ "# Left Cue\n", "tfr, itc = tfr_morlet(epochs['LeftCue'], freqs=frequencies, \n", " n_cycles=wave_cycles, return_itc=True)\n", - "tfr = tfr.apply_baseline([-1,-.5],mode='mean')\n", + "tfr = tfr.apply_baseline((-1,-.5),mode='mean')\n", "tfr.plot(picks=[0], mode='logratio', \n", " title='TP9 - Ipsi');\n", "tfr.plot(picks=[1], mode='logratio', \n", @@ -540,7 +540,7 @@ "# Right Cue\n", "tfr, itc = tfr_morlet(epochs['RightCue'], freqs=frequencies, \n", " n_cycles=wave_cycles, return_itc=True)\n", - "tfr = tfr.apply_baseline([-1,-.5],mode='mean')\n", + "tfr = tfr.apply_baseline((-1,-.5),mode='mean')\n", "tfr.plot(picks=[0], mode='logratio', \n", " title='TP9 - Contra');\n", "tfr.plot(picks=[1], mode='logratio', \n", diff --git a/examples/visual_cueing/cueing_group_analysis.ipynb b/examples/visual_cueing/cueing_group_analysis.ipynb index bd781d91..44dcbc79 100755 --- a/examples/visual_cueing/cueing_group_analysis.ipynb +++ b/examples/visual_cueing/cueing_group_analysis.ipynb @@ -225,7 +225,7 @@ " # Left Cue\n", " tfr, itc = tfr_morlet(epochs['LeftCue'], freqs=frequencies, \n", " n_cycles=wave_cycles, return_itc=True)\n", - " tfr = tfr.apply_baseline([-1,-.5],mode='mean')\n", + " tfr = tfr.apply_baseline((-1,-.5),mode='mean')\n", " #tfr.plot(picks=[0], mode='logratio', \n", " # title='TP9 - Ipsi');\n", " #tfr.plot(picks=[3], mode='logratio', \n", @@ -236,7 +236,7 @@ " # Right Cue\n", " tfr, itc = tfr_morlet(epochs['RightCue'], freqs=frequencies, \n", " n_cycles=wave_cycles, return_itc=True)\n", - " tfr = tfr.apply_baseline([-1,-.5],mode='mean')\n", + " tfr = tfr.apply_baseline((-1,-.5),mode='mean')\n", " #tfr.plot(picks=[0], mode='logratio', \n", " # title='TP9 - Contra');\n", " #tfr.plot(picks=[3], mode='logratio', \n", diff --git a/examples/visual_cueing/cueing_loop.ipynb b/examples/visual_cueing/cueing_loop.ipynb index 969c08d0..8894dcfe 100644 --- a/examples/visual_cueing/cueing_loop.ipynb +++ b/examples/visual_cueing/cueing_loop.ipynb @@ -601,7 +601,7 @@ " # Left Cue\n", " tfr, itc = tfr_morlet(epochs['LeftCue'], freqs=frequencies, \n", " n_cycles=wave_cycles, return_itc=True)\n", - " tfr = tfr.apply_baseline([-1,-.5],mode='mean')\n", + " tfr = tfr.apply_baseline((-1,-.5),mode='mean')\n", " #tfr.plot(picks=[0], mode='logratio', \n", " # title='TP9 - Ipsi');\n", " #tfr.plot(picks=[3], mode='logratio', \n", @@ -612,7 +612,7 @@ " # Right Cue\n", " tfr, itc = tfr_morlet(epochs['RightCue'], freqs=frequencies, \n", " n_cycles=wave_cycles, return_itc=True)\n", - " tfr = tfr.apply_baseline([-1,-.5],mode='mean')\n", + " tfr = tfr.apply_baseline((-1,-.5),mode='mean')\n", " #tfr.plot(picks=[0], mode='logratio', \n", " # title='TP9 - Contra');\n", " #tfr.plot(picks=[3], mode='logratio', \n", diff --git a/examples/visual_ssvep/01r__ssvep_viz.py b/examples/visual_ssvep/01r__ssvep_viz.py index 91d9ad50..501c6857 100644 --- a/examples/visual_ssvep/01r__ssvep_viz.py +++ b/examples/visual_ssvep/01r__ssvep_viz.py @@ -101,8 +101,9 @@ axs[0].plot(freq1, psd1_mean[[0, 3], :].mean(0), color='b', label='30 Hz') axs[0].plot(freq2, psd2_mean[[0, 3], :].mean(0), color='r', label='20 Hz') -axs[1].plot(freq1, psd1_mean[4, :], color='b', label='30 Hz') -axs[1].plot(freq2, psd2_mean[4, :], color='r', label='20 Hz') +# TODO fix: IndexError: index 4 is out of bounds for axis 0 with size 4 +# axs[1].plot(freq1, psd1_mean[4, :], color='b', label='30 Hz') +# axs[1].plot(freq2, psd2_mean[4, :], color='r', label='20 Hz') axs[0].set_title('TP9 and TP10') axs[1].set_title('POz') From a0aa01e1f30c40258e7fdf72da35d21488275db6 Mon Sep 17 00:00:00 2001 From: Ben Pettit Date: Tue, 25 Oct 2022 13:30:19 +1000 Subject: [PATCH 2/3] reverted some changes --- .github/workflows/docs.yml | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/.github/workflows/docs.yml b/.github/workflows/docs.yml index b74b87cf..67ad74d8 100644 --- a/.github/workflows/docs.yml +++ b/.github/workflows/docs.yml @@ -2,9 +2,9 @@ name: Docs on: push: - branches: [ '**' ] + branches: [ master, develop, 'dev/*' ] pull_request: - branches: [ '**' ] + branches: [ master, develop ] jobs: build: @@ -22,7 +22,7 @@ jobs: # Install wxPython wheels since they are distribution-specific and therefore not on PyPI # See: https://wxpython.org/pages/downloads/index.html - pip install -f https://extras.wxpython.org/wxPython4/extras/linux/gtk3/ubuntu-20.04 wxPython + pip install -U -f https://extras.wxpython.org/wxPython4/extras/linux/gtk3/ubuntu-20.04 wxPython pip install . - name: Build docs From bd4aaf4aa99b77760ab678563b5dfd5158a14052 Mon Sep 17 00:00:00 2001 From: John Griffiths Date: Thu, 27 Oct 2022 00:17:38 -0400 Subject: [PATCH 3/3] Update 01r__ssvep_viz.py --- examples/visual_ssvep/01r__ssvep_viz.py | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/examples/visual_ssvep/01r__ssvep_viz.py b/examples/visual_ssvep/01r__ssvep_viz.py index 501c6857..d812681c 100644 --- a/examples/visual_ssvep/01r__ssvep_viz.py +++ b/examples/visual_ssvep/01r__ssvep_viz.py @@ -59,6 +59,7 @@ experiment='visual-SSVEP', site='eegnb_examples', device_name='muse2016', data_dir = eegnb_data_path, replace_ch_names={'Right AUX': 'POz'}) +raw.set_channel_types({'POz': 'eeg'}) ################################################################################################### # Visualize the power spectrum @@ -101,9 +102,8 @@ axs[0].plot(freq1, psd1_mean[[0, 3], :].mean(0), color='b', label='30 Hz') axs[0].plot(freq2, psd2_mean[[0, 3], :].mean(0), color='r', label='20 Hz') -# TODO fix: IndexError: index 4 is out of bounds for axis 0 with size 4 -# axs[1].plot(freq1, psd1_mean[4, :], color='b', label='30 Hz') -# axs[1].plot(freq2, psd2_mean[4, :], color='r', label='20 Hz') +axs[1].plot(freq1, psd1_mean[4, :], color='b', label='30 Hz') +axs[1].plot(freq2, psd2_mean[4, :], color='r', label='20 Hz') axs[0].set_title('TP9 and TP10') axs[1].set_title('POz')