diff --git a/.github/workflows/non_omv.yml b/.github/workflows/non_omv.yml index 02f227d8..d4e2b40d 100644 --- a/.github/workflows/non_omv.yml +++ b/.github/workflows/non_omv.yml @@ -29,6 +29,7 @@ jobs: - name: Install c302 run: | pip install . + pip install WormNeuroAtlas pip list - name: Test OpenWormReader with owmeta @@ -36,6 +37,10 @@ jobs: owm bundle remote --user add ow 'https://raw.githubusercontent.com/openworm/owmeta-bundles/master/index.json' python -m c302.OpenWormReader + - name: Test WormNeuroAtlasReader + run: | + python -m c302.WormNeuroAtlasReader + - name: Run some examples run: | cd c302 diff --git a/c302/__version__.py b/c302/__version__.py index 6a22e39b..32a90a3b 100644 --- a/c302/__version__.py +++ b/c302/__version__.py @@ -1 +1 @@ -__version__ = '0.7.12' +__version__ = '0.8.0' diff --git a/examples/parametersweep/Canonical_C.json b/examples/parametersweep/Canonical_C.json index c6541830..a1f8be8b 100644 --- a/examples/parametersweep/Canonical_C.json +++ b/examples/parametersweep/Canonical_C.json @@ -1,6 +1,6 @@ { "Canonical_C": { - "version": "NeuroMLlite v0.5.7", + "version": "NeuroMLlite v0.5.9", "parameters": { "stim_duration": "2000ms", "stim_amp": "3.5pA", diff --git a/examples/parametersweep/Canonical_C.net.nml b/examples/parametersweep/Canonical_C.net.nml index c224e0fe..81179aa1 100644 --- a/examples/parametersweep/Canonical_C.net.nml +++ b/examples/parametersweep/Canonical_C.net.nml @@ -1,5 +1,5 @@ - Generated by NeuroMLlite v0.5.7 + Generated by NeuroMLlite v0.5.9 Generated network: Canonical_C Generation seed: 1234 NeuroMLlite parameters: diff --git a/examples/parametersweep/Canonical_X.json b/examples/parametersweep/Canonical_X.json index a92e8750..5896839e 100644 --- a/examples/parametersweep/Canonical_X.json +++ b/examples/parametersweep/Canonical_X.json @@ -1,6 +1,6 @@ { "Canonical_X": { - "version": "NeuroMLlite v0.5.7", + "version": "NeuroMLlite v0.5.9", "parameters": { "stim_duration": "250ms", "stim_amp": "1pA", diff --git a/examples/parametersweep/Canonical_X.net.nml b/examples/parametersweep/Canonical_X.net.nml index bbe97693..e16cea32 100644 --- a/examples/parametersweep/Canonical_X.net.nml +++ b/examples/parametersweep/Canonical_X.net.nml @@ -1,5 +1,5 @@ - Generated by NeuroMLlite v0.5.7 + Generated by NeuroMLlite v0.5.9 Generated network: Canonical_X Generation seed: 1234 NeuroMLlite parameters: diff --git a/examples/parametersweep/IClamp_GenericMuscleCell.json b/examples/parametersweep/IClamp_GenericMuscleCell.json index d300bdd4..dbcd8bb2 100644 --- a/examples/parametersweep/IClamp_GenericMuscleCell.json +++ b/examples/parametersweep/IClamp_GenericMuscleCell.json @@ -1,6 +1,6 @@ { "IClamp_GenericMuscleCell": { - "version": "NeuroMLlite v0.5.7", + "version": "NeuroMLlite v0.5.9", "notes": "A network model: IClamp_GenericMuscleCell", "parameters": { "stim_amp": "4pA" diff --git a/examples/parametersweep/IClamp_GenericMuscleCell.net.nml b/examples/parametersweep/IClamp_GenericMuscleCell.net.nml index cf9252b2..46bdcf05 100644 --- a/examples/parametersweep/IClamp_GenericMuscleCell.net.nml +++ b/examples/parametersweep/IClamp_GenericMuscleCell.net.nml @@ -1,5 +1,5 @@ - Generated by NeuroMLlite v0.5.7 + Generated by NeuroMLlite v0.5.9 Generated network: IClamp_GenericMuscleCell Generation seed: 1234 NeuroMLlite parameters: diff --git a/examples/parametersweep/IClamp_GenericNeuronCell.json b/examples/parametersweep/IClamp_GenericNeuronCell.json index f845b88d..88183997 100644 --- a/examples/parametersweep/IClamp_GenericNeuronCell.json +++ b/examples/parametersweep/IClamp_GenericNeuronCell.json @@ -1,6 +1,6 @@ { "IClamp_GenericNeuronCell": { - "version": "NeuroMLlite v0.5.7", + "version": "NeuroMLlite v0.5.9", "notes": "A network model: IClamp_GenericNeuronCell", "parameters": { "stim_amp": "4pA" diff --git a/examples/parametersweep/IClamp_GenericNeuronCell.net.nml b/examples/parametersweep/IClamp_GenericNeuronCell.net.nml index d336088f..ac41d297 100644 --- a/examples/parametersweep/IClamp_GenericNeuronCell.net.nml +++ b/examples/parametersweep/IClamp_GenericNeuronCell.net.nml @@ -1,5 +1,5 @@ - Generated by NeuroMLlite v0.5.7 + Generated by NeuroMLlite v0.5.9 Generated network: IClamp_GenericNeuronCell Generation seed: 1234 NeuroMLlite parameters: diff --git a/examples/parametersweep/README.md b/examples/parametersweep/README.md index 75a305db..87aaf08f 100644 --- a/examples/parametersweep/README.md +++ b/examples/parametersweep/README.md @@ -21,6 +21,27 @@ ? + + GenericNeuronCellX + + ? + + + ? + + + ? + + + ? + + + ? + + + ? + + GenericMuscleCell diff --git a/examples/parametersweep/SimCanonical_C.json b/examples/parametersweep/SimCanonical_C.json index 5e58abdf..3e96661f 100644 --- a/examples/parametersweep/SimCanonical_C.json +++ b/examples/parametersweep/SimCanonical_C.json @@ -1,6 +1,6 @@ { "SimCanonical_C": { - "version": "NeuroMLlite v0.5.7", + "version": "NeuroMLlite v0.5.9", "network": "Canonical_C.json", "duration": 3000.0, "dt": 0.1, diff --git a/examples/parametersweep/SimCanonical_X.json b/examples/parametersweep/SimCanonical_X.json index 27519739..b182dbe5 100644 --- a/examples/parametersweep/SimCanonical_X.json +++ b/examples/parametersweep/SimCanonical_X.json @@ -1,6 +1,6 @@ { "SimCanonical_X": { - "version": "NeuroMLlite v0.5.7", + "version": "NeuroMLlite v0.5.9", "network": "Canonical_X.json", "duration": 3000.0, "dt": 0.1, diff --git a/examples/parametersweep/Sim_IClamp_GenericMuscleCell.json b/examples/parametersweep/Sim_IClamp_GenericMuscleCell.json index fd609e75..136c7955 100644 --- a/examples/parametersweep/Sim_IClamp_GenericMuscleCell.json +++ b/examples/parametersweep/Sim_IClamp_GenericMuscleCell.json @@ -1,6 +1,6 @@ { "Sim_IClamp_GenericMuscleCell": { - "version": "NeuroMLlite v0.5.7", + "version": "NeuroMLlite v0.5.9", "network": "IClamp_GenericMuscleCell.json", "duration": 3000.0, "dt": 0.025, diff --git a/examples/parametersweep/Sim_IClamp_GenericNeuronCell.json b/examples/parametersweep/Sim_IClamp_GenericNeuronCell.json index 4a476255..47a3ee6b 100644 --- a/examples/parametersweep/Sim_IClamp_GenericNeuronCell.json +++ b/examples/parametersweep/Sim_IClamp_GenericNeuronCell.json @@ -1,6 +1,6 @@ { "Sim_IClamp_GenericNeuronCell": { - "version": "NeuroMLlite v0.5.7", + "version": "NeuroMLlite v0.5.9", "network": "IClamp_GenericNeuronCell.json", "duration": 3000.0, "dt": 0.025, diff --git a/examples/parametersweep/Sweep.py b/examples/parametersweep/Sweep.py index 24282852..eadd428d 100644 --- a/examples/parametersweep/Sweep.py +++ b/examples/parametersweep/Sweep.py @@ -12,7 +12,7 @@ heatmap_lims=[-110,20] - standard_stim_amps = ['%spA'%(i/10.0) for i in xrange(-5,70,1)] + standard_stim_amps = ['%spA'%(i/10.0) for i in range(-5,70,1)] if '-all' in sys.argv: @@ -24,7 +24,7 @@ vary = {'stim_amp':standard_stim_amps} - #vary = {'stim_amp':['%spA'%(i/10.0) for i in xrange(-10,20,5)]} + #vary = {'stim_amp':['%spA'%(i/10.0) for i in range(-10,20,5)]} #vary = {'stim_amp':['-100pA','0pA','100pA','200pA','300pA','400pA']} cells = colors.keys() @@ -146,9 +146,9 @@ vary = {'stim_amp':standard_stim_amps} - #vary = {'number_per_cell':[i for i in xrange(0,250,10)]} + #vary = {'number_per_cell':[i for i in range(0,250,10)]} vary = {'stim_amp':['-1pA','0pA','1.5pA','2pA']} - vary = {'stim_amp':['%spA'%(i/10.0) for i in xrange(-20,60,5)]} + vary = {'stim_amp':['%spA'%(i/10.0) for i in range(-20,60,5)]} type = 'GenericMuscleCell' type = 'GenericNeuronCell' @@ -197,9 +197,9 @@ vary = {'dt':[0.1,0.05,0.025,0.01,0.005,0.0025,0.001]} vary = {'dt':[0.1,0.05,0.025,0.01,0.005]} - #vary = {'number_per_cell':[i for i in xrange(0,250,10)]} + #vary = {'number_per_cell':[i for i in range(0,250,10)]} #vary = {'stim_amp':['1pA','1.5pA','2pA']} - vary = {'stim_amp':['%spA'%(i/10.0) for i in xrange(-3,60,1)]} + vary = {'stim_amp':['%spA'%(i/10.0) for i in range(-3,60,1)]} type = 'GenericMuscleCell' type = 'GenericNeuronCell' diff --git a/examples/parametersweep/firing_rates_GenericMuscleCell.png b/examples/parametersweep/firing_rates_GenericMuscleCell.png index cedf2350..b815c3d9 100644 Binary files a/examples/parametersweep/firing_rates_GenericMuscleCell.png and b/examples/parametersweep/firing_rates_GenericMuscleCell.png differ diff --git a/examples/parametersweep/firing_rates_GenericNeuronCell.png b/examples/parametersweep/firing_rates_GenericNeuronCell.png index f8af711d..28c9c2ee 100644 Binary files a/examples/parametersweep/firing_rates_GenericNeuronCell.png and b/examples/parametersweep/firing_rates_GenericNeuronCell.png differ diff --git a/examples/parametersweep/firing_rates_GenericNeuronCellX.png b/examples/parametersweep/firing_rates_GenericNeuronCellX.png new file mode 100644 index 00000000..fe16f78a Binary files /dev/null and b/examples/parametersweep/firing_rates_GenericNeuronCellX.png differ diff --git a/examples/parametersweep/heatmap_GenericMuscleCell.png b/examples/parametersweep/heatmap_GenericMuscleCell.png index 43747042..94368ec6 100644 Binary files a/examples/parametersweep/heatmap_GenericMuscleCell.png and b/examples/parametersweep/heatmap_GenericMuscleCell.png differ diff --git a/examples/parametersweep/heatmap_GenericNeuronCell.png b/examples/parametersweep/heatmap_GenericNeuronCell.png index cb36ba62..492c3486 100644 Binary files a/examples/parametersweep/heatmap_GenericNeuronCell.png and b/examples/parametersweep/heatmap_GenericNeuronCell.png differ diff --git a/examples/parametersweep/heatmap_GenericNeuronCellX.png b/examples/parametersweep/heatmap_GenericNeuronCellX.png new file mode 100644 index 00000000..9bda1b58 Binary files /dev/null and b/examples/parametersweep/heatmap_GenericNeuronCellX.png differ diff --git a/examples/parametersweep/info.html b/examples/parametersweep/info.html index 3a531682..aab9d38a 100644 --- a/examples/parametersweep/info.html +++ b/examples/parametersweep/info.html @@ -21,6 +21,27 @@ ? + + GenericNeuronCellX + + ? + + + ? + + + ? + + + ? + + + ? + + + ? + + GenericMuscleCell diff --git a/examples/parametersweep/mean_spike_frequency_GenericMuscleCell.png b/examples/parametersweep/mean_spike_frequency_GenericMuscleCell.png index 40342bf7..9e6235f8 100644 Binary files a/examples/parametersweep/mean_spike_frequency_GenericMuscleCell.png and b/examples/parametersweep/mean_spike_frequency_GenericMuscleCell.png differ diff --git a/examples/parametersweep/mean_spike_frequency_GenericNeuronCell.png b/examples/parametersweep/mean_spike_frequency_GenericNeuronCell.png index 019bf45a..6f424e92 100644 Binary files a/examples/parametersweep/mean_spike_frequency_GenericNeuronCell.png and b/examples/parametersweep/mean_spike_frequency_GenericNeuronCell.png differ diff --git a/examples/parametersweep/mean_spike_frequency_GenericNeuronCellX.png b/examples/parametersweep/mean_spike_frequency_GenericNeuronCellX.png new file mode 100644 index 00000000..d19c9cfd Binary files /dev/null and b/examples/parametersweep/mean_spike_frequency_GenericNeuronCellX.png differ