diff --git a/.github/workflows/omv-ci.yml b/.github/workflows/omv-ci.yml index 9410753..88ae919 100644 --- a/.github/workflows/omv-ci.yml +++ b/.github/workflows/omv-ci.yml @@ -3,19 +3,20 @@ name: Continuous build using OMV on: push: - branches: [ master, development, experimental ] + branches: [ master, development, experimental, test* ] pull_request: - branches: [ master, development, experimental ] + branches: [ master, development, experimental, test* ] jobs: build: - runs-on: ubuntu-latest + runs-on: ${{ matrix.runs-on }} strategy: fail-fast: false matrix: python-version: [ 3.9 ] - engine: [ NEURON, jNeuroML, jNeuroML_NEURON, jNeuroML_validate, jNeuroML_validatev1, "NEURON:7.6", "NEURON:7.7" ] + engine: [ jNeuroML, jNeuroML_NEURON, jNeuroML_validate, jNeuroML_validatev1, "NEURON:8.1" ] + runs-on: [ubuntu-latest, macos-latest] steps: diff --git a/.gitignore b/.gitignore index d5121b7..15503e0 100644 --- a/.gitignore +++ b/.gitignore @@ -45,3 +45,4 @@ simulations /NEURON/tests.log /tests.log /NEURON_2007/*.log +arm64 diff --git a/NEURON/test/.test.mep b/NEURON/test/.test.mep index 6d9e339..e22e5f9 100644 --- a/NEURON/test/.test.mep +++ b/NEURON/test/.test.mep @@ -5,4 +5,4 @@ system: Testing Golgi experiments: pacemaking: expected: - spike times: [0.041427, 0.199477, 0.362728, 0.525695, 0.688318, 0.850665, 1.012798, 1.174768, 1.33661, 1.498353, 1.660013, 1.821605, 1.983138, 2.144618, 2.30605, 2.467442, 2.628792, 2.790105, 2.951385, 3.112597, 3.273812, 3.434997, 3.596155, 3.757285, 3.91839] \ No newline at end of file + spike times: [0.041427, 0.199485, 0.362743, 0.525715, 0.688348, 0.8507, 1.01284, 1.174815, 1.336665, 1.49842, 1.659113, 1.820678, 1.982223, 2.143723, 2.305175, 2.466582, 2.627947, 2.789275, 2.950565, 3.111822, 3.273047, 3.434245, 3.59541, 3.75655, 3.917665] \ No newline at end of file diff --git a/NEURON/test/.test.neuron.omt b/NEURON/test/.test.neuron.omt index 270db8e..41ad957 100644 --- a/NEURON/test/.test.neuron.omt +++ b/NEURON/test/.test.neuron.omt @@ -15,5 +15,5 @@ experiments: spike detection: method: threshold threshold: 0 - tolerance: 0 + tolerance: 0.000631 # non zero tolerance due to differences in times between ubuntu and mac... diff --git a/NEURON/test/.test.soma.mep b/NEURON/test/.test.soma.mep index e7775e6..91e4c30 100644 --- a/NEURON/test/.test.soma.mep +++ b/NEURON/test/.test.soma.mep @@ -5,4 +5,4 @@ system: Testing Golgi experiments: pacemaking: expected: - spike times: [0.057706, 0.072057, 0.086836, 0.103116, 0.121569, 0.142782, 0.167439, 0.195775, 0.458494, 0.488709, 0.522085, 0.559345, 0.600174, 0.643928, 0.689896, 0.737449, 0.786095, 0.806101, 0.813874, 0.821581, 0.829287, 0.837015, 0.844757, 0.852513, 0.860291, 0.868099, 0.875931, 0.88378, 0.891642, 0.899523, 0.907423, 0.915341, 0.923276, 0.931227, 0.939195, 0.947179, 0.955187, 0.963198, 0.971223, 0.979261, 0.987313, 0.995386, 1.00904, 1.0601, 1.11279, 1.16507, 1.217, 1.26868, 1.32018, 1.37154, 1.4228, 1.47408] \ No newline at end of file + spike times: [0.057707, 0.072137, 0.086924, 0.10321, 0.12167, 0.142889, 0.167422, 0.195745, 0.458496, 0.488716, 0.522098, 0.559362, 0.600192, 0.643945, 0.689911, 0.73746, 0.786102, 0.806101, 0.813874, 0.82158, 0.829284, 0.837, 0.844736, 0.852509, 0.860287, 0.868093, 0.875914, 0.883755, 0.891616, 0.899497, 0.907396, 0.915313, 0.923248, 0.931199, 0.939166, 0.947148, 0.955145, 0.963156, 0.97118, 0.979218, 0.987269, 0.995341, 1.00884, 1.05986, 1.11267, 1.16507, 1.21696, 1.26861, 1.32009, 1.37159, 1.42282, 1.47398] \ No newline at end of file diff --git a/NEURON/test/.test_fig3A.mep b/NEURON/test/.test_fig3A.mep index 419f085..fdaab5d 100644 --- a/NEURON/test/.test_fig3A.mep +++ b/NEURON/test/.test_fig3A.mep @@ -5,6 +5,6 @@ system: Testing Golgi experiments: rebound: expected: - spike times: [0.134225, 0.42035, 0.7035, 6.107725, 6.247675, 6.43055, 6.6215, 6.8208, 7.027025, 7.23885] + spike times: [0.134225, 0.420275, 0.713525, 6.107725, 6.2477, 6.430575, 6.62155, 6.82085, 7.027075, 7.238925] diff --git a/NEURON/test/.test_fig4A.mep b/NEURON/test/.test_fig4A.mep index 618c359..c948a0f 100644 --- a/NEURON/test/.test_fig4A.mep +++ b/NEURON/test/.test_fig4A.mep @@ -5,12 +5,11 @@ system: Testing Golgi experiments: dep1: expected: - spike times: [0.515175, 0.55125, 0.6069, 0.66235, 0.7174, 0.771775, 0.8256, 0.87895, 0.931975, 0.9847, 1.037225, 1.089575, 1.141775, 1.193875, 1.2459, 1.297875, 1.349775, 1.401675, 1.453525, 1.505375] - + spike times: [0.515175, 0.55125, 0.606925, 0.662375, 0.717425, 0.7718, 0.825625, 0.878975, 0.932, 0.98475, 1.037275, 1.0896, 1.141825, 1.193925, 1.24595, 1.297925, 1.34985, 1.40175, 1.4536, 1.505475] + dep2: expected: - spike times: [0.509, 0.52755, 0.565725, 0.602875, 0.640475, 0.6776, 0.714275, 0.7505, 0.78635, 0.821825, 0.857025, 0.89195, 0.92665, 0.96115, 0.995475, 1.02965, 1.063775, 1.0935, 1.1283, 1.16185, 1.195475, 1.229, 1.2625, 1.295925, 1.3293, 1.36265, 1.395975, 1.429275, 1.46255, 1.495775] - + spike times: [0.509, 0.52755, 0.565725, 0.602875, 0.640475, 0.677625, 0.7143, 0.750525, 0.786375, 0.82185, 0.85705, 0.892, 0.9267, 0.9612, 0.995525, 1.0297, 1.06375, 1.09765, 1.131475, 1.1652, 1.19885, 1.23245, 1.26595, 1.299425, 1.33285, 1.366225, 1.399575, 1.4329, 1.466175, 1.49945] dep3: expected: - spike times: [0.506425, 0.519175, 0.5487, 0.5783, 0.604475, 0.6349, 0.664075, 0.69305, 0.72165, 0.74995, 0.77795, 0.805725, 0.833275, 0.8606, 0.88775, 0.914725, 0.94155, 0.968225, 0.994775, 1.021225, 1.047575, 1.073825, 1.1, 1.126075, 1.1521, 1.17805, 1.20395, 1.2298, 1.2556, 1.281375, 1.3071, 1.332775, 1.358425, 1.38405, 1.40965, 1.435225, 1.460775, 1.4863, 1.511825] + spike times: [0.506425, 0.519175, 0.5487, 0.578225, 0.6081, 0.637725, 0.667025, 0.69595, 0.72455, 0.75285, 0.780875, 0.808625, 0.836175, 0.8635, 0.89065, 0.9176, 0.944425, 0.971125, 0.997675, 1.024125, 1.050475, 1.076725, 1.1029, 1.128975, 1.155, 1.18095, 1.20685, 1.2327, 1.258525, 1.284275, 1.31, 1.335675, 1.361325, 1.386975, 1.41255, 1.43815, 1.4637, 1.489225, 1.515075] \ No newline at end of file diff --git a/NEURON/test/.test_fig4Bii.mep b/NEURON/test/.test_fig4Bii.mep index d9e91ab..05f839b 100644 --- a/NEURON/test/.test_fig4Bii.mep +++ b/NEURON/test/.test_fig4Bii.mep @@ -6,76 +6,78 @@ experiments: frate1: expected: - spike times: [0.0817, 0.255725, 0.436825, 0.620375, 0.8065, 0.994775] + spike times: [0.0817, 0.255725, 0.43685, 0.6204, 0.806525, 0.994825] frate2: expected: - spike times: [0.056725, 0.168925, 0.291875, 0.414375, 0.537025, 0.660125, 0.783775, 0.907975] + spike times: [0.056725, 0.168925, 0.2919, 0.4144, 0.53705, 0.66015, 0.783825, 0.908025] frate3: expected: - spike times: [0.04485, 0.12535, 0.220675, 0.3153, 0.409225, 0.50285, 0.596375, 0.689975, 0.7837, 0.8776, 0.971675] + spike times: [0.04485, 0.12535, 0.2207, 0.315325, 0.40925, 0.502875, 0.596425, 0.690025, 0.78375, 0.87765, 0.97175] frate4: expected: - spike times: [0.037775, 0.098875, 0.17755, 0.255775, 0.33305, 0.40965, 0.485825, 0.56175, 0.637525, 0.71325, 0.788975, 0.864725, 0.940525, 1.0164] + spike times: [0.037775, 0.098875, 0.17755, 0.2558, 0.333075, 0.409675, 0.48585, 0.561775, 0.637575, 0.7133, 0.789025, 0.8648, 0.9406, 1.016475] frate5: expected: - spike times: [0.03305, 0.0814, 0.14895, 0.21625, 0.28265, 0.348225, 0.413225, 0.47775, 0.542, 0.606025, 0.6699, 0.733675, 0.797425, 0.861125, 0.924825, 0.988525] + spike times: [0.03305, 0.0814, 0.148975, 0.216275, 0.282675, 0.34825, 0.41325, 0.4778, 0.542025, 0.606075, 0.66995, 0.73375, 0.797475, 0.861175, 0.924875, 0.9886] frate6: expected: - spike times: [0.02965, 0.069225, 0.1289, 0.18835, 0.247075, 0.304925, 0.362125, 0.418775, 0.47505, 0.531, 0.5867, 0.64225, 0.69765, 0.75295, 0.808175, 0.86335, 0.9185, 0.97365] + spike times: [0.02965, 0.069225, 0.128925, 0.18835, 0.247075, 0.30495, 0.36215, 0.418825, 0.475075, 0.53105, 0.58675, 0.6423, 0.6977, 0.753, 0.808225, 0.863425, 0.918575, 0.973725] frate7: expected: - spike times: [0.0271, 0.060375, 0.1142, 0.16765, 0.22065, 0.272825, 0.324275, 0.375175, 0.425625, 0.4757, 0.525475, 0.575025, 0.624375, 0.673575, 0.722675, 0.771675, 0.8206, 0.86945, 0.918275, 0.967075, 1.01585] + spike times: [0.0271, 0.060375, 0.114225, 0.167675, 0.220675, 0.272825, 0.3243, 0.3752, 0.42565, 0.475725, 0.525525, 0.575075, 0.624425, 0.673625, 0.722725, 0.771725, 0.82065, 0.869525, 0.91835, 0.96715, 1.01595] frate8: expected: - spike times: [0.025125, 0.05375, 0.103, 0.15175, 0.200275, 0.24805, 0.2951, 0.3416, 0.387625, 0.433225, 0.478525, 0.523525, 0.568325, 0.612925, 0.657375, 0.7017, 0.745925, 0.79005, 0.834125, 0.87815, 0.922125, 0.96605, 1.009975] + spike times: [0.025125, 0.05375, 0.103025, 0.151775, 0.2003, 0.24805, 0.295125, 0.341625, 0.38765, 0.43325, 0.47855, 0.523575, 0.56835, 0.612975, 0.657425, 0.70175, 0.745975, 0.790125, 0.8342, 0.878225, 0.9222, 0.966125, 1.01005] frate9: expected: - spike times: [0.023525, 0.04865, 0.094225, 0.13915, 0.1841, 0.228325, 0.271925, 0.314925, 0.357425, 0.39955, 0.4413, 0.48285, 0.519175, 0.561175, 0.601825, 0.64245, 0.68295, 0.72335, 0.763675, 0.803925, 0.844125, 0.884275, 0.9244, 0.964475, 1.004525] + spike times: [0.023525, 0.04865, 0.094225, 0.139175, 0.184125, 0.22835, 0.271925, 0.31495, 0.357475, 0.399575, 0.441325, 0.4828, 0.524025, 0.56505, 0.605875, 0.64655, 0.687125, 0.727575, 0.767925, 0.808225, 0.84845, 0.888625, 0.928775, 0.968875, 1.00895] frate10: expected: - spike times: [0.02225, 0.0446, 0.087125, 0.128925, 0.170925, 0.212275, 0.253, 0.293175, 0.33285, 0.372125, 0.41105, 0.44965, 0.488, 0.5261, 0.564025, 0.6018, 0.6394, 0.6769, 0.7143, 0.7516, 0.788825, 0.825975, 0.863075, 0.900125, 0.93715, 0.974125, 1.0111] - + spike times: [0.02225, 0.0446, 0.08715, 0.12895, 0.17095, 0.2123, 0.253025, 0.2932, 0.332875, 0.37215, 0.411075, 0.449675, 0.488025, 0.52615, 0.564075, 0.60185, 0.63945, 0.67695, 0.71435, 0.75165, 0.788875, 0.82605, 0.86315, 0.9002, 0.937225, 0.9742, 1.011175] + frate11: expected: - spike times: [0.021175, 0.04135, 0.0813, 0.120475, 0.16, 0.198925, 0.237275, 0.275075, 0.3124, 0.349325, 0.3859, 0.42215, 0.458125, 0.49385, 0.5294, 0.56475, 0.59995, 0.635025, 0.669975, 0.70485, 0.7396, 0.7743, 0.8089, 0.843475, 0.877975, 0.91245, 0.9469, 0.9813, 1.015675] + spike times: [0.021175, 0.04135, 0.0813, 0.1205, 0.16, 0.198925, 0.237275, 0.2751, 0.312425, 0.34935, 0.385925, 0.422175, 0.45815, 0.4939, 0.529425, 0.5648, 0.6, 0.635075, 0.670025, 0.7049, 0.73965, 0.77435, 0.808975, 0.84355, 0.87805, 0.912525, 0.946975, 0.981375, 1.01575] + frate12: expected: - spike times: [0.020275, 0.0387, 0.0764, 0.113375, 0.15075, 0.187625, 0.224025, 0.255525, 0.291775, 0.3266, 0.361175, 0.395425, 0.4294, 0.46315, 0.496675, 0.530025, 0.5632, 0.596225, 0.62915, 0.66195, 0.69465, 0.727275, 0.7598, 0.792275, 0.8247, 0.857075, 0.8894, 0.9217, 0.95395, 0.986175, 1.018375] - + spike times: [0.020275, 0.0387, 0.0764, 0.113375, 0.150775, 0.18765, 0.223975, 0.25985, 0.290925, 0.3268, 0.361225, 0.3955, 0.429475, 0.4632, 0.496725, 0.530075, 0.56325, 0.5963, 0.6292, 0.662, 0.6947, 0.727325, 0.759875, 0.79235, 0.824775, 0.85715, 0.889475, 0.92175, 0.954025, 0.98625, 1.01845] + frate13: expected: - spike times: [0.0195, 0.036475, 0.072225, 0.1073, 0.14285, 0.177925, 0.2125, 0.246575, 0.280225, 0.31345, 0.34635, 0.3789, 0.4112, 0.44325, 0.475075, 0.506725, 0.5382, 0.569525, 0.6007, 0.631775, 0.66275, 0.6936, 0.7244, 0.755125, 0.785775, 0.81635, 0.8469, 0.8774, 0.907875, 0.938275, 0.968675, 0.99905] - + spike times: [0.0195, 0.036475, 0.072225, 0.1073, 0.14285, 0.17795, 0.212525, 0.2466, 0.28025, 0.313475, 0.346375, 0.37895, 0.4111, 0.44315, 0.474975, 0.506625, 0.5381, 0.569425, 0.600625, 0.6317, 0.66265, 0.693525, 0.724325, 0.75505, 0.7857, 0.8163, 0.84685, 0.87735, 0.9078, 0.938225, 0.968625, 0.999] + frate14: expected: - spike times: [0.01885, 0.0346, 0.0686, 0.10205, 0.135975, 0.1695, 0.20255, 0.235125, 0.267275, 0.299025, 0.33045, 0.36155, 0.392375, 0.42295, 0.4533, 0.483475, 0.513475, 0.5433, 0.573, 0.602575, 0.632025, 0.6614, 0.690675, 0.719875, 0.749, 0.77805, 0.807075, 0.836025, 0.864925, 0.8938, 0.92265, 0.95145, 0.980225, 1.008975] - + spike times: [0.01885, 0.0346, 0.068625, 0.10205, 0.136, 0.169525, 0.202575, 0.23515, 0.2673, 0.29905, 0.330475, 0.361575, 0.3924, 0.422975, 0.45335, 0.4835, 0.5135, 0.54335, 0.572925, 0.6025, 0.63195, 0.661325, 0.6906, 0.7198, 0.748925, 0.778, 0.807, 0.835975, 0.864875, 0.89375, 0.922675, 0.948075, 0.977675, 1.006275] + frate15: expected: - spike times: [0.018275, 0.033, 0.065425, 0.09745, 0.12995, 0.1621, 0.193775, 0.22505, 0.255875, 0.286325, 0.31645, 0.346275, 0.3758, 0.4051, 0.434175, 0.46305, 0.49175, 0.520275, 0.548675,0.577025, 0.60175, 0.630625, 0.65835, 0.6862, 0.713975, 0.741675, 0.769325, 0.796925, 0.824475, 0.851975, 0.87945, 0.906875, 0.9343, 0.961675, 0.989025, 1.01635] - + spike times: [0.018275, 0.033, 0.065425, 0.09745, 0.12995, 0.1621, 0.1938, 0.22505, 0.2559, 0.28635, 0.316475, 0.3463, 0.375825, 0.405125, 0.4342, 0.463075, 0.491775, 0.520325, 0.548725, 0.577, 0.60515, 0.6332, 0.66115, 0.689025, 0.716825, 0.74465, 0.76895, 0.797375, 0.8248, 0.852325, 0.879775, 0.9072, 0.934575, 0.96195, 0.9893, 1.016625] + frate16: expected: - spike times: [0.017775, 0.031625, 0.062575, 0.093375, 0.1246, 0.1555, 0.186, 0.216075, 0.245725, 0.275025, 0.304, 0.332675, 0.361075, 0.389225, 0.417175, 0.4449, 0.472475, 0.499875, 0.527125, 0.554225, 0.58125, 0.608125, 0.634925, 0.66165, 0.688275, 0.71485, 0.741325, 0.767775, 0.79415, 0.8205, 0.8468, 0.87305, 0.899275, 0.92545, 0.951625, 0.97775, 1.003875] - + spike times: [0.017775, 0.031625, 0.0626, 0.093375, 0.1246, 0.1555, 0.186, 0.216075, 0.24575, 0.27505, 0.304025, 0.3327, 0.3611, 0.389275, 0.4172, 0.44495, 0.4725, 0.4999, 0.52715, 0.554275, 0.581275, 0.608175, 0.634975, 0.6617, 0.688325, 0.7149, 0.7414, 0.767825, 0.794225, 0.82055, 0.84685, 0.873125, 0.89935, 0.925525, 0.9517, 0.977825, 1.00395] + frate17: expected: - spike times: [0.017325, 0.0304, 0.06, 0.0897, 0.119775, 0.149575, 0.178975, 0.208, 0.236625, 0.2649, 0.292825, 0.320475, 0.347875, 0.375, 0.401925, 0.42865, 0.4552, 0.481575, 0.507825, 0.533925, 0.5599, 0.585775, 0.61155, 0.637225, 0.662825, 0.68835, 0.7138, 0.7392, 0.764525, 0.789825, 0.81505, 0.84025, 0.865425, 0.89055, 0.915625, 0.9407, 0.965725, 0.99075, 1.01575] - + spike times: [0.017325, 0.0304, 0.06, 0.0897, 0.119775, 0.149575, 0.179, 0.208, 0.23665, 0.2649, 0.29285, 0.3205, 0.347975, 0.37185, 0.3995, 0.426125, 0.452675, 0.47905, 0.505275, 0.53135, 0.557325, 0.5832, 0.60895, 0.634625, 0.660225, 0.685725, 0.711175, 0.736575, 0.7619, 0.7872, 0.812425, 0.837625, 0.862775, 0.8879, 0.913, 0.938075, 0.9631, 0.988125, 1.013125] + frate18: expected: - spike times: [0.016925, 0.02935, 0.0576, 0.08635, 0.115375, 0.144175, 0.172625, 0.200675, 0.22835, 0.2557, 0.2827, 0.30945, 0.3359, 0.36215, 0.38815, 0.413975, 0.4396, 0.465075, 0.4904, 0.515575, 0.54065, 0.5656, 0.59045, 0.6152, 0.639875, 0.664475, 0.689, 0.71345, 0.737875, 0.7622, 0.7865, 0.810775, 0.834975, 0.85915, 0.8833, 0.9074, 0.931475, 0.95555, 0.979575, 1.0036] - + spike times: [0.016925, 0.02935, 0.057625, 0.08635, 0.115375, 0.1442, 0.172625, 0.200675, 0.228375, 0.2557, 0.282725, 0.309475, 0.33595, 0.362175, 0.388175, 0.414, 0.439625, 0.4651, 0.490425, 0.515625, 0.5407, 0.56565, 0.5905, 0.61525, 0.639925, 0.664525, 0.68905, 0.713525, 0.737925, 0.762275, 0.786575, 0.810825, 0.83505, 0.859225, 0.88335, 0.907475, 0.93155, 0.955625, 0.97965, 1.003675] + frate19: expected: - spike times: [0.016575, 0.0284, 0.05535, 0.08325, 0.111325, 0.139225, 0.166775, 0.19395, 0.220775, 0.247275, 0.27345, 0.29935, 0.325, 0.3504, 0.3756, 0.400575, 0.4254, 0.45005, 0.47455, 0.4989, 0.52315, 0.547275, 0.5713, 0.595225, 0.619075, 0.642825, 0.6665, 0.690125, 0.7137, 0.737125, 0.76055, 0.783975, 0.807325, 0.83065, 0.853925, 0.877175, 0.9004, 0.9236, 0.946775, 0.969925, 0.993025, 1.01615] + spike times: [0.016575, 0.0284, 0.05535, 0.083275, 0.11135, 0.139225, 0.166775, 0.193975, 0.2208, 0.2473, 0.273475, 0.299375, 0.325025, 0.350425, 0.375625, 0.4006, 0.425425, 0.450075, 0.474575, 0.49895, 0.5232, 0.547325, 0.57135, 0.595175, 0.619025, 0.642775, 0.666475, 0.6901, 0.71365, 0.73715, 0.7606, 0.784025, 0.807375, 0.8307, 0.854, 0.87725, 0.900475, 0.923675, 0.946825, 0.969975, 0.9931, 1.0162] + \ No newline at end of file diff --git a/NEURON/test/.test_fig5A.mep b/NEURON/test/.test_fig5A.mep index 28aec39..5631d12 100644 --- a/NEURON/test/.test_fig5A.mep +++ b/NEURON/test/.test_fig5A.mep @@ -5,11 +5,11 @@ system: Testing Golgi experiments: phar_pacemaking_control: expected: - spike times: [0.0872, 0.289275, 0.499225, 0.7139, 0.9327, 1.154625, 1.378925, 1.605025, 1.832675] + spike times: [0.0872, 0.289275, 0.49925, 0.713925, 0.932725, 1.154675, 1.378975, 1.605075, 1.83265] phar_pacemaking_Ih: expected: - spike times: [0.1737, 0.546925, 0.944375, 1.367, 1.810675] + spike times: [0.1737, 0.54695, 0.9444, 1.367075, 1.81075] phar_pacemaking_INaP: diff --git a/NEURON/test/.test_fig5Bi.mep b/NEURON/test/.test_fig5Bi.mep index 354cc0e..8fb08c9 100644 --- a/NEURON/test/.test_fig5Bi.mep +++ b/NEURON/test/.test_fig5Bi.mep @@ -5,11 +5,11 @@ system: Testing Golgi experiments: phar_pacemaking_control: expected: - spike times: [0.22245, 0.2839, 0.3618, 0.439575, 0.5166, 0.593125, 0.6693, 0.7453, 0.8212, 0.897075, 0.97295, 1.04885, 1.1248, 1.2009] + spike times: [0.22245, 0.283925, 0.361825, 0.439575, 0.516625, 0.59315, 0.66935, 0.74535, 0.82125, 0.897125, 0.973, 1.0489, 1.124875, 1.200975] phar_pacemaking_IK_slow_shift: expected: - spike times: [0.2273, 0.312, 0.413075, 0.513075, 0.6124, 0.71155, 0.8107, 0.909975, 1.009425, 1.109025] + spike times: [0.2273, 0.312025, 0.413075, 0.513075, 0.612425, 0.711575, 0.810725, 0.910025, 1.009225, 1.108825] diff --git a/NEURON/test/.test_fig5Bii.mep b/NEURON/test/.test_fig5Bii.mep index 70d5493..7253ac8 100644 --- a/NEURON/test/.test_fig5Bii.mep +++ b/NEURON/test/.test_fig5Bii.mep @@ -6,65 +6,65 @@ experiments: Control1: expected: - spike times: [0.22245, 0.2839, 0.3618, 0.439575, 0.5166, 0.593125, 0.6693, 0.7453, 0.8212, 0.897075, 0.97295, 1.04885, 1.1248, 1.2009] + spike times: [0.22245, 0.283925, 0.361825, 0.439575, 0.516625, 0.59315, 0.66935, 0.74535, 0.82125, 0.897125, 0.973, 1.0489, 1.124875, 1.200975] Control2: expected: - spike times: [0.2147, 0.250725, 0.306425, 0.3619, 0.41695, 0.4713, 0.525075, 0.578375, 0.631325, 0.683975, 0.7364, 0.788675, 0.840775, 0.8928, 0.944725, 0.9966, 1.048425, 1.100225, 1.152025] + spike times: [0.2147, 0.250725, 0.306425, 0.3619, 0.416975, 0.471325, 0.5251, 0.5784, 0.63135, 0.684025, 0.73645, 0.788725, 0.840825, 0.89285, 0.9448, 0.996675, 1.0485, 1.1003, 1.1521] Control3: expected: - spike times: [0.21095, 0.2356, 0.280525, 0.32465, 0.368925, 0.412575, 0.45565, 0.49825, 0.54045, 0.58235, 0.61895, 0.6612, 0.7021, 0.74295, 0.783625, 0.824175, 0.86465, 0.905025, 0.945325, 0.98555, 1.02575, 1.0659, 1.106, 1.1461, 1.18615] + spike times: [0.21095, 0.2356, 0.28055, 0.324675, 0.368925, 0.412575, 0.455675, 0.498275, 0.540475, 0.5823, 0.623825, 0.665125, 0.706175, 0.747075, 0.7878, 0.828425, 0.868925, 0.909325, 0.94965, 0.989925, 1.03015, 1.070325, 1.11045, 1.15055, 1.190625] Control4: expected: - spike times: [0.208725, 0.227425, 0.2657, 0.302975, 0.3407, 0.37795, 0.414725, 0.451025, 0.486925, 0.522475, 0.5577, 0.592675, 0.6274, 0.6619, 0.69625, 0.730425, 0.76445, 0.7984, 0.83035, 0.864475, 0.898025, 0.931575, 0.96505, 0.998475, 1.03185, 1.0652, 1.0985, 1.1318, 1.16505, 1.198275] + spike times: [0.208725, 0.227425, 0.265725, 0.303, 0.340725, 0.377975, 0.414725, 0.45105, 0.48695, 0.5225, 0.557725, 0.5927, 0.627425, 0.66195, 0.696275, 0.73045, 0.7645, 0.798425, 0.832225, 0.86595, 0.899575, 0.93315, 0.96665, 1.0001, 1.0335, 1.06685, 1.100175, 1.133475, 1.166725, 1.199975] Control5: expected: - spike times: [0.207275, 0.22245, 0.256, 0.28875, 0.322025, 0.354925, 0.38745, 0.41955, 0.451125, 0.482525, 0.5136, 0.5444, 0.574975, 0.605325, 0.635475, 0.665475, 0.6953, 0.725, 0.754575, 0.78405, 0.813425, 0.8427, 0.8719, 0.901025, 0.9301, 0.959125, 0.9881, 1.017025, 1.0459, 1.07475, 1.103575, 1.13235, 1.161125, 1.189875] + spike times: [0.207275, 0.22245, 0.256, 0.28875, 0.322025, 0.35495, 0.38745, 0.41955, 0.451275, 0.482675, 0.51375, 0.54455, 0.575125, 0.605475, 0.63565, 0.665625, 0.695475, 0.725175, 0.75475, 0.784225, 0.813575, 0.842875, 0.872075, 0.901225, 0.9303, 0.9593, 0.988275, 1.0172, 1.0461, 1.07495, 1.103775, 1.13255, 1.161325, 1.190075] Control6: expected: - spike times: [0.20625, 0.219125, 0.248875, 0.2785, 0.308475, 0.33825, 0.36765, 0.3967, 0.4254, 0.453775, 0.481875, 0.5097, 0.5373, 0.564675, 0.59185, 0.618875, 0.645725, 0.672425, 0.699025, 0.725475, 0.75185, 0.7781, 0.804275, 0.830375, 0.8564, 0.882375, 0.908275, 0.934125, 0.959925, 0.985675, 1.011375, 1.037075, 1.0627, 1.088325, 1.113925, 1.139475, 1.165025, 1.19055] + spike times: [0.20625, 0.219125, 0.248875, 0.2785, 0.3085, 0.33825, 0.367675, 0.3967, 0.4254, 0.4538, 0.481875, 0.509725, 0.537325, 0.5647, 0.5919, 0.6189, 0.64575, 0.672475, 0.69905, 0.725525, 0.751875, 0.77815, 0.804325, 0.830425, 0.85645, 0.882425, 0.908325, 0.934175, 0.959975, 0.985725, 1.01145, 1.037125, 1.062775, 1.088475, 1.11105, 1.137325, 1.162775, 1.188275] Control7: expected: - spike times: [0.205475, 0.216775, 0.242925, 0.27035, 0.2978, 0.325125, 0.35215, 0.378875, 0.40525, 0.43135, 0.457175, 0.48275, 0.508075, 0.533225, 0.558175, 0.58285, 0.60745, 0.631925, 0.65625, 0.680475, 0.704575, 0.728575, 0.752475, 0.776325, 0.80005, 0.82375, 0.84735, 0.8709, 0.8944, 0.91785, 0.94125, 0.9646, 0.987925, 1.011225, 1.034475, 1.0577, 1.080875, 1.10405, 1.1272, 1.150325, 1.173425, 1.196525] + spike times: [0.205475, 0.216775, 0.242925, 0.27035, 0.2978, 0.32515, 0.352175, 0.378875, 0.405275, 0.431375, 0.4572, 0.482775, 0.5081, 0.53325, 0.5582, 0.582975, 0.607575, 0.63205, 0.6564, 0.6806, 0.7047, 0.728725, 0.752625, 0.77645, 0.8002, 0.823875, 0.8475, 0.87105, 0.89455, 0.918, 0.9414, 0.96475, 0.988075, 1.011375, 1.034625, 1.05785, 1.08105, 1.104225, 1.127375, 1.1505, 1.1736, 1.1967] Control8: expected: - spike times: [0.204875, 0.215025, 0.237375, 0.263325, 0.288725, 0.314125, 0.339275, 0.3641, 0.388675, 0.41295, 0.436975, 0.46075, 0.484325, 0.5077, 0.530875, 0.5539, 0.57675, 0.59945, 0.622025, 0.6445, 0.666825, 0.689075, 0.7112, 0.733275, 0.75525, 0.777125, 0.798975, 0.820725, 0.842425, 0.864075, 0.885675, 0.907225, 0.92875, 0.950225, 0.97165, 0.99305, 1.014425, 1.03575, 1.057075, 1.07835, 1.099625, 1.12085, 1.142075, 1.163275, 1.184475] + spike times: [0.204875, 0.215025, 0.237375, 0.263325, 0.28875, 0.31415, 0.339275, 0.364125, 0.388675, 0.412975, 0.437, 0.460775, 0.48435, 0.507725, 0.5309, 0.553925, 0.576775, 0.5995, 0.622075, 0.644525, 0.666875, 0.6891, 0.71125, 0.7333, 0.755275, 0.777175, 0.799, 0.820775, 0.842475, 0.864125, 0.885725, 0.9073, 0.9288, 0.950275, 0.9717, 0.9931, 1.014475, 1.035825, 1.057125, 1.078425, 1.099675, 1.120925, 1.14215, 1.16335, 1.18455] Control1_Ik_slow: expected: - spike times: [0.2273, 0.312, 0.413075, 0.513075, 0.6124, 0.71155, 0.8107, 0.909975, 1.009425, 1.109025] + spike times: [0.2273, 0.312025, 0.413075, 0.513075, 0.612425, 0.711575, 0.810725, 0.910025, 1.009225, 1.108825] Control2_Ik_slow: expected: - spike times: [0.217, 0.26225, 0.33005, 0.398175, 0.46545, 0.53195, 0.598, 0.6637, 0.7292, 0.794575, 0.859825, 0.92505, 0.99025, 1.055425, 1.120625, 1.185825] + spike times: [0.217, 0.26225, 0.330075, 0.3982, 0.46545, 0.531975, 0.598025, 0.663725, 0.729225, 0.7946, 0.859875, 0.9251, 0.9903, 1.055475, 1.120675, 1.185875] Control3_Ik_slow: expected: - spike times: [0.21235, 0.241225, 0.2933, 0.346, 0.398425, 0.4501, 0.501125, 0.5517, 0.6019, 0.651775, 0.70145, 0.750925, 0.800275, 0.849475, 0.8986, 0.947675, 0.996675, 1.045625, 1.09455, 1.143475, 1.19235] + spike times: [0.21235, 0.241225, 0.293325, 0.346, 0.398425, 0.4501, 0.50115, 0.551725, 0.601925, 0.651825, 0.701475, 0.750975, 0.8003, 0.849525, 0.89865, 0.947725, 0.996725, 1.045675, 1.094625, 1.143525, 1.192425] Control4_Ik_slow: expected: - spike times: [0.2097, 0.230625, 0.273675, 0.317025, 0.3607, 0.403775, 0.44625, 0.4882, 0.52975, 0.57095, 0.61185, 0.6525, 0.69295, 0.733225, 0.77335, 0.81335, 0.853225, 0.893025, 0.93275, 0.972425, 1.012025, 1.051575, 1.0911, 1.1306, 1.170075] + spike times: [0.2097, 0.230625, 0.2737, 0.317025, 0.360725, 0.40365, 0.446125, 0.4881, 0.52965, 0.57085, 0.61175, 0.6524, 0.69285, 0.733125, 0.77325, 0.81325, 0.85315, 0.89295, 0.932675, 0.972325, 1.01195, 1.0515, 1.091025, 1.130525, 1.17] Control5_Ik_slow: expected: - spike times: [0.208, 0.224525, 0.261575, 0.2988, 0.33665, 0.374025, 0.4109, 0.4473, 0.4833, 0.518925, 0.554225, 0.589275, 0.624075, 0.658675, 0.6931, 0.72735, 0.761475, 0.7955, 0.8294, 0.863225, 0.89695, 0.930625, 0.964225, 0.997775, 1.031275, 1.06475, 1.098175, 1.131575, 1.16495, 1.1983] + spike times: [0.208, 0.224525, 0.2616, 0.298825, 0.33665, 0.37405, 0.410925, 0.447325, 0.4833, 0.518925, 0.55425, 0.5893, 0.6241, 0.6587, 0.693125, 0.7274, 0.761375, 0.7954, 0.8293, 0.863125, 0.89685, 0.930525, 0.96415, 0.9977, 1.0312, 1.064675, 1.0981, 1.1315, 1.164875, 1.19825] Control6_Ik_slow: expected: - spike times: [0.2068, 0.220625, 0.2532, 0.2862, 0.319825, 0.35315, 0.38605, 0.418525, 0.4506, 0.482325, 0.51375, 0.544875, 0.575775, 0.60645, 0.63695, 0.66735, 0.694375, 0.725125, 0.75495, 0.784725, 0.814425, 0.844025, 0.87355, 0.903, 0.9324, 0.96175, 0.99105, 1.0203, 1.049525, 1.078725, 1.107875, 1.137, 1.166125, 1.1952] + spike times: [0.2068, 0.220625, 0.25325, 0.2831, 0.317325, 0.350575, 0.3835, 0.415975, 0.448075, 0.4798, 0.511225, 0.542375, 0.573275, 0.603975, 0.634475, 0.6648, 0.694975, 0.725, 0.754925, 0.78475, 0.81445, 0.844075, 0.873625, 0.9031, 0.932525, 0.9619, 0.991225, 1.0205, 1.049725, 1.078925, 1.1081, 1.13725, 1.16635, 1.19545] Control7_Ik_slow: expected: - spike times: [0.205925, 0.2179, 0.2466, 0.276625, 0.307075, 0.337325, 0.36725, 0.39675, 0.425925, 0.45475, 0.483275, 0.511525, 0.53955, 0.56735, 0.59495, 0.6224, 0.64965, 0.6768, 0.703775, 0.730675, 0.75735, 0.7839, 0.8105, 0.837, 0.86345, 0.889825, 0.91615, 0.942425, 0.96865, 0.994825, 1.02095, 1.04705, 1.073125, 1.099175, 1.125175, 1.151175, 1.177125] + spike times: [0.205925, 0.2179, 0.2466, 0.27665, 0.307075, 0.33735, 0.36725, 0.396775, 0.425925, 0.454775, 0.4833, 0.51155, 0.539575, 0.567375, 0.595, 0.622425, 0.6497, 0.676825, 0.703825, 0.7307, 0.757475, 0.78415, 0.81075, 0.837275, 0.8637, 0.8901, 0.916425, 0.942675, 0.9689, 0.995075, 1.021225, 1.047325, 1.0734, 1.099425, 1.125525, 1.1487, 1.175325] Control8_Ik_slow: expected: - spike times: [0.205275, 0.215925, 0.240725, 0.268675, 0.296575, 0.32445, 0.352, 0.379225, 0.4061, 0.432675, 0.458975, 0.485025, 0.5108, 0.5364, 0.561775, 0.587075, 0.6095, 0.63485, 0.659575, 0.6842, 0.708725, 0.73315, 0.757475, 0.781725, 0.8059, 0.83, 0.854025, 0.878, 0.901925, 0.9258, 0.949625, 0.9734, 0.99715, 1.02085, 1.04455, 1.0682, 1.091825, 1.115425, 1.139, 1.16255, 1.186075] + spike times: [0.205275, 0.215925, 0.240725, 0.268675, 0.296575, 0.32445, 0.352025, 0.379225, 0.406125, 0.4327, 0.459075, 0.482325, 0.508725, 0.53425, 0.55965, 0.58485, 0.6099, 0.6348, 0.65955, 0.6842, 0.708725, 0.73315, 0.7575, 0.78175, 0.806, 0.827525, 0.8521, 0.876025, 0.89995, 0.9238, 0.947625, 0.9714, 0.995125, 1.018825, 1.0425, 1.06615, 1.08975, 1.11335, 1.136925, 1.160475, 1.184] diff --git a/NEURON/test/.test_fig6A.mep b/NEURON/test/.test_fig6A.mep index 1f6f3ca..b85f1d0 100644 --- a/NEURON/test/.test_fig6A.mep +++ b/NEURON/test/.test_fig6A.mep @@ -5,4 +5,4 @@ system: Testing Golgi experiments: ionic_currents_and_calcium: expected: - spike times: [0.0872, 0.289275, 0.40795, 0.42785, 0.4671, 0.505025, 0.54345, 0.58145, 0.61905, 0.6563, 0.693225, 0.97475, 1.195625, 1.700725, 1.833325, 1.973525, 2.116175] + spike times: [0.0872, 0.289275, 0.40795, 0.427975, 0.46725, 0.5052, 0.543625, 0.5817, 0.61495, 0.6531, 0.6899, 0.9723, 1.193425, 1.700725, 1.83335, 1.9736, 2.11625] diff --git a/NEURON/test/.test_fig9A.mep b/NEURON/test/.test_fig9A.mep index 3d66c43..a27df6b 100644 --- a/NEURON/test/.test_fig9A.mep +++ b/NEURON/test/.test_fig9A.mep @@ -5,15 +5,15 @@ system: Testing Golgi experiments: subthreshold oscillations and spike coupling control: expected: - spike times: [0.0872, 0.289275, 0.499225, 0.7139, 0.9327, 1.154625] + spike times: [0.0872, 0.289275, 0.49925, 0.713925, 0.932725, 1.154675] subthreshold oscillations and spike coupling INa IK-V IK-C block: expected: - spike times: [0.0733, 0.342575, 0.638525, 0.9371, 1.2367] + spike times: [0.0733, 0.342575, 0.638525, 0.937125, 1.236725] subthreshold oscillations and spike coupling INa IK-V IK-C and Ihcn2 block: expected: - spike times: [0.10235, 0.437725, 0.801825, 1.1689] + spike times: [0.10235, 0.437725, 0.80185, 1.168925] subthreshold oscillations and spike coupling INa IK-V IK-C and Ihcn2 block and 10pA: expected: - spike times: [0.070075, 0.331475, 0.618775, 0.908225, 1.198325] + spike times: [0.070075, 0.331475, 0.6188, 0.908225, 1.198325] diff --git a/NEURON/test/.test_fig9B.mep b/NEURON/test/.test_fig9B.mep index 1ef2017..d6e0ce7 100644 --- a/NEURON/test/.test_fig9B.mep +++ b/NEURON/test/.test_fig9B.mep @@ -11,7 +11,7 @@ experiments: resting: -57 Subthreshold oscillations:Control block+50% I Na-P +120pA (mV): expected: - spike times: [0.0153, 0.165075, 0.2855, 0.40615, 0.5275, 0.6495, 0.772025, 0.894925, 1.01815, 1.1416, 1.26525] + spike times: [0.0153, 0.165075, 0.2855, 0.40615, 0.527525, 0.6495, 0.772025, 0.894925, 1.01815, 1.1416, 1.26525] Subthreshold oscillations:Control block+I k-slow=0 (mV): expected: spike times: [0.0677, 0.4529, 0.831, 1.20845] diff --git a/NEURON_2007/.test.mep b/NEURON_2007/.test.mep index b14fdf1..118dbde 100644 --- a/NEURON_2007/.test.mep +++ b/NEURON_2007/.test.mep @@ -5,4 +5,4 @@ system: Testing Golgi experiments: pacemaking: expected: - spike times: [0.041561, 0.195603, 0.355507, 0.515022, 0.674439, 0.83347, 0.992308, 1.151057, 1.309555, 1.468005, 1.626376, 1.784619, 1.943082, 2.10146, 2.259849, 2.418057, 2.576202, 2.73465, 2.892927, 3.05111, 3.209347, 3.367301, 3.525396, 3.683457, 3.841568, 3.999519] \ No newline at end of file + spike times: [0.041561, 0.195611, 0.35543, 0.515107, 0.674487, 0.833386, 0.992174, 1.150798, 1.309438, 1.467905, 1.626437, 1.784724, 1.94288, 2.101167, 2.259283, 2.4175, 2.575905, 2.734135, 2.892377, 3.050474, 3.208362, 3.366376, 3.524493, 3.682585, 3.840519, 3.998588] \ No newline at end of file diff --git a/NEURON_2007/.test.neuron.omt b/NEURON_2007/.test.neuron.omt index 121fa94..aa7cdce 100644 --- a/NEURON_2007/.test.neuron.omt +++ b/NEURON_2007/.test.neuron.omt @@ -15,5 +15,5 @@ experiments: spike detection: method: threshold threshold: 0 - tolerance: 0.000391680240993 + tolerance: 0.00203 # non zero tolerance due to differences in times between ubuntu and mac... diff --git a/NeuroML2/.test.golgi.jnmlnrn.omt b/NeuroML2/.test.golgi.jnmlnrn.omt index f948fee..ecb607d 100644 --- a/NeuroML2/.test.golgi.jnmlnrn.omt +++ b/NeuroML2/.test.golgi.jnmlnrn.omt @@ -15,4 +15,4 @@ experiments: spike detection: method: threshold threshold: 0 - tolerance: 0.003232 + tolerance: 0.003491210203843143 diff --git a/NeuroML2/.test.kahp.jnml.omt b/NeuroML2/.test.kahp.jnml.omt index ec84684..4375ab6 100644 --- a/NeuroML2/.test.kahp.jnml.omt +++ b/NeuroML2/.test.kahp.jnml.omt @@ -14,7 +14,7 @@ experiments: spike detection: method: threshold threshold: 0.018 - tolerance: 0.00063 + tolerance: 0.0006253908692932503 o2: observables: spike times: @@ -24,7 +24,7 @@ experiments: spike detection: method: threshold threshold: 0.5 - tolerance: 0.00066 + tolerance: 0.0006540816511928143 c2: observables: spike times: @@ -34,7 +34,7 @@ experiments: spike detection: method: threshold threshold: 0.1065 - tolerance: 0.00058 + tolerance: 0.0005743251679277049 c3: observables: spike times: @@ -44,4 +44,4 @@ experiments: spike detection: method: threshold threshold: 0.1065 - tolerance: 0.00071 + tolerance: 0.0007027685120114187 diff --git a/NeuroML2/.test.kahp.jnmlnrn.omt b/NeuroML2/.test.kahp.jnmlnrn.omt index 9c81c1f..fe76bb8 100644 --- a/NeuroML2/.test.kahp.jnmlnrn.omt +++ b/NeuroML2/.test.kahp.jnmlnrn.omt @@ -14,7 +14,7 @@ experiments: spike detection: method: threshold threshold: 0.018 - tolerance: 0.00012 + tolerance: 0.00011779083292854516 o2: observables: spike times: @@ -24,7 +24,7 @@ experiments: spike detection: method: threshold threshold: 0.5 - tolerance: 2.8e-5 + tolerance: 2.7253402132934124e-05 c2: observables: spike times: @@ -34,7 +34,7 @@ experiments: spike detection: method: threshold threshold: 0.1065 - tolerance: 0.00025 + tolerance: 0.00024330558713847594 c3: observables: spike times: @@ -44,4 +44,4 @@ experiments: spike detection: method: threshold threshold: 0.1065 - tolerance: 6.8e-5 + tolerance: 6.70269572492118e-05 diff --git a/NeuroML2/.test.soma2.jnml.omt b/NeuroML2/.test.soma2.jnml.omt index f257b75..87c3191 100644 --- a/NeuroML2/.test.soma2.jnml.omt +++ b/NeuroML2/.test.soma2.jnml.omt @@ -15,4 +15,4 @@ experiments: spike detection: method: threshold threshold: 0 - tolerance: 0.0028 + tolerance: 0.0029551072783196956 diff --git a/NeuroML2/.test.soma2.jnmlnrn.omt b/NeuroML2/.test.soma2.jnmlnrn.omt index 4bd396d..6ccf045 100644 --- a/NeuroML2/.test.soma2.jnmlnrn.omt +++ b/NeuroML2/.test.soma2.jnmlnrn.omt @@ -15,4 +15,4 @@ experiments: spike detection: method: threshold threshold: 0 - tolerance: 0.0111 + tolerance: 0.010764004189123592 diff --git a/neuroConstruct/generatedNeuroML2/.test.validate.omt b/neuroConstruct/generatedNeuroML2/.test.validate.omt index 0f95929..3fe7b8e 100644 --- a/neuroConstruct/generatedNeuroML2/.test.validate.omt +++ b/neuroConstruct/generatedNeuroML2/.test.validate.omt @@ -2,5 +2,5 @@ # This test will validate all of the NeuroML 2 files in the current directory using: jnml -validate *.nml # Missing KAHP_CML.channel.nml -target: "CaHVA_CML.channel.nml hcn1f_CML.channel.nml hcn2f_CML.channel.nml KA_CML.channel.nml Kslow_CML.channel.nml LeakCond.channel.nml NaR_CML.channel.nml CaLVA_CML.channel.nml hcn1s_CML.channel.nml hcn2s_CML.channel.nml KV_CML.channel.nml NaP_CML.channel.nml NaT_CML.channel.nml*.cell.nml *.net.nml" +target: "CaHVA_CML.channel.nml hcn1f_CML.channel.nml hcn2f_CML.channel.nml KA_CML.channel.nml Kslow_CML.channel.nml LeakCond.channel.nml NaR_CML.channel.nml CaLVA_CML.channel.nml hcn1s_CML.channel.nml hcn2s_CML.channel.nml KV_CML.channel.nml NaP_CML.channel.nml NaT_CML.channel.nml *.cell.nml *.net.nml" engine: jNeuroML_validate