From 6d7e45e7db0924b5f96c9c44e9b43a5c12dd05c2 Mon Sep 17 00:00:00 2001 From: Padraig Gleeson Date: Wed, 22 Mar 2023 10:37:56 +0000 Subject: [PATCH 1/7] Tweak test script to pip install --- test-ghactions.sh | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/test-ghactions.sh b/test-ghactions.sh index 0fd0c846..df71fa6b 100755 --- a/test-ghactions.sh +++ b/test-ghactions.sh @@ -1,6 +1,6 @@ set -e -python setup.py install +pip install . echo echo "################################################" From 333634a66f0f29ffe183552e49df8eb25d4e9641 Mon Sep 17 00:00:00 2001 From: Padraig Gleeson Date: Wed, 12 Apr 2023 11:58:25 +0100 Subject: [PATCH 2/7] Ignore arm64 dir on new mac chip --- .gitignore | 1 + 1 file changed, 1 insertion(+) diff --git a/.gitignore b/.gitignore index cc71c8d6..ac99070f 100644 --- a/.gitignore +++ b/.gitignore @@ -151,3 +151,4 @@ examples/results/*.dat /tests/iv_izh2007RS0.net.nml /tests/leak_chan.channel.nml /tests/test_cell_analysis.cell.nml +arm64 From 3194a9ea1093101954f12827afda8e20da28725c Mon Sep 17 00:00:00 2001 From: pgleeson Date: Wed, 3 May 2023 13:29:15 +0100 Subject: [PATCH 3/7] Fix some issues with plot (was using marker='o' by default) --- pyneuroml/plot/Plot.py | 8 +++----- 1 file changed, 3 insertions(+), 5 deletions(-) diff --git a/pyneuroml/plot/Plot.py b/pyneuroml/plot/Plot.py index 0e84a88f..9387aa6a 100644 --- a/pyneuroml/plot/Plot.py +++ b/pyneuroml/plot/Plot.py @@ -177,15 +177,14 @@ def generate_plot( label = "" if not labels else labels[i] marker = None if not markers else markers[i] linewidth = 1 if not linewidths else linewidths[i] - markersize = 6 if not markersizes else markersizes[i] + markersize = None if not markersizes else markersizes[i] if colors: plt.plot( xvalues[i], yvalues[i], - "o", - color=colors[i], marker=marker, + color=colors[i], markersize=markersize, linestyle=linestyle, linewidth=linewidth, @@ -195,7 +194,6 @@ def generate_plot( plt.plot( xvalues[i], yvalues[i], - "o", marker=marker, markersize=markersize, linestyle=linestyle, @@ -385,7 +383,7 @@ def generate_interactive_plot( raise ValueError("labels not provided correctly") if not markersizes: - markersizes = len(xvalues) * [6.0] + markersizes = len(xvalues) * [6] if not markers: markers = len(xvalues) * [0] if not linestyles: From 94e510810de429b8189e8a95dff82c0108e78b55 Mon Sep 17 00:00:00 2001 From: pgleeson Date: Wed, 3 May 2023 14:05:03 +0100 Subject: [PATCH 4/7] Test without argparse requirement --- .gitignore | 2 ++ setup.py | 1 - 2 files changed, 2 insertions(+), 1 deletion(-) diff --git a/.gitignore b/.gitignore index cc0a451f..c8329ab7 100644 --- a/.gitignore +++ b/.gitignore @@ -153,3 +153,5 @@ examples/results/*.dat /tests/test_cell_analysis.cell.nml arm64 *.neux +/test_*plot*png +/examples/plot.py diff --git a/setup.py b/setup.py index 7b665516..f5ced29f 100644 --- a/setup.py +++ b/setup.py @@ -92,7 +92,6 @@ long_description=open("README.md").read(), long_description_content_type="text/markdown", install_requires=[ - "argparse", "pylems>=0.5.7", "airspeed>=0.5.5", "neuromllite>=0.4.1", # sets dependency for libNeuroML also From e09ec7519b0a79180c515368beff8d1c53398125 Mon Sep 17 00:00:00 2001 From: Padraig Gleeson Date: Thu, 4 May 2023 10:03:53 +0100 Subject: [PATCH 5/7] Remove travis badge --- README.md | 2 -- 1 file changed, 2 deletions(-) diff --git a/README.md b/README.md index 75448d72..0ba2ee55 100644 --- a/README.md +++ b/README.md @@ -144,5 +144,3 @@ Builds on [Neurotune](https://github.com/NeuralEnsemble/neurotune) and [pyelectr Built in viewer of cells in 3D? Mayavi? More closely tied to PyNN? - -[![Build Status](https://travis-ci.com/NeuroML/pyNeuroML.svg?branch=master)](https://travis-ci.com/NeuroML/pyNeuroML) From 3af5ab2e7bc25d2de2282b246ef9610efa4d8130 Mon Sep 17 00:00:00 2001 From: Padraig Gleeson Date: Thu, 4 May 2023 10:38:27 +0100 Subject: [PATCH 6/7] Remove py2.7 in master tests --- .github/workflows/ci.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml index a2162e05..794ab6ee 100644 --- a/.github/workflows/ci.yml +++ b/.github/workflows/ci.yml @@ -12,7 +12,7 @@ jobs: runs-on: ubuntu-latest strategy: matrix: - python-version: [2.7, 3.7, 3.8, 3.9] + python-version: [3.7, 3.8, 3.9] fail-fast: false steps: From 0e4cbf34f8e0687e6ef6334911ffc774a7ff11cd Mon Sep 17 00:00:00 2001 From: pgleeson Date: Thu, 4 May 2023 10:55:25 +0100 Subject: [PATCH 7/7] Add plot spike support for nest 3.0 spiketime files --- pyneuroml/plot/PlotSpikes.py | 17 +++++++++++------ 1 file changed, 11 insertions(+), 6 deletions(-) diff --git a/pyneuroml/plot/PlotSpikes.py b/pyneuroml/plot/PlotSpikes.py index 0534773a..647fa9c7 100644 --- a/pyneuroml/plot/PlotSpikes.py +++ b/pyneuroml/plot/PlotSpikes.py @@ -12,9 +12,13 @@ logger = logging.getLogger(__name__) +FORMAT_ID_T = "id_t" +FORMAT_ID_TIME_NEST_DAT = "id_t_nest_dat" +FORMAT_T_ID = "t_id" + DEFAULTS = { - "format": "id_t", + "format": FORMAT_ID_T, "rates": False, "save_spike_plot_to": None, "rate_window": 50, @@ -74,8 +78,9 @@ def process_args(): metavar="", default=DEFAULTS["format"], help="How the spiketimes are represented on each line of file: \n" - + "id_t: id of cell, space(s) / tab(s), time of spike (default);\n" - + "t_id: time of spike, space(s) / tab(s), id of cell;\n" + + "%s: id of cell, space(s) / tab(s), time of spike (default);\n"%FORMAT_ID_T + + "%s: id of cell, space(s) / tab(s), time of spike, allowing NEST dat file comments/metadata;\n"%FORMAT_ID_TIME_NEST_DAT + + "%s: time of spike, space(s) / tab(s), id of cell;\n"%FORMAT_T_ID + "sonata: SONATA format HDF5 file containing spike times", ) @@ -288,10 +293,10 @@ def run(a=None, **kwargs): ids_in_file[name] = [] for line in spikes_file: - if not line.startswith("#"): - if a.format == "id_t": + if not line.startswith("#") and not (line.startswith("sender") and a.format == FORMAT_ID_TIME_NEST_DAT): + if a.format == FORMAT_ID_T or a.format == FORMAT_ID_TIME_NEST_DAT: [id, t] = line.split() - elif a.format == "t_id": + elif a.format == FORMAT_T_ID: [t, id] = line.split() id_shifted = offset_id + int(float(id)) max_id = max(max_id, id_shifted)