From c683a1f77f4ccc96d2a20ec3604cc11727eda759 Mon Sep 17 00:00:00 2001
From: Brent Huisman <brenthuisman@users.noreply.github.com>
Date: Thu, 22 Dec 2022 16:09:33 +0100
Subject: [PATCH] v0.8.1 (#2072)
Co-authored-by: boeschf <48126478+boeschf@users.noreply.github.com>
---
.../workflows/{ciwheel.yml => release.yml} | 30 +++++++++++-
CHANGELOG.md | 26 ++++++++++
VERSION | 2 +-
doc/contrib/release.rst | 39 ++++++++-------
python/example/calcium_stdp.py | 5 +-
python/example/example_requirements.txt | 1 +
python/example/gap_junctions.py | 2 +-
python/example/network_ring.py | 6 +--
python/example/network_ring_gpu.py | 6 +--
python/example/network_ring_mpi_plot.py | 6 +--
.../network_two_cells_gap_junctions.py | 2 +-
python/example/single_cell_allen.py | 4 +-
python/example/single_cell_bluepyopt_l5pc.py | 8 ++-
.../single_cell_bluepyopt_simplecell.py | 8 ++-
python/example/single_cell_cable.py | 6 +--
python/example/single_cell_detailed.py | 8 ++-
python/example/single_cell_detailed_recipe.py | 8 ++-
python/example/single_cell_model.py | 2 +-
python/example/single_cell_nml.py | 8 ++-
python/example/single_cell_recipe.py | 2 +-
python/example/single_cell_stdp.py | 4 +-
python/example/single_cell_swc.py | 8 ++-
python/example/v-clamp.py | 8 ++-
scripts/run_python_examples.sh | 49 ++++++++++---------
24 files changed, 171 insertions(+), 77 deletions(-)
rename .github/workflows/{ciwheel.yml => release.yml} (75%)
diff --git a/.github/workflows/ciwheel.yml b/.github/workflows/release.yml
similarity index 75%
rename from .github/workflows/ciwheel.yml
rename to .github/workflows/release.yml
index 809c978e..895a20e6 100644
--- a/.github/workflows/ciwheel.yml
+++ b/.github/workflows/release.yml
@@ -1,5 +1,4 @@
-
-name: Arbor on Wheels
+name: Produce Arbor release artifacts
on:
push:
@@ -107,3 +106,30 @@ jobs:
env:
TWINE_USERNAME: __token__
TWINE_PASSWORD: ${{ secrets.TESTPYPI_SECRET }}
+
+ make_release:
+ name: draft new GitHub release
+ if: startsWith(github.ref, 'refs/tags/v')
+ runs-on: ubuntu-20.04
+ needs: [build_binary_wheels, build_sdist]
+ steps:
+ - name: "Clone w/ submodules"
+ uses: actions/checkout@v3
+ with:
+ fetch-depth: 0
+ submodules: "recursive"
+ path: arbor
+ - name: Make full tarball
+ run: |
+ the_ref=${{ github.ref }}
+ the_tag="${the_ref/refs\/tags\//}"
+ $GITHUB_WORKSPACE/arbor/scripts/create_tarball $GITHUB_WORKSPACE/arbor $the_tag $GITHUB_WORKSPACE/arbor-$the_tag-full.tar.gz
+ - name: "Make Release"
+ uses: ncipollo/release-action@v1
+ with:
+ omitBody: false
+ draft: true
+ prerelease: false
+ generateReleaseNotes: true
+ artifacts: '*.whl,*full.tar.gz'
+ token: ${{ secrets.GITHUB_TOKEN }}
diff --git a/CHANGELOG.md b/CHANGELOG.md
index 537d089b..55405a5e 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -1,3 +1,29 @@
+# v0.8.1
+
+** 2022 12 20 **
+
+A 🎄 holiday release! Not much has changed in a month, but we'd like to share it all the same. Notably, the [Arbor GUI](https://github.com/arbor-sim/gui/) [is co-released](https://github.com/arbor-sim/gui/releases/tag/v0.8) as of Arbor v0.8, and v0.8.1 will be no different.
+
+## Major new features
+
+- Voltage Processes: add the VOLTAGE_PROCESS mechanism kind to modcc, allowing for direct writing to the membrane voltage (#2033)
+- Spack gpu option: added conditional variant for cuda builds to enable GPU-based random number generation (#2043)
+- SDE Tutorial (#2044)
+
+## Breaking changes since v0.7
+
+- None 💃!
+
+## Bug fixed
+
+- Fix ornstein_uhlenbeck example on gpu (#2039)
+- Setting ARB_MODCC was broken and nunfunctional. Fixed. (#2029)
+- The `--cxx` flag in `arbor-build-catalogue` is now properly used; falls back to `c++`. (#2051)
+
+## Full commit log
+
+...
+
# v0.8
** 2022 11 15 **
diff --git a/VERSION b/VERSION
index d182dc91..6f4eebdf 100644
--- a/VERSION
+++ b/VERSION
@@ -1 +1 @@
-0.8.1-dev
+0.8.1
diff --git a/doc/contrib/release.rst b/doc/contrib/release.rst
index 699f6200..22a5b1d6 100644
--- a/doc/contrib/release.rst
+++ b/doc/contrib/release.rst
@@ -82,7 +82,7 @@ Release
#. Change ``VERSION``. Make sure does not end with ``-rc`` or ``-dev``.
-#. Update ``scripts/check-all-tags.sh`` to check the current tag.
+#. Merge the PR.
#. Tag
@@ -94,6 +94,8 @@ Release
#. Upload to pypi & verify
+ Get the wheels from test PyPI or the Github Action that produced the release artifacts.
+
.. code-block:: bash
twine upload -r arborpypi dist/*
@@ -102,34 +104,33 @@ Release
pip install arbor
python -c 'import arbor; print(arbor.__config__)'
-#. Create tarball with
+#. Create Github Release: https://github.com/arbor-sim/arbor/releases
+
+ - The Github action that produced the release artifacts should have prepared a draft Release.
+ - If not:
+ - Go to `GH tags`_ and click “…†and “Create releaseâ€
+ - Categorize/edit Github's autogenerated release notes (alternatively go through merged PRs to come up with a changelog).
+ - Manually build full tarball:
+
``scripts/create_tarball ~/loc/of/arbor tagname outputfile``
- eg ``scripts/create_tarball /full/path/to/arbor v0.5.1 ~/arbor-v0.5.1-full.tar.gz``
-
-#. Download output of wheel action associated to this release commit and extract (verify the wheels and
- source targz is in /dist)
- - Of course, the above action must have passed the tests successfully.
-
-#. Update ``spack/package.py``. The checksum of the targz is the sha256sum.
+Post Release
+------------
-#. Start a new release on Zenodo, this allocated a DOI, but you don't have to finish it right away. Add new Zenodo badge/link to docs/README.
+#. Place the Github generated release notes in ``CHANGELOG``.
-#. Create Github Release: https://github.com/arbor-sim/arbor/releases
+#. Start a new release on Zenodo, this allocated a DOI, but you don't have to finish it right away. Add new Zenodo badge/link to docs/README.
- - Go to `GH tags`_ and click “…†and “Create releaseâ€
- - Categorize/edit Github's autogenerated release notes (alternatively go through merged PRs to come up with a changelog).
- - add tarball to release, created in previous step.
-
#. Update Zenodo with authors and changelog created in previous step and submit.
-Post Release
-------------
-
#. Make a new PR setting ``VERSION`` to the next with a trailing ``-dev``. E.g. if you just release ``3.14``, change ``VERSION`` to ``3.15-dev``
-
- - Include changes such as to ``spack/package.py``, ``CITATIONS``, ``doc/index.rst`` in postrel PR. Copy Zenodo BibTex export to ``CITATIONS``.
+
+ - Update ``spack/package.py``. The checksum of the targz is the sha256sum.
+ - Include changes such as to ``CITATIONS``, ``doc/index.rst`` in postrel PR. Copy Zenodo BibTex export to ``CITATIONS``.
+
+#. Update ``scripts/check-all-tags.sh`` to check the current tag.
#. Update spack package / Ebrains Lab / Opensourcebrain
diff --git a/python/example/calcium_stdp.py b/python/example/calcium_stdp.py
index ba86050f..6f287184 100644
--- a/python/example/calcium_stdp.py
+++ b/python/example/calcium_stdp.py
@@ -224,9 +224,8 @@ ref = numpy.array(
)
df_ref = pandas.DataFrame({"ds": ref[:, 1], "ms": ref[:, 0], "type": "Reference"})
-seaborn.set_theme()
-df = pandas.concat(results)
-df = pandas.concat([df, df_ref])
+df = pandas.concat(results, ignore_index=True)
+df = pandas.concat([df, df_ref], ignore_index=True)
plt = seaborn.relplot(kind="line", data=df, x="ms", y="ds", hue="type")
plt.set_xlabels("lag time difference (ms)")
plt.set_ylabels("change in synaptic strenght (after/before)")
diff --git a/python/example/example_requirements.txt b/python/example/example_requirements.txt
index 05a99b1d..c06bf62e 100644
--- a/python/example/example_requirements.txt
+++ b/python/example/example_requirements.txt
@@ -1,4 +1,5 @@
# pip requirements file
+numpy!=1.24.0 # See https://github.com/numpy/numpy/issues/22826
LFPykit>=0.3
pandas
seaborn
diff --git a/python/example/gap_junctions.py b/python/example/gap_junctions.py
index a06bc8de..50da0589 100644
--- a/python/example/gap_junctions.py
+++ b/python/example/gap_junctions.py
@@ -160,5 +160,5 @@ for gid in range(ncells):
)
df = pandas.concat(df_list, ignore_index=True)
-seaborn.relplot(data=df, kind="line", x="t/ms", y="U/mV", hue="Cell", ci=None)
+seaborn.relplot(data=df, kind="line", x="t/ms", y="U/mV", hue="Cell", errorbar=None)
plt.show()
diff --git a/python/example/network_ring.py b/python/example/network_ring.py
index d30e83a4..786c8cba 100755
--- a/python/example/network_ring.py
+++ b/python/example/network_ring.py
@@ -152,6 +152,6 @@ for gid in range(ncells):
)
df = pandas.concat(df_list, ignore_index=True)
-seaborn.relplot(data=df, kind="line", x="t/ms", y="U/mV", hue="Cell", ci=None).savefig(
- "network_ring_result.svg"
-)
+seaborn.relplot(
+ data=df, kind="line", x="t/ms", y="U/mV", hue="Cell", errorbar=None
+).savefig("network_ring_result.svg")
diff --git a/python/example/network_ring_gpu.py b/python/example/network_ring_gpu.py
index 22a9b43d..ff4682c9 100644
--- a/python/example/network_ring_gpu.py
+++ b/python/example/network_ring_gpu.py
@@ -179,6 +179,6 @@ for gid in range(ncells):
)
df = pandas.concat(df_list, ignore_index=True)
-seaborn.relplot(data=df, kind="line", x="t/ms", y="U/mV", hue="Cell", ci=None).savefig(
- "network_ring_gpu_result.svg"
-)
+seaborn.relplot(
+ data=df, kind="line", x="t/ms", y="U/mV", hue="Cell", errorbar=None
+).savefig("network_ring_gpu_result.svg")
diff --git a/python/example/network_ring_mpi_plot.py b/python/example/network_ring_mpi_plot.py
index d5ea5d32..36db6a6a 100644
--- a/python/example/network_ring_mpi_plot.py
+++ b/python/example/network_ring_mpi_plot.py
@@ -12,6 +12,6 @@ for result in results:
df_list.append(pandas.read_csv(result))
df = pandas.concat(df_list, ignore_index=True)
-seaborn.relplot(data=df, kind="line", x="t/ms", y="U/mV", hue="Cell", ci=None).savefig(
- "mpi_result.svg"
-)
+seaborn.relplot(
+ data=df, kind="line", x="t/ms", y="U/mV", hue="Cell", errorbar=None
+).savefig("mpi_result.svg")
diff --git a/python/example/network_two_cells_gap_junctions.py b/python/example/network_two_cells_gap_junctions.py
index 1eeec49f..181833f9 100755
--- a/python/example/network_two_cells_gap_junctions.py
+++ b/python/example/network_two_cells_gap_junctions.py
@@ -183,7 +183,7 @@ if __name__ == "__main__":
fig, ax = plt.subplots()
# plot the membrane potentials of the two cells as function of time
- seaborn.lineplot(ax=ax, data=df, x="t/ms", y="U/mV", hue="Cell", ci=None)
+ seaborn.lineplot(ax=ax, data=df, x="t/ms", y="U/mV", hue="Cell", errorbar=None)
# area of cells
area = args.length * 1e-6 * 2 * np.pi * args.radius * 1e-6
diff --git a/python/example/single_cell_allen.py b/python/example/single_cell_allen.py
index dade963a..df961492 100644
--- a/python/example/single_cell_allen.py
+++ b/python/example/single_cell_allen.py
@@ -153,7 +153,9 @@ df_list.append(
)
)
df = pandas.concat(df_list, ignore_index=True)
-seaborn.relplot(data=df, kind="line", x="t/ms", y="U/mV", hue="Simulator", ci=None)
+seaborn.relplot(
+ data=df, kind="line", x="t/ms", y="U/mV", hue="Simulator", errorbar=None
+)
plt.scatter(
model.spikes, [-40] * len(model.spikes), color=seaborn.color_palette()[2], zorder=20
)
diff --git a/python/example/single_cell_bluepyopt_l5pc.py b/python/example/single_cell_bluepyopt_l5pc.py
index 6af3d21a..2a8b6f39 100755
--- a/python/example/single_cell_bluepyopt_l5pc.py
+++ b/python/example/single_cell_bluepyopt_l5pc.py
@@ -129,5 +129,11 @@ for i in range(len(data)):
)
df = pandas.concat(df_list, ignore_index=True)
seaborn.relplot(
- data=df, kind="line", x="t/ms", y="U/mV", hue="Location", col="Variable", ci=None
+ data=df,
+ kind="line",
+ x="t/ms",
+ y="U/mV",
+ hue="Location",
+ col="Variable",
+ errorbar=None,
).savefig("single_cell_bluepyopt_l5pc_bAP_dend1.svg")
diff --git a/python/example/single_cell_bluepyopt_simplecell.py b/python/example/single_cell_bluepyopt_simplecell.py
index 1b413164..1e7a993b 100755
--- a/python/example/single_cell_bluepyopt_simplecell.py
+++ b/python/example/single_cell_bluepyopt_simplecell.py
@@ -81,5 +81,11 @@ for t in m.traces:
df = pandas.concat(df_list, ignore_index=True)
seaborn.relplot(
- data=df, kind="line", x="t/ms", y="U/mV", hue="Location", col="Variable", ci=None
+ data=df,
+ kind="line",
+ x="t/ms",
+ y="U/mV",
+ hue="Location",
+ col="Variable",
+ errorbar=None,
).savefig("single_cell_bluepyopt_simplecell.svg")
diff --git a/python/example/single_cell_cable.py b/python/example/single_cell_cable.py
index 25f6aa14..348fad91 100755
--- a/python/example/single_cell_cable.py
+++ b/python/example/single_cell_cable.py
@@ -222,9 +222,9 @@ if __name__ == "__main__":
)
df = pandas.concat(df_list, ignore_index=True)
- seaborn.relplot(data=df, kind="line", x="t/ms", y="U/mV", hue="Probe", ci=None).set(
- xlim=(9, 14)
- ).savefig("single_cell_cable_result.svg")
+ seaborn.relplot(
+ data=df, kind="line", x="t/ms", y="U/mV", hue="Probe", errorbar=None
+ ).set(xlim=(9, 14)).savefig("single_cell_cable_result.svg")
# calculcate the idealized conduction velocity, cf. cable equation
data = [sim.samples(handle)[0][0] for handle in handles]
diff --git a/python/example/single_cell_detailed.py b/python/example/single_cell_detailed.py
index 25495c51..0d2222ed 100755
--- a/python/example/single_cell_detailed.py
+++ b/python/example/single_cell_detailed.py
@@ -117,5 +117,11 @@ for t in model.traces:
)
df = pandas.concat(df_list, ignore_index=True)
seaborn.relplot(
- data=df, kind="line", x="t/ms", y="U/mV", hue="Location", col="Variable", ci=None
+ data=df,
+ kind="line",
+ x="t/ms",
+ y="U/mV",
+ hue="Location",
+ col="Variable",
+ errorbar=None,
).savefig("single_cell_detailed_result.svg")
diff --git a/python/example/single_cell_detailed_recipe.py b/python/example/single_cell_detailed_recipe.py
index b5056254..cefb4dc9 100644
--- a/python/example/single_cell_detailed_recipe.py
+++ b/python/example/single_cell_detailed_recipe.py
@@ -151,5 +151,11 @@ for i in range(len(data)):
)
df = pandas.concat(df_list, ignore_index=True)
seaborn.relplot(
- data=df, kind="line", x="t/ms", y="U/mV", hue="Location", col="Variable", ci=None
+ data=df,
+ kind="line",
+ x="t/ms",
+ y="U/mV",
+ hue="Location",
+ col="Variable",
+ errorbar=None,
).savefig("single_cell_recipe_result.svg")
diff --git a/python/example/single_cell_model.py b/python/example/single_cell_model.py
index 0737983f..054443e2 100755
--- a/python/example/single_cell_model.py
+++ b/python/example/single_cell_model.py
@@ -46,7 +46,7 @@ else:
print("Plotting results ...")
seaborn.set_theme() # Apply some styling to the plot
df = pandas.DataFrame({"t/ms": m.traces[0].time, "U/mV": m.traces[0].value})
-seaborn.relplot(data=df, kind="line", x="t/ms", y="U/mV", ci=None).savefig(
+seaborn.relplot(data=df, kind="line", x="t/ms", y="U/mV", errorbar=None).savefig(
"single_cell_model_result.svg"
)
diff --git a/python/example/single_cell_nml.py b/python/example/single_cell_nml.py
index f69b195f..8992ca1e 100755
--- a/python/example/single_cell_nml.py
+++ b/python/example/single_cell_nml.py
@@ -112,5 +112,11 @@ for t in m.traces:
df = pandas.concat(df_list, ignore_index=True)
seaborn.relplot(
- data=df, kind="line", x="t/ms", y="U/mV", hue="Location", col="Variable", ci=None
+ data=df,
+ kind="line",
+ x="t/ms",
+ y="U/mV",
+ hue="Location",
+ col="Variable",
+ errorbar=None,
).savefig("single_cell_nml.svg")
diff --git a/python/example/single_cell_recipe.py b/python/example/single_cell_recipe.py
index 447266e5..3d498eae 100644
--- a/python/example/single_cell_recipe.py
+++ b/python/example/single_cell_recipe.py
@@ -92,7 +92,7 @@ else:
print("Plotting results ...")
df = pandas.DataFrame({"t/ms": data[:, 0], "U/mV": data[:, 1]})
-seaborn.relplot(data=df, kind="line", x="t/ms", y="U/mV", ci=None).savefig(
+seaborn.relplot(data=df, kind="line", x="t/ms", y="U/mV", errorbar=None).savefig(
"single_cell_recipe_result.svg"
)
diff --git a/python/example/single_cell_stdp.py b/python/example/single_cell_stdp.py
index 9799d69f..b67d45f2 100755
--- a/python/example/single_cell_stdp.py
+++ b/python/example/single_cell_stdp.py
@@ -100,7 +100,7 @@ def run(dT, n_pairs=1, do_plots=False):
data, meta = sim.samples(handle)[0]
df = pd.DataFrame({"t/ms": data[:, 0], var: data[:, 1]})
- sns.relplot(data=df, kind="line", x="t/ms", y=var, ci=None).savefig(
+ sns.relplot(data=df, kind="line", x="t/ms", y=var, errorbar=None).savefig(
f"single_cell_stdp_result_{var}.svg"
)
@@ -111,6 +111,6 @@ def run(dT, n_pairs=1, do_plots=False):
data = np.array([(dT, run(dT)) for dT in np.arange(-20, 20, 0.5)])
df = pd.DataFrame({"t/ms": data[:, 0], "dw": data[:, 1]})
print("Plotting results ...")
-sns.relplot(data=df, x="t/ms", y="dw", kind="line", ci=None).savefig(
+sns.relplot(data=df, x="t/ms", y="dw", kind="line", errorbar=None).savefig(
"single_cell_stdp.svg"
)
diff --git a/python/example/single_cell_swc.py b/python/example/single_cell_swc.py
index 4edaec7b..febfe774 100755
--- a/python/example/single_cell_swc.py
+++ b/python/example/single_cell_swc.py
@@ -102,5 +102,11 @@ for t in m.traces:
df = pandas.concat(df_list, ignore_index=True)
seaborn.relplot(
- data=df, kind="line", x="t/ms", y="U/mV", hue="Location", col="Variable", ci=None
+ data=df,
+ kind="line",
+ x="t/ms",
+ y="U/mV",
+ hue="Location",
+ col="Variable",
+ errorbar=None,
).savefig("single_cell_swc.svg")
diff --git a/python/example/v-clamp.py b/python/example/v-clamp.py
index 27469177..ba34ebd7 100755
--- a/python/example/v-clamp.py
+++ b/python/example/v-clamp.py
@@ -1,5 +1,4 @@
#!/usr/bin/env python3
-# This script is included in documentation. Adapt line numbers if touched.
import arbor
import pandas # You may have to pip install these.
@@ -45,11 +44,10 @@ else:
# (9) Plot the recorded voltages over time.
print("Plotting results ...")
-seaborn.set_theme() # Apply some styling to the plot
df = pandas.DataFrame({"t/ms": m.traces[0].time, "U/mV": m.traces[0].value})
-seaborn.relplot(data=df, kind="line", x="t/ms", y="U/mV", ci=None).savefig(
- "single_cell_model_result.svg"
+seaborn.relplot(data=df, kind="line", x="t/ms", y="U/mV", errorbar=None).savefig(
+ "v-clamp.svg"
)
# (10) Optionally, you can store your results for later processing.
-df.to_csv("single_cell_model_result.csv", float_format="%g")
+df.to_csv("v-clamp.csv", float_format="%g")
diff --git a/scripts/run_python_examples.sh b/scripts/run_python_examples.sh
index e561ca58..e79b34d5 100755
--- a/scripts/run_python_examples.sh
+++ b/scripts/run_python_examples.sh
@@ -10,26 +10,31 @@ fi
PREFIX=${1:-}
-$PREFIX python -m pip install -r python/example/example_requirements.txt
+$PREFIX python3 -m pip install -r python/example/example_requirements.txt -U
-$PREFIX python python/example/brunel.py -n 400 -m 100 -e 20 -p 0.1 -w 1.2 -d 1 -g 0.5 -l 5 -t 100 -s 1 -G 50 -S 123
-# $PREFIX python python/dynamic-catalogue.py # arbor-build-catalog is a test already
-$PREFIX python python/example/gap_junctions.py
-$PREFIX python python/example/single_cell_cable.py
-$PREFIX python python/example/single_cell_detailed_recipe.py python/example/single_cell_detailed.swc
-$PREFIX python python/example/single_cell_detailed.py python/example/single_cell_detailed.swc
-$PREFIX python python/example/probe_lfpykit.py python/example/single_cell_detailed.swc
-$PREFIX python python/example/single_cell_model.py
-$PREFIX python python/example/single_cell_nml.py python/example/morph.nml
-$PREFIX python python/example/single_cell_recipe.py
-$PREFIX python python/example/single_cell_stdp.py
-$PREFIX python python/example/single_cell_swc.py python/example/single_cell_detailed.swc
-$PREFIX python python/example/network_ring.py
-# $PREFIX python python/example/network_ring_mpi.py # requires MPI
-# $PREFIX python python/example/network_ring_mpi_plot.py # no need to test
-$PREFIX python python/example/network_ring_gpu.py # by default, gpu_id=None
-$PREFIX python python/example/network_two_cells_gap_junctions.py
-$PREFIX python python/example/diffusion.py
-$PREFIX python python/example/plasticity.py
-$PREFIX python python/example/v-clamp.py
-$PREFIX python python/example/calcium_stdp.py
+runpyex () {
+ echo "=== Executing $1 ======================================"
+ $PREFIX python3 python/example/$*
+}
+
+runpyex brunel.py -n 400 -m 100 -e 20 -p 0.1 -w 1.2 -d 1 -g 0.5 -l 5 -t 100 -s 1 -G 50 -S 123
+# runpyex dynamic-catalogue.py # arbor-build-catalog is a test already
+runpyex gap_junctions.py
+runpyex single_cell_cable.py
+runpyex single_cell_detailed_recipe.py python/example/single_cell_detailed.swc
+runpyex single_cell_detailed.py python/example/single_cell_detailed.swc
+runpyex probe_lfpykit.py python/example/single_cell_detailed.swc
+runpyex single_cell_model.py
+runpyex single_cell_nml.py python/example/morph.nml
+runpyex single_cell_recipe.py
+runpyex single_cell_stdp.py
+runpyex single_cell_swc.py python/example/single_cell_detailed.swc
+runpyex network_ring.py
+# runpyex network_ring_mpi.py # requires MPI
+# runpyex network_ring_mpi_plot.py # no need to test
+runpyex network_ring_gpu.py # by default, gpu_id=None
+runpyex network_two_cells_gap_junctions.py
+runpyex diffusion.py
+runpyex plasticity.py
+runpyex v-clamp.py
+runpyex calcium_stdp.py
--
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