Joss paper

.compile_mod.sh

@@ -1,12 +1,26 @@
 #!/bin/sh
 
+# Copyright 2012-2024 Blue Brain Project / EPFL
+
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+
+#     http://www.apache.org/licenses/LICENSE-2.0
+
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+
 set -e
 
 INSTALL_DIR=$1
 MOD_DIR=$2
 
 cd ${INSTALL_DIR}
- 
+
 echo "Building mod files"
 rm -rf x86_64
 nrnivmodl ${MOD_DIR} >nrnivmodl.log 2>&1

.github/workflows/draft-pdf.yml

@@ -0,0 +1,25 @@
+# Prepares a draft PDF of the paper using the Open Journals draft action.
+name: Draft JOSS Paper PDF
+on: push
+
+jobs:
+  paper:
+    runs-on: ubuntu-latest
+    name: Paper Draft
+    steps:
+    - name: Checkout
+      uses: actions/checkout@v4
+    - name: Build draft PDF
+      uses: openjournals/openjournals-draft-action@master
+      with:
+        journal: joss
+        # This should be the path to the paper within your repo.
+        paper-path: paper/paper.md
+    - name: Upload
+      uses: actions/upload-artifact@v1
+      with:
+        name: paper
+        # This is the output path where Pandoc will write the compiled
+        # PDF. Note, this should be the same directory as the input
+        # paper.md
+        path: paper/paper.pdf

.github/workflows/release.yml

@@ -25,7 +25,7 @@ jobs:
           python-version: "3.10"
 
       - name: Fetch the tag, if any. If not tagged, create a patch tag
-        uses: anothrNick/github-tag-action@1.69.0
+        uses: anothrNick/github-tag-action@1.70.0
         if: ${{ !startsWith(github.ref, 'refs/tags/') }}
         id: tag
         env:

CONTRIBUTING.rst

@@ -0,0 +1,27 @@
+Contributing to BlueCelluLab
+============================
+
+Thank you for taking the time to contribute!
+
+Reporting Bugs and Suggesting Enhancements
+------------------------------------------
+
+1. Search existing `issues <https://github.com/BlueBrain/BlueCelluLab/issues>`_.
+2. Open a new issue with a clear title and detailed description.
+3. Include steps to reproduce, expected and actual behavior for bugs, or the current and expected behavior for enhancements.
+4. Attach any relevant screenshots or files.
+5. If applicable specify the versions of BlueCelluLab, Python and any relevant dependencies.
+
+Pull Requests
+-------------
+
+1. Fork the repository and create a new branch.
+2. Make your changes.
+3. Run `tox -e lint` to check the code format.
+4. Run the tests with `tox -e py3`.
+5. Add unit tests for the new code.
+6. If applicable add type hints and docstrings.
+7. If applicable update the documentation.
+8. Submit a pull request with a clear description.
+
+Thank you for contributing to BlueCelluLab!

README.rst

@@ -116,6 +116,11 @@ Testing is set up using `tox`:
     tox -e py3  # runs the tests
     tox -e lint  # runs the format checks
 
+Contributing
+============
+
+We welcome contributions to BlueCelluLab! Please see the `CONTRIBUTING.rst <https://github.com/BlueBrain/BlueCelluLab/blob/main/CONTRIBUTING.rst>`_ for guidelines on how to contribute.
+
 Funding & Acknowledgements
 ==========================
 

bluecellulab-bb5-tests/.compile_mod.sh

@@ -0,0 +1,26 @@
+#!/bin/sh
+
+# Copyright 2024 Blue Brain Project / EPFL
+
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+
+#     http://www.apache.org/licenses/LICENSE-2.0
+
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+
+set -e
+
+INSTALL_DIR=$1
+MOD_DIR=$2
+
+cd ${INSTALL_DIR}
+
+echo "Building mod files"
+rm -rf x86_64
+nrnivmodl ${MOD_DIR} >nrnivmodl.log 2>&1

bluecellulab-bb5-tests/.gitignore

@@ -0,0 +1,11 @@
+*.nrndat
+bin
+lib
+share
+.pytest_cache
+.tox-info.json
+.tox
+.neurodamus
+__pycache__
+x86_64
+nrnivmodl.log

bluecellulab-bb5-tests/Makefile

@@ -0,0 +1,26 @@
+# Variables
+PIP_INDEX_URL := https://pypi.python.org/simple
+NEURON_MODULE_OPTIONS := '-nogui'
+TESTS_DIR := tests
+MECHANISMS_DIR := ./../tests/mechanisms/
+PYTEST_OPTS := --numprocesses=auto --timeout=600 -vsx --forked
+
+# Default rule (similar to 'testenv' in tox)
+default: install_deps compile_mod run_lint run_tests
+
+# Rule for installing dependencies (similar to 'deps' in tox)
+install_deps:
+	python -m pip install --index-url $(PIP_INDEX_URL) -r test_requirements.txt
+
+# Rule for compiling mod (similar to the first 'commands' in tox)
+compile_mod:
+	chmod +x ./.compile_mod.sh
+	./.compile_mod.sh . $(MECHANISMS_DIR)
+
+# Rule for running tests (similar to the second 'commands' in tox)
+run_tests:
+	NEURON_MODULE_OPTIONS=$(NEURON_MODULE_OPTIONS) pytest $(TESTS_DIR) $(PYTEST_OPTS)
+
+run_lint:
+	ruff check $(TESTS_DIR)
+	mypy $(TESTS_DIR) --ignore-missing-imports

bluecellulab-bb5-tests/README.md

@@ -0,0 +1,60 @@
+# bluecellulab-bb5-tests
+
+## Description
+
+This folder contains tests for bluecellulab on the large circuits located on bb5. Please note that these tests are not directly usable as they are, due to dependencies.
+
+## How to run locally
+
+Simply clone the repository, install tox and type `tox` in the root directory of the repository.
+
+## Continous Integration
+
+This module will continue to be part of the continuous integration (CI) pipeline on GitLab until the end of the year. The scheduled CI tasks will run the tests for this module periodically until 2024.12.31. After this date, the tests will no longer be included in the CI pipeline.
+
+## Mechanisms
+
+The mechanisms for these tests have been merged into the [tests/mechanisms/](./../tests/mechanisms/) folder. Here is the list of mechanisms used for these tests. The original list is provided below, and files marked with an asterisk (*) were added to the tests folder as they were not already present:
+- `Ca.mod`
+- `CaDynamics_DC0.mod`
+- `CaDynamics_E2.mod`
+- `Ca_HVA.mod`
+- `Ca_HVA2.mod`
+- `Ca_LVAst.mod`
+- `DetAMPANMDA.mod`
+- `DetGABAAB.mod`
+- `GluSynapse.mod`
+- *`IN_Ih_Halnes2011.mod`
+- *`IN_iT.mod`
+- `Ih.mod`
+- `Im.mod`
+- `K_Pst.mod`
+- `K_Tst.mod`
+- `KdShu2007.mod`
+- `NaTa_t.mod`
+- `NaTg.mod`
+- `NaTs2_t.mod`
+- `Nap_Et2.mod`
+- `ProbAMPANMDA_EMS.mod`
+- `ProbGABAAB_EMS.mod`
+- *`RC_IT_Des92.mod`
+- `SK_E2.mod`
+- `SKv3_1.mod`
+- `StochKv.mod`
+- `StochKv3.mod`
+- *`TC_HH.mod`
+- *`TC_ITGHK_Des98.mod`
+- *`TC_Ih_Bud97.mod`
+- *`TC_Ih_CaMod.mod`
+- *`TC_Kleak.mod`
+- *`TC_Naleak.mod`
+- *`TC_Nap_Et2.mod`
+- *`TC_cadecay.mod`
+- *`TC_iA.mod`
+- *`TC_iL.mod`
+- *`TC_kir_Con15.mod`
+- `TTXDynamicsSwitch.mod`
+- `VecStim.mod`
+- `gap.mod`
+- *`ican.mod`
+- `netstim_inhpoisson.mod`

bluecellulab-bb5-tests/pytest.ini

@@ -0,0 +1,5 @@
+[pytest]
+markers =
+    v5: tests on the neocortex circuit version 5.
+    v6: tests on the neocortex circuit version 6.
+    thal: tests on the thalamus circuit.

bluecellulab-bb5-tests/pyvenv.cfg

@@ -0,0 +1,8 @@
+home = /gpfs/bbp.cscs.ch/ssd/apps/bsd/2022-01-10/stage_externals/install_gcc-11.2.0-skylake/python-3.9.7-yj5alh/bin
+implementation = CPython
+version_info = 3.9.7.final.0
+virtualenv = 20.17.1
+include-system-site-packages = false
+base-prefix = /gpfs/bbp.cscs.ch/ssd/apps/bsd/2022-01-10/stage_externals/install_gcc-11.2.0-skylake/python-3.9.7-yj5alh
+base-exec-prefix = /gpfs/bbp.cscs.ch/ssd/apps/bsd/2022-01-10/stage_externals/install_gcc-11.2.0-skylake/python-3.9.7-yj5alh
+base-executable = /gpfs/bbp.cscs.ch/ssd/apps/bsd/2022-01-10/stage_externals/install_gcc-11.2.0-skylake/python-3.9.7-yj5alh/bin/python3.9

bluecellulab-bb5-tests/test_requirements.txt

@@ -0,0 +1,8 @@
+bluepy-configfile>=0.1.18
+bluepy[bbp]>=2.5.0
+pytest
+pytest-timeout
+pytest-xdist
+pytest-forked
+ruff>=0.0.40
+mypy>=1.2.0

bluecellulab-bb5-tests/tests/examples/circuit_twocell_example1/CircuitConfig

@@ -0,0 +1,14 @@
+Run Default
+{
+
+  MorphologyPath /bgscratch/bbp/l5/release/2012.07.23/morphologies/h5
+  METypePath ../circuit_twocell_example1/ccells/
+  MeshPath /bgscratch/bbp/l5/release/2012.07.23/meshes
+  CircuitPath ../circuit_twocell_example1
+  nrnPath ../circuit_twocell_example1/ncsFunctionalAllRecipePathways
+  TargetFile /bgscratch/bbp/l5/release/2012.07.23/circuit/SomatosensoryCxS1-v4.lowerCellDensity.r151/O1/merged_circuit/default_user.target
+  BioName SomatosensoryCxS1-v4.lowerCellDensity.r151
+  CentralHyperColumn 2
+
+}
+