From 196e7168ef0bf4a2a3a8f1af62c67c9a59e4a3e9 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Jaquier=20Aur=C3=A9lien=20Tristan?= Date: Wed, 24 Apr 2024 10:38:49 +0200 Subject: [PATCH 01/12] small fix in documentation --- docs/source/eFeatures.rst | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/docs/source/eFeatures.rst b/docs/source/eFeatures.rst index fa89614d..775cff7a 100644 --- a/docs/source/eFeatures.rst +++ b/docs/source/eFeatures.rst @@ -134,8 +134,8 @@ The interspike intervals, i.e., the time intervals between adjacent peaks. else: inv_last_ISI = 0 -`Python efeature`: inv_ISI_values -~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +`Python efeature`_ : inv_ISI_values +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Computes all inverse spike interval values. From 2d0b98eb49edb0990b321df33d1f2b9d07afe76f Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Jaquier=20Aur=C3=A9lien=20Tristan?= Date: Wed, 24 Apr 2024 14:18:12 +0200 Subject: [PATCH 02/12] try removing architecture in wheel building --- .github/workflows/build-wheels.yml | 13 +++---------- 1 file changed, 3 insertions(+), 10 deletions(-) diff --git a/.github/workflows/build-wheels.yml b/.github/workflows/build-wheels.yml index 6fce2b8b..c3a2f612 100644 --- a/.github/workflows/build-wheels.yml +++ b/.github/workflows/build-wheels.yml @@ -12,16 +12,9 @@ jobs: matrix: os: [ubuntu-22.04, macos-latest, windows-latest] python: [cp39, cp310, cp311, cp312] - arch: [x86_64, amd64] - exclude: - - os: macos-latest - arch: amd64 - - os: ubuntu-22.04 - arch: amd64 - - os: windows-latest - arch: x86_64 + env: - CIBW_BUILD: ${{ matrix.python }}*${{ matrix.arch }} + CIBW_BUILD: ${{ matrix.python }} CIBW_TEST_REQUIRES: pytest neo[neomatlabio]>=0.5.1 pytest-xdist>=3.3.1 CIBW_TEST_COMMAND: pytest -sx -n auto {project}/tests CIBW_SKIP: "*-musllinux_*" @@ -39,5 +32,5 @@ jobs: run: cibuildwheel --output-dir wheelhouse - uses: actions/upload-artifact@v4 with: - name: wheels-${{ matrix.os }}-${{ matrix.python }}-${{ matrix.arch }} + name: wheels-${{ matrix.os }}-${{ matrix.python }} path: ./wheelhouse/*.whl From 09f4174d6c90c766f103cfec37f34ef2a7d0988a Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Jaquier=20Aur=C3=A9lien=20Tristan?= Date: Wed, 24 Apr 2024 15:22:09 +0200 Subject: [PATCH 03/12] restoring architectures in wheel building --- .github/workflows/build-wheels.yml | 13 ++++++++++--- 1 file changed, 10 insertions(+), 3 deletions(-) diff --git a/.github/workflows/build-wheels.yml b/.github/workflows/build-wheels.yml index c3a2f612..6fce2b8b 100644 --- a/.github/workflows/build-wheels.yml +++ b/.github/workflows/build-wheels.yml @@ -12,9 +12,16 @@ jobs: matrix: os: [ubuntu-22.04, macos-latest, windows-latest] python: [cp39, cp310, cp311, cp312] - + arch: [x86_64, amd64] + exclude: + - os: macos-latest + arch: amd64 + - os: ubuntu-22.04 + arch: amd64 + - os: windows-latest + arch: x86_64 env: - CIBW_BUILD: ${{ matrix.python }} + CIBW_BUILD: ${{ matrix.python }}*${{ matrix.arch }} CIBW_TEST_REQUIRES: pytest neo[neomatlabio]>=0.5.1 pytest-xdist>=3.3.1 CIBW_TEST_COMMAND: pytest -sx -n auto {project}/tests CIBW_SKIP: "*-musllinux_*" @@ -32,5 +39,5 @@ jobs: run: cibuildwheel --output-dir wheelhouse - uses: actions/upload-artifact@v4 with: - name: wheels-${{ matrix.os }}-${{ matrix.python }} + name: wheels-${{ matrix.os }}-${{ matrix.python }}-${{ matrix.arch }} path: ./wheelhouse/*.whl From ff699309d3ca961928e9e6f6edabebb1c5d6e53a Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Jaquier=20Aur=C3=A9lien=20Tristan?= Date: Wed, 24 Apr 2024 17:28:42 +0200 Subject: [PATCH 04/12] add nmc-portal and sonata-network examples to docs --- docs/source/python_examples.rst | 2 ++ examples/nmc-portal/L5TTPC2.ipynb | 2 +- tox.ini | 9 +++++++++ 3 files changed, 12 insertions(+), 1 deletion(-) diff --git a/docs/source/python_examples.rst b/docs/source/python_examples.rst index 444adde7..5a70b765 100644 --- a/docs/source/python_examples.rst +++ b/docs/source/python_examples.rst @@ -6,4 +6,6 @@ Python python_example1 deap_optimisation neoIO_example + nmc-portal + sonata-network diff --git a/examples/nmc-portal/L5TTPC2.ipynb b/examples/nmc-portal/L5TTPC2.ipynb index bd988b45..297d26ac 100644 --- a/examples/nmc-portal/L5TTPC2.ipynb +++ b/examples/nmc-portal/L5TTPC2.ipynb @@ -5,7 +5,7 @@ "cell_type": "markdown", "metadata": {}, "source": [ - "Example of the use of the eFEL (eFeature Extraction Library) in conjunction with models downloaded from the Neocortical Microcircuit Portal website\n", + "# Example of the use of the eFEL (eFeature Extraction Library) in conjunction with models downloaded from the Neocortical Microcircuit Portal website\n", "\n", "Requirements:\n", "- Python 3.9+, including Pip (https://pip.readthedocs.org)\n", diff --git a/tox.ini b/tox.ini index f458d4a0..dab0ac2e 100644 --- a/tox.ini +++ b/tox.ini @@ -72,11 +72,20 @@ envdir = {toxworkdir}/docs deps = -r{toxinidir}/requirements_docs.txt pytest>=7.4.4 + ipython allowlist_externals = make + jupyter + cp changedir = docs commands = + jupyter nbconvert --to rst ../examples/sonata-network/sonata-network.ipynb + jupyter nbconvert --to rst ../examples/nmc-portal/L5TTPC2.ipynb + cp ../examples/sonata-network/sonata-network.rst source/ + cp -r ../examples/sonata-network/sonata-network_files source/ + cp ../examples/nmc-portal/L5TTPC2.rst source/nmc-portal.rst + cp -r ../examples/nmc-portal/L5TTPC2_files source/ # build the docs to see if it builds fine make html SPHINXOPTS=-W # make sure the feature names and units are up-to-date From e786587cb372dfc6044ef1ca959912580615a07c Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Jaquier=20Aur=C3=A9lien=20Tristan?= Date: Wed, 24 Apr 2024 17:42:57 +0200 Subject: [PATCH 05/12] adding dependency in tox --- tox.ini | 1 + 1 file changed, 1 insertion(+) diff --git a/tox.ini b/tox.ini index dab0ac2e..ed55e162 100644 --- a/tox.ini +++ b/tox.ini @@ -73,6 +73,7 @@ deps = -r{toxinidir}/requirements_docs.txt pytest>=7.4.4 ipython + jupyter allowlist_externals = make jupyter From 9dd1197dbd8bd709f82aed0a260a1a3cca4d6dc7 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Jaquier=20Aur=C3=A9lien=20Tristan?= Date: Wed, 24 Apr 2024 17:50:56 +0200 Subject: [PATCH 06/12] adding pandoc dependency in tox --- tox.ini | 1 + 1 file changed, 1 insertion(+) diff --git a/tox.ini b/tox.ini index ed55e162..2a36c481 100644 --- a/tox.ini +++ b/tox.ini @@ -74,6 +74,7 @@ deps = pytest>=7.4.4 ipython jupyter + pandoc allowlist_externals = make jupyter From cae5dee854ef04ae95de537db738bef380909a3f Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Jaquier=20Aur=C3=A9lien=20Tristan?= Date: Thu, 25 Apr 2024 09:11:16 +0200 Subject: [PATCH 07/12] adding pandoc docker to docs github action --- .github/workflows/test.yml | 1 + 1 file changed, 1 insertion(+) diff --git a/.github/workflows/test.yml b/.github/workflows/test.yml index 407224e3..ca78e1cf 100644 --- a/.github/workflows/test.yml +++ b/.github/workflows/test.yml @@ -84,6 +84,7 @@ jobs: run: | python -m pip install --upgrade pip setuptools pip install tox tox-gh-actions + - uses: docker://pandoc/core:2.9 - name: Run tox run: tox -e docs From 9c635681420907d13ac7f0cf2c020d790cb90bac Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Jaquier=20Aur=C3=A9lien=20Tristan?= Date: Thu, 25 Apr 2024 09:18:23 +0200 Subject: [PATCH 08/12] install pandoc without docker image --- .github/workflows/test.yml | 5 ++++- 1 file changed, 4 insertions(+), 1 deletion(-) diff --git a/.github/workflows/test.yml b/.github/workflows/test.yml index ca78e1cf..d0bba8a0 100644 --- a/.github/workflows/test.yml +++ b/.github/workflows/test.yml @@ -84,7 +84,10 @@ jobs: run: | python -m pip install --upgrade pip setuptools pip install tox tox-gh-actions - - uses: docker://pandoc/core:2.9 + - name: Install pandoc # needed by nbconvert + uses: pandoc/actions/setup@{main} + with: + version: 2.19 - name: Run tox run: tox -e docs From e181aaf77533ba454cde3cb341ee525275837781 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Jaquier=20Aur=C3=A9lien=20Tristan?= Date: Thu, 25 Apr 2024 09:19:14 +0200 Subject: [PATCH 09/12] use macos-12 for building wheels --- .github/workflows/build-wheels.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/build-wheels.yml b/.github/workflows/build-wheels.yml index 6fce2b8b..529d9ceb 100644 --- a/.github/workflows/build-wheels.yml +++ b/.github/workflows/build-wheels.yml @@ -10,7 +10,7 @@ jobs: strategy: fail-fast: false matrix: - os: [ubuntu-22.04, macos-latest, windows-latest] + os: [ubuntu-22.04, macos-12, windows-latest] python: [cp39, cp310, cp311, cp312] arch: [x86_64, amd64] exclude: From 5fdf86f4ef42e36eef99320e8cf38dcd7b38c9be Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Jaquier=20Aur=C3=A9lien=20Tristan?= Date: Thu, 25 Apr 2024 09:21:47 +0200 Subject: [PATCH 10/12] fix macos version in exclude --- .github/workflows/build-wheels.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/build-wheels.yml b/.github/workflows/build-wheels.yml index 529d9ceb..ebf2775c 100644 --- a/.github/workflows/build-wheels.yml +++ b/.github/workflows/build-wheels.yml @@ -14,7 +14,7 @@ jobs: python: [cp39, cp310, cp311, cp312] arch: [x86_64, amd64] exclude: - - os: macos-latest + - os: macos-12 arch: amd64 - os: ubuntu-22.04 arch: amd64 From 67f5d3a502bc6d51b6ae2f441df04477b8cf2fdf Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Jaquier=20Aur=C3=A9lien=20Tristan?= Date: Thu, 25 Apr 2024 09:23:34 +0200 Subject: [PATCH 11/12] fix typo in test.yml --- .github/workflows/test.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/test.yml b/.github/workflows/test.yml index d0bba8a0..1f6f13e5 100644 --- a/.github/workflows/test.yml +++ b/.github/workflows/test.yml @@ -85,7 +85,7 @@ jobs: python -m pip install --upgrade pip setuptools pip install tox tox-gh-actions - name: Install pandoc # needed by nbconvert - uses: pandoc/actions/setup@{main} + uses: pandoc/actions/setup@main with: version: 2.19 - name: Run tox From 708defec207d4c46d3372752247aeae3cfa11d11 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Jaquier=20Aur=C3=A9lien=20Tristan?= Date: Thu, 25 Apr 2024 09:31:20 +0200 Subject: [PATCH 12/12] moved new doc requirements to requirements_docs.txt --- requirements_docs.txt | 3 +++ tox.ini | 3 --- 2 files changed, 3 insertions(+), 3 deletions(-) diff --git a/requirements_docs.txt b/requirements_docs.txt index 1aeaefe1..62bc658e 100644 --- a/requirements_docs.txt +++ b/requirements_docs.txt @@ -29,3 +29,6 @@ sphinx_rtd_theme>=2.0.0 sphinx-autobuild>=2021.3.14 sphinx-autorun>=1.1.1 sphinx-autodoc-typehints>=1.25.2 +ipython +jupyter +pandoc diff --git a/tox.ini b/tox.ini index 2a36c481..34c5c8a0 100644 --- a/tox.ini +++ b/tox.ini @@ -72,9 +72,6 @@ envdir = {toxworkdir}/docs deps = -r{toxinidir}/requirements_docs.txt pytest>=7.4.4 - ipython - jupyter - pandoc allowlist_externals = make jupyter