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Merged
mihaic merged 1 commit into from
Jan 6, 2025
Merged

Fix Docker and add v0.12 release notes #559

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18 changes: 13 additions & 5 deletions Dockerfile
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@@ -1,4 +1,4 @@
FROM ubuntu:18.04
FROM ubuntu:24.04

ARG DEBIAN_FRONTEND=noninteractive
# Group 1 must be synced with README
Expand Down Expand Up @@ -30,17 +30,25 @@ RUN apt-get update && apt-get install -y \
libssl-dev \
&& rm -rf /var/lib/apt/lists/*

COPY brainiak-* /mnt/brainiak
COPY dist/brainiak-* /mnt

WORKDIR /mnt

RUN set -e \
&& tar -xf brainiak-*.tar.gz \
&& mv brainiak-*.tar.gz sdist.tar.gz \
&& mv brainiak-* brainiak

WORKDIR /mnt/brainiak

COPY tutorials/tutorials tutorials

RUN set -e \
&& python3 -m pip install --user -U pip \
&& python3 -m pip install --user -U -r tutorials/requirements.txt \
&& python3 -m pip install --user --break-system-packages -U pip \
&& python3 -m pip install --user --break-system-packages -U . \
&& python3 -m pip install --user --break-system-packages -U -r tutorials/requirements.txt \
&& for example in examples/*/requirements.txt; \
do python3 -m pip install --user -U -r $example ; done \
do python3 -m pip install --user --break-system-packages -U -r $example ; done \
&& rm -rf ~/.cache/pip

RUN echo PATH=\"\$HOME/.local/bin:\$PATH\" >> $HOME/.profile \
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26 changes: 26 additions & 0 deletions NEWS.rst
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Expand Up @@ -2,6 +2,32 @@

.. towncrier release notes start

BrainIAK 0.12 (2024-12-24)
==========================

Features
--------

- Add support for Windows (`#549 <https://github.com/brainiak/brainiak/issues/549>`_)
- Publish wheels (`#549 <https://github.com/brainiak/brainiak/issues/549>`_)

Bugfixes
--------

- Fix Docker image.

Documentation improvements
--------------------------

- fmrisim: Burn in is removed so that the size of the signal and noise volumes are the same (`#542 <https://github.com/brainiak/brainiak/issues/542>`_)

Deprecations and removals
-------------------------

- Refactor package to generally recommended src layout (`#549 <https://github.com/brainiak/brainiak/issues/549>`_)
- Drop support for Python < 3.9 (`#549 <https://github.com/brainiak/brainiak/issues/549>`_)


BrainIAK 0.11 (2020-10-14)
==========================

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9 changes: 2 additions & 7 deletions README.rst
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Expand Up @@ -44,14 +44,9 @@ Docker
You can also test BrainIAK without installing it using Docker::

docker pull brainiak/brainiak
docker run -it -p 8888:8888 -v brainiak:/mnt --name demo brainiak/brainiak
docker run -it -p 8899:8899 brainiak/brainiak

To run Jupyter notebooks in the running container, try::

python3 -m notebook --allow-root --no-browser --ip=0.0.0.0

Then visit http://localhost:8888 in your browser and enter the token. Protip:
run ``screen`` before running the notebook command.
Jupyter Notebook will start automatically; visit the URL shown in the Docker command output to access it. You can then run the BrainIAK examples or create new notebooks. You can also try a `sample example <http://127.0.0.1:8899/notebooks/examples/funcalign/rsrm_synthetic_reconstruction.ipynb>`_.

Note that we do not support MPI execution using Docker containers and that performance will not be optimal.

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8 changes: 4 additions & 4 deletions examples/funcalign/rsrm_synthetic_reconstruction.ipynb
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Expand Up @@ -156,13 +156,13 @@
"outputs": [],
"source": [
"fig = plt.figure()\n",
"ax = fig.gca(projection='3d')\n",
"ax.plot(curve[0, :], curve[1, :], curve[2, :], '-g', label='original', lineWidth=5)\n",
"ax = fig.add_subplot(projection='3d')\n",
"ax.plot(curve[0, :], curve[1, :], curve[2, :], '-g', label='original', linewidth=5)\n",
"\n",
"proj = find_orthogonal_transform(algo_srm.s_, curve)\n",
"ax.plot(proj[0, :], proj[1, :], proj[2, :], '-b', label='SRM', lineWidth=3)\n",
"ax.plot(proj[0, :], proj[1, :], proj[2, :], '-b', label='SRM', linewidth=3)\n",
"proj = find_orthogonal_transform(algo_rsrm.r_, curve)\n",
"ax.plot(proj[0, :], proj[1, :], proj[2, :], '-r', label='RSRM', lineWidth=3)\n",
"ax.plot(proj[0, :], proj[1, :], proj[2, :], '-r', label='RSRM', linewidth=3)\n",
"plt.legend()"
]
}
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6 changes: 5 additions & 1 deletion pyproject.toml
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Expand Up @@ -141,7 +141,11 @@ write_to = "src/brainiak/_version.py"
minimum-version = "0.4"
build-dir = "build/{wheel_tag}"
metadata.version.provider = "scikit_build_core.metadata.setuptools_scm"
sdist.include = ["src/brainiak/_version.py", "src/brainiak/utils/sim_parameters"]
sdist.include = [
"tests/io/data/*",
"src/brainiak/_version.py",
"src/brainiak/utils/sim_parameters",
]
cmake.build-type = "Release"

[tool.cibuildwheel]
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