diff --git a/.github/workflows/docker-push.yaml b/.github/workflows/docker-push.yaml index 5453265..503fe74 100644 --- a/.github/workflows/docker-push.yaml +++ b/.github/workflows/docker-push.yaml @@ -5,7 +5,7 @@ on: branches: - main paths: - - 'Dockerfile*' + - 'images/Dockerfile*' workflow_dispatch: jobs: diff --git a/.github/workflows/docker-test.yaml b/.github/workflows/docker-test.yaml index b13db86..0b17cad 100644 --- a/.github/workflows/docker-test.yaml +++ b/.github/workflows/docker-test.yaml @@ -3,7 +3,7 @@ name: Build Docker Images on: pull_request: paths: - - 'Dockerfile*' + - 'images/Dockerfile*' workflow_dispatch: jobs: diff --git a/images/Dockerfile b/images/Dockerfile index 8b0ce42..770d57d 100644 --- a/images/Dockerfile +++ b/images/Dockerfile @@ -53,7 +53,7 @@ RUN mamba install --yes 'datalad>=0.18' rclone 'h5py>3.3=mpi*' ipykernel zarr bl RUN pip install --no-cache-dir -U plotly jupyter_bokeh jupytext nbgitpuller datalad_container \ datalad-osf dandi nibabel nilearn pybids spikeinterface neo itkwidgets \ - 'pydra>=0.17' 'pynwb>=2.8.3' 'nwbwidgets>=0.10.2' hdf5plugin s3fs h5netcdf "xarray[io]" \ + 'pydra>=0.25' 'pynwb>=2.8.3' 'nwbwidgets>=0.10.2' hdf5plugin s3fs h5netcdf "xarray[io]" \ aicsimageio kerchunk 'neuroglancer>=2.28' cloud-volume ipywidgets ome-zarr \ webio_jupyter_extension https://github.com/balbasty/dandi-io/archive/refs/heads/main.zip \ tensorstore anndata diff --git a/images/Dockerfile.allensdk b/images/Dockerfile.allensdk index 37c64ad..124fac1 100644 --- a/images/Dockerfile.allensdk +++ b/images/Dockerfile.allensdk @@ -61,7 +61,7 @@ RUN /opt/conda/envs/allen/bin/python -m ipykernel install --user --name allen \ RUN pip install --no-cache-dir -U plotly jupyter_bokeh jupytext nbgitpuller datalad_container \ datalad-osf dandi pybids spikeinterface neo itkwidgets \ - 'pydra>=0.17' 'pynwb>=2.8.3' 'nwbwidgets>=0.10.2' hdf5plugin s3fs h5netcdf "xarray[io]" \ + 'pydra>=0.25' 'pynwb>=2.8.3' 'nwbwidgets>=0.10.2' hdf5plugin s3fs h5netcdf "xarray[io]" \ aicsimageio kerchunk cloud-volume ipywidgets ome-zarr \ webio_jupyter_extension https://github.com/balbasty/dandi-io/archive/refs/heads/main.zip \ tensorstore anndata diff --git a/images/Dockerfile.gpu b/images/Dockerfile.gpu index 607199d..543fc89 100644 --- a/images/Dockerfile.gpu +++ b/images/Dockerfile.gpu @@ -53,7 +53,7 @@ RUN mamba install --yes datalad rclone 'h5py>3.3=mpi*' ipykernel zarr blosc ecco RUN pip install --no-cache-dir -U plotly jupyter_bokeh jupytext nbgitpuller datalad_container \ datalad-osf dandi nibabel nilearn pybids spikeinterface neo itkwidgets \ - 'pydra>=0.17' 'pynwb>=2.8.3' 'nwbwidgets>=0.10.2' hdf5plugin s3fs h5netcdf "xarray[io]" \ + 'pydra>=0.25' 'pynwb>=2.8.3' 'nwbwidgets>=0.10.2' hdf5plugin s3fs h5netcdf "xarray[io]" \ aicsimageio kerchunk 'neuroglancer>=2.28' cloud-volume ipywidgets ome-zarr \ webio_jupyter_extension https://github.com/balbasty/dandi-io/archive/refs/heads/main.zip \ tensorstore anndata && rm -rf /tmp/* diff --git a/images/Dockerfile.gpu.allensdk b/images/Dockerfile.gpu.allensdk index ef35404..5a6a636 100644 --- a/images/Dockerfile.gpu.allensdk +++ b/images/Dockerfile.gpu.allensdk @@ -61,7 +61,7 @@ RUN /opt/conda/envs/allen/bin/python -m ipykernel install --user --name allen \ RUN pip install --no-cache-dir -U plotly jupyter_bokeh jupytext nbgitpuller datalad_container \ datalad-osf dandi pybids spikeinterface neo itkwidgets \ - 'pydra>=0.17' 'pynwb>=2.8.3' 'nwbwidgets>=0.10.2' hdf5plugin s3fs h5netcdf "xarray[io]" \ + 'pydra>=0.25' 'pynwb>=2.8.3' 'nwbwidgets>=0.10.2' hdf5plugin s3fs h5netcdf "xarray[io]" \ aicsimageio kerchunk cloud-volume ipywidgets ome-zarr \ webio_jupyter_extension https://github.com/balbasty/dandi-io/archive/refs/heads/main.zip \ tensorstore anndata && rm -rf /tmp/* diff --git a/images/Dockerfile.gpu.matlab b/images/Dockerfile.gpu.matlab index 8e40bcf..904f23e 100644 --- a/images/Dockerfile.gpu.matlab +++ b/images/Dockerfile.gpu.matlab @@ -74,7 +74,7 @@ RUN mamba install --yes datalad rclone 'h5py>3.3=mpi*' ipykernel zarr blosc gcc RUN pip install --no-cache-dir plotly jupyter_bokeh jupytext nbgitpuller datalad_container \ datalad-osf dandi nibabel nilearn pybids spikeinterface neo \ - 'pydra>=0.17' 'pynwb>=2.8.3' 'nwbwidgets>=0.10.2' hdf5plugin s3fs h5netcdf "xarray[io]" \ + 'pydra>=0.25' 'pynwb>=2.8.3' 'nwbwidgets>=0.10.2' hdf5plugin s3fs h5netcdf "xarray[io]" \ aicsimageio kerchunk 'neuroglancer>=2.28' cloud-volume ipywidgets ome-zarr \ webio_jupyter_extension https://github.com/balbasty/dandi-io/archive/refs/heads/main.zip \ tensorstore anndata "tensorflow[and-cuda]==2.14" diff --git a/images/Dockerfile.matlab b/images/Dockerfile.matlab index 60eac31..8ea37b6 100644 --- a/images/Dockerfile.matlab +++ b/images/Dockerfile.matlab @@ -64,7 +64,7 @@ RUN mamba install --yes datalad rclone 'h5py>3.3=mpi*' ipykernel zarr blosc gcc RUN pip install --no-cache-dir plotly jupyter_bokeh jupytext nbgitpuller datalad_container \ datalad-osf dandi nibabel nilearn pybids spikeinterface neo \ - 'pydra>=0.17' 'pynwb>=2.8.3' 'nwbwidgets>=0.10.2' hdf5plugin s3fs h5netcdf "xarray[io]" \ + 'pydra>=0.25' 'pynwb>=2.8.3' 'nwbwidgets>=0.10.2' hdf5plugin s3fs h5netcdf "xarray[io]" \ aicsimageio kerchunk 'neuroglancer>=2.28' cloud-volume ipywidgets ome-zarr \ webio_jupyter_extension https://github.com/balbasty/dandi-io/archive/refs/heads/main.zip \ tensorstore anndata tensorflow