From b72cc85b414e7813c10b9f09f1b9163421a06488 Mon Sep 17 00:00:00 2001 From: Sebastian Luna-Valero Date: Fri, 16 Feb 2024 08:40:35 +0000 Subject: [PATCH 01/11] update Dockerfile to work with conda-lock and change base image --- single-user-sobigdata/Dockerfile | 142 +- single-user-sobigdata/README.md | 21 + single-user-sobigdata/conda-lock.yml | 10934 +++++++++++++++++++++++++ single-user-sobigdata/sbd.yml | 114 + 4 files changed, 11088 insertions(+), 123 deletions(-) create mode 100644 single-user-sobigdata/README.md create mode 100644 single-user-sobigdata/conda-lock.yml create mode 100644 single-user-sobigdata/sbd.yml diff --git a/single-user-sobigdata/Dockerfile b/single-user-sobigdata/Dockerfile index 7a4f63c0..dba7d36d 100644 --- a/single-user-sobigdata/Dockerfile +++ b/single-user-sobigdata/Dockerfile @@ -1,135 +1,31 @@ -# _____ ____ _ _____ _ -# / ____| | _ \(_) | __ \ | | _ _ -# | (___ ___ | |_) |_ __ _| | | | __ _| |_ __ _ _| |_ _| |_ -# \___ \ / _ \| _ <| |/ _` | | | |/ _` | __/ _` |_ _|_ _| -# ____) | (_) | |_) | | (_| | |__| | (_| | || (_| | |_| |_| -# |_____/ \___/|____/|_|\__, |_____/ \__,_|\__\__,_| -# __/ | -# |___/ - -ARG BASE_IMAGE=eginotebooks/d4science-base:latest -# hadolint ignore=DL3006 -FROM $BASE_IMAGE +FROM quay.io/jupyter/minimal-notebook:x86_64-2024-02-12 USER root RUN apt-get update \ && apt-get install --no-install-recommends -y \ - nco \ - cdo \ - cmake \ - g++ \ + less \ + openssh-client \ && apt-get clean \ && rm -rf /var/lib/apt/lists/* USER $NB_UID -ARG SKLEARN_ALLOW_DEPRECATED_SKLEARN_PACKAGE_INSTALL=True - -RUN mamba install -y --quiet \ - basemap \ - beakerx \ - xgboost \ - lightgbm \ - catboost \ - netcdf4 \ - aiohttp \ - graph-tool \ - scikit-learn \ - scikit-mobility \ - dask-jobqueue \ - fs \ - rasterio \ - contextily \ - nb_conda_kernels \ - nb_conda \ - && conda clean -tipy - -# Pinned networkx to 2.6.3 as 2.7 makes networksns fail -RUN pip install --no-cache-dir \ - bicm \ - rdp \ - sentinelhub \ - import_ipynb \ - nbresuse \ - ndlib \ - motuclient \ - panel==0.9.* \ - cdlib[C]==0.2.3 \ - cython \ - node_conformity \ - git+https://github.com/geopython/OWSLib.git \ - git+https://github.com/guglielmocola/RetweetCascade.git \ - fast-forward-indexes \ - NEMtropy \ - folium==0.11.0 \ - geopy==2.0.0 \ - hvplot==0.6.0 \ - intake==0.6.0 \ - intake-esm==2020.8.15 \ - hda \ - seaborn==0.11.0 \ - zarr==2.5.0 \ - holoviews \ - networkx==2.6.3 \ - networksns \ - eventclf \ - XAI-Library \ - convrewriting \ - git+https://github.com/guglielmocola/TwitterMonitorLib_v2.git \ - pygm \ - structify-net - -# ------------------------------- -# SoBigData ++ specific libraries -# ------------------------------- -RUN mamba install -y --quiet \ - pyspark \ - transformers \ - rtree \ - geopandas \ - nltk \ - pydotplus \ - plotly \ - graphviz \ - keras \ - selenium \ - tweepy \ - openjdk=8 \ - && conda clean --all - -RUN pip install --no-cache-dir \ - torch \ - torchvision \ - torchaudio \ - --index-url https://download.pytorch.org/whl/cpu - -RUN pip install --no-cache-dir \ - pyfim \ - pyclustering \ - import_ipynb \ - opencv-python \ - simpletransformers \ - shuffle-graph \ - privlib \ - ash_model \ - cdlib==0.3.0 \ - bayanpy \ - dynetx==0.3.2 \ - geolet \ - triplex \ - glocalx \ - cliqs \ - quantum-distance-based-classifier - -RUN pip install --no-cache-dir \ - -i https://test.pypi.org/pypi/ \ - --extra-index-url https://pypi.org/simple \ +COPY conda-lock.yml /conda/conda-lock.yml + +RUN . /opt/conda/etc/profile.d/conda.sh && \ + conda create --name lock -c conda-forge conda-lock --yes && \ + conda activate lock && \ + conda-lock install --mamba --copy --name sbd /conda/conda-lock.yml && \ + conda activate sbd && \ + pip install privlib && \ + pip install git+https://github.com/guglielmocola/RetweetCascade.git && \ + pip install git+https://github.com/guglielmocola/TwitterMonitorLib_v2.git && \ + pip install git+https://github.com/vitiugin/cliqs.git && \ + pip install -i https://test.pypi.org/pypi/ --extra-index-url https://pypi.org/simple \ anonymization-crisesURV \ - antiDiscrimination-crisesURV + antiDiscrimination-crisesURV && \ + conda clean --all --force-pkgs-dirs --yes && \ + pip cache purge -# ------------------------------- -# JupyterLab extensions -# ------------------------------- -RUN pip install --no-cache-dir jupyterlab-topbar -RUN jupyter labextension disable @jupyterlab/filebrowser-extension:share-file +WORKDIR "${HOME}" diff --git a/single-user-sobigdata/README.md b/single-user-sobigdata/README.md new file mode 100644 index 00000000..8ead04a7 --- /dev/null +++ b/single-user-sobigdata/README.md @@ -0,0 +1,21 @@ +# How to + +## Create a conda-lock file + +Steps: + +```shell +conda create -n conda-lock -c conda-forge conda-lock --yes +conda activate conda-lock +conda-lock --file=sbd-extended.yml --platform=linux-64 +``` + +## Install conda-lock file + +Steps: + +```shell +conda create -n conda-lock -c conda-forge conda-lock --yes +conda activate conda-lock +conda-lock install --name sbd conda-lock.yml +``` diff --git a/single-user-sobigdata/conda-lock.yml b/single-user-sobigdata/conda-lock.yml new file mode 100644 index 00000000..25f44ed4 --- /dev/null +++ b/single-user-sobigdata/conda-lock.yml @@ -0,0 +1,10934 @@ +# This lock file was generated by conda-lock (https://github.com/conda/conda-lock). DO NOT EDIT! +# +# A "lock file" contains a concrete list of package versions (with checksums) to be installed. Unlike +# e.g. `conda env create`, the resulting environment will not change as new package versions become +# available, unless you explicitly update the lock file. +# +# Install this environment as "YOURENV" with: +# conda-lock install -n YOURENV --file conda-lock.yml +# To update a single package to the latest version compatible with the version constraints in the source: +# conda-lock lock --lockfile conda-lock.yml --update PACKAGE +# To re-solve the entire environment, e.g. after changing a version constraint in the source file: +# conda-lock -f sbd-extended.yml --lockfile conda-lock.yml +version: 1 +metadata: + content_hash: + linux-64: 09631011cc21d2a3e5cee9daf7af72309e2aa4994fa4370b2a799bcb5cd586b2 + channels: + - url: conda-forge + used_env_vars: [] + - url: pytorch + used_env_vars: [] + - url: defaults + used_env_vars: [] + platforms: + - linux-64 + sources: + - sbd-extended.yml +package: +- name: _libgcc_mutex + version: '0.1' + manager: conda + platform: linux-64 + 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a/single-user-sobigdata/sbd.yml b/single-user-sobigdata/sbd.yml new file mode 100644 index 00000000..cef4852e --- /dev/null +++ b/single-user-sobigdata/sbd.yml @@ -0,0 +1,114 @@ +name: sbd +channels: + - conda-forge +# new + - pytorch + - defaults +dependencies: + # extended + - python 3.9.* + - cxx-compiler + # 1st mamba command + - basemap + - beakerx + - xgboost + - lightgbm + - catboost + - netcdf4 + - aiohttp + - graph-tool + - scikit-learn + - scikit-mobility + - dask-jobqueue + - fs + - rasterio + - contextily + - nb_conda_kernels + - nb_conda + # 2nd mamba command + - pyspark + - transformers + - rtree + - geopandas + - nltk + - pydotplus + - plotly + - graphviz + - keras 2.15.0 + - selenium + - tweepy + - openjdk=8 + # new + - sentinelhub + - networkx + - nbresuse + - motuclient + - panel 0.9.* + - cython + - owslib + - folium 0.11.0 + - geopy 2.0.0 + - hvplot 0.6.0 + - intake 0.6.0 + - intake-esm 2020.8.15 + - hda + - seaborn 0.11.0 + - zarr 2.5.0 + - holoviews + - pyfim + - pyclustering + - py-opencv + - jupyterlab-topbar + # https://pytorch.org/get-started/locally/#linux-anaconda + - cpuonly + - pytorch 1.13.1 + - torchvision + - torchaudio + # d4science-base + - shortid + - rdflib + - prov + - pydot + - lxml + - geojson + - pydap + - xarray + - cartopy + - ipyleaflet + - nbgitpuller + - nomkl + - pip + - pip: + - bicm + - rdp + - import_ipynb + - ndlib + - cdlib==0.3.0 + - node_conformity + - fast-forward-indexes + - NEMtropy + - networksns + - eventclf + - XAI-Library + - convrewriting +# gcc needed +# https://github.com/gvinciguerra/PyGM/issues/3 + - pygm + - structify-net + - simpletransformers + - shuffle-graph +# https://github.com/conda-forge/pyfim-feedstock/issues/14 +# - privlib + - ash_model + - bayanpy + - dynetx==0.3.2 + - geolet + - triplex + - glocalx +# https://github.com/vitiugin/cliqs/pull/1 +# - cliqs + - quantum-distance-based-classifier + - demv +# do not work with conda-lock +# - git+https://github.com/guglielmocola/RetweetCascade.git +# - git+https://github.com/guglielmocola/TwitterMonitorLib_v2.git From 4507dd9c300ca83096d48683474d56c4d626a2e0 Mon Sep 17 00:00:00 2001 From: Sebastian Luna-Valero Date: Fri, 16 Feb 2024 09:25:49 +0000 Subject: [PATCH 02/11] temporarily avoid building base image --- .github/workflows/d4science-images.yml | 49 -------------------------- 1 file changed, 49 deletions(-) diff --git a/.github/workflows/d4science-images.yml b/.github/workflows/d4science-images.yml index 59842f03..d3ce733e 100644 --- a/.github/workflows/d4science-images.yml +++ b/.github/workflows/d4science-images.yml @@ -23,45 +23,6 @@ jobs: "single-user-sobigdata-lipari23/Dockerfile" "single-user-sobigdata-aaai24/Dockerfile" - base-image: - name: Build base image - needs: detect-changes - if: needs.detect-changes.outputs.build-base == 1 - runs-on: ubuntu-latest - outputs: - base: ${{ steps.docker_meta_base.outputs.tags }} - steps: - - name: try to make free space - run: | - sudo rm -rf /usr/share/dotnet - sudo rm -rf /usr/local/lib/android - sudo rm -rf /opt/ghc - - name: Checkout - uses: actions/checkout@v4 - - name: Docker meta - id: docker_meta_base - uses: docker/metadata-action@v5 - with: - images: ${{ github.repository_owner }}/notebooks-d4science-base - tags: | - type=sha - - name: Set up QEMU - uses: docker/setup-qemu-action@v3 - - name: Set up Docker Buildx - uses: docker/setup-buildx-action@v3 - - name: Build base - uses: docker/build-push-action@v5 - with: - context: d4science-base - tags: ${{ steps.docker_meta_base.outputs.tags }} - labels: ${{ steps.docker_meta_base.outputs.labels }} - outputs: type=docker,dest=/tmp/base.tar - - name: Upload docker image as artifact - uses: actions/upload-artifact@v4 - with: - name: images - path: /tmp/base.tar - user-images: name: Build and push images if: fromJson(needs.detect-changes.outputs.matrix).image @@ -88,16 +49,6 @@ jobs: type=sha - name: Set up QEMU uses: docker/setup-qemu-action@v3 - - name: Get previous build base - uses: actions/download-artifact@v4 - with: - name: images - path: /tmp - - name: Load Docker images - run: | - docker load --input /tmp/base.tar - # we are so scarce on storage that this needs to be cleared - rm -rf /tmp/base.tar - name: Login to DockerHub uses: docker/login-action@v3 with: From cb84a4c5ee4b39cf428765d022c8e5016b63ced4 Mon Sep 17 00:00:00 2001 From: Sebastian Luna-Valero Date: Fri, 16 Feb 2024 09:32:07 +0000 Subject: [PATCH 03/11] temporarily remove base-image from needs in user-images --- .github/workflows/d4science-images.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/d4science-images.yml b/.github/workflows/d4science-images.yml index d3ce733e..953604c3 100644 --- a/.github/workflows/d4science-images.yml +++ b/.github/workflows/d4science-images.yml @@ -26,7 +26,7 @@ jobs: user-images: name: Build and push images if: fromJson(needs.detect-changes.outputs.matrix).image - needs: [base-image, detect-changes] + needs: [detect-changes] runs-on: ubuntu-latest strategy: From 0876e1b88744c0e2a158b92bc5070659ffb9c29f Mon Sep 17 00:00:00 2001 From: Sebastian Luna-Valero Date: Fri, 16 Feb 2024 09:36:31 +0000 Subject: [PATCH 04/11] temporarily remove base-image from docker build --- .github/workflows/d4science-images.yml | 1 - 1 file changed, 1 deletion(-) diff --git a/.github/workflows/d4science-images.yml b/.github/workflows/d4science-images.yml index 953604c3..a8c904a8 100644 --- a/.github/workflows/d4science-images.yml +++ b/.github/workflows/d4science-images.yml @@ -61,7 +61,6 @@ jobs: - name: Build full image run: | docker build \ - --build-arg BASE_IMAGE=${{ needs.base-image.outputs.base }} \ --tag ${{ steps.docker_meta.outputs.tags }} \ --tag eginotebooks/${{ matrix.image }}:latest \ ${{ matrix.image }} From 3942fa35f796feab6c1369a1ba2f13e7dfc0659a Mon Sep 17 00:00:00 2001 From: Sebastian Luna-Valero Date: Fri, 16 Feb 2024 13:02:04 +0000 Subject: [PATCH 05/11] conda-lock --without-cuda --- single-user-sobigdata/conda-lock.yml | 192 +++++++-------------------- 1 file changed, 45 insertions(+), 147 deletions(-) diff --git a/single-user-sobigdata/conda-lock.yml b/single-user-sobigdata/conda-lock.yml index 25f44ed4..849ceaf0 100644 --- a/single-user-sobigdata/conda-lock.yml +++ b/single-user-sobigdata/conda-lock.yml @@ -55,10 +55,10 @@ package: manager: conda platform: linux-64 dependencies: {} - url: https://conda.anaconda.org/conda-forge/linux-64/_py-xgboost-mutex-2.0-gpu_0.tar.bz2 + url: https://conda.anaconda.org/conda-forge/linux-64/_py-xgboost-mutex-2.0-cpu_0.tar.bz2 hash: - md5: 7702188077361f43a4d61e64c694f850 - sha256: ef6bccb4e2114a7be586416f5e1a8656ffa11c6fddef926b5c6d5ff5179157fa + md5: 23b8f98a355030331f40d0245492f715 + sha256: 504b46c85d81269b24e7b22309064886cfc873955e77daf0eb794d8e7ec8cc06 category: main optional: false - name: aenum @@ -1342,48 +1342,6 @@ package: sha256: 56b8d01515d58bf5e368f01286485f9f3095bbede487ffa9f9367f6978eba07f 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sha256: 15120c9a1ff5ceb88314e883002bb99cd88df8ec61ffeffdd38f23a3d10c1954 category: main optional: false - name: py4j @@ -6913,30 +6822,22 @@ package: manager: conda platform: linux-64 dependencies: - __cuda: '' __glibc: '>=2.17,<3.0.a0' _openmp_mutex: '>=4.5' - cffi: '' - cudatoolkit: '>=11.2,<12' - cudnn: '>=8.4.1.50,<9.0a0' libcblas: '>=3.9.0,<4.0a0' libgcc-ng: '>=12' libprotobuf: '>=3.21.12,<3.22.0a0' libstdcxx-ng: '>=12' - magma: '>=2.6.2,<2.6.3.0a0' mkl: '>=2022.2.1,<2023.0a0' - nccl: '>=2.14.3.1,<3.0a0' - ninja: '' numpy: '>=1.20.3,<2.0a0' python: '>=3.9,<3.10.0a0' python_abi: 3.9.* - setuptools: '' sleef: '>=3.5.1,<4.0a0' typing_extensions: '' - url: https://conda.anaconda.org/conda-forge/linux-64/pytorch-1.13.1-cuda112py39hb0b7ed5_200.conda + url: https://conda.anaconda.org/conda-forge/linux-64/pytorch-1.13.1-cpu_py39h14c4022_1.conda hash: - md5: adfcd34b46ec298bd84c3b55bdd36b7e - sha256: 5fdc38777ec4077599820297333ff05004440617fc466f0793606ab61ae56918 + md5: b7d869dbfae95c9fb7776c26450f9a88 + sha256: 04055a517df97b4b02287e1545e896f62026dbf1bad0c073fb66057a6c66daa0 category: main optional: false - name: pytorch-mutex @@ -7311,7 +7212,7 @@ package: category: main optional: false - name: scikit-learn - version: 1.4.0 + version: 1.4.1.post1 manager: conda platform: linux-64 dependencies: @@ -7324,10 +7225,10 @@ package: python_abi: 3.9.* scipy: '' threadpoolctl: '>=2.0.0' - url: https://conda.anaconda.org/conda-forge/linux-64/scikit-learn-1.4.0-py39ha22ef79_0.conda + url: https://conda.anaconda.org/conda-forge/linux-64/scikit-learn-1.4.1.post1-py39ha22ef79_0.conda hash: - md5: cb8da9a55b56e7fda3553c919f89431b - sha256: 29080f3b936839256acbd3a686e912f2d00e97c84e79357e26ad7a7cfb67a4e9 + md5: 34570aedcdc0281c66ce0ed300844111 + sha256: 72fe5a1a19a4ed66a8e0aeceee256e58c7a7b3dd9a97139c6e7b2ba73e0c9f63 category: main optional: false - name: scikit-mobility @@ -7709,10 +7610,10 @@ package: platform: linux-64 dependencies: kernel-headers_linux-64: 2.6.32 - url: https://conda.anaconda.org/conda-forge/noarch/sysroot_linux-64-2.12-he073ed8_16.conda + url: https://conda.anaconda.org/conda-forge/noarch/sysroot_linux-64-2.12-he073ed8_17.conda hash: - md5: 071ea8dceff4d30ac511f4a2f8437cd1 - sha256: 4c024b2eee24c6da7d3e08723111ec02665c578844c5b3e9e6b38f89000bec41 + md5: 595db67e32b276298ff3d94d07d47fbf + sha256: b4e4d685e41cb36cfb16f0cb15d2c61f8f94f56fab38987a44eff95d8a673fb5 category: main optional: false - name: tbb @@ -7926,8 +7827,6 @@ package: platform: linux-64 dependencies: __glibc: '>=2.17,<3.0.a0' - cudatoolkit: '>=11.2,<12' - cudnn: '>=8.4.1.50,<9.0a0' libgcc-ng: '>=12' libjpeg-turbo: '>=2.1.5.1,<3.0a0' libpng: '>=1.6.39,<1.7.0a0' @@ -7938,10 +7837,10 @@ package: python_abi: 3.9.* pytorch: '>=1.13.1,<1.14.0a0' requests: '' - url: https://conda.anaconda.org/conda-forge/linux-64/torchvision-0.14.1-cuda112py39hb350dc8_1.conda + url: https://conda.anaconda.org/conda-forge/linux-64/torchvision-0.14.1-cpu_py39h39206e8_1.conda hash: - md5: 841cac0f50f4a3a5c10e0f12d4e68a21 - sha256: 000597edb2257c75c678286589dcb1e0f87ec1cdb83f860be9515ef8477e8ff5 + md5: e02e710914fa6562b0a0d7f19a781a01 + sha256: 57f1db0342730123c944dc8ff096968aeeca83bbdf4636d9cc4dee271e910a42 category: main optional: false - name: tornado @@ -8476,13 +8375,12 @@ package: manager: conda platform: linux-64 dependencies: - __cuda: '' py-xgboost: 2.0.3 python: '' - url: https://conda.anaconda.org/conda-forge/noarch/xgboost-2.0.3-cuda118_pyh5ebfdf7_1.conda + url: https://conda.anaconda.org/conda-forge/noarch/xgboost-2.0.3-cpu_pyhb06c54e_1.conda hash: - md5: 9ca04fca5cb67e6f2e51d0eb0277cf67 - sha256: 463d7be77f991cdd197f690e09b793017e9fca3af40e747cea902ee143dd0cfc + md5: d2bef907bb183fe4ca29e6080ded7632 + sha256: d5829eb907e668b01fc0a67c02c5c43a27e91171bfdb2cd6f7fc6455845b8295 category: main optional: false - name: xkeyboard-config From b088e72bfb8d1b8ae4c6cd77911658775e7c41e1 Mon Sep 17 00:00:00 2001 From: Sebastian Luna-Valero Date: Fri, 16 Feb 2024 14:11:09 +0000 Subject: [PATCH 06/11] try activating conda env for test --- single-user-sobigdata/tests/anon_anti.ipynb | 1 + 1 file changed, 1 insertion(+) diff --git a/single-user-sobigdata/tests/anon_anti.ipynb b/single-user-sobigdata/tests/anon_anti.ipynb index 120502ce..9a6d2463 100644 --- a/single-user-sobigdata/tests/anon_anti.ipynb +++ b/single-user-sobigdata/tests/anon_anti.ipynb @@ -9,6 +9,7 @@ }, "outputs": [], "source": [ + "%conda activate sdb\n", "from anonymization.entities.dataset_CSV import Dataset_CSV\n", "from anonymization.entities.dataset_DataFrame import Dataset_DataFrame\n", "from anonymization.algorithms.anonymization_scheme import Anonymization_scheme\n", From a9b96762a9d5b22612a3fcf3a64d42802c5965e7 Mon Sep 17 00:00:00 2001 From: Sebastian Luna-Valero Date: Fri, 16 Feb 2024 15:21:16 +0000 Subject: [PATCH 07/11] try activating conda env for test --- single-user-sobigdata/tests/anon_anti.ipynb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/single-user-sobigdata/tests/anon_anti.ipynb b/single-user-sobigdata/tests/anon_anti.ipynb index 9a6d2463..fba38b1a 100644 --- a/single-user-sobigdata/tests/anon_anti.ipynb +++ b/single-user-sobigdata/tests/anon_anti.ipynb @@ -9,7 +9,7 @@ }, "outputs": [], "source": [ - "%conda activate sdb\n", + "!. /opt/conda/etc/profile.d/conda.sh && conda activate sbd\n", "from anonymization.entities.dataset_CSV import Dataset_CSV\n", "from anonymization.entities.dataset_DataFrame import Dataset_DataFrame\n", "from anonymization.algorithms.anonymization_scheme import Anonymization_scheme\n", From c11f1aed1f1994bc7858c493bb6fdb4f114692a0 Mon Sep 17 00:00:00 2001 From: Sebastian Luna-Valero Date: Fri, 16 Feb 2024 15:54:59 +0000 Subject: [PATCH 08/11] try activating conda env for test --- .github/workflows/d4science-images.yml | 1 + single-user-sobigdata/tests/anon_anti.ipynb | 1 - 2 files changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/d4science-images.yml b/.github/workflows/d4science-images.yml index a8c904a8..b379a28d 100644 --- a/.github/workflows/d4science-images.yml +++ b/.github/workflows/d4science-images.yml @@ -74,6 +74,7 @@ jobs: image: ${{ steps.docker_meta.outputs.tags }} options: -v ${{ github.workspace }}/${{ matrix.image }}:/image-data run: | + . /opt/conda/etc/profile.d/conda.sh && conda activate sbd for f in /image-data/tests/*.ipynb; do if [ -e "$f" ]; then jupyter nbconvert --ExecutePreprocessor.timeout=600 --to rst \ diff --git a/single-user-sobigdata/tests/anon_anti.ipynb b/single-user-sobigdata/tests/anon_anti.ipynb index fba38b1a..120502ce 100644 --- a/single-user-sobigdata/tests/anon_anti.ipynb +++ b/single-user-sobigdata/tests/anon_anti.ipynb @@ -9,7 +9,6 @@ }, "outputs": [], "source": [ - "!. /opt/conda/etc/profile.d/conda.sh && conda activate sbd\n", "from anonymization.entities.dataset_CSV import Dataset_CSV\n", "from anonymization.entities.dataset_DataFrame import Dataset_DataFrame\n", "from anonymization.algorithms.anonymization_scheme import Anonymization_scheme\n", From 448e2095d9b140e9491cdbd89a185483ab5543f8 Mon Sep 17 00:00:00 2001 From: Sebastian Luna-Valero Date: Fri, 16 Feb 2024 16:09:19 +0000 Subject: [PATCH 09/11] Revert "temporarily remove base-image from docker build" This reverts commit 0876e1b88744c0e2a158b92bc5070659ffb9c29f. --- .github/workflows/d4science-images.yml | 1 + 1 file changed, 1 insertion(+) diff --git a/.github/workflows/d4science-images.yml b/.github/workflows/d4science-images.yml index b379a28d..6c9475d5 100644 --- a/.github/workflows/d4science-images.yml +++ b/.github/workflows/d4science-images.yml @@ -61,6 +61,7 @@ jobs: - name: Build full image run: | docker build \ + --build-arg BASE_IMAGE=${{ needs.base-image.outputs.base }} \ --tag ${{ steps.docker_meta.outputs.tags }} \ --tag eginotebooks/${{ matrix.image }}:latest \ ${{ matrix.image }} From bc53061098a73791e4d46af72e15a073a1b211c2 Mon Sep 17 00:00:00 2001 From: Sebastian Luna-Valero Date: Fri, 16 Feb 2024 16:09:46 +0000 Subject: [PATCH 10/11] Revert "temporarily remove base-image from needs in user-images" This reverts commit cb84a4c5ee4b39cf428765d022c8e5016b63ced4. --- .github/workflows/d4science-images.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/d4science-images.yml b/.github/workflows/d4science-images.yml index 6c9475d5..0a2127cc 100644 --- a/.github/workflows/d4science-images.yml +++ b/.github/workflows/d4science-images.yml @@ -26,7 +26,7 @@ jobs: user-images: name: Build and push images if: fromJson(needs.detect-changes.outputs.matrix).image - needs: [detect-changes] + needs: [base-image, detect-changes] runs-on: ubuntu-latest strategy: From 7cd245547bfafd53d0f6c8315ca32d3cf08c9de1 Mon Sep 17 00:00:00 2001 From: Sebastian Luna-Valero Date: Fri, 16 Feb 2024 16:09:54 +0000 Subject: [PATCH 11/11] Revert "temporarily avoid building base image" This reverts commit 4507dd9c300ca83096d48683474d56c4d626a2e0. --- .github/workflows/d4science-images.yml | 49 ++++++++++++++++++++++++++ 1 file changed, 49 insertions(+) diff --git a/.github/workflows/d4science-images.yml b/.github/workflows/d4science-images.yml index 0a2127cc..5f15b358 100644 --- a/.github/workflows/d4science-images.yml +++ b/.github/workflows/d4science-images.yml @@ -23,6 +23,45 @@ jobs: "single-user-sobigdata-lipari23/Dockerfile" "single-user-sobigdata-aaai24/Dockerfile" + base-image: + name: Build base image + needs: detect-changes + if: needs.detect-changes.outputs.build-base == 1 + runs-on: ubuntu-latest + outputs: + base: ${{ steps.docker_meta_base.outputs.tags }} + steps: + - name: try to make free space + run: | + sudo rm -rf /usr/share/dotnet + sudo rm -rf /usr/local/lib/android + sudo rm -rf /opt/ghc + - name: Checkout + uses: actions/checkout@v4 + - name: Docker meta + id: docker_meta_base + uses: docker/metadata-action@v5 + with: + images: ${{ github.repository_owner }}/notebooks-d4science-base + tags: | + type=sha + - name: Set up QEMU + uses: docker/setup-qemu-action@v3 + - name: Set up Docker Buildx + uses: docker/setup-buildx-action@v3 + - name: Build base + uses: docker/build-push-action@v5 + with: + context: d4science-base + tags: ${{ steps.docker_meta_base.outputs.tags }} + labels: ${{ steps.docker_meta_base.outputs.labels }} + outputs: type=docker,dest=/tmp/base.tar + - name: Upload docker image as artifact + uses: actions/upload-artifact@v4 + with: + name: images + path: /tmp/base.tar + user-images: name: Build and push images if: fromJson(needs.detect-changes.outputs.matrix).image @@ -49,6 +88,16 @@ jobs: type=sha - name: Set up QEMU uses: docker/setup-qemu-action@v3 + - name: Get previous build base + uses: actions/download-artifact@v4 + with: + name: images + path: /tmp + - name: Load Docker images + run: | + docker load --input /tmp/base.tar + # we are so scarce on storage that this needs to be cleared + rm -rf /tmp/base.tar - name: Login to DockerHub uses: docker/login-action@v3 with: