From 3a33cac4506b11076ce467bf79b97c32a2f3a9db Mon Sep 17 00:00:00 2001 From: Abdu Zoghbi Date: Thu, 9 May 2024 12:04:25 -0400 Subject: [PATCH 01/16] starting with a new structure --- README.md | 18 ++++++++++++++---- base-image/Dockerfile | 0 fornax_forced_photometry/README.md | 1 - 3 files changed, 14 insertions(+), 5 deletions(-) create mode 100644 base-image/Dockerfile delete mode 100644 fornax_forced_photometry/README.md diff --git a/README.md b/README.md index 04491c1..ba5e3a7 100644 --- a/README.md +++ b/README.md @@ -1,8 +1,18 @@ # fornax-images -Customised Jupyterhub images for the Fornax Platform deployments +This repo contains the Docker images for the Fornax Platform deployments. +It captures reproducible computing environments, and it follows the +structure used by [Pangeo](https://github.com/pangeo-data/pangeo-docker-images). -Have separate subdirectories for the different images, and please list them below for documentation purposes. +Each image is in its own directory. +`base-image` is a base image that contains basic JupyterHub and Lab setup. +Other images should use it as a starting point. +# Content +- `base_image`: is the base image that all other images should start from. It contains jupyter and the basic tools needed for deployment in the fornax project. -#### fornax_forced_photometry - - Basic image with tractor installed +- `tractor`: Main Astro image that was used for the demo. It contains tractor and other general useful tools. + +- `heasoft`: high energy image containing heasoft. + +# Adding New Images +TODO diff --git a/base-image/Dockerfile b/base-image/Dockerfile new file mode 100644 index 0000000..e69de29 diff --git a/fornax_forced_photometry/README.md b/fornax_forced_photometry/README.md deleted file mode 100644 index 7cbc55b..0000000 --- a/fornax_forced_photometry/README.md +++ /dev/null @@ -1 +0,0 @@ -Packages from the astropy ecosystem + tractor and its deepndencies From f504707b5cb28b781e9d99db8c7252ecf348ba1b Mon Sep 17 00:00:00 2001 From: Abdu Zoghbi Date: Wed, 15 May 2024 12:26:21 -0400 Subject: [PATCH 02/16] add environment-lock.yml to base-image --- base-image/Dockerfile | 36 ++++ base-image/apt.txt | 6 + base-image/environment-lock.yml | 334 ++++++++++++++++++++++++++++++++ base-image/environment.yml | 16 ++ build.py | 102 ++++++++++ 5 files changed, 494 insertions(+) create mode 100644 base-image/apt.txt create mode 100644 base-image/environment-lock.yml create mode 100644 base-image/environment.yml create mode 100755 build.py diff --git a/base-image/Dockerfile b/base-image/Dockerfile index e69de29..a7a380f 100644 --- a/base-image/Dockerfile +++ b/base-image/Dockerfile @@ -0,0 +1,36 @@ +FROM jupyter/base-notebook:2023-04-17 + +LABEL org.opencontainers.image.source=https://github.com/fornax-navo/fornax-images +LABEL org.opencontainers.image.ref.name="Fornax Base Image" +LABEL org.opencontainers.image.version=0.1 +LABEL maintainer="Fornax Project" + +SHELL ["/bin/bash", "-o", "pipefail", "-c"] + +# copy anything we have so we can use it +COPY --chown=jovyan:jovyan . /home/jovyan + + +# Install OS packages and then clean up +USER root +RUN apt-get update --fix-missing > /dev/null \ + # Read apt.txt line by line, and execute apt-get install -y for each line in apt.txt + && xargs -a apt.txt apt-get install -y \ + && apt-get clean \ + && apt-get -y autoremove \ + && rm -rf /var/lib/apt/lists/* +USER $NB_USER +# ------------------------------------ # + +# if we have base-lock.txt, use it +RUN LOCKFILE="environment-lock.yml" ENVFILE="environment.yml" \ + && echo "Checking for lock or environment files" \ + ; if test -f $LOCKFILE; then \ + echo "Found $LOCKFILE, using it ..." \ + && echo "Found $LOCKFILE" > /tmp/tmp.txt \ + && mamba env update -n base --file $LOCKFILE \ + ; elif test -f $ENVFILE; then \ + echo "Found $ENVFILE, using it ..." > /tmp/tmp.txt \ + && echo "Found $ENVFILE" > /tmp/tmp.txt \ + && mamba env update -n base --file $ENVFILE \ + ; fi \ diff --git a/base-image/apt.txt b/base-image/apt.txt new file mode 100644 index 0000000..729e171 --- /dev/null +++ b/base-image/apt.txt @@ -0,0 +1,6 @@ +vim +nano +fuse +bzip2 +git +curl \ No newline at end of file diff --git a/base-image/environment-lock.yml b/base-image/environment-lock.yml new file mode 100644 index 0000000..b113ef4 --- /dev/null +++ b/base-image/environment-lock.yml @@ -0,0 +1,334 @@ +name: base +channels: + - conda-forge +dependencies: + - _libgcc_mutex=0.1=conda_forge + - _openmp_mutex=4.5=2_gnu + - aiofiles=22.1.0=pyhd8ed1ab_0 + - aiohttp=3.9.5=py310h2372a71_0 + - aiosignal=1.3.1=pyhd8ed1ab_0 + - aiosqlite=0.18.0=pyhd8ed1ab_0 + - alembic=1.10.3=pyhd8ed1ab_0 + - anyio=3.6.2=pyhd8ed1ab_0 + - argon2-cffi=21.3.0=pyhd8ed1ab_0 + - argon2-cffi-bindings=21.2.0=py310h5764c6d_3 + - arrow-cpp=12.0.0=ha770c72_1_cpu + - asttokens=2.2.1=pyhd8ed1ab_0 + - async-lru=2.0.4=pyhd8ed1ab_0 + - async-timeout=4.0.3=pyhd8ed1ab_0 + - async_generator=1.10=py_0 + - attrs=22.2.0=pyh71513ae_0 + - aws-c-auth=0.6.26=h2c7c9e7_6 + - aws-c-cal=0.5.26=h71eb795_0 + - aws-c-common=0.8.17=hd590300_0 + - aws-c-compression=0.2.16=h4f47f36_6 + - aws-c-event-stream=0.2.20=h69ce273_6 + - aws-c-http=0.7.7=h7b8353a_3 + - aws-c-io=0.13.21=h2c99d58_4 + - aws-c-mqtt=0.8.6=h3a1964a_15 + - aws-c-s3=0.2.8=h0933b68_4 + - aws-c-sdkutils=0.1.9=h4f47f36_1 + - aws-checksums=0.1.14=h4f47f36_6 + - aws-crt-cpp=0.19.9=h85076f6_5 + - aws-sdk-cpp=1.10.57=hf40e4db_10 + - babel=2.12.1=pyhd8ed1ab_1 + - backcall=0.2.0=pyh9f0ad1d_0 + - backports=1.0=pyhd8ed1ab_3 + - backports.functools_lru_cache=1.6.4=pyhd8ed1ab_0 + - beautifulsoup4=4.12.2=pyha770c72_0 + - bleach=6.0.0=pyhd8ed1ab_0 + - blinker=1.6.2=pyhd8ed1ab_0 + - bokeh=3.4.1=pyhd8ed1ab_0 + - boltons=23.0.0=pyhd8ed1ab_0 + - brotlipy=0.7.0=py310h5764c6d_1005 + - bzip2=1.0.8=h7f98852_4 + - c-ares=1.18.1=h7f98852_0 + - ca-certificates=2022.12.7=ha878542_0 + - certifi=2022.12.7=pyhd8ed1ab_0 + - certipy=0.1.3=py_0 + - cffi=1.15.1=py310h255011f_3 + - charset-normalizer=3.1.0=pyhd8ed1ab_0 + - click=8.1.7=unix_pyh707e725_0 + - cloudpickle=3.0.0=pyhd8ed1ab_0 + - colorama=0.4.6=pyhd8ed1ab_0 + - comm=0.1.3=pyhd8ed1ab_0 + - conda=23.3.1=py310hff52083_0 + - conda-package-handling=2.0.2=pyh38be061_0 + - conda-package-streaming=0.7.0=pyhd8ed1ab_1 + - configurable-http-proxy=4.5.4=h3b247e2_2 + - contourpy=1.2.1=py310hd41b1e2_0 + - cryptography=40.0.2=py310h34c0648_0 + - cytoolz=0.12.3=py310h2372a71_0 + - dask=2024.5.0=pyhd8ed1ab_0 + - dask-core=2024.5.0=pyhd8ed1ab_0 + - dask-expr=1.1.0=pyhd8ed1ab_0 + - dask-labextension=7.0.0=pyhd8ed1ab_0 + - debugpy=1.6.7=py310heca2aa9_0 + - decorator=5.1.1=pyhd8ed1ab_0 + - defusedxml=0.7.1=pyhd8ed1ab_0 + - distributed=2024.5.0=pyhd8ed1ab_0 + - entrypoints=0.4=pyhd8ed1ab_0 + - executing=1.2.0=pyhd8ed1ab_0 + - flit-core=3.8.0=pyhd8ed1ab_0 + - fmt=9.1.0=h924138e_0 + - freetype=2.12.1=h267a509_2 + - frozenlist=1.4.1=py310h2372a71_0 + - gflags=2.2.2=he1b5a44_1004 + - glog=0.6.0=h6f12383_0 + - greenlet=2.0.2=py310heca2aa9_0 + - h11=0.14.0=pyhd8ed1ab_0 + - h2=4.1.0=pyhd8ed1ab_0 + - hpack=4.0.0=pyh9f0ad1d_0 + - httpcore=1.0.5=pyhd8ed1ab_0 + - httpx=0.27.0=pyhd8ed1ab_0 + - hyperframe=6.0.1=pyhd8ed1ab_0 + - icu=72.1=hcb278e6_0 + - idna=3.4=pyhd8ed1ab_0 + - importlib-metadata=6.4.1=pyha770c72_0 + - importlib_metadata=6.4.1=hd8ed1ab_0 + - importlib_resources=5.12.0=pyhd8ed1ab_0 + - ipykernel=6.22.0=pyh210e3f2_0 + - ipython=8.12.0=pyh41d4057_0 + - ipython_genutils=0.2.0=py_1 + - jedi=0.18.2=pyhd8ed1ab_0 + - 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reproc-cpp=14.2.4=hcb278e6_0 + - requests=2.31.0=pyhd8ed1ab_0 + - rfc3339-validator=0.1.4=pyhd8ed1ab_0 + - rfc3986-validator=0.1.1=pyh9f0ad1d_0 + - rpds-py=0.18.1=py310he421c4c_0 + - ruamel.yaml=0.17.21=py310h1fa729e_3 + - ruamel.yaml.clib=0.2.7=py310h1fa729e_1 + - s2n=1.3.44=h06160fa_0 + - send2trash=1.8.0=pyhd8ed1ab_0 + - setuptools=67.6.1=pyhd8ed1ab_0 + - simpervisor=1.0.0=pyhd8ed1ab_0 + - six=1.16.0=pyh6c4a22f_0 + - snappy=1.1.10=hdb0a2a9_1 + - sniffio=1.3.0=pyhd8ed1ab_0 + - sortedcontainers=2.4.0=pyhd8ed1ab_0 + - soupsieve=2.3.2.post1=pyhd8ed1ab_0 + - sqlalchemy=2.0.9=py310h1fa729e_0 + - stack_data=0.6.2=pyhd8ed1ab_0 + - tblib=3.0.0=pyhd8ed1ab_0 + - terminado=0.17.1=pyh41d4057_0 + - tinycss2=1.2.1=pyhd8ed1ab_0 + - tk=8.6.12=h27826a3_0 + - tomli=2.0.1=pyhd8ed1ab_0 + - toolz=0.12.0=pyhd8ed1ab_0 + - tornado=6.2=py310h5764c6d_1 + - tqdm=4.65.0=pyhd8ed1ab_1 + - traitlets=5.9.0=pyhd8ed1ab_0 + - typing-extensions=4.5.0=hd8ed1ab_0 + - typing_extensions=4.5.0=pyha770c72_0 + - tzdata=2023c=h71feb2d_0 + - ucx=1.14.1=h64cca9d_5 + - urllib3=1.26.15=pyhd8ed1ab_0 + - wcwidth=0.2.6=pyhd8ed1ab_0 + - webencodings=0.5.1=py_1 + - websocket-client=1.5.1=pyhd8ed1ab_0 + - wheel=0.40.0=pyhd8ed1ab_0 + - xorg-libxau=1.0.11=hd590300_0 + - xorg-libxdmcp=1.1.3=h7f98852_0 + - xyzservices=2024.4.0=pyhd8ed1ab_0 + - xz=5.2.6=h166bdaf_0 + - y-py=0.5.9=py310h4426083_0 + - yaml=0.2.5=h7f98852_2 + - yaml-cpp=0.7.0=h27087fc_2 + - yarl=1.9.4=py310h2372a71_0 + - ypy-websocket=0.8.2=pyhd8ed1ab_0 + - zeromq=4.3.4=h9c3ff4c_1 + - zict=3.0.0=pyhd8ed1ab_0 + - zipp=3.15.0=pyhd8ed1ab_0 + - zlib=1.2.13=h166bdaf_4 + - zstandard=0.19.0=py310hdeb6495_1 + - zstd=1.5.2=h3eb15da_6 + - pip: + - aiobotocore==2.12.3 + - aioitertools==0.11.0 + - arrow==1.3.0 + - astropy==6.1.0 + - astropy-iers-data==0.2024.5.13.0.30.12 + - boto3==1.34.69 + - boto3-stubs==1.34.105 + - botocore==1.34.69 + - botocore-stubs==1.34.94 + - fqdn==1.5.1 + - fsspec==2024.5.0 + - gitdb==4.0.11 + - gitpython==3.1.43 + - isoduration==20.11.0 + - jmespath==1.0.1 + - jupyter-server-mathjax==0.2.6 + - jupyterlab-bxplorer==0.1.24 + - jupyterlab-git==0.50.0 + - jupyterlab-s3-browser==0.12.0 + - mypy-boto3-s3==1.34.105 + - nbdime==4.0.1 + - opencv-python==4.9.0.80 + - oss-pasarela==0.1.6 + - pyerfa==2.0.1.4 + - s3fs==2024.5.0 + - s3transfer==0.10.1 + - singleton-decorator==1.0.0 + - smmap==5.0.1 + - types-awscrt==0.20.9 + - types-python-dateutil==2.9.0.20240316 + - types-s3transfer==0.10.1 + - tzlocal==5.2 + - uri-template==1.3.0 + - validators==0.28.1 + - webcolors==1.13 + - werkzeug==3.0.3 + - wrapt==1.16.0 +prefix: /opt/conda diff --git a/base-image/environment.yml b/base-image/environment.yml new file mode 100644 index 0000000..c1bdd28 --- /dev/null +++ b/base-image/environment.yml @@ -0,0 +1,16 @@ +channels: + - conda-forge + - nodefaults +dependencies: + - jupyterlab + - dask + - jupytext + - dask-labextension + - pip + - pip: + - opencv-python + - jupyterlab-git + - oss-pasarela + - jupyterlab-bxplorer + - jupyterlab-s3-browser + \ No newline at end of file diff --git a/build.py b/build.py new file mode 100755 index 0000000..6d8bd5a --- /dev/null +++ b/build.py @@ -0,0 +1,102 @@ +#!/usr/bin/env python3 + +""" + +Description: +------------ +A python script for building docker images on sciserver. + +""" + +import argparse +import glob +import subprocess +import os +import json +import time +import logging +import sys + + + +def build_images(image, dryrun, build_args, update_lock, lock_file): + """call 'docker build' on each element in images + + Parameters + ---------- + images: str + The name of the image to build. + dryrun: bool + Print docker command without running. + build_args: dict + extra build arguments. + update_lock: bool + update lock file? + lock_file: str + name of the lock file + + """ + + # loop through requested images + logging.debug(f'Working on image {image} ...') + if os.path.exists(image) and os.path.exists(f'{image}/Dockerfile'): + logging.debug(f'Found {image}/Dockerfile ...') + else: + raise ValueError(f'No image folder found for {image}') + + # check build_args + extra_args = [] + if build_args is not None: + for arg in build_args: + if '=' not in arg: + raise ValueError(f'build_args should be of the form "name=value". Got "{arg}".') + args = arg.split('=') + args = f'{args[0].upper()}={args[1]}' + extra_args = [i for arg in build_args for i in ['--build-arg', args]] + + # build the image # + logging.debug(f'\tBuilding {image}') + cmd = [ + 'docker', 'build', '--network=host', '-t', + f'fornax/{image}:latest' + ] + extra_args + [f'./{image}'] + logging.debug('\t' + (' '.join(cmd))) + + if not dryrun: + if update_lock and os.path.exists(f'{image}/{lock_file}'): + os.system(f'rm {image}/{lock_file}') + + out = subprocess.call(cmd) + if out: + logging.error('\tError encountered.') + sys.exit(1) + + # update lock-file? + if update_lock: + logging.debug(f'Updating the lock file for {image}') + cmd = [ + 'docker', 'run', '--rm', + f'fornax/{image}:latest', + 'mamba', 'env', 'export', '-f', f'{image}/{lock_file}' + ] + logging.debug('\t' + (' '.join(cmd))) + + if not dryrun: + out = subprocess.call(cmd) + +if __name__ == '__main__': + + ap = argparse.ArgumentParser() + ap.add_argument('--dryrun', action='store_true', default=False) + ap.add_argument('--update-lock', action='store_true', help='update lock file', default=False) + ap.add_argument('--lock_file', type=str, help='name of the lock file', default='environment-lock.yml') + ap.add_argument('image', help='image to build') + ap.add_argument('--build-args', nargs='*', help='Extra arguments passed to docker build') + args = ap.parse_args() + + + logging.basicConfig(format='%(asctime)s|%(levelname)5s| %(message)s', + datefmt='%Y-%m-%d|%H:%M:%S') + logging.getLogger().setLevel(logging.DEBUG) + + build_images(args.image, args.dryrun, args.build_args, args.update_lock, args.lock_file) From 5bcb36c2225f546bd4df1bd53b6675bfa2740b66 Mon Sep 17 00:00:00 2001 From: Abdu Zoghbi Date: Fri, 17 May 2024 16:23:26 -0400 Subject: [PATCH 03/16] switched to conda-lock --- base-image/Dockerfile | 73 +- base-image/apt.txt | 3 +- base-image/conda-notebook-lock.yml | 3910 +++++++++++++++++ .../{environment.yml => conda-notebook.yml} | 0 base-image/environment-lock.yml | 334 -- base-image/packages.txt | 279 ++ base-image/scripts/apt-install.sh | 11 + base-image/scripts/conda-env-install.sh | 26 + build.py | 53 +- generate-package-list.py | 69 + 10 files changed, 4391 insertions(+), 367 deletions(-) create mode 100644 base-image/conda-notebook-lock.yml rename base-image/{environment.yml => conda-notebook.yml} (100%) delete mode 100644 base-image/environment-lock.yml create mode 100644 base-image/packages.txt create mode 100644 base-image/scripts/apt-install.sh create mode 100644 base-image/scripts/conda-env-install.sh create mode 100644 generate-package-list.py diff --git a/base-image/Dockerfile b/base-image/Dockerfile index a7a380f..537dd37 100644 --- a/base-image/Dockerfile +++ b/base-image/Dockerfile @@ -1,36 +1,63 @@ -FROM jupyter/base-notebook:2023-04-17 +FROM quay.io/jupyter/base-notebook:2024-05-16 LABEL org.opencontainers.image.source=https://github.com/fornax-navo/fornax-images LABEL org.opencontainers.image.ref.name="Fornax Base Image" LABEL org.opencontainers.image.version=0.1 LABEL maintainer="Fornax Project" -SHELL ["/bin/bash", "-o", "pipefail", "-c"] +# clear the jupyter stack from base +RUN mamba remove jupyterlab notebook jupyterhub nbclassic ipykernel \ + && mamba clean -afy \ + && find ${CONDA_DIR} -follow -type f -name '*.a' -delete -# copy anything we have so we can use it -COPY --chown=jovyan:jovyan . /home/jovyan +ENV CONDA_ENV=notebook + + +# Ask dask to read config from ${CONDA_DIR}/etc rather than +# the default of /etc, since the non-root jovyan user can write +# to ${CONDA_DIR}/etc but not to /etc +ENV DASK_ROOT_CONFIG=${CONDA_DIR}/etc -# Install OS packages and then clean up USER root -RUN apt-get update --fix-missing > /dev/null \ - # Read apt.txt line by line, and execute apt-get install -y for each line in apt.txt - && xargs -a apt.txt apt-get install -y \ - && apt-get clean \ - && apt-get -y autoremove \ - && rm -rf /var/lib/apt/lists/* + +# Install OS packages and then clean up +COPY --chown=$NB_USER:$NB_USER scripts /opt/scripts +COPY --chown=$NB_USER:$NB_USER apt.txt* $HOME/build/ +# Read apt.txt line by line, and execute apt-get install for each line +RUN cd build && bash /opt/scripts/apt-install.sh + + +# update start.sh (user as ENTRYPOINT) to a simple one +RUN printf "#!/bin/bash -l\n\nexec \"\$@\"" > /usr/local/bin/start.sh \ + && chmod +x /usr/local/bin/start.sh +CMD ["/bin/bash"] + + USER $NB_USER +# setup conda environments +COPY --chown=$NB_USER:$NB_USER conda-*yml $HOME/build/ +RUN mamba install conda-lock \ + && cd build && bash /opt/scripts/conda-env-install.sh + +# reset user and location +USER ${NB_USER} +WORKDIR ${HOME} + +# Make $CONDA_ENV default +RUN printf "\nif ! [ -z \$CONDA_ENV ]; then\n conda activate \$CONDA_ENV\nfi\n" >> $HOME/.bashrc +ENV PATH=$CONDA_DIR/envs/$CONDA_ENV/bin:$PATH + + +# Install OS packages and then clean up +ONBUILD USER root +ONBUILD COPY --chown=$NB_USER:$NB_USER apt.txt* $HOME/build/ +ONBUILD RUN cd build && bash /opt/scripts/apt-install.sh +ONBUILD USER $NB_USER # ------------------------------------ # -# if we have base-lock.txt, use it -RUN LOCKFILE="environment-lock.yml" ENVFILE="environment.yml" \ - && echo "Checking for lock or environment files" \ - ; if test -f $LOCKFILE; then \ - echo "Found $LOCKFILE, using it ..." \ - && echo "Found $LOCKFILE" > /tmp/tmp.txt \ - && mamba env update -n base --file $LOCKFILE \ - ; elif test -f $ENVFILE; then \ - echo "Found $ENVFILE, using it ..." > /tmp/tmp.txt \ - && echo "Found $ENVFILE" > /tmp/tmp.txt \ - && mamba env update -n base --file $ENVFILE \ - ; fi \ + +# setup conda environments +ONBUILD COPY --chown=$NB_USER:$NB_USER conda-*yml $HOME/build/ +ONBUILD RUN cd build && bash /opt/scripts/conda-env-install.sh +# ----------------------- # diff --git a/base-image/apt.txt b/base-image/apt.txt index 729e171..3d8f908 100644 --- a/base-image/apt.txt +++ b/base-image/apt.txt @@ -3,4 +3,5 @@ nano fuse bzip2 git -curl \ No newline at end of file +curl +zip \ No newline at end of file diff --git a/base-image/conda-notebook-lock.yml b/base-image/conda-notebook-lock.yml new file mode 100644 index 0000000..aeb8618 --- /dev/null +++ b/base-image/conda-notebook-lock.yml @@ -0,0 +1,3910 @@ +# 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 conda-notebook-lock.yml +# To update a single package to the latest version compatible with the version constraints in the source: +# conda-lock lock --lockfile conda-notebook-lock.yml --update PACKAGE +# To re-solve the entire environment, e.g. after changing a version constraint in the source file: +# conda-lock -f tmp-notebook-lock.yml --lockfile conda-notebook-lock.yml +version: 1 +metadata: + content_hash: + linux-64: 59d338ed7abc6c801ebf5b779dca11ede4a98385c4f266983b9bc5d76778a844 + channels: + - url: conda-forge + used_env_vars: [] + platforms: + - linux-64 + sources: + - tmp-notebook-lock.yml +package: +- name: _libgcc_mutex + version: '0.1' + manager: conda + platform: linux-64 + dependencies: {} + url: 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soupsieve=2.3.2.post1=pyhd8ed1ab_0 - - sqlalchemy=2.0.9=py310h1fa729e_0 - - stack_data=0.6.2=pyhd8ed1ab_0 - - tblib=3.0.0=pyhd8ed1ab_0 - - terminado=0.17.1=pyh41d4057_0 - - tinycss2=1.2.1=pyhd8ed1ab_0 - - tk=8.6.12=h27826a3_0 - - tomli=2.0.1=pyhd8ed1ab_0 - - toolz=0.12.0=pyhd8ed1ab_0 - - tornado=6.2=py310h5764c6d_1 - - tqdm=4.65.0=pyhd8ed1ab_1 - - traitlets=5.9.0=pyhd8ed1ab_0 - - typing-extensions=4.5.0=hd8ed1ab_0 - - typing_extensions=4.5.0=pyha770c72_0 - - tzdata=2023c=h71feb2d_0 - - ucx=1.14.1=h64cca9d_5 - - urllib3=1.26.15=pyhd8ed1ab_0 - - wcwidth=0.2.6=pyhd8ed1ab_0 - - webencodings=0.5.1=py_1 - - websocket-client=1.5.1=pyhd8ed1ab_0 - - wheel=0.40.0=pyhd8ed1ab_0 - - xorg-libxau=1.0.11=hd590300_0 - - xorg-libxdmcp=1.1.3=h7f98852_0 - - xyzservices=2024.4.0=pyhd8ed1ab_0 - - xz=5.2.6=h166bdaf_0 - - y-py=0.5.9=py310h4426083_0 - - yaml=0.2.5=h7f98852_2 - - yaml-cpp=0.7.0=h27087fc_2 - - yarl=1.9.4=py310h2372a71_0 - - ypy-websocket=0.8.2=pyhd8ed1ab_0 - - zeromq=4.3.4=h9c3ff4c_1 - - zict=3.0.0=pyhd8ed1ab_0 - - zipp=3.15.0=pyhd8ed1ab_0 - - zlib=1.2.13=h166bdaf_4 - - zstandard=0.19.0=py310hdeb6495_1 - - zstd=1.5.2=h3eb15da_6 - - pip: - - aiobotocore==2.12.3 - - aioitertools==0.11.0 - - arrow==1.3.0 - - astropy==6.1.0 - - astropy-iers-data==0.2024.5.13.0.30.12 - - boto3==1.34.69 - - boto3-stubs==1.34.105 - - botocore==1.34.69 - - botocore-stubs==1.34.94 - - fqdn==1.5.1 - - fsspec==2024.5.0 - - gitdb==4.0.11 - - gitpython==3.1.43 - - isoduration==20.11.0 - - jmespath==1.0.1 - - jupyter-server-mathjax==0.2.6 - - jupyterlab-bxplorer==0.1.24 - - jupyterlab-git==0.50.0 - - jupyterlab-s3-browser==0.12.0 - - mypy-boto3-s3==1.34.105 - - nbdime==4.0.1 - - opencv-python==4.9.0.80 - - oss-pasarela==0.1.6 - - pyerfa==2.0.1.4 - - s3fs==2024.5.0 - - s3transfer==0.10.1 - - singleton-decorator==1.0.0 - - smmap==5.0.1 - - types-awscrt==0.20.9 - - types-python-dateutil==2.9.0.20240316 - - types-s3transfer==0.10.1 - - tzlocal==5.2 - - uri-template==1.3.0 - - validators==0.28.1 - - webcolors==1.13 - - werkzeug==3.0.3 - - wrapt==1.16.0 -prefix: /opt/conda diff --git a/base-image/packages.txt b/base-image/packages.txt new file mode 100644 index 0000000..2d8db85 --- /dev/null +++ b/base-image/packages.txt @@ -0,0 +1,279 @@ +# List of packages and versions installed in the environment +# Generated by parsing base-image/conda-notebook-lock.yml, please use that as source of truth +GitPython==3.1.43 +SQLAlchemy==2.0.30 +_libgcc_mutex==0.1 +_openmp_mutex==4.5 +aiobotocore==2.13.0 +aiohttp==3.9.5 +aioitertools==0.11.0 +aiosignal==1.3.1 +anyio==4.3.0 +argon2-cffi==23.1.0 +argon2-cffi-bindings==21.2.0 +arrow==1.3.0 +astropy==6.1.0 +astropy-iers-data==0.2024.5.13.0.30.12 +asttokens==2.4.1 +async-lru==2.0.4 +attrs==23.2.0 +aws-c-auth==0.7.20 +aws-c-cal==0.6.12 +aws-c-common==0.9.17 +aws-c-compression==0.2.18 +aws-c-event-stream==0.4.2 +aws-c-http==0.8.1 +aws-c-io==0.14.8 +aws-c-mqtt==0.10.4 +aws-c-s3==0.5.8 +aws-c-sdkutils==0.1.16 +aws-checksums==0.1.18 +aws-crt-cpp==0.26.8 +aws-sdk-cpp==1.11.267 +babel==2.14.0 +beautifulsoup4==4.12.3 +bleach==6.1.0 +bokeh==3.4.1 +boto3==1.34.106 +boto3-stubs==1.34.108 +botocore==1.34.106 +botocore-stubs==1.34.94 +brotli-python==1.1.0 +bzip2==1.0.8 +c-ares==1.28.1 +ca-certificates==2024.2.2 +cached-property==1.5.2 +cached_property==1.5.2 +certifi==2024.2.2 +cffi==1.16.0 +charset-normalizer==3.3.2 +click==8.1.7 +cloudpickle==3.0.0 +colorama==0.4.6 +comm==0.2.2 +contourpy==1.2.1 +cytoolz==0.12.3 +dask==2024.5.0 +dask-core==2024.5.0 +dask-expr==1.1.0 +dask-labextension==7.0.0 +debugpy==1.8.1 +decorator==5.1.1 +defusedxml==0.7.1 +distributed==2024.5.0 +entrypoints==0.4 +exceptiongroup==1.2.0 +executing==2.0.1 +fqdn==1.5.1 +freetype==2.12.1 +frozenlist==1.4.1 +fsspec==2024.5.0 +gflags==2.2.2 +gitdb==4.0.11 +glog==0.7.0 +greenlet==3.0.3 +h11==0.14.0 +h2==4.1.0 +hpack==4.0.0 +httpcore==1.0.5 +httpx==0.27.0 +hyperframe==6.0.1 +idna==3.7 +importlib-metadata==7.1.0 +importlib_metadata==7.1.0 +importlib_resources==6.4.0 +ipykernel==6.29.3 +ipython==8.24.0 +isoduration==20.11.0 +jedi==0.19.1 +jinja2==3.1.4 +jmespath==1.0.1 +json5==0.9.25 +jsonpointer==2.4 +jsonschema==4.22.0 +jsonschema-specifications==2023.12.1 +jsonschema-with-format-nongpl==4.22.0 +jupyter-lsp==2.2.5 +jupyter-server-mathjax==0.2.6 +jupyter-server-proxy==4.1.2 +jupyter_client==8.6.1 +jupyter_core==5.7.2 +jupyter_events==0.10.0 +jupyter_server==2.14.0 +jupyter_server_terminals==0.5.3 +jupyterlab==4.2.0 +jupyterlab-bxplorer==0.1.24 +jupyterlab-git==0.50.1 +jupyterlab-s3-browser==0.12.0 +jupyterlab_pygments==0.3.0 +jupyterlab_server==2.27.1 +jupytext==1.16.2 +keyutils==1.6.1 +krb5==1.21.2 +lcms2==2.16 +ld_impl_linux-64==2.40 +lerc==4.0.0 +libabseil==20240116.2 +libarrow==16.0.0 +libarrow-acero==16.0.0 +libarrow-dataset==16.0.0 +libarrow-substrait==16.0.0 +libblas==3.9.0 +libbrotlicommon==1.1.0 +libbrotlidec==1.1.0 +libbrotlienc==1.1.0 +libcblas==3.9.0 +libcrc32c==1.1.2 +libcurl==8.7.1 +libdeflate==1.20 +libedit==3.1.20191231 +libev==4.33 +libevent==2.1.12 +libexpat==2.6.2 +libffi==3.4.2 +libgcc-ng==13.2.0 +libgfortran-ng==13.2.0 +libgfortran5==13.2.0 +libgomp==13.2.0 +libgoogle-cloud==2.23.0 +libgoogle-cloud-storage==2.23.0 +libgrpc==1.62.2 +libjpeg-turbo==3.0.0 +liblapack==3.9.0 +libnghttp2==1.58.0 +libnsl==2.0.1 +libopenblas==0.3.27 +libparquet==16.0.0 +libpng==1.6.43 +libprotobuf==4.25.3 +libre2-11==2023.09.01 +libsodium==1.0.18 +libsqlite==3.45.3 +libssh2==1.11.0 +libstdcxx-ng==13.2.0 +libthrift==0.19.0 +libtiff==4.6.0 +libutf8proc==2.8.0 +libuuid==2.38.1 +libwebp-base==1.4.0 +libxcb==1.15 +libxcrypt==4.4.36 +libzlib==1.2.13 +locket==1.0.0 +lz4==4.3.3 +lz4-c==1.9.4 +markdown-it-py==3.0.0 +markupsafe==2.1.5 +matplotlib-inline==0.1.7 +mdit-py-plugins==0.4.1 +mdurl==0.1.2 +mistune==3.0.2 +msgpack-python==1.0.8 +multidict==6.0.5 +mypy-boto3-s3==1.34.105 +nbclient==0.10.0 +nbconvert==7.16.4 +nbconvert-core==7.16.4 +nbdime==4.0.1 +nbformat==5.10.4 +ncurses==6.5 +nest-asyncio==1.6.0 +notebook==7.2.0 +notebook-shim==0.2.4 +numpy==1.26.4 +opencv-python==4.9.0.80 +openjpeg==2.5.2 +openssl==3.3.0 +orc==2.0.0 +oss-pasarela==0.1.6 +overrides==7.7.0 +packaging==24.0 +pandas==2.2.2 +pandocfilters==1.5.0 +parso==0.8.4 +partd==1.4.2 +pexpect==4.9.0 +pickleshare==0.7.5 +pillow==10.3.0 +pip==24.0 +pkgutil-resolve-name==1.3.10 +platformdirs==4.2.2 +prometheus_client==0.20.0 +prompt-toolkit==3.0.42 +psutil==5.9.8 +pthread-stubs==0.4 +ptyprocess==0.7.0 +pure_eval==0.2.2 +pyarrow==16.0.0 +pyarrow-core==16.0.0 +pyarrow-hotfix==0.6 +pycparser==2.22 +pyerfa==2.0.1.4 +pygments==2.18.0 +pysocks==1.7.1 +python==3.12.3 +python-dateutil==2.9.0 +python-fastjsonschema==2.19.1 +python-json-logger==2.0.7 +python-tzdata==2024.1 +python_abi==3.12 +pytz==2024.1 +pyyaml==6.0.1 +pyzmq==26.0.3 +re2==2023.09.01 +readline==8.2 +referencing==0.35.1 +requests==2.31.0 +rfc3339-validator==0.1.4 +rfc3986-validator==0.1.1 +rpds-py==0.18.1 +s2n==1.4.13 +s3fs==2024.5.0 +s3transfer==0.10.1 +send2trash==1.8.3 +setuptools==69.5.1 +simpervisor==1.0.0 +singleton==decorator-1.0.0 +six==1.16.0 +smmap==5.0.1 +snappy==1.2.0 +sniffio==1.3.1 +sortedcontainers==2.4.0 +soupsieve==2.5 +stack_data==0.6.2 +tblib==3.0.0 +terminado==0.18.1 +tinycss2==1.3.0 +tk==8.6.13 +tomli==2.0.1 +toolz==0.12.1 +tornado==6.4 +traitlets==5.14.3 +types-awscrt==0.20.9 +types-python-dateutil==2.9.0.20240316 +types-s3transfer==0.10.1 +typing-extensions==4.11.0 +typing_extensions==4.11.0 +typing_utils==0.1.0 +tzdata==2024a +tzlocal==5.2 +uri-template==1.3.0 +urllib3==2.2.1 +validators==0.28.1 +wcwidth==0.2.13 +webcolors==1.13 +webencodings==0.5.1 +websocket-client==1.8.0 +werkzeug==3.0.3 +wheel==0.43.0 +wrapt==1.16.0 +xorg-libxau==1.0.11 +xorg-libxdmcp==1.1.3 +xyzservices==2024.4.0 +xz==5.2.6 +yaml==0.2.5 +yarl==1.9.4 +zeromq==4.3.5 +zict==3.0.0 +zipp==3.17.0 +zstd==1.5.6 diff --git a/base-image/scripts/apt-install.sh b/base-image/scripts/apt-install.sh new file mode 100644 index 0000000..f0dcf68 --- /dev/null +++ b/base-image/scripts/apt-install.sh @@ -0,0 +1,11 @@ +#!/bin/bash +# This will be run as root inside Dockerfile + +if test -f "apt.txt" ; then + echo "Found apt.txt; using it ..." + apt-get update --fix-missing > /dev/null + xargs -a apt.txt apt-get install -y + apt-get clean + apt-get -y autoremove + rm -rf /var/lib/apt/lists/* +fi \ No newline at end of file diff --git a/base-image/scripts/conda-env-install.sh b/base-image/scripts/conda-env-install.sh new file mode 100644 index 0000000..9b9b041 --- /dev/null +++ b/base-image/scripts/conda-env-install.sh @@ -0,0 +1,26 @@ +#!/bin/bash + +# handle conda environment and lock files +# look for conda-{env}-lock.yml and conda-{env}.yml files + +for envfile in `ls conda-*.yml | grep -v lock`; do + echo "Found env file ${envfile}" + env=`echo $envfile | sed -n 's/conda-\(.*\)\.yml/\1/p'` + LOCKFILE="conda-${env}-lock.yml" + ENVFILE="conda-${env}.yml" + if test -f $LOCKFILE; then + echo "Found $LOCKFILE, using it ..." + conda-lock install --name ${env} $LOCKFILE + elif test -f $ENVFILE; then + echo "Found $ENVFILE, using it ..." + mamba env create -n ${env} -f $ENVFILE + elif [[ "$env"=="$CONDA_ENV" ]]; then + echo "Defaulting to basic env ..." + mamba create --name $env python=3.11 jupyterlab + fi +done + +# clean +mamba clean -yaf +find ${CONDA_DIR} -follow -type f -name '*.a' -delete +find ${CONDA_DIR} -follow -type f -name '*.js.map' -delete diff --git a/build.py b/build.py index 6d8bd5a..34548f5 100755 --- a/build.py +++ b/build.py @@ -12,6 +12,7 @@ import glob import subprocess import os +import re import json import time import logging @@ -19,7 +20,7 @@ -def build_images(image, dryrun, build_args, update_lock, lock_file): +def build_images(image, dryrun, build_args, update_lock): """call 'docker build' on each element in images Parameters @@ -32,8 +33,6 @@ def build_images(image, dryrun, build_args, update_lock, lock_file): extra build arguments. update_lock: bool update lock file? - lock_file: str - name of the lock file """ @@ -63,8 +62,11 @@ def build_images(image, dryrun, build_args, update_lock, lock_file): logging.debug('\t' + (' '.join(cmd))) if not dryrun: - if update_lock and os.path.exists(f'{image}/{lock_file}'): - os.system(f'rm {image}/{lock_file}') + if update_lock and len(glob.glob(f'{image}/conda-*-lock.yml')): + # If update_lock, remove the old ones so the build does + # not use them + # TODO: handle individual files separately + os.system(f'rm {image}/conda-*-lock.yml') out = subprocess.call(cmd) if out: @@ -74,22 +76,55 @@ def build_images(image, dryrun, build_args, update_lock, lock_file): # update lock-file? if update_lock: logging.debug(f'Updating the lock file for {image}') + envfiles = [ + env for env in glob.glob(f'{image}/conda-*.yml') if 'lock' not in env + ] + for env in envfiles: + match = re.match(rf'{image}/conda-(.*).yml', env) + if match: + env_name = match[1] + else: + env_name = 'base' + # first create an env file cmd = [ 'docker', 'run', '--rm', f'fornax/{image}:latest', - 'mamba', 'env', 'export', '-f', f'{image}/{lock_file}' + 'mamba', 'env', 'export', '-n', env_name ] logging.debug('\t' + (' '.join(cmd))) + if not dryrun: + out = subprocess.check_output(cmd) + with open(f'{image}/tmp-{env_name}-lock.yml', 'wb') as fp: + fp.write(out) + + # then call conda-lock on it + # conda-lock -f tmp.yml -p linux-64 --lockfile tmp-lock.yml + cmd = [ + 'conda-lock', '-f', f'{image}/tmp-{env_name}-lock.yml', + '-p', 'linux-64', '--lockfile', f'{image}/conda-{env_name}-lock.yml' + ] + logging.debug('\t' + (' '.join(cmd))) if not dryrun: out = subprocess.call(cmd) + if out: + logging.error('\tError encountered.') + sys.exit(1) + os.system(f'rm {image}/tmp-{env_name}-lock.yml') + + # Now generate the packages-list.txt file that contain the list for reference + cmd = [sys.executable, 'generate-package-list.py', f'{image}/conda-{env_name}-lock.yml'] + logging.debug('\t' + (' '.join(cmd))) + if not dryrun: + out = subprocess.check_output(cmd) + with open(f'{image}/packages.txt', 'wb') as fp: + fp.write(out) if __name__ == '__main__': ap = argparse.ArgumentParser() ap.add_argument('--dryrun', action='store_true', default=False) - ap.add_argument('--update-lock', action='store_true', help='update lock file', default=False) - ap.add_argument('--lock_file', type=str, help='name of the lock file', default='environment-lock.yml') + ap.add_argument('--update-lock', action='store_true', help='update conda lock file', default=False) ap.add_argument('image', help='image to build') ap.add_argument('--build-args', nargs='*', help='Extra arguments passed to docker build') args = ap.parse_args() @@ -99,4 +134,4 @@ def build_images(image, dryrun, build_args, update_lock, lock_file): datefmt='%Y-%m-%d|%H:%M:%S') logging.getLogger().setLevel(logging.DEBUG) - build_images(args.image, args.dryrun, args.build_args, args.update_lock, args.lock_file) + build_images(args.image, args.dryrun, args.build_args, args.update_lock) diff --git a/generate-package-list.py b/generate-package-list.py new file mode 100644 index 0000000..076f21e --- /dev/null +++ b/generate-package-list.py @@ -0,0 +1,69 @@ +#!/usr/bin/env python3 +""" +Generate human readable packages.txt file from a conda-lock file. +""" +import argparse + +def parse_package_url(line): + """ + Parse a single conda-lock line and return name + + Supports both conda and pip pins. + + Returns name of package and version as tuple + """ + + if 'pythonhosted.org' in line: # pip + # Get just the URL + full_url = line.split()[-1] + # Remove hash from URL + url = full_url.split('#', 1)[0] + # Get just the name of file we're getting + filename = url.split('/')[-1] + if filename.endswith('.whl'): + # Wheels are in the format -- + underscored_pkg_name, version, _ = filename.split('-', 2) + elif filename.endswith('.tar.gz'): + # tarballs are just ---. + # Since can have dashes, use rsplit to split the whole + # thing into 3 components, starting from the right. + pkg_name, version, _ = full_pkg.rsplit('-', 2) + return pkg_name, version + +def main(): + argparser = argparse.ArgumentParser() + argparser.add_argument('lock_file', help='Path to conda-lock file to parse', default='conda-linux-64.lock') + args = argparser.parse_args() + + print('# List of packages and versions installed in the environment') + print(f'# Generated by parsing {args.lock_file}, please use that as source of truth') + with open(args.lock_file) as fp: + # Remove comments + lines = [line for line in fp.readlines() if line.strip() and not line.startswith('#')] + packages = [] + for line in lines: + if 'url: https:' not in line: + continue + packages.append(parse_package_url(line)) + # print sort listed of pacakges + for pkg_name, version in sorted(packages): + print(f'{pkg_name}=={version}') + +if __name__ == '__main__': + main() \ No newline at end of file From 70d8d19077e5f941dd39e8d6ed0d3357695b8d51 Mon Sep 17 00:00:00 2001 From: Abdu Zoghbi Date: Mon, 20 May 2024 22:10:13 -0400 Subject: [PATCH 04/16] add image infrastructure and tractor image to test it --- base-image/Dockerfile | 15 + build.py | 86 +- generate-package-list.py | 69 - tractor/Dockerfile | 6 + tractor/apt.txt | 4 + tractor/conda-science_demo-lock.yml | 6117 +++++++++++++++++++++++++++ tractor/conda-science_demo.yml | 37 + tractor/packages.txt | 410 ++ tractor/postBuild.sh | 27 + 9 files changed, 6694 insertions(+), 77 deletions(-) delete mode 100644 generate-package-list.py create mode 100644 tractor/Dockerfile create mode 100644 tractor/apt.txt create mode 100644 tractor/conda-science_demo-lock.yml create mode 100644 tractor/conda-science_demo.yml create mode 100644 tractor/packages.txt create mode 100644 tractor/postBuild.sh diff --git a/base-image/Dockerfile b/base-image/Dockerfile index 537dd37..c56f759 100644 --- a/base-image/Dockerfile +++ b/base-image/Dockerfile @@ -41,6 +41,7 @@ RUN mamba install conda-lock \ && cd build && bash /opt/scripts/conda-env-install.sh # reset user and location +RUN rm -r $HOME/build $HOME/work /tmp/* USER ${NB_USER} WORKDIR ${HOME} @@ -61,3 +62,17 @@ ONBUILD USER $NB_USER ONBUILD COPY --chown=$NB_USER:$NB_USER conda-*yml $HOME/build/ ONBUILD RUN cd build && bash /opt/scripts/conda-env-install.sh # ----------------------- # + +# Any other postBuild scripts # +ONBUILD COPY --chown=$NB_USER:$NB_USER postBuild* $HOME/build/ +ONBUILD RUN cd build \ + ; for script in `ls postBuild*`; do \ + echo "Found script ${script} ..." \ + && chmod +x $script \ + && ./$script \ + ; done +# --------------------------- # + +ONBUILD RUN rm -r $HOME/build +ONBUILD USER ${NB_USER} +ONBUILD WORKDIR ${HOME} diff --git a/build.py b/build.py index 34548f5..1587741 100755 --- a/build.py +++ b/build.py @@ -89,7 +89,7 @@ def build_images(image, dryrun, build_args, update_lock): cmd = [ 'docker', 'run', '--rm', f'fornax/{image}:latest', - 'mamba', 'env', 'export', '-n', env_name + 'mamba', 'env', 'export', '-n', env_name, ] logging.debug('\t' + (' '.join(cmd))) @@ -112,13 +112,83 @@ def build_images(image, dryrun, build_args, update_lock): sys.exit(1) os.system(f'rm {image}/tmp-{env_name}-lock.yml') - # Now generate the packages-list.txt file that contain the list for reference - cmd = [sys.executable, 'generate-package-list.py', f'{image}/conda-{env_name}-lock.yml'] - logging.debug('\t' + (' '.join(cmd))) - if not dryrun: - out = subprocess.check_output(cmd) - with open(f'{image}/packages.txt', 'wb') as fp: - fp.write(out) + # Now generate the packages-list.txt file that contains the list for reference + logging.debug('Generating list of packages to pacakges.txt') + generate_package_list( + lock_file=f'{image}/conda-{env_name}-lock.yml', + out_file=f'{image}/packages.txt' + ) + +def _parse_package_url(line): + """ + Parse a single conda-lock line and return name + + Supports both conda and pip pins. + + Returns name of package and version as tuple + """ + + if 'pythonhosted.org' in line: # pip + # Get just the URL + full_url = line.split()[-1] + # Remove hash from URL + url = full_url.split('#', 1)[0] + # Get just the name of file we're getting + filename = url.split('/')[-1] + if filename.endswith('.whl'): + # Wheels are in the format -- + underscored_pkg_name, version, _ = filename.split('-', 2) + elif filename.endswith('.tar.gz'): + # tarballs are just ---. + # Since can have dashes, use rsplit to split the whole + # thing into 3 components, starting from the right. + pkg_name, version, _ = full_pkg.rsplit('-', 2) + return pkg_name, version + +def generate_package_list(lock_file, out_file): + """Generate a reference list of pacakges from lock file + + Parameters + ---------- + lock_file: str + Name of lock file generated by conda-lock + out_file: str + Name of the output file + + """ + out_txt = '# List of packages and versions installed in the environment\n' + out_txt += f'# Generated by parsing {lock_file}, please use that as source of truth\n' + with open(lock_file) as fp: + # Remove comments + lines = [line for line in fp.readlines() if line.strip() and not line.startswith('#')] + packages = [] + for line in lines: + if 'url: https:' not in line: + continue + packages.append(_parse_package_url(line)) + # print sort listed of pacakges + for pkg_name, version in sorted(packages): + out_txt += f'{pkg_name}=={version}\n' + + with open(out_file, 'w') as fp: + fp.write(out_txt) + if __name__ == '__main__': diff --git a/generate-package-list.py b/generate-package-list.py deleted file mode 100644 index 076f21e..0000000 --- a/generate-package-list.py +++ /dev/null @@ -1,69 +0,0 @@ -#!/usr/bin/env python3 -""" -Generate human readable packages.txt file from a conda-lock file. -""" -import argparse - -def parse_package_url(line): - """ - Parse a single conda-lock line and return name - - Supports both conda and pip pins. - - Returns name of package and version as tuple - """ - - if 'pythonhosted.org' in line: # pip - # Get just the URL - full_url = line.split()[-1] - # Remove hash from URL - url = full_url.split('#', 1)[0] - # Get just the name of file we're getting - filename = url.split('/')[-1] - if filename.endswith('.whl'): - # Wheels are in the format -- - underscored_pkg_name, version, _ = filename.split('-', 2) - elif filename.endswith('.tar.gz'): - # tarballs are just ---. - # Since can have dashes, use rsplit to split the whole - # thing into 3 components, starting from the right. - pkg_name, version, _ = full_pkg.rsplit('-', 2) - return pkg_name, version - -def main(): - argparser = argparse.ArgumentParser() - argparser.add_argument('lock_file', help='Path to conda-lock file to parse', default='conda-linux-64.lock') - args = argparser.parse_args() - - print('# List of packages and versions installed in the environment') - print(f'# Generated by parsing {args.lock_file}, please use that as source of truth') - with open(args.lock_file) as fp: - # Remove comments - lines = [line for line in fp.readlines() if line.strip() and not line.startswith('#')] - packages = [] - for line in lines: - if 'url: https:' not in line: - continue - packages.append(parse_package_url(line)) - # print sort listed of pacakges - for pkg_name, version in sorted(packages): - print(f'{pkg_name}=={version}') - -if __name__ == '__main__': - main() \ No newline at end of file diff --git a/tractor/Dockerfile b/tractor/Dockerfile new file mode 100644 index 0000000..8e848e3 --- /dev/null +++ b/tractor/Dockerfile @@ -0,0 +1,6 @@ +# ONBUILD instructions in base-image/Dockerfile are used to +# perform certain actions based on the presence of specific +# files (such as conda-linux-64.lock, start) in this repo. +# Refer to the base-image/Dockerfile for documentation. +ARG IMAGE_TAG=latest +FROM fornax/base-image:${IMAGE_TAG} diff --git a/tractor/apt.txt b/tractor/apt.txt new file mode 100644 index 0000000..d3b877a --- /dev/null +++ b/tractor/apt.txt @@ -0,0 +1,4 @@ +build-essential +gcc +make +gfortran \ No newline at end of file diff --git a/tractor/conda-science_demo-lock.yml 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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 conda-science_demo-lock.yml +# To update a single package to the latest version compatible with the version constraints in the source: +# conda-lock lock --lockfile conda-science_demo-lock.yml --update PACKAGE +# To re-solve the entire environment, e.g. after changing a version constraint in the source file: +# conda-lock -f tmp-science_demo-lock.yml --lockfile conda-science_demo-lock.yml +version: 1 +metadata: + content_hash: + linux-64: 0cf64d12c1bbc2eb49934c8b6c9369766973a78aef3b7d1c996e2e87d1e0edcd + channels: + - url: conda-forge + used_env_vars: [] + platforms: + - linux-64 + sources: + - tmp-science_demo-lock.yml +package: +- name: _libgcc_mutex + version: '0.1' + manager: conda + platform: linux-64 + dependencies: {} + url: 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a/tractor/conda-science_demo.yml b/tractor/conda-science_demo.yml new file mode 100644 index 0000000..61abe1d --- /dev/null +++ b/tractor/conda-science_demo.yml @@ -0,0 +1,37 @@ +name: science_demo +channels: + - conda-forge + - nodefaults +dependencies: + - python=3.11 + - numpy + - pandas + - scipy + - pyarrow + - swig + - ipykernel + - cairo + - cython + - "ceres-solver<2.2.0" + - pkg-config + - setuptools + - wcslib + - libjpeg-turbo + - netpbm + - acstools + - astropy + - astroquery + - boto3 + - firefly-client + - hpgeom + - lightkurve + - matplotlib + - seaborn + - mpld3 + - seaborn + - reproject + - s3fs + - scikit-image + - statsmodels + - tqdm +prefix: /opt/conda/envs/science_demo \ No newline at end of file diff --git a/tractor/packages.txt b/tractor/packages.txt new file mode 100644 index 0000000..6e50201 --- /dev/null +++ b/tractor/packages.txt @@ -0,0 +1,410 @@ +# List of packages and versions installed in the environment +# Generated by parsing tractor/conda-science_demo-lock.yml, please use that as source of truth +_libgcc_mutex==0.1 +_openmp_mutex==4.5 +acstools==3.7.1 +affine==2.4.0 +aiobotocore==2.13.0 +aiohttp==3.9.5 +aioitertools==0.11.0 +aiosignal==1.3.1 +alsa-lib==1.2.11 +aom==3.9.0 +asciitree==0.3.3 +asdf==3.2.0 +asdf-astropy==0.6.1 +asdf-coordinates-schemas==0.3.0 +asdf-standard==1.1.1 +asdf-transform-schemas==0.5.0 +asdf-wcs-schemas==0.4.0 +astropy==6.1.0 +astropy-healpix==1.0.3 +astropy-iers-data==0.2024.5.20.0.29.40 +astroquery==0.4.7 +asttokens==2.4.1 +attr==2.5.1 +attrs==23.2.0 +autograd==1.6.2 +aws-c-auth==0.7.16 +aws-c-cal==0.6.10 +aws-c-common==0.9.13 +aws-c-compression==0.2.18 +aws-c-event-stream==0.4.2 +aws-c-http==0.8.1 +aws-c-io==0.14.5 +aws-c-mqtt==0.10.2 +aws-c-s3==0.5.2 +aws-c-sdkutils==0.1.15 +aws-checksums==0.1.18 +aws-crt-cpp==0.26.2 +aws-sdk-cpp==1.11.267 +azure-core-cpp==1.10.3 +azure-storage-blobs-cpp==12.10.0 +azure-storage-common-cpp==12.5.0 +backports==1.0 +backports.tarfile==1.0.0 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+python_abi==3.11 +pytz==2024.1 +pyvo==1.5.1 +pywavelets==1.4.1 +pyyaml==6.0.1 +pyzmq==26.0.3 +qt-main==5.15.8 +rasterio==1.3.9 +rav1e==0.6.6 +rdma-core==51.0 +re2==2023.09.01 +readline==8.2 +reproject==0.13.1 +requests==2.31.0 +s2n==1.4.5 +s3fs==2024.5.0 +s3transfer==0.10.1 +scikit-image==0.22.0 +scikit-learn==1.4.2 +scipy==1.13.0 +seaborn==0.13.2 +seaborn-base==0.13.2 +secretstorage==3.3.3 +semantic_version==2.10.0 +setuptools==69.5.1 +shapely==2.0.4 +sip==6.7.12 +six==1.16.0 +snappy==1.1.10 +snuggs==1.4.7 +sortedcontainers==2.4.0 +soupsieve==2.5 +sqlite==3.45.3 +stack_data==0.6.2 +statsmodels==0.14.2 +suitesparse==5.10.1 +svt-av1==2.1.0 +swig==4.2.1 +tbb==2021.12.0 +tblib==3.0.0 +threadpoolctl==3.5.0 +tifffile==2024.5.10 +tiledb==2.20.1 +tk==8.6.13 +toml==0.10.2 +tomli==2.0.1 +toolz==0.12.1 +tornado==6.4 +tqdm==4.66.4 +traitlets==5.14.3 +typing_extensions==4.11.0 +tzcode==2024a +tzdata==2024a +ucx==1.15.0 +uncertainties==3.1.7 +uriparser==0.9.8 +urllib3==2.2.1 +wcslib==8.2.2 +wcwidth==0.2.13 +webencodings==0.5.1 +websocket-client==1.8.0 +wheel==0.43.0 +wrapt==1.16.0 +xcb-util==0.4.0 +xcb-util-image==0.4.0 +xcb-util-keysyms==0.4.0 +xcb-util-renderutil==0.3.9 +xcb-util-wm==0.4.1 +xerces-c==3.2.5 +xkeyboard-config==2.41 +xorg-kbproto==1.0.7 +xorg-libice==1.1.1 +xorg-libsm==1.2.4 +xorg-libx11==1.8.9 +xorg-libxau==1.0.11 +xorg-libxdmcp==1.1.3 +xorg-libxext==1.3.4 +xorg-libxrender==0.9.11 +xorg-renderproto==0.11.1 +xorg-xextproto==7.3.0 +xorg-xf86vidmodeproto==2.3.1 +xorg-xproto==7.0.31 +xyzservices==2024.4.0 +xz==5.2.6 +yaml==0.2.5 +yarl==1.9.4 +zarr==2.18.1 +zeromq==4.3.5 +zfp==1.0.1 +zict==3.0.0 +zipp==3.17.0 +zlib==1.2.13 +zlib-ng==2.0.7 +zstd==1.5.6 diff --git a/tractor/postBuild.sh b/tractor/postBuild.sh new file mode 100644 index 0000000..25fc142 --- /dev/null +++ b/tractor/postBuild.sh @@ -0,0 +1,27 @@ +#!/bin/bash + +pythonenv=science_demo +astrometry_commit=fbca48e +tractor_commit=cdb8200 + +# Install astrometry.net and tractor +cd /tmp +git clone https://github.com/dstndstn/astrometry.net.git +cd astrometry.net +git config --global --add safe.directory $PWD +git checkout $astrometry_commit +conda run -n $pythonenv make +conda run -n $pythonenv make py +conda run -n $pythonenv make extra +conda run -n $pythonenv make install INSTALL_DIR=${CONDA_DIR}/envs/${pythonenv} +mv ${CONDA_DIR}/envs/$pythonenv/lib/python/astrometry \ + ${CONDA_DIR}/envs/$pythonenv/lib/python3.??/ + +cd /tmp +git clone https://github.com/dstndstn/tractor.git +cd tractor +git checkout $tractor_commit +conda run -n $pythonenv python setup.py build_ext --inplace --with-ceres --with-cython +cp -r build +conda run -n $pythonenv pip install --no-cache-dir . --target ${CONDA_DIR}/envs/$pythonenv/lib/python3.??/ +rm -r /tmp/astrometry.net /tmp/tractor From da6268039572765e69c4312eb73cf8cb0e85b31c Mon Sep 17 00:00:00 2001 From: Abdu Zoghbi Date: Tue, 21 May 2024 10:00:56 -0400 Subject: [PATCH 05/16] update the readme file --- README.md | 39 ++++++++++++++++++++++++++++++++------- 1 file changed, 32 insertions(+), 7 deletions(-) diff --git a/README.md b/README.md index ba5e3a7..670f278 100644 --- a/README.md +++ b/README.md @@ -1,18 +1,43 @@ # fornax-images This repo contains the Docker images for the Fornax Platform deployments. -It captures reproducible computing environments, and it follows the -structure used by [Pangeo](https://github.com/pangeo-data/pangeo-docker-images). +It produces reproducible computing environments. Some of the parts are +adapted from the [Pangeo](https://github.com/pangeo-data/pangeo-docker-images) project. -Each image is in its own directory. -`base-image` is a base image that contains basic JupyterHub and Lab setup. +Reproducibility is achived by keeping track of the software environments using conda-lock. +The following is a general description of the images: + +- Each image is in its own directory (e.g. `base-image` and `tractor`). +- `base-image` is a base image that contains basic JupyterHub and Lab setup. Other images should use it as a starting point. +- Jupyterlab is installed in a conda environment called `notebook`, and it is the +default environment when running the images. +- The `build.py` script should be used when building the image. It takes as parameter +the name of the folder that contains Dockerfile, which is also the name of the image. +For example: `python build.py base-image` build the base image, and +`python build.py tractor` builds the tractor image. +- The Dockerfile of each image (other than `base-image`) should start from the base image: +`FROM fornax/base-image:latest`. That will trigger the `ONBUILD` sections defined in the +`base-image/Dockerfile`, which include: + - If `apt.txt` exits, it will parsed for the list of the system software to be installed with `apt-get`. + - If `postBuild*` files exist, the scripts are run during the build. + - If `conda-{env}.yml` exists, it defines a conda environment called `{env}`. + - Additionally, if `conda-{env}-lock.yml` exists, it defines a `conda-lock` file that locks +the versions of the installed libraries. To create it, or updated it, pass `--update-lock` to the +build script `build.py`. This will first generate a conda environment file from what is installed in the +conda environment, then use `conda-lock` to lock the versions, and then generate human-readable `packages.txt` +that contains a list of installed libraries and their versions. + +The recommonded workflow is therefore like this: +- Define the libraries requirement from some conda environment `{env}` in `conda-{env}.yml`. +- Build the image with `python build.py {image-name} --update-lock`. +- This will generate: `conda-{env}-lock.yml` and `packages.txt`. Both these should be kept under +verson control. The next time the image is built with `python build.py {image-name}`, the lock +file will be used inside Dockerfile to reproduce the exact build. -# Content +# The image - `base_image`: is the base image that all other images should start from. It contains jupyter and the basic tools needed for deployment in the fornax project. - `tractor`: Main Astro image that was used for the demo. It contains tractor and other general useful tools. - `heasoft`: high energy image containing heasoft. -# Adding New Images -TODO From 46f31364cdc609db76d36397d734c82f2fd6f3e3 Mon Sep 17 00:00:00 2001 From: Abdu Zoghbi Date: Tue, 16 Jul 2024 12:04:20 -0400 Subject: [PATCH 06/16] fix typos in readme --- README.md | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/README.md b/README.md index 670f278..3c71c2e 100644 --- a/README.md +++ b/README.md @@ -31,13 +31,13 @@ The recommonded workflow is therefore like this: - Define the libraries requirement from some conda environment `{env}` in `conda-{env}.yml`. - Build the image with `python build.py {image-name} --update-lock`. - This will generate: `conda-{env}-lock.yml` and `packages.txt`. Both these should be kept under -verson control. The next time the image is built with `python build.py {image-name}`, the lock -file will be used inside Dockerfile to reproduce the exact build. +version control. The next time the image is built with `python build.py {image-name}`, the lock +file will be used inside the Dockerfile to reproduce the exact build. # The image - `base_image`: is the base image that all other images should start from. It contains jupyter and the basic tools needed for deployment in the fornax project. - `tractor`: Main Astro image that was used for the demo. It contains tractor and other general useful tools. -- `heasoft`: high energy image containing heasoft. +- `heasoft`: high energy image containing heasoft (TODO). From f4a7106f095e091cc0a7432b7f99aa115524b186 Mon Sep 17 00:00:00 2001 From: Abdu Zoghbi Date: Mon, 12 Aug 2024 11:16:35 -0400 Subject: [PATCH 07/16] add more explicit astro-dependencies to base-image --- base-image/apt.txt | 1 + base-image/conda-notebook-lock.yml | 3947 +++++++++++++++++++++++----- base-image/conda-notebook.yml | 18 +- base-image/packages-notebook.txt | 434 +++ base-image/packages.txt | 279 -- build.py | 70 +- tractor/conda-science_demo.yml | 1 + 7 files changed, 3743 insertions(+), 1007 deletions(-) create mode 100644 base-image/packages-notebook.txt delete mode 100644 base-image/packages.txt diff --git a/base-image/apt.txt b/base-image/apt.txt index 3d8f908..294442d 100644 --- a/base-image/apt.txt +++ b/base-image/apt.txt @@ -1,5 +1,6 @@ vim nano +emacs fuse bzip2 git diff --git a/base-image/conda-notebook-lock.yml b/base-image/conda-notebook-lock.yml index aeb8618..d98f585 100644 --- a/base-image/conda-notebook-lock.yml +++ b/base-image/conda-notebook-lock.yml @@ -13,7 +13,7 @@ version: 1 metadata: content_hash: - linux-64: 59d338ed7abc6c801ebf5b779dca11ede4a98385c4f266983b9bc5d76778a844 + linux-64: 0f7cde59eec4e81fa63faed4d647b834d0933e6ea8c70bfdac724f9f8469acd2 channels: - url: conda-forge used_env_vars: [] @@ -46,11 +46,37 @@ package: sha256: fbe2c5e56a653bebb982eda4876a9178aedfc2b545f25d0ce9c4c0b508253d22 category: main optional: false +- name: affine + version: 2.4.0 + manager: conda + platform: linux-64 + dependencies: + python: '>=3.7' + url: https://conda.anaconda.org/conda-forge/noarch/affine-2.4.0-pyhd8ed1ab_0.conda + hash: + md5: ae5f4ad87126c55ba3f690ef07f81d64 + sha256: fbf0288cae7c6e5005280436ff73c95a36c5a4c978ba50175cc8e3eb22abc5f9 + category: main + optional: false +- name: aiohappyeyeballs + version: 2.3.5 + manager: conda + platform: linux-64 + dependencies: + python: '>=3.8.0' + url: https://conda.anaconda.org/conda-forge/noarch/aiohappyeyeballs-2.3.5-pyhd8ed1ab_0.conda + hash: + md5: d904abda207d2dba054fd820d34bbaee + sha256: 37ac19a57d429670dcd2c716232e6f842b7f357cecd0977b1d4fd30b8446a30a + category: main + optional: false - name: aiohttp - version: 3.9.5 + version: 3.10.3 manager: conda platform: linux-64 dependencies: + __glibc: '>=2.17,<3.0.a0' + aiohappyeyeballs: '>=2.3.0' aiosignal: '>=1.1.2' attrs: '>=17.3.0' frozenlist: '>=1.1.1' @@ -59,10 +85,10 @@ package: python: '>=3.12,<3.13.0a0' python_abi: 3.12.* yarl: '>=1.0,<2.0' - url: https://conda.anaconda.org/conda-forge/linux-64/aiohttp-3.9.5-py312h98912ed_0.conda + url: https://conda.anaconda.org/conda-forge/linux-64/aiohttp-3.10.3-py312h41a817b_0.conda hash: - md5: edc01db954d139fe398a5f378f96ab4d - sha256: 4727041c2bf3ee90f1a3bba68f846f6ea34f59b292bf5bc390db3bc4ae56d315 + md5: 9efe6ef5d30d2788edbaec60b0aaad45 + sha256: 34e82fc499682a959d4f1203895ae56d45ab43a1701f50bfa861157e609dff74 category: main optional: false - name: aiosignal @@ -79,7 +105,7 @@ package: category: main optional: false - name: anyio - version: 4.3.0 + version: 4.4.0 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+cached_property==1.5.2 +cairo==1.18.0 +ccdproc==2.4.2 +certifi==2024.7.4 +cffi==1.17.0 +cfitsio==4.4.1 +charls==2.4.2 +charset-normalizer==3.3.2 +click==8.1.7 +click-plugins==1.1.1 +cligj==0.7.2 +cloudpickle==3.0.0 +colorama==0.4.6 +comm==0.2.2 +contourpy==1.2.1 +cryptography==43.0.0 +cycler==0.12.1 +cytoolz==0.12.3 +dask==2024.8.0 +dask-core==2024.8.0 +dask-expr==1.1.10 +dask-labextension==7.0.0 +dav1d==1.2.1 +dbus==1.13.6 +debugpy==1.8.5 +decorator==5.1.1 +defusedxml==0.7.1 +distributed==2024.8.0 +entrypoints==0.4 +exceptiongroup==1.2.2 +executing==2.0.1 +expat==2.6.2 +fasteners==0.17.3 +fmt==11.0.2 +font-ttf-dejavu-sans-mono==2.37 +font-ttf-inconsolata==3.000 +font-ttf-source-code-pro==2.038 +font-ttf-ubuntu==0.83 +fontconfig==2.14.2 +fonts-conda-ecosystem==1 +fonts-conda-forge==1 +fonttools==4.53.1 +fqdn==1.5.1 +freetype==2.12.1 +freexl==2.0.0 +frozenlist==1.4.1 +fsspec==2024.6.1 +geos==3.12.2 +geotiff==1.7.3 +gflags==2.2.2 +giflib==5.2.2 +gitdb==4.0.11 +glog==0.7.1 +greenlet==3.0.3 +gwcs==0.21.0 +h11==0.14.0 +h2==4.1.0 +hdf4==4.2.15 +hdf5==1.14.3 +hpack==4.0.0 +html5lib==1.1 +httpcore==1.0.5 +httpx==0.27.0 +hyperframe==6.0.1 +icu==75.1 +idna==3.7 +imagecodecs==2024.6.1 +imageio==2.34.2 +importlib-metadata==8.2.0 +importlib_metadata==8.2.0 +importlib_resources==6.4.0 +ipykernel==6.29.5 +ipython==8.26.0 +isoduration==20.11.0 +jaraco.classes==3.4.0 +jaraco.context==5.3.0 +jaraco.functools==4.0.0 +jedi==0.19.1 +jeepney==0.8.0 +jinja2==3.1.4 +jmespath==1.0.1 +joblib==1.4.2 +json-c==0.17 +json5==0.9.25 +jsonpointer==3.0.0 +jsonschema==4.23.0 +jsonschema-specifications==2023.12.1 +jsonschema-with-format-nongpl==4.23.0 +jupyter-lsp==2.2.5 +jupyter-server-mathjax==0.2.6 +jupyter-server-proxy==4.3.0 +jupyter_client==8.6.2 +jupyter_core==5.7.2 +jupyter_events==0.10.0 +jupyter_server==2.14.2 +jupyter_server_terminals==0.5.3 +jupyterlab==4.2.4 +jupyterlab-bxplorer==0.1.24 +jupyterlab-git==0.50.1 +jupyterlab-myst==2.4.2 +jupyterlab-s3-browser==0.12.0 +jupyterlab_pygments==0.3.0 +jupyterlab_server==2.27.3 +jupytext==1.16.4 +jxrlib==1.1 +kealib==1.5.3 +keyring==25.3.0 +keyutils==1.6.1 +kiwisolver==1.4.5 +krb5==1.21.3 +lazy_loader==0.4 +lcms2==2.16 +ld_impl_linux-64==2.40 +lerc==4.0.0 +libabseil==20240116.2 +libaec==1.1.3 +libarchive==3.7.4 +libarrow==17.0.0 +libarrow-acero==17.0.0 +libarrow-dataset==17.0.0 +libarrow-substrait==17.0.0 +libavif16==1.1.1 +libblas==3.9.0 +libbrotlicommon==1.1.0 +libbrotlidec==1.1.0 +libbrotlienc==1.1.0 +libcblas==3.9.0 +libcrc32c==1.1.2 +libcurl==8.9.1 +libdeflate==1.21 +libedit==3.1.20191231 +libev==4.33 +libevent==2.1.12 +libexpat==2.6.2 +libffi==3.4.2 +libgcc-ng==14.1.0 +libgdal==3.9.1 +libgdal-core==3.9.1 +libgdal-fits==3.9.1 +libgdal-grib==3.9.1 +libgdal-hdf4==3.9.1 +libgdal-hdf5==3.9.1 +libgdal-jp2openjpeg==3.9.1 +libgdal-kea==3.9.1 +libgdal-netcdf==3.9.1 +libgdal-pdf==3.9.1 +libgdal-pg==3.9.1 +libgdal-postgisraster==3.9.1 +libgdal-tiledb==3.9.1 +libgdal-xls==3.9.1 +libgfortran-ng==14.1.0 +libgfortran5==14.1.0 +libglib==2.80.3 +libgomp==14.1.0 +libgoogle-cloud==2.28.0 +libgoogle-cloud-storage==2.28.0 +libgrpc==1.62.2 +libhwy==1.1.0 +libiconv==1.17 +libjpeg-turbo==3.0.0 +libjxl==0.10.3 +libkml==1.3.0 +liblapack==3.9.0 +libnetcdf==4.9.2 +libnghttp2==1.58.0 +libnsl==2.0.1 +libopenblas==0.3.27 +libparquet==17.0.0 +libpng==1.6.43 +libpq==16.4 +libprotobuf==4.25.3 +libre2-11==2023.09.01 +librttopo==1.1.0 +libsodium==1.0.18 +libspatialite==5.1.0 +libsqlite==3.46.0 +libssh2==1.11.0 +libstdcxx-ng==14.1.0 +libthrift==0.19.0 +libtiff==4.6.0 +libutf8proc==2.8.0 +libuuid==2.38.1 +libwebp-base==1.4.0 +libxcb==1.16 +libxcrypt==4.4.36 +libxml2==2.12.7 +libzip==1.10.1 +libzlib==1.3.1 +libzopfli==1.0.3 +locket==1.0.0 +lz4==4.3.3 +lz4-c==1.9.4 +lzo==2.10 +markdown-it-py==3.0.0 +markupsafe==2.1.5 +matplotlib-base==3.9.1 +matplotlib-inline==0.1.7 +mdit-py-plugins==0.4.1 +mdurl==0.1.2 +minizip==4.0.7 +mistune==3.0.2 +more-itertools==10.4.0 +mpl_animators==1.1.1 +msgpack-python==1.0.8 +multidict==6.0.5 +munkres==1.1.4 +mypy-boto3-s3==1.34.158 +nbclient==0.10.0 +nbconvert==7.16.4 +nbconvert-core==7.16.4 +nbdime==4.0.1 +nbformat==5.10.4 +ncurses==6.5 +ndcube==2.2.2 +nest-asyncio==1.6.0 +networkx==3.3 +notebook==7.2.1 +notebook-shim==0.2.4 +nspr==4.35 +nss==3.103 +numcodecs==0.12.1 +numpy==2.0.1 +openjpeg==2.5.2 +openssl==3.3.1 +orc==2.0.1 +overrides==7.7.0 +packaging==24.1 +pandas==2.2.2 +pandocfilters==1.5.0 +parso==0.8.4 +partd==1.4.2 +pcre2==10.44 +pexpect==4.9.0 +photutils==1.13.0 +pickleshare==0.7.5 +pillow==10.4.0 +pip==24.2 +pixman==0.43.2 +pkgutil-resolve-name==1.3.10 +platformdirs==4.2.2 +poppler==24.07.0 +poppler-data==0.4.12 +postgresql==16.4 +proj==9.4.1 +prometheus_client==0.20.0 +prompt-toolkit==3.0.47 +psutil==6.0.0 +pthread-stubs==0.4 +ptyprocess==0.7.0 +pure_eval==0.2.3 +pyarrow==17.0.0 +pyarrow-core==17.0.0 +pyarrow-hotfix==0.6 +pycparser==2.22 +pyerfa==2.0.1.4 +pygments==2.18.0 +pyparsing==3.1.2 +pysocks==1.7.1 +python==3.12.5 +python-dateutil==2.9.0 +python-fastjsonschema==2.20.0 +python-json-logger==2.0.7 +python-tzdata==2024.1 +python_abi==3.12 +pytz==2024.1 +pyvo==1.5.2 +pywavelets==1.6.0 +pyyaml==6.0.2 +pyzmq==26.1.0 +qhull==2020.2 +rasterio==1.3.10 +rav1e==0.6.6 +re2==2023.09.01 +readline==8.2 +referencing==0.35.1 +regions==0.9 +reproject==0.14.0 +requests==2.32.3 +rfc3339-validator==0.1.4 +rfc3986-validator==0.1.1 +rpds-py==0.20.0 +s2n==1.4.19 +s3fs==2024.6.1 +s3transfer==0.10.2 +scikit-image==0.24.0 +scikit-learn==1.5.1 +scipy==1.14.0 +secretstorage==3.3.3 +semantic_version==2.10.0 +send2trash==1.8.3 +setuptools==72.1.0 +shapely==2.0.5 +simpervisor==1.0.0 +singleton==decorator-1.0.0 +six==1.16.0 +smmap==5.0.1 +snappy==1.2.1 +sniffio==1.3.1 +snuggs==1.4.7 +sortedcontainers==2.4.0 +soupsieve==2.5 +spdlog==1.14.1 +specreduce==1.4.1 +specutils==1.16.0 +sqlite==3.46.0 +stack_data==0.6.2 +svt-av1==2.1.2 +tblib==3.0.0 +terminado==0.18.1 +threadpoolctl==3.5.0 +tifffile==2024.8.10 +tiledb==2.25.0 +tinycss2==1.3.0 +tk==8.6.13 +tomli==2.0.1 +toolz==0.12.1 +tornado==6.4.1 +tqdm==4.66.5 +traitlets==5.14.3 +types-awscrt==0.21.2 +types-python-dateutil==2.9.0.20240316 +types-s3transfer==0.10.1 +typing-extensions==4.12.2 +typing_extensions==4.12.2 +typing_utils==0.1.0 +tzcode==2024a +tzdata==2024a +tzlocal==5.2 +uri-template==1.3.0 +uriparser==0.9.8 +urllib3==2.2.2 +wcwidth==0.2.13 +webcolors==24.8.0 +webencodings==0.5.1 +websocket-client==1.8.0 +werkzeug==3.0.3 +wheel==0.44.0 +wrapt==1.16.0 +xerces-c==3.2.5 +xorg-kbproto==1.0.7 +xorg-libice==1.1.1 +xorg-libsm==1.2.4 +xorg-libx11==1.8.9 +xorg-libxau==1.0.11 +xorg-libxdmcp==1.1.3 +xorg-libxext==1.3.4 +xorg-libxrender==0.9.11 +xorg-renderproto==0.11.1 +xorg-xextproto==7.3.0 +xorg-xproto==7.0.31 +xyzservices==2024.6.0 +xz==5.2.6 +yaml==0.2.5 +yarl==1.9.4 +zarr==2.18.2 +zeromq==4.3.5 +zfp==1.0.1 +zict==3.0.0 +zipp==3.19.2 +zlib==1.3.1 +zlib-ng==2.2.1 +zstandard==0.23.0 +zstd==1.5.6 diff --git a/base-image/packages.txt b/base-image/packages.txt deleted file mode 100644 index 2d8db85..0000000 --- a/base-image/packages.txt +++ /dev/null @@ -1,279 +0,0 @@ -# List of packages and versions installed in the environment -# Generated by parsing base-image/conda-notebook-lock.yml, please use that as source of truth -GitPython==3.1.43 -SQLAlchemy==2.0.30 -_libgcc_mutex==0.1 -_openmp_mutex==4.5 -aiobotocore==2.13.0 -aiohttp==3.9.5 -aioitertools==0.11.0 -aiosignal==1.3.1 -anyio==4.3.0 -argon2-cffi==23.1.0 -argon2-cffi-bindings==21.2.0 -arrow==1.3.0 -astropy==6.1.0 -astropy-iers-data==0.2024.5.13.0.30.12 -asttokens==2.4.1 -async-lru==2.0.4 -attrs==23.2.0 -aws-c-auth==0.7.20 -aws-c-cal==0.6.12 -aws-c-common==0.9.17 -aws-c-compression==0.2.18 -aws-c-event-stream==0.4.2 -aws-c-http==0.8.1 -aws-c-io==0.14.8 -aws-c-mqtt==0.10.4 -aws-c-s3==0.5.8 -aws-c-sdkutils==0.1.16 -aws-checksums==0.1.18 -aws-crt-cpp==0.26.8 -aws-sdk-cpp==1.11.267 -babel==2.14.0 -beautifulsoup4==4.12.3 -bleach==6.1.0 -bokeh==3.4.1 -boto3==1.34.106 -boto3-stubs==1.34.108 -botocore==1.34.106 -botocore-stubs==1.34.94 -brotli-python==1.1.0 -bzip2==1.0.8 -c-ares==1.28.1 -ca-certificates==2024.2.2 -cached-property==1.5.2 -cached_property==1.5.2 -certifi==2024.2.2 -cffi==1.16.0 -charset-normalizer==3.3.2 -click==8.1.7 -cloudpickle==3.0.0 -colorama==0.4.6 -comm==0.2.2 -contourpy==1.2.1 -cytoolz==0.12.3 -dask==2024.5.0 -dask-core==2024.5.0 -dask-expr==1.1.0 -dask-labextension==7.0.0 -debugpy==1.8.1 -decorator==5.1.1 -defusedxml==0.7.1 -distributed==2024.5.0 -entrypoints==0.4 -exceptiongroup==1.2.0 -executing==2.0.1 -fqdn==1.5.1 -freetype==2.12.1 -frozenlist==1.4.1 -fsspec==2024.5.0 -gflags==2.2.2 -gitdb==4.0.11 -glog==0.7.0 -greenlet==3.0.3 -h11==0.14.0 -h2==4.1.0 -hpack==4.0.0 -httpcore==1.0.5 -httpx==0.27.0 -hyperframe==6.0.1 -idna==3.7 -importlib-metadata==7.1.0 -importlib_metadata==7.1.0 -importlib_resources==6.4.0 -ipykernel==6.29.3 -ipython==8.24.0 -isoduration==20.11.0 -jedi==0.19.1 -jinja2==3.1.4 -jmespath==1.0.1 -json5==0.9.25 -jsonpointer==2.4 -jsonschema==4.22.0 -jsonschema-specifications==2023.12.1 -jsonschema-with-format-nongpl==4.22.0 -jupyter-lsp==2.2.5 -jupyter-server-mathjax==0.2.6 -jupyter-server-proxy==4.1.2 -jupyter_client==8.6.1 -jupyter_core==5.7.2 -jupyter_events==0.10.0 -jupyter_server==2.14.0 -jupyter_server_terminals==0.5.3 -jupyterlab==4.2.0 -jupyterlab-bxplorer==0.1.24 -jupyterlab-git==0.50.1 -jupyterlab-s3-browser==0.12.0 -jupyterlab_pygments==0.3.0 -jupyterlab_server==2.27.1 -jupytext==1.16.2 -keyutils==1.6.1 -krb5==1.21.2 -lcms2==2.16 -ld_impl_linux-64==2.40 -lerc==4.0.0 -libabseil==20240116.2 -libarrow==16.0.0 -libarrow-acero==16.0.0 -libarrow-dataset==16.0.0 -libarrow-substrait==16.0.0 -libblas==3.9.0 -libbrotlicommon==1.1.0 -libbrotlidec==1.1.0 -libbrotlienc==1.1.0 -libcblas==3.9.0 -libcrc32c==1.1.2 -libcurl==8.7.1 -libdeflate==1.20 -libedit==3.1.20191231 -libev==4.33 -libevent==2.1.12 -libexpat==2.6.2 -libffi==3.4.2 -libgcc-ng==13.2.0 -libgfortran-ng==13.2.0 -libgfortran5==13.2.0 -libgomp==13.2.0 -libgoogle-cloud==2.23.0 -libgoogle-cloud-storage==2.23.0 -libgrpc==1.62.2 -libjpeg-turbo==3.0.0 -liblapack==3.9.0 -libnghttp2==1.58.0 -libnsl==2.0.1 -libopenblas==0.3.27 -libparquet==16.0.0 -libpng==1.6.43 -libprotobuf==4.25.3 -libre2-11==2023.09.01 -libsodium==1.0.18 -libsqlite==3.45.3 -libssh2==1.11.0 -libstdcxx-ng==13.2.0 -libthrift==0.19.0 -libtiff==4.6.0 -libutf8proc==2.8.0 -libuuid==2.38.1 -libwebp-base==1.4.0 -libxcb==1.15 -libxcrypt==4.4.36 -libzlib==1.2.13 -locket==1.0.0 -lz4==4.3.3 -lz4-c==1.9.4 -markdown-it-py==3.0.0 -markupsafe==2.1.5 -matplotlib-inline==0.1.7 -mdit-py-plugins==0.4.1 -mdurl==0.1.2 -mistune==3.0.2 -msgpack-python==1.0.8 -multidict==6.0.5 -mypy-boto3-s3==1.34.105 -nbclient==0.10.0 -nbconvert==7.16.4 -nbconvert-core==7.16.4 -nbdime==4.0.1 -nbformat==5.10.4 -ncurses==6.5 -nest-asyncio==1.6.0 -notebook==7.2.0 -notebook-shim==0.2.4 -numpy==1.26.4 -opencv-python==4.9.0.80 -openjpeg==2.5.2 -openssl==3.3.0 -orc==2.0.0 -oss-pasarela==0.1.6 -overrides==7.7.0 -packaging==24.0 -pandas==2.2.2 -pandocfilters==1.5.0 -parso==0.8.4 -partd==1.4.2 -pexpect==4.9.0 -pickleshare==0.7.5 -pillow==10.3.0 -pip==24.0 -pkgutil-resolve-name==1.3.10 -platformdirs==4.2.2 -prometheus_client==0.20.0 -prompt-toolkit==3.0.42 -psutil==5.9.8 -pthread-stubs==0.4 -ptyprocess==0.7.0 -pure_eval==0.2.2 -pyarrow==16.0.0 -pyarrow-core==16.0.0 -pyarrow-hotfix==0.6 -pycparser==2.22 -pyerfa==2.0.1.4 -pygments==2.18.0 -pysocks==1.7.1 -python==3.12.3 -python-dateutil==2.9.0 -python-fastjsonschema==2.19.1 -python-json-logger==2.0.7 -python-tzdata==2024.1 -python_abi==3.12 -pytz==2024.1 -pyyaml==6.0.1 -pyzmq==26.0.3 -re2==2023.09.01 -readline==8.2 -referencing==0.35.1 -requests==2.31.0 -rfc3339-validator==0.1.4 -rfc3986-validator==0.1.1 -rpds-py==0.18.1 -s2n==1.4.13 -s3fs==2024.5.0 -s3transfer==0.10.1 -send2trash==1.8.3 -setuptools==69.5.1 -simpervisor==1.0.0 -singleton==decorator-1.0.0 -six==1.16.0 -smmap==5.0.1 -snappy==1.2.0 -sniffio==1.3.1 -sortedcontainers==2.4.0 -soupsieve==2.5 -stack_data==0.6.2 -tblib==3.0.0 -terminado==0.18.1 -tinycss2==1.3.0 -tk==8.6.13 -tomli==2.0.1 -toolz==0.12.1 -tornado==6.4 -traitlets==5.14.3 -types-awscrt==0.20.9 -types-python-dateutil==2.9.0.20240316 -types-s3transfer==0.10.1 -typing-extensions==4.11.0 -typing_extensions==4.11.0 -typing_utils==0.1.0 -tzdata==2024a -tzlocal==5.2 -uri-template==1.3.0 -urllib3==2.2.1 -validators==0.28.1 -wcwidth==0.2.13 -webcolors==1.13 -webencodings==0.5.1 -websocket-client==1.8.0 -werkzeug==3.0.3 -wheel==0.43.0 -wrapt==1.16.0 -xorg-libxau==1.0.11 -xorg-libxdmcp==1.1.3 -xyzservices==2024.4.0 -xz==5.2.6 -yaml==0.2.5 -yarl==1.9.4 -zeromq==4.3.5 -zict==3.0.0 -zipp==3.17.0 -zstd==1.5.6 diff --git a/build.py b/build.py index 1587741..4610c63 100755 --- a/build.py +++ b/build.py @@ -4,7 +4,7 @@ Description: ------------ -A python script for building docker images on sciserver. +A python script for building docker images on fornax. """ @@ -85,39 +85,41 @@ def build_images(image, dryrun, build_args, update_lock): env_name = match[1] else: env_name = 'base' - # first create an env file - cmd = [ - 'docker', 'run', '--rm', - f'fornax/{image}:latest', - 'mamba', 'env', 'export', '-n', env_name, - ] - logging.debug('\t' + (' '.join(cmd))) - - if not dryrun: - out = subprocess.check_output(cmd) - with open(f'{image}/tmp-{env_name}-lock.yml', 'wb') as fp: - fp.write(out) - - # then call conda-lock on it - # conda-lock -f tmp.yml -p linux-64 --lockfile tmp-lock.yml - cmd = [ - 'conda-lock', '-f', f'{image}/tmp-{env_name}-lock.yml', - '-p', 'linux-64', '--lockfile', f'{image}/conda-{env_name}-lock.yml' - ] - logging.debug('\t' + (' '.join(cmd))) - if not dryrun: - out = subprocess.call(cmd) - if out: - logging.error('\tError encountered.') - sys.exit(1) - os.system(f'rm {image}/tmp-{env_name}-lock.yml') - - # Now generate the packages-list.txt file that contains the list for reference - logging.debug('Generating list of packages to pacakges.txt') - generate_package_list( - lock_file=f'{image}/conda-{env_name}-lock.yml', - out_file=f'{image}/packages.txt' - ) + # first create an env file + cmd = [ + 'docker', 'run', '--rm', + f'fornax/{image}:latest', + 'mamba', 'env', 'export', '-n', env_name, + ] + logging.debug('\t' + (' '.join(cmd))) + + if not dryrun: + out = subprocess.check_output(cmd) + with open(f'{image}/tmp-{env_name}-lock.yml', 'wb') as fp: + fp.write(out) + + # then call conda-lock on it + # conda-lock -f tmp.yml -p linux-64 --lockfile tmp-lock.yml + cmd = [ + 'conda-lock', '-f', f'{image}/tmp-{env_name}-lock.yml', + '-p', 'linux-64', '--lockfile', f'{image}/conda-{env_name}-lock.yml' + ] + logging.debug('\t' + (' '.join(cmd))) + if not dryrun: + out = subprocess.call(cmd) + if out: + logging.error('\tError encountered.') + sys.exit(1) + os.system(f'rm {image}/tmp-{env_name}-lock.yml') + + # Now generate the packages-list.txt file that contains the list for reference + packages_file = f'{image}/packages-{env_name}.txt' + logging.debug(f'Generating list of packages to {packages_file}') + if not dryrun: + generate_package_list( + lock_file=f'{image}/conda-{env_name}-lock.yml', + out_file=packages_file + ) def _parse_package_url(line): """ diff --git a/tractor/conda-science_demo.yml b/tractor/conda-science_demo.yml index 61abe1d..aeb6641 100644 --- a/tractor/conda-science_demo.yml +++ b/tractor/conda-science_demo.yml @@ -20,6 +20,7 @@ dependencies: - netpbm - acstools - astropy + - pyvo - astroquery - boto3 - firefly-client From 4335e76710f855298a273af4bf2baa1b49256671 Mon Sep 17 00:00:00 2001 From: Abdu Zoghbi Date: Mon, 12 Aug 2024 15:27:51 -0400 Subject: [PATCH 08/16] switch to updating the main conda env rather than creating new ones --- base-image/Dockerfile | 5 +- base-image/apt.txt | 6 +- base-image/conda-notebook-lock.yml | 626 +-- base-image/conda-notebook.yml | 6 + base-image/packages-notebook.txt | 13 +- base-image/scripts/conda-env-install.sh | 4 +- tractor/apt.txt | 4 - ..._demo-lock.yml => conda-notebook-lock.yml} | 4449 +++++++++++------ ...da-science_demo.yml => conda-notebook.yml} | 0 tractor/packages-notebook.txt | 489 ++ tractor/packages.txt | 410 -- 11 files changed, 3699 insertions(+), 2313 deletions(-) delete mode 100644 tractor/apt.txt rename tractor/{conda-science_demo-lock.yml => conda-notebook-lock.yml} (58%) rename tractor/{conda-science_demo.yml => conda-notebook.yml} (100%) create mode 100644 tractor/packages-notebook.txt delete mode 100644 tractor/packages.txt diff --git a/base-image/Dockerfile b/base-image/Dockerfile index c56f759..d720520 100644 --- a/base-image/Dockerfile +++ b/base-image/Dockerfile @@ -18,7 +18,7 @@ ENV CONDA_ENV=notebook # to ${CONDA_DIR}/etc but not to /etc ENV DASK_ROOT_CONFIG=${CONDA_DIR}/etc - +RUN mkdir -p build USER root # Install OS packages and then clean up @@ -51,9 +51,10 @@ ENV PATH=$CONDA_DIR/envs/$CONDA_ENV/bin:$PATH # Install OS packages and then clean up +ONBUILD RUN mkdir -p build ONBUILD USER root ONBUILD COPY --chown=$NB_USER:$NB_USER apt.txt* $HOME/build/ -ONBUILD RUN cd build && bash /opt/scripts/apt-install.sh +ONBUILD RUN mkdir -p build && cd build && bash /opt/scripts/apt-install.sh ONBUILD USER $NB_USER # ------------------------------------ # diff --git a/base-image/apt.txt b/base-image/apt.txt index 294442d..31ff88b 100644 --- a/base-image/apt.txt +++ b/base-image/apt.txt @@ -5,4 +5,8 @@ fuse bzip2 git curl -zip \ No newline at end of file +zip +build-essential +gcc +make +gfortran \ No newline at end of file diff --git a/base-image/conda-notebook-lock.yml b/base-image/conda-notebook-lock.yml index d98f585..0ec726c 100644 --- a/base-image/conda-notebook-lock.yml +++ b/base-image/conda-notebook-lock.yml @@ -13,7 +13,7 @@ version: 1 metadata: content_hash: - linux-64: 0f7cde59eec4e81fa63faed4d647b834d0933e6ea8c70bfdac724f9f8469acd2 + linux-64: cd92786ef71b3463d3394a5cb2069bf886efdaee43be07f34611c36c7ccb659c channels: - url: conda-forge used_env_vars: [] @@ -82,13 +82,13 @@ package: frozenlist: '>=1.1.1' libgcc-ng: '>=12' multidict: '>=4.5,<7.0' - python: '>=3.12,<3.13.0a0' - python_abi: 3.12.* + python: '>=3.11,<3.12.0a0' + python_abi: 3.11.* yarl: '>=1.0,<2.0' - url: https://conda.anaconda.org/conda-forge/linux-64/aiohttp-3.10.3-py312h41a817b_0.conda + url: https://conda.anaconda.org/conda-forge/linux-64/aiohttp-3.10.3-py311h61187de_0.conda hash: - md5: 9efe6ef5d30d2788edbaec60b0aaad45 - sha256: 34e82fc499682a959d4f1203895ae56d45ab43a1701f50bfa861157e609dff74 + md5: b3b58253d1691fafecc512f7a995e12b + sha256: 18075c677baa159d97d879ab5c678707c62954ed3744114d32b4c67610141ee7 category: main optional: false - name: aiosignal @@ -154,12 +154,12 @@ package: dependencies: cffi: '>=1.0.1' libgcc-ng: '>=12' - python: '>=3.12.0rc3,<3.13.0a0' - python_abi: 3.12.* - url: https://conda.anaconda.org/conda-forge/linux-64/argon2-cffi-bindings-21.2.0-py312h98912ed_4.conda + python: '>=3.11,<3.12.0a0' + python_abi: 3.11.* + url: https://conda.anaconda.org/conda-forge/linux-64/argon2-cffi-bindings-21.2.0-py311h459d7ec_4.conda hash: - md5: 00536e0a1734dcde9815fe227f32fc5a - sha256: 8ddb4a586bc128f1b9484f82c5cb0226340527fbfe093adf3b76b7e755e11477 + md5: de5b16869a430949b02161b04b844a30 + sha256: 104194af519b4e667aa5341068b94b521a791aaaa05ec0091f8f0bdba43a60ac category: main optional: false - name: arrow @@ -294,13 +294,13 @@ package: numpy: '>=1.23' packaging: '>=19.0' pyerfa: '>=2.0.1.1' - python: '>=3.12,<3.13.0a0' - python_abi: 3.12.* + python: '>=3.11,<3.12.0a0' + python_abi: 3.11.* pyyaml: '>=3.13' - url: https://conda.anaconda.org/conda-forge/linux-64/astropy-6.1.2-py312h4fc7734_0.conda + url: https://conda.anaconda.org/conda-forge/linux-64/astropy-6.1.2-py311h07ce7c0_0.conda hash: - md5: da0cc3d397ef1db55bdca0884ff991ab - sha256: b0a1974b9631b68d7eee79ffb37ecacdcd5d9f9bc4f6c75d1dca7df59a210ce4 + md5: fab697e4797d4c0ce8f1053902fa9de5 + sha256: 2ade9c28adb3d9b58c4b1a3d8c3c21df9ad6297cb940629591c511bf5c524557 category: main optional: false - name: astropy-healpix @@ -311,12 +311,12 @@ package: astropy: '>=3' libgcc-ng: '>=12' numpy: '>=1.19,<3' - python: '>=3.12,<3.13.0a0' - python_abi: 3.12.* - url: https://conda.anaconda.org/conda-forge/linux-64/astropy-healpix-1.0.3-py312h085067d_1.conda + python: '>=3.11,<3.12.0a0' + python_abi: 3.11.* + url: https://conda.anaconda.org/conda-forge/linux-64/astropy-healpix-1.0.3-py311h18e1886_1.conda hash: - md5: d167f5e2d7245e8730547a1104b2aba6 - sha256: ba8ede9af757c7910ad06e1b4cc2fb2061af38400f5dc52f720edba767290fc5 + md5: 6a1190ae6373568c9e1c9676f68de218 + sha256: 1672a20c0f7edec1652d50e2c93eca4783bb5926b7c2d3461063b55016127ff7 category: main optional: false - name: astropy-iers-data @@ -359,12 +359,12 @@ package: astropy: '' libgcc-ng: '>=12' numpy: '>=1.23' - python: '>=3.12,<3.13.0a0' - python_abi: 3.12.* - url: https://conda.anaconda.org/conda-forge/linux-64/astroscrappy-1.2.0-py312h41a817b_0.conda + python: '>=3.11,<3.12.0a0' + python_abi: 3.11.* + url: https://conda.anaconda.org/conda-forge/linux-64/astroscrappy-1.2.0-py311h61187de_0.conda hash: - md5: b1d5b0a6bedec0b460e2232eb01878b0 - sha256: 5aad6ae0add4c89bccdc5ddae613908ca84e66f794541fb8ef86442b56ceb3bc + md5: 2809f48faf1fc4bab5834ab0db5f94f0 + sha256: 3a58436ab6cf77155b7375ce640f616764e5655667b6065fc852fd8a945c2c6b category: main optional: false - name: asttokens @@ -508,11 +508,11 @@ package: aws-c-cal: '>=0.7.2,<0.7.3.0a0' aws-c-common: '>=0.9.25,<0.9.26.0a0' libgcc-ng: '>=12' - s2n: '>=1.4.19,<1.4.20.0a0' - url: https://conda.anaconda.org/conda-forge/linux-64/aws-c-io-0.14.18-h41d8d95_1.conda + s2n: '>=1.5.0,<1.5.1.0a0' + url: https://conda.anaconda.org/conda-forge/linux-64/aws-c-io-0.14.18-h3e50d33_2.conda hash: - md5: 32ce11d5b2c86e5b1adad2a401d54cbf - sha256: 86d4a08d358432feb5c8f8ebbe076865d4f4f5983c0b227a14c8e2722298655f + md5: 9b0aca26d579311a918a0f03047fc447 + sha256: 8b94d550344392429931aa69f16c38cfd2dbb49ce1e5d2705cb10c8b735dd0ee category: main optional: false - name: aws-c-mqtt @@ -818,12 +818,12 @@ package: dependencies: libgcc-ng: '>=12' numpy: '>=1.19,<3' - python: '>=3.12,<3.13.0a0' - python_abi: 3.12.* - url: https://conda.anaconda.org/conda-forge/linux-64/bottleneck-1.4.0-py312h085067d_1.conda + python: '>=3.11,<3.12.0a0' + python_abi: 3.11.* + url: https://conda.anaconda.org/conda-forge/linux-64/bottleneck-1.4.0-py311h18e1886_1.conda hash: - md5: 465afba0490075f44a3f6ae1bb087352 - sha256: 47da3473b782494c254d4a7cd761bea4ce464b47435c170036f99ab8c389d8a3 + md5: 5f30101a9040203522a168a75ad4e50b + sha256: 1823d680856eec582206f18851036e6d2a7d5d08c472d5d722fddad8e71c752d category: main optional: false - name: brotli @@ -862,12 +862,12 @@ package: dependencies: libgcc-ng: '>=12' libstdcxx-ng: '>=12' - python: '>=3.12.0rc3,<3.13.0a0' - python_abi: 3.12.* - url: https://conda.anaconda.org/conda-forge/linux-64/brotli-python-1.1.0-py312h30efb56_1.conda + python: '>=3.11,<3.12.0a0' + python_abi: 3.11.* + url: https://conda.anaconda.org/conda-forge/linux-64/brotli-python-1.1.0-py311hb755f60_1.conda hash: - md5: 45801a89533d3336a365284d93298e36 - sha256: b68706698b6ac0d31196a8bcb061f0d1f35264bcd967ea45e03e108149a74c6f + md5: cce9e7c3f1c307f2a5fb08a2922d6164 + sha256: 559093679e9fdb6061b7b80ca0f9a31fe6ffc213f1dae65bc5c82e2cd1a94107 category: main optional: false - name: brunsli @@ -1030,12 +1030,12 @@ package: libffi: '>=3.4,<4.0a0' libgcc-ng: '>=12' pycparser: '' - python: '>=3.12,<3.13.0a0' - python_abi: 3.12.* - url: https://conda.anaconda.org/conda-forge/linux-64/cffi-1.17.0-py312h1671c18_0.conda + python: '>=3.11,<3.12.0a0' + python_abi: 3.11.* + url: https://conda.anaconda.org/conda-forge/linux-64/cffi-1.17.0-py311ha8e6434_0.conda hash: - md5: 33dee889f41b0ba6dbe5ddbe70ebf263 - sha256: 20fe2f88dd7c0ef16e464fa46757821cf569bc71f40a832e7767d3a87250f251 + md5: 32259cd17741b52be10cd23a26cca23a + sha256: 88edb3161c8fda6df36db5643a3721123c371273c6375a2307b4ccafe060c5a0 category: main optional: false - name: cfitsio @@ -1164,12 +1164,12 @@ package: libgcc-ng: '>=12' libstdcxx-ng: '>=12' numpy: '>=1.20' - python: '>=3.12,<3.13.0a0' - python_abi: 3.12.* - url: https://conda.anaconda.org/conda-forge/linux-64/contourpy-1.2.1-py312h8572e83_0.conda + python: '>=3.11,<3.12.0a0' + python_abi: 3.11.* + url: https://conda.anaconda.org/conda-forge/linux-64/contourpy-1.2.1-py311h9547e67_0.conda hash: - md5: 12c6a831ef734f0b2dd4caff514cbb7f - sha256: b0731336b9788c247b11a592352f700a647119340b549aba9e933835c7c77df0 + md5: 74ad0ae64f1ef565e27eda87fa749e84 + sha256: 82cec326aa81b9b6b40d9f4dab5045f0553092405efd0de9d2daf71179f20607 category: main optional: false - name: cryptography @@ -1181,12 +1181,12 @@ package: cffi: '>=1.12' libgcc-ng: '>=12' openssl: '>=3.3.1,<4.0a0' - python: '>=3.12,<3.13.0a0' - python_abi: 3.12.* - url: https://conda.anaconda.org/conda-forge/linux-64/cryptography-43.0.0-py312h8aaac84_0.conda + python: '>=3.11,<3.12.0a0' + python_abi: 3.11.* + url: 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category: main optional: false - name: dask @@ -1324,12 +1324,12 @@ package: __glibc: '>=2.17,<3.0.a0' libgcc-ng: '>=12' libstdcxx-ng: '>=12' - python: '>=3.12,<3.13.0a0' - python_abi: 3.12.* - url: https://conda.anaconda.org/conda-forge/linux-64/debugpy-1.8.5-py312hca68cad_0.conda + python: '>=3.11,<3.12.0a0' + python_abi: 3.11.* + url: https://conda.anaconda.org/conda-forge/linux-64/debugpy-1.8.5-py311hf86e51f_0.conda hash: - md5: 6c56579c537feaafdf62d6c3b5424c53 - sha256: 129964de45b48cb44a377ba926fd96a081ef11ca3d47f5f1b969c2609de30816 + md5: 748a22f229ec0e62963b8045b8e6786c + sha256: 92a719cca475ba58ca9d9b6287c5880fc8fd99d8518f22ae6f66c69a6995fe05 category: main optional: false - name: decorator @@ -1555,12 +1555,12 @@ package: brotli: '' libgcc-ng: '>=12' munkres: '' - python: '>=3.12,<3.13.0a0' - python_abi: 3.12.* - url: https://conda.anaconda.org/conda-forge/linux-64/fonttools-4.53.1-py312h41a817b_0.conda + python: '>=3.11,<3.12.0a0' + python_abi: 3.11.* + url: 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false - name: fsspec @@ -1914,16 +1914,16 @@ package: lz4-c: '>=1.9.3,<1.10.0a0' numpy: '>=1.19,<3' openjpeg: '>=2.5.2,<3.0a0' - python: '>=3.12,<3.13.0a0' - python_abi: 3.12.* + python: '>=3.11,<3.12.0a0' + python_abi: 3.11.* snappy: '>=1.2.1,<1.3.0a0' xz: '>=5.2.6,<6.0a0' zfp: '>=1.0.1,<2.0a0' zstd: '>=1.5.6,<1.6.0a0' - url: https://conda.anaconda.org/conda-forge/linux-64/imagecodecs-2024.6.1-py312h36edd9b_3.conda + url: https://conda.anaconda.org/conda-forge/linux-64/imagecodecs-2024.6.1-py311h732c098_3.conda hash: - md5: c309596a0ff59342f52e59046bbe3a8c - sha256: b8cb061810628487fb02f9f8d7cb110e94b99cf6dd6bb14b85c5cb601770d62d + md5: 34ee94453a09c0abc94b194207917b50 + sha256: e64844785a22e007c7e8dce66517c7bc80a1df3b5df80e9e8d5c83da1bbafb11 category: main optional: false - name: imageio @@ -2172,12 +2172,12 @@ package: manager: conda platform: linux-64 dependencies: - python: '>=3.12,<3.13.0a0' - python_abi: 3.12.* - url: 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+boto3-stubs==1.34.159 botocore==1.34.131 botocore-stubs==1.34.158 bottleneck==1.4.0 @@ -253,7 +253,6 @@ libutf8proc==2.8.0 libuuid==2.38.1 libwebp-base==1.4.0 libxcb==1.16 -libxcrypt==4.4.36 libxml2==2.12.7 libzip==1.10.1 libzlib==1.3.1 @@ -300,6 +299,7 @@ pandas==2.2.2 pandocfilters==1.5.0 parso==0.8.4 partd==1.4.2 +patsy==0.5.6 pcre2==10.44 pexpect==4.9.0 photutils==1.13.0 @@ -327,12 +327,12 @@ pyerfa==2.0.1.4 pygments==2.18.0 pyparsing==3.1.2 pysocks==1.7.1 -python==3.12.5 +python==3.11.0 python-dateutil==2.9.0 python-fastjsonschema==2.20.0 python-json-logger==2.0.7 python-tzdata==2024.1 -python_abi==3.12 +python_abi==3.11 pytz==2024.1 pyvo==1.5.2 pywavelets==1.6.0 @@ -350,12 +350,14 @@ requests==2.32.3 rfc3339-validator==0.1.4 rfc3986-validator==0.1.1 rpds-py==0.20.0 -s2n==1.4.19 +s2n==1.5.0 s3fs==2024.6.1 s3transfer==0.10.2 scikit-image==0.24.0 scikit-learn==1.5.1 scipy==1.14.0 +seaborn==0.13.2 +seaborn-base==0.13.2 secretstorage==3.3.3 semantic_version==2.10.0 send2trash==1.8.3 @@ -375,6 +377,7 @@ specreduce==1.4.1 specutils==1.16.0 sqlite==3.46.0 stack_data==0.6.2 +statsmodels==0.14.2 svt-av1==2.1.2 tblib==3.0.0 terminado==0.18.1 diff --git a/base-image/scripts/conda-env-install.sh b/base-image/scripts/conda-env-install.sh index 9b9b041..81d0b62 100644 --- a/base-image/scripts/conda-env-install.sh +++ b/base-image/scripts/conda-env-install.sh @@ -13,10 +13,10 @@ for envfile in `ls conda-*.yml | grep -v lock`; do conda-lock install --name ${env} $LOCKFILE elif test -f $ENVFILE; then echo "Found $ENVFILE, using it ..." - mamba env create -n ${env} -f $ENVFILE + mamba env update -n ${env} -f $ENVFILE elif [[ "$env"=="$CONDA_ENV" ]]; then echo "Defaulting to basic env ..." - mamba create --name $env python=3.11 jupyterlab + mamba update --name $env python=3.11 jupyterlab fi done diff --git a/tractor/apt.txt b/tractor/apt.txt deleted file mode 100644 index d3b877a..0000000 --- a/tractor/apt.txt +++ /dev/null @@ -1,4 +0,0 @@ -build-essential -gcc -make -gfortran \ No newline at end of file diff --git a/tractor/conda-science_demo-lock.yml b/tractor/conda-notebook-lock.yml similarity index 58% rename from tractor/conda-science_demo-lock.yml rename to tractor/conda-notebook-lock.yml index c07cdbd..7ad93d4 100644 --- a/tractor/conda-science_demo-lock.yml +++ b/tractor/conda-notebook-lock.yml @@ -5,22 +5,22 @@ # available, unless you explicitly update the lock file. # # Install this environment as "YOURENV" with: -# conda-lock install -n YOURENV conda-science_demo-lock.yml +# conda-lock install -n YOURENV conda-notebook-lock.yml # To update a single package to the latest version compatible with the version constraints in the source: -# conda-lock lock --lockfile conda-science_demo-lock.yml --update PACKAGE +# conda-lock lock --lockfile conda-notebook-lock.yml --update PACKAGE # To re-solve the entire environment, e.g. after changing a version constraint in the source file: -# conda-lock -f tmp-science_demo-lock.yml --lockfile conda-science_demo-lock.yml +# conda-lock -f tmp-notebook-lock.yml --lockfile conda-notebook-lock.yml version: 1 metadata: content_hash: - linux-64: 0cf64d12c1bbc2eb49934c8b6c9369766973a78aef3b7d1c996e2e87d1e0edcd + linux-64: e1798a4139fe66cfe17f98c783f2bcdeae0dff62bb5dd0ddee4c93c572bc9971 channels: - url: conda-forge used_env_vars: [] platforms: - linux-64 sources: - - tmp-science_demo-lock.yml + - tmp-notebook-lock.yml package: - name: _libgcc_mutex version: '0.1' @@ -79,26 +79,40 @@ package: category: main optional: false - name: aiobotocore - version: 2.13.0 + version: 2.13.2 manager: conda platform: linux-64 dependencies: aiohttp: '>=3.9.2,<4.0.0' aioitertools: '>=0.5.1,<1.0.0' - botocore: '>=1.34.70,<1.34.107' + botocore: '>=1.34.70,<1.34.132' python: '>=3.8' wrapt: '>=1.10.10,<2.0.0' - url: https://conda.anaconda.org/conda-forge/noarch/aiobotocore-2.13.0-pyhd8ed1ab_0.conda + url: https://conda.anaconda.org/conda-forge/noarch/aiobotocore-2.13.2-pyhd8ed1ab_0.conda hash: - md5: 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diff --git a/tractor/packages-notebook.txt b/tractor/packages-notebook.txt new file mode 100644 index 0000000..e1f0f97 --- /dev/null +++ b/tractor/packages-notebook.txt @@ -0,0 +1,489 @@ +# List of packages and versions installed in the environment +# Generated by parsing tractor/conda-notebook-lock.yml, please use that as source of truth +GitPython==3.1.43 +SQLAlchemy==2.0.32 +_libgcc_mutex==0.1 +_openmp_mutex==4.5 +acstools==3.7.1 +affine==2.4.0 +aiobotocore==2.13.2 +aiohappyeyeballs==2.3.5 +aiohttp==3.10.3 +aioitertools==0.11.0 +aiosignal==1.3.1 +alsa-lib==1.2.12 +anyio==4.4.0 +aom==3.9.1 +argon2-cffi==23.1.0 +argon2-cffi-bindings==21.2.0 +arrow==1.3.0 +asciitree==0.3.3 +asdf==3.4.0 +asdf-astropy==0.6.1 +asdf-coordinates-schemas==0.3.0 +asdf-standard==1.1.1 +asdf-transform-schemas==0.5.0 +asdf-wcs-schemas==0.4.0 +astropy==6.1.2 +astropy-healpix==1.0.3 +astropy-iers-data==0.2024.8.5.0.32.23 +astroquery==0.4.7 +astroscrappy==1.2.0 +asttokens==2.4.1 +async-lru==2.0.4 +attrs==24.2.0 +autograd==1.6.2 +aws-c-auth==0.7.25 +aws-c-cal==0.7.2 +aws-c-common==0.9.25 +aws-c-compression==0.2.18 +aws-c-event-stream==0.4.2 +aws-c-http==0.8.7 +aws-c-io==0.14.18 +aws-c-mqtt==0.10.4 +aws-c-s3==0.6.4 +aws-c-sdkutils==0.1.19 +aws-checksums==0.1.18 +aws-crt-cpp==0.27.5 +aws-sdk-cpp==1.11.379 +azure-core-cpp==1.13.0 +azure-identity-cpp==1.8.0 +azure-storage-blobs-cpp==12.12.0 +azure-storage-common-cpp==12.7.0 +azure-storage-files-datalake-cpp==12.11.0 +babel==2.14.0 +backports==1.0 +backports.tarfile==1.0.0 +beautifulsoup4==4.12.3 +bleach==6.1.0 +blosc==1.21.6 +bokeh==3.5.1 +boto3==1.34.131 +boto3-stubs==1.34.159 +botocore==1.34.131 +botocore-stubs==1.34.158 +bottleneck==1.4.0 +brotli==1.1.0 +brotli-bin==1.1.0 +brotli-python==1.1.0 +brunsli==0.1 +bzip2==1.0.8 +c-ares==1.32.3 +c-blosc2==2.15.1 +ca-certificates==2024.7.4 +cached-property==1.5.2 +cached_property==1.5.2 +cairo==1.18.0 +ccdproc==2.4.2 +ceres-solver==1.14.0 +certifi==2024.7.4 +cffi==1.17.0 +cfitsio==4.4.1 +charls==2.4.2 +charset-normalizer==3.3.2 +click==8.1.7 +click-plugins==1.1.1 +cligj==0.7.2 +cloudpickle==3.0.0 +colorama==0.4.6 +comm==0.2.2 +contourpy==1.2.1 +cryptography==43.0.0 +cycler==0.12.1 +cython==3.0.11 +cytoolz==0.12.3 +dask==2024.8.0 +dask-core==2024.8.0 +dask-expr==1.1.10 +dask-labextension==7.0.0 +dav1d==1.2.1 +dbus==1.13.6 +debugpy==1.8.5 +decorator==5.1.1 +defusedxml==0.7.1 +distributed==2024.8.0 +double-conversion==3.3.0 +eigen==3.4.0 +entrypoints==0.4 +exceptiongroup==1.2.2 +executing==2.0.1 +expat==2.6.2 +fasteners==0.17.3 +fbpca==1.0 +firefly-client==3.0.2 +fmt==11.0.2 +font-ttf-dejavu-sans-mono==2.37 +font-ttf-inconsolata==3.000 +font-ttf-source-code-pro==2.038 +font-ttf-ubuntu==0.83 +fontconfig==2.14.2 +fonts-conda-ecosystem==1 +fonts-conda-forge==1 +fonttools==4.53.1 +fqdn==1.5.1 +freetype==2.12.1 +freexl==2.0.0 +frozenlist==1.4.1 +fsspec==2024.6.1 +future==1.0.0 +geos==3.12.2 +geotiff==1.7.3 +gflags==2.2.2 +ghostscript==10.03.1 +giflib==5.2.2 +gitdb==4.0.11 +glog==0.7.1 +gmp==6.3.0 +graphite2==1.3.13 +greenlet==3.0.3 +gwcs==0.21.0 +h11==0.14.0 +h2==4.1.0 +harfbuzz==9.0.0 +hdf4==4.2.15 +hdf5==1.14.3 +hpack==4.0.0 +hpgeom==1.3.0 +html5lib==1.1 +httpcore==1.0.5 +httpx==0.27.0 +hyperframe==6.0.1 +icu==75.1 +idna==3.7 +imagecodecs==2024.6.1 +imageio==2.34.2 +importlib-metadata==8.2.0 +importlib_metadata==8.2.0 +importlib_resources==6.4.0 +ipykernel==6.29.5 +ipython==8.26.0 +isoduration==20.11.0 +jaraco.classes==3.4.0 +jaraco.context==5.3.0 +jaraco.functools==4.0.0 +jedi==0.19.1 +jeepney==0.8.0 +jinja2==3.1.4 +jmespath==1.0.1 +joblib==1.4.2 +json-c==0.17 +json5==0.9.25 +jsonpointer==3.0.0 +jsonschema==4.23.0 +jsonschema-specifications==2023.12.1 +jsonschema-with-format-nongpl==4.23.0 +jupyter-lsp==2.2.5 +jupyter-server-mathjax==0.2.6 +jupyter-server-proxy==4.3.0 +jupyter_client==8.6.2 +jupyter_core==5.7.2 +jupyter_events==0.10.0 +jupyter_server==2.14.2 +jupyter_server_terminals==0.5.3 +jupyterlab==4.2.4 +jupyterlab-bxplorer==0.1.24 +jupyterlab-git==0.50.1 +jupyterlab-myst==2.4.2 +jupyterlab-s3-browser==0.12.0 +jupyterlab_pygments==0.3.0 +jupyterlab_server==2.27.3 +jupytext==1.16.4 +jxrlib==1.1 +kealib==1.5.3 +keyring==25.3.0 +keyutils==1.6.1 +kiwisolver==1.4.5 +krb5==1.21.3 +lazy_loader==0.4 +lcms2==2.16 +ld_impl_linux-64==2.40 +lerc==4.0.0 +libabseil==20240116.2 +libaec==1.1.3 +libarchive==3.7.4 +libarrow==17.0.0 +libarrow-acero==17.0.0 +libarrow-dataset==17.0.0 +libarrow-substrait==17.0.0 +libavif16==1.1.1 +libblas==3.9.0 +libbrotlicommon==1.1.0 +libbrotlidec==1.1.0 +libbrotlienc==1.1.0 +libcblas==3.9.0 +libclang-cpp18.1==18.1.8 +libclang13==18.1.8 +libcrc32c==1.1.2 +libcups==2.3.3 +libcurl==8.9.1 +libdeflate==1.21 +libdrm==2.4.122 +libedit==3.1.20191231 +libev==4.33 +libevent==2.1.12 +libexpat==2.6.2 +libffi==3.4.2 +libgcc-ng==14.1.0 +libgdal==3.9.1 +libgdal-core==3.9.1 +libgdal-fits==3.9.1 +libgdal-grib==3.9.1 +libgdal-hdf4==3.9.1 +libgdal-hdf5==3.9.1 +libgdal-jp2openjpeg==3.9.1 +libgdal-kea==3.9.1 +libgdal-netcdf==3.9.1 +libgdal-pdf==3.9.1 +libgdal-pg==3.9.1 +libgdal-postgisraster==3.9.1 +libgdal-tiledb==3.9.1 +libgdal-xls==3.9.1 +libgfortran-ng==14.1.0 +libgfortran5==14.1.0 +libglib==2.80.3 +libgomp==14.1.0 +libgoogle-cloud==2.28.0 +libgoogle-cloud-storage==2.28.0 +libgrpc==1.62.2 +libhwy==1.1.0 +libiconv==1.17 +libjpeg-turbo==3.0.0 +libjxl==0.10.3 +libkml==1.3.0 +liblapack==3.9.0 +libllvm18==18.1.8 +libnetcdf==4.9.2 +libnghttp2==1.58.0 +libnsl==2.0.1 +libopenblas==0.3.27 +libparquet==17.0.0 +libpciaccess==0.18 +libpng==1.6.43 +libpq==16.4 +libprotobuf==4.25.3 +libre2-11==2023.09.01 +librttopo==1.1.0 +libsodium==1.0.18 +libspatialite==5.1.0 +libsqlite==3.46.0 +libssh2==1.11.0 +libstdcxx-ng==14.1.0 +libthrift==0.19.0 +libtiff==4.6.0 +libutf8proc==2.8.0 +libuuid==2.38.1 +libwebp-base==1.4.0 +libxcb==1.16 +libxcrypt==4.4.36 +libxkbcommon==1.7.0 +libxml2==2.12.7 +libxslt==1.1.39 +libzip==1.10.1 +libzlib==1.3.1 +libzopfli==1.0.3 +lightkurve==2.4.2 +locket==1.0.0 +lz4==4.3.3 +lz4-c==1.9.4 +lzo==2.10 +markdown-it-py==3.0.0 +markupsafe==2.1.5 +matplotlib==3.9.1 +matplotlib-base==3.9.1 +matplotlib-inline==0.1.7 +mdit-py-plugins==0.4.1 +mdurl==0.1.2 +memoization==0.4.0 +metis==5.1.0 +minizip==4.0.7 +mistune==3.0.2 +more-itertools==10.4.0 +mpfr==4.2.1 +mpl_animators==1.1.1 +mpld3==0.5.10 +msgpack-python==1.0.8 +multidict==6.0.5 +munkres==1.1.4 +mypy-boto3-s3==1.34.158 +mysql-common==8.3.0 +mysql-libs==8.3.0 +nbclient==0.10.0 +nbconvert==7.16.4 +nbconvert-core==7.16.4 +nbdime==4.0.1 +nbformat==5.10.4 +ncurses==6.5 +ndcube==2.2.2 +nest-asyncio==1.6.0 +netpbm==10.73.43 +networkx==3.3 +notebook==7.2.1 +notebook-shim==0.2.4 +nspr==4.35 +nss==3.103 +numcodecs==0.12.1 +numpy==1.26.4 +oktopus==0.1.2 +openjpeg==2.5.2 +openssl==3.3.1 +orc==2.0.1 +overrides==7.7.0 +packaging==24.1 +pandas==2.2.2 +pandocfilters==1.5.0 +parso==0.8.4 +partd==1.4.2 +patsy==0.5.6 +pcre2==10.44 +perl==5.32.1 +pexpect==4.9.0 +pgplot==5.2.2 +photutils==1.13.0 +pickleshare==0.7.5 +pillow==10.4.0 +pip==24.2 +pixman==0.43.2 +pkg-config==0.29.2 +pkgutil-resolve-name==1.3.10 +platformdirs==4.2.2 +poppler==24.07.0 +poppler-data==0.4.12 +postgresql==16.4 +proj==9.4.1 +prometheus_client==0.20.0 +prompt-toolkit==3.0.47 +psutil==6.0.0 +pthread-stubs==0.4 +ptyprocess==0.7.0 +pure_eval==0.2.3 +pyarrow==17.0.0 +pyarrow-core==17.0.0 +pyarrow-hotfix==0.6 +pycparser==2.22 +pyerfa==2.0.1.4 +pygments==2.18.0 +pyparsing==3.1.2 +pyside6==6.7.2 +pysocks==1.7.1 +python==3.11.9 +python-dateutil==2.9.0 +python-fastjsonschema==2.20.0 +python-json-logger==2.0.7 +python-tzdata==2024.1 +python_abi==3.11 +pytz==2024.1 +pyvo==1.5.2 +pywavelets==1.6.0 +pyyaml==6.0.2 +pyzmq==26.1.0 +qhull==2020.2 +qt6-main==6.7.2 +rasterio==1.3.10 +rav1e==0.6.6 +re2==2023.09.01 +readline==8.2 +referencing==0.35.1 +regions==0.9 +reproject==0.14.0 +requests==2.32.3 +rfc3339-validator==0.1.4 +rfc3986-validator==0.1.1 +rpds-py==0.20.0 +s2n==1.5.0 +s3fs==2024.6.1 +s3transfer==0.10.2 +scikit-image==0.24.0 +scikit-learn==1.5.1 +scipy==1.14.0 +seaborn==0.13.2 +seaborn-base==0.13.2 +secretstorage==3.3.3 +semantic_version==2.10.0 +send2trash==1.8.3 +setuptools==72.1.0 +shapely==2.0.5 +simpervisor==1.0.0 +singleton==decorator-1.0.0 +six==1.16.0 +smmap==5.0.1 +snappy==1.2.1 +sniffio==1.3.1 +snuggs==1.4.7 +sortedcontainers==2.4.0 +soupsieve==2.5 +spdlog==1.14.1 +specreduce==1.4.1 +specutils==1.16.0 +sqlite==3.46.0 +stack_data==0.6.2 +statsmodels==0.14.2 +suitesparse==5.10.1 +svt-av1==2.1.2 +swig==4.2.1 +tbb==2020.2 +tblib==3.0.0 +terminado==0.18.1 +threadpoolctl==3.5.0 +tifffile==2024.8.10 +tiledb==2.25.0 +tinycss2==1.3.0 +tk==8.6.13 +tomli==2.0.1 +toolz==0.12.1 +tornado==6.4.1 +tqdm==4.66.5 +traitlets==5.14.3 +types-awscrt==0.21.2 +types-python-dateutil==2.9.0.20240316 +types-s3transfer==0.10.1 +typing-extensions==4.12.2 +typing_extensions==4.12.2 +typing_utils==0.1.0 +tzcode==2024a +tzdata==2024a +tzlocal==5.2 +uncertainties==3.2.2 +uri-template==1.3.0 +uriparser==0.9.8 +urllib3==2.2.2 +wayland==1.23.0 +wcslib==8.2.2 +wcwidth==0.2.13 +webcolors==24.8.0 +webencodings==0.5.1 +websocket-client==1.8.0 +werkzeug==3.0.3 +wheel==0.44.0 +wrapt==1.16.0 +xcb-util==0.4.1 +xcb-util-cursor==0.1.4 +xcb-util-image==0.4.0 +xcb-util-keysyms==0.4.1 +xcb-util-renderutil==0.3.10 +xcb-util-wm==0.4.2 +xerces-c==3.2.5 +xkeyboard-config==2.42 +xorg-kbproto==1.0.7 +xorg-libice==1.1.1 +xorg-libsm==1.2.4 +xorg-libx11==1.8.9 +xorg-libxau==1.0.11 +xorg-libxdmcp==1.1.3 +xorg-libxext==1.3.4 +xorg-libxrender==0.9.11 +xorg-renderproto==0.11.1 +xorg-xextproto==7.3.0 +xorg-xproto==7.0.31 +xyzservices==2024.6.0 +xz==5.2.6 +yaml==0.2.5 +yarl==1.9.4 +zarr==2.18.2 +zeromq==4.3.5 +zfp==1.0.1 +zict==3.0.0 +zipp==3.19.2 +zlib==1.3.1 +zlib-ng==2.2.1 +zstandard==0.23.0 +zstd==1.5.6 diff --git a/tractor/packages.txt b/tractor/packages.txt deleted file mode 100644 index 6e50201..0000000 --- a/tractor/packages.txt +++ /dev/null @@ -1,410 +0,0 @@ -# List of packages and versions installed in the environment -# Generated by parsing tractor/conda-science_demo-lock.yml, please use that as source of truth -_libgcc_mutex==0.1 -_openmp_mutex==4.5 -acstools==3.7.1 -affine==2.4.0 -aiobotocore==2.13.0 -aiohttp==3.9.5 -aioitertools==0.11.0 -aiosignal==1.3.1 -alsa-lib==1.2.11 -aom==3.9.0 -asciitree==0.3.3 -asdf==3.2.0 -asdf-astropy==0.6.1 -asdf-coordinates-schemas==0.3.0 -asdf-standard==1.1.1 -asdf-transform-schemas==0.5.0 -asdf-wcs-schemas==0.4.0 -astropy==6.1.0 -astropy-healpix==1.0.3 -astropy-iers-data==0.2024.5.20.0.29.40 -astroquery==0.4.7 -asttokens==2.4.1 -attr==2.5.1 -attrs==23.2.0 -autograd==1.6.2 -aws-c-auth==0.7.16 -aws-c-cal==0.6.10 -aws-c-common==0.9.13 -aws-c-compression==0.2.18 -aws-c-event-stream==0.4.2 -aws-c-http==0.8.1 -aws-c-io==0.14.5 -aws-c-mqtt==0.10.2 -aws-c-s3==0.5.2 -aws-c-sdkutils==0.1.15 -aws-checksums==0.1.18 -aws-crt-cpp==0.26.2 -aws-sdk-cpp==1.11.267 -azure-core-cpp==1.10.3 -azure-storage-blobs-cpp==12.10.0 -azure-storage-common-cpp==12.5.0 -backports==1.0 -backports.tarfile==1.0.0 -beautifulsoup4==4.12.3 -blosc==1.21.5 -bokeh==3.4.1 -boto3==1.34.106 -botocore==1.34.106 -bottleneck==1.3.8 -brotli==1.1.0 -brotli-bin==1.1.0 -brotli-python==1.1.0 -brunsli==0.1 -bzip2==1.0.8 -c-ares==1.28.1 -c-blosc2==2.14.3 -ca-certificates==2024.2.2 -cairo==1.18.0 -ceres-solver==2.1.0 -certifi==2024.2.2 -cffi==1.16.0 -cfitsio==4.4.0 -charls==2.4.2 -charset-normalizer==3.3.2 -click==8.1.7 -click-plugins==1.1.1 -cligj==0.7.2 -cloudpickle==3.0.0 -colorama==0.4.6 -comm==0.2.2 -contourpy==1.2.1 -cryptography==42.0.7 -cycler==0.12.1 -cython==3.0.10 -cytoolz==0.12.3 -dask==2024.5.1 -dask-core==2024.5.1 -dask-expr==1.1.1 -dav1d==1.2.1 -dbus==1.13.6 -debugpy==1.8.1 -decorator==5.1.1 -distributed==2024.5.1 -eigen==3.4.0 -exceptiongroup==1.2.0 -executing==2.0.1 -expat==2.6.2 -fasteners==0.17.3 -fbpca==1.0 -firefly-client==2.9.0 -font-ttf-dejavu-sans-mono==2.37 -font-ttf-inconsolata==3.000 -font-ttf-source-code-pro==2.038 -font-ttf-ubuntu==0.83 -fontconfig==2.14.2 -fonts-conda-ecosystem==1 -fonts-conda-forge==1 -fonttools==4.51.0 -freetype==2.12.1 -freexl==2.0.0 -frozenlist==1.4.1 -fsspec==2024.5.0 -future==1.0.0 -geos==3.12.1 -geotiff==1.7.1 -gettext==0.22.5 -gettext-tools==0.22.5 -gflags==2.2.2 -ghostscript==10.03.0 -giflib==5.2.2 -glib==2.80.2 -glib-tools==2.80.2 -glog==0.6.0 -gmp==6.3.0 -graphite2==1.3.13 -gst-plugins-base==1.24.3 -gstreamer==1.24.3 -gwcs==0.21.0 -harfbuzz==8.5.0 -hdf4==4.2.15 -hdf5==1.14.3 -hpgeom==1.3.0 -html5lib==1.1 -icu==73.2 -idna==3.7 -imagecodecs==2024.1.1 -imageio==2.34.1 -importlib-metadata==7.1.0 -importlib_metadata==7.1.0 -importlib_resources==6.4.0 -ipykernel==6.29.3 -ipython==8.24.0 -jaraco.classes==3.4.0 -jaraco.context==5.3.0 -jaraco.functools==4.0.0 -jedi==0.19.1 -jeepney==0.8.0 -jinja2==3.1.4 -jmespath==1.0.1 -joblib==1.4.2 -json-c==0.17 -jupyter_client==8.6.1 -jupyter_core==5.7.2 -jxrlib==1.1 -kealib==1.5.3 -keyring==25.2.1 -keyutils==1.6.1 -kiwisolver==1.4.5 -krb5==1.21.2 -lame==3.100 -lazy_loader==0.4 -lcms2==2.16 -ld_impl_linux-64==2.40 -lerc==4.0.0 -libabseil==20230802.1 -libaec==1.1.3 -libarchive==3.7.2 -libarrow==15.0.0 -libarrow-acero==15.0.0 -libarrow-dataset==15.0.0 -libarrow-flight==15.0.0 -libarrow-flight-sql==15.0.0 -libarrow-gandiva==15.0.0 -libarrow-substrait==15.0.0 -libasprintf==0.22.5 -libasprintf-devel==0.22.5 -libavif16==1.0.4 -libblas==3.9.0 -libboost-headers==1.85.0 -libbrotlicommon==1.1.0 -libbrotlidec==1.1.0 -libbrotlienc==1.1.0 -libcap==2.69 -libcblas==3.9.0 -libclang-cpp15==15.0.7 -libclang13==18.1.5 -libcrc32c==1.1.2 -libcups==2.3.3 -libcurl==8.7.1 -libdeflate==1.19 -libedit==3.1.20191231 -libev==4.33 -libevent==2.1.12 -libexpat==2.6.2 -libffi==3.4.2 -libflac==1.4.3 -libgcc-ng==13.2.0 -libgcrypt==1.10.3 -libgdal==3.8.4 -libgettextpo==0.22.5 -libgettextpo-devel==0.22.5 -libgfortran-ng==13.2.0 -libgfortran5==13.2.0 -libglib==2.80.2 -libgomp==13.2.0 -libgoogle-cloud==2.17.0 -libgoogle-cloud-storage==2.17.0 -libgpg-error==1.49 -libgrpc==1.60.1 -libhwloc==2.10.0 -libhwy==1.1.0 -libiconv==1.17 -libjpeg-turbo==3.0.0 -libjxl==0.10.2 -libkml==1.3.0 -liblapack==3.9.0 -libllvm15==15.0.7 -libllvm16==16.0.6 -libllvm18==18.1.5 -libnetcdf==4.9.2 -libnghttp2==1.58.0 -libnl==3.9.0 -libnsl==2.0.1 -libogg==1.3.4 -libopenblas==0.3.27 -libopus==1.3.1 -libparquet==15.0.0 -libpng==1.6.43 -libpq==16.3 -libprotobuf==4.25.1 -libre2-11==2023.09.01 -librttopo==1.1.0 -libsndfile==1.2.2 -libsodium==1.0.18 -libspatialite==5.1.0 -libsqlite==3.45.3 -libssh2==1.11.0 -libstdcxx-ng==13.2.0 -libsystemd0==255 -libthrift==0.19.0 -libtiff==4.6.0 -libutf8proc==2.8.0 -libuuid==2.38.1 -libvorbis==1.3.7 -libwebp-base==1.4.0 -libxcb==1.15 -libxcrypt==4.4.36 -libxkbcommon==1.7.0 -libxml2==2.12.7 -libzip==1.10.1 -libzlib==1.2.13 -libzopfli==1.0.3 -lightkurve==2.4.2 -locket==1.0.0 -lz4==4.3.3 -lz4-c==1.9.4 -lzo==2.10 -markupsafe==2.1.5 -matplotlib==3.8.4 -matplotlib-base==3.8.4 -matplotlib-inline==0.1.7 -memoization==0.4.0 -metis==5.1.0 -minizip==4.0.5 -more-itertools==10.2.0 -mpfr==4.2.1 -mpg123==1.32.6 -mpld3==0.5.10 -msgpack-python==1.0.8 -multidict==6.0.5 -munkres==1.1.4 -mysql-common==8.3.0 -mysql-libs==8.3.0 -ncurses==6.5 -nest-asyncio==1.6.0 -netpbm==10.73.43 -networkx==3.3 -nspr==4.35 -nss==3.100 -numcodecs==0.12.1 -numpy==1.26.4 -oktopus==0.1.2 -openjpeg==2.5.2 -openssl==3.3.0 -orc==1.9.2 -packaging==24.0 -pandas==2.2.2 -parso==0.8.4 -partd==1.4.2 -patsy==0.5.6 -pcre2==10.43 -perl==5.32.1 -pexpect==4.9.0 -pgplot==5.2.2 -photutils==1.12.0 -pickleshare==0.7.5 -pillow==10.3.0 -pip==24.0 -pixman==0.43.2 -pkg-config==0.29.2 -platformdirs==4.2.2 -ply==3.11 -poppler==24.03.0 -poppler-data==0.4.12 -postgresql==16.3 -proj==9.3.1 -prompt-toolkit==3.0.42 -psutil==5.9.8 -pthread-stubs==0.4 -ptyprocess==0.7.0 -pulseaudio-client==17.0 -pure_eval==0.2.2 -pyarrow==15.0.0 -pyarrow-hotfix==0.6 -pycparser==2.22 -pyerfa==2.0.1.4 -pygments==2.18.0 -pyparsing==3.1.2 -pyqt==5.15.9 -pyqt5-sip==12.12.2 -pysocks==1.7.1 -python==3.11.9 -python-dateutil==2.9.0 -python-tzdata==2024.1 -python_abi==3.11 -pytz==2024.1 -pyvo==1.5.1 -pywavelets==1.4.1 -pyyaml==6.0.1 -pyzmq==26.0.3 -qt-main==5.15.8 -rasterio==1.3.9 -rav1e==0.6.6 -rdma-core==51.0 -re2==2023.09.01 -readline==8.2 -reproject==0.13.1 -requests==2.31.0 -s2n==1.4.5 -s3fs==2024.5.0 -s3transfer==0.10.1 -scikit-image==0.22.0 -scikit-learn==1.4.2 -scipy==1.13.0 -seaborn==0.13.2 -seaborn-base==0.13.2 -secretstorage==3.3.3 -semantic_version==2.10.0 -setuptools==69.5.1 -shapely==2.0.4 -sip==6.7.12 -six==1.16.0 -snappy==1.1.10 -snuggs==1.4.7 -sortedcontainers==2.4.0 -soupsieve==2.5 -sqlite==3.45.3 -stack_data==0.6.2 -statsmodels==0.14.2 -suitesparse==5.10.1 -svt-av1==2.1.0 -swig==4.2.1 -tbb==2021.12.0 -tblib==3.0.0 -threadpoolctl==3.5.0 -tifffile==2024.5.10 -tiledb==2.20.1 -tk==8.6.13 -toml==0.10.2 -tomli==2.0.1 -toolz==0.12.1 -tornado==6.4 -tqdm==4.66.4 -traitlets==5.14.3 -typing_extensions==4.11.0 -tzcode==2024a -tzdata==2024a -ucx==1.15.0 -uncertainties==3.1.7 -uriparser==0.9.8 -urllib3==2.2.1 -wcslib==8.2.2 -wcwidth==0.2.13 -webencodings==0.5.1 -websocket-client==1.8.0 -wheel==0.43.0 -wrapt==1.16.0 -xcb-util==0.4.0 -xcb-util-image==0.4.0 -xcb-util-keysyms==0.4.0 -xcb-util-renderutil==0.3.9 -xcb-util-wm==0.4.1 -xerces-c==3.2.5 -xkeyboard-config==2.41 -xorg-kbproto==1.0.7 -xorg-libice==1.1.1 -xorg-libsm==1.2.4 -xorg-libx11==1.8.9 -xorg-libxau==1.0.11 -xorg-libxdmcp==1.1.3 -xorg-libxext==1.3.4 -xorg-libxrender==0.9.11 -xorg-renderproto==0.11.1 -xorg-xextproto==7.3.0 -xorg-xf86vidmodeproto==2.3.1 -xorg-xproto==7.0.31 -xyzservices==2024.4.0 -xz==5.2.6 -yaml==0.2.5 -yarl==1.9.4 -zarr==2.18.1 -zeromq==4.3.5 -zfp==1.0.1 -zict==3.0.0 -zipp==3.17.0 -zlib==1.2.13 -zlib-ng==2.0.7 -zstd==1.5.6 From 4fe4d39d1e898ef90c52057330403d6c733fbb35 Mon Sep 17 00:00:00 2001 From: Abdu Zoghbi Date: Wed, 14 Aug 2024 12:02:27 -0400 Subject: [PATCH 09/16] update jupyter base image; use default entrypoint; make notebook default kernel; add config scripts --- base-image/Dockerfile | 33 +- base-image/conda-notebook-lock.yml | 437 ++++++------------------ base-image/conda-notebook.yml | 5 +- base-image/overrides.json | 7 + base-image/packages-notebook.txt | 29 +- base-image/postBuild-config.sh | 10 + base-image/scripts/conda-env-install.sh | 6 +- build.py | 13 +- tractor/conda-notebook-lock.yml | 353 ++++++------------- tractor/packages-notebook.txt | 22 +- tractor/postBuild.sh | 2 +- 11 files changed, 276 insertions(+), 641 deletions(-) create mode 100644 base-image/overrides.json create mode 100644 base-image/postBuild-config.sh diff --git a/base-image/Dockerfile b/base-image/Dockerfile index d720520..f7fd5b2 100644 --- a/base-image/Dockerfile +++ b/base-image/Dockerfile @@ -1,4 +1,4 @@ -FROM quay.io/jupyter/base-notebook:2024-05-16 +FROM quay.io/jupyter/base-notebook:2024-08-12 LABEL org.opencontainers.image.source=https://github.com/fornax-navo/fornax-images LABEL org.opencontainers.image.ref.name="Fornax Base Image" @@ -18,28 +18,37 @@ ENV CONDA_ENV=notebook # to ${CONDA_DIR}/etc but not to /etc ENV DASK_ROOT_CONFIG=${CONDA_DIR}/etc -RUN mkdir -p build +# COPY the current content to $HOME/build +RUN mkdir -p $HOME/build/ +COPY --chown=$NB_USER:$NB_USER apt* conda*yml postBuild* $HOME/build/ +COPY --chown=$NB_USER:$NB_USER overrides.json $HOME/build/ + USER root # Install OS packages and then clean up COPY --chown=$NB_USER:$NB_USER scripts /opt/scripts -COPY --chown=$NB_USER:$NB_USER apt.txt* $HOME/build/ # Read apt.txt line by line, and execute apt-get install for each line RUN cd build && bash /opt/scripts/apt-install.sh -# update start.sh (user as ENTRYPOINT) to a simple one -RUN printf "#!/bin/bash -l\n\nexec \"\$@\"" > /usr/local/bin/start.sh \ - && chmod +x /usr/local/bin/start.sh -CMD ["/bin/bash"] - USER $NB_USER # setup conda environments -COPY --chown=$NB_USER:$NB_USER conda-*yml $HOME/build/ RUN mamba install conda-lock \ && cd build && bash /opt/scripts/conda-env-install.sh +# Change dispaly name of the default kernel +RUN mamba run -n $CONDA_ENV python -m ipykernel install --sys-prefix --display-name "$CONDA_ENV" + +# Any other postBuild scripts # +RUN cd $HOME/build \ + ; for script in `ls postBuild*`; do \ + echo "Found script ${script} ..." \ + && chmod +x $script \ + && ./$script \ + ; done +# --------------------------- # + # reset user and location RUN rm -r $HOME/build $HOME/work /tmp/* USER ${NB_USER} @@ -51,21 +60,19 @@ ENV PATH=$CONDA_DIR/envs/$CONDA_ENV/bin:$PATH # Install OS packages and then clean up -ONBUILD RUN mkdir -p build +ONBUILD RUN mkdir -p $HOME/build +ONBUILD COPY --chown=$NB_USER:$NB_USER apt* conda*yml postBuild* $HOME/build/ ONBUILD USER root -ONBUILD COPY --chown=$NB_USER:$NB_USER apt.txt* $HOME/build/ ONBUILD RUN mkdir -p build && cd build && bash /opt/scripts/apt-install.sh ONBUILD USER $NB_USER # ------------------------------------ # # setup conda environments -ONBUILD COPY --chown=$NB_USER:$NB_USER conda-*yml $HOME/build/ ONBUILD RUN cd build && bash /opt/scripts/conda-env-install.sh # ----------------------- # # Any other postBuild scripts # -ONBUILD COPY --chown=$NB_USER:$NB_USER postBuild* $HOME/build/ ONBUILD RUN cd build \ ; for script in `ls postBuild*`; do \ echo "Found script ${script} ..." \ diff --git a/base-image/conda-notebook-lock.yml b/base-image/conda-notebook-lock.yml index 0ec726c..8ea3748 100644 --- a/base-image/conda-notebook-lock.yml +++ b/base-image/conda-notebook-lock.yml @@ -13,7 +13,7 @@ version: 1 metadata: content_hash: - linux-64: cd92786ef71b3463d3394a5cb2069bf886efdaee43be07f34611c36c7ccb659c + linux-64: 5a8e0c19e5cf4bac06ec0ed43466b4142e2d2ae4500cdf62f40a7d34861a513f channels: - url: conda-forge used_env_vars: [] @@ -898,16 +898,16 @@ package: category: main optional: false - name: c-ares - version: 1.32.3 + version: 1.33.0 manager: conda platform: linux-64 dependencies: - __glibc: '>=2.17,<3.0.a0' + __glibc: '>=2.28,<3.0.a0' libgcc-ng: '>=12' - url: https://conda.anaconda.org/conda-forge/linux-64/c-ares-1.32.3-h4bc722e_0.conda + url: https://conda.anaconda.org/conda-forge/linux-64/c-ares-1.33.0-ha66036c_0.conda hash: - md5: 7624e34ee6baebfc80d67bac76cc9d9d - sha256: 3c5a844bb60b0d52d89c3f1bd828c9856417fe33a6102fd8bbd5c13c3351704a + md5: b6927f788e85267beef6cbb292aaebdd + sha256: 3dec5fdb5d1e1758510af0ca163d82ea10109fec8af7d0cd7af38f01068c365b category: main optional: false - name: c-blosc2 @@ -2656,10 +2656,10 @@ package: re2: '' snappy: '>=1.2.1,<1.3.0a0' zstd: '>=1.5.6,<1.6.0a0' - url: https://conda.anaconda.org/conda-forge/linux-64/libarrow-17.0.0-h03aeac6_6_cpu.conda + url: https://conda.anaconda.org/conda-forge/linux-64/libarrow-17.0.0-h03aeac6_7_cpu.conda hash: - md5: c0d3c973e49d549ba10003c3c985f027 - sha256: 0ac58206b1b3bbe8acc897797287c856a10e750275649637b971454b15ecb386 + md5: 25225d90d4fb125c5fbb6f87cc1aa309 + sha256: 745e9f84761da075f0bbe0f0279f0b74aeb1c29811e3eaa9d46f8de1ad897887 category: main optional: false - name: libarrow-acero @@ -2671,10 +2671,10 @@ package: libarrow: 17.0.0 libgcc-ng: '>=12' libstdcxx-ng: '>=12' - url: https://conda.anaconda.org/conda-forge/linux-64/libarrow-acero-17.0.0-he02047a_6_cpu.conda + url: https://conda.anaconda.org/conda-forge/linux-64/libarrow-acero-17.0.0-he02047a_7_cpu.conda hash: - md5: f38e5ee8bb811b2a465598a4bfc41e22 - sha256: fdaafc46c8df76efadb1a74e31ee2465da21eef07f9e36e229ff068cdbd64311 + md5: 64ba31c035986db4e46f98410607498e + sha256: d0f5d0ae8266d83de7b1398c061d5b499c6899742029d80a262f34d3b613012d category: main optional: false - name: libarrow-dataset @@ -2688,10 +2688,10 @@ package: libgcc-ng: '>=12' libparquet: 17.0.0 libstdcxx-ng: '>=12' - url: https://conda.anaconda.org/conda-forge/linux-64/libarrow-dataset-17.0.0-he02047a_6_cpu.conda + url: https://conda.anaconda.org/conda-forge/linux-64/libarrow-dataset-17.0.0-he02047a_7_cpu.conda hash: - md5: 94b84127d9f697b4ac0eba53e58583b6 - sha256: 3b17f7e3ec3ea9df53274b5f3d8a5f6d1aa783e706ac81ccbd6c095a712505d4 + md5: ad26d57360f2019840af562ddf3cb7d2 + sha256: 8ff60afa166498ec5372e851c80a7616c3298c1ac4bcfb386767c62c0acf6a35 category: main optional: false - name: libarrow-substrait @@ -2707,10 +2707,10 @@ package: libgcc-ng: '>=12' libprotobuf: '>=4.25.3,<4.25.4.0a0' libstdcxx-ng: '>=12' - url: https://conda.anaconda.org/conda-forge/linux-64/libarrow-substrait-17.0.0-hc9a23c6_6_cpu.conda + url: https://conda.anaconda.org/conda-forge/linux-64/libarrow-substrait-17.0.0-hc9a23c6_7_cpu.conda hash: - md5: f6fd0b0822f00c963b31ac3fec2b6905 - sha256: 5455c7cad87df0ee6c50dcf7a1dd7fa62ed8677fe042c98f8464007824c685c0 + md5: a0207293ee147d04b46b44d60266d964 + sha256: 88177f0e86b87579e1fbb3f7c8bc9a128d364d342efb971f65df2f514ddb96f3 category: main optional: false - name: libavif16 @@ -2929,10 +2929,10 @@ package: libgdal-postgisraster: 3.9.1.* libgdal-tiledb: 3.9.1.* libgdal-xls: 3.9.1.* - url: https://conda.anaconda.org/conda-forge/linux-64/libgdal-3.9.1-ha770c72_11.conda + url: https://conda.anaconda.org/conda-forge/linux-64/libgdal-3.9.1-ha770c72_13.conda hash: - md5: 80c879dc94effb21cc8989da2a16e95b - sha256: 287c8a14c6273b3f68007bd1a284ead2ed9155ed270ec249b4659880119b54db + md5: 65d475b84d3c1b7a49709aedd9b1233a + sha256: 7b3a50005225391995ebb5f7282871584a4b551a21c6b34a6eee0f748785119b category: main optional: false - name: libgdal-core @@ -2971,10 +2971,10 @@ package: xerces-c: '>=3.2.5,<3.3.0a0' xz: '>=5.2.6,<6.0a0' zstd: '>=1.5.6,<1.6.0a0' - url: https://conda.anaconda.org/conda-forge/linux-64/libgdal-core-3.9.1-hba09cee_11.conda + url: https://conda.anaconda.org/conda-forge/linux-64/libgdal-core-3.9.1-hba09cee_13.conda hash: - md5: b525df1c074f391fbcfbf6de41154382 - sha256: d4be97134610ff3a222874f672db76fdf5c56e4a586546ea53aeaa64a68573df + md5: 938517f031db6905837a822552bd5998 + sha256: 54871769b8e93fc92df1cb5edb58582c847460218ff341ce7c4ead86378641a2 category: main optional: false - name: libgdal-fits @@ -2988,10 +2988,10 @@ package: libgdal-core: '>=3.9' libkml: '>=1.3.0,<1.4.0a0' libstdcxx-ng: '>=12' - url: https://conda.anaconda.org/conda-forge/linux-64/libgdal-fits-3.9.1-hdd6600c_11.conda + url: https://conda.anaconda.org/conda-forge/linux-64/libgdal-fits-3.9.1-hdd6600c_13.conda hash: - md5: 0871f081fde06b0fba25e8a18cf84510 - sha256: ad67985038e987284cd10d901e086d1dd0f955ae7ce1e229fcb4cbf29ef12e3e + md5: 10eef4dbf39a26c5a4bcf8c51027950b + sha256: f261cc355dec8956a084aba14eee581bf667e681909de11c3bb3bfa93cf981e4 category: main optional: false - name: libgdal-grib @@ -3005,10 +3005,10 @@ package: libgdal-core: '>=3.9' libkml: '>=1.3.0,<1.4.0a0' libstdcxx-ng: '>=12' - url: https://conda.anaconda.org/conda-forge/linux-64/libgdal-grib-3.9.1-h5f34788_11.conda + url: https://conda.anaconda.org/conda-forge/linux-64/libgdal-grib-3.9.1-h5f34788_13.conda hash: - md5: 31de2a91c892ad97e162e3d033cf1f4e - sha256: 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1666b39..6bd1553 100644 --- a/base-image/conda-notebook.yml +++ b/base-image/conda-notebook.yml @@ -4,6 +4,8 @@ channels: dependencies: - python==3.11 - jupyterlab + - notebook + - ipykernel - jupytext - dask - dask-labextension @@ -29,6 +31,5 @@ dependencies: - specreduce - jupyterlab-git - jupyterlab-myst - - jupyterlab-bxplorer - - jupyterlab-s3-browser + #- jupyterlab-s3-browser \ No newline at end of file diff --git a/base-image/overrides.json b/base-image/overrides.json new file mode 100644 index 0000000..62aff58 --- /dev/null +++ b/base-image/overrides.json @@ -0,0 +1,7 @@ +{ + "@jupyterlab/docmanager-extension:plugin": { + "defaultViewers": { + "markdown": "Jupytext Notebook" + } + } +} \ No newline at end of file diff --git a/base-image/packages-notebook.txt b/base-image/packages-notebook.txt index 6aff468..2f81af7 100644 --- a/base-image/packages-notebook.txt +++ b/base-image/packages-notebook.txt @@ -1,14 +1,11 @@ # List of packages and versions installed in the environment # Generated by parsing base-image/conda-notebook-lock.yml, please use that as source of truth GitPython==3.1.43 -SQLAlchemy==2.0.32 _libgcc_mutex==0.1 _openmp_mutex==4.5 affine==2.4.0 -aiobotocore==2.13.2 aiohappyeyeballs==2.3.5 aiohttp==3.10.3 -aioitertools==0.11.0 aiosignal==1.3.1 anyio==4.4.0 aom==3.9.1 @@ -55,17 +52,13 @@ beautifulsoup4==4.12.3 bleach==6.1.0 blosc==1.21.6 bokeh==3.5.1 -boto3==1.34.131 -boto3-stubs==1.34.159 -botocore==1.34.131 -botocore-stubs==1.34.158 bottleneck==1.4.0 brotli==1.1.0 brotli-bin==1.1.0 brotli-python==1.1.0 brunsli==0.1 bzip2==1.0.8 -c-ares==1.32.3 +c-ares==1.33.0 c-blosc2==2.15.1 ca-certificates==2024.7.4 cached-property==1.5.2 @@ -122,7 +115,6 @@ gflags==2.2.2 giflib==5.2.2 gitdb==4.0.11 glog==0.7.1 -greenlet==3.0.3 gwcs==0.21.0 h11==0.14.0 h2==4.1.0 @@ -166,10 +158,8 @@ jupyter_events==0.10.0 jupyter_server==2.14.2 jupyter_server_terminals==0.5.3 jupyterlab==4.2.4 -jupyterlab-bxplorer==0.1.24 jupyterlab-git==0.50.1 jupyterlab-myst==2.4.2 -jupyterlab-s3-browser==0.12.0 jupyterlab_pygments==0.3.0 jupyterlab_server==2.27.3 jupytext==1.16.4 @@ -247,7 +237,7 @@ libspatialite==5.1.0 libsqlite==3.46.0 libssh2==1.11.0 libstdcxx-ng==14.1.0 -libthrift==0.19.0 +libthrift==0.20.0 libtiff==4.6.0 libutf8proc==2.8.0 libuuid==2.38.1 @@ -274,7 +264,6 @@ mpl_animators==1.1.1 msgpack-python==1.0.8 multidict==6.0.5 munkres==1.1.4 -mypy-boto3-s3==1.34.158 nbclient==0.10.0 nbconvert==7.16.4 nbconvert-core==7.16.4 @@ -309,7 +298,7 @@ pip==24.2 pixman==0.43.2 pkgutil-resolve-name==1.3.10 platformdirs==4.2.2 -poppler==24.07.0 +poppler==24.08.0 poppler-data==0.4.12 postgresql==16.4 proj==9.4.1 @@ -335,7 +324,7 @@ python-tzdata==2024.1 python_abi==3.11 pytz==2024.1 pyvo==1.5.2 -pywavelets==1.6.0 +pywavelets==1.7.0 pyyaml==6.0.2 pyzmq==26.1.0 qhull==2020.2 @@ -351,8 +340,6 @@ rfc3339-validator==0.1.4 rfc3986-validator==0.1.1 rpds-py==0.20.0 s2n==1.5.0 -s3fs==2024.6.1 -s3transfer==0.10.2 scikit-image==0.24.0 scikit-learn==1.5.1 scipy==1.14.0 @@ -364,7 +351,6 @@ send2trash==1.8.3 setuptools==72.1.0 shapely==2.0.5 simpervisor==1.0.0 -singleton==decorator-1.0.0 six==1.16.0 smmap==5.0.1 snappy==1.2.1 @@ -391,15 +377,12 @@ toolz==0.12.1 tornado==6.4.1 tqdm==4.66.5 traitlets==5.14.3 -types-awscrt==0.21.2 types-python-dateutil==2.9.0.20240316 -types-s3transfer==0.10.1 typing-extensions==4.12.2 typing_extensions==4.12.2 typing_utils==0.1.0 tzcode==2024a tzdata==2024a -tzlocal==5.2 uri-template==1.3.0 uriparser==0.9.8 urllib3==2.2.2 @@ -407,9 +390,7 @@ wcwidth==0.2.13 webcolors==24.8.0 webencodings==0.5.1 websocket-client==1.8.0 -werkzeug==3.0.3 wheel==0.44.0 -wrapt==1.16.0 xerces-c==3.2.5 xorg-kbproto==1.0.7 xorg-libice==1.1.1 @@ -430,7 +411,7 @@ zarr==2.18.2 zeromq==4.3.5 zfp==1.0.1 zict==3.0.0 -zipp==3.19.2 +zipp==3.20.0 zlib==1.3.1 zlib-ng==2.2.1 zstandard==0.23.0 diff --git a/base-image/postBuild-config.sh b/base-image/postBuild-config.sh new file mode 100644 index 0000000..25c06a2 --- /dev/null +++ b/base-image/postBuild-config.sh @@ -0,0 +1,10 @@ +#!/bin/bash + +env=notebook + +# jupyter overrides +mkdir -p $CONDA_DIR/envs/$env/share/jupyter/lab/settings/ +mv ~/build/overrides.json $CONDA_DIR/envs/$env/share/jupyter/lab/settings/ + +# disable the annoucement extension +mamba run -n $env jupyter labextension disable "@jupyterlab/apputils-extension:announcements" \ No newline at end of file diff --git a/base-image/scripts/conda-env-install.sh b/base-image/scripts/conda-env-install.sh index 81d0b62..5d02c37 100644 --- a/base-image/scripts/conda-env-install.sh +++ b/base-image/scripts/conda-env-install.sh @@ -16,7 +16,11 @@ for envfile in `ls conda-*.yml | grep -v lock`; do mamba env update -n ${env} -f $ENVFILE elif [[ "$env"=="$CONDA_ENV" ]]; then echo "Defaulting to basic env ..." - mamba update --name $env python=3.11 jupyterlab + mamba create --name $env python=3.11 jupyterlab + fi + if [ "$env" != "notebook" ]; then + mamba install ipykernel -n $env + mamba run -n $env python -m ipykernel install --sys-prefix --name $env fi done diff --git a/build.py b/build.py index 4610c63..ae49641 100755 --- a/build.py +++ b/build.py @@ -56,7 +56,7 @@ def build_images(image, dryrun, build_args, update_lock): # build the image # logging.debug(f'\tBuilding {image}') cmd = [ - 'docker', 'build', '--network=host', '-t', + 'docker', 'build', '--network=host', '--progress=plain', '-t', f'fornax/{image}:latest' ] + extra_args + [f'./{image}'] logging.debug('\t' + (' '.join(cmd))) @@ -95,8 +95,15 @@ def build_images(image, dryrun, build_args, update_lock): if not dryrun: out = subprocess.check_output(cmd) - with open(f'{image}/tmp-{env_name}-lock.yml', 'wb') as fp: - fp.write(out) + lines = [] + include = False + for line in out.decode().split('\n'): + if 'name:' in line: + include = True + if include: + lines.append(line) + with open(f'{image}/tmp-{env_name}-lock.yml', 'w') as fp: + fp.write('\n'.join(lines)) # then call conda-lock on it # conda-lock -f tmp.yml -p linux-64 --lockfile tmp-lock.yml diff --git a/tractor/conda-notebook-lock.yml b/tractor/conda-notebook-lock.yml index 7ad93d4..179bebb 100644 --- a/tractor/conda-notebook-lock.yml +++ b/tractor/conda-notebook-lock.yml @@ -13,7 +13,7 @@ version: 1 metadata: content_hash: - linux-64: e1798a4139fe66cfe17f98c783f2bcdeae0dff62bb5dd0ddee4c93c572bc9971 + linux-64: 63071e67a87c429e28979b845353d4f24b50210d0bc5c0935087e3a517cb7346 channels: - url: conda-forge used_env_vars: [] @@ -1004,16 +1004,16 @@ package: category: main optional: false - name: c-ares - version: 1.32.3 + version: 1.33.0 manager: conda platform: linux-64 dependencies: - __glibc: '>=2.17,<3.0.a0' + __glibc: '>=2.28,<3.0.a0' libgcc-ng: '>=12' - url: https://conda.anaconda.org/conda-forge/linux-64/c-ares-1.32.3-h4bc722e_0.conda + url: https://conda.anaconda.org/conda-forge/linux-64/c-ares-1.33.0-ha66036c_0.conda hash: - md5: 7624e34ee6baebfc80d67bac76cc9d9d - sha256: 3c5a844bb60b0d52d89c3f1bd828c9856417fe33a6102fd8bbd5c13c3351704a + md5: 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https://files.pythonhosted.org/packages/9d/a4/cbf63143ecc169378dae8150a4c8774b35bb1d760996c842024c8a07a5db/mypy_boto3_s3-1.34.158-py3-none-any.whl - hash: - sha256: c01f1b2304ba7718c8561aaa2b6dc70fe438c91964256aa6ddc508d1cc553c66 - category: main - optional: false - name: nbconvert version: 7.16.4 manager: pip @@ -7259,31 +7194,6 @@ package: sha256: 82538e2b52e0834e9c07607e2dea27aceaaf7e8cf2269a4607c67ea9aa625404 category: main optional: false -- name: notebook - version: 7.2.1 - manager: pip - platform: linux-64 - dependencies: - jupyter-server: '>=2.4.0,<3' - jupyterlab-server: '>=2.27.1,<3' - jupyterlab: '>=4.2.0,<4.3' - notebook-shim: '>=0.2,<0.3' - tornado: '>=6.2.0' - url: https://files.pythonhosted.org/packages/32/b4/b0cdaf52c35a3a40633136bee5152d6670acb555c698d23a3458dca65781/notebook-7.2.1-py3-none-any.whl - hash: - sha256: f45489a3995746f2195a137e0773e2130960b51c9ac3ce257dbc2705aab3a6ca - category: main - optional: false -- name: singleton-decorator - version: 1.0.0 - manager: pip - platform: linux-64 - dependencies: {} - url: https://files.pythonhosted.org/packages/33/98/a8b5c919bee1152a9a1afd82014431f8db5882699754de50d1b3aba4d136/singleton-decorator-1.0.0.tar.gz - hash: - sha256: 1a90ad8a8a738be591c9c167fdd677c5d4a43d1bc6b1c128227be1c5e03bee07 - category: main - optional: false - name: smmap version: 5.0.1 manager: pip @@ -7309,56 +7219,3 @@ package: sha256: dfcf23bdeda9b8c9ada7e0b51d6eeceb905654cd8b6f004d633a6b491c2b6ded category: main optional: false -- name: sqlalchemy - version: 2.0.32 - manager: pip - platform: linux-64 - dependencies: - greenlet: '!=0.4.17' - typing-extensions: '>=4.6.0' - url: https://files.pythonhosted.org/packages/ca/af/379f8695ab751acf61868b0098c8d66e2b2ad8b11d9939d5144c82d05bc5/SQLAlchemy-2.0.32-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl - hash: - sha256: 295ff8689544f7ee7e819529633d058bd458c1fd7f7e3eebd0f9268ebc56c2a0 - category: main - optional: false -- name: types-awscrt - version: 0.21.2 - manager: 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- category: main - optional: false -- name: werkzeug - version: 3.0.3 - manager: pip - platform: linux-64 - dependencies: - markupsafe: '>=2.1.1' - url: https://files.pythonhosted.org/packages/9d/6e/e792999e816d19d7fcbfa94c730936750036d65656a76a5a688b57a656c4/werkzeug-3.0.3-py3-none-any.whl - hash: - sha256: fc9645dc43e03e4d630d23143a04a7f947a9a3b5727cd535fdfe155a17cc48c8 - category: main - optional: false diff --git a/tractor/packages-notebook.txt b/tractor/packages-notebook.txt index e1f0f97..0f741b4 100644 --- a/tractor/packages-notebook.txt +++ b/tractor/packages-notebook.txt @@ -1,7 +1,6 @@ # List of packages and versions installed in the environment # Generated by parsing tractor/conda-notebook-lock.yml, please use that as source of truth GitPython==3.1.43 -SQLAlchemy==2.0.32 _libgcc_mutex==0.1 _openmp_mutex==4.5 acstools==3.7.1 @@ -59,16 +58,14 @@ bleach==6.1.0 blosc==1.21.6 bokeh==3.5.1 boto3==1.34.131 -boto3-stubs==1.34.159 botocore==1.34.131 -botocore-stubs==1.34.158 bottleneck==1.4.0 brotli==1.1.0 brotli-bin==1.1.0 brotli-python==1.1.0 brunsli==0.1 bzip2==1.0.8 -c-ares==1.32.3 +c-ares==1.33.0 c-blosc2==2.15.1 ca-certificates==2024.7.4 cached-property==1.5.2 @@ -135,7 +132,6 @@ gitdb==4.0.11 glog==0.7.1 gmp==6.3.0 graphite2==1.3.13 -greenlet==3.0.3 gwcs==0.21.0 h11==0.14.0 h2==4.1.0 @@ -181,10 +177,8 @@ jupyter_events==0.10.0 jupyter_server==2.14.2 jupyter_server_terminals==0.5.3 jupyterlab==4.2.4 -jupyterlab-bxplorer==0.1.24 jupyterlab-git==0.50.1 jupyterlab-myst==2.4.2 -jupyterlab-s3-browser==0.12.0 jupyterlab_pygments==0.3.0 jupyterlab_server==2.27.3 jupytext==1.16.4 @@ -268,7 +262,7 @@ libspatialite==5.1.0 libsqlite==3.46.0 libssh2==1.11.0 libstdcxx-ng==14.1.0 -libthrift==0.19.0 +libthrift==0.20.0 libtiff==4.6.0 libutf8proc==2.8.0 libuuid==2.38.1 @@ -304,7 +298,6 @@ mpld3==0.5.10 msgpack-python==1.0.8 multidict==6.0.5 munkres==1.1.4 -mypy-boto3-s3==1.34.158 mysql-common==8.3.0 mysql-libs==8.3.0 nbclient==0.10.0 @@ -346,7 +339,7 @@ pixman==0.43.2 pkg-config==0.29.2 pkgutil-resolve-name==1.3.10 platformdirs==4.2.2 -poppler==24.07.0 +poppler==24.08.0 poppler-data==0.4.12 postgresql==16.4 proj==9.4.1 @@ -373,7 +366,7 @@ python-tzdata==2024.1 python_abi==3.11 pytz==2024.1 pyvo==1.5.2 -pywavelets==1.6.0 +pywavelets==1.7.0 pyyaml==6.0.2 pyzmq==26.1.0 qhull==2020.2 @@ -403,7 +396,6 @@ send2trash==1.8.3 setuptools==72.1.0 shapely==2.0.5 simpervisor==1.0.0 -singleton==decorator-1.0.0 six==1.16.0 smmap==5.0.1 snappy==1.2.1 @@ -433,15 +425,12 @@ toolz==0.12.1 tornado==6.4.1 tqdm==4.66.5 traitlets==5.14.3 -types-awscrt==0.21.2 types-python-dateutil==2.9.0.20240316 -types-s3transfer==0.10.1 typing-extensions==4.12.2 typing_extensions==4.12.2 typing_utils==0.1.0 tzcode==2024a tzdata==2024a -tzlocal==5.2 uncertainties==3.2.2 uri-template==1.3.0 uriparser==0.9.8 @@ -452,7 +441,6 @@ wcwidth==0.2.13 webcolors==24.8.0 webencodings==0.5.1 websocket-client==1.8.0 -werkzeug==3.0.3 wheel==0.44.0 wrapt==1.16.0 xcb-util==0.4.1 @@ -482,7 +470,7 @@ zarr==2.18.2 zeromq==4.3.5 zfp==1.0.1 zict==3.0.0 -zipp==3.19.2 +zipp==3.20.0 zlib==1.3.1 zlib-ng==2.2.1 zstandard==0.23.0 diff --git a/tractor/postBuild.sh b/tractor/postBuild.sh index 25fc142..433a588 100644 --- a/tractor/postBuild.sh +++ b/tractor/postBuild.sh @@ -1,6 +1,6 @@ #!/bin/bash -pythonenv=science_demo +pythonenv=notebook astrometry_commit=fbca48e tractor_commit=cdb8200 From e5b2565242ce1efb95c45abfb0301bf63b857fc3 Mon Sep 17 00:00:00 2001 From: Abdu Zoghbi Date: Wed, 14 Aug 2024 12:08:17 -0400 Subject: [PATCH 10/16] update image labels --- base-image/Dockerfile | 2 +- tractor/Dockerfile | 4 ++++ 2 files changed, 5 insertions(+), 1 deletion(-) diff --git a/base-image/Dockerfile b/base-image/Dockerfile index f7fd5b2..10db513 100644 --- a/base-image/Dockerfile +++ b/base-image/Dockerfile @@ -2,7 +2,7 @@ FROM quay.io/jupyter/base-notebook:2024-08-12 LABEL org.opencontainers.image.source=https://github.com/fornax-navo/fornax-images LABEL org.opencontainers.image.ref.name="Fornax Base Image" -LABEL org.opencontainers.image.version=0.1 +LABEL org.opencontainers.image.version=0.2 LABEL maintainer="Fornax Project" # clear the jupyter stack from base diff --git a/tractor/Dockerfile b/tractor/Dockerfile index 8e848e3..d4b77e2 100644 --- a/tractor/Dockerfile +++ b/tractor/Dockerfile @@ -2,5 +2,9 @@ # perform certain actions based on the presence of specific # files (such as conda-linux-64.lock, start) in this repo. # Refer to the base-image/Dockerfile for documentation. +LABEL org.opencontainers.image.ref.name="Fornax Tractor Image" +LABEL org.opencontainers.image.version=0.2 +LABEL maintainer="Fornax Project" + ARG IMAGE_TAG=latest FROM fornax/base-image:${IMAGE_TAG} From d5905dc9c07d3a41d262d568637a65d114aa1715 Mon Sep 17 00:00:00 2001 From: Abdu Zoghbi Date: Wed, 14 Aug 2024 12:11:51 -0400 Subject: [PATCH 11/16] fix names in tractor/conda-notebook.yml --- tractor/conda-notebook.yml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/tractor/conda-notebook.yml b/tractor/conda-notebook.yml index aeb6641..f3ce732 100644 --- a/tractor/conda-notebook.yml +++ b/tractor/conda-notebook.yml @@ -1,4 +1,4 @@ -name: science_demo +name: notebook channels: - conda-forge - nodefaults @@ -35,4 +35,4 @@ dependencies: - scikit-image - statsmodels - tqdm -prefix: /opt/conda/envs/science_demo \ No newline at end of file +prefix: /opt/conda/envs/notebook \ No newline at end of file From 34e4a490cd5de25bc73166ad8700fadd211ae129 Mon Sep 17 00:00:00 2001 From: Abdu Zoghbi Date: Wed, 14 Aug 2024 12:21:48 -0400 Subject: [PATCH 12/16] move conda activate to /etc/bash.bashrc --- base-image/Dockerfile | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/base-image/Dockerfile b/base-image/Dockerfile index 10db513..4134eb0 100644 --- a/base-image/Dockerfile +++ b/base-image/Dockerfile @@ -55,7 +55,7 @@ USER ${NB_USER} WORKDIR ${HOME} # Make $CONDA_ENV default -RUN printf "\nif ! [ -z \$CONDA_ENV ]; then\n conda activate \$CONDA_ENV\nfi\n" >> $HOME/.bashrc +RUN printf "\nif ! [ -z \$CONDA_ENV ]; then\n conda activate \$CONDA_ENV\nfi\n" >> /etc/bash.bashrc ENV PATH=$CONDA_DIR/envs/$CONDA_ENV/bin:$PATH From 1dcfeeb62623cfe8714d04108bc76a22f7a02eca Mon Sep 17 00:00:00 2001 From: Abdu Zoghbi Date: Wed, 14 Aug 2024 12:27:27 -0400 Subject: [PATCH 13/16] undo label change as it does not work --- tractor/Dockerfile | 4 ---- 1 file changed, 4 deletions(-) diff --git a/tractor/Dockerfile b/tractor/Dockerfile index d4b77e2..8e848e3 100644 --- a/tractor/Dockerfile +++ b/tractor/Dockerfile @@ -2,9 +2,5 @@ # perform certain actions based on the presence of specific # files (such as conda-linux-64.lock, start) in this repo. # Refer to the base-image/Dockerfile for documentation. -LABEL org.opencontainers.image.ref.name="Fornax Tractor Image" -LABEL org.opencontainers.image.version=0.2 -LABEL maintainer="Fornax Project" - ARG IMAGE_TAG=latest FROM fornax/base-image:${IMAGE_TAG} From ee631f7aa34786adbc261eb71552b7fd83ab7d27 Mon Sep 17 00:00:00 2001 From: Abdu Zoghbi Date: Thu, 15 Aug 2024 15:52:44 -0400 Subject: [PATCH 14/16] changes how the default env is set so it does not rely on ~/.bashrc --- base-image/Dockerfile | 18 ++++++++--- base-image/conda-notebook-lock.yml | 50 +++++++++++++++--------------- base-image/packages-notebook.txt | 2 +- tractor/conda-notebook-lock.yml | 50 +++++++++++++++--------------- tractor/packages-notebook.txt | 2 +- 5 files changed, 65 insertions(+), 57 deletions(-) diff --git a/base-image/Dockerfile b/base-image/Dockerfile index 4134eb0..22fc4e3 100644 --- a/base-image/Dockerfile +++ b/base-image/Dockerfile @@ -25,6 +25,9 @@ COPY --chown=$NB_USER:$NB_USER overrides.json $HOME/build/ USER root +# Make /opt/ user writeable so it can be used by postBuild scripts +RUN fix-permissions /opt/ + # Install OS packages and then clean up COPY --chown=$NB_USER:$NB_USER scripts /opt/scripts # Read apt.txt line by line, and execute apt-get install for each line @@ -49,15 +52,20 @@ RUN cd $HOME/build \ ; done # --------------------------- # +# Make $CONDA_ENV default; do it at the global level +# because ~/.bashrc is not loaded when user space is mounted +USER root +ENV PATH=$CONDA_DIR/envs/$CONDA_ENV/bin:$PATH +RUN cat $HOME/.bashrc >> /etc/bash.bashrc \ + && printf "\nconda activate \$CONDA_ENV\n" >> /etc/bash.bashrc \ + && printf "" > $HOME/.bashrc +USER $NB_USER + + # reset user and location RUN rm -r $HOME/build $HOME/work /tmp/* -USER ${NB_USER} WORKDIR ${HOME} -# Make $CONDA_ENV default -RUN printf "\nif ! [ -z \$CONDA_ENV ]; then\n conda activate \$CONDA_ENV\nfi\n" >> /etc/bash.bashrc -ENV PATH=$CONDA_DIR/envs/$CONDA_ENV/bin:$PATH - # Install OS packages and then clean up ONBUILD RUN mkdir -p $HOME/build diff --git a/base-image/conda-notebook-lock.yml b/base-image/conda-notebook-lock.yml index 8ea3748..7c29dba 100644 --- a/base-image/conda-notebook-lock.yml +++ b/base-image/conda-notebook-lock.yml @@ -13,7 +13,7 @@ version: 1 metadata: content_hash: - linux-64: 5a8e0c19e5cf4bac06ec0ed43466b4142e2d2ae4500cdf62f40a7d34861a513f + linux-64: d092121de70efb995343eed7a5b782f6ccbe59be459a633f189f4e487f4d0524 channels: - url: conda-forge used_env_vars: [] @@ -411,20 +411,20 @@ package: platform: linux-64 dependencies: __glibc: '>=2.17,<3.0.a0' - aws-c-cal: '>=0.7.2,<0.7.3.0a0' + aws-c-cal: '>=0.7.3,<0.7.4.0a0' aws-c-common: '>=0.9.25,<0.9.26.0a0' aws-c-http: '>=0.8.7,<0.8.8.0a0' aws-c-io: '>=0.14.18,<0.14.19.0a0' aws-c-sdkutils: '>=0.1.19,<0.1.20.0a0' libgcc-ng: '>=12' - url: https://conda.anaconda.org/conda-forge/linux-64/aws-c-auth-0.7.25-h8a0f778_4.conda + url: https://conda.anaconda.org/conda-forge/linux-64/aws-c-auth-0.7.25-hff137af_5.conda hash: - md5: aa51e240a99df535e64e3472f54652c9 - sha256: 06f0fd8fdcee90c45d3f711dae3f7439f5895e3ef0c498484a2a67c781eff748 + md5: 1f05e3e75005a8e7cce98322e19cde41 + sha256: 7e927e0da639cb9a873f7cab0b42102488d3a1a74fd8d301653d0a3044a8141a category: main optional: false - name: aws-c-cal - version: 0.7.2 + version: 0.7.3 manager: conda platform: linux-64 dependencies: @@ -432,10 +432,10 @@ package: aws-c-common: '>=0.9.25,<0.9.26.0a0' libgcc-ng: '>=12' openssl: '>=3.3.1,<4.0a0' - url: https://conda.anaconda.org/conda-forge/linux-64/aws-c-cal-0.7.2-h7970872_1.conda + url: https://conda.anaconda.org/conda-forge/linux-64/aws-c-cal-0.7.3-h7970872_0.conda hash: - md5: f7f648ab6e51b66d2ada922498547732 - sha256: 060d9fba6b18781aff862ca84b5b11f4681f6dc364c70856e5ab5d61cf5eb324 + md5: 902105f82c52abed505e1e1917c1c23b + sha256: 8a5a0f661e1a4cc3bf0bf2ba7cd980c5a932c12db70a634de6aab8683e6c07e0 category: main optional: false - name: aws-c-common @@ -488,15 +488,15 @@ package: platform: linux-64 dependencies: __glibc: '>=2.17,<3.0.a0' - aws-c-cal: '>=0.7.2,<0.7.3.0a0' + aws-c-cal: '>=0.7.3,<0.7.4.0a0' aws-c-common: '>=0.9.25,<0.9.26.0a0' aws-c-compression: '>=0.2.18,<0.2.19.0a0' aws-c-io: '>=0.14.18,<0.14.19.0a0' libgcc-ng: '>=12' - url: https://conda.anaconda.org/conda-forge/linux-64/aws-c-http-0.8.7-hc9bb02b_2.conda + url: https://conda.anaconda.org/conda-forge/linux-64/aws-c-http-0.8.7-he2d3600_3.conda hash: - md5: 1fa3da862ddcc9e9b0538fd58273a65e - sha256: 58a5830a4bb878568b231e3215d2eedfd713e1ee9ea58dbc5e54e1793ea017e5 + md5: 3beadf1544937956b66eef343734d71e + sha256: 7e8452ce2e51bd344003e77ffee717dfe71e96031fc4e7d4891b7f8fc26dec45 category: main optional: false - name: aws-c-io @@ -505,14 +505,14 @@ package: platform: linux-64 dependencies: __glibc: '>=2.17,<3.0.a0' - aws-c-cal: '>=0.7.2,<0.7.3.0a0' + aws-c-cal: '>=0.7.3,<0.7.4.0a0' aws-c-common: '>=0.9.25,<0.9.26.0a0' libgcc-ng: '>=12' s2n: '>=1.5.0,<1.5.1.0a0' - url: https://conda.anaconda.org/conda-forge/linux-64/aws-c-io-0.14.18-h3e50d33_2.conda + url: https://conda.anaconda.org/conda-forge/linux-64/aws-c-io-0.14.18-h7d46f39_3.conda hash: - md5: 9b0aca26d579311a918a0f03047fc447 - sha256: 8b94d550344392429931aa69f16c38cfd2dbb49ce1e5d2705cb10c8b735dd0ee + md5: cf970c7fde2c61b82759f3d3c141b0ec + sha256: d0c7c5105a7fd48ad6b5419f20602232ec42fd057b99d005dfdd78ab231bc102 category: main optional: false - name: aws-c-mqtt @@ -538,17 +538,17 @@ package: dependencies: __glibc: '>=2.17,<3.0.a0' aws-c-auth: '>=0.7.25,<0.7.26.0a0' - aws-c-cal: '>=0.7.2,<0.7.3.0a0' + aws-c-cal: '>=0.7.3,<0.7.4.0a0' aws-c-common: '>=0.9.25,<0.9.26.0a0' aws-c-http: '>=0.8.7,<0.8.8.0a0' aws-c-io: '>=0.14.18,<0.14.19.0a0' aws-checksums: '>=0.1.18,<0.1.19.0a0' libgcc-ng: '>=12' openssl: '>=3.3.1,<4.0a0' - url: https://conda.anaconda.org/conda-forge/linux-64/aws-c-s3-0.6.4-hbe604ca_6.conda + url: https://conda.anaconda.org/conda-forge/linux-64/aws-c-s3-0.6.4-h28a8003_7.conda hash: - md5: a57d5bbd0559aed25766420bbd371aa0 - sha256: c184511cf6d733bbdfc80d68b3087d8743c735d7bb40176cef73d9521c8d921d + md5: 5d1ea2ae5ca0de171c81c77e0e7e247c + sha256: 0ddb4ccd1adf6f49ffbfd365acb7687a54ef3bba3437c04bf04390a64bdee51f category: main optional: false - name: aws-c-sdkutils @@ -586,7 +586,7 @@ package: dependencies: __glibc: '>=2.17,<3.0.a0' aws-c-auth: '>=0.7.25,<0.7.26.0a0' - aws-c-cal: '>=0.7.2,<0.7.3.0a0' + aws-c-cal: '>=0.7.3,<0.7.4.0a0' aws-c-common: '>=0.9.25,<0.9.26.0a0' aws-c-event-stream: '>=0.4.2,<0.4.3.0a0' aws-c-http: '>=0.8.7,<0.8.8.0a0' @@ -596,10 +596,10 @@ package: aws-c-sdkutils: '>=0.1.19,<0.1.20.0a0' libgcc-ng: '>=12' libstdcxx-ng: '>=12' - url: https://conda.anaconda.org/conda-forge/linux-64/aws-crt-cpp-0.27.5-hba11562_5.conda + url: https://conda.anaconda.org/conda-forge/linux-64/aws-crt-cpp-0.27.5-heec6497_6.conda hash: - md5: 3b97f88120ba6bc6c53b428954a15895 - sha256: 6c2d72591495d68b17d6f428b32517a9b59b710eafdc8200e627780812886e6f + md5: d99cb216fba6ec1576db0bb5901b956f + sha256: 17ebb0d468354e85986f2e8137c43e9714353238fe039086bda070746455cfd2 category: main optional: false - name: aws-sdk-cpp diff --git a/base-image/packages-notebook.txt b/base-image/packages-notebook.txt index 2f81af7..fc68dbc 100644 --- a/base-image/packages-notebook.txt +++ b/base-image/packages-notebook.txt @@ -28,7 +28,7 @@ asttokens==2.4.1 async-lru==2.0.4 attrs==24.2.0 aws-c-auth==0.7.25 -aws-c-cal==0.7.2 +aws-c-cal==0.7.3 aws-c-common==0.9.25 aws-c-compression==0.2.18 aws-c-event-stream==0.4.2 diff --git a/tractor/conda-notebook-lock.yml b/tractor/conda-notebook-lock.yml index 179bebb..86a211b 100644 --- a/tractor/conda-notebook-lock.yml +++ b/tractor/conda-notebook-lock.yml @@ -13,7 +13,7 @@ version: 1 metadata: content_hash: - linux-64: 63071e67a87c429e28979b845353d4f24b50210d0bc5c0935087e3a517cb7346 + linux-64: af6286c797d86e8fca06e7f159737fe0411556f7e92026307037a84081e62cd9 channels: - url: conda-forge used_env_vars: [] @@ -487,20 +487,20 @@ package: platform: linux-64 dependencies: __glibc: '>=2.17,<3.0.a0' - aws-c-cal: '>=0.7.2,<0.7.3.0a0' + aws-c-cal: '>=0.7.3,<0.7.4.0a0' aws-c-common: '>=0.9.25,<0.9.26.0a0' aws-c-http: '>=0.8.7,<0.8.8.0a0' aws-c-io: '>=0.14.18,<0.14.19.0a0' aws-c-sdkutils: '>=0.1.19,<0.1.20.0a0' libgcc-ng: '>=12' - url: https://conda.anaconda.org/conda-forge/linux-64/aws-c-auth-0.7.25-h8a0f778_4.conda + url: https://conda.anaconda.org/conda-forge/linux-64/aws-c-auth-0.7.25-hff137af_5.conda hash: - md5: aa51e240a99df535e64e3472f54652c9 - sha256: 06f0fd8fdcee90c45d3f711dae3f7439f5895e3ef0c498484a2a67c781eff748 + md5: 1f05e3e75005a8e7cce98322e19cde41 + sha256: 7e927e0da639cb9a873f7cab0b42102488d3a1a74fd8d301653d0a3044a8141a category: main optional: false - name: aws-c-cal - version: 0.7.2 + version: 0.7.3 manager: conda platform: linux-64 dependencies: @@ -508,10 +508,10 @@ package: aws-c-common: '>=0.9.25,<0.9.26.0a0' libgcc-ng: '>=12' openssl: '>=3.3.1,<4.0a0' - url: https://conda.anaconda.org/conda-forge/linux-64/aws-c-cal-0.7.2-h7970872_1.conda + url: https://conda.anaconda.org/conda-forge/linux-64/aws-c-cal-0.7.3-h7970872_0.conda hash: - md5: f7f648ab6e51b66d2ada922498547732 - sha256: 060d9fba6b18781aff862ca84b5b11f4681f6dc364c70856e5ab5d61cf5eb324 + md5: 902105f82c52abed505e1e1917c1c23b + sha256: 8a5a0f661e1a4cc3bf0bf2ba7cd980c5a932c12db70a634de6aab8683e6c07e0 category: main optional: false - name: aws-c-common @@ -564,15 +564,15 @@ package: platform: linux-64 dependencies: __glibc: '>=2.17,<3.0.a0' - aws-c-cal: '>=0.7.2,<0.7.3.0a0' + aws-c-cal: '>=0.7.3,<0.7.4.0a0' aws-c-common: '>=0.9.25,<0.9.26.0a0' aws-c-compression: '>=0.2.18,<0.2.19.0a0' aws-c-io: '>=0.14.18,<0.14.19.0a0' libgcc-ng: '>=12' - url: https://conda.anaconda.org/conda-forge/linux-64/aws-c-http-0.8.7-hc9bb02b_2.conda + url: https://conda.anaconda.org/conda-forge/linux-64/aws-c-http-0.8.7-he2d3600_3.conda hash: - md5: 1fa3da862ddcc9e9b0538fd58273a65e - sha256: 58a5830a4bb878568b231e3215d2eedfd713e1ee9ea58dbc5e54e1793ea017e5 + md5: 3beadf1544937956b66eef343734d71e + sha256: 7e8452ce2e51bd344003e77ffee717dfe71e96031fc4e7d4891b7f8fc26dec45 category: main optional: false - name: aws-c-io @@ -581,14 +581,14 @@ package: platform: linux-64 dependencies: __glibc: '>=2.17,<3.0.a0' - aws-c-cal: '>=0.7.2,<0.7.3.0a0' + aws-c-cal: '>=0.7.3,<0.7.4.0a0' aws-c-common: '>=0.9.25,<0.9.26.0a0' libgcc-ng: '>=12' s2n: '>=1.5.0,<1.5.1.0a0' - url: https://conda.anaconda.org/conda-forge/linux-64/aws-c-io-0.14.18-h3e50d33_2.conda + url: https://conda.anaconda.org/conda-forge/linux-64/aws-c-io-0.14.18-h7d46f39_3.conda hash: - md5: 9b0aca26d579311a918a0f03047fc447 - sha256: 8b94d550344392429931aa69f16c38cfd2dbb49ce1e5d2705cb10c8b735dd0ee + md5: cf970c7fde2c61b82759f3d3c141b0ec + sha256: d0c7c5105a7fd48ad6b5419f20602232ec42fd057b99d005dfdd78ab231bc102 category: main optional: false - name: aws-c-mqtt @@ -614,17 +614,17 @@ package: dependencies: __glibc: '>=2.17,<3.0.a0' aws-c-auth: '>=0.7.25,<0.7.26.0a0' - aws-c-cal: '>=0.7.2,<0.7.3.0a0' + aws-c-cal: '>=0.7.3,<0.7.4.0a0' aws-c-common: '>=0.9.25,<0.9.26.0a0' aws-c-http: '>=0.8.7,<0.8.8.0a0' aws-c-io: '>=0.14.18,<0.14.19.0a0' aws-checksums: '>=0.1.18,<0.1.19.0a0' libgcc-ng: '>=12' openssl: '>=3.3.1,<4.0a0' - url: https://conda.anaconda.org/conda-forge/linux-64/aws-c-s3-0.6.4-hbe604ca_6.conda + url: https://conda.anaconda.org/conda-forge/linux-64/aws-c-s3-0.6.4-h28a8003_7.conda hash: - md5: a57d5bbd0559aed25766420bbd371aa0 - sha256: c184511cf6d733bbdfc80d68b3087d8743c735d7bb40176cef73d9521c8d921d + md5: 5d1ea2ae5ca0de171c81c77e0e7e247c + sha256: 0ddb4ccd1adf6f49ffbfd365acb7687a54ef3bba3437c04bf04390a64bdee51f category: main optional: false - name: aws-c-sdkutils @@ -662,7 +662,7 @@ package: dependencies: __glibc: '>=2.17,<3.0.a0' aws-c-auth: '>=0.7.25,<0.7.26.0a0' - aws-c-cal: '>=0.7.2,<0.7.3.0a0' + aws-c-cal: '>=0.7.3,<0.7.4.0a0' aws-c-common: '>=0.9.25,<0.9.26.0a0' aws-c-event-stream: '>=0.4.2,<0.4.3.0a0' aws-c-http: '>=0.8.7,<0.8.8.0a0' @@ -672,10 +672,10 @@ package: aws-c-sdkutils: '>=0.1.19,<0.1.20.0a0' libgcc-ng: '>=12' libstdcxx-ng: '>=12' - url: https://conda.anaconda.org/conda-forge/linux-64/aws-crt-cpp-0.27.5-hba11562_5.conda + url: https://conda.anaconda.org/conda-forge/linux-64/aws-crt-cpp-0.27.5-heec6497_6.conda hash: - md5: 3b97f88120ba6bc6c53b428954a15895 - sha256: 6c2d72591495d68b17d6f428b32517a9b59b710eafdc8200e627780812886e6f + md5: d99cb216fba6ec1576db0bb5901b956f + sha256: 17ebb0d468354e85986f2e8137c43e9714353238fe039086bda070746455cfd2 category: main optional: false - name: aws-sdk-cpp diff --git a/tractor/packages-notebook.txt b/tractor/packages-notebook.txt index 0f741b4..00ca6a9 100644 --- a/tractor/packages-notebook.txt +++ b/tractor/packages-notebook.txt @@ -33,7 +33,7 @@ async-lru==2.0.4 attrs==24.2.0 autograd==1.6.2 aws-c-auth==0.7.25 -aws-c-cal==0.7.2 +aws-c-cal==0.7.3 aws-c-common==0.9.25 aws-c-compression==0.2.18 aws-c-event-stream==0.4.2 From ece889edcf76528f65d5570699483c0594853047 Mon Sep 17 00:00:00 2001 From: Abdu Zoghbi Date: Fri, 16 Aug 2024 06:15:47 -0400 Subject: [PATCH 15/16] fix new kernel installations --- base-image/Dockerfile | 2 +- base-image/conda-notebook-lock.yml | 18 +++++++++--------- base-image/packages-notebook.txt | 4 ++-- base-image/scripts/conda-env-install.sh | 4 ++-- 4 files changed, 14 insertions(+), 14 deletions(-) diff --git a/base-image/Dockerfile b/base-image/Dockerfile index 22fc4e3..5532da9 100644 --- a/base-image/Dockerfile +++ b/base-image/Dockerfile @@ -29,7 +29,7 @@ USER root RUN fix-permissions /opt/ # Install OS packages and then clean up -COPY --chown=$NB_USER:$NB_USER scripts /opt/scripts +COPY --chown=$NB_USER:$NB_USER scripts/*.sh /opt/scripts/ # Read apt.txt line by line, and execute apt-get install for each line RUN cd build && bash /opt/scripts/apt-install.sh diff --git a/base-image/conda-notebook-lock.yml b/base-image/conda-notebook-lock.yml index 7c29dba..1d69cb5 100644 --- a/base-image/conda-notebook-lock.yml +++ b/base-image/conda-notebook-lock.yml @@ -13,7 +13,7 @@ version: 1 metadata: content_hash: - linux-64: d092121de70efb995343eed7a5b782f6ccbe59be459a633f189f4e487f4d0524 + linux-64: 46f1324661d875acee5cc3fff3bf3a5bf3b5d8cd58520c76a1572746bfbd0a60 channels: - url: conda-forge used_env_vars: [] @@ -1966,16 +1966,16 @@ package: category: main optional: false - name: importlib_resources - version: 6.4.0 + version: 6.4.2 manager: conda platform: linux-64 dependencies: python: '>=3.8' zipp: '>=3.1.0' - url: https://conda.anaconda.org/conda-forge/noarch/importlib_resources-6.4.0-pyhd8ed1ab_0.conda + url: https://conda.anaconda.org/conda-forge/noarch/importlib_resources-6.4.2-pyhd8ed1ab_0.conda hash: - md5: c5d3907ad8bd7bf557521a1833cf7e6d - sha256: c6ae80c0beaeabb342c5b041f19669992ae6e937dbec56ced766cb035900f9de + md5: ff64113bd700cf0f892ebf4b223e56aa + sha256: 1304c2ff6c1879628c13a0713fd070192910d1a250a2366e91208ceda1b6d2bf category: main optional: false - name: ipykernel @@ -3840,7 +3840,7 @@ package: category: main optional: false - name: matplotlib-base - version: 3.9.1 + version: 3.9.2 manager: conda platform: linux-64 dependencies: @@ -3862,10 +3862,10 @@ package: python_abi: 3.11.* qhull: '>=2020.2,<2020.3.0a0' tk: '>=8.6.13,<8.7.0a0' - url: https://conda.anaconda.org/conda-forge/linux-64/matplotlib-base-3.9.1-py311h74b4f7c_2.conda + url: https://conda.anaconda.org/conda-forge/linux-64/matplotlib-base-3.9.2-py311h74b4f7c_0.conda hash: - md5: e4a26e6bd32d4af38492ba68caaa16d1 - sha256: d35b8a68d6d803d4977ccf3354abe14a0d1037c06f7519701c0c3247265d489a + md5: de8e36c9792f14eed7e11e672f03fbf0 + sha256: a914061120a15618dacefc7268fca6c2e77631c801f58a5771f40f77ed200943 category: main optional: false - name: matplotlib-inline diff --git a/base-image/packages-notebook.txt b/base-image/packages-notebook.txt index fc68dbc..1982002 100644 --- a/base-image/packages-notebook.txt +++ b/base-image/packages-notebook.txt @@ -131,7 +131,7 @@ imagecodecs==2024.6.1 imageio==2.34.2 importlib-metadata==8.2.0 importlib_metadata==8.2.0 -importlib_resources==6.4.0 +importlib_resources==6.4.2 ipykernel==6.29.5 ipython==8.26.0 isoduration==20.11.0 @@ -253,7 +253,7 @@ lz4-c==1.9.4 lzo==2.10 markdown-it-py==3.0.0 markupsafe==2.1.5 -matplotlib-base==3.9.1 +matplotlib-base==3.9.2 matplotlib-inline==0.1.7 mdit-py-plugins==0.4.1 mdurl==0.1.2 diff --git a/base-image/scripts/conda-env-install.sh b/base-image/scripts/conda-env-install.sh index 5d02c37..b565625 100644 --- a/base-image/scripts/conda-env-install.sh +++ b/base-image/scripts/conda-env-install.sh @@ -19,8 +19,8 @@ for envfile in `ls conda-*.yml | grep -v lock`; do mamba create --name $env python=3.11 jupyterlab fi if [ "$env" != "notebook" ]; then - mamba install ipykernel -n $env - mamba run -n $env python -m ipykernel install --sys-prefix --name $env + mamba install -n $env ipykernel + mamba run -n $env python -m ipykernel install --name $env --prefix $CONDA_DIR/envs/notebook fi done From 87029b4f29c62c8645ef2c404a354fd6faca1991 Mon Sep 17 00:00:00 2001 From: Abdu Zoghbi Date: Fri, 16 Aug 2024 06:16:29 -0400 Subject: [PATCH 16/16] add heasoft image --- heasoft/Dockerfile | 13 + heasoft/apt.txt | 11 + heasoft/conda-heasoft-lock.yml | 2286 ++++++++++++++++++++++++++++++++ heasoft/conda-heasoft.yml | 12 + heasoft/packages-heasoft.txt | 161 +++ heasoft/postBuild.sh | 67 + 6 files changed, 2550 insertions(+) create mode 100644 heasoft/Dockerfile create mode 100644 heasoft/apt.txt create mode 100644 heasoft/conda-heasoft-lock.yml create mode 100644 heasoft/conda-heasoft.yml create mode 100644 heasoft/packages-heasoft.txt create mode 100644 heasoft/postBuild.sh diff --git a/heasoft/Dockerfile b/heasoft/Dockerfile new file mode 100644 index 0000000..bc0902f --- /dev/null +++ b/heasoft/Dockerfile @@ -0,0 +1,13 @@ +# ONBUILD instructions in base-image/Dockerfile are used to +# perform certain actions based on the presence of specific +# files (such as conda-linux-64.lock, start) in this repo. +# Refer to the base-image/Dockerfile for documentation. +ARG IMAGE_TAG=latest +FROM fornax/base-image:${IMAGE_TAG} + +# set default conda env +ENV CONDA_ENV=heasoft + +USER root +RUN mamba run -n $CONDA_ENV python -m ipykernel install --sys-prefix --name $CONDA_ENV +USER $NB_USER \ No newline at end of file diff --git a/heasoft/apt.txt b/heasoft/apt.txt new file mode 100644 index 0000000..2bad9a4 --- /dev/null +++ b/heasoft/apt.txt @@ -0,0 +1,11 @@ +g++ +libncurses-dev +libreadline-dev +make +ncurses-dev +perl-modules +tcsh +wget +xorg-dev +libcurl4 +libssl3 \ No newline at end of file diff --git a/heasoft/conda-heasoft-lock.yml b/heasoft/conda-heasoft-lock.yml new file mode 100644 index 0000000..e01cfd1 --- /dev/null +++ b/heasoft/conda-heasoft-lock.yml @@ -0,0 +1,2286 @@ +# 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 conda-heasoft-lock.yml +# To update a single package to the latest version compatible with the version constraints in the source: +# conda-lock lock --lockfile conda-heasoft-lock.yml --update PACKAGE +# To re-solve the entire environment, e.g. after changing a version constraint in the source file: +# conda-lock -f tmp-heasoft-lock.yml --lockfile conda-heasoft-lock.yml +version: 1 +metadata: + content_hash: + linux-64: 7cadeea695daddf00619e5e46d30029cb360422d91bb2250359118419e5f6208 + channels: + - url: conda-forge + used_env_vars: [] + platforms: + - linux-64 + sources: + - tmp-heasoft-lock.yml +package: +- name: _libgcc_mutex + version: '0.1' + manager: conda + platform: linux-64 + dependencies: {} + url: 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+asttokens==2.4.1 +brotli==1.1.0 +brotli-bin==1.1.0 +bzip2==1.0.8 +ca-certificates==2024.7.4 +cairo==1.18.0 +certifi==2024.7.4 +comm==0.2.2 +contourpy==1.2.1 +cycler==0.12.1 +dbus==1.13.6 +debugpy==1.8.5 +decorator==5.1.1 +double-conversion==3.3.0 +exceptiongroup==1.2.2 +executing==2.0.1 +expat==2.6.2 +font-ttf-dejavu-sans-mono==2.37 +font-ttf-inconsolata==3.000 +font-ttf-source-code-pro==2.038 +font-ttf-ubuntu==0.83 +fontconfig==2.14.2 +fonts-conda-ecosystem==1 +fonts-conda-forge==1 +fonttools==4.53.1 +freetype==2.12.1 +graphite2==1.3.13 +harfbuzz==9.0.0 +icu==75.1 +importlib-metadata==8.2.0 +importlib_metadata==8.2.0 +ipykernel==6.29.5 +ipython==8.26.0 +jedi==0.19.1 +jupyter_client==8.6.2 +jupyter_core==5.7.2 +keyutils==1.6.1 +kiwisolver==1.4.5 +krb5==1.21.3 +lcms2==2.16 +ld_impl_linux-64==2.40 +lerc==4.0.0 +libblas==3.9.0 +libbrotlicommon==1.1.0 +libbrotlidec==1.1.0 +libbrotlienc==1.1.0 +libcblas==3.9.0 +libclang-cpp18.1==18.1.8 +libclang13==18.1.8 +libcups==2.3.3 +libdeflate==1.21 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/dev/null +++ b/heasoft/postBuild.sh @@ -0,0 +1,67 @@ +#!/bin/bash + +pythonenv=heasoft +heasoft_version=6.33.1 + +export PYTHON=${CONDA_DIR}/envs/${pythonenv}/bin/python +heasoft_tarfile_suffix=src_no_xspec_modeldata +echo " --- Downloading heasoft ---" +wget https://heasarc.gsfc.nasa.gov/FTP/software/lheasoft/lheasoft${heasoft_version}/heasoft-${heasoft_version}${heasoft_tarfile_suffix}.tar.gz +tar xzvf heasoft-${heasoft_version}${heasoft_tarfile_suffix}.tar.gz +rm -f heasoft-${heasoft_version}${heasoft_tarfile_suffix}.tar.gz +cd heasoft-${heasoft_version} + + +## Configure, make, and install ... +echo " --- Configure heasoft ---" +cd BUILD_DIR/ +./configure --prefix=/opt/heasoft 2>&1 | tee config.log.txt + +echo " --- Build heasoft ---" +make 2>&1 | tee build.log.txt +make install 2>&1 | tee install.log.txt +make clean 2>&1 +gzip -9 *.log.txt && mv *.log.txt.gz /opt/heasoft +cd .. +cp -p Xspec/BUILD_DIR/hmakerc /opt/heasoft/x86_64*/bin/ +cp -p Xspec/BUILD_DIR/Makefile-std /opt/heasoft/x86_64*/bin/ +mv Release_Notes* /opt/heasoft/ +cd heasoft-${heasoft_version} + +# Tweak Xspec settings for a no-X11 environment +printf "setplot splashpage off\ncpd /GIF\n" >> /opt/heasoft/spectral/scripts/global_customize.tcl + +# enable remote CALDB for now. +export CALDBCONFIG=/opt/caldb/caldb.config +export CALDBALIAS=/opt/caldb/alias_config.fits +export CALDB=/home/jovyan/efs/caldb +mkdir -p /opt/caldb/ +cd /opt/caldb +wget -q https://heasarc.gsfc.nasa.gov/FTP/caldb/software/tools/caldb.config +wget -q https://heasarc.gsfc.nasa.gov/FTP/caldb/software/tools/alias_config.fits + +# setup scripts so it runs when (heasoft) is activated +HEADAS=`ls -d /opt/heasoft/x86_64*` +CALDB=https://heasarc.gsfc.nasa.gov/FTP/caldb + +# bash +echo " +export HEADAS=$HEADAS +export CALDB=$CALDB +source \$HEADAS/headas-init.sh +if [ -z \$CALDB ] ; then + printf \"\\\n** No CALDB data. **\\\n\" +elif [[ \$CALDB == http* ]]; then + printf \"\\\n** Using Remote CALDB **\\\n\" +elif [ -d \$CALDB ]; then + printf \"\\\n** Using CALDB in \$CALDB **\\\n\" + source \$CALDB/software/tools/caldbinit.sh +else + printf \"\\\n** No CALDB data. **\\\n\" +fi +" > activate_heasoft.sh + +_activatedir=$CONDA_DIR/envs/heasoft/etc/conda/activate.d/ +mkdir -p $_activatedir +mv activate_heasoft.sh $_activatedir +