diff --git a/README.md b/README.md index 04491c1..3c71c2e 100644 --- a/README.md +++ b/README.md @@ -1,8 +1,43 @@ # fornax-images -Customised Jupyterhub images for the Fornax Platform deployments +This repo contains the Docker images for the Fornax Platform deployments. +It produces reproducible computing environments. Some of the parts are +adapted from the [Pangeo](https://github.com/pangeo-data/pangeo-docker-images) project. -Have separate subdirectories for the different images, and please list them below for documentation purposes. +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 +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 (TODO). -#### fornax_forced_photometry - - Basic image with tractor installed diff --git a/base-image/Dockerfile b/base-image/Dockerfile new file mode 100644 index 0000000..5532da9 --- /dev/null +++ b/base-image/Dockerfile @@ -0,0 +1,94 @@ +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=0.2 +LABEL maintainer="Fornax Project" + +# 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 + +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 + +# 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 $HOME/build/ + +USER root + +# Make /opt/ user writeable so it can be used by postBuild scripts +RUN fix-permissions /opt/ + +# Install OS packages and then clean up +COPY --chown=$NB_USER:$NB_USER scripts/*.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 + + + +USER $NB_USER +# setup conda environments +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 +# --------------------------- # + +# 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/* +WORKDIR ${HOME} + + +# Install OS packages and then clean up +ONBUILD RUN mkdir -p $HOME/build +ONBUILD COPY --chown=$NB_USER:$NB_USER apt* conda*yml postBuild* $HOME/build/ +ONBUILD USER root +ONBUILD RUN mkdir -p build && cd build && bash /opt/scripts/apt-install.sh +ONBUILD USER $NB_USER +# ------------------------------------ # + + +# setup conda environments +ONBUILD RUN cd build && bash /opt/scripts/conda-env-install.sh +# ----------------------- # + +# Any other postBuild scripts # +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/base-image/apt.txt b/base-image/apt.txt new file mode 100644 index 0000000..31ff88b --- /dev/null +++ b/base-image/apt.txt @@ -0,0 +1,12 @@ +vim +nano +emacs +fuse +bzip2 +git +curl +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 new file mode 100644 index 0000000..1d69cb5 --- /dev/null +++ b/base-image/conda-notebook-lock.yml @@ -0,0 +1,6298 @@ +# 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: 46f1324661d875acee5cc3fff3bf3a5bf3b5d8cd58520c76a1572746bfbd0a60 + 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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+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==0.20.0 +libtiff==4.6.0 +libutf8proc==2.8.0 +libuuid==2.38.1 +libwebp-base==1.4.0 +libxcb==1.16 +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==3.9.2 +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 +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 +patsy==0.5.6 +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==24.08.0 +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==3.11.0 +python-dateutil==2.9.0 +python-fastjsonschema==2.20.0 +python-json-logger==2.0.7 +python-tzdata==2024.1 +python_abi==3.11 +pytz==2024.1 +pyvo==1.5.2 +pywavelets==1.7.0 +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==1.5.0 +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 +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 +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-python-dateutil==2.9.0.20240316 +typing-extensions==4.12.2 +typing_extensions==4.12.2 +typing_utils==0.1.0 +tzcode==2024a +tzdata==2024a +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 +wheel==0.44.0 +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==3.20.0 +zlib==1.3.1 +zlib-ng==2.2.1 +zstandard==0.23.0 +zstd==1.5.6 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/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..b565625 --- /dev/null +++ b/base-image/scripts/conda-env-install.sh @@ -0,0 +1,30 @@ +#!/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 update -n ${env} -f $ENVFILE + elif [[ "$env"=="$CONDA_ENV" ]]; then + echo "Defaulting to basic env ..." + mamba create --name $env python=3.11 jupyterlab + fi + if [ "$env" != "notebook" ]; then + mamba install -n $env ipykernel + mamba run -n $env python -m ipykernel install --name $env --prefix $CONDA_DIR/envs/notebook + 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 new file mode 100755 index 0000000..ae49641 --- /dev/null +++ b/build.py @@ -0,0 +1,216 @@ +#!/usr/bin/env python3 + +""" + +Description: +------------ +A python script for building docker images on fornax. + +""" + +import argparse +import glob +import subprocess +import os +import re +import json +import time +import logging +import sys + + + +def build_images(image, dryrun, build_args, update_lock): + """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? + + """ + + # 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', '--progress=plain', '-t', + f'fornax/{image}:latest' + ] + extra_args + [f'./{image}'] + logging.debug('\t' + (' '.join(cmd))) + + if not dryrun: + 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: + logging.error('\tError encountered.') + sys.exit(1) + + # 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', '-n', env_name, + ] + logging.debug('\t' + (' '.join(cmd))) + + if not dryrun: + out = subprocess.check_output(cmd) + 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 + 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): + """ + 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__': + + ap = argparse.ArgumentParser() + ap.add_argument('--dryrun', action='store_true', default=False) + 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() + + + 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) 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 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 +libdrm==2.4.122 +libedit==3.1.20191231 +libexpat==2.6.2 +libffi==3.4.2 +libgcc-ng==14.1.0 +libgfortran-ng==14.1.0 +libgfortran5==14.1.0 +libglib==2.80.3 +libgomp==14.1.0 +libiconv==1.17 +libjpeg-turbo==3.0.0 +liblapack==3.9.0 +libllvm18==18.1.8 +libnsl==2.0.1 +libopenblas==0.3.27 +libpciaccess==0.18 +libpng==1.6.43 +libpq==16.4 +libsodium==1.0.18 +libsqlite==3.46.0 +libstdcxx-ng==14.1.0 +libtiff==4.6.0 +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 +libzlib==1.3.1 +matplotlib==3.9.2 +matplotlib-base==3.9.2 +matplotlib-inline==0.1.7 +munkres==1.1.4 +mysql-common==8.3.0 +mysql-libs==8.3.0 +ncurses==6.5 +nest-asyncio==1.6.0 +numpy==2.0.1 +openjpeg==2.5.2 +openssl==3.3.1 +packaging==24.1 +parso==0.8.4 +pcre2==10.44 +pexpect==4.9.0 +pickleshare==0.7.5 +pillow==10.4.0 +pip==24.2 +pixman==0.43.2 +platformdirs==4.2.2 +prompt-toolkit==3.0.47 +psutil==6.0.0 +pthread-stubs==0.4 +ptyprocess==0.7.0 +pure_eval==0.2.3 +pyerfa==2.0.1.4 +pygments==2.18.0 +pyparsing==3.1.2 +pyside6==6.7.2 +python==3.11.9 +python-dateutil==2.9.0 +python_abi==3.11 +pyyaml==6.0.2 +pyzmq==26.1.0 +qhull==2020.2 +qt6-main==6.7.2 +readline==8.2 +scipy==1.14.0 +setuptools==72.1.0 +six==1.16.0 +stack_data==0.6.2 +tk==8.6.13 +tornado==6.4.1 +traitlets==5.14.3 +typing_extensions==4.12.2 +tzdata==2024a +wayland==1.23.0 +wcwidth==0.2.13 +wheel==0.44.0 +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 +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 +xz==5.2.6 +yaml==0.2.5 +zeromq==4.3.5 +zipp==3.20.0 +zlib==1.3.1 +zstd==1.5.6 diff --git a/heasoft/postBuild.sh b/heasoft/postBuild.sh new file mode 100644 index 0000000..4b2d9ec --- /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 $_activatedir + diff --git a/tractor/Dockerfile b/tractor/Dockerfile new file mode 100644 index 0000000..8e848e3 --- /dev/null +++ b/tractor/Dockerfile @@ -0,0 +1,6 @@ +# ONBUILD instructions in base-image/Dockerfile are used to +# perform certain actions based on the presence of specific +# files (such as conda-linux-64.lock, start) in this repo. +# Refer to the base-image/Dockerfile for documentation. +ARG IMAGE_TAG=latest +FROM fornax/base-image:${IMAGE_TAG} diff --git a/tractor/conda-notebook-lock.yml b/tractor/conda-notebook-lock.yml new file mode 100644 index 0000000..86a211b --- /dev/null +++ b/tractor/conda-notebook-lock.yml @@ -0,0 +1,7221 @@ +# 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: af6286c797d86e8fca06e7f159737fe0411556f7e92026307037a84081e62cd9 + 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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tqdm +prefix: /opt/conda/envs/notebook \ No newline at end of file diff --git a/tractor/packages-notebook.txt b/tractor/packages-notebook.txt new file mode 100644 index 0000000..00ca6a9 --- /dev/null +++ b/tractor/packages-notebook.txt @@ -0,0 +1,477 @@ +# 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 +_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 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+semantic_version==2.10.0 +send2trash==1.8.3 +setuptools==72.1.0 +shapely==2.0.5 +simpervisor==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-python-dateutil==2.9.0.20240316 +typing-extensions==4.12.2 +typing_extensions==4.12.2 +typing_utils==0.1.0 +tzcode==2024a +tzdata==2024a +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 +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==3.20.0 +zlib==1.3.1 +zlib-ng==2.2.1 +zstandard==0.23.0 +zstd==1.5.6 diff --git a/tractor/postBuild.sh b/tractor/postBuild.sh new file mode 100644 index 0000000..433a588 --- /dev/null +++ b/tractor/postBuild.sh @@ -0,0 +1,27 @@ +#!/bin/bash + +pythonenv=notebook +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