PycWB 0.30.2__tar.gz → 0.31.0__tar.gz

pycwb-0.31.0/.gitlab-ci.yml

@@ -0,0 +1,57 @@
+image: buildpack-deps:jammy
+
+stages:          # List of stages for jobs, and their order of execution
+  - build
+  - test
+  - deploy
+
+
+include:
+  - component: git.ligo.org/computing/gitlab/components/docker/build@2.3.1
+    inputs:
+      dockerfile: envs/Dockerfile.ci
+      job_name: build
+      image_tag: ${CI_COMMIT_TAG:-$CI_COMMIT_REF_SLUG}
+
+  - component: git.ligo.org/computing/gitlab/components/docker/build@2.3.1
+    inputs:
+      dockerfile: envs/Dockerfile.ci
+      job_name: build-latest
+      image_tag: latest
+
+  - component: git.ligo.org/computing/gitlab/components/docker/test@2.3.1
+    inputs:
+      test_script:
+        - cd /opt && pycwb --version # change dir to prevent use the source code
+
+build-latest:
+  rules:
+    - if: $CI_COMMIT_TAG
+
+container_scanning:
+  needs:
+    - job: build-latest
+      optional: true
+
+build-sdist:
+  image: python:3.11
+  stage: build
+  script:
+    - python3 -m pip install build
+    - python3 -m build --sdist
+  only:
+    - tags
+  artifacts:
+    paths:
+      - dist/*
+
+publish:
+  image: python:3.10
+  stage: deploy  # It only runs when *both* jobs in the test stage complete successfully.
+  environment: production
+  only:
+    - tags
+  script:
+    - echo "Deploying to PyPI..."
+    - pip install twine
+    - TWINE_PASSWORD=${PYPI_TOKEN} TWINE_USERNAME=__token__ python -m twine upload dist/*.tar.gz

pycwb-0.31.0/Dockerfile

@@ -0,0 +1,29 @@
+# CI-ready image for PycWB (mirrors .gitlab-ci.yml install steps)
+FROM buildpack-deps:jammy
+
+ARG ROOT_VERSION=6.26.14
+ARG ROOT_ARCH=Linux-ubuntu22-x86_64-gcc11.4
+ENV ROOTSYS=/usr/local
+ENV PYTHONPATH=${ROOTSYS}/lib:${PYTHONPATH}
+ENV CLING_STANDARD_PCH=none
+
+# System deps and ROOT + healpix
+RUN set -eux; \
+    wget -q https://root.cern/download/root_v${ROOT_VERSION}.${ROOT_ARCH}.tar.gz; \
+    tar -xf root_v${ROOT_VERSION}.${ROOT_ARCH}.tar.gz --strip-components=1 -C /usr/local/; \
+    apt-get update; \
+    apt-get -y install git dpkg-dev cmake pkg-config g++ gcc binutils libx11-dev libxpm-dev libxft-dev libxext-dev tar gfortran subversion; \
+    apt-get -y install libfftw3-dev libcfitsio9 libsharp0 python3-pip; \
+    wget -q http://archive.ubuntu.com/ubuntu/pool/main/o/openssl/libssl1.1_1.1.1f-1ubuntu2_amd64.deb; \
+    dpkg -i libssl1.1_1.1.1f-1ubuntu2_amd64.deb; \
+    wget -q https://launchpad.net/ubuntu/+archive/primary/+files/libhealpix-cxx3_3.80.0-5_amd64.deb; \
+    wget -q https://launchpad.net/ubuntu/+archive/primary/+files/libhealpix-cxx-dev_3.80.0-5_amd64.deb; \
+    dpkg -i libhealpix-cxx3_3.80.0-5_amd64.deb; \
+    dpkg -i libhealpix-cxx-dev_3.80.0-5_amd64.deb; \
+    apt-get -y install python3-venv; \
+    ln -sf /usr/bin/python3 /usr/bin/python; \
+    python3 -m pip install --upgrade pip setuptools; \
+    rm -rf /var/lib/apt/lists/*
+
+WORKDIR /workspace
+CMD ["python3", "--version"]

{pycwb-0.30.2 → pycwb-0.31.0}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: PycWB
-Version: 0.30.2
+Version: 0.31.0
 Summary: A Python package for coherent gravitational wave burst analysis
 Home-page: https://git.ligo.org/yumeng.xu/pycwb
 Author-email: The PycWB team <yumeng.xu@ligo.org>
@@ -17,6 +17,7 @@ Requires-Dist: numpy
 Requires-Dist: numba
 Requires-Dist: gwpy
 Requires-Dist: ligo-segments
+Requires-Dist: ligo-gracedb
 Requires-Dist: aiohttp
 Requires-Dist: pycbc
 Requires-Dist: filelock
@@ -33,10 +34,14 @@ Requires-Dist: dask_jobqueue
 Requires-Dist: htcondor
 Requires-Dist: psutil
 Requires-Dist: memspectrum
+Requires-Dist: exceptiongroup>=1.0.0; python_version < "3.11"
 Requires-Dist: python-ligo-lw<2.0.0
 Requires-Dist: scikit-learn
 Requires-Dist: jinja2
 Requires-Dist: plotly
+Requires-Dist: healpy
+Requires-Dist: wdm-wavelet
+Requires-Dist: burst-waveform
 Dynamic: description
 Dynamic: description-content-type
 Dynamic: home-page

{pycwb-0.30.2 → pycwb-0.31.0}/PycWB.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: PycWB
-Version: 0.30.2
+Version: 0.31.0
 Summary: A Python package for coherent gravitational wave burst analysis
 Home-page: https://git.ligo.org/yumeng.xu/pycwb
 Author-email: The PycWB team <yumeng.xu@ligo.org>
@@ -17,6 +17,7 @@ Requires-Dist: numpy
 Requires-Dist: numba
 Requires-Dist: gwpy
 Requires-Dist: ligo-segments
+Requires-Dist: ligo-gracedb
 Requires-Dist: aiohttp
 Requires-Dist: pycbc
 Requires-Dist: filelock
@@ -33,10 +34,14 @@ Requires-Dist: dask_jobqueue
 Requires-Dist: htcondor
 Requires-Dist: psutil
 Requires-Dist: memspectrum
+Requires-Dist: exceptiongroup>=1.0.0; python_version < "3.11"
 Requires-Dist: python-ligo-lw<2.0.0
 Requires-Dist: scikit-learn
 Requires-Dist: jinja2
 Requires-Dist: plotly
+Requires-Dist: healpy
+Requires-Dist: wdm-wavelet
+Requires-Dist: burst-waveform
 Dynamic: description
 Dynamic: description-content-type
 Dynamic: home-page

{pycwb-0.30.2 → pycwb-0.31.0}/PycWB.egg-info/SOURCES.txt

@@ -1,6 +1,7 @@
 .gitignore
 .gitlab-ci.yml
 .readthedocs.yaml
+Dockerfile
 LICENSE
 MANIFEST.in
 Makefile
@@ -157,7 +158,10 @@ docs/source/workflow.png
 docs/source/_static/.keep
 docs/source/_templates/.keep
 envs/Dockerfile
+envs/Dockerfile.ci
+envs/Dockerfile.ci-conda
 envs/environment.yml
+envs/pycwb.def
 envs/mamba/Dockerfile
 examples/GW190521_search/README.md
 examples/GW190521_search/user_parameters.yaml
@@ -405,6 +409,7 @@ pycwb/modules/read_data/read_data.py
 pycwb/modules/read_data/tests/__init__.py
 pycwb/modules/read_data/tests/test_mdc.py
 pycwb/modules/reconstruction/__init__.py
+pycwb/modules/reconstruction/getINJwaveform.py
 pycwb/modules/reconstruction/getMRAwaveform.py
 pycwb/modules/reconstruction/module.yaml
 pycwb/modules/report/__init__.py

{pycwb-0.30.2 → pycwb-0.31.0}/PycWB.egg-info/requires.txt

@@ -7,6 +7,7 @@ numpy
 numba
 gwpy
 ligo-segments
+ligo-gracedb
 aiohttp
 pycbc
 filelock
@@ -27,3 +28,9 @@ python-ligo-lw<2.0.0
 scikit-learn
 jinja2
 plotly
+healpy
+wdm-wavelet
+burst-waveform
+
+[:python_version < "3.11"]
+exceptiongroup>=1.0.0

{pycwb-0.30.2 → pycwb-0.31.0}/bin/pycwb

@@ -15,11 +15,15 @@ import pycwb.cli.post_process as post_process
 import pycwb.cli.gwosc as gwosc
 import pycwb.cli.gwosc_data as gwosc_data
 import pycwb.cli.get_external_modules as get_external_modules
+from pycwb import __version__
 
 def main():
     parser = argparse.ArgumentParser(prog='pycwb')
     subparsers = parser.add_subparsers(help='commands')
 
+    # Show version
+    parser.add_argument('-v', '--version', action='version', version=f'pycwb {__version__}')
+
     # Create subcommand
     create_parser = subparsers.add_parser('server', help='Run a simple server to show the results')
     server.init_parser(create_parser)

{pycwb-0.30.2 → pycwb-0.31.0}/cwb-core/CMakeLists.txt

@@ -50,9 +50,13 @@ if(NOT DEFINED XIFO)
    set(XIFO 4)
 endif()
 
-# Fix the macso cross-compilation issue, see git.ligo.org issue#4
-set(CWB_OPTS "XIFO=${XIFO}" "_USE_CPP" "_Float16=short")
-
+# Fix the macOS cross-compilation issue, see git.ligo.org issue#4
+# Only apply the `_Float16=short` workaround on Apple Silicon (arm64)
+# FIXME: could not find a robust way to detect Apple Silicon when rosseta is used
+set(CWB_OPTS "XIFO=${XIFO}" "_USE_CPP")
+if(APPLE)
+   list(APPEND CWB_OPTS "_Float16=short")
+endif()
 
 #Find ROOT
 list(APPEND CMAKE_PREFIX_PATH $ENV{ROOTSYS})

{pycwb-0.30.2 → pycwb-0.31.0}/cwb-core/wat.hh

@@ -68,6 +68,10 @@ inline bool USE_ICC() {return false;}
 
 } // end namespace
 
+#ifndef XIFO
+#define XIFO 4
+#endif
+
 #define _ALIGNED        __attribute__((aligned(32)))
 
 #if XIFO < 5

pycwb-0.31.0/envs/Dockerfile.ci

@@ -0,0 +1,61 @@
+FROM buildpack-deps:jammy
+
+# ---- Install ROOT ----
+WORKDIR /tmp
+RUN wget -q https://root.cern/download/root_v6.32.20.Linux-ubuntu22.04-x86_64-gcc11.4.tar.gz \
+ && tar -xf root_v6.32.20.Linux-ubuntu22.04-x86_64-gcc11.4.tar.gz \
+      --strip-components=1 -C /usr/local/
+
+# ---- Environment ----
+ENV ROOTSYS=/usr/local
+ENV PYTHONPATH=${ROOTSYS}/lib:${PYTHONPATH}
+ENV CLING_STANDARD_PCH=none
+
+# ---- System dependencies ----
+RUN apt-get update && apt-get -y install \
+    git dpkg-dev cmake pkg-config g++ gcc binutils \
+    libx11-dev libxpm-dev libxft-dev libxext-dev \
+    tar gfortran subversion \
+    libfftw3-dev libcfitsio9 libsharp0 \
+    python3-pip python3-venv nlohmann-json3-dev libtbb12 \
+ && rm -rf /var/lib/apt/lists/*
+
+# ---- OpenSSL 1.1 ----
+RUN wget -q http://archive.ubuntu.com/ubuntu/pool/main/o/openssl/libssl1.1_1.1.1f-1ubuntu2_amd64.deb \
+ && dpkg -i libssl1.1_1.1.1f-1ubuntu2_amd64.deb
+
+# ---- HEALPix ----
+RUN wget -q https://launchpad.net/ubuntu/+archive/primary/+files/libhealpix-cxx3_3.80.0-5_amd64.deb \
+ && wget -q https://launchpad.net/ubuntu/+archive/primary/+files/libhealpix-cxx-dev_3.80.0-5_amd64.deb \
+ && dpkg -i libhealpix-cxx3_3.80.0-5_amd64.deb \
+ && dpkg -i libhealpix-cxx-dev_3.80.0-5_amd64.deb
+
+# Copy source to a temporary build directory
+WORKDIR /tmp/build
+COPY . /tmp/build
+
+# Build wheel and install into site-packages
+RUN python3 -m pip install --upgrade pip setuptools setuptools_scm build \
+ && python3 -m build
+
+# Change to another dir to prevent not installing pycwb itself
+WORKDIR /opt/pycwb
+
+RUN python3 -m pip install /tmp/build/dist/*.whl -v
+
+# ----------------------------
+# Remove tmp files
+# ----------------------------
+RUN rm -rf /tmp/build
+
+# ----------------------------
+# Sanity checks
+# ----------------------------
+RUN python3 -m pip show pycwb
+
+RUN python3 - <<EOF
+import pycwb
+print("pycwb version:", pycwb.__version__)
+EOF
+
+RUN which pycwb && pycwb --version || true

pycwb-0.31.0/envs/Dockerfile.ci-conda

@@ -0,0 +1,74 @@
+FROM buildpack-deps:jammy
+
+ENV DEBIAN_FRONTEND=noninteractive
+WORKDIR /opt
+
+# ---- System dependencies (minimal) ----
+RUN apt-get update && apt-get install -y \
+    git \
+    build-essential \
+    wget \
+    ca-certificates \
+ && rm -rf /var/lib/apt/lists/*
+
+# ---- Install Miniforge ----
+ENV CONDA_DIR=/opt/conda
+RUN wget -q https://github.com/conda-forge/miniforge/releases/latest/download/Miniforge3-Linux-x86_64.sh \
+ && bash Miniforge3-Linux-x86_64.sh -b -p ${CONDA_DIR} \
+ && rm Miniforge3-Linux-x86_64.sh
+
+ENV PATH=${CONDA_DIR}/bin:${PATH}
+
+# ---- Configure conda ----
+RUN conda config --set channel_priority strict \
+ && conda update -y conda
+
+# ---- Create pycwb environment ----
+RUN conda create -y -n pycwb "python>=3.9,<3.11"
+
+# ---- Install dependencies from conda-forge ----
+RUN conda install -y -n pycwb -c conda-forge \
+    root=6.26.10 \
+    healpix_cxx=3.81 \
+    nds2-client \
+    python-nds2-client \
+    lalsuite \
+    setuptools_scm \
+    cmake \
+    pkg-config \
+ && conda clean -afy
+
+# ---- Make pycwb env the default ----
+SHELL ["bash", "-c"]
+ENV CONDA_DEFAULT_ENV=pycwb
+ENV PATH=${CONDA_DIR}/envs/pycwb/bin:${PATH}
+
+# Copy source to a temporary build directory
+WORKDIR /tmp/build
+COPY . /tmp/build
+
+# Build wheel and install into site-packages
+RUN python3 -m pip install --upgrade pip setuptools setuptools_scm build \
+ && python3 -m build
+
+# Change to another dir to prevent not installing pycwb itself
+WORKDIR /opt/pycwb
+
+RUN python3 -m pip install /tmp/build/dist/*.whl -v
+
+# ----------------------------
+# Remove tmp files
+# ----------------------------
+RUN rm -rf /tmp/build
+
+# ----------------------------
+# Sanity checks
+# ----------------------------
+RUN python3 -m pip show pycwb
+
+RUN python3 - <<EOF
+import pycwb
+print("pycwb version:", pycwb.__version__)
+EOF
+
+RUN which pycwb && pycwb --version || true

pycwb-0.31.0/envs/pycwb.def

@@ -0,0 +1,67 @@
+Bootstrap: docker
+From: buildpack-deps:jammy
+
+%labels
+    Author your-name
+    Description CI-ready image for PycWB (converted from Dockerfile)
+
+%environment
+    export ROOTSYS=/usr/local
+    export PYTHONPATH=${ROOTSYS}/lib:${PYTHONPATH}
+    export CLING_STANDARD_PCH=none
+    export WORKSPACE=/workspace
+
+%post
+    set -eux
+
+    # ---- build args (hard-coded in Singularity) ----
+    ROOT_VERSION=6.26.14
+    ROOT_ARCH=Linux-ubuntu22-x86_64-gcc11.4
+
+    echo "Installing ROOT"
+    cd /tmp
+    wget -q https://root.cern/download/root_v${ROOT_VERSION}.${ROOT_ARCH}.tar.gz
+    tar -xf root_v${ROOT_VERSION}.${ROOT_ARCH}.tar.gz --strip-components=1 -C /usr/local/
+
+    echo "Installing system dependencies"
+    apt-get update
+    apt-get -y install \
+        git dpkg-dev cmake pkg-config g++ gcc binutils \
+        libx11-dev libxpm-dev libxft-dev libxext-dev \
+        tar gfortran subversion \
+        libfftw3-dev libcfitsio9 libsharp0 \
+        python3-pip python3-venv
+
+    echo "Installing legacy OpenSSL 1.1"
+    wget -q http://archive.ubuntu.com/ubuntu/pool/main/o/openssl/libssl1.1_1.1.1f-1ubuntu2_amd64.deb
+    dpkg -i libssl1.1_1.1.1f-1ubuntu2_amd64.deb
+
+    echo "Installing HEALPix"
+    wget -q https://launchpad.net/ubuntu/+archive/primary/+files/libhealpix-cxx3_3.80.0-5_amd64.deb
+    wget -q https://launchpad.net/ubuntu/+archive/primary/+files/libhealpix-cxx-dev_3.80.0-5_amd64.deb
+    dpkg -i libhealpix-cxx3_3.80.0-5_amd64.deb
+    dpkg -i libhealpix-cxx-dev_3.80.0-5_amd64.deb
+
+    echo "Python setup"
+    ln -sf /usr/bin/python3 /usr/bin/python
+    python3 -m pip install --upgrade pip setuptools
+    python3 -m pip install build 
+
+    echo "==== Install pycwb ===="
+    cd /opt
+    git clone https://git.ligo.org/yumeng.xu/pycwb.git
+    cd pycwb
+    python3 -m build --sdist
+    pip install dist/*.tar.gz
+
+    echo "Create workspace"
+    mkdir -p /workspace
+
+    echo "Cleanup"
+    rm -rf /var/lib/apt/lists/*
+    rm -rf /tmp/root_v6.26.04.Linux-ubuntu22-x86_64-gcc11.2.tar.gz
+    rm -rf /tmp/libssl1.1_1.1.1f-1ubuntu2_amd64.deb
+    rm -rf /tmp/libhealpix-cxx*.deb
+    
+%runscript
+    exec python3 --version

{pycwb-0.30.2 → pycwb-0.31.0}/pycwb/_version.py

@@ -28,7 +28,7 @@ version_tuple: VERSION_TUPLE
 commit_id: COMMIT_ID
 __commit_id__: COMMIT_ID
 
-__version__ = version = '0.30.2'
-__version_tuple__ = version_tuple = (0, 30, 2)
+__version__ = version = '0.31.0'
+__version_tuple__ = version_tuple = (0, 31, 0)
 
-__commit_id__ = commit_id = 'g27e3ff7bf'
+__commit_id__ = commit_id = 'g5f80524f4'

{pycwb-0.30.2 → pycwb-0.31.0}/pycwb/cli/batch_setup.py

@@ -26,7 +26,6 @@ def init_parser(parser):
                         metavar='job_submission_system',
                         type=str,
                         choices=['condor', 'slurm'],
-                        default='condor',
                         help='the submit option, the available options are condor and slurm')
 
     parser.add_argument('--submit',
@@ -55,7 +54,6 @@ def init_parser(parser):
                         '-e',
                         metavar='conda_env',
                         type=str,
-                        default=os.environ.get('CONDA_DEFAULT_ENV'),
                         help='the conda environment')
 
     # additional init
@@ -88,13 +86,25 @@ def init_parser(parser):
                         type=int,
                         default=1,
                         help='the number of jobs per worker')
+    
+    # container_image
+    parser.add_argument('--container-image',
+                        '--image',
+                        metavar='container_image',
+                        type=str,
+                        help='the URI to the container image')
+
+    # should_transfer_files
+    parser.add_argument('--should-transfer-files',
+                        action='store_true',
+                        default=False,
+                        help='whether transfer files to computing node, set this if the shared file system does not exist')   
 
     # memory
     parser.add_argument('--memory',
                         '-m',
                         metavar='memory',
                         type=str,
-                        default='6GB',
                         help='the memory for each job')
 
     # disk
@@ -102,7 +112,6 @@ def init_parser(parser):
                         '-k',
                         metavar='disk',
                         type=str,
-                        default='4GB',
                         help='the disk space for each job')
 
     # compress json
@@ -158,6 +167,8 @@ def command(args):
                 disk=args.disk,
                 accounting_group=args.accounting_group,
                 job_per_worker=args.job_per_worker,
+                should_transfer_files=args.should_transfer_files,
+                container_image=args.container_image,
                 submit=args.submit,
                 overwrite=args.force_overwrite, 
                 config_vars=args.config_vars)

{pycwb-0.30.2 → pycwb-0.31.0}/pycwb/constants/user_parameters_schema.py

@@ -110,6 +110,69 @@ schema = {
             "default": 4,
             "cwb": False
         },
+        "cluster": {
+            "type": "string",
+            "description": "cluster type for batch processing (condor or slurm)",
+            "default": "",
+            "cwb": False,
+            "category": "job_submission"
+        },
+        "conda_env": {
+            "type": "string",
+            "description": "conda environment name for batch jobs",
+            "default": "",
+            "cwb": False,
+            "category": "job_submission"
+        },
+        "additional_init": {
+            "type": "string",
+            "description": "additional initialization commands for batch jobs",
+            "default": "",
+            "cwb": False,
+            "category": "job_submission"
+        },
+        "accounting_group": {
+            "type": "string",
+            "description": "accounting group for HTCondor batch jobs",
+            "default": "",
+            "cwb": False,
+            "category": "job_submission"
+        },
+        "job_per_worker": {
+            "type": "integer",
+            "description": "number of jobs per worker in batch processing",
+            "default": 1,
+            "cwb": False,
+            "category": "job_submission"
+        },
+        "job_memory": {
+            "type": "string",
+            "description": "memory allocation for batch jobs (e.g., '6GB')",
+            "default": "6GB",
+            "cwb": False,
+            "category": "job_submission"
+        },
+        "job_disk": {
+            "type": "string",
+            "description": "disk allocation for batch jobs (e.g., '8GB')",
+            "default": "8GB",
+            "cwb": False,
+            "category": "job_submission"
+        },
+        "container_image": {
+            "type": "string",
+            "description": "container image for HTCondor batch jobs",
+            "default": "",
+            "cwb": False,
+            "category": "job_submission"
+        },
+        "should_transfer_files": {
+            "type": "boolean",
+            "description": "whether to transfer files in HTCondor batch jobs",
+            "default": False,
+            "cwb": False,
+            "category": "job_submission"
+        },
         "skip_no_injection": {
             "type": "boolean",
             "description": "skip jobs without injection",