PycWB 0.23.0__tar.gz → 0.23.2__tar.gz

pycwb-0.23.2/.readthedocs.yaml

@@ -0,0 +1,68 @@
+version: 2
+
+build:
+  os: "ubuntu-22.04"
+  tools:
+    python: "mambaforge-22.9"
+
+conda:
+  environment: envs/environment.yml
+#  commands:
+#    - wget -q https://root.cern/download/root_v6.26.14.Linux-ubuntu22-x86_64-gcc11.4.tar.gz
+#    - tar -xf root_v6.26.14.Linux-ubuntu22-x86_64-gcc11.4.tar.gz --strip-components=1 -C /usr/local/
+#    - export ROOTSYS=/usr/local
+#    - export PYTHONPATH=$ROOTSYS/lib:$PYTHONPATH
+#    - export CLING_STANDARD_PCH=none
+#    - 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-pip python3-venv
+#    - ln -s /usr/bin/python3 /usr/bin/python
+#    - python3 -m pip install pip setuptools -U
+
+python:
+  install:
+    #- requirements: docs/requirements.txt
+    - method: pip
+      path: .
+
+sphinx:
+  configuration: docs/source/conf.py
+
+#environment:
+#  ROOTSYS: /usr/local
+#  PYTHONPATH: /usr/local/lib:$PYTHONPATH
+
+#apt_packages:
+#  - wget
+#  - cmake
+#  - g++
+#  - gcc
+#  - gfortran
+#  - libx11-dev
+#  - libxpm-dev
+#  - libxft-dev
+#  - libxext-dev
+#  - libfftw3-dev
+#  - libcfitsio9
+#  - libsharp0
+#  - libssl1.1
+#
+#pre_build:
+#  - wget -q https://root.cern/download/root_v6.26.14.Linux-ubuntu22-x86_64-gcc11.4.tar.gz
+#  - tar -xf root_v6.26.14.Linux-ubuntu22-x86_64-gcc11.4.tar.gz --strip-components=1 -C /usr/local/
+#  - 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
+#
+#exclude:
+#  - "dist/*"
+#  - "*.tar.gz"
+#  - "*.deb"

{pycwb-0.23.0 → pycwb-0.23.2}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: PycWB
-Version: 0.23.0
+Version: 0.23.2
 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>
@@ -34,12 +34,14 @@ Requires-Dist: htcondor
 
 # PycWB
 
+[![Documentations](https://readthedocs.org/projects/pycwb/badge/?version=latest)](https://pycwb.readthedocs.io)
 [![Build Status](https://git.ligo.org/yumeng.xu/pycwb/badges/main/pipeline.svg)](https://git.ligo.org/yumeng.xu/pycwb/-/pipelines)
 [![Releases](https://git.ligo.org/yumeng.xu/pycwb/-/badges/release.svg)](https://git.ligo.org/yumeng.xu/pycwb/-/releases)
 [![PyPI version](https://badge.fury.io/py/pycWB.svg)](https://badge.fury.io/py/pycWB)
 [![License](https://img.shields.io/badge/license-GPLv3-blue)](https://git.ligo.org/yumeng.xu/pycwb/-/blob/main/LICENSE)
 
 PycWB is a modularized Python package for gravitational wave burst search based on the core function of cWB.
+The documentation can be found at [pycwb.readthedocs.io](https://pycwb.readthedocs.io).
 
 ## Installation
 
@@ -56,6 +58,19 @@ conda install -c conda-forge root=6.26.10 healpix_cxx=3.81 nds2-client python-nd
 python3 -m pip install pycwb
 ```
 
+Currently, pycWB is only available for x64 architecture.
+For Apple Silicon users, you can install the dependencies with the following commands:
+
+```bash
+# make sure rosetta is installed
+softwareupdate --install-rosetta --agree-to-license
+# Optional: export CONDA_BUILD=1
+conda create -n pycwb
+conda activate pycwb
+conda config --env --set subdir osx-64
+conda install -c conda-forge "python>=3.9,<3.11" root=6.26.10 healpix_cxx=3.81 nds2-client python-nds2-client lalsuite setuptools_scm cmake pkg-config ruamel.yaml htcondor
+```
+
 ### Install pycWB from source
 
 ```bash
@@ -72,7 +87,7 @@ make install
 Example project can be found in [examples](https://git.ligo.org/yumeng.xu/pycwb/-/tree/main/examples)
 
 ```python
-from pycwb.search import search
+from pycwb.workflow.run import search
 
 search('./user_parameters.yaml')
 ```
@@ -80,14 +95,9 @@ search('./user_parameters.yaml')
 or run with command line
 
 ```bash
-pycwb_search ./user_parameters.yaml
+pycwb run ./user_parameters.yaml
 ```
 
 ## Interactive tutorial
 
  - Google Colab tutorial: [pycWB_GW150914.ipynb](https://colab.research.google.com/github/PycWB/pycwb/blob/main/examples/colab/pycWB_GW150914.ipynb)
-
-
-## Documentation
-
-Documentation can be found in [https://yumeng.xu.docs.ligo.org/pycwb](https://yumeng.xu.docs.ligo.org/pycwb)

{pycwb-0.23.0 → pycwb-0.23.2}/PycWB.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: PycWB
-Version: 0.23.0
+Version: 0.23.2
 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>
@@ -34,12 +34,14 @@ Requires-Dist: htcondor
 
 # PycWB
 
+[![Documentations](https://readthedocs.org/projects/pycwb/badge/?version=latest)](https://pycwb.readthedocs.io)
 [![Build Status](https://git.ligo.org/yumeng.xu/pycwb/badges/main/pipeline.svg)](https://git.ligo.org/yumeng.xu/pycwb/-/pipelines)
 [![Releases](https://git.ligo.org/yumeng.xu/pycwb/-/badges/release.svg)](https://git.ligo.org/yumeng.xu/pycwb/-/releases)
 [![PyPI version](https://badge.fury.io/py/pycWB.svg)](https://badge.fury.io/py/pycWB)
 [![License](https://img.shields.io/badge/license-GPLv3-blue)](https://git.ligo.org/yumeng.xu/pycwb/-/blob/main/LICENSE)
 
 PycWB is a modularized Python package for gravitational wave burst search based on the core function of cWB.
+The documentation can be found at [pycwb.readthedocs.io](https://pycwb.readthedocs.io).
 
 ## Installation
 
@@ -56,6 +58,19 @@ conda install -c conda-forge root=6.26.10 healpix_cxx=3.81 nds2-client python-nd
 python3 -m pip install pycwb
 ```
 
+Currently, pycWB is only available for x64 architecture.
+For Apple Silicon users, you can install the dependencies with the following commands:
+
+```bash
+# make sure rosetta is installed
+softwareupdate --install-rosetta --agree-to-license
+# Optional: export CONDA_BUILD=1
+conda create -n pycwb
+conda activate pycwb
+conda config --env --set subdir osx-64
+conda install -c conda-forge "python>=3.9,<3.11" root=6.26.10 healpix_cxx=3.81 nds2-client python-nds2-client lalsuite setuptools_scm cmake pkg-config ruamel.yaml htcondor
+```
+
 ### Install pycWB from source
 
 ```bash
@@ -72,7 +87,7 @@ make install
 Example project can be found in [examples](https://git.ligo.org/yumeng.xu/pycwb/-/tree/main/examples)
 
 ```python
-from pycwb.search import search
+from pycwb.workflow.run import search
 
 search('./user_parameters.yaml')
 ```
@@ -80,14 +95,9 @@ search('./user_parameters.yaml')
 or run with command line
 
 ```bash
-pycwb_search ./user_parameters.yaml
+pycwb run ./user_parameters.yaml
 ```
 
 ## Interactive tutorial
 
  - Google Colab tutorial: [pycWB_GW150914.ipynb](https://colab.research.google.com/github/PycWB/pycwb/blob/main/examples/colab/pycWB_GW150914.ipynb)
-
-
-## Documentation
-
-Documentation can be found in [https://yumeng.xu.docs.ligo.org/pycwb](https://yumeng.xu.docs.ligo.org/pycwb)

{pycwb-0.23.0 → pycwb-0.23.2}/PycWB.egg-info/SOURCES.txt

@@ -1,5 +1,6 @@
 .gitignore
 .gitlab-ci.yml
+.readthedocs.yaml
 LICENSE
 MANIFEST.in
 Makefile
@@ -150,6 +151,7 @@ docs/source/workflow.png
 docs/source/_static/.keep
 docs/source/_templates/.keep
 envs/Dockerfile
+envs/environment.yml
 envs/mamba/Dockerfile
 examples/autoencoder/pycwb_injection.ipynb
 examples/autoencoder/user_parameters_injection.yaml
@@ -174,8 +176,8 @@ examples/benchmark/input/OPBM_H1.frames
 examples/benchmark/input/OPBM_L1.frames
 examples/colab/pycWB_GW150914.ipynb
 examples/injection/pycwb_injection.ipynb
-examples/injection/pycwb_injection.py
 examples/injection/user_parameters_injection.yaml
+examples/injection/wdmXTalk/OverlapCatalog16-1024.bin
 examples/lvk_sep_2023/demo.ipynb
 examples/lvk_sep_2023/user_parameters.yaml
 examples/multiple_injection/pycwb_injection.py

{pycwb-0.23.0 → pycwb-0.23.2}/README.md

@@ -1,11 +1,13 @@
 # PycWB
 
+[![Documentations](https://readthedocs.org/projects/pycwb/badge/?version=latest)](https://pycwb.readthedocs.io)
 [![Build Status](https://git.ligo.org/yumeng.xu/pycwb/badges/main/pipeline.svg)](https://git.ligo.org/yumeng.xu/pycwb/-/pipelines)
 [![Releases](https://git.ligo.org/yumeng.xu/pycwb/-/badges/release.svg)](https://git.ligo.org/yumeng.xu/pycwb/-/releases)
 [![PyPI version](https://badge.fury.io/py/pycWB.svg)](https://badge.fury.io/py/pycWB)
 [![License](https://img.shields.io/badge/license-GPLv3-blue)](https://git.ligo.org/yumeng.xu/pycwb/-/blob/main/LICENSE)
 
 PycWB is a modularized Python package for gravitational wave burst search based on the core function of cWB.
+The documentation can be found at [pycwb.readthedocs.io](https://pycwb.readthedocs.io).
 
 ## Installation
 
@@ -22,6 +24,19 @@ conda install -c conda-forge root=6.26.10 healpix_cxx=3.81 nds2-client python-nd
 python3 -m pip install pycwb
 ```
 
+Currently, pycWB is only available for x64 architecture.
+For Apple Silicon users, you can install the dependencies with the following commands:
+
+```bash
+# make sure rosetta is installed
+softwareupdate --install-rosetta --agree-to-license
+# Optional: export CONDA_BUILD=1
+conda create -n pycwb
+conda activate pycwb
+conda config --env --set subdir osx-64
+conda install -c conda-forge "python>=3.9,<3.11" root=6.26.10 healpix_cxx=3.81 nds2-client python-nds2-client lalsuite setuptools_scm cmake pkg-config ruamel.yaml htcondor
+```
+
 ### Install pycWB from source
 
 ```bash
@@ -38,7 +53,7 @@ make install
 Example project can be found in [examples](https://git.ligo.org/yumeng.xu/pycwb/-/tree/main/examples)
 
 ```python
-from pycwb.search import search
+from pycwb.workflow.run import search
 
 search('./user_parameters.yaml')
 ```
@@ -46,14 +61,9 @@ search('./user_parameters.yaml')
 or run with command line
 
 ```bash
-pycwb_search ./user_parameters.yaml
+pycwb run ./user_parameters.yaml
 ```
 
 ## Interactive tutorial
 
  - Google Colab tutorial: [pycWB_GW150914.ipynb](https://colab.research.google.com/github/PycWB/pycwb/blob/main/examples/colab/pycWB_GW150914.ipynb)
-
-
-## Documentation
-
-Documentation can be found in [https://yumeng.xu.docs.ligo.org/pycwb](https://yumeng.xu.docs.ligo.org/pycwb)

{pycwb-0.23.0 → pycwb-0.23.2}/cwb-core/CMakeLists.txt

@@ -1,4 +1,4 @@
-cmake_minimum_required(VERSION 3.14.0 FATAL_ERROR)
+cmake_minimum_required(VERSION 3.15.0 FATAL_ERROR)
 project(
     WAT
     LANGUAGES CXX ASM
@@ -6,6 +6,8 @@ project(
     DESCRIPTION "cWB pipeline source library"
 )
 
+set(CMAKE_OSX_ARCHITECTURES "x86_64" CACHE INTERNAL "" FORCE)
+
 if(NOT CMAKE_BUILD_TYPE)
    set(CMAKE_BUILD_TYPE "Release" CACHE STRING
            "Choose the type of build, options are: Debug Release
@@ -48,7 +50,8 @@ if(NOT DEFINED XIFO)
    set(XIFO 4)
 endif()
 
-set(CWB_OPTS "XIFO=${XIFO}" "_USE_CPP")
+# Fix the macso cross-compilation issue, see git.ligo.org issue#4
+set(CWB_OPTS "XIFO=${XIFO}" "_USE_CPP" "_Float16=short")
 
 
 #Find ROOT

pycwb-0.23.2/docs/source/index.rst

@@ -0,0 +1,148 @@
+.. pycWB documentation master file, created by
+   sphinx-quickstart on Wed Mar  8 13:16:45 2023.
+   You can adapt this file completely to your liking, but it should at least
+   contain the root `toctree` directive.
+
+Welcome to pycWB's documentation!
+===================================
+
+.. image:: https://readthedocs.org/projects/pycwb/badge/?version=latest
+   :target: https://pycwb.readthedocs.io/en/latest/
+   :alt: Documentations
+
+.. image:: https://git.ligo.org/yumeng.xu/pycwb/badges/main/pipeline.svg
+   :target: https://git.ligo.org/yumeng.xu/pycwb/-/pipelines
+   :alt: Build Status
+
+.. image:: https://git.ligo.org/yumeng.xu/pycwb/-/badges/release.svg
+   :target: https://git.ligo.org/yumeng.xu/pycwb/-/releases
+   :alt: Releases
+
+.. image:: https://badge.fury.io/py/pycWB.svg
+   :target: https://badge.fury.io/py/pycWB
+   :alt: PyPI version
+
+.. image:: https://img.shields.io/badge/license-GPLv3-blue
+   :target: https://git.ligo.org/yumeng.xu/pycwb/-/blob/main/LICENSE
+   :alt: License
+
+
+pycWB is a modularized Python package for gravitational wave burst search based on the core function of cWB.
+
+
+.. toctree::
+   :hidden:
+   :maxdepth: 5
+
+   install
+   credit
+   pycWB <modules>
+   genindex
+
+.. toctree::
+   :hidden:
+   :caption: User Guides
+   :maxdepth: 1
+
+   tutorials
+   schema
+
+.. toctree::
+   :hidden:
+   :caption: Developer Guides
+   :maxdepth: 1
+
+   mod_cwb
+
+
+Getting Started
+===============
+
+Installation
+------------
+
+PycWB is available on `PyPI <https://pypi.org/project/pycWB/>`_. You can install it with pip.
+Some dependencies are required to be installed before installing pycWB with pip.
+The easiest way is to install them with conda.
+
+.. code-block:: bash
+
+   conda create -n pycwb "python>=3.9,<3.11"
+   conda activate pycwb
+   conda install -c conda-forge root=6.26.10 healpix_cxx=3.81 nds2-client python-nds2-client lalsuite setuptools_scm cmake pkg-config
+   python3 -m pip install pycwb
+
+
+Run your first burst search
+---------------------------
+
+In your first burst search, we will use a built-in noise generator and waveform generator
+to minimize the requirement for external data. What you need is just one configuration file in YAML format.
+
+To start with, copy the example configuration folder from the source code or download the
+``user_parameters_injection.yaml`` manually from `here <https://git.ligo.org/yumeng.xu/pycwb/-/blob/main/examples/injection/user_parameters_injection.yaml>`_.
+
+.. code-block:: bash
+
+    cp -r [path_to_source_code]/examples/injection my_first_search
+
+Now, you are all set! You can directly run the example in the terminal with the ``pycwb run`` command
+
+.. code-block:: bash
+
+    pycwb run user_parameters_injection.yaml
+
+Or you can open the juptyer notebook ``pycwb_injection.ipynb`` (download `here <https://git.ligo.org/yumeng.xu/pycwb/-/blob/main/examples/injection/pycwb_injection.ipynb>`_)
+and run the search step by step
+
+Go deeper into pycWB.search
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+
+If you want to know more about the search process, please refer to
+:ref:`tutorial_search`
+
+Step by step injection!
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+
+If you want to know more about the injection process step by step, please refer to
+:ref:`tutorial_injection` or the juptyer notebook `pycwb_injection.ipynb`
+
+Command line interfaces (CLI)
+------------------------------
+
+It is recommended to use the command line interfaces (CLI) to run the search.
+You can get help by running the command with the ``-h`` option. Here are the current available commands:
+
+.. list-table:: Available Commands
+   :header-rows: 1
+
+   * - Command
+     - Description
+   * - ``pycwb run``
+     - Run a single search
+   * - ``pycwb batch-setup``
+     - Setup batch run
+   * - ``pycwb batch-runner``
+     - Runner for batch run, used for the job submission
+   * - ``pycwb flow``
+     - Run search with prefect flow
+   * - ``pycwb xtalk``
+     - Convert xtalk file
+   * - ``pycwb merge-catalog``
+     - Merge catalog files
+   * - ``pycwb server``
+     - Run a simple server to show the results
+
+
+Basic Workflow
+==============
+.. image:: workflow.png
+   :width: 100%
+   :align: center
+
+Indices and tables
+==================
+
+* :ref:`genindex`
+* :ref:`modindex`
+* :ref:`search`

{pycwb-0.23.0 → pycwb-0.23.2}/docs/source/tutorial_injection.rst

@@ -25,10 +25,6 @@ Next, load the environment and the configuration file:
     from pycwb.config import Config
     from pycwb.modules.logger import logger_init
 
-    if not os.environ.get('HOME_WAT_FILTERS'):
-        pyburst_path = os.path.dirname(os.path.abspath(pycwb.__file__))
-        os.environ['HOME_WAT_FILTERS'] = f"{os.path.abspath(pyburst_path)}/vendor"
-
     logger_init()
 
     config = Config('./user_parameters_injection.yaml')
@@ -39,12 +35,13 @@ Now, create an injection job using the parameters specified in the configuration
 
 .. code-block:: python
 
-    from pycwb.modules.read_data import generate_injection
+    from pycwb.modules.read_data import generate_injection, generate_noise_for_job_seg
     from pycwb.modules.job_segment import create_job_segment_from_injection
 
     job_segments = create_job_segment_from_injection(config.ifo, config.simulation, config.injection)
 
-    data = generate_injection(config, job_segments[0])
+    data = generate_noise_for_job_seg(job_segments[0], config.inRate)
+    data = generate_injection(config, job_segments[0], data)
 
 A pyCBC time series is generated for each detector defined in the configuration file.
 
@@ -85,7 +82,7 @@ Finally, calculate the likelihood for each supercluster:
 
     from pycwb.modules.likelihood import likelihood
 
-    events, clusters = likelihood(config, network, pwc_list)
+    events, clusters, skymap_statistics = likelihood(config, network, pwc_list)
 
 You can use the following code to plot the events on the spectrogram:
 

{pycwb-0.23.0 → pycwb-0.23.2}/docs/source/tutorial_search.rst

@@ -13,7 +13,7 @@ three parts: job generation and data analysis
 Job Control
 -----------------
 
-The job control part is done by :py:func:`pycwb.search.search`.
+The job control part is done by the functions in :py:func:`pycwb.workflow`.
 
 Initialize logger with log_file and log_level, if log_file is None, log will be printed to stdout.
 
@@ -22,15 +22,6 @@ Initialize logger with log_file and log_level, if log_file is None, log will be
    from pycwb.modules.logger import logger_init
    logger_init(log_file, log_level)
 
-set env HOME_WAT_FILTERS to the path of xdmXTalk. pycWB contains a sample xdmXTalk file in vendor folder.
-You can also use your own xdmXTalk file.
-
-.. code-block:: python
-
-   import os, pycwb
-
-   pycwb_path = os.path.dirname(os.path.abspath(pycwb.__file__))
-   os.environ['HOME_WAT_FILTERS'] = f"{os.path.abspath(pycwb_path)}/vendor"
 
 read user parameters from user_parameters.yaml to a :py:class:`.Config` object.
 

pycwb-0.23.2/envs/environment.yml

@@ -0,0 +1,15 @@
+name: pycwb
+channels:
+  - conda-forge
+  - igwn
+dependencies:
+  - cmake
+  - healpix_cxx=3.81
+  - lalsuite
+  - nds2-client
+  - pkg-config
+  - python-nds2-client
+  - python=3.10
+  - root=6.26.10
+  - setuptools_scm
+  - sphinx_rtd_theme