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‎.gitattributes‎

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external/** filter=lfs diff=lfs merge=lfs -text
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*.webp filter=lfs diff=lfs merge=lfs -text
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*.png filter=lfs diff=lfs merge=lfs -text

‎.gitignore‎

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*pyp_original/
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*.sif
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*.vscode
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src/pyp/*.vscode
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*.code-workspace
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*.nfs*
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*.pyc
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*.*.pyc
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*.nfs*
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*__pycache__
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*_regtest_outputs
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*cache
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singularity-example
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docs/_build/
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external/CSP/src/.currentRefine3D.dff
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external/CSP/src/CMakeCache.txt
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.CalculateFSC.dff
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.currentCtffind.dff
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.currentResample.dff
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.currentResize.dff
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external/CSP/src/csp_05_03_2021
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config/config.toml
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/.idea/
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external/CSP/csp_fboost
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external/CSP/csp
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external/CSP/csp_nofboost
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.pyp_history

‎LICENSE‎

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Copyright (c) 2023, Bartesaghi Lab
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Redistribution and use in source and binary forms, with or without
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modification, are permitted provided that the following conditions are met:
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1. Redistributions of source code must retain the above copyright notice, this
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list of conditions and the following disclaimer.
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2. Redistributions in binary form must reproduce the above copyright notice,
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this list of conditions and the following disclaimer in the documentation
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and/or other materials provided with the distribution.
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3. Neither the name of the copyright holder nor the names of its
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contributors may be used to endorse or promote products derived from
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this software without specific prior written permission.
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THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
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AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
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IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
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DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE
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FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
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DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
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SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
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CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
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OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
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OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.

‎Makefile‎

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init:
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git config core.hooksPath .githooks

‎README.rst‎

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============
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Introduction
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============
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PYP is a comprehensive package for Single-Particle Analysis (SPA) and Cryo-Electron Tomography (TOMO) image processing.
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The software is developed and maintained by the `Bartesaghi Lab <http://cryoem.cs.duke.edu>`_ at `Duke University <http://www.duke.edu>`_.
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Documentation
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=============
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The `documentation <https://nextpyp.app/files/pyp/latest/docs/reference/cli.html>`_ contains installation instructions and tutorials for Single-Particle and Tomography.

‎bin/3davg‎

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../src/launcher/bin/launcher

‎bin/byp‎

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../src/launcher/bin/launcher

‎bin/csp‎

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../src/pyp_csp.sh

‎bin/fyp‎

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../src/launcher/bin/launcher

‎bin/gyp‎

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../src/pyp_gain.sh

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