keyword stringclasses 7
values | repo_name stringlengths 8 98 | file_path stringlengths 4 244 | file_extension stringclasses 29
values | file_size int64 0 84.1M | line_count int64 0 1.6M | content stringlengths 1 84.1M ⌀ | language stringclasses 14
values |
|---|---|---|---|---|---|---|---|
3D | lvqiujie/Mol2Context-vec | tasks/lipop/test.py | .py | 1,506 | 40 | import torch
import torch.nn as nn
from torch.nn.utils.rnn import pack_padded_sequence, pad_packed_sequence
from tasks.lipop.train import LSTM, MyDataset
import torch.nn.functional as F
import torch.utils.data as data
import pandas as pd
from sklearn.externals import joblib
import numpy as np
# 设置超参数
input_size = 512
... | Python |
3D | lvqiujie/Mol2Context-vec | tasks/muv/get_muv_data.py | .py | 5,651 | 185 | import sys
sys.path.append('./')
import pandas as pd
import numpy as np
from rdkit import Chem
import os
from rdkit.Chem import Descriptors
from sklearn.externals import joblib
# step 1
filepath="muv/muv.csv"
df = pd.read_csv(filepath, header=0, encoding="gbk")
w_file = open("muv/muv.smi", mode='w', encoding="utf-8")
... | Python |
3D | lvqiujie/Mol2Context-vec | tasks/muv/muv_train.py | .py | 21,864 | 461 | import os
import torch
import torch.nn as nn
from torch.nn.utils.rnn import pack_padded_sequence, pad_packed_sequence
import torch.nn.functional as F
import torch.utils.data as data
import pandas as pd
from sklearn.externals import joblib
import numpy as np
import math
import random
from sklearn import metrics
from skl... | Python |
3D | lvqiujie/Mol2Context-vec | tasks/sider/sider_train.py | .py | 12,877 | 262 | import os
import torch
import torch.nn as nn
from torch.nn.utils.rnn import pack_padded_sequence, pad_packed_sequence
import torch.nn.functional as F
import torch.utils.data as data
import pandas as pd
from sklearn.externals import joblib
import numpy as np
import random
from sklearn import metrics
from sklearn.metrics... | Python |
3D | lvqiujie/Mol2Context-vec | tasks/sider/get_sider_data.py | .py | 5,522 | 179 | import pandas as pd
import numpy as np
from rdkit import Chem
import os
from rdkit.Chem import Descriptors
from sklearn.externals import joblib
# step 1
filepath="sider/sider.csv"
df = pd.read_csv(filepath, header=0, encoding="gbk")
w_file = open("sider/sider.smi", mode='w', encoding="utf-8")
all_label = []
all_smi =... | Python |
3D | lvqiujie/Mol2Context-vec | tasks/BBBP/get_BBBP_data.py | .py | 4,709 | 162 | import sys
sys.path.append('./')
import pandas as pd
import joblib
import numpy as np
import os
# step 1
filepath="BBBP/BBBP.csv"
df = pd.read_csv(filepath, header=0, encoding="gbk")
w_file = open("BBBP/BBBP.smi", mode='w', encoding="utf-8")
all_label = []
all_smi = []
for line in df.values:
smi = line[1]
if ... | Python |
3D | lvqiujie/Mol2Context-vec | tasks/BBBP/__init__.py | .py | 0 | 0 | null | Python |
3D | lvqiujie/Mol2Context-vec | tasks/BBBP/BBBP_train.py | .py | 9,523 | 215 | import os
import torch
import torch.nn as nn
from torch.nn.utils.rnn import pack_padded_sequence, pad_packed_sequence
import torch.nn.functional as F
import torch.utils.data as data
import pandas as pd
from sklearn.externals import joblib
import numpy as np
import math
import random
from sklearn import metrics
from skl... | Python |
3D | lvqiujie/Mol2Context-vec | context_vec/smi_model.py | .py | 20,741 | 414 | import sys
sys.path.append('./')
import os
import time
import gc
import numpy as np
from keras import backend as K
from keras.callbacks import ModelCheckpoint, EarlyStopping
from keras.layers import Dense, Input, SpatialDropout1D
from keras.layers import LSTM, CuDNNLSTM, Activation
from keras.layers import Lambda, Embe... | Python |
3D | lvqiujie/Mol2Context-vec | context_vec/train.py | .py | 5,463 | 143 | import os
import keras.backend as K
os.environ["CUDA_VISIBLE_DEVICES"] = "0"
from context_vec.smi_generator import SMIDataGenerator
from context_vec.smi_model import Context_vec
import tensorflow as tf
from tensorflow import keras
config = tf.ConfigProto()
config.gpu_options.allow_growth = True
sess = tf.Session(config... | Python |
3D | lvqiujie/Mol2Context-vec | context_vec/__init__.py | .py | 0 | 0 | null | Python |
3D | lvqiujie/Mol2Context-vec | context_vec/smi_generator.py | .py | 6,425 | 140 | import numpy as np
import keras
class SMIDataGenerator(keras.utils.Sequence):
"""Generates data for Keras"""
def __len__(self):
"""Denotes the number of batches per epoch"""
return int(np.ceil(len(self.indices)/self.batch_size))
def __init__(self, corpus, vocab, sentence_maxlen=100, toke... | Python |
3D | lvqiujie/Mol2Context-vec | context_vec/split.py | .py | 2,539 | 85 | import numpy as np
import os
import random
mols_src_all = []
all_dict = {}
with open("data/datasets/my_smi_0/mols.cp_UNK") as fp:
for i, line in enumerate(fp):
mols_src_all.append(line)
for j, token in enumerate(line.split()):
token = token.strip()
if token in all_dict:
... | Python |
3D | lvqiujie/Mol2Context-vec | context_vec/custom_layers/__init__.py | .py | 141 | 4 | from .dropout import TimestepDropout
from .masking import Camouflage
from .highway import Highway
from .sampled_softmax import SampledSoftmax | Python |
3D | lvqiujie/Mol2Context-vec | context_vec/custom_layers/masking.py | .py | 1,345 | 40 | # -*- coding: utf-8 -*-
"""Core Keras layers.
"""
from __future__ import absolute_import
from __future__ import division
from __future__ import print_function
from keras import backend as K
from keras.engine.base_layer import Layer
class Camouflage(Layer):
"""Masks a sequence by using a mask value to skip times... | Python |
3D | lvqiujie/Mol2Context-vec | context_vec/custom_layers/sampled_softmax.py | .py | 3,026 | 64 | from keras.layers import Layer
import keras.backend as K
class SampledSoftmax(Layer):
"""Sampled Softmax, a faster way to train a softmax classifier over a huge number of classes.
# Arguments
num_classes: number of classes
num_sampled: number of classes to be sampled at each batch
tie... | Python |
3D | lvqiujie/Mol2Context-vec | context_vec/custom_layers/dropout.py | .py | 985 | 38 | # -*- coding: utf-8 -*-
from __future__ import absolute_import
from __future__ import division
from keras import backend as K
from keras.engine import InputSpec
from keras.layers import Dropout
class TimestepDropout(Dropout):
"""Word Dropout.
This version performs the same function as Dropout, however it dr... | Python |
3D | lvqiujie/Mol2Context-vec | context_vec/custom_layers/highway.py | .py | 7,259 | 140 | from keras.layers.core import Layer
from keras import initializers, regularizers, constraints, activations
from keras.initializers import Constant
from keras import backend as K
class Highway(Layer):
"""Highway network, a natural extension of LSTMs to feedforward networks.
# Arguments
activation: Act... | Python |
3D | czimaginginstitute/2024_czii_mlchallenge_notebooks | blob_detector_inference.ipynb | .ipynb | 17,911 | 448 | {
"cells": [
{
"cell_type": "markdown",
"metadata": {},
"source": [
"This is a blob detector that does a poor job but is an example of a fast running solution that processes all tomograms and generates a submission without training."
]
},
{
"cell_type": "code",
"execution_count": null,
"... | Unknown |
3D | czimaginginstitute/2024_czii_mlchallenge_notebooks | SECURITY.md | .md | 193 | 4 | ## Reporting Security Issues
If you believe you have found a security issue, please responsibly disclose by contacting us at [security@chanzuckerberg.com](mailto:security@chanzuckerberg.com).
| Markdown |
3D | czimaginginstitute/2024_czii_mlchallenge_notebooks | overview.ipynb | .ipynb | 805,308 | 808 | {
"cells": [
{
"cell_type": "code",
"execution_count": 1,
"metadata": {},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"Collecting napari\n",
" Downloading napari-0.5.3-py3-none-any.whl.metadata (13 kB)\n",
"Collecting monai\n",
" Using ... | Unknown |
3D | czimaginginstitute/2024_czii_mlchallenge_notebooks | tomotwin_picking_notebook/copick_tools.py | .py | 17,174 | 520 | import json
import os
from typing import Any, Dict, List
import copick
import numpy as np
import ome_zarr.writer
import starfile
import zarr
from scipy.spatial.transform import Rotation as R
def get_copick_project_tomo_ids(copickRoot):
copickRoot = copick.from_file(copickRoot)
tomoIDs = [run.name for run in ... | Python |
3D | czimaginginstitute/2024_czii_mlchallenge_notebooks | tomotwin_picking_notebook/tomotwin_notebook_helper.py | .py | 14,350 | 447 | import subprocess
import numpy as np
import pandas as pd
from pathlib import Path
def save_mrc(
mic: np.ndarray,
filename: str | Path,
*,
overwrite: bool = True,
voxel_size: list | tuple = None,
):
"""
Save a numpy array to MRC format.
Parameters:
mic (np.ndarray): The numpy ... | Python |
3D | czimaginginstitute/2024_czii_mlchallenge_notebooks | tomotwin_picking_notebook/tomotwin_notebook_inference.ipynb | .ipynb | 396,036 | 1,052 | {
"cells": [
{
"cell_type": "markdown",
"metadata": {},
"source": [
"# <span style=\"color:#cc241d\">Using TomoTwin for particle picking</span>\n",
"\n",
"TomoTwin is an embedding-based cryo-ET particle picking procedure for cryo-ET [[1](https://tomotwin-cryoet.readthedocs.io/en/stable/index.htm... | Unknown |
3D | czimaginginstitute/2024_czii_mlchallenge_notebooks | 3d_unet_monai/train.ipynb | .ipynb | 589,540 | 2,500 | {
"cells": [
{
"cell_type": "markdown",
"id": "d8cbcb34-b7a9-4bd3-af85-6263ac3ee83d",
"metadata": {},
"source": [
"# Training 3D U-Net model for multi-class semantic segmentation"
]
},
{
"cell_type": "markdown",
"id": "936c827d-9270-4137-8049-3b2b8845f6f1",
"metadata": {},
"source"... | Unknown |
3D | czimaginginstitute/2024_czii_mlchallenge_notebooks | 3d_unet_monai/inference.ipynb | .ipynb | 633,135 | 508 | {
"cells": [
{
"cell_type": "code",
"execution_count": 11,
"id": "60fecd04-06e4-4544-8329-7393e2817ea8",
"metadata": {},
"outputs": [],
"source": [
"import torch\n",
"from monai.networks.nets import UNet\n",
"from monai.inferers import sliding_window_inference"
]
},
{
"cell_ty... | Unknown |
3D | czimaginginstitute/2024_czii_mlchallenge_notebooks | DeepFindET/train.ipynb | .ipynb | 962,774 | 1,025 | {
"cells": [
{
"cell_type": "markdown",
"metadata": {},
"source": [
"## 3D CNN Instance Segmentation of Proteins in Cryo-ET Tomograms\n",
"\n",
"This tutorial guides you through the process of training 3D U-Nets for instance segmentation of proteins in Cryo-ET tomograms. It draws inspiration fro... | Unknown |
3D | czimaginginstitute/2024_czii_mlchallenge_notebooks | DeepFindET/inference.ipynb | .ipynb | 933,033 | 5,248 | {
"cells": [
{
"cell_type": "markdown",
"metadata": {},
"source": [
"## 3D CNN Instance Segmentation of Proteins in Cryo-ET Tomograms (Inference / Prediction)\n",
"\n",
"This tutorial walks you through the process of using trained 3D U-Nets for instance segmentation of proteins within Cryo-ET to... | Unknown |
3D | febiosoftware/FEBio | BUILD.md | .md | 12,568 | 117 | # FEBio Build Guide
### Table of contents
- [Prerequisites](#prereq)
- [Running CMake](#runCMake)
- [Building FEBio](#build)
- [Limitations of CMake](#limits)
- [Troubleshooting](#trouble)
## Prerequisites <a name="prereq"></a>
### CMake
FEBio's build process utilizes CMake, an open-source, cross-platform tool des... | Markdown |
3D | febiosoftware/FEBio | ROADMAP.md | .md | 2,318 | 35 | # Roadmap
This roadmap briefly discusses some planned milestones for the FEBio project.
Please check out our [contribution guidelines](CONTRIBUTING.md) and [code of conduct](CODE_OF_CONDUCT.md) for information on how to contribute to the FEBio project.
## Main Milestones
The main focus at this point is the impleme... | Markdown |
3D | febiosoftware/FEBio | CONTRIBUTING.md | .md | 2,003 | 29 | # Contribution Guidelines
## Reporting issues
- **Search for existing issues.** Please check to see if someone else has reported the same issue.
- **Share as much information as possible.** Include operating system and version, browser and version. Also, include steps to reproduce the bug.
## Project Setup
Refer to ... | Markdown |
3D | febiosoftware/FEBio | CODE_OF_CONDUCT.md | .md | 5,217 | 128 | # Contributor Covenant Code of Conduct
## Our Pledge
We as members, contributors, and leaders pledge to make participation in our
community a harassment-free experience for everyone, regardless of age, body
size, visible or invisible disability, ethnicity, sex characteristics, gender
identity and expression, level of... | Markdown |
3D | febiosoftware/FEBio | infrastructure/common/linux/apt.sh | .sh | 772 | 23 | #!/bin/bash
set -e
export DEBIAN_FRONTEND=noninteractive
SUDO=""
if command -v sudo &> /dev/null
then
SUDO=$(which sudo)
fi
$SUDO apt-get update
$SUDO apt-get install linux-headers-generic -y
$SUDO apt-get install software-properties-common wget gpg sudo -y
$SUDO apt-get update --fix-missing
wget -O- https://apt.re... | Shell |
3D | febiosoftware/FEBio | infrastructure/common/linux/aws.sh | .sh | 203 | 8 | #!/bin/bash
# set -e
export DEBIAN_FRONTEND=noninteractive
sudo curl "https://awscli.amazonaws.com/awscli-exe-linux-x86_64.zip" -o "awscliv2.zip"
sudo unzip awscliv2.zip
sudo ./aws/install
aws --version
| Shell |
3D | febiosoftware/FEBio | infrastructure/common/linux/cmake.sh | .sh | 141 | 8 | #!/bin/bash
set -e
export DEBIAN_FRONTEND=noninteractive
sudo apt update
sudo apt install libssl3 cmake cmake-curses-gui -y
cmake --version
| Shell |
3D | febiosoftware/FEBio | infrastructure/common/linux/git.sh | .sh | 218 | 13 | #!/bin/bash
set -e
export DEBIAN_FRONTEND=noninteractive
if command -v git &> /dev/null
then
git --version
fi
sudo add-apt-repository ppa:git-core/ppa -y
sudo apt-get update
sudo apt-get install git -y
git --version
| Shell |
3D | febiosoftware/FEBio | infrastructure/common/linux/openapi.sh | .sh | 429 | 14 | #!/bin/bash
set -e
export DEBIAN_FRONTEND=noninteractive
SUDO=""
if command -v sudo &> /dev/null
then
SUDO=$(which sudo)
fi
INSTALLER="intel-oneapi-base-toolkit-2025.0.1.46_offline.sh"
aws s3 cp "s3://febiosoftware/linux/oneapi/${INSTALLER}" .
chmod +x ./$INSTALLER
$SUDO ./intel-oneapi-base-toolkit-2025.0.1.46_offlin... | Shell |
3D | febiosoftware/FEBio | infrastructure/common/linux/qt.sh | .sh | 226 | 12 | #!/bin/bash
set -e
export DEBIAN_FRONTEND=noninteractive
SUDO=""
if command -v sudo &> /dev/null
then
SUDO=$(which sudo)
fi
$SUDO pip install aqtinstall -v
$SUDO aqt install-qt --outputdir /opt/Qt linux desktop 6.9.3 -m all
| Shell |
3D | febiosoftware/FEBio | infrastructure/common/linux/install-builder.sh | .sh | 381 | 15 | #!/bin/bash
set -ex
export DEBIAN_FRONTEND=noninteractive
pushd /tmp
INSTALLER="installbuilder-enterprise-23.11.0-linux-x64-installer.run"
aws s3 cp "s3://febiosoftware/linux/installbuilder/${INSTALLER}" .
chmod +x ./$INSTALLER
sudo ./$INSTALLER \
--mode unattended \
--installer-language en
sudo ln -s /opt/installb... | Shell |
3D | febiosoftware/FEBio | infrastructure/common/linux/dependencies/mmg.sh | .sh | 599 | 34 | #! /bin/bash
set -o errexit
set -o verbose
# shellcheck disable=1091
. ./common-functions.sh
MMG="https://github.com/MmgTools/mmg.git"
BRANCH="v5.7.3"
build_and_install() {
local source=$1
local branch=$2
git clone --depth 1 --branch "$branch" "$source" "$branch"
pushd $branch || exit 1
cmake . -B cmbuild \... | Shell |
3D | febiosoftware/FEBio | infrastructure/common/linux/dependencies/levmar.sh | .sh | 488 | 31 | #! /bin/bash
set -o errexit
set -o verbose
REPO=https://github.com/jturney/levmar.git
DIR=levmar
build_and_install() {
local repo=$1
local dir=$2
git clone $repo $dir
pushd $dir
cmake . -B cmbuild \
-DCMAKE_INSTALL_PREFIX="/usr/local" \
-DCMAKE_POSITION_INDEPENDENT_CODE=ON \
-DBUILD_DEMO:BOOLEAN=false
pu... | Shell |
3D | febiosoftware/FEBio | infrastructure/common/linux/dependencies/netgen.sh | .sh | 1,099 | 51 | #! /bin/bash
set -o errexit
set -o verbose
NETGEN="https://github.com/NGSolve/netgen.git"
BRANCH="v6.2.2406"
build_and_install() {
local source=$1
local branch=$2
git clone --depth 1 --branch "$branch" "$source" "$branch"
pushd $branch || exit 1
git submodule update --init --recursive
cmake . -LA -B cmbuild \... | Shell |
3D | febiosoftware/FEBio | infrastructure/common/linux/dependencies/hypre.sh | .sh | 751 | 37 | #! /bin/bash
set -o errexit
set -o verbose
# shellcheck disable=1091
. ./common-functions.sh
HYPRE_SOURCE="https://github.com/hypre-space/hypre/archive/refs/tags/v2.23.0.zip"
HYPRE_ARCHIVE=$(basename $HYPRE_SOURCE)
HYPRE_PATH="hypre-2.23.0"
build_and_install() {
local source=$1
pushd "$source" || exit 1
pushd src... | Shell |
3D | febiosoftware/FEBio | infrastructure/common/linux/dependencies/tetgen.sh | .sh | 672 | 33 | #! /bin/bash
set -o errexit
set -o verbose
# shellcheck disable=1091
. ./common-functions.sh
TETGEN_GIT="https://github.com/ufz/tetgen.git"
TETGEN_FILENAME=$(basename $TETGEN_GIT)
TETGEN_SOURCE_DIR="${TETGEN_FILENAME%.*}"
build_and_install() {
local git_remote=$1
local src_dir=$2
git clone $git_remote $src_dir
... | Shell |
3D | febiosoftware/FEBio | infrastructure/common/linux/dependencies/libzip.sh | .sh | 965 | 49 | #! /bin/bash
set -o errexit
set -o verbose
# shellcheck disable=1091
. ./common-functions.sh
SOURCE="https://github.com/nih-at/libzip.git"
BRANCH="v1.10.1"
build_and_install() {
local source=$1
local branch=$2
git clone --depth 1 --branch "$branch" "$source" "$branch"
pushd $branch || exit 1
cmake . -LA -B cm... | Shell |
3D | febiosoftware/FEBio | infrastructure/common/linux/dependencies/python.sh | .sh | 166 | 10 | curl https://pyenv.run | bash
export PYENV_ROOT="$HOME/.pyenv"
export PATH="$PYENV_ROOT/bin:$PATH"
eval "$(pyenv init -)"
pyenv install 3.13.1
pyenv global 3.13.1
| Shell |
3D | febiosoftware/FEBio | infrastructure/common/linux/dependencies/itk.sh | .sh | 759 | 39 | #! /bin/bash
set -o errexit
set -o verbose
# shellcheck disable=1091
. ./common-functions.sh
ITK="https://github.com/InsightSoftwareConsortium/ITK.git"
BRANCH="v5.2.1"
build_and_install() {
local source=$1
local branch=$2
git clone --depth 1 --branch "$branch" "$source" "$branch"
pushd $branch || exit 1
cmake .... | Shell |
3D | febiosoftware/FEBio | infrastructure/common/linux/dependencies/quazip.sh | .sh | 558 | 33 | #! /bin/bash
set -o errexit
set -o verbose
# shellcheck disable=1091
. ./common-functions.sh
QUAZIP="https://github.com/stachenov/quazip.git"
BRANCH="v1.4"
build_and_install() {
local source=$1
local branch=$2
git clone --depth 1 --branch "$branch" "$source" "$branch"
pushd $branch || exit 1
cmake . -LA -B cmb... | Shell |
3D | febiosoftware/FEBio | infrastructure/common/linux/dependencies/sitk.sh | .sh | 723 | 38 | #! /bin/bash
set -o errexit
set -o verbose
# shellcheck disable=1091
. ./common-functions.sh
SITK="https://github.com/SimpleITK/SimpleITK.git"
BRANCH="v2.1.1.2"
build_and_install() {
local source=$1
local branch=$2
git clone --depth 1 --branch "$branch" "$source" "$branch"
pushd $branch || exit 1
cmake . -LA -... | Shell |
3D | febiosoftware/FEBio | infrastructure/common/linux/dependencies/ffmpeg.sh | .sh | 617 | 38 | #!/bin/bash
set -e
REPO="https://github.com/FFmpeg/FFmpeg.git"
BRANCH="n6.1"
build_and_install() {
local source=$1
local branch=$2
git clone --depth 1 --branch "$branch" "$source" "$branch"
pushd $BRANCH
./configure \
--disable-everything \
--disable-programs \
--disable-doc \
--disable-stat... | Shell |
3D | febiosoftware/FEBio | infrastructure/common/linux/dependencies/occt.sh | .sh | 1,528 | 62 | #! /bin/bash
set -o errexit
set -o verbose
# shellcheck disable=1091
. ./common-functions.sh
OCCT="https://github.com/Open-Cascade-SAS/OCCT.git"
BRANCH="V7_7_2"
build_and_install() {
local source=$1
local branch=$2
git clone --depth 1 --branch "$branch" "$source" "$branch"
pushd $branch || exit 1
cmake . -B cmb... | Shell |
3D | febiosoftware/FEBio | infrastructure/common/linux/dependencies/install.sh | .sh | 377 | 24 | #! /bin/bash
set -o errexit
set -o verbose
export BUILD_PATH=/tmp/src
mkdir -p $BUILD_PATH
SETVARS="${SETVARS:-/opt/intel/oneapi/setvars.sh}"
. $SETVARS
main() {
local dir=$1
pushd $dir
local installers=(hypre levmar mmg tetgen itk sitk occt netgen libzip ffmpeg python)
for installer in ${installers[@]}; do
.... | Shell |
3D | febiosoftware/FEBio | infrastructure/common/linux/dependencies/common-functions.sh | .sh | 138 | 14 | #! /bin/bash
download_source() {
local source=$1
curl -L -O "$source"
}
extract_source() {
local archive=$1
unzip -o "$archive"
}
| Shell |
3D | febiosoftware/FEBio | infrastructure/common/macos/installation_prep.sh | .sh | 296 | 16 | #!/bin/zsh
set -ex
if [ -d "${INSTALLATION_PATH}" ]; then
echo "Paths already configured"
exit
fi
mkdir -p "${SOURCE_PATH}"
mkdir -p "${INSTALLATION_PATH}"
chown -R "${SSH_USER}" "${INSTALLATION_PATH}"
cat << EOF >> /Users/$SSH_USER/.zprofile
export PATH="\$PATH:${INSTALLATION_PATH}"
EOF
| Shell |
3D | febiosoftware/FEBio | infrastructure/common/macos/mmg.sh | .sh | 343 | 18 | #!/bin/zsh
pushd $SOURCE_PATH
git clone https://github.com/MmgTools/mmg.git
pushd mmg
git checkout v5.7.3
cmake . -L -B cmbuild \
-DCMAKE_INSTALL_PREFIX="/Users/gitRunner/local/x86_64" \
-DCMAKE_OSX_ARCHITECTURES="x86_64" \
-DCMAKE_OSX_DEPLOYMENT_TARGET=10.15
pushd cmbuild
make install -j $(sysctl -n hw.ncpu)
pop... | Shell |
3D | febiosoftware/FEBio | infrastructure/common/macos/levmar.sh | .sh | 390 | 19 | #!/bin/zsh
pushd $SOURCE_PATH
git clone https://github.com/jturney/levmar.git
pushd levmar
cmake . -LA -B cmbuild \
-DCMAKE_INSTALL_PREFIX="$INSTALLATION_PATH" \
-DCMAKE_POSITION_INDEPENDENT_CODE=ON \
-DBUILD_DEMO:BOOLEAN=false \
-DCMAKE_OSX_ARCHITECTURES="x86_64" \
-DCMAKE_OSX_DEPLOYMENT_TARGET=10.15
pushd cmbu... | Shell |
3D | febiosoftware/FEBio | infrastructure/common/macos/netgen.sh | .sh | 910 | 38 | #!/bin/zsh
pushd $SOURCE_PATH
git clone --depth 1 --branch "v6.2.2406" "https://github.com/NGSolve/netgen.git"
pushd netgen
cmake . -L -B cmbuild \
-DCMAKE_BUILD_TYPE=Release \
-DCMAKE_INSTALL_PREFIX="$INSTALLATION_PATH" \
-DUSE_CCACHE:BOOL=OFF \
-DUSE_CGNS:BOOL=OFF \
-DUSE_CSG:BOOL=ON \
-DUSE_GEOM2D:BOO... | Shell |
3D | febiosoftware/FEBio | infrastructure/common/macos/hypre.sh | .sh | 373 | 19 | #!/bin/zsh
pushd $SOURCE_PATH
git clone https://github.com/hypre-space/hypre.git
pushd hypre/src
cmake . -L -B cmbuild \
-DCMAKE_INSTALL_PREFIX="$INSTALLATION_PATH" \
-DHYPRE_HAVE_MPI=Off \
-DHYPRE_WITH_MPI=Off \
-DCMAKE_OSX_ARCHITECTURES="x86_64" \
-DCMAKE_OSX_DEPLOYMENT_TARGET=10.15
pushd cmbuild
make install... | Shell |
3D | febiosoftware/FEBio | infrastructure/common/macos/tetgen.sh | .sh | 324 | 19 | #!/bin/zsh
pushd $SOURCE_PATH
git clone "https://github.com/ufz/tetgen.git"
pushd tetgen
cmake . -L -B cmbuild \
-DCMAKE_INSTALL_PREFIX="$INSTALLATION_PATH" \
-DCMAKE_OSX_ARCHITECTURES="x86_64" \
-DCMAKE_OSX_DEPLOYMENT_TARGET=10.15
pushd cmbuild
make -j $(sysctl -n hw.ncpu)
make install
popd
popd
rm -rf tetgen
p... | Shell |
3D | febiosoftware/FEBio | infrastructure/common/macos/libzip.sh | .sh | 804 | 36 | #!/bin/zsh
pushd $SOURCE_PATH
repo="https://github.com/nih-at/libzip.git"
branch="v1.10.1"
git clone --depth 1 --branch "$branch" "$repo" "$branch"
pushd $branch
cmake . -LA -B cmbuild \
-DCMAKE_INSTALL_PREFIX="$INSTALLATION_PATH" \
-DBUILD_DOC=OFF \
-DBUILD_EXAMPLES=OFF \
-DBUILD_OSSFUZZ=OFF \
-DBUILD_REG... | Shell |
3D | febiosoftware/FEBio | infrastructure/common/macos/homebrew-packages.sh | .sh | 177 | 7 | #!/bin/zsh
set -ex
packages=(jq awscli eigen glew libssh libssh2 yasm zstd pcre2 harfbuzz freetype pkg-config jpeg-turbo)
arch -x86_64 $HOMEBREW_BIN install "${packages[@]}"
| Shell |
3D | febiosoftware/FEBio | infrastructure/common/macos/itk.sh | .sh | 580 | 24 | #!/bin/zsh
pushd $SOURCE_PATH
git clone --depth 1 --branch "v5.2.1" "https://github.com/InsightSoftwareConsortium/ITK.git"
pushd ITK
cmake . -L -B cmbuild \
-DCMAKE_INSTALL_PREFIX="$INSTALLATION_PATH" \
-DBUILD_EXAMPLES:BOOL=OFF \
-DBUILD_SHARED_LIBS:BOOL=OFF \
-DBUILD_TESTING:BOOL=OFF \
-DITK_USE_SYSTEM_EIG... | Shell |
3D | febiosoftware/FEBio | infrastructure/common/macos/sitk.sh | .sh | 514 | 22 | #!/bin/zsh
pushd $SOURCE_PATH
git clone --depth 1 --branch "v2.1.1.2" "https://github.com/SimpleITK/SimpleITK.git"
pushd SimpleITK
cmake . -L -B cmbuild \
-DCMAKE_INSTALL_PREFIX="$INSTALLATION_PATH" \
-DWRAP_DEFAULT:BOOL=OFF \
-DBUILD_EXAMPLES:BOOL=OFF \
-DBUILD_TESTING:BOOL=OFF \
-DBUILD_SHARED_LIBS:BOOL=OF... | Shell |
3D | febiosoftware/FEBio | infrastructure/common/macos/ffmpeg.sh | .sh | 627 | 34 | #!/bin/zsh
set -e
REPO="https://github.com/FFmpeg/FFmpeg.git"
BRANCH="n6.1"
pushd $SOURCE_PATH
rm -rf "${SOURCE_PATH}/${BRANCH}"
export MACOSX_DEPLOYMENT_TARGET=10.15
export MACOSX_DEPLOYMENT_ARCHITECTURES=x86_64
git clone --depth 1 --branch $BRANCH $REPO $BRANCH
pushd $BRANCH
arch -x86_64 ./configure \
--disab... | Shell |
3D | febiosoftware/FEBio | infrastructure/common/macos/occt.sh | .sh | 1,326 | 46 | #!/bin/zsh
pushd $SOURCE_PATH
git clone --depth 1 --branch "V7_7_2" "https://github.com/Open-Cascade-SAS/OCCT.git"
pushd OCCT
cmake . -L -B cmbuild \
-DCMAKE_INSTALL_PREFIX="$INSTALLATION_PATH" \
-DBUILD_DOC_Overview:BOOL=OFF \
-DBUILD_ENABLE_FPE_SIGNAL_HANDLER:BOOL=OFF \
-DBUILD_Inspector:BOOL=OFF \
-DBUIL... | Shell |
3D | febiosoftware/FEBio | infrastructure/common/macos/openapi.sh | .sh | 622 | 20 | #!/bin/bash
set -e
if [ -f /opt/intel/oneapi/setvars.sh ]; then
echo "Oneapi was previously installed"
exit 0
fi
TARGET_DIR="/tmp/intel"
ONEAPI_FILE="m_BaseKit_p_2023.2.0.49398_offline"
ONEAPI_DMG="$ONEAPI_FILE.dmg"
ONEAPI_URI="https://registrationcenter-download.intel.com/akdlm/IRC_NAS/cd013e6c-49c4-488b-8b86-25df... | Shell |
3D | febiosoftware/FEBio | infrastructure/common/macos/lua.sh | .sh | 165 | 9 | #!/bin/zsh
set -ex
arch -x86_64 $HOMEBREW_BIN install lua@5.3
cat << EOF >> /Users/$SSH_USER/.zprofile
export PATH="${HOMEBREW_PREFIX}/opt/lua@5.3/bin:\$PATH"
EOF
| Shell |
3D | febiosoftware/FEBio | infrastructure/common/macos/rosetta.sh | .sh | 177 | 9 | #!/bin/bash
set -e
if arch -x86_64 /usr/bin/true 2> /dev/null; then
echo "Rosetta previously installed"
else
/usr/sbin/softwareupdate --install-rosetta --agree-to-license
fi
| Shell |
3D | febiosoftware/FEBio | infrastructure/common/macos/homebrew-x86.sh | .sh | 389 | 15 | #!/bin/bash
set -ex
if [ -f "${HOMEBREW_BIN}" ]; then
echo "Homebrew already installed at: ${HOMEBREW_PREFIX}"
exit
fi
git clone https://github.com/Homebrew/brew.git $HOMEBREW_PREFIX
cat << EOF >> /Users/$SSH_USER/.zprofile
export HOMEBREW_PREFIX="${HOMEBREW_PREFIX}"
export PATH="\$PATH:${HOMEBREW_PREFIX}:${HOMEBR... | Shell |
3D | febiosoftware/FEBio | infrastructure/common/macos/qt.sh | .sh | 846 | 38 | #!/bin/zsh
set -e
REPO="https://github.com/qt/qtbase.git"
BRANCH="v6.6.1"
pushd $SOURCE_PATH
rm -rf "${SOURCE_PATH}/${BRANCH}"
git clone --depth 1 --branch $BRANCH $REPO $BRANCH
pushd $BRANCH
cmake . -G Ninja -L -B cmbuild \
-DCMAKE_OSX_ARCHITECTURES="x86_64" \
-DCMAKE_OSX_DEPLOYMENT_TARGET=10.15 \
-DCMAKE_IN... | Shell |
3D | febiosoftware/FEBio | FEBioRVE/FE2OMicroConstraint.cpp | .cpp | 11,063 | 432 | /*This file is part of the FEBio source code and is licensed under the MIT license
listed below.
See Copyright-FEBio.txt for details.
Copyright (c) 2021 University of Utah, The Trustees of Columbia University in
the City of New York, and others.
Permission is hereby granted, free of charge, to any person obtaining a... | C++ |
3D | febiosoftware/FEBio | FEBioRVE/FEElasticMaterial2O.h | .h | 3,253 | 99 | /*This file is part of the FEBio source code and is licensed under the MIT license
listed below.
See Copyright-FEBio.txt for details.
Copyright (c) 2021 University of Utah, The Trustees of Columbia University in
the City of New York, and others.
Permission is hereby granted, free of charge, to any person obtaining a... | Unknown |
3D | febiosoftware/FEBio | FEBioRVE/febiorve_api.h | .h | 1,531 | 44 | /*This file is part of the FEBio source code and is licensed under the MIT license
listed below.
See Copyright-FEBio.txt for details.
Copyright (c) 2021 University of Utah, The Trustees of Columbia University in
the City of New York, and others.
Permission is hereby granted, free of charge, to any person obtaining a... | Unknown |
3D | febiosoftware/FEBio | FEBioRVE/FEMultiscaleDomainFactory.cpp | .cpp | 859 | 25 | #include "stdafx.h"
#include "FEMultiscaleDomainFactory.h"
#include "FEMicroMaterial.h"
#include "FEMicroMaterial2O.h"
#include "FEElasticMultiscaleDomain1O.h"
#include "FEElasticMultiscaleDomain2O.h"
//==========================================================================================
FEDomain* FEMultiScaleDom... | C++ |
3D | febiosoftware/FEBio | FEBioRVE/FEElasticSolidDomain2O.cpp | .cpp | 65,319 | 2,119 | /*This file is part of the FEBio source code and is licensed under the MIT license
listed below.
See Copyright-FEBio.txt for details.
Copyright (c) 2021 University of Utah, The Trustees of Columbia University in
the City of New York, and others.
Permission is hereby granted, free of charge, to any person obtaining a... | C++ |
3D | febiosoftware/FEBio | FEBioRVE/stdafx.h | .h | 13 | 2 | #pragma once
| Unknown |
3D | febiosoftware/FEBio | FEBioRVE/FEElasticMultiscaleDomain1O.h | .h | 1,815 | 43 | /*This file is part of the FEBio source code and is licensed under the MIT license
listed below.
See Copyright-FEBio.txt for details.
Copyright (c) 2021 University of Utah, The Trustees of Columbia University in
the City of New York, and others.
Permission is hereby granted, free of charge, to any person obtaining a... | Unknown |
3D | febiosoftware/FEBio | FEBioRVE/FERVEProbe.h | .h | 2,609 | 80 | /*This file is part of the FEBio source code and is licensed under the MIT license
listed below.
See Copyright-FEBio.txt for details.
Copyright (c) 2021 University of Utah, The Trustees of Columbia University in
the City of New York, and others.
Permission is hereby granted, free of charge, to any person obtaining a... | Unknown |
3D | febiosoftware/FEBio | FEBioRVE/FERVEModel.h | .h | 3,385 | 111 | /*This file is part of the FEBio source code and is licensed under the MIT license
listed below.
See Copyright-FEBio.txt for details.
Copyright (c) 2021 University of Utah, The Trustees of Columbia University in
the City of New York, and others.
Permission is hereby granted, free of charge, to any person obtaining a... | Unknown |
3D | febiosoftware/FEBio | FEBioRVE/FEElasticMaterial2O.cpp | .cpp | 3,722 | 107 | /*This file is part of the FEBio source code and is licensed under the MIT license
listed below.
See Copyright-FEBio.txt for details.
Copyright (c) 2021 University of Utah, The Trustees of Columbia University in
the City of New York, and others.
Permission is hereby granted, free of charge, to any person obtaining a... | C++ |
3D | febiosoftware/FEBio | FEBioRVE/FEElasticMultiscaleDomain2O.h | .h | 1,971 | 52 | /*This file is part of the FEBio source code and is licensed under the MIT license
listed below.
See Copyright-FEBio.txt for details.
Copyright (c) 2021 University of Utah, The Trustees of Columbia University in
the City of New York, and others.
Permission is hereby granted, free of charge, to any person obtaining a... | Unknown |
3D | febiosoftware/FEBio | FEBioRVE/FEPeriodicBoundary2O.cpp | .cpp | 16,710 | 688 | /*This file is part of the FEBio source code and is licensed under the MIT license
listed below.
See Copyright-FEBio.txt for details.
Copyright (c) 2021 University of Utah, The Trustees of Columbia University in
the City of New York, and others.
Permission is hereby granted, free of charge, to any person obtaining a... | C++ |
3D | febiosoftware/FEBio | FEBioRVE/FEPeriodicBoundary2O.h | .h | 3,348 | 102 | /*This file is part of the FEBio source code and is licensed under the MIT license
listed below.
See Copyright-FEBio.txt for details.
Copyright (c) 2021 University of Utah, The Trustees of Columbia University in
the City of New York, and others.
Permission is hereby granted, free of charge, to any person obtaining a... | Unknown |
3D | febiosoftware/FEBio | FEBioRVE/FEMicroMaterial2O.cpp | .cpp | 5,218 | 155 | /*This file is part of the FEBio source code and is licensed under the MIT license
listed below.
See Copyright-FEBio.txt for details.
Copyright (c) 2021 University of Utah, The Trustees of Columbia University in
the City of New York, and others.
Permission is hereby granted, free of charge, to any person obtaining a... | C++ |
3D | febiosoftware/FEBio | FEBioRVE/FEPeriodicBoundary1O.h | .h | 3,233 | 98 | /*This file is part of the FEBio source code and is licensed under the MIT license
listed below.
See Copyright-FEBio.txt for details.
Copyright (c) 2021 University of Utah, The Trustees of Columbia University in
the City of New York, and others.
Permission is hereby granted, free of charge, to any person obtaining a... | Unknown |
3D | febiosoftware/FEBio | FEBioRVE/FEPeriodicLinearConstraint2O.h | .h | 2,038 | 65 | /*This file is part of the FEBio source code and is licensed under the MIT license
listed below.
See Copyright-FEBio.txt for details.
Copyright (c) 2021 University of Utah, The Trustees of Columbia University in
the City of New York, and others.
Permission is hereby granted, free of charge, to any person obtaining a... | Unknown |
3D | febiosoftware/FEBio | FEBioRVE/FERVEModel.cpp | .cpp | 18,588 | 707 | /*This file is part of the FEBio source code and is licensed under the MIT license
listed below.
See Copyright-FEBio.txt for details.
Copyright (c) 2021 University of Utah, The Trustees of Columbia University in
the City of New York, and others.
Permission is hereby granted, free of charge, to any person obtaining a... | C++ |
3D | febiosoftware/FEBio | FEBioRVE/FEPeriodicLinearConstraint2O.cpp | .cpp | 7,057 | 278 | /*This file is part of the FEBio source code and is licensed under the MIT license
listed below.
See Copyright-FEBio.txt for details.
Copyright (c) 2021 University of Utah, The Trustees of Columbia University in
the City of New York, and others.
Permission is hereby granted, free of charge, to any person obtaining a... | C++ |
3D | febiosoftware/FEBio | FEBioRVE/FEElasticMultiscaleDomain2O.cpp | .cpp | 5,795 | 198 | /*This file is part of the FEBio source code and is licensed under the MIT license
listed below.
See Copyright-FEBio.txt for details.
Copyright (c) 2021 University of Utah, The Trustees of Columbia University in
the City of New York, and others.
Permission is hereby granted, free of charge, to any person obtaining a... | C++ |
3D | febiosoftware/FEBio | FEBioRVE/FEPeriodicBoundary1O.cpp | .cpp | 16,542 | 685 | /*This file is part of the FEBio source code and is licensed under the MIT license
listed below.
See Copyright-FEBio.txt for details.
Copyright (c) 2021 University of Utah, The Trustees of Columbia University in
the City of New York, and others.
Permission is hereby granted, free of charge, to any person obtaining a... | C++ |
3D | febiosoftware/FEBio | FEBioRVE/FEBioRVE.cpp | .cpp | 2,913 | 69 | /*This file is part of the FEBio source code and is licensed under the MIT license
listed below.
See Copyright-FEBio.txt for details.
Copyright (c) 2021 University of Utah, The Trustees of Columbia University in
the City of New York, and others.
Permission is hereby granted, free of charge, to any person obtaining a... | C++ |
3D | febiosoftware/FEBio | FEBioRVE/FEMindlinElastic2O.cpp | .cpp | 4,306 | 155 | /*This file is part of the FEBio source code and is licensed under the MIT license
listed below.
See Copyright-FEBio.txt for details.
Copyright (c) 2021 University of Utah, The Trustees of Columbia University in
the City of New York, and others.
Permission is hereby granted, free of charge, to any person obtaining a... | C++ |
3D | febiosoftware/FEBio | FEBioRVE/FE2OMicroConstraint.h | .h | 3,254 | 103 | /*This file is part of the FEBio source code and is licensed under the MIT license
listed below.
See Copyright-FEBio.txt for details.
Copyright (c) 2021 University of Utah, The Trustees of Columbia University in
the City of New York, and others.
Permission is hereby granted, free of charge, to any person obtaining a... | Unknown |
3D | febiosoftware/FEBio | FEBioRVE/FEMultiscaleDomainFactory.h | .h | 1,563 | 35 | /*This file is part of the FEBio source code and is licensed under the MIT license
listed below.
See Copyright-FEBio.txt for details.
Copyright (c) 2021 University of Utah, The Trustees of Columbia University in
the City of New York, and others.
Permission is hereby granted, free of charge, to any person obtaining a... | Unknown |
3D | febiosoftware/FEBio | FEBioRVE/FEMicroMaterial.cpp | .cpp | 11,179 | 356 | /*This file is part of the FEBio source code and is licensed under the MIT license
listed below.
See Copyright-FEBio.txt for details.
Copyright (c) 2021 University of Utah, The Trustees of Columbia University in
the City of New York, and others.
Permission is hereby granted, free of charge, to any person obtaining a... | C++ |
3D | febiosoftware/FEBio | FEBioRVE/FERVEModel2O.cpp | .cpp | 25,902 | 963 | /*This file is part of the FEBio source code and is licensed under the MIT license
listed below.
See Copyright-FEBio.txt for details.
Copyright (c) 2021 University of Utah, The Trustees of Columbia University in
the City of New York, and others.
Permission is hereby granted, free of charge, to any person obtaining a... | C++ |
3D | febiosoftware/FEBio | FEBioRVE/FEMicroMaterial2O.h | .h | 3,371 | 101 | /*This file is part of the FEBio source code and is licensed under the MIT license
listed below.
See Copyright-FEBio.txt for details.
Copyright (c) 2021 University of Utah, The Trustees of Columbia University in
the City of New York, and others.
Permission is hereby granted, free of charge, to any person obtaining a... | Unknown |
3D | febiosoftware/FEBio | FEBioRVE/FEElasticSolidDomain2O.h | .h | 5,373 | 153 | /*This file is part of the FEBio source code and is licensed under the MIT license
listed below.
See Copyright-FEBio.txt for details.
Copyright (c) 2021 University of Utah, The Trustees of Columbia University in
the City of New York, and others.
Permission is hereby granted, free of charge, to any person obtaining a... | Unknown |
3D | febiosoftware/FEBio | FEBioRVE/FEMicroMaterial.h | .h | 4,115 | 122 | /*This file is part of the FEBio source code and is licensed under the MIT license
listed below.
See Copyright-FEBio.txt for details.
Copyright (c) 2021 University of Utah, The Trustees of Columbia University in
the City of New York, and others.
Permission is hereby granted, free of charge, to any person obtaining a... | Unknown |
3D | febiosoftware/FEBio | FEBioRVE/FEMindlinElastic2O.h | .h | 1,864 | 58 | /*This file is part of the FEBio source code and is licensed under the MIT license
listed below.
See Copyright-FEBio.txt for details.
Copyright (c) 2021 University of Utah, The Trustees of Columbia University in
the City of New York, and others.
Permission is hereby granted, free of charge, to any person obtaining a... | Unknown |
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