Automated deployment to update software database 2022-06-08 (#24)

Co-authored-by: github-actions <github-actions@users.noreply.github.com>
rseng · Jun 8, 2022 · 02e9e14 · 02e9e14
1 parent 81c6a94
commit 02e9e14
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Showing 54 changed files with 22,148 additions and 18,068 deletions.
diff --git a/_data/language_counts.json b/_data/language_counts.json
@@ -1,19 +1,19 @@
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+    "Jupyter Notebook": 103,
     "Modelica": 1,
     "Shell": 16,
     "HTML": 42,
     "Perl": 11,
-    "R": 497,
+    "R": 499,
     "C++": 145,
     "Java": 50,
     "C": 46,
     "Rust": 6,
     "JavaScript": 52,
     "AMPL": 1,
-    "MATLAB": 26,
+    "MATLAB": 28,
     "Haskell": 1,
     "Fortran": 22,
     "Clojure": 1,
@@ -37,7 +37,7 @@
     "NCL": 1,
     "Rich Text Format": 1,
     "Cuda": 1,
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+    "TeX": 8,
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diff --git a/_data/repos.json b/_data/repos.json
@@ -8325,7 +8325,47 @@
             "finite-elements",
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+        "github/siminegroup/E2EDNA2": [],
+        "github/LiuJJ0327/CCPE": [],
+        "github/wangsiwei2010/FPMVS-CAG": [],
+        "github/RudolfCardinal/camcops": [],
+        "github/chrisaberson/BetterReg": [],
+        "github/rudeboybert/forestecology": [
+            "forestecology",
+            "tidyverse"
+        ],
+        "github/maxibor/sam2lca": [],
+        "github/VeinsOfTheEarth/rabpro": [
+            "python",
+            "manuscript"
+        ],
+        "github/NKI-AI/direct": [
+            "pytorch",
+            "deep-learning",
+            "mri-reconstruction",
+            "inverse-problems",
+            "medical-imaging",
+            "fastmri-challenge"
+        ],
+        "github/aomlomics/tourmaline": [
+            "noaa-omics-software",
+            "amplicon-sequence-variants",
+            "dada2",
+            "deblur",
+            "snakemake"
+        ],
+        "github/ScialdoneLab/MitoHEAR": [
+            "bioinformatics-analysis",
+            "heteroplasmy",
+            "open-source",
+            "rstats-package"
+        ],
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+        "github/szwiep/py_SBeLT": [],
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@@ -10110,7 +10150,23 @@
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         "github/paulmorio/gincco": "Python",
         "github/davidechicco/geneExpressionFromGEO": "R",
-        "github/FEniCS/basix": "C++"
+        "github/FEniCS/basix": "C++",
+        "github/dfki-ric-underactuated-lab/torque_limited_simple_pendulum": "Python",
+        "github/siminegroup/E2EDNA2": "Python",
+        "github/LiuJJ0327/CCPE": "MATLAB",
+        "github/wangsiwei2010/FPMVS-CAG": "MATLAB",
+        "github/RudolfCardinal/camcops": "Python",
+        "github/chrisaberson/BetterReg": "R",
+        "github/rudeboybert/forestecology": "TeX",
+        "github/maxibor/sam2lca": "Python",
+        "github/VeinsOfTheEarth/rabpro": "Python",
+        "github/NKI-AI/direct": "Python",
+        "github/aomlomics/tourmaline": "Python",
+        "github/ScialdoneLab/MitoHEAR": "R",
+        "github/seung-lab/FlyWirePaper": "Jupyter Notebook",
+        "github/icredd-cheminfo/CGRdb2": "Python",
+        "github/szwiep/py_SBeLT": "Python",
+        "github/TingMAC/FrMLNet": "Python"
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@@ -11895,7 +11951,23 @@
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         "github/paulmorio/gincco": "https://github.com/paulmorio/gincco",
         "github/davidechicco/geneExpressionFromGEO": "https://github.com/davidechicco/geneExpressionFromGEO",
-        "github/FEniCS/basix": "https://github.com/FEniCS/basix"
+        "github/FEniCS/basix": "https://github.com/FEniCS/basix",
+        "github/dfki-ric-underactuated-lab/torque_limited_simple_pendulum": "https://github.com/dfki-ric-underactuated-lab/torque_limited_simple_pendulum",
+        "github/siminegroup/E2EDNA2": "https://github.com/siminegroup/E2EDNA2",
+        "github/LiuJJ0327/CCPE": "https://github.com/LiuJJ0327/CCPE",
+        "github/wangsiwei2010/FPMVS-CAG": "https://github.com/wangsiwei2010/FPMVS-CAG",
+        "github/RudolfCardinal/camcops": "https://github.com/ucam-department-of-psychiatry/camcops",
+        "github/chrisaberson/BetterReg": "https://github.com/chrisaberson/BetterReg",
+        "github/rudeboybert/forestecology": "https://github.com/rudeboybert/forestecology",
+        "github/maxibor/sam2lca": "https://github.com/maxibor/sam2lca",
+        "github/VeinsOfTheEarth/rabpro": "https://github.com/VeinsOfTheEarth/rabpro",
+        "github/NKI-AI/direct": "https://github.com/NKI-AI/direct",
+        "github/aomlomics/tourmaline": "https://github.com/aomlomics/tourmaline",
+        "github/ScialdoneLab/MitoHEAR": "https://github.com/ScialdoneLab/MitoHEAR",
+        "github/seung-lab/FlyWirePaper": "https://github.com/seung-lab/FlyWirePaper",
+        "github/icredd-cheminfo/CGRdb2": "https://github.com/icredd-cheminfo/CGRdb2",
+        "github/szwiep/py_SBeLT": "https://github.com/szwiep/py_SBeLT",
+        "github/TingMAC/FrMLNet": "https://github.com/TingMAC/FrMLNet"
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@@ -13680,6 +13752,22 @@
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         "github/paulmorio/gincco": "Source code for GINCCo Paper",
         "github/davidechicco/geneExpressionFromGEO": "geneExpressionFromGEO",
-        "github/FEniCS/basix": "FEniCS finite element basis evaluation library"
+        "github/FEniCS/basix": "FEniCS finite element basis evaluation library",
+        "github/dfki-ric-underactuated-lab/torque_limited_simple_pendulum": "Torque Limited Simple Pendulum Underactuated System",
+        "github/siminegroup/E2EDNA2": null,
+        "github/LiuJJ0327/CCPE": "Cell cycle pseudotome estimation for scRNA-seq data",
+        "github/wangsiwei2010/FPMVS-CAG": "code of \"Fast Parameter-free Multi-view Subspace Clustering with Consensus Anchor Guidance \" published in IEEE TIP2022",
+        "github/RudolfCardinal/camcops": "Cambridge Cognitive and Psychiatric Test Kit (CamCOPS)",
+        "github/chrisaberson/BetterReg": "Better statistics for regression (OLS and logistic)",
+        "github/rudeboybert/forestecology": "forestecology R package of Methods and Data for Forest Ecology Model Fitting and Assessment",
+        "github/maxibor/sam2lca": "Lowest Common Ancestor from a SAM/BAM/CRAM alignment file",
+        "github/VeinsOfTheEarth/rabpro": "River and basin profiler",
+        "github/NKI-AI/direct": "Deep learning framework for MRI reconstruction",
+        "github/aomlomics/tourmaline": "Amplicon sequence processing workflow using QIIME 2 and Snakemake",
+        "github/ScialdoneLab/MitoHEAR": "MitoHEAR (Mitochondrial HEteroplasmy AnalyzeR) is an R package that allows the estimation as well as downstream statistical analysis of the mtDNA heteroplasmy calculated from single-cell datasets.",
+        "github/seung-lab/FlyWirePaper": "Source code and data to reproduce analyses from the FlyWire paper.",
+        "github/icredd-cheminfo/CGRdb2": null,
+        "github/szwiep/py_SBeLT": "A Markov-type numerical model of sediment particle transport in rivers",
+        "github/TingMAC/FrMLNet": "This is a implementation of training code of this paper \u201cFrMLNet: Framelet-based Multi-level Network for Pansharpening\u201d"
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diff --git a/_data/repos_counts_languages.json b/_data/repos_counts_languages.json
@@ -1,7 +1,7 @@
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diff --git a/_data/stats.json b/_data/stats.json
@@ -1,9 +1,9 @@
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diff --git a/_repos/github/NKI-AI/direct/README.md b/_repos/github/NKI-AI/direct/README.md
@@ -0,0 +1,103 @@
+---
+title: github/NKI-AI/direct
+layout: repo
+tipue_search_active: true
+exclude_from_search: true
+---
+# Software Credit
+
+|Manager|Name|Credit|
+|-------|----|------|
+|pypi|[numpy](https://www.numpy.org)|0.147|
+|pypi|[typing-extensions](https://typing.readthedocs.io/)|0.131|
+|pypi|[protobuf](https://developers.google.com/protocol-buffers/)|0.107|
+|pypi|[h5py](http://www.h5py.org)|0.099|
+|pypi|[dataclasses](https://github.com/ericvsmith/dataclasses)|0.033|
+|pypi|[PyYAML](https://pyyaml.org/)|0.033|
+|pypi|[antlr4-python3-runtime](http://www.antlr.org)|0.033|
+|pypi|[requests](https://requests.readthedocs.io)|0.02|
+|pypi|[wheel](https://pypi.org/project/wheel)|0.02|
+|pypi|[ipywidgets](https://pypi.org/project/ipywidgets)|0.015|
+|pypi|[slack-sdk](https://pypi.org/project/slack-sdk)|0.012|
+|pypi|[twine](https://pypi.org/project/twine)|0.012|
+|pypi|[py-make](https://pypi.org/project/py-make)|0.012|
+|pypi|[importlib-resources](https://pypi.org/project/importlib-resources)|0.012|
+|pypi|[colorama](https://pypi.org/project/colorama)|0.012|
+|pypi|[pytest](https://pypi.org/project/pytest)|0.011|
+|pypi|[werkzeug](https://pypi.org/project/werkzeug)|0.01|
+|setup.py|github/NKI-AI/direct|0.01|
+|pypi|[pytest-cov](https://github.com/pytest-dev/pytest-cov)|0.008|
+|pypi|[sphinx](https://pypi.org/project/sphinx)|0.008|
+|pypi|[scipy](https://www.scipy.org)|0.008|
+|pypi|[tensorboard-plugin-wit](https://pypi.org/project/tensorboard-plugin-wit)|0.008|
+|pypi|[tensorboard-data-server](https://pypi.org/project/tensorboard-data-server)|0.008|
+|pypi|[setuptools](https://pypi.org/project/setuptools)|0.008|
+|pypi|[markdown](https://pypi.org/project/markdown)|0.008|
+|pypi|[google-auth-oauthlib](https://pypi.org/project/google-auth-oauthlib)|0.008|
+|pypi|[google-auth](https://pypi.org/project/google-auth)|0.008|
+|pypi|[grpcio](https://pypi.org/project/grpcio)|0.008|
+|pypi|[absl-py](https://pypi.org/project/absl-py)|0.008|
+|pypi|[flake8](https://pypi.org/project/flake8)|0.007|
+|pypi|[pyamg](https://pypi.org/project/pyamg)|0.007|
+|pypi|[seaborn](https://pypi.org/project/seaborn)|0.007|
+|pypi|[pandas](https://pypi.org/project/pandas)|0.007|
+|pypi|[matplotlib](https://pypi.org/project/matplotlib)|0.007|
+|pypi|[numpydoc](https://pypi.org/project/numpydoc)|0.007|
+|pypi|[sphinx-gallery](https://pypi.org/project/sphinx-gallery)|0.007|
+|pypi|[sphinxext-opengraph](https://pypi.org/project/sphinxext-opengraph)|0.006|
+|pypi|[scikit-image](https://scikit-image.org)|0.006|
+|pypi|[mypy](https://pypi.org/project/mypy)|0.005|
+|pypi|[black](https://pypi.org/project/black)|0.005|
+|pypi|[sphinx-prompt](https://pypi.org/project/sphinx-prompt)|0.005|
+|pypi|[Pillow](https://pypi.org/project/Pillow)|0.005|
+|pypi|[memory-profiler](https://pypi.org/project/memory-profiler)|0.005|
+|pypi|[threadpoolctl](https://pypi.org/project/threadpoolctl)|0.005|
+|pypi|[joblib](https://pypi.org/project/joblib)|0.005|
+|pypi|[sphinx-copybutton](https://pypi.org/project/sphinx-copybutton)|0.004|
+|pypi|[packaging](https://pypi.org/project/packaging)|0.004|
+|pypi|[scikit-learn](http://scikit-learn.org)|0.004|
+|pypi|[pillow](https://python-pillow.org)|0.003|
+|pypi|[codecov](https://pypi.org/project/codecov)|0.003|
+|pypi|[asv](https://pypi.org/project/asv)|0.003|
+|pypi|[qtpy](https://pypi.org/project/qtpy)|0.003|
+|pypi|[astropy](https://pypi.org/project/astropy)|0.003|
+|pypi|[SimpleITK](https://pypi.org/project/SimpleITK)|0.003|
+|pypi|[kaleido](https://pypi.org/project/kaleido)|0.003|
+|pypi|[plotly](https://pypi.org/project/plotly)|0.003|
+|pypi|[myst-parser](https://pypi.org/project/myst-parser)|0.003|
+|pypi|[cloudpickle](https://pypi.org/project/cloudpickle)|0.003|
+|pypi|[dask](https://pypi.org/project/dask)|0.003|
+|pypi|[pytest-runner](https://pypi.org/project/pytest-runner)|0.003|
+|pypi|[pooch](https://pypi.org/project/pooch)|0.003|
+|pypi|[PyWavelets](https://pypi.org/project/PyWavelets)|0.003|
+|pypi|[tifffile](https://pypi.org/project/tifffile)|0.003|
+|pypi|[imageio](https://pypi.org/project/imageio)|0.003|
+|pypi|[networkx](https://pypi.org/project/networkx)|0.003|
+|pypi|[win-inet-pton](https://pypi.org/project/win-inet-pton)|0.002|
+|pypi|[PySocks](https://pypi.org/project/PySocks)|0.002|
+|pypi|[charset-normalizer](https://pypi.org/project/charset-normalizer)|0.002|
+|pypi|[idna](https://pypi.org/project/idna)|0.002|
+|pypi|[chardet](https://pypi.org/project/chardet)|0.002|
+|pypi|[certifi](https://pypi.org/project/certifi)|0.002|
+|pypi|[urllib3](https://pypi.org/project/urllib3)|0.002|
+|pypi|[torch](https://pytorch.org/)|0.001|
+|pypi|[pytest-timeout](https://pypi.org/project/pytest-timeout)|0.001|
+|pypi|[pyroma](https://pypi.org/project/pyroma)|0.001|
+|pypi|[markdown2](https://pypi.org/project/markdown2)|0.001|
+|pypi|[defusedxml](https://pypi.org/project/defusedxml)|0.001|
+|pypi|[coverage](https://pypi.org/project/coverage)|0.001|
+|pypi|[check-manifest](https://pypi.org/project/check-manifest)|0.001|
+|pypi|[sphinx-rtd-theme](https://pypi.org/project/sphinx-rtd-theme)|0.001|
+|pypi|[sphinx-removed-in](https://pypi.org/project/sphinx-removed-in)|0.001|
+|pypi|[sphinx-issues](https://pypi.org/project/sphinx-issues)|0.001|
+|pypi|[olefile](https://pypi.org/project/olefile)|0.001|
+|pypi|[omegaconf](https://github.com/omry/omegaconf)|0.001|
+|pypi|[torchvision](https://github.com/pytorch/vision)|0.001|
+|pypi|[tensorboard](https://github.com/tensorflow/tensorboard)|0.001|
+|pypi|[tqdm](https://tqdm.github.io)|0.001|
+
+
+> Note that credit values are rounded and expanded (so shared dependencies are represented as one record) and may not add to 1.0. Rounded values that hit zero are removed.
+
+
+- Generated by [CiteLang](https://github.com/vsoch/citelang)
diff --git a/_repos/github/NKI-AI/direct/badge.png b/_repos/github/NKI-AI/direct/badge.png