Automated deployment to update software database 2023-01-25 (#55)

Co-authored-by: github-actions <github-actions@users.noreply.github.com>
rseng · Jan 25, 2023 · 27f54ca · 27f54ca
1 parent 22fb6b9
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Showing 50 changed files with 31,776 additions and 28,339 deletions.
diff --git a/_data/language_counts.json b/_data/language_counts.json
@@ -1,15 +1,15 @@
 {
-    "unknown": 145,
-    "Python": 1757,
-    "Jupyter Notebook": 328,
+    "unknown": 147,
+    "Python": 1761,
+    "Jupyter Notebook": 330,
     "Modelica": 1,
-    "Shell": 25,
+    "Shell": 26,
     "HTML": 72,
     "Perl": 44,
-    "R": 589,
-    "C++": 473,
+    "R": 594,
+    "C++": 475,
     "Java": 93,
-    "C": 291,
+    "C": 292,
     "Rust": 22,
     "JavaScript": 75,
     "AMPL": 1,
@@ -37,7 +37,7 @@
     "NCL": 1,
     "Rich Text Format": 1,
     "Cuda": 9,
-    "TeX": 19,
+    "TeX": 20,
     "Ruby": 11,
     "Mathematica": 17,
     "OCaml": 2,
@@ -75,5 +75,6 @@
     "FreeMarker": 1,
     "Slash": 1,
     "Component Pascal": 1,
-    "ImageJ Macro": 1
+    "ImageJ Macro": 1,
+    "Yacc": 1
 }
diff --git a/_data/repos.json b/_data/repos.json
@@ -16297,7 +16297,83 @@
         ],
         "github/ComputationalPhysiology/simcardems": [],
         "gitlab/ProjectRHEA/flowsolverrhea": [],
-        "gitlab/programgreg/tagginglatencyestimator": []
+        "gitlab/programgreg/tagginglatencyestimator": [],
+        "github/BioGenies/AMPBenchmark": [],
+        "github/Ge-Lab/USAT": [],
+        "github/D-Crake/HEADSS": [],
+        "github/apcamargo/prodigal-gv": [],
+        "github/andreyshabalin/TwinEQTL": [],
+        "github/tiberioap/grav_waldo": [],
+        "github/SciOmicsLab/PhenoComb": [],
+        "github/tobiasrausch/wally": [
+            "genomics",
+            "sequencing",
+            "visualization",
+            "alignment",
+            "sequencing-data",
+            "mapping",
+            "plotting",
+            "assembly",
+            "contigs"
+        ],
+        "github/rmaphoh/AutoMorph": [],
+        "github/johnschwenck/bp": [],
+        "github/mgm8/pyngham": [],
+        "github/sjbeckett/localcovid19now": [],
+        "github/AnthonyOfSeattle/pyAscoreValidation": [],
+        "github/ianfhunter/GNOLL": [
+            "dice",
+            "dice-roller",
+            "dice-notation",
+            "board-game",
+            "c",
+            "cpp",
+            "dice-rolls",
+            "python",
+            "roleplaying-games",
+            "ttrpg",
+            "perl",
+            "golang",
+            "javascript",
+            "go",
+            "js",
+            "rpg-dice-roller",
+            "julia",
+            "r",
+            "java",
+            "haskell"
+        ],
+        "github/ICESat2-SlideRule/paper": [],
+        "github/N-Wouda/ALNS": [
+            "adaptive-large-neighbourhood-search",
+            "alns",
+            "metaheuristic",
+            "operations-research",
+            "python",
+            "travelling-salesman-problem",
+            "cutting-stock-problem",
+            "vehicle-routing-problem",
+            "rcpsp",
+            "scheduling-problem",
+            "tsp",
+            "vrp",
+            "flow-shop"
+        ],
+        "github/cwieder/py-ssPA": [
+            "bioinformatics",
+            "identifier-mapping",
+            "pathway-analysis",
+            "pathway-enrichment-analysis",
+            "pathway-databases",
+            "metabolomics",
+            "omics"
+        ],
+        "github/lorenzo-rovigatti/oxDNA": [
+            "simulation",
+            "physics-simulation",
+            "dna"
+        ],
+        "gitlab/fibreglass/pivc": []
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@@ -20758,7 +20834,26 @@
         "github/Jacks0nJ/PyFPT": "Python",
         "github/ComputationalPhysiology/simcardems": "Python",
         "gitlab/ProjectRHEA/flowsolverrhea": "unknown",
-        "gitlab/programgreg/tagginglatencyestimator": "unknown"
+        "gitlab/programgreg/tagginglatencyestimator": "unknown",
+        "github/BioGenies/AMPBenchmark": "R",
+        "github/Ge-Lab/USAT": "Shell",
+        "github/D-Crake/HEADSS": "Jupyter Notebook",
+        "github/apcamargo/prodigal-gv": "C",
+        "github/andreyshabalin/TwinEQTL": "R",
+        "github/tiberioap/grav_waldo": "Python",
+        "github/SciOmicsLab/PhenoComb": "R",
+        "github/tobiasrausch/wally": "C++",
+        "github/rmaphoh/AutoMorph": "Python",
+        "github/johnschwenck/bp": "R",
+        "github/mgm8/pyngham": "Python",
+        "github/sjbeckett/localcovid19now": "R",
+        "github/AnthonyOfSeattle/pyAscoreValidation": "unknown",
+        "github/ianfhunter/GNOLL": "Yacc",
+        "github/ICESat2-SlideRule/paper": "TeX",
+        "github/N-Wouda/ALNS": "Python",
+        "github/cwieder/py-ssPA": "Jupyter Notebook",
+        "github/lorenzo-rovigatti/oxDNA": "C++",
+        "gitlab/fibreglass/pivc": "unknown"
     },
     "url": {
         "gitlab/chiemotono/mdcontactcom": "https://gitlab.com/chiemotono/mdcontactcom",
@@ -25219,7 +25314,26 @@
         "github/Jacks0nJ/PyFPT": "https://github.com/Jacks0nJ/PyFPT",
         "github/ComputationalPhysiology/simcardems": "https://github.com/ComputationalPhysiology/simcardems",
         "gitlab/ProjectRHEA/flowsolverrhea": "https://gitlab.com/ProjectRHEA/flowsolverrhea",
-        "gitlab/programgreg/tagginglatencyestimator": "https://gitlab.com/programgreg/tagginglatencyestimator"
+        "gitlab/programgreg/tagginglatencyestimator": "https://gitlab.com/programgreg/tagginglatencyestimator",
+        "github/BioGenies/AMPBenchmark": "https://github.com/BioGenies/AMPBenchmark",
+        "github/Ge-Lab/USAT": "https://github.com/Ge-Lab/USAT",
+        "github/D-Crake/HEADSS": "https://github.com/D-Crake/HEADSS",
+        "github/apcamargo/prodigal-gv": "https://github.com/apcamargo/prodigal-gv",
+        "github/andreyshabalin/TwinEQTL": "https://github.com/andreyshabalin/TwinEQTL",
+        "github/tiberioap/grav_waldo": "https://github.com/tiberioap/grav_waldo",
+        "github/SciOmicsLab/PhenoComb": "https://github.com/SciOmicsLab/PhenoComb",
+        "github/tobiasrausch/wally": "https://github.com/tobiasrausch/wally",
+        "github/rmaphoh/AutoMorph": "https://github.com/rmaphoh/AutoMorph",
+        "github/johnschwenck/bp": "https://github.com/johnschwenck/bp",
+        "github/mgm8/pyngham": "https://github.com/mgm8/pyngham",
+        "github/sjbeckett/localcovid19now": "https://github.com/sjbeckett/localcovid19now",
+        "github/AnthonyOfSeattle/pyAscoreValidation": "https://github.com/AnthonyOfSeattle/pyAscoreValidation",
+        "github/ianfhunter/GNOLL": "https://github.com/ianfhunter/GNOLL",
+        "github/ICESat2-SlideRule/paper": "https://github.com/ICESat2-SlideRule/paper",
+        "github/N-Wouda/ALNS": "https://github.com/N-Wouda/ALNS",
+        "github/cwieder/py-ssPA": "https://github.com/cwieder/py-ssPA",
+        "github/lorenzo-rovigatti/oxDNA": "https://github.com/lorenzo-rovigatti/oxDNA",
+        "gitlab/fibreglass/pivc": "https://gitlab.com/fibreglass/pivc"
     },
     "description": {
         "gitlab/chiemotono/mdcontactcom": "",
@@ -29680,6 +29794,25 @@
         "github/Jacks0nJ/PyFPT": "Stochastic first-passage time (FPT) simulations using importance sampling.",
         "github/ComputationalPhysiology/simcardems": "Simula Cardiac ElectroMechanics Solver",
         "gitlab/ProjectRHEA/flowsolverrhea": "RHEA: an open-source Reproducible and Hybrid-architecture flow solver Engineered for Academia",
-        "gitlab/programgreg/tagginglatencyestimator": "Software to estimate the latency of the tagging process."
+        "gitlab/programgreg/tagginglatencyestimator": "Software to estimate the latency of the tagging process.",
+        "github/BioGenies/AMPBenchmark": null,
+        "github/Ge-Lab/USAT": "USAT is a software for analyzing and visualizing the Tandem Repeat (TR) alleles",
+        "github/D-Crake/HEADSS": "HiErArchical Data Splitting and Stitching Software for Non-Distributed Clustering Algorithms",
+        "github/apcamargo/prodigal-gv": "A fork of Prodigal meant to improve gene calling for giant viruses and viruses that use alternative genetic codes",
+        "github/andreyshabalin/TwinEQTL": "TwinMeta: Fast and Powerful Association Analysis for eQTL and GWAS in Twin Studies",
+        "github/tiberioap/grav_waldo": "Waveform anomaly detector",
+        "github/SciOmicsLab/PhenoComb": "An R package for combinatorial analysis of phenotypes",
+        "github/tobiasrausch/wally": "Wally: Visualization of aligned sequencing reads and contigs",
+        "github/rmaphoh/AutoMorph": "vessel segmentation, artery and vein, optic disc, vascular feature analysis",
+        "github/johnschwenck/bp": "An R package for analyzing blood pressure data",
+        "github/mgm8/pyngham": "Python library of the NGHam protocol",
+        "github/sjbeckett/localcovid19now": "processing and mapping COVID-19 case data at subnational scales",
+        "github/AnthonyOfSeattle/pyAscoreValidation": "Validation experiments for the pyAscore python package.",
+        "github/ianfhunter/GNOLL": "GNOLL is an efficient dice notation parser for multiple programming languages that supports a wide set of dice notation",
+        "github/ICESat2-SlideRule/paper": "JOSS paper materials",
+        "github/N-Wouda/ALNS": "Adaptive large neighbourhood search (and more!) in Python.",
+        "github/cwieder/py-ssPA": "Single sample pathway analysis tools for omics data",
+        "github/lorenzo-rovigatti/oxDNA": "A new version of the code to simulate the oxDNA/oxRNA models, now equipped with Python bindings",
+        "gitlab/fibreglass/pivc": null
     }
 }
diff --git a/_data/repos_counts_languages.json b/_data/repos_counts_languages.json
@@ -1,6 +1,6 @@
 {
-    "Python": 4887,
-    "R": 2106,
+    "Python": 4893,
+    "R": 2117,
     "Cpp": 394,
     "Js": 1462,
     "Go": 245

diff --git a/_data/stats.json b/_data/stats.json
@@ -1,9 +1,9 @@
 {
-    "python_deps": 3998,
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     "go_deps": 245,
-    "total_repos": 4459,
-    "total_parsed": 2329
+    "total_repos": 4478,
+    "total_parsed": 2337
 }
diff --git a/_repos/github/N-Wouda/ALNS/README.md b/_repos/github/N-Wouda/ALNS/README.md
@@ -0,0 +1,50 @@
+---
+title: github/N-Wouda/ALNS
+layout: repo
+tipue_search_active: true
+exclude_from_search: true
+---
+# Software Credit
+
+|Manager|Name|Credit|
+|-------|----|------|
+|pypi|[docutils](http://docutils.sourceforge.net/)|0.129|
+|pypi|[numpy](https://www.numpy.org)|0.124|
+|pypi|[matplotlib](https://matplotlib.org)|0.124|
+|pypi|[tomli](https://pypi.org/project/tomli)|0.124|
+|pypi|[nbsphinx](https://nbsphinx.readthedocs.io/)|0.124|
+|pypi|[ipython](https://ipython.org)|0.124|
+|pypi|[numpydoc](https://numpydoc.readthedocs.io)|0.124|
+|requirements.txt|github/N-Wouda/ALNS|0.01|
+|pypi|[pytest](https://docs.pytest.org/en/latest/)|0.005|
+|pypi|[types-requests](https://pypi.org/project/types-requests)|0.005|
+|pypi|[types-typed-ast](https://pypi.org/project/types-typed-ast)|0.005|
+|pypi|[docutils-stubs](https://pypi.org/project/docutils-stubs)|0.005|
+|pypi|[mypy](https://pypi.org/project/mypy)|0.005|
+|pypi|[isort](https://pypi.org/project/isort)|0.005|
+|pypi|[flake8](https://pypi.org/project/flake8)|0.005|
+|pypi|[sphinxcontrib-websupport](https://pypi.org/project/sphinxcontrib-websupport)|0.005|
+|pypi|[colorama](https://pypi.org/project/colorama)|0.005|
+|pypi|[importlib-metadata](https://pypi.org/project/importlib-metadata)|0.005|
+|pypi|[packaging](https://pypi.org/project/packaging)|0.005|
+|pypi|[requests](https://pypi.org/project/requests)|0.005|
+|pypi|[imagesize](https://pypi.org/project/imagesize)|0.005|
+|pypi|[alabaster](https://pypi.org/project/alabaster)|0.005|
+|pypi|[babel](https://pypi.org/project/babel)|0.005|
+|pypi|[snowballstemmer](https://pypi.org/project/snowballstemmer)|0.005|
+|pypi|[Pygments](https://pypi.org/project/Pygments)|0.005|
+|pypi|[Jinja2](https://pypi.org/project/Jinja2)|0.005|
+|pypi|[sphinxcontrib-qthelp](https://pypi.org/project/sphinxcontrib-qthelp)|0.005|
+|pypi|[sphinxcontrib-serializinghtml](https://pypi.org/project/sphinxcontrib-serializinghtml)|0.005|
+|pypi|[sphinxcontrib-htmlhelp](https://pypi.org/project/sphinxcontrib-htmlhelp)|0.005|
+|pypi|[sphinxcontrib-jsmath](https://pypi.org/project/sphinxcontrib-jsmath)|0.005|
+|pypi|[sphinxcontrib-devhelp](https://pypi.org/project/sphinxcontrib-devhelp)|0.005|
+|pypi|[sphinxcontrib-applehelp](https://pypi.org/project/sphinxcontrib-applehelp)|0.005|
+|pypi|[sphinx_rtd_theme](https://github.com/rtfd/sphinx_rtd_theme/)|0.001|
+|pypi|[sphinx](https://www.sphinx-doc.org/)|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/N-Wouda/ALNS/badge.png b/_repos/github/N-Wouda/ALNS/badge.png