Updated R and Python package files. Updated README.

sociality-task
Primoz 2022-07-07 15:30:07 +00:00
parent 5a777ac79f
commit 6c8014ba8e
3 changed files with 54 additions and 9 deletions

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@ -16,11 +16,55 @@ By [MoSHI](https://www.moshi.pitt.edu/), [University of Pittsburgh](https://www.
For RAPIDS installation refer to to the [documentation](https://www.rapids.science/1.8/setup/installation/)
## For the installation of the Docker version
1. Follow the [instructions](https://www.rapids.science/1.8/setup/installation/) to setup RAPIDS via Docker (from scratch).
2. Delete current contents in /rapids/ folder when in a container session.
```
cd ..
rm -rf rapids/{*,.*}
cd rapids
```
3. Clone RAPIDS workspace from Git and checkout a specific branch.
```
git clone "https://repo.ijs.si/junoslukan/rapids.git" .
git checkout <branch_name>
```
4. Install missing “libpq-dev” dependency with bash.
```
apt-get update -y
apt-get install -y libpq-dev
```
5. Restore R venv.
Type R to go to the interactive R session and then:
```
renv::restore()
```
6. Install cr-features module
From: https://repo.ijs.si/matjazbostic/calculatingfeatures.git -> branch calculations_for_rapids.
Then follow the CalculatingFeatures section below.
7. Install all required packages from environment.yml, prune also deletes conda packages not present in environment file.
conda env update --file environment.yml prune
8. If you wish to update your R or Python venvs.
```
R interactive session renv::snapshot()
Python: conda env export --no-builds | sed 's/^.*libgfortran.*$/ - libgfortran/' | sed 's/^.*mkl=.*$/ - mkl/' > environment.ym
```
## CalculatingFeatures
This RAPIDS extension uses CalculatingFeatures library accessible [here](https://repo.ijs.si/matjazbostic/calculatingfeatures).
To use CalculatingFeatures library:
- For now, use the "modifications_for_rapids" branch to get the newest version of cr-features that is functional for RAPIDS-STRAW analysis.
- Follow the installation instructions in the [README.md](https://repo.ijs.si/matjazbostic/calculatingfeatures/-/blob/master/README.md).
- Copy built calculatingfeatures folder into the RAPIDS workspace.
@ -28,5 +72,6 @@ To use CalculatingFeatures library:
- Install the CalculatingFeatures package by:
```
pip install "path/to/the/calculatingfeatures/folder"
e.g. "./calculatingfeatures" if the folder is copied to main parent directory
CalculatingFeatures package has to be built and installed everytime to get the newest version.
```

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@ -111,7 +111,7 @@ dependencies:
- biosppy==0.8.0
- cached-property==1.5.2
- configargparse==0.15.1
- cr-features==0.1.15
- cr-features==0.1.20
- cycler==0.11.0
- decorator==4.4.2
- fonttools==4.33.2

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@ -111,7 +111,7 @@
"Package": "Rcpp",
"Version": "1.0.7",
"Source": "Repository",
"Repository": "RSPM",
"Repository": "CRAN",
"Hash": "dab19adae4440ae55aa8a9d238b246bb"
},
"RcppArmadillo": {
@ -356,7 +356,7 @@
"Package": "dbplyr",
"Version": "2.1.1",
"Source": "Repository",
"Repository": "RSPM",
"Repository": "CRAN",
"Hash": "1f37fa4ab2f5f7eded42f78b9a887182"
},
"desc": {
@ -405,7 +405,7 @@
"Package": "ellipsis",
"Version": "0.3.2",
"Source": "Repository",
"Repository": "RSPM",
"Repository": "CRAN",
"Hash": "bb0eec2fe32e88d9e2836c2f73ea2077"
},
"entropy": {
@ -566,7 +566,7 @@
"Package": "gower",
"Version": "0.2.2",
"Source": "Repository",
"Repository": "RSPM",
"Repository": "CRAN",
"Hash": "be6a2b3529928bd803d1c437d1d43152"
},
"graphlayouts": {
@ -615,7 +615,7 @@
"Package": "hms",
"Version": "1.1.1",
"Source": "Repository",
"Repository": "RSPM",
"Repository": "CRAN",
"Hash": "5b8a2dd0fdbe2ab4f6081e6c7be6dfca"
},
"htmlTable": {
@ -888,7 +888,7 @@
"Package": "parallelly",
"Version": "1.29.0",
"Source": "Repository",
"Repository": "RSPM",
"Repository": "CRAN",
"Hash": "b5f399c9ce96977e22ef32c20b6cfe87"
},
"pbapply": {
@ -1000,7 +1000,7 @@
"Package": "progressr",
"Version": "0.9.0",
"Source": "Repository",
"Repository": "RSPM",
"Repository": "CRAN",
"Hash": "ca0d80ecc29903f7579edbabd91f4199"
},
"promises": {
@ -1343,7 +1343,7 @@
"Package": "vctrs",
"Version": "0.3.8",
"Source": "Repository",
"Repository": "RSPM",
"Repository": "CRAN",
"Hash": "ecf749a1b39ea72bd9b51b76292261f1"
},
"viridis": {