Refactoring and cran prep v0.1.6

.Rbuildignore

@@ -4,3 +4,9 @@
 ^docs$
 ^pkgdown$
 ^\.github$
+^INSTALLATION\.md$
+^environment\.yml$
+^CONTRIBUTING\.md$
+^CODE_OF_CONDUCT\.md$
+^dev$
+^cran-comments\.md$

.github/ISSUE_TEMPLATE/bug_report.md

@@ -0,0 +1,37 @@
+---
+name: Bug report
+about: Report a bug or unexpected behaviour in SelectSim
+title: "[BUG] "
+labels: bug
+assignees: ''
+---
+
+## Describe the bug
+
+A clear and concise description of what the bug is.
+
+## Minimal reproducible example
+
+```r
+library(SelectSim)
+# paste the smallest code that reproduces the issue
+```
+
+## Expected behaviour
+
+What you expected to happen.
+
+## Actual behaviour
+
+What actually happened. Include the full error message or unexpected output.
+
+## Environment
+
+- SelectSim version: <!-- packageVersion("SelectSim") -->
+- R version: <!-- R.version.string -->
+- OS: <!-- e.g. macOS 14.5, Ubuntu 22.04 -->
+- Installation method: <!-- devtools::install_github / local build -->
+
+## Additional context
+
+Any other context that may be relevant (e.g. dataset size, number of cores used).

.github/ISSUE_TEMPLATE/feature_request.md

@@ -0,0 +1,23 @@
+---
+name: Feature request
+about: Suggest a new feature or improvement for SelectSim
+title: "[FEATURE] "
+labels: enhancement
+assignees: ''
+---
+
+## Is your feature request related to a problem?
+
+A clear and concise description of the problem or limitation you are experiencing.
+
+## Proposed solution
+
+Describe the feature or change you would like to see, including any API design ideas if relevant.
+
+## Alternatives considered
+
+Any alternative approaches you have considered, and why you prefer the proposed solution.
+
+## Additional context
+
+Any other context, references, or examples that support the request.

.github/PULL_REQUEST_TEMPLATE.md

@@ -0,0 +1,14 @@
+## Summary
+
+<!-- What does this PR do? Reference any related issues with "Fixes #N" or "Closes #N". -->
+
+## Changes
+
+- 
+
+## Test plan
+
+- [ ] `devtools::document()` run to regenerate NAMESPACE / man pages
+- [ ] `devtools::check()` passes with 0 errors, 0 warnings, 0 notes
+- [ ] New or changed behaviour covered by tests in `tests/testthat/`
+- [ ] Documentation updated (roxygen tags, vignette, README) if applicable

.github/workflows/R-CMD-check.yaml

@@ -0,0 +1,47 @@
+on:
+  push:
+    branches: [main]
+  pull_request:
+    branches: [main]
+
+name: R-CMD-check
+
+jobs:
+  R-CMD-check:
+    runs-on: ${{ matrix.config.os }}
+
+    name: ${{ matrix.config.os }} (R ${{ matrix.config.r }})
+
+    strategy:
+      fail-fast: false
+      matrix:
+        config:
+          - {os: macos-latest,   r: 'release'}
+          - {os: windows-latest, r: 'release'}
+          - {os: ubuntu-latest,  r: 'release'}
+          - {os: ubuntu-latest,  r: 'devel', http-user-agent: 'release'}
+
+    env:
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+      R_KEEP_PKG_SOURCE: yes
+
+    steps:
+      - uses: actions/checkout@v4
+
+      - uses: r-lib/actions/setup-pandoc@v2
+
+      - uses: r-lib/actions/setup-r@v2
+        with:
+          r-version: ${{ matrix.config.r }}
+          http-user-agent: ${{ matrix.config.http-user-agent }}
+          use-public-rspm: true
+
+      - uses: r-lib/actions/setup-r-dependencies@v2
+        with:
+          extra-packages: any::rcmdcheck
+          needs: check
+
+      - uses: r-lib/actions/check-r-package@v2
+        with:
+          upload-snapshots: true
+          build_args: 'c("--no-manual", "--compact-vignettes=gs+qpdf")'

.gitignore

@@ -7,4 +7,5 @@
 .ipynb_checkpoints
 inst/doc
 .*
-!/.gitignore
+!/.gitignore
+!/.github

CODE_OF_CONDUCT.md

@@ -0,0 +1,41 @@
+# 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 experience, education, socio-economic status, nationality, personal appearance, race, caste, colour, religion, or sexual identity and orientation.
+
+We pledge to act and interact in ways that contribute to an open, welcoming, diverse, inclusive, and healthy community.
+
+## Our Standards
+
+Examples of behaviour that contributes to a positive environment:
+
+- Demonstrating empathy and kindness toward other people
+- Being respectful of differing opinions, viewpoints, and experiences
+- Giving and gracefully accepting constructive feedback
+- Accepting responsibility and apologising to those affected by our mistakes, and learning from the experience
+- Focusing on what is best not just for us as individuals, but for the overall community
+
+Examples of unacceptable behaviour:
+
+- The use of sexualised language or imagery, and sexual attention or advances of any kind
+- Trolling, insulting or derogatory comments, and personal or political attacks
+- Public or private harassment
+- Publishing others' private information, such as a physical or email address, without their explicit permission
+- Other conduct which could reasonably be considered inappropriate in a professional setting
+
+## Enforcement Responsibilities
+
+Community leaders are responsible for clarifying and enforcing our standards of acceptable behaviour and will take appropriate and fair corrective action in response to any behaviour that they deem inappropriate, threatening, offensive, or harmful.
+
+## Scope
+
+This Code of Conduct applies within all community spaces, and also applies when an individual is officially representing the community in public spaces.
+
+## Enforcement
+
+Instances of abusive, harassing, or otherwise unacceptable behaviour may be reported to the community leaders responsible for enforcement at giovanni.ciriello@unil.ch. All complaints will be reviewed and investigated promptly and fairly.
+
+## Attribution
+
+This Code of Conduct is adapted from the [Contributor Covenant](https://www.contributor-covenant.org), version 2.1.

CONTRIBUTING.md

@@ -0,0 +1,33 @@
+# Contributing to SelectSim
+
+Thank you for your interest in contributing to SelectSim. This document explains how to report bugs, suggest features, and submit code.
+
+## Reporting bugs
+
+Please use the [issue tracker](https://github.com/CSOgroup/SelectSim/issues) and select the **Bug report** template. Include:
+
+- SelectSim version (`packageVersion("SelectSim")`)
+- R version and OS
+- A minimal reproducible example (preferably using the bundled `luad_run_data`)
+- The full error message or unexpected output
+
+## Suggesting features
+
+Open an issue using the **Feature request** template. Describe the use case and why it would benefit users of the package.
+
+## Contributing code
+
+1. Fork the repository and create a branch from `main`.
+2. Follow the existing code style (base R where possible; tidyverse only via already-imported packages).
+3. Add or update tests in `tests/testthat/` for any new or changed behaviour.
+4. Run `devtools::check()` and ensure 0 errors, 0 warnings, and 0 notes before opening a pull request.
+5. Update roxygen2 documentation (`devtools::document()`) if you change function signatures or add new functions.
+6. Open a pull request against `main` using the provided PR template.
+
+## Code of conduct
+
+This project follows the [Contributor Covenant Code of Conduct](CODE_OF_CONDUCT.md). By participating you agree to abide by its terms.
+
+## Questions
+
+For questions about the SelectSim methodology, contact Giovanni Ciriello (giovanni.ciriello@unil.ch) or Arvind Iyer (ayalurarvind@gmail.com).

DESCRIPTION

@@ -1,17 +1,22 @@
 Package: SelectSim
-Title: Selected Events Linked by Evolutionary Conditions across human Tumors
-Version: 0.0.1.5
-Authors@R: 
-    c(person("Arvind", "Iyer", , "ayalurarvind@gamil.com", role = c("aut", "cre"),comment = c(ORCID = "0000-0002-8247-700X")),
-    person("Marco", "Mina", , "marco.mina.85@gmail.com", role = c("aut")),
-    person("Miljan", "Petrovic", , "miljanpet93@gmail.com", role = c("aut")),
-    person("Giovanni", "Ciriello", , "givoanni.cirello@unil.ch", role = c("aut"),comment = c(ORCID ="0000-0003-2021-8683")))
-Description: This R package implements the SelectSim methodology to infer co-mutations between functional alterations in cancer.
+Title: Selected Events Linked by Evolutionary Conditions Across Human Tumors
+Version: 0.1.6
+Authors@R: c(
+    person("Arvind", "Iyer", , "ayalurarvind@gmail.com", role = c("aut", "cre"),
+           comment = c(ORCID = "0000-0002-8247-700X")),
+    person("Marco", "Mina", , "marco.mina.85@gmail.com", role = "aut"),
+    person("Miljan", "Petrovic", , "miljanpet93@gmail.com", role = "aut"),
+    person("Giovanni", "Ciriello", , "giovanni.ciriello@unil.ch", role = "aut",
+           comment = c(ORCID = "0000-0003-2021-8683"))
+  )
+Description: This R package implements the SelectSim methodology to infer
+    co-mutations between functional alterations in cancer.
 License: MIT + file LICENSE
-Encoding: UTF-8
-Roxygen: list(markdown = TRUE)
-RoxygenNote: 7.3.2
-Imports: 
+URL: https://csogroup.github.io/SelectSim/
+BugReports: https://github.com/CSOgroup/SelectSim/issues
+Depends:
+    R (>= 3.5)
+Imports:
     doParallel,
     doRNG,
     dplyr,
@@ -20,20 +25,24 @@ Imports:
     ggpubr,
     ggridges,
     Matrix,
+    parallel,
     Rcpp,
-    reshape2,
     Rfast,
-    tictoc
-Suggests: 
+    stats
+Suggests:
     knitr,
     rmarkdown,
-    testthat (>= 3.0.0)
-Config/testthat/edition: 3
-Depends: 
-    R (>= 3.5)
-LazyData: true
-VignetteBuilder: knitr
-URL: https://csogroup.github.io/SelectSim/
-LinkingTo: 
+    testthat (>= 3.0.0),
+    tictoc
+LinkingTo:
     Rcpp,
     RcppArmadillo
+VignetteBuilder: 
+    knitr
+Config/testthat/edition: 3
+Encoding: UTF-8
+LazyData: true
+LazyDataCompression: xz
+Roxygen: list(markdown = TRUE)
+RoxygenNote: 8.0.0
+Language: en-US

NAMESPACE

@@ -46,7 +46,7 @@ export(selectX)
 export(stat_maf_column)
 export(stat_maf_gene)
 export(stat_maf_sample)
-export(templeate.obj.gen)
+export(template.obj.gen)
 export(theme_Publication)
 export(w.r.am.pairwise.alteration.overlap)
 import(doParallel)
@@ -55,8 +55,6 @@ import(foreach)
 import(ggplot2)
 import(ggpubr)
 import(ggridges)
-import(graphics)
-import(parallel)
 importFrom(Matrix,Matrix)
 importFrom(Matrix,sparseMatrix)
 importFrom(Matrix,t)
@@ -65,20 +63,19 @@ importFrom(Rfast,rowSort)
 importFrom(dplyr,"%>%")
 importFrom(dplyr,arrange)
 importFrom(dplyr,case_when)
+importFrom(dplyr,distinct)
 importFrom(dplyr,filter)
 importFrom(dplyr,group_by)
 importFrom(dplyr,left_join)
 importFrom(dplyr,mutate)
 importFrom(dplyr,row_number)
 importFrom(dplyr,ungroup)
-importFrom(reshape2,acast)
-importFrom(reshape2,melt)
+importFrom(parallel,makeCluster)
+importFrom(parallel,stopCluster)
 importFrom(stats,as.dist)
 importFrom(stats,density)
 importFrom(stats,ecdf)
 importFrom(stats,median)
 importFrom(stats,runif)
 importFrom(stats,setNames)
-importFrom(tictoc,tic)
-importFrom(tictoc,toc)
 useDynLib(SelectSim, .registration = TRUE)

NEWS.md

@@ -1,21 +1,31 @@
-# SelectSim (development version)
+# SelectSim 0.1.6
 
+* Removed `reshape2` dependency; replaced with base R equivalents (`tapply`, `as.data.frame.table`).
+* Fixed `theme_ridges()` partial argument match (`center` → `center_axis_labels`).
+* Fixed parallel log file leak in `null_model_parallel` using `tempfile()` and `on.exit()`.
+* Refactored `selectX()` to eliminate duplicate verbose/non-verbose code paths.
+* Added `utils::globalVariables()` declarations to suppress R CMD check NOTEs for ggplot2 aesthetics.
+* Dropped `SystemRequirements: C++14` from DESCRIPTION.
+* Added GitHub community health files: `CONTRIBUTING.md`, `CODE_OF_CONDUCT.md`, issue templates, PR template, and CI workflow.
+* Expanded test coverage with `test-gam_utils.R`.
+* Repository migrated: development moved from personal branches to [CSOgroup/SelectSim](https://github.com/CSOgroup/SelectSim); `dev` branch merged into `main` for initial public release.
+* Bumped version to 0.1.6 across all source files
 
-# SelectX 0.0.1.3
+# SelectSim 0.0.1.3
 
 * Added a `NEWS.md` file to track changes to the package.
-* Rename the pacakge SelectX to SelectSim by creating a new git folder.
+* Rename the pacakge SelectSim to SelectSim by creating a new git folder.
 * Create CSO group repositroy and move the code there.
 * Created the website for github
 
-# SelectX 0.0.1.4
+# SelectSim 0.0.1.4
 
 * Added Mijan in author's list
 * Remove C/C++ code dependecny to avoid installation diffculties in different systems.
   * Hence move to using `Matrix` library functions and removed `RCpp` functions and code.
 * Update the website and vignette accordingly. 
 
-# SelectX 0.0.1.5
+# SelectSim 0.0.1.5
 
 * Fixed bug of outlier functions and added C/C++ code back.
 * More description in functions