refactor: code improvements and automatization by visze · Pull Request #15 · kircherlab/BCalm

visze · 2026-02-26T12:20:13Z

No description provided.

…kage improvements

…rove automation

github-actions · 2026-02-26T12:40:22Z

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R	Fail ❌
YAML	Pass ✅

Super-linter detected linting errors

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R

Error in `lint_impl_()`:
! Linter `linter()` failed in '/github/workspace/R/analyze.R':
Caused by error in `linter_fun()`:
! cyclocomp_linter is disabled due to lack of the cyclocomp package
Backtrace:
     ▆
  1. └─lintr::lint("/github/workspace/R/analyze.R")
  2.   └─lintr:::lint_impl_(linters, lint_cache, filename, source_expressions)
  3.     ├─base::withCallingHandlers(...)
  4.     └─lintr:::get_lints(...)
  5.       ├─lintr:::flatten_lints(linter_fun(expr))
  6.       │ └─lintr:::flatten_list(x, class = "lint")
  7.       │   └─lintr (local) assign_item(x)
  8.       └─lintr (local) linter_fun(expr)
  9.         └─cli::cli_abort("cyclocomp_linter is disabled due to lack of the {.pkg cyclocomp} package")
 10.           └─rlang::abort(...)
Warning message:
Warning encountered while loading config:
Caused by warning:
! Warning from config setting `linters`.
Caused by warning:
! Cyclocomp complexity is computed using `cyclocomp::cyclocomp()`.
ℹ Please install the needed cyclocomp package.
Execution halted
Error in `lint_impl_()`:
! Linter `linter()` failed in '/github/workspace/R/fit.R':
Caused by error in `linter_fun()`:
! cyclocomp_linter is disabled due to lack of the cyclocomp package
Backtrace:
     ▆
  1. └─lintr::lint("/github/workspace/R/fit.R")
  2.   └─lintr:::lint_impl_(linters, lint_cache, filename, source_expressions)
  3.     ├─base::withCallingHandlers(...)
  4.     └─lintr:::get_lints(...)
  5.       ├─lintr:::flatten_lints(linter_fun(expr))
  6.       │ └─lintr:::flatten_list(x, class = "lint")
  7.       │   └─lintr (local) assign_item(x)
  8.       └─lintr (local) linter_fun(expr)
  9.         └─cli::cli_abort("cyclocomp_linter is disabled due to lack of the {.pkg cyclocomp} package")
 10.           └─rlang::abort(...)
Warning message:
Warning encountered while loading config:
Caused by warning:
! Warning from config setting `linters`.
Caused by warning:
! Cyclocomp complexity is computed using `cyclocomp::cyclocomp()`.
ℹ Please install the needed cyclocomp package.
Execution halted
Error in `lint_impl_()`:
! Linter `linter()` failed in '/github/workspace/R/mpra_set.R':
Caused by error in `linter_fun()`:
! cyclocomp_linter is disabled due to lack of the cyclocomp package
Backtrace:
     ▆
  1. └─lintr::lint("/github/workspace/R/mpra_set.R")
  2.   └─lintr:::lint_impl_(linters, lint_cache, filename, source_expressions)
  3.     ├─base::withCallingHandlers(...)
  4.     └─lintr:::get_lints(...)
  5.       ├─lintr:::flatten_lints(linter_fun(expr))
  6.       │ └─lintr:::flatten_list(x, class = "lint")
  7.       │   └─lintr (local) assign_item(x)
  8.       └─lintr (local) linter_fun(expr)
  9.         └─cli::cli_abort("cyclocomp_linter is disabled due to lack of the {.pkg cyclocomp} package")
 10.           └─rlang::abort(...)
Warning message:
Warning encountered while loading config:
Caused by warning:
! Warning from config setting `linters`.
Caused by warning:
! Cyclocomp complexity is computed using `cyclocomp::cyclocomp()`.
ℹ Please install the needed cyclocomp package.
Execution halted
Error in `lint_impl_()`:
! Linter `linter()` failed in '/github/workspace/R/preprocess.R':
Caused by error in `linter_fun()`:
! cyclocomp_linter is disabled due to lack of the cyclocomp package
Backtrace:
     ▆
  1. └─lintr::lint("/github/workspace/R/preprocess.R")
  2.   └─lintr:::lint_impl_(linters, lint_cache, filename, source_expressions)
  3.     ├─base::withCallingHandlers(...)
  4.     └─lintr:::get_lints(...)
  5.       ├─lintr:::flatten_lints(linter_fun(expr))
  6.       │ └─lintr:::flatten_list(x, class = "lint")
  7.       │   └─lintr (local) assign_item(x)
  8.       └─lintr (local) linter_fun(expr)
  9.         └─cli::cli_abort("cyclocomp_linter is disabled due to lack of the {.pkg cyclocomp} package")
 10.           └─rlang::abort(...)
Warning message:
Warning encountered while loading config:
Caused by warning:
! Warning from config setting `linters`.
Caused by warning:
! Cyclocomp complexity is computed using `cyclocomp::cyclocomp()`.
ℹ Please install the needed cyclocomp package.
Execution halted
Error in `lint_impl_()`:
! Linter `linter()` failed in '/github/workspace/R/utils.R':
Caused by error in `linter_fun()`:
! cyclocomp_linter is disabled due to lack of the cyclocomp package
Backtrace:
     ▆
  1. └─lintr::lint("/github/workspace/R/utils.R")
  2.   └─lintr:::lint_impl_(linters, lint_cache, filename, source_expressions)
  3.     ├─base::withCallingHandlers(...)
  4.     └─lintr:::get_lints(...)
  5.       ├─lintr:::flatten_lints(linter_fun(expr))
  6.       │ └─lintr:::flatten_list(x, class = "lint")
  7.       │   └─lintr (local) assign_item(x)
  8.       └─lintr (local) linter_fun(expr)
  9.         └─cli::cli_abort("cyclocomp_linter is disabled due to lack of the {.pkg cyclocomp} package")
 10.           └─rlang::abort(...)
Warning message:
Warning encountered while loading config:
Caused by warning:
! Warning from config setting `linters`.
Caused by warning:
! Cyclocomp complexity is computed using `cyclocomp::cyclocomp()`.
ℹ Please install the needed cyclocomp package.
Execution halted
Error in `lint_impl_()`:
! Linter `linter()` failed in
  '/github/workspace/inst/scripts/makeMpraSetExample.R':
Caused by error in `linter_fun()`:
! cyclocomp_linter is disabled due to lack of the cyclocomp package
Backtrace:
     ▆
  1. └─lintr::lint("/github/workspace/inst/scripts/makeMpraSetExample.R")
  2.   └─lintr:::lint_impl_(linters, lint_cache, filename, source_expressions)
  3.     ├─base::withCallingHandlers(...)
  4.     └─lintr:::get_lints(...)
  5.       ├─lintr:::flatten_lints(linter_fun(expr))
  6.       │ └─lintr:::flatten_list(x, class = "lint")
  7.       │   └─lintr (local) assign_item(x)
  8.       └─lintr (local) linter_fun(expr)
  9.         └─cli::cli_abort("cyclocomp_linter is disabled due to lack of the {.pkg cyclocomp} package")
 10.           └─rlang::abort(...)
Warning message:
Warning encountered while loading config:
Caused by warning:
! Warning from config setting `linters`.
Caused by warning:
! Cyclocomp complexity is computed using `cyclocomp::cyclocomp()`.
ℹ Please install the needed cyclocomp package.
Execution halted
Error in `lint_impl_()`:
! Linter `linter()` failed in '/github/workspace/tests/runTests.R':
Caused by error in `linter_fun()`:
! cyclocomp_linter is disabled due to lack of the cyclocomp package
Backtrace:
     ▆
  1. └─lintr::lint("/github/workspace/tests/runTests.R")
  2.   └─lintr:::lint_impl_(linters, lint_cache, filename, source_expressions)
  3.     ├─base::withCallingHandlers(...)
  4.     └─lintr:::get_lints(...)
  5.       ├─lintr:::flatten_lints(linter_fun(expr))
  6.       │ └─lintr:::flatten_list(x, class = "lint")
  7.       │   └─lintr (local) assign_item(x)
  8.       └─lintr (local) linter_fun(expr)
  9.         └─cli::cli_abort("cyclocomp_linter is disabled due to lack of the {.pkg cyclocomp} package")
 10.           └─rlang::abort(...)
Warning message:
Warning encountered while loading config:
Caused by warning:
! Warning from config setting `linters`.
Caused by warning:
! Cyclocomp complexity is computed using `cyclocomp::cyclocomp()`.
ℹ Please install the needed cyclocomp package.
Execution halted
Error in `lint_impl_()`:
! Linter `linter()` failed in
  '/github/workspace/tests/testthat/test-analyze.R':
Caused by error in `linter_fun()`:
! cyclocomp_linter is disabled due to lack of the cyclocomp package
Backtrace:
     ▆
  1. └─lintr::lint("/github/workspace/tests/testthat/test-analyze.R")
  2.   └─lintr:::lint_impl_(linters, lint_cache, filename, source_expressions)
  3.     ├─base::withCallingHandlers(...)
  4.     └─lintr:::get_lints(...)
  5.       ├─lintr:::flatten_lints(linter_fun(expr))
  6.       │ └─lintr:::flatten_list(x, class = "lint")
  7.       │   └─lintr (local) assign_item(x)
  8.       └─lintr (local) linter_fun(expr)
  9.         └─cli::cli_abort("cyclocomp_linter is disabled due to lack of the {.pkg cyclocomp} package")
 10.           └─rlang::abort(...)
Warning message:
Warning encountered while loading config:
Caused by warning:
! Warning from config setting `linters`.
Caused by warning:
! Cyclocomp complexity is computed using `cyclocomp::cyclocomp()`.
ℹ Please install the needed cyclocomp package.
Execution halted
Error in `lint_impl_()`:
! Linter `linter()` failed in
  '/github/workspace/tests/testthat/test-fit.R':
Caused by error in `linter_fun()`:
! cyclocomp_linter is disabled due to lack of the cyclocomp package
Backtrace:
     ▆
  1. └─lintr::lint("/github/workspace/tests/testthat/test-fit.R")
  2.   └─lintr:::lint_impl_(linters, lint_cache, filename, source_expressions)
  3.     ├─base::withCallingHandlers(...)
  4.     └─lintr:::get_lints(...)
  5.       ├─lintr:::flatten_lints(linter_fun(expr))
  6.       │ └─lintr:::flatten_list(x, class = "lint")
  7.       │   └─lintr (local) assign_item(x)
  8.       └─lintr (local) linter_fun(expr)
  9.         └─cli::cli_abort("cyclocomp_linter is disabled due to lack of the {.pkg cyclocomp} package")
 10.           └─rlang::abort(...)
Warning message:
Warning encountered while loading config:
Caused by warning:
! Warning from config setting `linters`.
Caused by warning:
! Cyclocomp complexity is computed using `cyclocomp::cyclocomp()`.
ℹ Please install the needed cyclocomp package.
Execution halted
Error in `lint_impl_()`:
! Linter `linter()` failed in
  '/github/workspace/tests/testthat/test-preprocess.R':
Caused by error in `linter_fun()`:
! cyclocomp_linter is disabled due to lack of the cyclocomp package
Backtrace:
     ▆
  1. └─lintr::lint("/github/workspace/tests/testthat/test-preprocess.R")
  2.   └─lintr:::lint_impl_(linters, lint_cache, filename, source_expressions)
  3.     ├─base::withCallingHandlers(...)
  4.     └─lintr:::get_lints(...)
  5.       ├─lintr:::flatten_lints(linter_fun(expr))
  6.       │ └─lintr:::flatten_list(x, class = "lint")
  7.       │   └─lintr (local) assign_item(x)
  8.       └─lintr (local) linter_fun(expr)
  9.         └─cli::cli_abort("cyclocomp_linter is disabled due to lack of the {.pkg cyclocomp} package")
 10.           └─rlang::abort(...)
Warning message:
Warning encountered while loading config:
Caused by warning:
! Warning from config setting `linters`.
Caused by warning:
! Cyclocomp complexity is computed using `cyclocomp::cyclocomp()`.
ℹ Please install the needed cyclocomp package.
Execution halted
Error in `lint_impl_()`:
! Linter `linter()` failed in '/github/workspace/vignettes/BCalm.Rmd':
Caused by error in `linter_fun()`:
! cyclocomp_linter is disabled due to lack of the cyclocomp package
Backtrace:
     ▆
  1. └─lintr::lint("/github/workspace/vignettes/BCalm.Rmd")
  2.   └─lintr:::lint_impl_(linters, lint_cache, filename, source_expressions)
  3.     ├─base::withCallingHandlers(...)
  4.     └─lintr:::get_lints(...)
  5.       ├─lintr:::flatten_lints(linter_fun(expr))
  6.       │ └─lintr:::flatten_list(x, class = "lint")
  7.       │   └─lintr (local) assign_item(x)
  8.       └─lintr (local) linter_fun(expr)
  9.         └─cli::cli_abort("cyclocomp_linter is disabled due to lack of the {.pkg cyclocomp} package")
 10.           └─rlang::abort(...)
Warning message:
Warning encountered while loading config:
Caused by warning:
! Warning from config setting `linters`.
Caused by warning:
! Cyclocomp complexity is computed using `cyclocomp::cyclocomp()`.
ℹ Please install the needed cyclocomp package.
Execution halted

…ove unnecessary linters

github-actions · 2026-02-26T12:48:36Z

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github-actions · 2026-02-26T13:36:42Z

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…mespace

github-actions · 2026-02-26T13:52:31Z

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…ratio binding in the mpra namespace

github-actions · 2026-02-26T14:26:09Z

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github-actions · 2026-02-26T14:34:06Z

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…, and LICENSE for improved organization and clarity

…st cases, and remove redundant parameters for clarity

…te_rna_df, create_var_df, downsample_barcodes, fit_elements, getLabel, mpra_treat, plot_groups, and BcSetExample

github-actions · 2026-02-27T09:27:58Z

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…and improve clarity in package documentation

… for consistency

…yr functions for improved clarity

github-actions · 2026-02-27T09:39:13Z

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github-actions · 2026-02-27T09:40:06Z

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github-actions · 2026-02-27T09:49:48Z

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github-actions · 2026-02-27T09:51:00Z

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github-actions · 2026-02-27T09:51:38Z

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github-actions · 2026-02-27T09:55:07Z

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github-actions · 2026-02-27T10:10:11Z

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…e versioning

github-actions · 2026-02-27T10:40:05Z

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…istently and update tests for class expectations based on endomorphic argument presence

github-actions · 2026-02-27T11:16:05Z

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…mn names in mpra_treat tests

github-actions · 2026-02-27T11:18:38Z

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github-actions · 2026-02-27T11:44:50Z

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github-actions · 2026-02-27T12:13:29Z

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…pralm and normalize_counts

github-actions · 2026-02-27T12:21:26Z

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visze added 8 commits February 26, 2026 12:37

Add EditorConfig, lintr, and update DESCRIPTION and NAMESPACE for pac…

364cff1

…kage improvements

linting and github action

7bebc8b

fixing spellings

02ec22a

github actions!

dc94164

check linter

46f9e23

Refactor GitHub Actions workflows and add YAML linting configuration

edb5898

Update GitHub Actions workflows to use latest action versions and imp…

20c7523

…rove automation

Add R-CMD-check workflow for automated R package checks

6c4f0fb

Refactor workflow files to improve YAML linting configuration and rem…

cd2bfd6

…ove unnecessary linters

Refactor utils and test files to streamline code and improve readability

a7b5f2b

Fix namespace assignment in .onLoad function to use utils::assignInNa…

3b5e9b5

…mespace

Refactor .onLoad function to properly unlock and lock the compute_log…

d6c8a75

…ratio binding in the mpra namespace

Use utils::assignInNamespace for compute_logratio in .onLoad function

1d74ba8

visze added 3 commits February 26, 2026 16:37

Refactor project files: update .Rbuildignore, .gitignore, DESCRIPTION…

52960c3

…, and LICENSE for improved organization and clarity

Refactor utils and test files: update global variables, streamline te…

41bb1b9

…st cases, and remove redundant parameters for clarity

Add documentation for new functions and datasets: create_dna_df, crea…

cba8422

…te_rna_df, create_var_df, downsample_barcodes, fit_elements, getLabel, mpra_treat, plot_groups, and BcSetExample

visze added 3 commits February 27, 2026 10:37

Refactor documentation and examples: standardize data loading syntax …

5533e48

…and improve clarity in package documentation

Refactor test files: update library references from 'mpra' to 'BCalm'…

d8048d8

… for consistency

Refactor NAMESPACE: streamline imports by consolidating stats and dpl…

a1d40c1

…yr functions for improved clarity

visze added 2 commits February 27, 2026 10:47

citations

d5f3963

build ignore

7879652

format

0368a56

ö to o

c05b7d1

documentation

067ffad

visze added 3 commits February 27, 2026 11:14

update doc

9f2e29d

newest bcalm vigniette

8131a43

Add warning for unavailable 'endomorphic' argument and update vignett…

341b480

…e versioning

Refactor fit_elements function to ensure label assignment occurs cons…

84b91c6

…istently and update tests for class expectations based on endomorphic argument presence

Remove unnecessary logFC column check and add warning for result colu…

bb9328f

…mn names in mpra_treat tests

Remove equality check between result and result_endo in mpra_treat tests

b04eff7

docs!

0906d4e

Update example data loading to specify package in documentation for m…

ad7d55c

…pralm and normalize_counts

visze merged commit e7c1178 into development Feb 27, 2026
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