Merge pull request #80 from DiseaseTranscriptomicsLab/main

v1.1.2

Author: ritamtbsilva

.Rbuildignore

@@ -20,4 +20,5 @@
 ^\\.git$
 ^codecov\.yml$
 ^vignettes/articles$
-^data_aux$
+^data_aux$ 
+^python(/.*)?$

.gitignore

@@ -18,3 +18,4 @@ markeR.Rproj
 inst/doc
 data_aux
 markeR.Rcheck 
+/python/.venv

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: markeR
 Title: An R Toolkit for Evaluating Gene Signatures as Phenotypic Markers
-Version: 1.1.1
+Version: 1.1.2
 Authors@R: 
     c(
       person("Rita", "Martins-Silva", 

NEWS.md

@@ -1,3 +1,13 @@
+# markeR 1.1.2 (12 Mar, 2026) 
+
+## Minor Changes
+- Moved Python bridge scripts from `inst/python/` to a top-level `python/` 
+  directory, as these are supplementary scripts not part of the R package itself.
+- Added `requirements.txt` to the `python/` directory listing all needed 
+  Python dependencies (`rpy2`, `pandas`, `numpy`, and optionally 
+  `ipython` and `jupyter`) for easier environment setup. 
+- Removed redundant code snippets from the Python bridge scripts.
+
 # markeR 1.1.1 (11 Mar, 2026) 
 
   - Added `p.adjust.method` parameter across all functions performing or

README.Rmd

@@ -30,7 +30,7 @@ knitr::opts_chunk$set(
 
 > **To cite `markeR` please use:** 
 >
-> Martins-Silva R, Kaizeler A, Barbosa-Morais NL (2025). _markeR: An R Toolkit for Evaluating Gene Signatures as Phenotypic Markers_. doi:10.18129/B9.bioc.markeR, R package version 1.1.1, https://bioconductor.org/packages/markeR.
+> Martins-Silva R, Kaizeler A, Barbosa-Morais NL (2025). _markeR: An R Toolkit for Evaluating Gene Signatures as Phenotypic Markers_. doi:10.18129/B9.bioc.markeR, R package version 1.1.2, https://bioconductor.org/packages/markeR.
  
 The folder `inst/Paper/` is in the **paper** branch and contains all scripts and materials used in the original `markeR` paper to reproduce analyses and figures.  You can browse it [here](https://github.com/DiseaseTranscriptomicsLab/markeR/tree/paper/inst/Paper).
 
@@ -241,10 +241,10 @@ Filters can be applied based on similarity thresholds (e.g., minimum Jaccard, OR
 ## Python Bridge
 
 For users who prefer Python, a lightweight bridge is available in
-`inst/python/` that allows calling any `markeR` function from a Python
+`python/` that allows calling any `markeR` function from a Python
 environment via [`rpy2`](https://rpy2.github.io/). It includes a tutorial
 workflow script and a generic command-line wrapper. See
-[`inst/python/README.md`](inst/python/README.md) for installation
+[`python/README.md`](inst/python/README.md) for installation
 instructions and usage examples.
 
 

README.md

@@ -26,7 +26,7 @@ across experimental and clinical phenotypes.
 >
 > Martins-Silva R, Kaizeler A, Barbosa-Morais NL (2025). *markeR: An R
 > Toolkit for Evaluating Gene Signatures as Phenotypic Markers*.
-> <doi:10.18129/B9.bioc.markeR>, R package version 1.1.1,
+> <doi:10.18129/B9.bioc.markeR>, R package version 1.1.2,
 > <https://bioconductor.org/packages/markeR>.
 
 The folder `inst/Paper/` is in the **paper** branch and contains all
@@ -288,10 +288,10 @@ Jaccard, OR, or Fisher’s test p-value).
 ## Python Bridge
 
 For users who prefer Python, a lightweight bridge is available in
-`inst/python/` that allows calling any `markeR` function from a Python
+`python/` that allows calling any `markeR` function from a Python
 environment via [`rpy2`](https://rpy2.github.io/). It includes a
 tutorial workflow script and a generic command-line wrapper. See
-[`inst/python/README.md`](inst/python/README.md) for installation
+[`python/README.md`](inst/python/README.md) for installation
 instructions and usage examples.
 
 ## Contact

inst/python/README.md python/README.mdinst/python/README.md renamed to python/README.md

@@ -12,14 +12,20 @@ Bioconductor R package **markeR** via `rpy2`.
 
 ## Prerequisites
 
-* R (>=.4.5) installed and on your `PATH`.
-* A Python virtual environment.  Install dependencies with:
-
-```bash
-python -m venv .venv
-source .venv/bin/activate
-pip install -r requirements.txt
-```
+* R (>=4.5) installed and on your `PATH`.
+* A Python virtual environment.  A `requirements.txt` file is provided in
+  this folder listing the needed packages (`rpy2`, `pandas`, `numpy` plus
+  optional `ipython`/`jupyter` for notebook usage).
+  To set up the environment:
+
+  ```bash
+  python -m venv .venv
+  source .venv/bin/activate
+  pip install -r requirements.txt
+  ```
+
+  After activation you can run the helper scripts using `python` from the
+  same environment.
 
 ## Quick start
 

inst/python/markeR_to_python.py python/markeR_to_python.pyinst/python/markeR_to_python.py renamed to python/markeR_to_python.py

@@ -60,12 +60,6 @@
 # converting.  helpers below wrap the recommended API.
 
 
-def _to_r(obj):
-    """Convert a pandas object to an R object using the current converter."""
-    with conversion.localconverter(ro.default_converter + pandas2ri.converter):
-        return conversion.py2rpy(obj)
-
-
 def _to_py(obj):
     """Convert an R object to a pandas/numpy equivalent."""
     with conversion.localconverter(ro.default_converter + pandas2ri.converter):
@@ -175,7 +169,6 @@ def plot_r_function(func_name: str, *args, width=800, height=600, filename=None,
 
 def ensure_bioc_installed() -> None:
     """Install Bioconductor's package manager if it is not already present."""
-    utils = importr("utils")
     biocinstaller = "BiocManager"
     if not isinstalled(biocinstaller):
         ro.r('install.packages("{0}")'.format(biocinstaller))
@@ -189,22 +182,17 @@ def install_markeR() -> None:
     the package should be loadable via `importr("markeR")`.
     """
     ensure_bioc_installed()
-    # use importr to check presence rather than only the isinstalled helper
-    try:
-        importr("markeR")
-    except Exception:
-        # attempt installation if import failed
+    if not isinstalled("markeR"):
         ro.r('BiocManager::install("markeR", ask=FALSE, update=FALSE)')
-        # load into namespace for side effects
-        ro.r('library(markeR)')
+    ro.r('library(markeR)')
 
 
 def get_markeR_functions() -> ro.Environment:
     """Return the markeR namespace so that functions can be accessed conveniently.
 
     Example:
         mark = get_markeR_functions()
-        imputed = mark.rgImpute(...)
+        scores = mark.CalculateScores(data=counts, metadata=metadata, gene_sets=genesets, method="logmedian")
     """
     install_markeR()
     # importing via importr is more reliable than accessing `ro.r['markeR']`.
@@ -330,4 +318,4 @@ def tutorial_benchmark(output_file=None):
             print("                            example: python markeR_to_python.py --tutorial --output my_plot.png")
     else:
         print("usage: python markeR_to_python.py --tutorial [--output FILENAME]")
-        print("See the module docstring for more details.")
+        print("See the module docstring for more details.")

python/requirements.txt

@@ -0,0 +1,9 @@
+# install packages for markeR_to_python script:
+#   pip install -r requirements.txt
+
+rpy2>=3.6
+pandas
+numpy
+# optional (for notebook inline display)
+ipython
+jupyter

inst/python/run_marker_function.py python/run_marker_function.pyinst/python/run_marker_function.py renamed to python/run_marker_function.py

@@ -25,6 +25,7 @@
 import argparse
 import json
 import os
+import re
 
 # Check dependencies
 _missing = []
@@ -42,7 +43,6 @@
 
 def ensure_bioc_installed() -> None:
     """Install Bioconductor's package manager if it is not already present."""
-    utils = importr("utils")
     biocinstaller = "BiocManager"
     if not isinstalled(biocinstaller):
         ro.r('install.packages("{0}")'.format(biocinstaller))
@@ -52,11 +52,9 @@ def ensure_bioc_installed() -> None:
 def install_markeR() -> None:
     """Install the markeR package from Bioconductor if not already installed."""
     ensure_bioc_installed()
-    try:
-        importr("markeR")
-    except Exception:
+    if not isinstalled("markeR"):
         ro.r('BiocManager::install("markeR", ask=FALSE, update=FALSE)')
-        ro.r('library(markeR)')
+    ro.r('library(markeR)')
 
 
 def load_example_data():
@@ -113,7 +111,8 @@ def parse_parameter(value: str):
     except (json.JSONDecodeError, ValueError):
         pass
 
-    # Default: treat as string
+    # Default: treat as string, escaping any internal quotes
+    value = value.replace('"', '\\"')
     return f'"{value}"'
 
 
@@ -272,6 +271,12 @@ def main():
         return
 
     func_name = sys.argv[1]
+    
+    # Validate function name to prevent code injection
+    if not re.match(r'^[A-Za-z][A-Za-z0-9_.]*$', func_name):
+        sys.exit(f"Error: invalid function name '{func_name}'. "
+                 "Function names must start with a letter and contain only letters, digits, dots or underscores.")
+    
     output_file = None
     width = 800
     height = 600
@@ -358,4 +363,4 @@ def main():
 
 
 if __name__ == "__main__":
-    main()
+    main()