remove rtransparent for now;

Dockerfile

@@ -21,13 +21,7 @@ RUN conda env create -f environment.yaml
 # Ensure the conda environment is activated
 RUN echo "source /opt/conda/etc/profile.d/conda.sh && conda activate osm" | tee -a ~/.bashrc /etc/profile /etc/profile.d/conda.sh /etc/skel/.bashrc /etc/skel/.profile > /dev/null
 
-RUN R -e '\
-install.packages("roadoi", repos = "http://cran.us.r-project.org"); \
-devtools::install_github("quest-bih/oddpub"); \
-devtools::install_github("cran/crminer"); \
-devtools::install_github("serghiou/metareadr")'
-COPY external /app/external
-RUN R -e 'devtools::install("external/rtransparent")'
+RUN R -e 'devtools::install_github("quest-bih/oddpub")'
 
 # Copy the project files and install the package
 COPY pyproject.toml /app

README.md

@@ -11,7 +11,7 @@ docker-compose -f compose.yaml run \
   --rm \
   -v $PWD:/app \
   app \
-  rtransparent \
+  extract_metrics \
   /mnt/docs/examples/pdf_inputs/test_sample.pdf \
   output.xml
 ```

environment.yaml

@@ -19,36 +19,20 @@ dependencies:
   - rich
   - rpy2
   - ruff=0.5.0
-  # Dependencies for rtransparent
-  - r-crul
   - r-devtools
   - r-dplyr
   - r-furrr
   - r-future
   - r-globals
-  - r-hoardr
   - r-httpcode
   - r-lazyeval
   - r-lubridate
   - r-magrittr
-  - r-pbapply
   - r-pdftools
-  - r-plyr
   - r-purrr
-  - r-qpdf
   - r-readr
-  - r-rentrez
   - r-rlang
   - r-stringr
   - r-tibble
   - r-tidyr
-  - r-tidyselect
-  - r-timechange
   - r-tokenizers
-  - r-triebeard
-  - r-urltools
-  - r-utf8
-  - r-XML
-  - r-xml2
-  - pip:
-    - metapub