remove .DS_Store

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

@@ -84,6 +84,7 @@ jobs:
       - uses: r-lib/actions/check-r-package@v2
         id: rcmdcheck
         with:
+<<<<<<< HEAD
           upload-snapshots: true
 
       # fail-fast but only if rcmdcheck step fails
@@ -92,3 +93,6 @@ jobs:
           GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
         if: always() && steps.rcmdcheck.outcome == 'failure'
         run: gh run cancel ${{ github.run_id }}
+=======
+          upload-snapshots: true
+>>>>>>> main

.github/workflows/pkgdown.yaml

@@ -80,4 +80,4 @@ jobs:
           # Also discussed in https://github.com/r-lib/actions/issues/484
           clean: ${{ github.event_name == 'release' }}
           branch: gh-pages
-          folder: docs
+          folder: docs

.github/workflows/render_readme.yml

@@ -42,7 +42,11 @@ jobs:
       GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
     steps:
       - name: Checkout repos
+<<<<<<< HEAD
         uses: actions/checkout@v3
+=======
+        uses: actions/checkout@v2
+>>>>>>> main
 
       - name: Setup R
         uses: r-lib/actions/setup-r@v2
@@ -51,11 +55,16 @@ jobs:
 
       - name: Setup pandoc
         uses: r-lib/actions/setup-pandoc@v2
+<<<<<<< HEAD
 
+=======
+
+>>>>>>> main
       - name: Install dependencies
         uses: r-lib/actions/setup-r-dependencies@v2
         with:
           extra-packages: any::rmarkdown, local::.
+<<<<<<< HEAD
 
       - name: Compile the readme
         run: |
@@ -72,6 +81,21 @@ jobs:
             output_file = "README.md",
             output_dir  = "."
           )
+=======
+
+      - name: Compile the readme
+        run: |
+          tf <- tempfile(fileext = ".Rmd")
+          writeLines(
+            knitr::knit_expand(
+              "README.Rmd", 
+              packagename = read.dcf("DESCRIPTION", "Package"), 
+              gh_repo = Sys.getenv("GITHUB_REPOSITORY")
+            ), 
+            tf
+          )
+          rmarkdown::render(tf, output_file = "README.md", output_dir = ".")
+>>>>>>> main
         shell: Rscript {0}
 
       - name: Commit files
@@ -85,4 +109,8 @@ jobs:
             git add man/figures/
           fi
           git diff-index --quiet HEAD || git commit -m "Automatic readme update"
+<<<<<<< HEAD
+          git push origin || echo "No changes to push"
+=======
           git push origin || echo "No changes to push"
+>>>>>>> main

.github/workflows/test-coverage.yaml

@@ -51,9 +51,13 @@ jobs:
 
       - name: Test coverage
         run: covr::codecov(quiet = FALSE)
+<<<<<<< HEAD
         shell: Rscript {0}
 
       - name: Upload coverage reports to Codecov
         uses: codecov/codecov-action@v3
         env:
           CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN }}
+=======
+        shell: Rscript {0}
+>>>>>>> main

DESCRIPTION

@@ -1,10 +1,16 @@
 Package: readepi
+<<<<<<< HEAD
 Title: Read Data From Health Information Systems
 Version: 1.0.0
+=======
+Title: Import Data From Files and Health Information Systems Into R
+Version: 0.0.1
+>>>>>>> main
 Authors@R: c(
     person("Karim", "Mané", , "[email protected]", role = c("aut", "cre"),
            comment = c(ORCID = "0000-0002-9892-2999")),
     person("Bubacarr", "Bah", , "[email protected]", role = "ctb",
+<<<<<<< HEAD
            comment = c(ORCID = "0000-0003-3318-6668")),
     person("Bankolé", "Ahadzie", , "[email protected]", role = "ctb"),
     person("Nuredin", "Mohammed", , "[email protected]", role = "ctb"),
@@ -19,11 +25,32 @@ Authors@R: c(
 Description: Data import from several sources including files and health
     information systems (HIS). The current version of the package covers
     HIS such as MS SQL, MySQL, PostGRESQL servers, REDCap, DHIS2 and
+=======
+            comment = c(ORCID = "0000-0003-3318-6668")),
+    person("Bankolé", "Ahadzie", , "[email protected]", role = "ctb"),
+    person("Nuredin", "Mohammed", , 
+            "[email protected]", role = "ctb"),
+    person("Hugo", "Gruson", , "[email protected]", role = "rev",
+           comment = c(ORCID = "0000-0002-4094-1476")),
+    person("Pratik", "Gupte", , "[email protected]", role = "rev",
+           comment = c(ORCID = "0000-0001-5294-7819")),
+    person("Andree", "Valle-Campos", , 
+            "[email protected]", role = "rev",
+            comment = c(ORCID = "0000-0002-7779-481X"))
+  )
+Description: Data import from several sources. These include files and
+    health information systems (HIS). The current version of the package
+    covers HIS such as REDCap, SQL, MySQL, PostGRESQL servers, DHIS2 and
+>>>>>>> main
     Fingertips.
 License: MIT + file LICENSE
 URL: https://github.com/epiverse-trace/readepi
 BugReports: https://github.com/epiverse-trace/readepi/issues
+<<<<<<< HEAD
 Imports: 
+=======
+Imports:
+>>>>>>> main
     checkmate,
     data.table,
     DBI,
@@ -34,6 +61,7 @@ Imports:
     magrittr,
     odbc,
     pool,
+<<<<<<< HEAD
     REDCapR,
     RMySQL
 Suggests: 
@@ -42,11 +70,30 @@ Suggests:
     knitr,
     rmarkdown,
     testthat (>= 3.0.0)
+=======
+    purrr,
+    R.utils,
+    readxl,
+    REDCapR,
+    rio,
+    RMySQL,
+    stringr
+Suggests: 
+    covr,
+    devtools,
+    knitr,
+    rmarkdown,
+    testthat (>= 3.0.0),
+    usethis
+>>>>>>> main
 VignetteBuilder: 
     knitr
 Remotes: 
     rOpenSci/fingertipsR
+<<<<<<< HEAD
 Config/Needs/website: epiverse-trace/epiversetheme
+=======
+>>>>>>> main
 Config/testthat/edition: 3
 Encoding: UTF-8
 Roxygen: list(markdown = TRUE)

NAMESPACE

@@ -1,9 +1,58 @@
 # Generated by roxygen2: do not edit by hand
 
+<<<<<<< HEAD
 export(get_dhis2_attributes)
 export(readepi)
 export(show_example_file)
 export(show_tables)
+=======
+export(check_dhis2_attributes)
+export(connect_to_server)
+export(detect_separator)
+export(dhis2_subset_fields)
+export(dhis2_subset_records)
+export(fetch_data_from_query)
+export(fingertips_subset_columns)
+export(fingertips_subset_rows)
+export(get_base_name)
+export(get_data_elements)
+export(get_data_sets)
+export(get_extension)
+export(get_fingertips_metadata)
+export(get_ind_id_from_domain_id)
+export(get_ind_id_from_domain_name)
+export(get_ind_id_from_ind_name)
+export(get_ind_id_from_profile)
+export(get_organisation_units)
+export(get_profile_name)
+export(get_read_file_args)
+export(get_read_fingertips_args)
+export(get_relevant_data_elt_group)
+export(get_relevant_dataset)
+export(get_relevant_organisation_unit)
+export(identify_table_name)
+export(import_redcap_data)
+export(read_credentials)
+export(read_from_dhis2)
+export(read_from_file)
+export(read_from_fingertips)
+export(read_from_redcap)
+export(read_multiple_files)
+export(readepi)
+export(redcap_get_results)
+export(redcap_read)
+export(redcap_read_fields)
+export(redcap_read_records)
+export(redcap_read_rows_columns)
+export(show_example_file)
+export(show_tables)
+export(sql_select_data)
+export(sql_select_entire_dataset)
+export(sql_select_fields_only)
+export(sql_select_records_and_fields)
+export(sql_select_records_only)
+export(sql_server_read_data)
+>>>>>>> main
 export(visualise_table)
 importFrom(magrittr,"%>%")
 importFrom(utils,read.table)