Release/1.0.0 (#50)

* restructure the README and the vignette

* restructure the README and the vignette

* restructure the README and the vignette

* add reading from DHIS2

* add reading from DHIS2

* add reading from DHIS2

* Automatic readme update

* update read_from_ms_sql_server to account for the new server

* Automatic readme update

* update read_from_ms_sql_server to account for the new server

* update read_from_ms_sql_server to account for the new server

* update readepi with new dependencies installation

* update readepi with new dependencies installation

* update readepi with new dependencies installation

* update install_dep.R

* update install_dep.R

* update install_dep.R

* update install_dep.R

* update install_dep.R

* update install_dep.R

* update readepi

* add reading from Fingertips

* update the SQL data base content

* update the test file for readepi function

* change redcap database source

* modify fingertips installation instructions

* update redcap project name in readme file

* remove R/install_dep

* remove tests/testthat/test-install_dep.R

* Change MS SQL test server to MySQL

* Change MS SQL test server to MySQL

* update how fingertipsR is defined as a dependency

* update how fingertipsR is defined as a dependency

* update how fingertipsR is defined as a dependency

* update the test REDCap server details

* update the test REDCap server details

* update the test REDCap server details

* remove install_dependencies.sh

* aplly styler on package

* Automatic readme update

* aplly styler on package

* aplly styler on package

* aplly styler on package

* fixed all lintr issues

* restructure reading from server by adding the possibility to submit an SQL query

* fixed new linter issues and impoved package coverage

* subdivide readepi_helpers into different helpers

* update the DESCRIPTION file

* Update R/read_from_redcap-helpers.R

Co-authored-by: Hugo Gruson <[email protected]>

* fix lintr issues

* add authors

* add Bubacarr's ORCID

* build package website

* update the README.Rmd

* update the README.Rmd and package website

* add the package logo

* replace DBI::dbConnect() with pool::dbPool()

* removed lint.yaml and lint-changed-files.yaml

* update the helper functions for read_servers.R

* exported and set examples for helper functions for read_from_fingertips

* update readme and vignette, fix lintr issue related to loading the package in tests/testthat.R

* fix typo error in readme

* comment the installation line in readme

* update the readme with vignette instructions

* update the readme with vignette instructions

* update the readme with vignette instructions

* updates on the .DS_Store file after merging PR and deleting develop branch

* Start of the review

* modify the file in ./github/workflow

* add functions to handle genomic data

* update readme

* update description file with github installation

* update package vignette

* comment out DHIS2 reading

* comment out DHIS2 reading

* update records and fields subsetting

* Automatic readme update

* correct for failed check of 07/02/2021

* Automatic readme update

* correct for failed check of 07/02/2021

* update credential file

* update function's documentation

* update function's documentation

* update on readepi following pull request

* update on readepi following pull request

* Automatic readme update

* add function to install MS driver

* restructure the README and the vignette

* restructure the README and the vignette

* restructure the README and the vignette

* restructure the README and the vignette

* add reading from DHIS2

* add reading from DHIS2

* add reading from DHIS2

* Automatic readme update

* update read_from_ms_sql_server to account for the new server

* Automatic readme update

* update read_from_ms_sql_server to account for the new server

* update read_from_ms_sql_server to account for the new server

* update readepi with new dependencies installation

* update readepi with new dependencies installation

* update readepi with new dependencies installation

* update install_dep.R

* update install_dep.R

* update install_dep.R

* update install_dep.R

* update install_dep.R

* update install_dep.R

* update readepi

* add reading from Fingertips

* update the SQL data base content

* update the test file for readepi function

* change redcap database source

* modify fingertips installation instructions

* update redcap project name in readme file

* remove R/install_dep

* remove tests/testthat/test-install_dep.R

* Change MS SQL test server to MySQL

* Change MS SQL test server to MySQL

* update how fingertipsR is defined as a dependency

* update how fingertipsR is defined as a dependency

* update how fingertipsR is defined as a dependency

* update the test REDCap server details

* update the test REDCap server details

* update the test REDCap server details

* remove install_dependencies.sh

* aplly styler on package

* Automatic readme update

* aplly styler on package

* aplly styler on package

* aplly styler on package

* fixed all lintr issues

* restructure reading from server by adding the possibility to submit an SQL query

* fixed new linter issues and impoved package coverage

* subdivide readepi_helpers into different helpers

* update the DESCRIPTION file

* Update R/read_from_redcap-helpers.R

Co-authored-by: Hugo Gruson <[email protected]>

* fix lintr issues

* add authors

* add Bubacarr's ORCID

* build package website

* update the README.Rmd

* update the README.Rmd and package website

* add the package logo

* replace DBI::dbConnect() with pool::dbPool()

* removed lint.yaml and lint-changed-files.yaml

* update the helper functions for read_servers.R

* exported and set examples for helper functions for read_from_fingertips

* update readme and vignette, fix lintr issue related to loading the package in tests/testthat.R

* fix typo error in readme

* comment the installation line in readme

* update the readme with vignette instructions

* update the readme with vignette instructions

* update the readme with vignette instructions

* Start of the review

* let github actions run from any branch on PR

* add package logo

* improved documentation

* Automatic readme update

* Captalize comments...

* update README

* Automatic readme update

* unexport internal functions and use file.path instead of paste0

* remove .DS_Store

* remove .Rhistory

* remove .Rhistory

* remove .DS_Store

* remove Meta/ folder

* remove ..Rcheck/ folder

* update return messages in different functions

* fix issues related to DESCRIPTION, Depencies, General technical sections raised by Pratik

* Automatic readme update

* fix issues related to DHIS2 sections raised by Pratik

* fix issues related to For local files sections raised by Pratik

* replace '-' by '_' in file names

* Automatic readme update

* general updates

* remove docs/ folder

* remove .github/.DS_Store file

* remove inst/.DS_Store file

* remove inst/.DS_Store files

* update functions documentation and test files

* update test files

* Automatic readme update

* update test files

* update readepi()

* update readepi() by swapping source and from arguments

* remove the .DS_Store files

* fix linters

* upated test-read_from_dhis2_helpers.R

* update readme and vignette

* Automatic readme update

* update readme, vignette and function documentation

* update readme, vignette and function documentation

* update test-read_from_dhis2_helpers.R

* remove reading from file-related files and functions

* Automatic readme update

* update readme and vignette

* update readepi_helpers.R

* update vignette

* fix-issue-16

* update readme and vignette

* update the github workflows files

* Automatic readme update

* update test files

* update test files

* update readme

* update workflow files to account for the develop branch

* update package version number in DESCRIPTION file

* Update CITATION.cff

* remove Meta folder and .DS_Store files

* remove .DS_Store files

* add citation file at inst/

* Update CITATION.cff

* update readme and vignette

* remove tests/.DS_Store

* fix conflicts with main

* Automatic readme update

* let the workflows run on the release branch

* fix linters

* fix issues with tests files

* Update Hugo's email

Co-authored-by: Hugo Gruson <[email protected]>

* enclose software and brand names with quotation

Co-authored-by: Hugo Gruson <[email protected]>

* Update {readepi} URL

Co-authored-by: Hugo Gruson <[email protected]>

* Update R/check_dhis2_attributes-helpers.R

Co-authored-by: Hugo Gruson <[email protected]>

* Update R/read_servers.R

Co-authored-by: Hugo Gruson <[email protected]>

* Update R/read_servers_helpers.R

Co-authored-by: Hugo Gruson <[email protected]>

* fix issues detected by Hugo

* fix issues detected by Hugo

* update desc

* create mock for fingertips

* update _pkgdown.yml

* update readme

* Automatic readme update

* update readme

* update package version

* update readme

* Automatic readme update

* update readme and vignette

* Update CITATION.cff

* updates

* remove CITATION.cff

* Automatic readme update

* update vignette

* update show_tables.R

---------

Co-authored-by: GitHub Action <[email protected]>
Co-authored-by: Hugo Gruson <[email protected]>
Co-authored-by: Karim Mane <[email protected]>
Co-authored-by: Karim Mane <[email protected]>
Co-authored-by: abdoelnaser-mahmood-degoot <[email protected]>

.Rbuildignore

@@ -10,3 +10,4 @@
 ^doc$
 ^Meta$
 ^\.lintr$
+^touchstone$