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---
title: "NEWS-ContDataQC"
output: github_document
#md_document:
# variant: markdown_github
---
<!-- NEWS.md is generated from NEWS.Rmd. Please edit that file -->
```{r, echo = FALSE}
knitr::opts_chunk$set(
collapse = TRUE,
comment = "#>",
fig.path = "NEWS-"
)
```
```{r, echo = FALSE}
cat(paste0("Last Update: ",Sys.time()))
```
# Version History
## v2.0.7.9049
2025-01-02
* refactor: Update HOBO U20 example data file
## v2.0.7.9048
2024-12-27
* refactor: Fix typo in Report_QC.rmd, Issue #167
+ inst/rmd
+ inst/shiny-examples/ContDataQC/rmd
## v2.0.7.9047
2024-12-27
* fix: Update shinyalalert for HOBO reformat, Issue #164
+ Shiny removes empty directories, add 'remove.text' file before upload
* tests: Add code to library creation script to add temp file to HOBO folder
+ Avoid having empty directory removed during upload to ShinyApps.io
## v2.0.7.9046
2024-12-26
* fix: Update shinyalert for HOBO reformat for multiple files, Issue #164
## v2.0.7.9045
2024-12-26
* fix: Update link to Shinay 3c3_QCThresh_Eval
## v2.0.7.9044
2024-12-23
* refactor: Update Excel file in Shiny 3c3_QCThresh_Eval
## v2.0.7.9043
2024-12-23
* refactor: Update workflow step 2 text (3a1_About)
## v2.0.7.9042
2024-12-23
* refactor: Text edits of flags in Report_QC.rmd
* refactor: Update Report_QC.rmd in shiny rmd folder
## v2.0.7.9041
2024-12-23
* refactor: Update thresholds display table
+ DO Spike
+ Add DO Adj, DO % Sat, and Salinity
## v2.0.7.9040
2024-12-23
* refactor: Remove extra mainPanel on 3c (Main_QCThresh_EditThresh)
+ Reclaim blank screen space
+ Space reserved for mainPanel not being used
## v2.0.7.9039
2024-12-17
* docs: Add vignettes to inst folder so can link to from GitHub
## v2.0.7.9038
2024-12-17
* docs: Build vignettes
## v2.0.7.9037
2024-12-02
* fix: Update Shiny file upload parameter check to use names from config, Issue #166
## v2.0.7.9036
2024-11-14
* fix: Update USGS gage data retreival for midnight entries, Issue #165
+ Same as miniDOT Issue #163
## v2.0.7.9035
2024-11-04
* refactor: Add pop up on HOBOware reformat for date time conversion, Issue #164
+ Success and failure
## v2.0.7.9034
2024-10-18
* refactor: Add error message for bad files in miniDOT concatenate in Shiny app
## v2.0.7.9033
2024-06-26
* fix: Update minidoct_cat() function to display midnight values, Issue #163
* refactor: Update config file, Issue #162
+ threshold for flat tolerance sensor depth from 0.0 to 0.01
+ ext
- config.ORIG.R
- config.COOL.R
- config.WARM.R
- config.Lakes.metric.R
+ shiny-examples\ContDataQC\www
- Config_Default.R
- Config_default.zip
- Config_Lakes_meters.zip
- Config_Lakes_metric.R
- Config_Template.R
- Config_Template.zip
- Config.R
## v2.0.7.9032
2024-03-01
* refactor: Update Shiny app
+ typos
+ indents
+ replace some tables with figures
## v2.0.7.9031
2024-02-27
* refactor: Update Shiny app text and tables, Issue #156
* refactor: Update Shiny app exit links, Issue #159
## v2.0.7.9030
2024-02-20
* refactor: Text updates on most tabs of Shiny app
* refactor: Remove Troubleshooting info in Shiny app, except for Console
* refactor: Figures of tables to tables in Shiny app, Issue #157
## v2.0.7.9029
2024-01-31
* refactor: Shiny app add "exit" tags to html links, Issue #159
## v2.0.7.9028
2024-01-31
* refactor: Replace images in Shiny, Issue #157
## v2.0.7.9027
2024-01-31
* refactor: Apply revised USEPA template (2023-12-15), Issue #155
## v2.0.7.9026
2024-01-31
* refactor: Move version number from title to about, Issue #161
* refactor: Add file identifiers to download links, Issue #160
## v2.0.7.9025
2024-01-25
* refactor: QC function to move QC columns, Issue #154
+ Flag. and Comment.MOD cols next to measurement columns
+ Ignore Date, Time, and Date.Time
## v2.0.7.9024
2023-09-28
* refactor: Use USEPA template
## v2.0.7.9023
2023-09-18
* refactor: Update stats plots with legend
+ fun.Stats.R
+ fun.Stats.File.R
## v2.0.7.9022
2023-09-18
* fix: Change stats N from total records to non-NA records, Issue #140
+ length(x) to sum(!is.na(x))
+ SumStats.updated.R
+ fun.Stats.R
+ fun.Stats.File.R
+ fun.PeriodStats.R
## v2.0.7.9021
2023-09-15
* refactor: Add text for tab references instead of links
## v2.0.7.9020
2023-09-14
* refactor: Added config file display name
+ Main Functions - Run Functions
+ Main Functions - QC Thresholds - Upload Custom Thresholds
## v2.0.7.9019
2023-09-14
* refactor: Edits to Shiny tabs
## v2.0.7.9018
2023-09-13
* refactor: Update period stats plots with legend
+ inst\RMD\Report_PeriodStats.rmd
* fix: Update example code in PeriodStats
## v2.0.7.9017
2023-09-12
* refactor: Change widths on Edit Thresholds tab
+ Some boxes too small
## v2.0.7.9016
2023-09-11
* refactor: Shiny tab text updates
+ miniDOT concatenate
+ miniDOT reformat
+ Advanced (new tab)
+ Formatting Files
## v2.0.7.9015
2023-09-08
* refactor: Shiny tab text updates
+ Check Input
+ Main
+ Organize Files
+ HOBOware Reformat
* refactor: Rename Sensor File Modification to Automated Reformatting
+ Add About tab
## v2.0.7.9014
2023-09-08
* refactor: Update Thresholds tab order
* refactor: Add text to Main - Import tab
## v2.0.7.9013
2023-09-08
* refactor: Update formatminiDOT function to remove columns with all NA values
+ Fixes issue with ContDataQC QC function
## v2.0.7.9012
2023-08-31
* refactor: Update config (lakes) in library and Shiny, Issue #153
* refactor: Shiny app updates
+ Update some images
+ Update text
## v2.0.7.9011
2023-08-31
* refactor: Shiny app updates
+ Main tab name Troubleshoot to Troubleshooting
+ Date format box text on HOBOware reformat
+ Move QC Tips from Main Functions to About
## v2.0.7.9010
2023-08-31
* refactor: Update base config file, Issue #153
* refactor: Update ThresholdsCheckWorksheet links in Shiny, Issue #153
## v2.0.7.9009
2023-08-14
* style: Update formating in global.R
* refactor: Change order, locations, and names of tabs in Shiny app, Issue #152
## v2.0.7.9008
2023-08-11
* style: Update Report_SiteSummary spacing
## v2.0.7.9007
2022-12-22
* fix: Shiny custom edit thresholds
+ Change default config to version without env statement
## v2.0.7.9006
2022-12-22
* update: Update Shiny app
+ QC Thresholds, Edit Thresholds, Issue #148
## v2.0.7.9005
2022-09-22
* update: update Shiny app
+ Fix numbered tabs 7 and 8
## v2.0.7.9004
2022-09-22
* update: update Shiny app
+ Update links
+ Remove (comment out) EPA template
+ Rearrange Console and Test Data tabs
## v2.0.7.9003
2022-09-19
* update: update Shiny app
+ Update text
## v2.0.7.9002
2022-09-15
* update: update Shiny app
+ Change names of navbar tabs and order
## v2.0.7.9001
2022-09-15
* style: Use EPA Template for shiny app
## v2.0.7
2022-06-15
* refactor: Bump to whole version number
## v2.0.6.9028
2022-06-15
* refactor: Add dummy files to blank Shiny app folders to avoid being deleted
## v2.0.6.9027
2022-06-15
* refactor: Update readme examples to use remotes instead of devtools package
## v2.0.6.9026
2022-06-15
* feature: Add miniDOT functions to Shiny, Issue #141
## v2.0.6.9025
2022-06-07
* fix: Modify config.R for salinity, Issue #138
+ Update other copies in package
## v2.0.6.9024
2022-05-31
* fix: Modify flags so can handle all na, Issue #143
+ fun.QC.file.R
+ fun.QC.R
+ Report_QC.rmd
- Base package and Shiny
## v2.0.6.9023
2022-05-25
* refactor: Update minidot_cat function, Issue #141
+ Remove filename parameter and use serial number from input file
* feature: Add format minidot function, Issue #141
## v2.0.6.9022
2022-05-25
* refactor: Updates to minidot_cat function, Issue #141
* refactor: Add missing return value for help script line 937
## v2.0.6.9021
2022-05-25
* feature: Add miniDOT concatenate function, Issue #141
+ Modified compile_do_folder.R from mnsentinellakes
## v2.0.6.9020
2022-05-24
* refactor: Update Report_QC.rmd used in Shiny app, Issue #117
* feature: Prototype site data summary report, Issue #142
* feature: Add google analytics to Shiny app
## v2.0.6.9019
2022-05-17
* fix: Update Report_QC.rmd table statements with useNA = ifany, Issue #117
* fix: Add new parameters to QC routine
+ DO adj, Issue #117
+ DO pct sat, Issue #117
+ Salinity, Issue #138
## v2.0.6.9018
2022-05-11
* feature: Add salinity to config file, Issue #138
* feature: Add salinity to config.out RMD, Issue #138
## v2.0.6.9017
2022-05-11
* fix: Modify config file for DO percent saturation
## v2.0.6.9016
2022-04-14
* refactor: Add keywords internal to two new functions
* fix: Rebuild package so new functions included
* docs: Add Yadong Xu as contributor
## v2.0.6.9015
2022-04-14
* feature: Add new functions from Yadong for EMVL project
+ Pull request #137
## v2.0.6.9014
2022-01-18
* refactor: Update Tim's Threshold Analysis zip file
## v2.0.6.9013
2022-01-18
* fix: Update broken links in Shiny to Config_Lakes_Metric.R, Issue #132
+ Linux case sensitive and wasn't working online
* refactor: Update text for readability in Shiny for Edit Thresholds
## v2.0.6.9012
2022-01-17
* refactor: Update QC Thresholds tab text in Shiny, Issue #131
## v2.0.6.9011
2022-01-17
* refactor: Update QC Thresholds tab in Shiny, Issue #131
+ Change order and names of tabs
+ Add Evaluate code as a download
## v2.0.6.9010
2021-12-22
* fix: Updated custom config thresholds to handle quotes, Issue #130
* docs: Added Ben Block as contributor for work on custom thresholds
## v2.0.6.9009
2021-12-22
* fix: Duplicate entry in config file, Issue #130
+ Updated all versions in package and shiny folders
+ Chlorophylla spike thresholds duplicated
## v2.0.6.9008
2021-12-21
* feature: Shiny, add custom thresholds for config file, Issue #130
+ merge pull request
## v2.0.6.9007
2021-10-25
* refactor: Rename "master" branch to "main".
## v2.0.6.9006
2021-10-25
* fix: Update fun.Stats.R and fun.Stats.File.R to use WaterLevel instead of
GageHeight, Issue #124
## v2.0.6.9005
2021-06-25
* refactor: Update config file with changes to units.
+ Correct some that were not correct
* refactor: Update config copy script in data-raw
* docs: Add markdown package to DESCRIPTION Suggests
+ Needed to to avoid GitHub Action build failure when creating vignettes
## v2.0.6.9004
2021-06-25
* style: Shiny, update code style in ui, server, and global
+ Not all code just code relevant to current refactor item
* refactor: Shiny add all parameters to table on 4MainFunction, CheckInput tab
+ Issue #127
## v2.0.6.9003
2021-06-23
* refactor: Updated version number in ui.R
## v2.0.6.9002
2021-06-23
* refactor: Shiny, pdated link locations to new repository (ShinyAppDocuments).
* style: Updated location of .rmd files to www/ folder.
## v2.0.6.9001
2021-06-23
* refactor: Shiny updates to app description text
## v2.0.6.9000
2021-06-23
* style: Removed Documents folder
+ Move to new repository
## v2.0.6
2021-06-21
* refactor: Create new version release
## v2.0.5.9109
2021-06-21
* refactor: Consolidate Shiny app updates from pull request, Issue #126
## v2.0.5.9108
2021-06-18
* refactor: Update Shiny
+ Final updates to section 7
## v2.0.5.9107
2021-06-18
* refactor: Update Shiny
+ Beginning updates to section 7
## v2.0.5.9106
2021-06-18
* refactor: Update Shiny
+ Updated section 8 text
## v2.0.5.9105
2021-06-18
* refactor: Update Shiny
+ Updated text in section 9
## v2.0.5.9104
2021-06-18
* refactor: Update Shiny
+ Updates to section 2 and section 3 - added sidebarpanels within tabsets rather than at bottom of pages
## v2.0.5.9103
2021-06-18
* refactor: Update Shiny
+ Updates sections 8 & 9.
## v2.0.5.9102
2021-06-18
* refactor: Update Shiny
+ Updated section 4a, 4b, and 5.
## v2.0.5.9101
2021-06-18
* refactor: Update Shiny
+ Updated 4a documents link
## v2.0.5.9100
2021-06-18
* refactor: Update Shiny
+ Made final updates to section 3a code and began section 4 code updates
## v2.0.5.9099
2021-06-18
* refactor: Update Shiny
+ Updated 3b files
## v2.0.5.9098
2021-06-18
* refactor: Update Shiny
+ Updated 3a section
## v2.0.5.9097
2021-06-18
* refactor: Update Shiny
+ Updated tab 6 information
## v2.0.5.9096
2021-06-18
* refactor: Update Shiny
+ Updated 2d HOBOware reformat
## v2.0.5.9095
2021-06-18
* refactor: Update Shiny
+ Added 2c info to rmd and documents
## v2.0.5.9094
2021-06-18
* refactor: Update Shiny
+ Updates to 2a and 2b text and data sources. Added files to documents folder.
## v2.0.5.9093
2021-06-18
* refactor: Update Shiny
+ Updated 2a text and created Documents folder
## v2.0.5.9092
2021-06-18
* refactor: Update Shiny
+ moved tab_Reformat.R under tab_2DataPrep subtab "Formatting files"
## v2.0.5.9091
2021-06-18
* refactor: Update Shiny
+ Update to ui.R subfiles - added all necessary new tab structures.
+ Added content to tab_1Overview using .rmd file.
## v2.0.5.9090
2021-06-18
* refactor: Update Shiny
+ Beginning updates in ui.R and subsequent code to accommodate application changes.
## v2.0.5.9089
2021-04-19
* refactor: Remove extra columns from QC routine, Issue #123
+ fun.QC.R
+ fun.QC.File.R
## v2.0.5.9088
2021-04-19
* refactor: Shiny, changes to tabs
## v2.0.5.9087
2021-04-19
* refactor: Shiny
+ Rearrange tabs
+ Split out Advanced tab into Console, Config, and Hobo
## v2.0.5.9086
2021-04-02
* style: Fix spelling, devtools::spell_check()
+ README
+ NEWS
+ fun.parseID.R
+ fun.Report.File.R
+ Vignette_ContDataQC.Rmd
+ Vignette_Config.RMD
+ fun.GageData.R
+ Vignette_Lakes.Rmd
* refactor: Reknit files
+ README
+ Vignettes
* style: Fix items from goodpractice::gp()
+ Trim lines to 80 characters
- CompSiteCDF.R
- test_export_rLakeAnalyzer.R
- RBIcalc.R
- format.Hobo.R
- fun.Helper.R
- Export.IHA.R
- Export.StreamThermal.R
- fun.CustomConfig.R
- fun.PeriodStats.R
- fun.Stats.R (partial)
- fun.DateFormat.R (partial)
+ Replace '=' with '<-'
- fun.Helper.R
+ Change T or F to TRUE or FALSE
- CompSiteCDF.R
## v2.0.5.9085
2021-03-31
* feature: Add custom config with metric units for Lakes, Issue #119
+ extdata\config.Lakes.metric.R
## v2.0.5.9084
2021-02-24
* feature: Shiny formatHobo add inputselect for date format, Issue #117
* refactor: Shiny server.R remove full.names from zip routine preventing
proper construction of download zip file, Issue #109
## v2.0.5.9083
2021-02-23
* refactor: Fix date in example reformatHobo for DO file, Issue #117
* refactor: Update reformatHobo date time conversion to account for no seconds
and 2 vs 4 digit years, Issue #117
## v2.0.5.9082
2021-02-23
* refactor: Shiny server, zip files add -j to strip folder names, Issue #109
* feature: Add additional DO parameters to config, Issue #117
* refactor: Update other versions of config, Issue #117
* docs: Update README install directions
* docs: README, trim lines to 80 characters
* docs: Move planned updates from NEWS to README
* refactor: Update Report_Config.rmd for new DO parameters, Issue #117
* refactor: Update Report_Config.rmd so sensor depth and water level are next
to each other
* refactor: Copy updated Report_Config.rmd to Shiny app, Issue #117
* feature: Add additional DO parameters (n=3) to reformatHobo function
, Issue #117
## v2.0.5.9081
2021-02-08
* refactor: Rework logger deployment start/end to use first non-NA date time
instead of first and last row; Issue #107
+ fun.QC.R
+ fun.QC.File.R
## v2.0.5.9080
2021-02-05
* style: Trim lines and fix spelling, fun.DateTimeFormat
## v2.0.5.9079
2021-02-04
* refactor: Update config spike flags for water level, Issue #116
+ Update other versions of config
## v2.0.5.9078
2021-02-04
* refactor: Update Config_Template.zip in Shiny, Issue #116
* docs: Retain NEWS.md for pkgdown to build changelog
## v2.0.5.9077
2021-02-04
* refactor: Update thresholds in config.R for sensor depth, Issue #116
## v2.0.5.9076
2021-02-04
* refactor: Modify "gross" check for water level, sensor depth, and discharge
, Issue #113
+ Was only checking for negative values
+ Set to evaluate like all other measured values
+ fun.Helper.R, fun.CalcQCStats()
* refactor: Update config.R comments for gross check as above, Issue #113
+ Update other copies of config
* refactor: Add missing spike thresholds for water level, config.R
* refactor: Set water level tests to values for sensor depth
## v2.0.5.9075
2021-01-27
* feature: Begin updates to add comparison of deployment periods, Issue #108
+ Add helper functions for rquery.t.test()
* feature: Add MonthDay to data during QC operation, Issue #111
* style: Trim some lines to 80 characters
+ fun.Stats.R
## v2.0.5.9074
2021-01-25
* docs: Update example in ContDataQC for aggregating lake/depth files, Issue #85
## v2.0.5.9073
2021-01-22
* refactor: Change ContDataQC() parameter fun.AddDeployCol from default FALSE to
TRUE
+ Shiny app will now auto add the deployment field
## v2.0.5.9072
2021-01-21
* refactor: Report_QC.rmd, add Water Level vs. Water Temp plots, Issue #110
* style: Report_QC.rmd, trim lines to 80 characters
* refactor: Copy Report_QC.rmd to shiny
## v2.0.5.9071
2021-01-21
* refactor: Revise Vignette_Config so it doesn't fail.
## v2.0.5.9070
2021-01-21
* refactor: Replace getwd() with tempdir() in examples
+ export_rLakeAnalyzer
+ PeriodStats
+ Export.IHA
of getwd() to save file
* feature: Create logger deployment column during QC routine, Issue #107
+ ContDataQC
+ fun.QC
+ fun.QC.File
* feature: Add logger deployment to config.R, Issue #107
+ myName.LoggerDeployment
+ myName.LoggerDeployment.start
+ myName.LoggerDeployment.end
+ Added to myNames.Order (add after DateTime)
* style: Trim lines to 80 characters
+ Export.rLakeAnalyzer
+ Vignette_Config
+ ContDataQC_Vignette
* refactor: Rename ContDataQC_Vignette to Vignette_ContDataQC
* refactor: Update config.R
* style: Updates to config.R, make order of Air and Water Pressure consistent
* refactor: Create data-raw file to propagate changes in config.R to shiny
* refactor: Update Vignette_Config with changes to config.R
* refactor: Update Config.R and its dependent versions
+ inst\extdata\config.ORIG.R
+ inst\shiny-examples\ContDataQC\www\Config_Template.R
+ inst\shiny-examples\ContDataQC\www\Config_Template.zip
* refactor: Replace getwd() with tempdir()
+ Vignette_Lakes
+ Vignette_ContDataQC
* docs: Update examples in Vignette_ContDataQC
* docs: Update example in Export.IHA with text from ContDataQC
## v2.0.5.9069
2021-01-20
* tests: Add test for export_rLakeAnalyzer
## v2.0.5.9068
2021-01-18
* refactor: Add "RAW" columns for flags in QC step Issue #106
## v2.0.5.9067
2021-01-18
* refactor: Shiny server, turn off renameAggOutput, Issue #104
## v2.0.5.9066
2021-01-15
* refactor: Add ability to Shiny to handle DOCX files to renameAggOutput in
global.R
* refactor: Redefine file name output for AggregateData.File
+ Use input file names to get date range
* docs: Remove docs folder for pkgdown site
+ Using GitHub Actions to build pkgdown in a different branch
* style: Trim to 80 character lines
+ zfun.AggregateData
+ zfun.AggregateData.File
## v2.0.5.9065
2021-01-14
* refactor: Update name of Config.zip to Config_Template.zip in shiny ui.R
## v2.0.5.9064
2021-01-14
* refactor: Rename custom config and add instructions, Issue #104
+ Won't work if use newenv() within custom file
* docs: Update text in config.out function about newenv()
## v2.0.5.9063
2021-01-13
* fix: Shiny app custom config not loading
## v2.0.5.9063
2021-01-13
* fix: Correct download of www/Config.zip
* fix: Replace unneeded concatenation without arguments
+ Aquarius_Data_Acquisition_PADEP
* style: Trim lines to 80 characters
+ fun.Config.Out
* fix: Example output to tempdir() rather than getwd()
+ fun.Config.Out
## v2.0.5.9062
2021-01-08
* refactor: Update version number display in Shiny app.
## v2.0.5.9061
2021-01-08
* feature: Update formatHobo to output water level, Issue #100
## v2.0.5.9060
2021-01-08
* refactor: Update CompSite.CDF 2nd example
## v2.0.5.9059
2021-01-08
* fix: Update CompSite.CDF so does not save to working directory
+ use tempdir in example and update code to use dir.output
* style: Trim to 80 character lines
+ fun.Helper.R
## v2.0.5.9058
2021-01-08
* refactor: Modify LakeID~Depth siteID to LakeID--Depth
+ File names with ~ are non-portable.
* style: Trim to 80 characters.
+ Vignette_Lakes
+ fun.ParseID
* refactor: Update help text in fun.ParseID for change in Lake ID delimiter
## v2.0.5.9057
2021-01-07
* feature: Modify formatHobo to use water level, issue #100
## v2.0.5.9056
2021-01-07
* feature: Add water level as a parameter for QC checks, Issue #100
* refactor: Remove gage height as a parameter for QC checks, Issue #100
* feature: Modify USGS download to change gage height to water level, Issue #100
+ Match HOBOware terminology (most of user base)
* style: Trim lines to 80 characters
+ config.R
+ fun.GageData.R
+ fun.Report.R
+ fun.Report.File.R
* fix: Update copies and version of config.R with edits, Issue #100
+ Package
- data\Config.R
- inst\extdata\config.COOL
- inst\extdata\config.ExcludeFailsFalse
- inst\extdata\config.ORIG
- inst\extdata\config.RMDdir
- inst\extdata\config.WARM
+ Shiny
- www\Config.R
- www\Config.zip
* feature: Update rmd files from GageHeight to WaterLevel
+ Report_Config
+ Report_QC
* refactor: Copy RMD files from package directory to shiny
* refactor: Remove unneeded concatenation of a constant
+ server.R
+ Export.rlakeAnalyzer.R
* feature: Change Gage Height to Water Level, fun.QC
* feature: Add Water Level, fun.QC.File
* refactor: Change getwd() to tempdir(), ContDataQC example
* refactor: Update ContDataQC example
+ getwd() to tempdir()
+ paste0() to file.path()
* fix: Fix typo in fun.Stats.File.R
+ seq_len(row... to seq_len(nrow...
* refactor: Remove use of installr package as is windows only
+ Move example text to details of ContDataQC function
## v2.0.5.9055
2021-01-04
* refactor: Add config_R.zip to shiny app in www folder
* refactor: server.R update fun.myReport.format to "" from "html"
## v2.0.5.9054
2021-01-04